def get_empty_fnames(subject, tasks, args):
utils.make_dir(op.join(MEG_DIR, subject))
utils.make_link(op.join(args.remote_subject_dir.format(subject=subject), 'bem'),
op.join(MEG_DIR, subject, 'bem'))
for task in tasks:
utils.make_dir(op.join(MEG_DIR, task, subject))
utils.make_link(op.join(MEG_DIR, subject, 'bem'), op.join(MEG_DIR, task, subject, 'bem'))
utils.make_link(op.join(MEG_DIR, subject, 'bem'), op.join(SUBJECTS_DIR, subject, 'bem'))
remote_meg_fol = '/autofs/space/lilli_003/users/DARPA-TRANSFER/meg/{}'.format(subject)
csv_fname = op.join(remote_meg_fol, 'cfg.txt')
if not op.isfile(csv_fname):
print('No cfg file!')
return {task:'' for task in tasks}
days, empty_fnames = {}, {}
for line in utils.csv_file_reader(csv_fname, ' '):
for task in tasks:
if line[4].lower() == task.lower():
days[task] = line[2]
print(days)
for line in utils.csv_file_reader(csv_fname, ' '):
if line[4] == 'empty':
for task in tasks:
empty_fnames[task] = op.join(MEG_DIR, task, subject, '{}_empty_raw.fif'.format(subject))
if op.isfile(empty_fnames[task]):
continue
task_day = days[task]
if line[2] == task_day:
empty_fname = op.join(remote_meg_fol, line[0].zfill(3), line[-1])
if not op.isfile(empty_fname):
raise Exception('empty file does not exist! {}'.format(empty_fname[task]))
utils.make_link(empty_fname, empty_fnames[task])
return empty_fnames
def get_meg_empty_fnames(subject,
remote_fol,
args,
ask_for_different_day_empty=False):
csv_fname = op.join(remote_fol, 'cfg.txt')
if not op.isfile(csv_fname):
print('No cfg file ({})!'.format(csv_fname))
return '', '', ''
day, empty_fname, cor_fname, local_rest_raw_fname = '', '', '', ''
for line in utils.csv_file_reader(csv_fname, ' '):
if line[4].lower() == 'resting':
day = line[2]
remote_rest_raw_fname = op.join(remote_fol, line[0].zfill(3),
line[-1])
if not op.isfile(remote_rest_raw_fname):
raise Exception('rest file does not exist! {}'.format(
remote_rest_raw_fname))
local_rest_raw_fname = op.join(
MEG_DIR, subject, '{}_resting_raw.fif'.format(subject))
if not op.isfile(local_rest_raw_fname):
utils.make_link(remote_rest_raw_fname, local_rest_raw_fname)
break
if day == '':
print('Couldn\'t find the resting day in the cfg!')
return '', '', ''
for line in utils.csv_file_reader(csv_fname, ' '):
if line[4] == 'empty':
empty_fname = op.join(MEG_DIR, subject,
'{}_empty_raw.fif'.format(subject))
if op.isfile(empty_fname):
continue
if line[2] == day:
remote_empty_fname = op.join(remote_fol, line[0].zfill(3),
line[-1])
if not op.isfile(remote_empty_fname):
raise Exception('empty file does not exist! {}'.format(
remote_empty_fname))
utils.make_link(remote_empty_fname, empty_fname)
if not op.isfile(empty_fname):
for line in utils.csv_file_reader(csv_fname, ' '):
if line[4] == 'empty':
ret = input('empty recordings from a different day were found, continue (y/n)? ') \
if ask_for_different_day_empty else True
if au.is_true(ret):
remote_empty_fname = op.join(remote_fol, line[0].zfill(3),
line[-1])
if not op.isfile(remote_empty_fname):
raise Exception('empty file does not exist! {}'.format(
remote_empty_fname))
utils.make_link(remote_empty_fname, empty_fname)
cor_dir = op.join(args.remote_subject_dir.format(subject=subject), 'mri',
'T1-neuromag', 'sets')
if op.isfile(op.join(cor_dir, 'COR-{}-resting.fif'.format(subject))):
cor_fname = op.join(cor_dir, 'COR-{}-resting.fif'.format(subject))
elif op.isfile(op.join(cor_dir, 'COR-{}-day{}.fif'.format(subject, day))):
cor_fname = op.join(cor_dir, 'COR-{}-day{}.fif'.format(subject, day))
return local_rest_raw_fname, empty_fname, cor_fname
def get_empty_fnames(subject, tasks, args, overwrite=False):
utils.make_dir(op.join(MEG_DIR, subject))
utils.make_link(op.join(args.remote_subject_dir.format(subject=subject),
'bem'),
op.join(MEG_DIR, subject, 'bem'),
overwrite=overwrite)
for task in tasks:
utils.make_dir(op.join(MEG_DIR, task, subject))
utils.make_link(op.join(MEG_DIR, subject, 'bem'),
op.join(MEG_DIR, task, subject, 'bem'),
overwrite=overwrite)
utils.make_link(op.join(MEG_DIR, subject, 'bem'),
op.join(SUBJECTS_DIR, subject, 'bem'),
overwrite=overwrite)
remote_meg_fol = op.join(args.remote_meg_dir, subject)
csv_fname = op.join(remote_meg_fol, 'cfg.txt')
empty_fnames, cors, days = '', '', ''
if not op.isfile(csv_fname):
print('No cfg file!')
return '', '', ''
days, empty_fnames, cors = {}, {}, {}
for line in utils.csv_file_reader(csv_fname, ' '):
for task in tasks:
if line[4].lower() == task.lower():
days[task] = line[2]
# print(days)
for line in utils.csv_file_reader(csv_fname, ' '):
if line[4] == 'empty':
for task in tasks:
empty_fnames[task] = op.join(
MEG_DIR, task, subject, '{}_empty_raw.fif'.format(subject))
if op.isfile(empty_fnames[task]):
continue
task_day = days[task]
if line[2] == task_day:
empty_fname = op.join(remote_meg_fol, line[0].zfill(3),
line[-1])
if not op.isfile(empty_fname):
raise Exception('empty file does not exist! {}'.format(
empty_fname[task]))
utils.make_link(empty_fname, empty_fnames[task])
cor_dir = op.join(args.remote_subject_dir.format(subject=subject), 'mri',
'T1-neuromag', 'sets')
for task in tasks:
if op.isfile(
op.join(cor_dir, 'COR-{}-{}.fif'.format(subject,
task.lower()))):
cors[task] = op.join(
cor_dir, 'COR-{}-{}.fif'.format('{subject}', task.lower()))
elif op.isfile(
op.join(cor_dir,
'COR-{}-day{}.fif'.format(subject, days[task]))):
cors[task] = op.join(
cor_dir, 'COR-{}-day{}.fif'.format('{subject}', days[task]))
return empty_fnames, cors, days
def get_fMRI_rest_fol(subject, remote_root):
remote_fol = op.join(remote_root, '{}_01'.format(subject.upper()))
csv_fname = op.join(remote_fol, 'cfg.txt')
if not op.isfile(csv_fname):
print('No cfg file!')
return '', '', ''
num = None
for line in utils.csv_file_reader(csv_fname, '\t'):
if line[1].lower() == 'resting':
num = line[0]
break
if num is None:
raise Exception(
'Can\'t find rest in the cfg file for {}!'.format(subject))
subject_folders = glob.glob(
op.join(remote_root, '{}_*'.format(subject.upper())))
rest_fols = []
for subject_fol in subject_folders:
rest_fols = glob.glob(op.join(subject_fol, '**', num.zfill(3)),
recursive=True)
if len(rest_fols) == 1:
break
if len(rest_fols) == 0:
raise Exception(
'Can\'t find rest in the cfg file for {}!'.format(subject))
return rest_fols[0]
def get_tal_coordaintes(files):
rois, errors = {}, {}
driver = None
for fname in tqdm(files):
# subject = utils.namebase(utils.get_parent_fol(fname, 3))
roi = utils.namebase(fname).split('.')[0]
if roi not in rois:
rois[roi] = {}
rois[roi]['tal'] = []
rois[roi]['mni'] = []
lines = list(utils.csv_file_reader(fname, delimiter=' '))
if len(lines) == 0:
errors[fname] = '{} is empty!'.format(fname)
continue
elif len(lines) > 1:
errors[fname] = 'More than one line in {}!'.format(fname)
continue
tal = [int(float(v)) for v in lines[0] if utils.is_float(v)]
rois[roi]['tal'].append(tal)
if driver is None:
driver = tu.yale_get_driver()
rois[roi]['mni'].append(tu.yale_tal2mni(tal, driver))
if len(errors) > 0:
print(errors)
del driver
return rois
def import_subs(movie_fol, subs_name='subs', delim=' '):
if op.isfile(op.join(movie_fol, subs_name)):
subs_fname = op.join(movie_fol, subs_name)
else:
subs_fnames = glob.glob(op.join(movie_fol, '{}.*'.format(subs_name)))
subs_fname = utils.select_one_file(subs_fnames)
if subs_fname is None:
return
subs = []
for line in utils.csv_file_reader(subs_fname, delim):
from_t, to_t = [utils.time_to_seconds(t, '%M:%S') for t in line[0].split('-')]
subs.append(((from_t, to_t), ' '.join(line[1:])))
return subs
def calc_distances_from_rois(subject, dist_threshold=0.05):
from scipy.spatial.distance import cdist
import nibabel as nib
dipoles_dict = utils.load(op.join(MMVT_DIR, subject, 'meg', 'dipoles.pkl'))
labels_times_fol = op.join(MMVT_DIR, subject, 'meg', 'time_accumulate')
labels = lu.read_labels(subject, SUBJECTS_DIR, 'laus125')
labels_center_of_mass = lu.calc_center_of_mass(labels)
labels_pos = np.array([labels_center_of_mass[l.name] for l in labels])
labels_dict = {l.name: labels_center_of_mass[l.name] for l in labels}
outer_skin_surf_fname = op.join(SUBJECTS_DIR, subject, 'surf', 'lh.seghead')
outer_skin_surf_verts, _ = nib.freesurfer.read_geometry(outer_skin_surf_fname)
for dipole_name, dipoles in dipoles_dict.items():
dipole_pos = np.array([dipoles[0][2], dipoles[0][3], dipoles[0][4]])
lables_times_fname = op.join(labels_times_fol, '{}_labels_times.txt'.format(dipole_name))
if not op.isfile(lables_times_fname):
print('Can\'t find {}!'.format(lables_times_fname))
continue
dists_from_outer_skin = np.min(cdist(outer_skin_surf_verts * 0.001, [dipole_pos]), 0)[0]
output_fname = op.join(labels_times_fol, '{}_labels_times_dists.txt'.format(dipole_name))
lines = utils.csv_file_reader(lables_times_fname, delimiter=':', skip_header=1)
output, dists = [], []
labels_dists = cdist(labels_pos, [dipole_pos])
dists_argmin = np.argmin(labels_dists, 0)[0]
dists_min = np.min(labels_dists, 0)[0]
closest_label = labels[dists_argmin].name
print('Parsing {} ({})'.format(dipole_name, closest_label))
for line in lines:
if len(line) == 0:
continue
elif len(line) != 2:
print('{}: Problem parsing "{}"'.format(lables_times_fname, line))
continue
label_name, label_time = line
label_pos = labels_dict.get(label_name, None)
if label_pos is not None:
dist_from_dipole = np.linalg.norm(dipole_pos - label_pos)
dists.append(dist_from_dipole)
else:
dist_from_dipole = -1
dists.append(np.nan)
output.append('{}: {} ({:.4f})'.format(label_name, label_time, dist_from_dipole))
for ind, dist in enumerate(dists):
if dist < dist_threshold:
output[ind] = '{} ***'.format(output[ind])
title = '{}: {} {:.4f} dist from outer skin: {:.4f} '.format(
dipole_name, closest_label, dists_min, dists_from_outer_skin)
utils.save_arr_to_file(output, output_fname, title)
def trans_tal_coords(roi,
file_name,
subjects_dir,
template='colin27',
overwrite=False):
subjects = {}
output_fol = utils.make_dir(op.join(MMVT_DIR, template, 'rois_peaks'))
csv_fname = op.join(output_fol, '{}.csv'.format(roi))
pkl_fname = op.join(output_fol, '{}.pkl'.format(roi))
if op.isfile(pkl_fname) and op.isfile(csv_fname) and not overwrite:
print('Data already exist for {}'.format(roi))
return
driver = tu.yale_get_driver()
files = list(utils.find_recursive(subjects_dir, file_name))
for fname in tqdm(files):
lines = list(utils.csv_file_reader(fname, delimiter=' '))
subject = utils.namebase(utils.get_parent_fol(fname, 3))
subjects[subject] = {}
if len(lines) == 0:
print()
subjects[subject]['error'] = '{} is empty!'.format(fname)
continue
elif len(lines) > 1:
print('More than one line in {}!'.format(fname))
subjects[subject] = '>1'
continue
tal = [int(float(v)) for v in lines[0] if utils.is_float(v)]
subjects[subject]['tal'] = tal
subjects[subject]['mni'] = tu.yale_tal2mni(tal, driver)
del driver
print(subjects)
with open(csv_fname, 'w') as csv_file:
csv_writer = csv.writer(csv_file, delimiter=',')
for subject, subject_data in subjects.items():
if 'mni' in subject_data:
csv_writer.writerow(subjects[subject]['mni'])
utils.save(subjects, pkl_fname)
