def read_xls(xls_fname,
subject_to='colin27',
atlas='aparc.DKTatlas',
overwrite=False,
check_morph_file=False):
bipolar = True
template_header = nib.load(
op.join(SUBJECTS_DIR, subject_to, 'mri', 'T1.mgz')).header
subjects_electrodes = defaultdict(list)
electrodes_colors = defaultdict(list)
for line in utils.xlsx_reader(xls_fname, skip_rows=1):
subject, _, elec_name, _, anat_group = line
subject = subject.replace('\'', '')
if subject == '':
break
if check_morph_file:
electrodes_fname = op.join(
MMVT_DIR, subject, 'electrodes',
'electrodes_morph_to_{}.txt'.format(subject_to))
if not op.isfile(electrodes_fname):
continue
elec_group, num1, num2 = utils.elec_group_number(elec_name, bipolar)
if '{}{}-{}'.format(elec_group, num2, num1) != elec_name:
num1, num2 = str(num1).zfill(2), str(num2).zfill(2)
if '{}{}-{}'.format(elec_group, num2, num1) != elec_name:
raise Exception('Wrong group or numbers!')
for num in [num1, num2]:
subjects_electrodes[subject].append('{}{}'.format(elec_group, num))
electrodes_colors[subject].append((elec_name, int(anat_group)))
subjects = list(subjects_electrodes.keys())
bad_subjects = []
for subject in subjects:
atlas = utils.fix_atlas_name(subject, atlas, SUBJECTS_DIR)
if not utils.both_hemi_files_exist(
op.join(SUBJECTS_DIR, subject, 'label', '{}.{}.annot'.format(
'{hemi}', atlas))):
anat.create_annotation(subject, atlas)
if not utils.both_hemi_files_exist(
op.join(SUBJECTS_DIR, subject, 'label',
'{}.{}.annot'.format('{hemi}', atlas))):
print('No atlas for {}!'.format(atlas))
bad_subjects.append((subject, 'No atlas'))
continue
try:
ela_morph_electrodes.calc_elas(subject,
subject_to,
subjects_electrodes[subject],
bipolar=False,
atlas=atlas,
overwrite=overwrite)
except:
err = utils.print_last_error_line()
bad_subjects.append((subject, err))
continue
print(bad_subjects)
def read_xls(xls_fname, specific_subjects=None):
subjects_electrodes = defaultdict(list)
for line in utils.xlsx_reader(xls_fname, skip_rows=1):
subject, elec1_name, elec2_name, cond, patient_id = line[:5]
subject = subject.lower()
if specific_subjects is not None and subject not in specific_subjects:
continue
elec1_coo, elec2_coo = line[5:8], line[8:11]
subjects_electrodes[subject].append((elec1_name, elec2_name))
return subjects_electrodes
def read_xlsx(xlsx_fname):
electrodes = {}
for line_ind, line in enumerate(utils.xlsx_reader(xlsx_fname)):
if line_ind == 0:
header = line
continue
subject = line[0].lower()
electrodes[subject] = defaultdict(list)
for k in range(len(header) - 1):
electrodes[subject][header[k + 1].lower()].extend(
read_electrodes_from_cell(line[k + 1]))
return electrodes
def read_onset_xlsx(xlsx_fname):
subjects = []
for vals in utils.xlsx_reader(xlsx_fname, skip_rows=1):
subject, _, elec_name = vals
subject = subject.replace('\'', '')
elec_group, elec_name = elec_name.replace('\'', '').split('.')
elec_name1, elec_name2 = elec_name.split('-')
elec_name = '{}{}-{}{}'.format(elec_group, elec_name2, elec_group,
elec_name1)
subjects.append("'{}'".format(subject))
# yield (subject, elec_name)
print(','.join(subjects))
def read_morphed_electrodes(xls_fname,
subject_to='colin27',
bipolar=True,
prefix='',
postfix=''):
output_fname = '{}electrodes{}_positions.npz'.format(
prefix, '_bipolar' if bipolar else '', postfix)
electrodes_colors = defaultdict(list)
bad_electrodes = []
template_electrodes = defaultdict(list)
morphed_electrodes_fname = op.join(MMVT_DIR, subject_to, 'electrodes',
'morphed_electrodes.pkl')
if op.isfile(morphed_electrodes_fname):
template_electrodes, electrodes_colors = utils.load(
morphed_electrodes_fname)
else:
for line in utils.xlsx_reader(xls_fname, skip_rows=1):
subject, _, elec_name, _, anat_group = line
subject = subject.replace('\'', '')
if subject == '':
break
elec_group, num1, num2 = utils.elec_group_number(
elec_name, bipolar)
if '{}{}-{}'.format(elec_group, num2, num1) != elec_name:
num1, num2 = str(num1).zfill(2), str(num2).zfill(2)
if '{}{}-{}'.format(elec_group, num2, num1) != elec_name:
raise Exception('Wrong group or numbers!')
elecs_pos = []
for num in num1, num2:
elec_input_fname = op.join(
MMVT_DIR, subject, 'electrodes',
'{}{}_ela_morphed.npz'.format(elec_group, num))
if not op.isfile(elec_input_fname):
print('{} not found!'.format(elec_input_fname))
bad_electrodes.append('{}_{}{}'.format(
subject, elec_group, num))
else:
d = np.load(elec_input_fname)
elecs_pos.append(d['pos'])
num1, num2 = (num1, num2) if num2 > num1 else (num2, num1)
if len(elecs_pos) == 2:
bipolar_ele_pos = np.mean(elecs_pos, axis=0)
elec_name = '{}_{}{}-{}'.format(subject, elec_group, num1,
num2)
template_electrodes[subject].append(
(elec_name, bipolar_ele_pos))
electrodes_colors[subject].append((elec_name, int(anat_group)))
utils.save((template_electrodes, electrodes_colors),
morphed_electrodes_fname)
write_electrode_colors(subject_to, electrodes_colors)
fol = utils.make_dir(op.join(MMVT_DIR, subject_to, 'electrodes'))
output_fname = op.join(fol, output_fname)
elecs_coordinates = np.array(
utils.flat_list_of_lists([[e[1] for e in template_electrodes[subject]]
for subject in template_electrodes.keys()]))
elecs_names = utils.flat_list_of_lists(
[[e[0] for e in template_electrodes[subject]]
for subject in template_electrodes.keys()])
print('Saving {} electrodes in {}:'.format(subject_to, output_fname))
print(elecs_names)
np.savez(output_fname,
pos=elecs_coordinates,
names=elecs_names,
pos_org=[])
print('Bad electrodes:')
print(bad_electrodes)
return template_electrodes, electrodes_colors