def load_edf_data_seizure_2(args):
args = elecs.read_cmd_args(
utils.Bag(
subject=args.subject,
atlas='laus125',
function='create_raw_data_for_blender',
task='seizure',
bipolar=args.bipolar,
raw_fname=op.join(
ELECTRODES_DIR, args.subject[0], 'DMphaseIISz_TG.edf'
), # '/cluster/neuromind/npeled/taha/dm04002705/edf/DMphaseIISz_TG.edf',
start_time='00:00:00',
seizure_onset='00:01:20',
seizure_end='00:02:00',
baseline_onset='00:00:00',
baseline_end='00:01:00',
lower_freq_filter=2,
upper_freq_filter=70,
power_line_notch_widths=5,
ref_elec='PST1',
normalize_data=False,
calc_zscore=False,
factor=1000,
channels_names_mismatches='LFO=LIF'))
pu.run_on_subjects(args, elecs.main)
def create_ictal_clips(subject,
ictal_events_dict,
ictal_template,
overwrite=False,
n_jobs=4):
mmvt_root = op.join(MMVT_DIR, subject, 'electrodes')
data_files, baseline_files = [], []
meta = utils.Bag(np.load(op.join(mmvt_root, 'electrodes_meta_data.npz')))
for ictal_id, times in ictal_events_dict.items():
output_fname = op.join(mmvt_root,
'electrodes_data_{}.npy'.format(ictal_id))
baseline_fname = op.join(mmvt_root,
'electrodes_baseline_{}.npy'.format(ictal_id))
if op.isfile(output_fname) and op.isfile(
baseline_fname) and not overwrite:
data_files.append(output_fname)
baseline_files.append(baseline_fname)
continue
event_fname = ictal_template.format(ictal_id=ictal_id)
if not op.isfile(event_fname):
print('Cannot find {}!'.format(event_fname))
continue
args = electrodes.read_cmd_args(
utils.Bag(
subject=subject,
function='create_raw_data_from_edf',
task='seizure',
bipolar=False,
raw_fname=event_fname,
start_time=0,
seizure_onset=times[0] - 5,
seizure_end=times[0] + 5, # times[1],
baseline_onset=0,
baseline_end=100,
time_format='seconds',
lower_freq_filter=1,
upper_freq_filter=150,
power_line_notch_widths=5,
remove_baseline=False,
normalize_data=False,
factor=1000,
overwrite_raw_data=True,
n_jobs=n_jobs))
electrodes.call_main(args)
temp_output_fname = op.join(mmvt_root, 'electrodes_data_diff.npy')
if op.isfile(temp_output_fname):
os.rename(temp_output_fname, output_fname)
data_files.append(output_fname)
else:
print('{}: no data!'.format(ictal_id))
temp_baseline_fname = op.join(mmvt_root, 'electrodes_baseline.npy')
if op.isfile(temp_baseline_fname):
os.rename(temp_baseline_fname, baseline_fname)
baseline_files.append(baseline_fname)
else:
print('{}: No baseline!'.format(ictal_id))
meta_fname = op.join(mmvt_root, 'electrodes_meta_data_diff.npz')
if op.isfile(meta_fname):
os.rename(meta_fname, op.join(mmvt_root, 'electrodes_meta_data.npz'))
return data_files, baseline_files
def load_edf_data_seizure(args):
args = elecs.read_cmd_args(
utils.Bag(
subject=args.subject,
atlas='laus125',
function='create_raw_data_from_edf',
task='seizure',
bipolar=args.bipolar,
raw_fname=op.join(ELECTRODES_DIR, args.subject[0],
'{}.edf'.format(args.edf)),
start_time='00:00:00',
seizure_onset='00:01:20',
seizure_end='00:02:00',
baseline_onset='00:00:00',
baseline_end='00:01:00',
lower_freq_filter=1,
upper_freq_filter=150,
power_line_notch_widths=5,
ref_elec='PST1',
normalize_data=False,
calc_zscore=False,
factor=1000,
# channels_names_mismatches='LFO=LIF'
))
pu.run_on_subjects(args, elecs.main)
def save_msit_single_trials_data(subject, bipolar):
args = elecs.read_cmd_args(['-s', subject, '-b', str(bipolar)])
args.task = 'MSIT'
args.function = 'create_electrode_data_file'
args.input_matlab_fname = 'electrodes_data_trials.mat'
args.electrodes_names_field = 'electrodes'
args.field_cond_template = '{}'
elecs.main(subject, args)
def save_msit_single_trials_data(subject, bipolar):
args = elecs_preproc.read_cmd_args(['-s', subject, '-b', str(bipolar)])
args.task = 'MSIT'
args.function = 'create_electrode_data_file'
args.input_matlab_fname = 'electrodes_data_trials.mat'
args.electrodes_names_field = 'electrodes'
args.field_cond_template = '{}'
elecs_preproc.main(subject, args)
def get_ras_from_mad(args):
args = elecs.read_cmd_args(
utils.Bag(
subject=args.subject,
function='get_ras_file',
remote_ras_fol=
'/mnt/cashlab/Original Data/MG/{subject}/{subject}_Notes_and_Images/{subject}_SurferOutput'
))
pu.run_on_subjects(args, elecs.main)
def load_edf_data_rest(args):
args = elecs.read_cmd_args(
utils.Bag(
subject=args.subject,
function='create_raw_data_for_blender',
task='rest',
bipolar=False,
remove_power_line_noise=True,
raw_fname='MG102_d3_Fri.edf',
# rest_onset_time='6:50:00',
# end_time='7:05:00',
normalize_data=False,
preload=False))
pu.run_on_subjects(args, elecs.main)
def calc_electrodes_power_spectrum(subject, edf_name, overwrite=False):
elecs_args = electrodes.read_cmd_args(utils.Bag(
subject=subject,
function='create_raw_data_from_edf,calc_epochs_power_spectrum',
task='rest',
bipolar=False,
remove_power_line_noise=True,
raw_fname='{}.edf'.format(edf_name),
normalize_data=False,
preload=True,
windows_length=10, # s
windows_shift=5,
# epochs_num=20,
overwrite_power_spectrum=overwrite
))
electrodes.call_main(elecs_args)
def get_electrodes_file_from_server(args):
args = elecs.read_cmd_args(
utils.Bag(subject=args.subject,
function='prepare_subject_folder',
sftp=True,
sftp_username='******',
sftp_domain='door.nmr.mgh.harvard.edu',
remote_subject_dir=
'/space/thibault/1/users/npeled/subjects/{subject}'))
# This line causes sometimes the sftp to hang, not sure why...
args.sftp_password = utils.ask_for_sftp_password(args.sftp_username)
for subject in args.subject:
upper_subject = subject[:2].upper() + subject[2:]
args.necessary_files['electrodes'] = \
['{}_RAS.{}'.format(upper_subject, file_type) for file_type in ['csv', 'xls', 'xlsx']] + \
['{}_RAS.{}'.format(subject, file_type) for file_type in ['csv', 'xls', 'xlsx']]
pu.run_on_subjects(args, elecs.main)
def load_electrodes_matlab_stim_file(args):
from src.preproc import stim
args = elecs.read_cmd_args(utils.Bag(subject=args.subject, bipolar=True))
args = pu.add_default_args(args, {
'error_radius': 3,
'elec_length': 4,
'file_frefix': ''
})
subject = args.subject[0]
mat_fname = op.join(elecs.ELECTRODES_DIR, subject,
'MG106_LVF56_continuous.mat')
d = mu.load_mat_to_bag(mat_fname)
labels = mu.matlab_cell_str_to_list(d.Label)
fs = d.fs[0][0]
T = d.data.shape[1]
# t1, t2 = 62000, 66000
t1, t2 = T - 5 * fs, T # Take last 5 seconds
data = d.data[:, t1:t2]
bad_electrodes = ['ROF04-05', 'ROF05-06', 'LPF14-NT']
labels, data = elecs.remove_bad_channels(labels, data, bad_electrodes)
data = data.reshape((*data.shape, 1))
args.stim_channel = 'LVF05-LVF06'
args.bipolar = '-' in args.stim_channel
elecs.convert_electrodes_coordinates_file_to_npy(subject, bipolar=False)
output_file = stim.create_stim_electrodes_positions(subject, args, labels)
# First you need to run find_rois in electrodes_rois project:
# python -m src.find_rois -s mg106 -b 1 --pos_fname '$MMVT/mg106/electrodes/electrodes_bipolar_stim_LVF04-LVF05_positions.npz' --output_postfix _stim_LVF04-LVF05
# stim.set_labels_colors(subject, args, stim_dict=dict(labels=labels, data=data, conditions=['rest']))
data_fname = op.join(
elecs.MMVT_DIR, subject, 'electrodes',
'electrodes{}_data.npy'.format('_bipolar' if args.bipolar else ''))
meta_fname = op.join(
elecs.MMVT_DIR, subject, 'electrodes',
'electrodes{}_meta_data.npz'.format(
'_bipolar' if args.bipolar else ''))
np.save(data_fname, data)
np.savez(meta_fname, names=labels, conditions=['rest'])
def load_edf_data_seizure(args):
args = elecs.read_cmd_args(
utils.Bag(
subject=args.subject,
atlas='laus250',
function='create_raw_data_for_blender',
task='seizure',
bipolar=False,
raw_fname='Bakhamis_Amal_1.edf',
start_time='00:01:34',
# seizure_onset='00:03:33',
seizure_onset='00:03:28',
seizure_end='00:03:50',
baseline_onset='00:01:34',
baseline_end='00:03:11',
lower_freq_filter=0.5,
upper_freq_filter=70,
power_line_notch_widths=5,
ref_elec='CII',
normalize_data=False,
calc_zscore=False,
factor=1000))
pu.run_on_subjects(args, elecs.main)
def load_electrodes_matlab_stim_file2(args):
from src.preproc import stim
args = elecs.read_cmd_args(utils.Bag(subject=args.subject, bipolar=True))
args = pu.add_default_args(args, {
'error_radius': 3,
'elec_length': 4,
'file_frefix': ''
})
subject = args.subject[0]
mat_fname = op.join(elecs.ELECTRODES_DIR, subject, 'MG106_HGP_sess2_3.mat')
d = mu.load_mat_to_bag(mat_fname)
labels = mu.matlab_cell_str_to_list(d.Label)
labels = [l.replace(' ', '-') for l in labels]
labels = [
'{0}{1}-{0}{2}'.format(*utils.elec_group_number(l, bipolar=True))
for l in labels
]
time = d.time2.squeeze()
data = d.Data2
data = data.reshape((*data.shape, 1))
args.stim_channel = 'sess2'
args.bipolar = '-' in labels[0]
elecs.convert_electrodes_coordinates_file_to_npy(subject, bipolar=False)
output_file = stim.create_stim_electrodes_positions(subject, args, labels)
data_fname = op.join(
elecs.MMVT_DIR, subject, 'electrodes',
'electrodes{}_data.npy'.format('_bipolar' if args.bipolar else ''))
meta_fname = op.join(
elecs.MMVT_DIR, subject, 'electrodes',
'electrodes{}_meta_data.npz'.format(
'_bipolar' if args.bipolar else ''))
np.save(data_fname, data)
np.savez(meta_fname, names=labels, conditions=['rest'], time=time)
print('Saving data in {} and {}'.format(data_fname, meta_fname))
def read_electrodes_coordiantes_from_specific_xlsx_sheet(subject, bipolar):
args = elecs.read_cmd_args(['-s', subject, '-b', str(bipolar)])
args.ras_xls_sheet_name = 'RAS_Snapped'
elecs.main(subject, args)
def read_electrodes_coordiantes_from_specific_xlsx_sheet(subject, bipolar):
args = elecs_preproc.read_cmd_args(['-s', subject, '-b', str(bipolar)])
args.ras_xls_sheet_name = 'RAS_Snapped'
elecs_preproc.main(subject, args)