def _run_func_in_parallel(parallel_params):
func, params, check_if_should_run, thread_ind, verbose = parallel_params
flags = []
now = time.time()
for run_num, p in enumerate(params):
if not check_if_should_run:
utils.time_to_go(now, run_num, len(params), 1, thread_ind)
subject, site, subject_dir, scan_rescan = [
p[key]
for key in ['subject', 'site', 'subject_dir', 'scan_rescan']
]
overwrite, print_only = [
p.get(key, False) for key in ['overwrite', 'print_only']
]
flag = False
if func.__name__ == 'register_cbf_to_t1':
flag = register_cbf_to_t1(subject, subject_dir, scan_rescan,
overwrite, print_only,
check_if_should_run, verbose)
elif func.__name__ == 'calc_volume_fractions':
flag = calc_volume_fractions(subject, subject_dir, scan_rescan,
overwrite, print_only,
check_if_should_run, verbose)
elif func.__name__ == 'register_aseg_to_cbf':
flag = register_aseg_to_cbf(subject, subject_dir, scan_rescan,
overwrite, print_only,
check_if_should_run, verbose)
flags.append(flag)
return flags
def calc_electrodes_coh(subject, conditions, mat_fname, t_max, from_t_ind, to_t_ind, sfreq=1000, fmin=55, fmax=110, bw=15,
dt=0.1, window_len=0.1, n_jobs=6):
from mne.connectivity import spectral_connectivity
import time
input_file = op.join(SUBJECTS_DIR, subject, 'electrodes', mat_fname)
d = sio.loadmat(input_file)
output_file = op.join(MMVT_DIR, subject, 'electrodes_coh.npy')
windows = np.linspace(0, t_max - dt, t_max / dt)
for cond, data in enumerate([d[cond] for cond in conditions]):
if cond == 0:
coh_mat = np.zeros((data.shape[1], data.shape[1], len(windows), 2))
# coh_mat = np.load(output_file)
# continue
ds_data = downsample_data(data)
ds_data = ds_data[:, :, from_t_ind:to_t_ind]
now = time.time()
for win, tmin in enumerate(windows):
print('cond {}, tmin {}'.format(cond, tmin))
utils.time_to_go(now, win + 1, len(windows))
con_cnd, _, _, _, _ = spectral_connectivity(
ds_data, method='coh', mode='multitaper', sfreq=sfreq,
fmin=fmin, fmax=fmax, mt_adaptive=True, n_jobs=n_jobs, mt_bandwidth=bw, mt_low_bias=True,
tmin=tmin, tmax=tmin + window_len)
con_cnd = np.mean(con_cnd, axis=2)
coh_mat[:, :, win, cond] = con_cnd
# plt.matshow(con_cnd)
# plt.show()
np.save(output_file[:-4], coh_mat)
return coh_mat
def transfer_electrodes_to_template_system(electrodes,
template_system,
use_mri_robust_lta=False,
vox2vox=False):
import time
teamplte_electrodes = defaultdict(list)
for subject in electrodes.keys():
# if subject != 'mg101':
# continue
now, N = time.time(), len(electrodes[subject])
for run, (elc_name, coords) in enumerate(electrodes[subject]):
utils.time_to_go(now, run, N, runs_num_to_print=5)
if use_mri_robust_lta:
if vox2vox:
template_cords = lta_transfer_vox2vox(subject, coords)
else:
template_cords = lta_transfer_ras2ras(subject, coords)
else:
if template_system == 'ras':
template_cords = fu.transform_subject_to_ras_coordinates(
subject, coords, SUBJECTS_DIR)
elif template_system == 'mni':
template_cords = fu.transform_subject_to_mni_coordinates(
subject, coords, SUBJECTS_DIR)
else:
template_cords = fu.transform_subject_to_subject_coordinates(
subject, template_system, coords, SUBJECTS_DIR)
if template_cords is not None:
teamplte_electrodes[subject].append((elc_name, template_cords))
return teamplte_electrodes
def split_cerebellum_hemis(subject, mask_fname, new_maks_name, subregions_num):
import time
if op.isfile(new_maks_name):
return subregions_num * 2
mask = nib.load(mask_fname)
mask_data = mask.get_data()
aseg_data = nib.load(op.join(SUBJECTS_DIR, subject, 'mri', 'aseg.mgz')).get_data()
new_mask_data = np.zeros(mask_data.shape)
lookup = utils.read_freesurfer_lookup_table(return_dict=True)
inv_lookup = {name:val for val,name in lookup.items()}
right_cerebral = inv_lookup['Right-Cerebellum-Cortex']
left_cerebral = inv_lookup['Left-Cerebellum-Cortex']
now = time.time()
for seg_id in range(1, subregions_num + 1):
utils.time_to_go(now, seg_id-1, subregions_num, 1)
seg_inds = np.where(mask_data == seg_id)
aseg_segs = aseg_data[seg_inds]
seg_inds = np.vstack((seg_inds[0], seg_inds[1], seg_inds[2]))
right_inds = seg_inds[:, np.where(aseg_segs == right_cerebral)[0]]
left_inds = seg_inds[:, np.where(aseg_segs == left_cerebral)[0]]
new_mask_data[right_inds[0], right_inds[1], right_inds[2]] = seg_id
new_mask_data[left_inds[0], left_inds[1], left_inds[2]] = seg_id + subregions_num
new_mask = nib.Nifti1Image(new_mask_data, affine=mask.get_affine())
print('Saving new mask to {}'.format(new_maks_name))
nib.save(new_mask, new_maks_name)
return subregions_num * 2
def calc_source_ttest(args):
# utils.run_parallel(_morph_stcs_pvals, args.subject, args.n_jobs)
import time
subjects = args.subject
now = time.time()
for run, subject in enumerate(subjects):
utils.time_to_go(now, run, len(subjects), 1)
print('subject: {}'.format(subject))
_calc_source_ttest(subject)
def update_img(image_index):
# print(image_fname)
utils.time_to_go(now, image_index, len(images))
image = mpimg.imread(images[image_index])
im.set_data(image)
if im2:
image2 = mpimg.imread(images2[image_index])
im2.set_data(image2)
current_t = get_t(images, image_index, time_range)
t_line.set_data([current_t, current_t], [ymin, ymax])
return [im]
def update_img(image_index):
# print(image_fname)
utils.time_to_go(now, image_index, len(images))
image = mpimg.imread(images[image_index])
im.set_data(image)
if im2:
image2 = mpimg.imread(images2[image_index])
im2.set_data(image2)
current_t = get_t(images, image_index, time_range)
t_line.set_data([current_t, current_t], [ymin, ymax])
return [im]
def analyze_graphs(subject,
fif_files,
graph_func,
bands,
modality,
overwrite=False,
n_jobs=4):
now = time.time()
for run, fif_fname in enumerate(fif_files):
utils.time_to_go(now, run, len(fif_files), runs_num_to_print=1)
for band_name in bands.keys():
analyze_graph(subject, fif_fname, band_name, graph_func, modality,
overwrite, n_jobs)
def calc_closeness_centrality(p):
con, times_chunk = p
vals = []
now = time.time()
for run, t in enumerate(times_chunk):
utils.time_to_go(now, run, len(times_chunk), 10)
con_t = con[:, :, t]
g = nx.from_numpy_matrix(con_t)
# x = nx.closeness_centrality(g)
x = nx.degree_centrality(g)
vals.append([x[k] for k in range(len(x))])
vals = np.array(vals)
return vals, times_chunk
def calc_electrodes_coh(subject,
conditions,
mat_fname,
t_max,
from_t_ind,
to_t_ind,
sfreq=1000,
fmin=55,
fmax=110,
bw=15,
dt=0.1,
window_len=0.1,
n_jobs=6):
from mne.connectivity import spectral_connectivity
import time
input_file = op.join(SUBJECTS_DIR, subject, 'electrodes', mat_fname)
d = sio.loadmat(input_file)
output_file = op.join(BLENDER_ROOT_DIR, subject, 'electrodes_coh.npy')
windows = np.linspace(0, t_max - dt, t_max / dt)
for cond, data in enumerate([d[cond] for cond in conditions]):
if cond == 0:
coh_mat = np.zeros((data.shape[1], data.shape[1], len(windows), 2))
# coh_mat = np.load(output_file)
# continue
ds_data = downsample_data(data)
ds_data = ds_data[:, :, from_t_ind:to_t_ind]
now = time.time()
for win, tmin in enumerate(windows):
print('cond {}, tmin {}'.format(cond, tmin))
utils.time_to_go(now, win + 1, len(windows))
con_cnd, _, _, _, _ = spectral_connectivity(ds_data,
method='coh',
mode='multitaper',
sfreq=sfreq,
fmin=fmin,
fmax=fmax,
mt_adaptive=True,
n_jobs=n_jobs,
mt_bandwidth=bw,
mt_low_bias=True,
tmin=tmin,
tmax=tmin + window_len)
con_cnd = np.mean(con_cnd, axis=2)
coh_mat[:, :, win, cond] = con_cnd
# plt.matshow(con_cnd)
# plt.show()
np.save(output_file[:-4], coh_mat)
return coh_mat
def update_img(image_index):
# print(image_fname)
utils.time_to_go(now, image_index, len(images))
image = mpimg.imread(images[image_index])
im.set_data(image)
if im2:
image2 = mpimg.imread(images2[image_index])
im2.set_data(image2)
current_t = get_t(images, image_index, time_range)
if not current_t is None:
t_line.set_data([current_t, current_t], [ymin, ymax])
# print('Reading image {}, current t {}'.format(images[image_index], current_t))
return [im]
else:
return None
def calc_connectivity(subject,
atlas,
connectivity_method,
files,
bands,
modality,
overwrite=False,
n_jobs=4):
conn_fol = op.join(MMVT_DIR, subject, 'connectivity')
now = time.time()
for run, fif_fname in enumerate(files):
utils.time_to_go(now, run, len(files), runs_num_to_print=1)
file_name = utils.namebase(fif_fname)
labels_data_name = 'labels_data_{}-epilepsy-{}-{}-{}_{}_mean_flip_{}.npz'.format(
subject, 'dSPM', modality, file_name, atlas, '{hemi}')
if not utils.both_hemi_files_exist(
op.join(MMVT_DIR, subject, modality, labels_data_name)):
print('labels data does not exist for {}!'.format(file_name))
for band_name, band_freqs in bands.items():
output_fname = op.join(
conn_fol,
'{}_{}_{}_{}.npy'.format(modality, file_name, band_name,
connectivity_method))
if op.isfile(output_fname) and not overwrite:
print('{} {} connectivity for {} already exist'.format(
connectivity_method, band_name, file_name))
continue
print('calc_meg_connectivity: {}'.format(band_name))
con_args = connectivity.read_cmd_args(
utils.Bag(
subject=subject,
atlas=atlas,
function='calc_lables_connectivity',
connectivity_modality=modality,
connectivity_method=connectivity_method,
labels_data_name=labels_data_name,
windows_length=500,
windows_shift=100,
identifier='{}_{}'.format(file_name, band_name),
fmin=band_freqs[0],
fmax=band_freqs[1],
sfreq=2035, # clin MEG
recalc_connectivity=False,
save_mmvt_connectivity=True,
threshold_percentile=80,
n_jobs=n_jobs))
connectivity.call_main(con_args)
def compare_coh_windows(subject, task, conditions, electrodes, freqs=((8, 12), (12, 25), (25,55), (55,110)), do_plot=False):
electrodes_coh = np.load(op.join(ELECTRODES_DIR, subject, task, 'electrodes_coh_windows.npy'))
meg_electrodes_coh = np.load(op.join(ELECTRODES_DIR, subject, task, 'meg_electrodes_ts_coh_windows.npy'))
figs_fol = op.join(MMVT_DIR, subject, 'figs', 'coh_windows')
utils.make_dir(figs_fol)
results = []
for cond_id, cond in enumerate(conditions):
now = time.time()
for freq_id, freq in enumerate(freqs):
freq = '{}-{}'.format(*freq)
indices = list(utils.lower_rec_indices(electrodes_coh.shape[0]))
for ind, (i, j) in enumerate(indices):
utils.time_to_go(now, ind, len(indices))
meg = meg_electrodes_coh[i, j, :, freq_id, cond_id][:22]
elc = electrodes_coh[i, j, :, freq_id, cond_id][:22]
elc_diff = np.max(elc) - np.min(elc)
meg *= elc_diff / (np.max(meg) - np.min(meg))
meg += np.mean(elc) - np.mean(meg)
if sum(meg) > len(meg) * 0.99:
continue
data_diff = meg - elc
# data_diff = data_diff / max(data_diff)
rms = np.sqrt(np.mean(np.power(data_diff, 2)))
corr = np.corrcoef(meg, elc)[0, 1]
results.append(dict(elc1=electrodes[i], elc2=electrodes[j], cond=cond, freq=freq, rms=rms, corr=corr))
if False: #do_plot and electrodes[i]=='RPT7' and electrodes[j] == 'RPT5': #corr > 10 and rms < 3:
plt.figure()
plt.plot(meg, label='pred')
plt.plot(elc, label='elec')
plt.legend()
# plt.title('{}-{} {} {}'.format(electrodes[i], electrodes[j], freq, cond)) # (rms:{:.2f})
plt.savefig(op.join(figs_fol, '{:.2f}-{}-{}-{}-{}.jpg'.format(rms, electrodes[i], electrodes[j], freq, cond)))
plt.close()
results_fname = op.join(figs_fol, 'results{}.csv'.format('_bipolar' if bipolar else ''))
rmss, corrs = [], []
with open(results_fname, 'w') as output_file:
for res in results:
output_file.write('{},{},{},{},{},{}\n'.format(
res['elc1'], res['elc2'], res['cond'], res['freq'], res['rms'], res['corr']))
rmss.append(res['rms'])
corrs.append(res['corr'])
rmss = np.array(rmss)
corrs = np.array(corrs)
pass
def compare_coh_windows(subject, task, conditions, electrodes, freqs=((8, 12), (12, 25), (25,55), (55,110)), do_plot=False):
electrodes_coh = np.load(op.join(ELECTRODES_DIR, subject, task, 'electrodes_coh_windows.npy'))
meg_electrodes_coh = np.load(op.join(ELECTRODES_DIR, subject, task, 'meg_electrodes_ts_coh_windows.npy'))
figs_fol = op.join(MMVT_DIR, subject, 'figs', 'coh_windows')
utils.make_dir(figs_fol)
results = []
for cond_id, cond in enumerate(conditions):
now = time.time()
for freq_id, freq in enumerate(freqs):
freq = '{}-{}'.format(*freq)
indices = list(utils.lower_rec_indices(electrodes_coh.shape[0]))
for ind, (i, j) in enumerate(indices):
utils.time_to_go(now, ind, len(indices))
meg = meg_electrodes_coh[i, j, :, freq_id, cond_id][:22]
elc = electrodes_coh[i, j, :, freq_id, cond_id][:22]
elc_diff = np.max(elc) - np.min(elc)
meg *= elc_diff / (np.max(meg) - np.min(meg))
meg += np.mean(elc) - np.mean(meg)
if sum(meg) > len(meg) * 0.99:
continue
data_diff = meg - elc
# data_diff = data_diff / max(data_diff)
rms = np.sqrt(np.mean(np.power(data_diff, 2)))
corr = np.corrcoef(meg, elc)[0, 1]
results.append(dict(elc1=electrodes[i], elc2=electrodes[j], cond=cond, freq=freq, rms=rms, corr=corr))
if electrodes[i]=='RAF6' and electrodes[j] == 'LOF4': #corr > 10 and rms < 3:
plt.figure()
plt.plot(meg, label='prediction')
plt.plot(elc, label='electrode')
plt.legend()
# plt.title('{}-{} {} {}'.format(electrodes[i], electrodes[j], freq, cond)) # (rms:{:.2f})
plt.savefig(op.join(figs_fol, '{:.2f}-{}-{}-{}-{}.jpg'.format(rms, electrodes[i], electrodes[j], freq, cond)))
plt.close()
results_fname = op.join(figs_fol, 'results{}.csv'.format('_bipolar' if bipolar else ''))
rmss, corrs = [], []
with open(results_fname, 'w') as output_file:
for res in results:
output_file.write('{},{},{},{},{},{}\n'.format(
res['elc1'], res['elc2'], res['cond'], res['freq'], res['rms'], res['corr']))
rmss.append(res['rms'])
corrs.append(res['corr'])
rmss = np.array(rmss)
corrs = np.array(corrs)
pass
def _calc_graph_func(p):
con, times_chunk, graph_func = p
vals = []
now = time.time()
for run, t in enumerate(times_chunk):
utils.time_to_go(now, run, len(times_chunk), 10)
con_t = con[:, :, t]
g = nx.from_numpy_matrix(con_t)
if graph_func == 'closeness_centrality':
x = nx.closeness_centrality(g)
elif graph_func == 'degree_centrality':
x = nx.degree_centrality(g)
elif graph_func == 'eigenvector_centrality':
x = nx.eigenvector_centrality(g, max_iter=10000)
elif graph_func == 'katz_centrality':
x = nx.katz_centrality(g, max_iter=100000)
else:
raise Exception('Wrong graph func!')
vals.append([x[k] for k in range(len(x))])
vals = np.array(vals)
return vals, times_chunk
def calc_electrodes_coh_windows(subject, input_fname, conditions, bipolar, meg_electordes_names, meg_electrodes_data, tmin=0, tmax=2.5, sfreq=1000,
freqs=((8, 12), (12, 25), (25,55), (55,110)), bw=15, dt=0.1, window_len=0.2, n_jobs=6):
output_file = op.join(ELECTRODES_DIR, subject, task, 'electrodes_coh_{}windows_{}.npy'.format('bipolar_' if bipolar else '', window_len))
if input_fname[-3:] == 'mat':
d = sio.loadmat(matlab_input_file)
conds_data = [d[conditions[0]], d[conditions[1]]]
electrodes = get_electrodes_names(subject, task)
elif input_fname[-3:] == 'npz':
d = np.load(input_fname)
conds_data = d['data']
conditions = d['conditions']
electrodes = d['names'].tolist()
pass
indices_to_remove, electrodes_indices = electrodes_tp_remove(electrodes, meg_electordes_names)
windows = np.linspace(tmin, tmax - dt, tmax / dt)
for cond, data in enumerate(conds_data):
data = scipy.delete(data, indices_to_remove, 1)
data = data[:, electrodes_indices, :]
data = downsample_data(data)
data = data[:, :, :meg_electrodes_data.shape[2]]
if cond == 0:
coh_mat = np.zeros((data.shape[1], data.shape[1], len(windows), len(freqs), 2))
# coh_mat = np.load(output_file)
# continue
now = time.time()
for freq_ind, (fmin, fmax) in enumerate(freqs):
for win, tmin in enumerate(windows):
try:
print('cond {}, tmin {}'.format(cond, tmin))
utils.time_to_go(now, win + 1, len(windows))
con_cnd, _, _, _, _ = spectral_connectivity(
data, method='coh', mode='multitaper', sfreq=sfreq,
fmin=fmin, fmax=fmax, mt_adaptive=True, n_jobs=n_jobs, mt_bandwidth=bw, mt_low_bias=True,
tmin=tmin, tmax=tmin + window_len)
con_cnd = np.mean(con_cnd, axis=2)
coh_mat[:, :, win, freq_ind, cond] = con_cnd
except:
print('Error with freq {} and win {}'.format(freq_ind, win))
np.save(output_file[:-4], coh_mat)
def calc_electrodes_coh_windows(subject, input_fname, conditions, bipolar, meg_electordes_names, meg_electrodes_data, tmin=0, tmax=2.5, sfreq=1000,
freqs=((8, 12), (12, 25), (25,55), (55,110)), bw=15, dt=0.1, window_len=0.2, n_jobs=6):
output_file = op.join(ELECTRODES_DIR, subject, task, 'electrodes_coh_{}windows_{}.npy'.format('bipolar_' if bipolar else '', window_len))
if input_fname[-3:] == 'mat':
d = sio.loadmat(matlab_input_file)
conds_data = [d[conditions[0]], d[conditions[1]]]
electrodes = get_electrodes_names(subject, task)
elif input_fname[-3:] == 'npz':
d = np.load(input_fname)
conds_data = d['data']
conditions = d['conditions']
electrodes = d['names'].tolist()
pass
indices_to_remove, electrodes_indices = electrodes_tp_remove(electrodes, meg_electordes_names)
windows = np.linspace(tmin, tmax - dt, tmax / dt)
for cond, data in enumerate(conds_data):
data = scipy.delete(data, indices_to_remove, 1)
data = data[:, electrodes_indices, :]
data = downsample_data(data)
data = data[:, :, :meg_electrodes_data.shape[2]]
if cond == 0:
coh_mat = np.zeros((data.shape[1], data.shape[1], len(windows), len(freqs), 2))
# coh_mat = np.load(output_file)
# continue
now = time.time()
for freq_ind, (fmin, fmax) in enumerate(freqs):
for win, tmin in enumerate(windows):
try:
print('cond {}, tmin {}'.format(cond, tmin))
utils.time_to_go(now, win + 1, len(windows))
con_cnd, _, _, _, _ = spectral_connectivity(
data, method='coh', mode='multitaper', sfreq=sfreq,
fmin=fmin, fmax=fmax, mt_adaptive=True, n_jobs=n_jobs, mt_bandwidth=bw, mt_low_bias=True,
tmin=tmin, tmax=tmin + window_len)
con_cnd = np.mean(con_cnd, axis=2)
coh_mat[:, :, win, freq_ind, cond] = con_cnd
except:
print('Error with freq {} and win {}'.format(freq_ind, win))
np.save(output_file[:-4], coh_mat)
def filter_meg_labels_ts(subject,
inv_method='dSPM',
em='mean_flip',
atlas='electrodes_labels',
low_freq_cut_off=10,
fs=1000,
do_plot=False,
n_jobs=4):
folders = glob.glob(
op.join(MMVT_DIR, subject, 'meg',
'{}_*_*_Resting_eeg_meg_Demi_ar-epo'.format(subject)))
now = time.time()
for fol_ind, fol in enumerate(folders):
utils.time_to_go(now, fol_ind, len(folders), runs_num_to_print=1)
files = glob.glob(
op.join(
fol, 'labels_data_rest_{}_{}_{}_?h.npz'.format(
atlas, inv_method, em)))
for fname in files:
hemi = lu.get_hemi_from_name(utils.namebase(fname))
d = utils.Bag(np.load(fname))
L = d.data.shape[0] # labels * time * epochs
filter_data = np.empty(d.data.shape)
params = [(d.data[label_ind], label_ind, fs, low_freq_cut_off,
do_plot) for label_ind in range(L)]
results = utils.run_parallel(_filter_meg_label_ts_parallel, params,
n_jobs)
for filter_label_data, label_ind in results:
filter_data[label_ind] = filter_label_data
new_fname = op.join(
fol, 'labels_data_rest_{}_{}_{}_filter_{}.npz'.format(
atlas, inv_method, em, hemi))
np.savez(new_fname,
data=filter_data,
names=d.names,
conditions=d.conditions)
def parcelate(subject,
atlas,
hemi,
surface_type,
vertices_labels_ids_lookup=None,
overwrite_vertices_labels_lookup=False):
output_fol = op.join(MMVT_DIR, subject, 'labels',
'{}.{}.{}'.format(atlas, surface_type, hemi))
utils.make_dir(output_fol)
vtx, fac = utils.read_ply_file(
op.join(MMVT_DIR, subject, 'surf',
'{}.{}.ply'.format(hemi, surface_type)))
if vertices_labels_ids_lookup is None or overwrite_vertices_labels_lookup:
vertices_labels_ids_lookup = lu.create_vertices_labels_lookup(
subject, atlas, True, overwrite_vertices_labels_lookup)[hemi]
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas, hemi=hemi)
if 'unknown-{}'.format(hemi) not in [l.name for l in labels]:
labels.append(lu.Label([], name='unknown-{}'.format(hemi), hemi=hemi))
nV = vtx.shape[0]
nF = fac.shape[0]
nL = len(labels)
# print('The number of unique labels is {}'.format(nL))
vtxL = [[] for _ in range(nL)]
facL = [[] for _ in range(nL)]
now = time.time()
for f in range(nF):
utils.time_to_go(now, f, nF, runs_num_to_print=50000)
# Current face & labels
Cfac = fac[f]
Cidx = [vertices_labels_ids_lookup[vert_ind] for vert_ind in Cfac]
# Depending on how many vertices of the current face
# are in different labels, behave differently
# nuCidx = len(np.unique(Cidx))
# if nuCidx == 1: # If all vertices share same label
# same_label = utils.all_items_equall(Cidx)
# if same_label:
if Cidx[0] == Cidx[1] == Cidx[2]:
# Add the current face to the list of faces of the
# respective label, and don't create new faces
facL[Cidx[0]] += [Cfac.tolist()]
else: # If 2 or 3 vertices are in different labels
# Create 3 new vertices at the midpoints of the 3 edges
vtxCfac = vtx[Cfac]
vtxnew = (vtxCfac + vtxCfac[[1, 2, 0]]) / 2
vtx = np.concatenate((vtx, vtxnew))
# Define 4 new faces, with care preserve normals (all CCW)
facnew = [[Cfac[0], nV, nV + 2], [nV, Cfac[1], nV + 1],
[nV + 2, nV + 1, Cfac[2]], [nV, nV + 1, nV + 2]]
# Update nV for the next loop
nV = vtx.shape[0]
# Add the new faces to their respective labels
facL[Cidx[0]] += [facnew[0]]
facL[Cidx[1]] += [facnew[1]]
facL[Cidx[2]] += [facnew[2]]
freq_Cidx = mode(Cidx)
facL[freq_Cidx] += [facnew[3]] # central face
# Having defined new faces and assigned all faces to labels, now
# select the vertices and redefine faces to use the new vertex indices
# Also, create the file for the indices
# fidx = fopen(sprintf('%s.index.csv', srfprefix), 'w');
# params = []
# for lab in range(nL):
# facL_lab = facL[lab]
# facL_lab_flat = utils.list_flatten(facL_lab)
# vidx = list(set(facL_lab_flat))
# vtxL_lab = vtx[vidx]
# params.append((facL_lab, vtxL_lab, vidx, nV, labels[lab].name, hemi, output_fol))
# utils.run_parallel(writing_ply_files_parallel, params, njobs=n_jobs)
#
ret = True
for lab in range(nL):
ret = ret and writing_ply_files(subject, surface_type, lab, facL[lab],
vtx, vtxL, labels, hemi, output_fol)
return ret
def calc_ieeg_connectivity(subject,
connectivity_method,
graph_func,
sfreq,
big_window_length,
windows_length,
windows_shift,
overwrite=False,
n_jobs=4):
mmvt_root = op.join(MMVT_DIR, subject, 'electrodes')
output_fol = utils.make_dir(
op.join(mmvt_root, '{}_{}'.format(connectivity_method, graph_func)))
files_dict = {}
data_files = glob.glob(op.join(mmvt_root, 'electrodes_data_*.npy'))
ictal_ids = sorted(
list(set([utils.namebase(f).split('_')[2] for f in data_files])))
now = time.time()
for run, id in enumerate(ictal_ids):
utils.time_to_go(now, run, len(ictal_ids), 1)
data_fname = op.join(mmvt_root, 'electrodes_data_{}.npy'.format(id))
files_dict[utils.namebase(data_fname)] = {
'baseline': [],
'ictal': [data_fname]
}
data = np.load(data_fname).squeeze()
for band_name, (fmin, fmax) in bands.items():
output_fname = op.join(
output_fol,
'{}_{}_{}_{}.npy'.format(utils.namebase(data_fname),
connectivity_method, graph_func,
band_name))
if op.isfile(output_fname) and not overwrite:
continue
print(utils.namebase(output_fname))
con = connectivity.calc_mi(data, windows_length, windows_shift,
sfreq, fmin, fmax, n_jobs)
graph_data = analyze_graph_data(con, n_jobs)
np.save(output_fname, graph_data)
baseline_fname = op.join(mmvt_root,
'electrodes_baseline_{}.npy'.format(id))
data = np.load(baseline_fname).squeeze()
w = sfreq * big_window_length
windows = connectivity.calc_windows(data.shape[1], w, w)
for base_ind, w in enumerate(windows):
for band_name, (fmin, fmax) in bands.items():
output_fname = op.join(
output_fol,
'{}_{}_{}_{}_{}.npy'.format(utils.namebase(baseline_fname),
connectivity_method,
graph_func, base_ind,
band_name))
files_dict[utils.namebase(data_fname)]['baseline'].append(
output_fname)
if op.isfile(output_fname) and not overwrite:
continue
print(utils.namebase(output_fname))
con = connectivity.calc_mi(data[:, w[0]:w[1]], windows_length,
windows_shift, sfreq, fmin, fmax,
n_jobs)
graph_data = analyze_graph_data(con, n_jobs)
np.save(output_fname, graph_data)
return files_dict
from src.utils import utils
from src.utils import preproc_utils as pu
from src.preproc import anatomy as anat
SUBJECTS_DIR, MMVT_DIR, FREESURFER_HOME = pu.get_links()
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)
if __name__ == '__main__':
subs = anat.load_subcortical_lookup_table()
now, N = time.time(), len(subs)
for ind, (k, name) in enumerate(subs.items()):
utils.time_to_go(now, ind, N, runs_num_to_print=1)
create_surf('mg116', k, name)
def post_meg_preproc(args):
inv_method, em, atlas = 'dSPM', 'mean_flip', 'darpa_atlas'
bands = dict(theta=[4, 8],
alpha=[8, 15],
beta=[15, 30],
gamma=[30, 55],
high_gamma=[65, 200])
norm_times = (500, 2500)
do_plot = False
subjects = args.subject
res_fol = utils.make_dir(
op.join(utils.get_parent_fol(MMVT_DIR), 'msit-ecr'))
subjects_with_results = {}
labels = lu.read_labels(subjects[0], SUBJECTS_DIR, atlas)
labels_names = [l.name for l in labels]
labels_num = len(labels_names)
epochs_max_num = 50
template_brain = 'colin27'
now = time.time()
bands_power_mmvt_all = []
for subject_ind, subject in enumerate(subjects):
utils.time_to_go(now, subject_ind, len(subjects), runs_num_to_print=1)
subjects_with_results[subject] = {}
input_fol = utils.make_dir(
op.join(MEG_DIR, subject, 'labels_induced_power'))
plots_fol = utils.make_dir(op.join(input_fol, 'plots'))
args.subject = subject
bands_power_mmvt = {'rh': {}, 'lh': {}}
for task_ind, task in enumerate(args.tasks):
task = task.lower()
input_fnames = glob.glob(
op.join(
input_fol, '{}_*_{}_{}_induced_power.npz'.format(
task, inv_method, em)))
if len(input_fnames) < 1: # labels_num:
print('No enough files for {} {}!'.format(subject, task))
subjects_with_results[subject][task] = False
continue
# input_dname = ecr_caudalanteriorcingulate-lh_dSPM_mean_flip_induced_power
# if not do_plot:
# continue
bands_power = np.empty((len(bands), labels_num, epochs_max_num))
for input_fname in input_fnames:
d = utils.Bag(np.load(input_fname)) # label_name, atlas, data
# label_power = np.empty((len(bands), epochs_num, T)) (5, 50, 3501)
label_power, label_name = d.data, d.label_name
# for band_ind in range(len(bands)):
# label_power[band_ind] /= label_power[band_ind][:, norm_times[0]:norm_times[1]].mean()
label_ind = labels_names.index(label_name)
hemi = labels[label_ind].hemi
for band_ind, band in enumerate(bands.keys()):
label_power_norm = label_power[
band_ind][:, norm_times[0]:norm_times[1]].mean(
axis=1)[:epochs_max_num]
if len(label_power_norm) != epochs_max_num:
print('{} does have {} epochs!'.format(
input_fname, len(label_power_norm)))
break
bands_power[band_ind, label_ind] = label_power_norm
if band not in bands_power_mmvt[hemi]:
bands_power_mmvt[hemi][band] = np.empty(
(len(labels_names), label_power[band_ind].shape[1],
1, len(args.tasks)))
bands_power_mmvt[hemi][band][
label_ind, :, 0,
task_ind] = label_power[band_ind].mean(axis=0)
fig_fname = op.join(plots_fol,
'power_{}_{}.jpg'.format(label_name, task))
if do_plot: # not op.isfile(fig_fname) and
times = np.arange(
0,
label_power.shape[2]) if 'times' not in d else d.times
plot_label_power(label_power, times, label_name, bands,
task, fig_fname)
for band_ind, band in enumerate(bands.keys()):
power_fname = op.join(
res_fol, subject, '{}_labels_{}_{}_{}_power.npz'.format(
task.lower(), inv_method, em, band))
np.savez(power_fname,
data=np.array(bands_power[band_ind]),
names=labels_names)
subjects_with_results[subject][task] = True
if all(subjects_with_results[subject].values()):
bands_power_mmvt_all.append(bands_power_mmvt)
else:
print('{} does not have both tasks data!'.format(subject))
labels_data_template = op.join(MMVT_DIR, template_brain, 'meg',
'labels_data_power_{}_{}_{}_{}_{}.npz'
) # task, atlas, extract_method, hemi
for hemi in utils.HEMIS:
for band_ind, band in enumerate(bands.keys()):
power = np.array([x[hemi][band]
for x in bands_power_mmvt_all]).mean(axis=0)
labels_output_fname = meg.get_labels_data_fname(
labels_data_template, inv_method, band, atlas, em, hemi)
utils.make_dir(utils.get_parent_fol(labels_output_fname))
np.savez(labels_output_fname,
data=power,
names=labels_names,
conditions=args.tasks)
have_all = len([
subject for subject, results in subjects_with_results.items()
if all(results.values())
])
print('{}/{} with all files'.format(have_all, len(subjects)))
print(subjects_with_results)