def calc_baseline_connectivity(ictals_clips, connectivity_template):
baseline_mat1, baseline_mat2 = None, None
for clip_fname in ictals_clips['baseline']:
clip_name = utils.namebase(clip_fname)
con_ictal_fname = connectivity_template.format(clip_name=clip_name)
print('concatenate {}'.format(utils.namebase(clip_fname)))
d = np.load(con_ictal_fname) # C, W, O = d['con_values'].shape
con_values = connectivity.find_best_ord(d['con_values'], False)
con_values2 = connectivity.find_best_ord(d['con_values2'], False)
if baseline_mat1 is None:
baseline_mat1 = con_values.copy()
baseline_mat2 = con_values2.copy()
else:
baseline_mat1 = np.concatenate((baseline_mat1, con_values), axis=1)
baseline_mat2 = np.concatenate((baseline_mat2, con_values2), axis=1)
return baseline_mat1, baseline_mat2
def norm_values(baseline_x,
cond_x,
divide_by_baseline_std,
threshold,
reduce_to_3d=False):
# cond_x = find_best_ord(cond_x)
# baseline_x = find_best_ord(baseline_x)
# Nodes x Time x Orders
baseline_mean = baseline_x.mean(axis=1, keepdims=True)
baseline_std = cond_x.std(
axis=1, keepdims=True) if divide_by_baseline_std else None
if threshold > 0:
mask_indices = np.where(np.max(np.abs(cond_x), axis=1) < threshold)
if divide_by_baseline_std:
cond_x = (cond_x - baseline_mean) / baseline_std
else:
cond_x = cond_x - baseline_mean
if threshold > 0:
cond_x[mask_indices[0]] = np.zeros(cond_x[mask_indices[0]].shape)
if reduce_to_3d and cond_x.ndim == 4:
from src.preproc import connectivity
cond_x = connectivity.find_best_ord(cond_x)
print('{:.4f} {:.4f}'.format(np.nanmin(cond_x), np.nanmax(cond_x)))
return cond_x
def normalize_connectivity(subject,
ictals_clips,
modality,
divide_by_baseline_std,
threshold,
reduce_to_3d,
overwrite=False,
n_jobs=6):
connectivity_template = connectivity.get_output_fname(
subject, 'gc', modality, 'mean_flip', 'all_{}_func_rois')
for clip_fname in ictals_clips:
clip_name = utils.namebase(clip_fname)
output_fname = '{}_zvals.npz'.format(
connectivity_template.format(clip_name)[:-4])
con_ictal_fname = connectivity_template.format(clip_name)
con_baseline_fname = connectivity_template.format(
'{}_baseline'.format(clip_name))
if not op.isfile(con_ictal_fname) or not op.isfile(con_baseline_fname):
for fname in [
f for f in [con_ictal_fname, con_baseline_fname]
if not op.isfile(f)
]:
print('{} is missing!'.format(fname))
continue
print('normalize_connectivity: {}:'.format(clip_name))
d_ictal = utils.Bag(np.load(con_ictal_fname, allow_pickle=True))
d_baseline = utils.Bag(np.load(con_baseline_fname, allow_pickle=True))
if reduce_to_3d:
d_ictal.con_values = connectivity.find_best_ord(
d_ictal.con_values, False)
d_ictal.con_values2 = connectivity.find_best_ord(
d_ictal.con_values2, False)
d_baseline.con_values = connectivity.find_best_ord(
d_baseline.con_values, False)
d_baseline.con_values2 = connectivity.find_best_ord(
d_baseline.con_values2, False)
d_ictal.con_values = epi_utils.norm_values(d_baseline.con_values,
d_ictal.con_values,
divide_by_baseline_std,
threshold, True)
if 'con_values2' in d_baseline:
d_ictal.con_values2 = epi_utils.norm_values(
d_baseline.con_values2, d_ictal.con_values2,
divide_by_baseline_std, threshold, True)
print('Saving norm connectivity in {}'.format(output_fname))
np.savez(output_fname, **d_ictal)
def calc_cond_and_basline(subject,
con_method,
modality,
condition,
extract_mode,
band_name,
con_indentifer,
use_zvals,
node_names,
nodes_names_includes_hemi=False,
use_abs=True,
threshold=0.7,
window_length=25,
stc_downsample=2,
cond_name='interictals',
stc_subfolder='zvals',
stc_name=''):
import mne
from src.preproc import connectivity
input_fname, baseline_fname = get_cond_and_baseline_fnames(
subject, con_method, modality, condition, extract_mode, band_name,
con_indentifer, use_zvals, cond_name)
if not op.isfile(input_fname) or not op.isfile(baseline_fname):
# print('Can\'t find {}'.format(input_fname))
return None, None, None, None, None, None, None
stcs_fol = op.join(MMVT_DIR, subject, 'meg', stc_subfolder)
if stc_name == '':
stc_name = '{}-epilepsy-dSPM-meg-{}-average-amplitude-zvals-rh.stc'.format(
subject, condition)
stc_fname = op.join(stcs_fol, stc_name)
if op.isfile(stc_fname):
stc = mne.read_source_estimate(stc_fname)
times = utils.downsample(stc.times, stc_downsample) # [window_length:]
stc_data = np.max(stc.data, axis=0)
stc_data = utils.downsample(stc_data,
stc_downsample) # [window_length:]
else:
stc_data, times = None, None
d_cond, d_baseline = np.load(input_fname), np.load(baseline_fname)
con_values1, con_values2 = fix_con_values(d_cond)
con_values1, best_ords1 = connectivity.find_best_ord(con_values1,
return_ords=True)
con_values2, best_ords2 = connectivity.find_best_ord(con_values2,
return_ords=True)
# baseline_values1 = epi_utils.set_new_ords(d_baseline['con_values'], best_ords1)
# baseline_values2 = epi_utils.set_new_ords(d_baseline['con_values2'], best_ords2)
baseline_values1, baseline_values2 = fix_con_values(d_baseline)
baseline_values1 = connectivity.find_best_ord(baseline_values1,
return_ords=False)
baseline_values2 = connectivity.find_best_ord(baseline_values2,
return_ords=False)
mask1 = epi_utils.filter_connections(
con_values1,
d_cond['con_names'],
threshold,
node_names,
'',
use_abs,
nodes_names_includes_hemi=nodes_names_includes_hemi)
mask2 = epi_utils.filter_connections(
con_values2,
d_cond['con_names2'],
threshold,
node_names,
'',
use_abs,
nodes_names_includes_hemi=nodes_names_includes_hemi)
names = np.concatenate(
(d_cond['con_names'][mask1], d_cond['con_names2'][mask2]))
if len(names) == 0:
print('{} no connections'.format(condition))
return None, None, None, None, None, None, None
x_cond = np.concatenate((con_values1[mask1], con_values2[mask2]))
x_baseline = np.concatenate(
(baseline_values1[mask1], baseline_values2[mask2]))
if best_ords1 is not None and best_ords2 is not None:
best_ords = np.concatenate((best_ords1[mask1], best_ords2[mask2]))
names = [
'{} {}'.format(name, int(best_ord))
for name, best_ord in zip(names, best_ords)
]
return d_cond, d_baseline, x_cond, x_baseline, names, stc_data, times
def normalize_connectivity(subject, ictals_clips, modality, atlas, divide_by_baseline_std, threshold,
reduce_to_3d, time_axis=None, overwrite=False, n_jobs=6):
# https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.stats.ttest_1samp.html
import scipy.stats # t, p = scipy.stats.ttest_1samp
import matplotlib.pyplot as plt
calc_method = 'baseline_correction'
top_k=5
include = None #('superiorfrontal', 'parstriangularis', 'rostralmiddlefrontal') #, 'insula')
baseline_con_fname = op.join(MMVT_DIR, subject, 'connectivity', '{}_baseline_{}_gc.npz'.format(modality, atlas))
connectivity_template = op.join(MMVT_DIR, subject, 'connectivity', '{}_all_{}_{}_gc.npz'.format(
modality, '{clip_name}', atlas))
figures_fol = utils.make_dir(op.join(MMVT_DIR, subject, 'figures', 'gc'))
if not op.isfile(baseline_con_fname) or overwrite:
baseline_con_values1, baseline_con_values2 = calc_baseline_connectivity(ictals_clips, connectivity_template)
print('Saving baseline connectivity {}'.format(baseline_con_fname))
np.savez(baseline_con_fname, con_values=baseline_con_values1, con_values2=baseline_con_values2)
else:
print('Loading baseline connectivity {}'.format(baseline_con_fname))
d_baseline = np.load(baseline_con_fname)
baseline_con_values1, baseline_con_values2 = d_baseline['con_values'], d_baseline['con_values2']
for clip_fname in ictals_clips['ictal']:
clip_name = utils.namebase(clip_fname)
print('\n\nAnalyzing {}'.format(clip_name))
output_fname = op.join(MMVT_DIR, subject, 'connectivity', '{}_{}_{}_sig_con.pkl'.format(
modality, clip_name, atlas))
if False: #op.isfile(output_fname) and not overwrite:
sig_con1, sig_con2, names1, names2 = utils.load(output_fname)
else:
con_ictal_fname = connectivity_template.format(clip_name=clip_name)
d_ictal = utils.Bag(np.load(con_ictal_fname, allow_pickle=True))
con_values1 = connectivity.find_best_ord(d_ictal.con_values, False)
con_values2 = connectivity.find_best_ord(d_ictal.con_values2, False)
# names = np.concatenate((d_cond['con_names'][mask1], d_cond['con_names2'][mask2]))
C, T = con_values1.shape
sig_con1, sig_con2, names1, names2 = [[]] * T, [[]] * T, [[]] * T, [[]] * T
for t in range(T):
inds = np.where(con_values1[:, t] < con_values2[:, t])
con_values1[inds, t] = 0
inds2 = np.where(con_values2[:, t] < con_values1[:, t])
con_values2[inds2, t] = 0
if calc_method == 'ttest_1samp':
res1 = scipy.stats.ttest_1samp(baseline_con_values1, con_values1[:, t], axis=1)[0]
res2 = scipy.stats.ttest_1samp(baseline_con_values2, con_values2[:, t], axis=1)[0]
elif calc_method == 'zvals':
res1 = (con_values1[:, t] - baseline_con_values1.mean(1)) / baseline_con_values1.std(1)
res2 = (con_values2[:, t] - baseline_con_values2.mean(1)) / baseline_con_values2.std(1)
elif calc_method == 'baseline_correction':
res1 = (con_values1[:, t] - baseline_con_values1.mean(1))
res2 = (con_values2[:, t] - baseline_con_values2.mean(1))
if include is None:
mask1 = np.where(res1 > sorted(res1)[-top_k])[0]
mask2 = np.where(res2 > sorted(res2)[-top_k])[0]
else:
mask1 = np.where(res1 > 0)[0] # sorted(ttest_res1)[-top_k])[0]
mask2 = np.where(res2 > 0)[0] #sorted(ttest_res2)[-top_k])[0]
sig_con1[t] = res1[mask1]
sig_con2[t] = res2[mask2]
names1[t] = d_ictal['con_names'][mask1]
names2[t] = d_ictal['con_names'][mask2]
# print('Time {}, x->y {} connections > {}, y->x {} connections > {}'.format(
# t, len(sig_con1[t]), p_val_threshold, len(sig_con2[t]), p_val_threshold))
print('Saving results in {}'.format(output_fname))
utils.save((sig_con1, sig_con2, names1, names2), output_fname)
plots.plot_pvalues(clip_name, time_axis, sig_con1, sig_con2, names1, names2, include, figures_fol)
def plot_norm_data(d_cond,
d_baseline,
x_axis,
condition,
threshold,
node_name,
stc_data,
stc_times,
windows_len=100,
windows_shift=10,
ax=None):
import matplotlib.pyplot as plt
from src.preproc import connectivity
# from src.mmvt_addon import colors_utils as cu
norm1 = d_cond['con_values'] - d_baseline['con_values'].mean(1,
keepdims=True)
norm2 = d_cond['con_values2'] - d_baseline['con_values2'].mean(
1, keepdims=True)
norm1, best_ords1 = connectivity.find_best_ord(norm1, return_ords=True)
norm2, best_ords2 = connectivity.find_best_ord(norm2, return_ords=True)
norm = {}
if ax is None:
fig = plt.figure()
ax = fig.add_subplot(111)
from itertools import product
conn_conditions = list(product(['within', 'between'], utils.HEMIS))
# colors = cu.get_distinct_colors(4)
colors = ['c', 'b', 'k', 'm']
lines, labels = [], []
# x_axis = x_axis [:-10]
for conn_type, color in zip(conn_conditions, colors):
mask1 = epi_utils.filter_connections(node_name,
norm1,
d_cond['con_names'],
threshold,
conn_type,
use_abs=False)
mask2 = epi_utils.filter_connections(node_name,
norm2,
d_cond['con_names2'],
threshold,
conn_type,
use_abs=False)
norm[conn_type] = np.concatenate(
(norm1[mask1], norm2[mask2])) #[:, :-10]
names = np.concatenate(
(d_cond['con_names'][mask1], d_cond['con_names2'][mask2]))
if best_ords1 is not None and best_ords2 is not None:
best_ords = np.concatenate((best_ords1[mask1], best_ords2[mask2]))
names = [
'{} {}'.format(name, int(best_ord))
for name, best_ord in zip(names, best_ords)
]
if len(names) == 0 or max(norm[conn_type].max(0)) < 0:
print('{} no connections {}'.format(condition, conn_type))
else:
windows_num = norm[conn_type].shape[1]
dt = (stc_times[-1] - stc_times[windows_len]) / windows_num
print(
'windows num: {} windows length: {:.2f}ms windows shift: {:2f}ms'
.format(windows_num,
(stc_times[windows_len] - stc_times[0]) * 1000,
dt * 1000))
time = np.arange(stc_times[windows_len], stc_times[-1], dt)
marker = '+' if conn_type[0] == 'within' else 'x'
l = ax.scatter(time, norm[conn_type].max(0),
color=color) #, marker=marker)
lines.append(l)
conn_type = (conn_type[0],
'right') if conn_type[1] == 'rh' else (conn_type[0],
'left')
labels.append(' '.join(conn_type) if conn_type[0] ==
'within' else '{} to {}'.format(*conn_type))
if stc_data is not None:
ax2 = ax.twinx()
l = ax2.plot(stc_times[windows_len:], stc_data[windows_len:].T,
'y--') # stc_data[:-100].T
lines.append(l[0])
labels.append('Source normalized activity')
ax2.set_ylim([0.5, 4.5])
# ax2.set_xlim([])
ax2.set_yticks(range(1, 5))
ax2.set_ylabel('Source z-values', fontsize=12)
# ax.set_xticks(time)
# xticklabels = ['{}-{}'.format(t, t + windows_shift) for t in time]
# xticklabels[2] = '{}\nonset'.format(xticklabels[2])
# ax.set_xticklabels(xticklabels, rotation=30)
ax.set_ylabel('Causality: Interictals\n minus Baseline', fontsize=12)
# ax.set_yticks([0, 0.5])
ax.set_ylim([0, 0.7])
# ax.axvline(x=x_axis[10], color='r', linestyle='--')
plt.title('{} interictals cluster'.format('Right' if condition ==
'R' else 'Left'))
# labs = [*conn_conditions, 'Source normalized activity']
# ax.legend([l1[conn_conditions[k]][0] for k in range(4)] + l2, labs, loc=0)
# ax.legend([l1[conn_conditions[0]]] + [l1[conn_conditions[1]]] + l2, labs, loc=0)
ax.legend(lines, labels, loc=0)
if ax is None:
plt.show()