import matplotlib.pyplot as plt
import numpy as np
import utils as ut
from definitions import SAVE_PATH_FIGURES
"""
Plot the mean coherence over subjects. select for every subject the channel with the largest amplitude in coherence.
"""
# load data
suffix = ''
window_length = 1024
data = ut.load_data_analysis('coh_icoh_allsubjects_w{}_{}.p'.format(
window_length, suffix))
# now make a plot of all selected channels and the histogram over peaks
f = data['frequs']
mask = ut.get_array_mask(f > 1, f < 30)
coh_mat = data['coh_mat'][:, :, mask]
icoh_mat = data['icoh_mat'][:, :, mask]
n_subjects, n_channels, n_frequ_samples = coh_mat.shape
max_coh_channels = np.zeros((n_subjects, n_frequ_samples))
max_icoh_channels = np.zeros((n_subjects, n_frequ_samples))
for subject_idx in range(n_subjects):
# select the channel with the largest coherence
channel_idx = np.argmax(np.max(coh_mat[subject_idx, ], axis=1))
max_coh_channels[subject_idx, ] = coh_mat[subject_idx, channel_idx, :]
max_icoh_channels[subject_idx, ] = icoh_mat[subject_idx, channel_idx, :]
# take mean and SE over subjects
# look at the pac data and select useful frequency ranges for every condition, hemisphere and mean channel
# look at left and right values separately
pac_left = pac_matrix[left_channel_idx, ].mean(
axis=(0, 2)) # mean over channels within a hemisphere
pac_right = pac_matrix[right_channel_idx, ].mean(
axis=(0, 2)) # , and over amp f?
# new shape: (phase-f)
# goal: find bands for every hemisphere
bands = dict(left=[], right=[])
for condition_idx, condition in enumerate(conditions):
# for left
# consider reasonable beta range
mask = ut.get_array_mask(f_phase > 10, f_phase < 40).squeeze()
f_mask = f_phase[mask]
data = pac_left[condition_idx, mask]
# smooth the mean PAC
smoother_pac_left = ut.smooth_with_mean_window(data, window_size=5)
max_idx = np.argmax(smoother_pac_left)
# plt.subplot(1, 2, 1)
# plt.title('Subject {}, {}'.format(subject_id, 'left'))
# plt.plot(f_mask, data, alpha=.5)
# plt.plot(f_mask, smoother_pac_left, label=condition)
# plt.plot(f_mask[max_idx], smoother_pac_left[max_idx], 'ro')
# plt.legend()
# select the band +-5 Hz around the peak
bands['left'].append([f_mask[max_idx] - 5, f_mask[max_idx] + 5])
rdsr = np.zeros(n_epochs)
mpl = np.zeros(n_epochs) # mean phase vector length
mpa = np.zeros(n_epochs) # amplitude
beta_amp = np.zeros(n_epochs)
# for every epoch
for epoch_idx, epoch in enumerate(channel_lfp.T):
# do preprocessing a la Cole et al
# low pass filter
lfp_pre = ut.low_pass_filter(y=epoch, fs=fs, cutoff=100, numtaps=250)
# extract beta amplitude
# calculate psd
frequs, psd = ut.calculate_psd(lfp_pre, fs=fs, window_length=1024)
# get the mask of the current band
band_mask = ut.get_array_mask(frequs >= beta_bands[subject_idx][0],
frequs <= beta_bands[subject_idx][1])
# calculate beta amplitude
beta_amp[epoch_idx] = np.mean(psd[band_mask])
# band pass filter
lfp_band = ut.band_pass_iir(y=lfp_pre,
fs=fs,
band=beta_bands[subject_idx])
# remove potential ringing artifacts
idx_167ms = int((fs / 1000) * 167)
lfp_band = lfp_band[idx_167ms:-idx_167ms]
lfp_band -= lfp_band.mean()
lfp_pre = lfp_pre[idx_167ms:-idx_167ms]
lfp_pre -= lfp_pre.mean()
for epoch_idx, epoch in enumerate(channel_lfp.T):
# do preprocessing a la Cole et al
# low pass filter
lfp_pre = ut.low_pass_filter(y=epoch,
fs=fs,
cutoff=100,
numtaps=250)
# extract beta amplitude
# calculate psd
frequs, psd = ut.calculate_psd(lfp_pre,
fs=fs,
window_length=1024)
# get the mask of the current band
band_mask = ut.get_array_mask(frequs >= current_band[0],
frequs <= current_band[1])
# calculate beta amplitude
beta_amp[epoch_idx] = np.mean(psd[band_mask])
# band pass filter
lfp_band = ut.band_pass_iir(y=lfp_pre,
fs=fs,
band=current_band)
# remove potential ringing artifacts
idx_167ms = int((fs / 1000) * 167)
lfp_band = lfp_band[idx_167ms:-idx_167ms]
lfp_band -= lfp_band.mean()
lfp_pre = lfp_pre[idx_167ms:-idx_167ms]
lfp_pre -= lfp_pre.mean()
def plot_beta_band_selection_illustration_for_poster(pac_matrix_sig,
pac_matrix_nonsig,
sig_matrix1,
sig_matrix2,
n_phase,
n_amplitude,
f_phase,
f_amp,
mask,
smoother_pac,
max_idx,
current_lfp_epochs,
subject_id,
fs,
save=False):
# plot both, the sig and the smoothed pac mean
fontsize = 20
y_tick_steps = 3
x_tick_steps = 5
tick_size = 15
legend_size = 15
vmin = pac_matrix_sig.min()
vmax = pac_matrix_sig.max()
plt.figure(figsize=(15, 6))
# plot the PAC matrix
plt.subplot2grid((2, 4), (0, 0), rowspan=2)
current_pac_data = pac_matrix_nonsig
plt.imshow(current_pac_data,
interpolation='None',
origin='lower',
vmin=vmin,
vmax=vmax)
# plot contours of significance
contours = measure.find_contours(sig_matrix2, 0)
for n, contour in enumerate(contours):
plt.plot(contour[:, 1], contour[:, 0], linewidth=.5, color='orange')
plt.xticks(np.linspace(0, n_phase, y_tick_steps),
np.linspace(f_phase.min(),
f_phase.max(),
y_tick_steps,
dtype=int),
fontsize=tick_size)
plt.yticks(np.linspace(0, n_amplitude, x_tick_steps),
np.linspace(f_amp.min(), f_amp.max(), x_tick_steps, dtype=int),
fontsize=tick_size)
plt.xlabel('Phase frequency [Hz]', fontsize=fontsize)
plt.ylabel('Amplitude frequency [Hz]', fontsize=fontsize)
plt.title('PAC, discarded', fontsize=fontsize)
plt.colorbar(
pad=0.02,
fraction=.09,
ticks=np.round(
[vmin + 0.01,
np.mean((vmin + 0.01, vmax - 0.01)), vmax - 0.01], 2))
plt.subplot2grid((2, 4), (0, 1), rowspan=2)
current_pac_data = pac_matrix_sig
plt.imshow(current_pac_data,
interpolation='None',
origin='lower',
vmin=vmin,
vmax=vmax)
# plot contours of significance
contours = measure.find_contours(sig_matrix1, 0)
for n, contour in enumerate(contours):
plt.plot(contour[:, 1], contour[:, 0], linewidth=.5, color='orange')
plt.xticks(np.linspace(0, n_phase, y_tick_steps),
np.linspace(f_phase.min(),
f_phase.max(),
y_tick_steps,
dtype=int),
fontsize=tick_size)
plt.yticks(np.linspace(0, n_amplitude, x_tick_steps),
np.linspace(f_amp.min(), f_amp.max(), x_tick_steps, dtype=int),
fontsize=tick_size)
plt.xlabel('Phase frequency [Hz]', fontsize=fontsize)
plt.title('PAC, accepted', fontsize=fontsize)
plt.tight_layout()
# plot the smoothed PAC values averaged over amplitude frequencies:
plt.subplot2grid((2, 4), (0, 2), colspan=2)
plt.title('Peak PAC and selected beta range', fontsize=fontsize)
plt.plot(f_phase[mask], smoother_pac)
plt.ylabel('PAC', fontsize=fontsize)
xtick_vals_smoothed = np.linspace(f_phase[mask].min(),
f_phase[mask].max(),
x_tick_steps,
dtype=int)
plt.xticks(np.linspace(f_phase[mask].min(), f_phase[mask].max(),
x_tick_steps),
xtick_vals_smoothed,
fontsize=tick_size)
y_tick_steps = 3
plt.yticks(np.linspace(smoother_pac.min(), smoother_pac.max(),
y_tick_steps),
np.round(
np.linspace(smoother_pac.min(), smoother_pac.max(),
y_tick_steps), 2),
fontsize=tick_size)
# plot the peak
plt.axvline(f_phase[mask][max_idx],
smoother_pac[max_idx],
alpha=.3,
color='C1')
plt.plot(f_phase[mask][max_idx],
smoother_pac[max_idx],
'o',
markersize=8,
label='peak PAC')
plt.legend(frameon=False, prop={'size': legend_size})
# plot the PSD of the corresponding LFP
plt.subplot2grid((2, 4), (1, 2), colspan=2)
# calculate psd for every epoch, average across epochs
f_psd, psd = ut.calculate_psd(y=current_lfp_epochs[:, 0],
fs=fs,
window_length=1024) # to get the dims
for epoch_idx, lfp_epoch in enumerate(current_lfp_epochs[:, 1:].T):
f_psd, psd_tmp = ut.calculate_psd(y=lfp_epoch,
fs=fs,
window_length=1024)
psd += psd_tmp
# divide by n epochs to average
psd /= current_lfp_epochs.shape[1]
# interpolate the psd to have the same sample point as in the PAC phase dimensions:
psd_inter_f = scipy.interpolate.interp1d(f_psd, psd)
psd = psd_inter_f(f_phase)
plt.plot(f_phase[mask], psd[mask])
plt.xticks(np.linspace(f_phase[mask].min(), f_phase[mask].max(),
x_tick_steps),
xtick_vals_smoothed,
fontsize=tick_size)
plt.yticks(np.linspace(psd[mask].min(), psd[mask].max(), y_tick_steps),
np.round(
np.linspace(psd[mask].min(), psd[mask].max(), y_tick_steps),
1),
fontsize=tick_size)
plt.xlabel('Frequency [Hz]', fontsize=fontsize)
plt.ylabel('PSD', fontsize=fontsize)
# plot the peak and the selected range
plt.axvline(f_phase[mask][max_idx],
smoother_pac[max_idx],
alpha=.5,
color='C1')
fill_mask = ut.get_array_mask(f_phase >= (f_phase[mask][max_idx] - 6),
f_phase <= (f_phase[mask][max_idx] + 6))
plt.fill_between(f_phase,
psd[mask].min(),
psd[mask].max(),
where=fill_mask,
color='C1',
alpha=0.1,
label='selected')
plt.legend(prop={'size': legend_size}, frameon=False)
plt.tight_layout()
if save:
plt.savefig(
os.path.join(
SAVE_PATH_FIGURES,
'example_beta_range_selection_subj{}.pdf'.format(subject_id)))
plt.show()
import matplotlib.pyplot as plt
import numpy as np
import utils as ut
from definitions import SAVE_PATH_FIGURES
"""
Plot figure figure 1A from the Neumann et al 2017 paper manuscript: the average psd over subjects
as well as the histogram over psd peaks in beta and in theta range
"""
# load data
suffix = '_linear_search_and_amp'
data = ut.load_data_analysis('psd_maxamp_theta_beta{}.p'.format(suffix))
# now make a plot of all selected channels and the histogram over peaks
frequs = data['frequs']
mask = ut.get_array_mask(frequs > 4, frequs < 40)
plt.figure(figsize=(7, 5))
# plot individual stectra
# plt.plot(frequs[mask], data['psd_beta'][:, mask].T, linewidth=.7, color='C1', alpha=.5)
# plt.plot(frequs[mask], data['psd_theta'][:, mask].T, linewidth=.7, color='C4', alpha=.5)
# plot std envelope
joined_psd_mean = np.mean(np.vstack((data['psd_theta'], data['psd_beta'])),
axis=0)
se = ut.standard_error(np.vstack((data['psd_theta'], data['psd_beta'])),
axis=0)
plt.fill_between(frequs[mask],
joined_psd_mean[mask] + se[mask],
joined_psd_mean[mask] - se[mask],
alpha=.2,
color='C3',
# for every subject file
for sub, sub_file in enumerate(file_list):
# load data
d = ut.load_data_analysis(sub_file, data_folder=data_folder)
# make new entries in the dict
d['freqs'] = {}
d['psd'] = {}
for i, c in enumerate(d['conditions']):
# notch filter around artefact in 24-26 Hz subharmonics of 50Hz noise
d['lfp'][c] = ut.band_stop_filter(d['lfp'][c], d['fs'][c], band=[23, 27])
# get psd and save it
freqs, psd = ut.calculate_psd(d['lfp'][c], d['fs'][c])
# interpolate between the neighboring bins to remove the dip
mask = ut.get_array_mask(freqs > 23, freqs < 27)
psd[mask] = np.mean(psd[[np.where(mask)[0][0]-1, np.where(mask)[0][-1]+1]])
d['freqs'][c], d['psd'][c] = freqs, psd
# plotting
mask = ut.get_array_mask(freqs > 2, freqs < 40)
plt.plot(d['freqs'][c][mask], d['psd'][c][mask], label=c)
plt.ylabel('power ')
plt.xlabel('Frequency [Hz]')
plt.title('Subject file {}, id {}'.format(sub_file[:-2], d['id']['rest']))
plt.legend()
# save data
ut.save_data(data_dict=d,
filename='subject_{}_cleaned_psd.p'.format(d['number']),
# collect the psd of this mask in a matrix over subjects
# prelocate with mask around the mean peak
mean_peak_theta = data['theta_peaks_all'].mean()
mean_peak_beta = data['beta_peaks_all'].mean()
frequ_samples = 12
psd_range_mat_theta = -1 * np.ones((subject_mask.sum(), frequ_samples))
psd_range_mat_beta = -1 * np.ones((n_subjects, frequ_samples))
for sub in range(n_subjects):
# get the peak
peak_beta = data['beta_peaks_max'][sub]
# build a mask -3, +8 Hz around the peak
mask_beta = ut.get_array_mask(frequs > (peak_beta - 3), frequs <
(peak_beta + 8))
beta_frequs = frequs[mask_beta]
# collect the psd of this mask in a matrix
psd_range_mat_beta[sub, ] = data['psd_beta'][sub, mask_beta]
for sub in range(np.sum(subject_mask)):
# get the peak
peak_theta = theta_peaks[sub]
# build a mask -3, +8 Hz around the peak
mask_theta = ut.get_array_mask(frequs > peak_theta - 3,
frequs < peak_theta + 8)
# collect the psd of this mask in a matrix
for file in file_list:
if file.startswith('spmeeg_'):
d = ut.load_data_spm(file)
fs = d['fsample'][0][0]
channel_labels = d['chanlabels'][0]
fig = plt.figure(figsize=(15, 8))
for i, lfp in enumerate(d['data']):
f, t, sxx = ut.calculate_spectrogram(lfp, fs=fs)
# transform to log
ssx_log = np.log(sxx)
# define a mask and build a grid
mask = ut.get_array_mask(f > 4, f < 12)
xgrid, ygrid = np.meshgrid(f[mask], t)
# plotting
ax = fig.add_subplot(3, 2, i + 1, projection='3d')
surf = ax.plot_surface(X=xgrid, Y=ygrid, Z=ssx_log[mask, :].T, cmap='viridis')
ax.set_xlabel('Frequency [Hz]')
ax.set_ylabel('Time [s]')
ax.set_zlabel('log power ')
fig.colorbar(surf, shrink=0.5, aspect=5)
# save figure
filename_save = file[:-4] + '_spectro.pdf'
plt.savefig(os.path.join(SAVE_PATH_FIGURES, filename_save))
# plt.show()
lfp = d['data'][idx]
if lfp is None:
raise ValueError(
'Could not find the specified channel in the data file: {}'.format(
channel_name))
# remove mean
lfp = lfp - np.mean(lfp)
# filter in theta range:
lfp_filt = band_pass_filter(y=lfp, fs=fs, band=[4, 12], plot_response=False)
# construct the time vector
dt = 1 / fs
t = np.arange(0, d['data'].shape[1] * dt, dt)
# design plotting mask
window_length = 3 # in sec
window_start = 250
mask = get_array_mask(t > window_start, t < window_start + window_length)
plt.figure(figsize=(7, 3))
plt.plot(t[mask], lfp[mask], label='raw')
plt.plot(t[mask], lfp_filt[mask], label='filtered')
plt.ylabel('[$\muV]')
plt.xlabel('time [s]')
plt.title('contact pair GPiR23 from case 19')
plt.legend()
plt.savefig(os.path.join(SAVE_PATH_FIGURES, 'figure_1C.pdf'))
# plt.show()
psds = np.zeros((n_channels, n_frequ_samples))
theta_peak_frequency = np.zeros(n_channels)
beta_peak_frequency = np.zeros(n_channels)
plt.figure(figsize=(10, 5))
for channel_idx, lfp in enumerate(d['data']):
# remove 50Hz noise
lfp_clean = lfp
# lfp_clean = ut.band_stop_filter(lfp, fs, band=[49, 51], plot_response=False)
# calculate psd
frequs, psd = ut.calculate_psd(lfp_clean,
fs=fs,
window_length=window_length)
# normalize like in the paper: take sd of the psd between 4-45 and 55-95Hz
mask = np.logical_or(ut.get_array_mask(frequs > 5, frequs < 45),
ut.get_array_mask(frequs > 55, frequs < 95))
psd /= np.std(psd[mask])
# remove 1 / f component
# frequs_linear, psd_linear = ut.remove_1f_component(frequs, psd)
# save for later
psds[channel_idx, ] = psd
# find peak in theta: use the linearized spectra for finding peaks
idx_theta, peak_amp_theta, ftheta, psd_theta = ut.find_peak_in_band(
frequs, psd, [4, 12], linearize=True)
# save the frequency at which the peak occured, in one long list for the histogram
theta_peaks[electrode_idx] = ftheta[idx_theta]
# save it in a matrix to select it per subject for the alignment
theta_peak_frequency[channel_idx] = ftheta[idx_theta]
# best band selection illustration plot
for channel_idx, channel_label in enumerate(channel_labels):
# the customized freqeuncy bands are saved per hemisphere, therefore we have to find the current hemi
current_hemi = 'left' if channel_label in left_channels else 'right'
# add a new list for condition bands of the current channel
bands[current_hemi][channel_label] = []
for condition_idx, condition in enumerate(conditions):
# get current lfp data
current_lfp_epochs = lfp_dict[condition]['data'][channel_idx]
# consider reasonable beta range
mask = ut.get_array_mask(f_phase >= 12, f_phase <= 40).squeeze()
f_mask = f_phase[mask]
data = pac_phase[channel_idx, condition_idx, mask]
# smooth the mean PAC
smoother_pac = ut.smooth_with_mean_window(data, window_size=3)
max_idx = np.argmax(smoother_pac)
# sum logical significance values across the amplitude frequency dimension
# calculate the binary groups in the significance map
lw, num = measurements.label(sig_matrix[channel_idx,
condition_idx, :, :])
# calculate the area of the clusters:
# from http://stackoverflow.com/questions/25664682/how-to-find-cluster-sizes-in-2d-numpy-array
area = measurements.sum(sig_matrix[channel_idx, condition_idx, ],
lw,
index=np.arange(lw.max() + 1))
# get the size of the largest group
# or conditions
# or both
bands = hemi_dict['bands']
f_phase = hemi_dict['f_phase']
# do it for every band
for band_idx, band in enumerate(bands):
# for PAC analysis
# average across low beta and high and across all HFO amplitude frequencies
# then average across channels
# or look at channels independently
# or conditions
# or both
# get the mask for the current band
phase_band_mask = ut.get_array_mask(f_phase >= band[0],
f_phase <= band[1]).squeeze()
# extract pac values for the current phase band
pac_phase_band = hemi_dict['pac_matrix'][:, :, :, phase_band_mask]
# average over frequency amplitude and over low beta frequencies
pac_phase_band = pac_phase_band.mean(axis=(-2, -1))
# save per condition and channel
pac_results['per_cond_channel'][band_idx,
hemi_idx, :, :] = pac_phase_band
# save pac per channel
pac_results['per_channel'][band_idx,
hemi_idx, :] = pac_phase_band.mean(
axis=1) # average over conditions