deploy: e03c52d

Author: JohnGriffiths

develop/.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: f43e356d84e74a6ccecdbab8dd44ba1e
+tags: 645f666f9bcd5a90fca523b33c5a78b7

develop/.nojekyll

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+"""
+Cueing Group Analysis Winter 2019
+===============================
+
+"""
+
+###################################################################################################
+# Setup
+# -----------------------------
+
+# Standard Pythonic imports
+import os,sys,glob,numpy as np, pandas as pd
+import scipy
+from collections import OrderedDict
+import warnings
+warnings.filterwarnings('ignore')
+from matplotlib import pyplot as plt
+import matplotlib.patches as patches
+
+# MNE functions
+from mne import Epochs, find_events, concatenate_raws
+from mne.time_frequency import tfr_morlet
+
+# EEG-Noteooks functions
+from eegnb.analysis.analysis_utils import load_data
+from eegnb.datasets import fetch_dataset
+
+# sphinx_gallery_thumbnail_number = 1
+
+###################################################################################################
+# Load the data
+# -----------------------------
+
+eegnb_data_path = os.path.join(os.path.expanduser('~/'),'.eegnb', 'data')
+cueing_data_path = os.path.join(eegnb_data_path, 'visual-cueing', 'kylemathlab_dev')
+
+# If dataset hasn't been downloaded yet, download it
+if not os.path.isdir(cueing_data_path):
+      fetch_dataset(data_dir=eegnb_data_path, experiment='visual-cueing', site='kylemathlab_dev')
+
+
+###################################################################################################
+# Put the data into MNE Epochs
+# -----------------------------
+#
+# Fall 2018
+# subs = [101, 102, 103, 104, 105, 106, 108, 109, 110, 111, 112,
+#         202, 203, 204, 205, 207, 208, 209, 210, 211, 
+#         301, 302, 303, 304, 305, 306, 307, 308, 309]
+#
+# Winter 2019
+subs = [1101, 1102, 1103, 1104, 1105, 1106, 1108, 1109, 1110,
+        1202, 1203, 1205, 1206, 1209, 1210, 1211, 1215,
+        1301, 1302, 1313, 
+        1401, 1402, 1403, 1404, 1405,  1408, 1410, 1411, 1412, 1413, 1413, 1414, 1415, 1416]
+#
+# Both
+# subs = [101, 102, 103, 104, 105, 106, 108, 109, 110, 111, 112,
+#         202, 203, 204, 205, 207, 208, 209, 210, 211, 
+#         301, 302, 303, 304, 305, 306, 307, 308, 309,
+#         1101, 1102, 1103, 1104, 1105, 1106, 1108, 1109, 1110,
+#         1202, 1203, 1205, 1206, 1209, 1210, 1211, 1215,
+#         1301, 1302, 1313, 
+#         1401, 1402, 1403, 1404, 1405,  1408, 1410, 1411, 1412, 1413, 1413, 1414, 1415, 1416]
+#
+#
+# placeholders to add to for each subject
+diff_out = []
+Ipsi_out = []
+Contra_out = []
+Ipsi_spectra_out = []
+Contra_spectra_out = []
+diff_spectra_out = []
+ERSP_diff_out = []
+ERSP_Ipsi_out = []
+ERSP_Contra_out = []
+
+frequencies =  np.linspace(6, 30, 100, endpoint=True)
+wave_cycles = 6
+
+# time frequency window for analysis
+f_low = 7 # Hz
+f_high = 10
+f_diff = f_high-f_low
+ 
+t_low = 0 # s
+t_high = 1
+t_diff = t_high-t_low
+
+bad_subs= [6, 7, 13, 26]
+really_bad_subs = [11, 12, 19]
+sub_count = 0    
+    
+    
+    
+for sub in subs:
+    print(sub)
+    
+    sub_count += 1
+
+    
+    if (sub_count in really_bad_subs):
+        rej_thresh_uV = 90
+    elif (sub_count in bad_subs):
+        rej_thresh_uV = 90
+    else:
+        rej_thresh_uV = 90
+
+    rej_thresh = rej_thresh_uV*1e-6
+    
+    
+    # Load both sessions
+    raw = load_data(sub,1, # subject, session
+                    experiment='visual-cueing',site='kylemathlab_dev',device_name='muse2016',
+                    data_dir = eegnb_data_path)
+                
+    raw.append(
+          load_data(sub,2, # subject, session
+                    experiment='visual-cueing', site='kylemathlab_dev', device_name='muse2016',
+                    data_dir = eegnb_data_path))
+    
+
+    # Filter Raw Data
+    raw.filter(1,30, method='iir')
+
+    #Select Events
+    events = find_events(raw)
+    event_id = {'LeftCue': 1, 'RightCue': 2}
+    epochs = Epochs(raw, events=events, event_id=event_id, 
+                    tmin=-1, tmax=2, baseline=(-1, 0), 
+                    reject={'eeg':rej_thresh}, preload=True,
+                    verbose=False, picks=[0, 3])
+    print('Trials Remaining: ' + str(len(epochs.events)) + '.')
+
+    # Compute morlet wavelet
+    # Left Cue
+    tfr, itc = tfr_morlet(epochs['LeftCue'], freqs=frequencies, 
+                          n_cycles=wave_cycles, return_itc=True)
+    tfr = tfr.apply_baseline((-1,-.5),mode='mean')
+    power_Ipsi_TP9 = tfr.data[0,:,:]
+    power_Contra_TP10 = tfr.data[1,:,:]
+
+    # Right Cue
+    tfr, itc = tfr_morlet(epochs['RightCue'], freqs=frequencies, 
+                          n_cycles=wave_cycles, return_itc=True)
+    tfr = tfr.apply_baseline((-1,-.5),mode='mean')
+    power_Contra_TP9 = tfr.data[0,:,:]
+    power_Ipsi_TP10 = tfr.data[1,:,:]
+
+    # Compute averages Differences
+    power_Avg_Ipsi =   (power_Ipsi_TP9+power_Ipsi_TP10)/2;
+    power_Avg_Contra = (power_Contra_TP9+power_Contra_TP10)/2;
+    power_Avg_Diff = power_Avg_Ipsi-power_Avg_Contra;
+    
+    #output data into array
+    times = epochs.times
+    Ipsi_out.append(np.mean(power_Avg_Ipsi[np.argmax(frequencies>f_low):
+                                           np.argmax(frequencies>f_high)-1,
+                            np.argmax(times>t_low):np.argmax(times>t_high)-1 ]
+                           )
+                   )            
+    Ipsi_spectra_out.append(np.mean(power_Avg_Ipsi[:,np.argmax(times>t_low):
+                                                   np.argmax(times>t_high)-1 ],1
+                                   )
+                           )
+        
+    Contra_out.append(np.mean(power_Avg_Contra[np.argmax(frequencies>f_low):
+                                               np.argmax(frequencies>f_high)-1,
+                            np.argmax(times>t_low):np.argmax(times>t_high)-1 ]
+                             )
+                     )
+    
+    Contra_spectra_out.append(np.mean(power_Avg_Contra[:,np.argmax(times>t_low):
+                                                       np.argmax(times>t_high)-1 ],1))
+    
+    
+    diff_out.append(np.mean(power_Avg_Diff[np.argmax(frequencies>f_low):
+                                           np.argmax(frequencies>f_high)-1,
+                            np.argmax(times>t_low):np.argmax(times>t_high)-1 ]
+                           )
+                   )
+    diff_spectra_out.append(np.mean(power_Avg_Diff[:,np.argmax(times>t_low):
+                                                   np.argmax(times>t_high)-1 ],1
+                                   )
+                           )
+    
+    #save the spectrograms to average over after
+    ERSP_diff_out.append(power_Avg_Diff)
+    ERSP_Ipsi_out.append(power_Avg_Ipsi)
+    ERSP_Contra_out.append(power_Avg_Contra)
+    
+    
+###################################################################################################
+# Combine subjects
+# ----------------------------
+
+#average spectrograms
+GrandAvg_diff = np.nanmean(ERSP_diff_out,0)
+GrandAvg_Ipsi = np.nanmean(ERSP_Ipsi_out,0)
+GrandAvg_Contra = np.nanmean(ERSP_Contra_out,0)
+
+#average spectra
+GrandAvg_spec_Ipsi = np.nanmean(Ipsi_spectra_out,0)
+GrandAvg_spec_Contra = np.nanmean(Contra_spectra_out,0)
+GrandAvg_spec_diff = np.nanmean(diff_spectra_out,0)
+
+#error bars for spectra (standard error)
+num_good = len(diff_out) - sum(np.isnan(diff_out))   
+GrandAvg_spec_Ipsi_ste = np.nanstd(Ipsi_spectra_out,0)/np.sqrt(num_good)
+GrandAvg_spec_Contra_ste = np.nanstd(Contra_spectra_out,0)/np.sqrt(num_good)
+GrandAvg_spec_diff_ste = np.nanstd(diff_spectra_out,0)/np.sqrt(num_good)
+
+###################################################################################################
+
+#Plot Spectra error bars
+fig, ax = plt.subplots(1)
+plt.errorbar(frequencies,GrandAvg_spec_Ipsi,yerr=GrandAvg_spec_Ipsi_ste)
+plt.errorbar(frequencies,GrandAvg_spec_Contra,yerr=GrandAvg_spec_Contra_ste)
+plt.legend(('Ipsi','Contra'))
+plt.xlabel('Frequency (Hz)')
+plt.ylabel('Power (uV^2)')   
+plt.hlines(0,3,33)
+
+###################################################################################################
+
+#Plot Spectra Diff error bars
+fig, ax = plt.subplots(1)
+plt.errorbar(frequencies,GrandAvg_spec_diff,yerr=GrandAvg_spec_diff_ste)
+plt.legend('Ipsi-Contra')
+plt.xlabel('Frequency (Hz)')
+plt.ylabel('Power (uV^2)')   
+plt.hlines(0,3,33)
+
+###################################################################################################
+#
+# Grand Average Ipsi
+plot_max = np.max([np.max(np.abs(GrandAvg_Ipsi)), np.max(np.abs(GrandAvg_Contra))])  
+fig, ax = plt.subplots(1)
+im = plt.imshow(GrandAvg_Ipsi,
+           extent=[times[0], times[-1], frequencies[0], frequencies[-1]],
+           aspect='auto', origin='lower', cmap='coolwarm', vmin=-plot_max, vmax=plot_max)
+plt.xlabel('Time (sec)')
+plt.ylabel('Frequency (Hz)')
+plt.title('Power Ipsi')
+cb = fig.colorbar(im)
+cb.set_label('Power')
+# Create a Rectangle patch
+rect = patches.Rectangle((t_low,f_low),t_diff,f_diff,linewidth=1,edgecolor='k',facecolor='none')
+# Add the patch to the Axes
+ax.add_patch(rect)
+#
+##e#################################################################################################
+#
+# Grand Average Contra
+#
+fig, ax = plt.subplots(1)
+im = plt.imshow(GrandAvg_Contra,
+           extent=[times[0], times[-1], frequencies[0], frequencies[-1]],
+           aspect='auto', origin='lower', cmap='coolwarm', vmin=-plot_max, vmax=plot_max)
+plt.xlabel('Time (sec)')
+plt.ylabel('Frequency (Hz)')
+plt.title('Power Contra')
+cb = fig.colorbar(im)
+cb.set_label('Power')
+# Create a Rectangle patch
+rect = patches.Rectangle((t_low,f_low),t_diff,f_diff,linewidth=1,edgecolor='k',facecolor='none')
+# Add the patch to the Axes
+ax.add_patch(rect)
+#
+###################################################################################################
+#
+# Grand Average Ipsi-Contra Difference
+#
+plot_max_diff = np.max(np.abs(GrandAvg_diff))
+fig, ax = plt.subplots(1)
+im = plt.imshow(GrandAvg_diff,
+           extent=[times[0], times[-1], frequencies[0], frequencies[-1]],
+           aspect='auto', origin='lower', cmap='coolwarm', vmin=-plot_max_diff, vmax=plot_max_diff)
+plt.xlabel('Time (sec)')
+plt.ylabel('Frequency (Hz)')
+plt.title('Power Difference Ipsi-Contra')
+cb = fig.colorbar(im)
+cb.set_label('Ipsi-Contra Power')
+# Create a Rectangle patch
+rect = patches.Rectangle((t_low,f_low),t_diff,f_diff,linewidth=1,edgecolor='k',facecolor='none')
+# Add the patch to the Axes
+ax.add_patch(rect)
+
+###################################################################################################
+# Compute t test
+# ----------------------------
+
+num_good = len(diff_out) - sum(np.isnan(diff_out))
+
+[tstat, pval] = scipy.stats.ttest_ind(diff_out,np.zeros(len(diff_out)),nan_policy='omit')
+print('Ipsi Mean: '+  str(np.nanmean(Ipsi_out))) 
+print('Contra Mean: '+  str(np.nanmean(Contra_out))) 
+print('Mean Diff: '+  str(np.nanmean(diff_out))) 
+print('t(' + str(num_good-1) + ') = ' + str(round(tstat,3)))
+print('p = ' + str(round(pval,3)))
+
+###################################################################################################
+# Save average powers ipsi and contra
+# ----------------------------
+
+print(diff_out)
+raw_data = {'Ipsi Power': Ipsi_out, 
+        'Contra Power': Contra_out}
+df = pd.DataFrame(raw_data, columns = ['Ipsi Power', 'Contra Power'])
+print(df)
+df.to_csv('375CueingEEG.csv')
+print('Saved subject averages for each condition to 375CueingEEG.csv file in present directory')
+
+###################################################################################################
+# Save spectra
+# ----------------------------
+
+df = pd.DataFrame(Ipsi_spectra_out,columns=frequencies)
+print(df)
+df.to_csv('375CueingIpsiSpec.csv')
+
+df = pd.DataFrame(Contra_spectra_out,columns=frequencies)
+df.to_csv('375CueingContraSpec.csv')
+print('Saved Spectra to 375CueingContraSpec.csv file in present directory')
+
+