% clear the memory
clear;
% close all open files and windows
close all;
% clear the command console
clc;

% key file variables we will need
pathName = '/Users/krigolson/Desktop/Frequency Tutorial Folder';
fileName = 'Oddball1.vhdr';

% load the data
EEG = doLoadBVData(pathName,fileName);

% keep track of the original channel locations
originalChannels = EEG.chanlocs;

% define the filter parameters
filterParameters.low = 0.5;
filterParameters.high = 30;
filterParameters.notch = 60;

% filter the data
EEG = doFilter(EEG,filterParameters);

% do some initial data cleaning
EEG = doCleanData(EEG);

% rereference the data to the average reference before ICA to improve
% results
EEG = doICAReference(EEG);

% run the ICA
EEG = doICA(EEG);

% remove ocular ICA components
EEG = doRemoveOcularICAComponents(EEG);

% interpolate the removed channels
EEG = doInterpolate(EEG,originalChannels);

% epoch the data into segments
epochMarkers = {'S202','S203'};
epochTimes = [-0.2 0.8];
EEG = doEpochData(EEG,epochMarkers,epochTimes);

% baseline correct the data
baselineWindow = [-0.2 0];
EEG = doBaseline(EEG,baselineWindow);

% run the Wavelet analysis. The time specified is the baseline window in
% ms. The next three numbers are the minimum frequency, the maximum
% frequency, and the number of frequency steps. I used 30 so the resolution
% will be 1 Hz. The last number if the mortlet parameter which shapes the
% wavelet. the recommended number is 6. 
WAV = doWAV(EEG,epochMarkers,[-200 0],1,30,30,6);

% plot the Wavelets for both conditions side by size for channel 52
condition1WaveletData = squeeze(WAV.data(52,:,:,1));
condition2WaveletData = squeeze(WAV.data(52,:,:,2));
% now the plotting is more complex as we are working with an image with 3D
% data
subplot(1,2,1);
imagesc(condition1WaveletData);
title('Channel Pz: Condition One');
xlabel('Samples');
ylabel('Frequency (Hz)');
set(gca,'YDir','normal');
subplot(1,2,2);
imagesc(condition2WaveletData);
title('Channel Pz: Condition Two');
xlabel('Samples');
set(gca,'YDir','normal');
ylabel('Frequency (Hz)');

% save the data
save('Subject Wavelet 1','WAV');