% The EEG data by default is recorded with reference to the hardware reference, which is Pz.
% This means that there was not a Pz channel in the recording file.
% We have to do some simple math to re-reference the data and reconstruct the Pz channel.
% 
% In this code, we are conducteding re-referencing for the EEG singnal with respect to Vref.
% Vref is the average between the electrodes A1 and A2

clc
clear
close all
warning off

for s=1:59  %number of subject
    Name = 'S%d_0.5_raw.csv';  %Change between speeds 0.5, 0.75, and 1. 
    filename = sprintf(Name,s);
    A=readmatrix(filename, 'HeaderLines', 16); %ignore the first 16 rows (trial description)
    
    LE=(A(:,11)+A(:,23))/2;  %Linked Ears = average of A1 and A2
    Pz=zeros(height(A), 1);  %Generate Pz channel with reference to Pz
    A(:,10)=Pz;  %Explaination: Replace Pz in A instead of CM channel
    channels=[2:10,12:17,20,21,24,25]; %the 19 EEG channels
    A1=A(:,channels);  %P3,C3,F3,Fz,F4,C4,P4,Cz,Pz,Fp1,Fp2,T3,T5,O1,O2,F7,F8,T6,T4

    %Rearrange channels to match EEGLAB and the default order as follows
    % 1	Fp1
    A11(:,1)=A1(:,10);
    % 2	Fp2
    A11(:,2)=A1(:,11);
    % 3	F7
    A11(:,3)=A1(:,16);
    % 4	F3
    A11(:,4)=A1(:,3);
    % 5	Fz
    A11(:,5)=A1(:,4);
    % 6	F4
    A11(:,6)=A1(:,5);
    % 7	F8
    A11(:,7)=A1(:,17);
    % 8	T7 (T3)
    A11(:,8)=A1(:,12);
    % 9	C3
    A11(:,9)=A1(:,2);
    % 10 Cz
    A11(:,10)=A1(:,8);
    % 11 C4
    A11(:,11)=A1(:,6);
    % 12 T8 (T4)
    A11(:,12)=A1(:,19);
    % 13 P7 (T5)
    A11(:,13)=A1(:,13);
    % 14 P3
    A11(:,14)=A1(:,1);
    % 15 Pz
    A11(:,15)=A1(:,9);
    % 16 P4
    A11(:,16)=A1(:,7);
    % 17 P8 (T6)
    A11(:,17)=A1(:,18);
    % 18 O1
    A11(:,18)=A1(:,14);
    % 19 O2
    A11(:,19)=A1(:,15);

    for ch=1:19  %Referencing the 19 EEG channels with respect to LE ... F1-LE, F2-LE,,,,,

        A_ref(s, 1, ch, :)=A11(:,ch)-LE; %Change between index 1,2,3 for the three speeds 0.5,0.75,1

        % ... A_ref: subjects(59), Speeds(3), Channels(19), Samples(17960)

    end
end

%.......................................%