main.m

EOG Correction program is used to work out the amount of ocular potential recorded by the electroenc

% Title: RAAA EOG Correction Program GUI 
% Author: Tony Tanoyo
% Year: Feb 2007 - Oct 2007
% Brain Sciences Institute
% -----------------------------------

function varargout = main(varargin)
% Last Modified by GUIDE v2.5 25-Oct-2007 23:51:37
% main: Display the selection for loading files and channel selections,
% correction for the EOG data. 
%
%      EOG Correction program is used to work out the amount of ocular
%      potential recorded by the electroencephalograph [EEG] (as a
%      proportion of the potentials recorded by the electrooculograph
%      [EOG]), and to subtract this from the EEG. By doing this we are able
%      to reduce the effect of ocular potentials on the EEG, and this in
%      turn allows us to increase the amount of usable data (we dont have
%      to discard data that correspond to eye movements), provides us with
%      greater confidence in data that correspond with small eye movements,
%      and reduces the restrictions that we place on participants' eye
%      movements.
% 
%      These proportions of EOG voltages that contaminate EEG recordings
%      are termed 'betas' or 'Bs'. We calculate separate Bs for vertical
%      (Bv), horizontal (Bh), and radial (Br) EOG channels, with separate
%      Bv, Bh, and Br values for EEG electrode. To increase accuracy of the
%      'Bs', they are calculated from specifically designed calibration
%      data collected separate to the main experimental data, in general
%      'Bs' remain constant across the EEG recording session. 
% 
%      This program has been designed to interface with Neuroscan Edit 
%      software, thus at present this will primarily be use to those with access
%      to this software. However, as the software uses the ascii ('.dat')
%      output from Neuroscan, if your data can be converted to that format
%      you will be able to use this correction algorithm. For example of
%      the ascii file format required are given in the package folder
%      /Extra Files/sample.... Note that the 'EOG Calibration' and
%      'To-Be-Corrected' files must have the same channels, but filter
%      settings and digitisation rates may differ. 
% 
%      Start the program by running the main file. 
% 
%      For more information, please see the help file.
%      ---------------------------------------------------------------- 
% 
%      H = MAIN returns the handle to a new MAIN or the handle to
%      the existing singleton*.
% 
%      MAIN('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in MAIN.M with the given input arguments.
% 
%      MAIN('Property','Value',...) creates a new MAIN or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before plotfig_OpeningFunction gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to plotfig_OpeningFcn via varargin.
% 
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
% 
%   See also: GUIDE, GUIDATA, GUIHANDLES
% 
%   Programmed and Copyright by Tony Tanoyo: [e-mail]
%   $Revision: 01 $  $Date: 24/10/2007s$
% 
%   Files Contribution:
%   Yair Altman for the statusbar function, May 2007.
%   Daniel Claxton for the workbar function, March 2005.
%   Xiaoning (David) Yang for the keep function, 1998. 

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @main_OpeningFcn, ...
                   'gui_OutputFcn',  @main_OutputFcn, ...
                   'gui_LayoutFcn',  [], ...
                   'gui_Callback',   []);
if nargin && ischar(varargin{1})
   gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
    gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT

% ----------------------------------------------------------
% --- Executes just before main is made visible.
function main_OpeningFcn(hObject, eventdata, handles, varargin)

handles.output = hObject;   % Choose default command line output for main

guidata(hObject, handles);  % Update handles structure

init_strings(handles);  % initialisation of string

setappdata(gcf,'pathname0',pwd);    % set pathname0 to the current program directory

setappdata(0,'hMainGui',gcf);   % set the hMainGui to the gcf(get current figure)

newpushbutton_Callback(hObject, eventdata, handles);

hMainGui = getappdata(0, 'hMainGui'); 

timeperchar=7e-7; % time taken per char to read data, found by experiment.

run_id=0;

setappdata(hMainGui,'run_id',run_id); 

starting_id=1;  % starting_id to indicate that the program just started and has not been run

setappdata(hMainGui,'starting_id',starting_id); 

setappdata(hMainGui,'timeperchar',timeperchar); % set the timeperchar to hMainGui

% set all the up, down, left, right, and blink popupmenu inactive at the start
set(handles.up_popupmenu,'enable','inactive');
set(handles.down_popupmenu,'enable','inactive');
set(handles.left_popupmenu,'enable','inactive');
set(handles.right_popupmenu,'enable','inactive');
set(handles.blink_popupmenu,'enable','inactive');

% set the editchannel1, 2 and 3 handles
setappdata(hMainGui,'edit_VE_main',handles.editchannel1);
setappdata(hMainGui,'edit_HE_main',handles.editchannel2);
setappdata(hMainGui,'edit_RE_main',handles.editchannel3);

% --- Outputs from this function are returned to the command line.
function varargout = main_OutputFcn(hObject, eventdata, handles)

varargout{1} = handles.output;  % Get default command line output from handles structure

% --------------------------------------------
% Push Button Callbacks
% --------------------------------------------
% --- Executes on button press in loadpushbutton1.
function loadpushbutton1_Callback(hObject, eventdata, handles)

hMainGui = getappdata(0, 'hMainGui');   % get the value of the hMainGUI from the root (handle 0) and assign it to hMainGui variable.
   
timeperchar=getappdata(hMainGui,'timeperchar');
pathname0=getappdata(hMainGui,'pathname0');     % root directory
pathname1=getappdata(hMainGui,'pathname1');     % eog calibration file directory
pathname2=getappdata(hMainGui,'pathname2');     % eog datapnts file directory
pathname3=getappdata(hMainGui,'pathname3');     % tbc directory
pathname1st2open=getappdata(hMainGui,'pathname1st2open');   % directory when the 1st file is open

if ~isempty(pathname1)&&isempty(pathname2)&&isempty(pathname3)
    cd(pathname1);
elseif isempty(pathname1)&&~isempty(pathname2)&&isempty(pathname3)
    cd(pathname2);
elseif isempty(pathname1)&&isempty(pathname2)&&~isempty(pathname3)
    cd(pathname3);
elseif ~isempty(pathname1st2open)
    cd(pathname1st2open);
end
select=1; invalid=1; data_type='cnt'; 

while(invalid==1)
    while(select~=0)
        [fname1, pathname1] = uigetfile('*.dat', 'Pick "eog calibration" file');
        if isempty(pathname2)&&isempty(pathname3)
            pathname1st2open=pathname1;
        end
        cd(pathname0);
        if isequal(fname1,0) || isequal(pathname1,0)
            return
        else
            select=0; invalid=0;  % to catch if user does not select a file.
        end
    end
    try
        set(handles.figure1,'Pointer','watch');
        [data,hdr]=read([pathname1 fname1],handles,timeperchar,data_type);    % Reading the eog file
        set(handles.figure1,'Pointer','arrow');
    catch
        statusbar;
        set(handles.figure1,'Pointer','arrow');
        warn_push1=msgbox('Please Select Continouous Type EOG Calibration File','Warning','warn','modal');
        waitfor(warn_push1);
        select=1; invalid=1;   % to catch if user selected wrong file.
    end
end

setappdata(hMainGui,'plot_id',0);   % plot_id =0 -> cannot be plotted

set(handles.editchannel1,'string','');
set(handles.editchannel2,'string','');
set(handles.editchannel3,'string','');

set(handles.fname1,'string',fname1);    % set the string of fname1 to fname1
setappdata(hMainGui,'pathname1',pathname1);
setappdata(hMainGui,'fname1',fname1); 
setappdata(hMainGui,'data',data); 
setappdata(hMainGui,'hdr',hdr);

elec_label=hdr{9,1};    % get line 9 of the header
lab_idx=regexp(elec_label,'([)*(])');
ch_label=cell(length(lab_idx),1);   % create length(lab_idx),1 empty matrices
for i=1:length(lab_idx)
    ch_label{i,1}=elec_label((lab_idx(i)-9):lab_idx(i));   % read every electrode label using the index, including the square brackets, since the char length varies from one to another.
end
ch_label=strrep(ch_label,'[','');
ch_label=strrep(ch_label,']',''); 
ch_label=strtrim(ch_label);     % get the channel labels

for ch_idx=1:length(ch_label)   % convert all the channel labels to capital
    try
        if isscalar(eval(ch_label{ch_idx}))
            ch_label{ch_idx}=['CH' ch_label{ch_idx}];
        end
    catch
        for j=1:length(ch_label{ch_idx})
            if ch_label{ch_idx}(j)>=97 && ch_label{ch_idx}(j)<=122
                ch_label{ch_idx}(j)=ch_label{ch_idx}(j)-32;
            end
        end
    end
end
setappdata(hMainGui,'ch_label',ch_label);

option=1; vech1_idx=1; vech2_idx=2*vech1_idx+1; 
while(option<3)
    for i=1:length(ch_label)
        switch(option)
            case 1
                if isequal('VE',ch_label{i})||isequal('VEOG',ch_label{i})
                    vech=ch_label{i};   % char type of variable
                    ve_count=i;
                elseif isequal('HE',ch_label{i})||isequal('HEOG',ch_label{i})
                    hech=ch_label{i};
                    he_count=i;
                elseif isequal('RE',ch_label{i})||isequal('REOG',ch_label{i})
                    rech=ch_label{i};
                    re_count=i;
                end
            case 2
                if isequal('E1',ch_label{i})||isequal('E2',ch_label{i}) % E1 & E2
                    try
                        try
                            if ~isequal(vech{vech1_idx-1},ch_label{i}) && vech1_idx<3  % check on the 2nd occurence possibility of double elect label
                                pass;
                            end
                        catch
                            if ~ischar(vech) && ~ischar(rech)
                                rech{vech1_idx}=ch_label{i};    % cell type of variable
                                vech{vech1_idx}=ch_label{i};    % vech1_idx takes the 1st and 3rd pos
                                vech1_idx=vech1_idx+1;
                            elseif ~ischar(vech) && ischar(rech) 
                                vech{vech1_idx}=ch_label{i};
                                vech1_idx=vech1_idx+1;
                            elseif ischar(vech) && ~ischar(rech)
                                rech{vech1_idx}=ch_label{i};
                                vech1_idx=vech1_idx+1;
                            end
                        end
                    catch
                        try                      
                            if ischar(vech)
                                rech{vech1_idx}=ch_label{i};
                                vech1_idx=vech1_idx+1;
                            end
                        catch
                            try
                                if ischar(rech)
                                    vech{vech1_idx}=ch_label{i};
                                    vech1_idx=vech1_idx+1;
                                end
                            catch
                                rech{vech1_idx}=ch_label{i};
                                vech{vech1_idx}=ch_label{i};
                                vech1_idx=vech1_idx+1;
                            end
                        end
                    end
                elseif isequal('E3',ch_label{i})||isequal('E4',ch_label{i})  %E3 & E4
                    try
                        try
                            if ~isequal(vech{vech2_idx-1},ch_label{i}) && vech2_idx<5 % check on the 2nd occurence possibility of double elect label
                                pass;
                            end
                        catch
                            if ~ischar(vech) && ~ischar(rech) 
                                rech{vech2_idx}=ch_label{i};
                                vech{vech2_idx}=ch_label{i};    % vech2_idx takes the 2nd and 4th pos
                                vech2_idx=vech2_idx+1;
                            elseif ~ischar(vech) && ischar(rech)
                                vech{vech2_idx}=ch_label{i};
                                vech2_idx=vech2_idx+1;
                            elseif ischar(vech) && ~ischar(rech) 
                                rech{vech2_idx}=ch_label{i};
                                vech2_idx=vech2_idx+1;
                            end
                        end
                    catch
                        try                      
                            if ischar(vech) 
                                rech{vech2_idx}=ch_label{i};
                                vech2_idx=vech2_idx+1;
                            end
                        catch
                            try
                                if ischar(rech)
                                    vech{vech2_idx}=ch_label{i};
                                    vech2_idx=vech2_idx+1;
                                end
                            catch
                                rech{vech2_idx}=ch_label{i};
                                vech{vech2_idx}=ch_label{i};
                                vech2_idx=vech2_idx+1;
                            end
                        end
                    end
                elseif isequal('E5',ch_label{i})    % E5
                    try
                        if ischar(hech)||ischar(hech{1}) && length(vech)<2
                            continue
                        end
                    catch
                        hech{1}=ch_label{i};
                    end
                elseif isequal('E6',ch_label{i})    % E6
                    try
                        if ischar(hech)||ischar(hech{2}) && length(vech)<2
                            continue
                        end
                    catch
                        hech{2}=ch_label{i};
                    end
                end
        end
    end
    try
        if ischar(vech)&& ischar(hech) && ischar(rech)
            option=3;
        else
            option=option+1;
        end
    catch
        option=option+1;
    end