function [time_arr,event_arr,eog_arr,epp_arr,header,trialcount,header2]  = readcortex(filename)

% function to read the cortex datafile 
% and put the timecodes, eventcodes, trialheaders
% in an array of arrays, and the nr of trials in a scalar.
% - - -
% USAGE: [times,events,eog_arr,epp_arr,header,trialcount,header2] = readcortex(path\file_name)
% - - - 
% adapted from get_ALLdata.m
%
% GDLH modified this 5/16/00 -- no need to preallocate the sizes of the arrays
% Matlab 5.2 will automatically pad with zeros when necessary.  How convenient!
% (But preallocating does seem to speed things up a bit.)
%
% GDLH modified this 4/2/01 -- Now returning the eog_arr as well.
%
% GDLH modified this 4/28/01 -- if we hit an error in the datafile, just
% return what we can.
% 
% MAS modified this 8/16/04 -- added in extra code to pull out the
% header from the new write_header() function in the timing file.
% Also changed use of "length" to "flength" for better compatibility.
%
% MAS modified this 10/15/04 -- Changed the fopen statement to use
% little endian, and added an error-checking statement in case there
% is an endian error. Also fixed an error in the write_header() reading
% code

MAXNUMTRIALS = 1000;
trialcount = 0;
% Old fopen statement:
%fid = fopen(filename, 'rb');
fid = fopen(filename, 'r','ieee-le');
%fid = fopen(filename, 'r','ieee-be');
if (fid == -1)
    error(['Cannot open file: ',filename]);
end
time_arr  = zeros(1, MAXNUMTRIALS);	% array of time_code arrays
event_arr = zeros(1, MAXNUMTRIALS);	% array of event_code arrays
eog_arr = zeros(1, MAXNUMTRIALS);	% array of eog_code arrays
eog_lengths = [];
epp_arr = zeros(1, MAXNUMTRIALS);	% array of epp_code arrays
epp_lengths = [];
header    = zeros(13, MAXNUMTRIALS);	% array of trial headers
header2 = [];
hd=zeros(1,13);					% a single header (read every trial)
while (~feof (fid))
    flength = fread(fid, 1, 'unsigned short');
    if (isempty(flength)~=1)
        hd(1,1:8)= (fread(fid, 8, 'unsigned short'))'; 
        hd(1,9:10) = (fread(fid, 2, 'unsigned char'))'; 
        hd(1,11:13)= (fread(fid, 3, 'unsigned short'))';
        hd(1,5)=hd(1,5)/4;	% reduce the size of the time_code array 
        hd(1,6)=hd(1,6)/2;	% idem for event_code array
        hd(1,7)=hd(1,7)/2;  	% and eogs
        hd(1,8)=hd(1,8)/2;	% and epp (not used)
        % This helps detect endian errors when opening the file
        %hddiff = hd - floor(hd);
        %if (~isempty(find(hddiff ~= 0)))
        if (sum(floor(hd) - hd) ~= 0)
            error('READCORTEX: Header data contains non-integers, endian needs to be changed');
        end
        % read the time codes, event_codes, eogs and epps (if any) for this trial
        try
            time_arr(1:(hd(1,5)),trialcount+1)   = (fread (fid,(hd(1,5)) , 'unsigned long'));   
            event_arr(1:(hd(1,6)),trialcount+1) = (fread (fid,(hd(1,6)), 'unsigned short'));
            
            % epp array is stored in the data file before the eog array
            epp_arr(1:(hd(1,8)),trialcount+1)        = fread (fid,(hd(1,8)), 'short');
            
            % must modify all epp entries
            for i = 1:1:(hd(1,8)),
                
                % Must extract the data from the raw epp values.
                % The epp value is made up of 12-bits of data, and 4-bits (the
                % low-order 4 bits) of the channel number.  
                % To extract the data, must right shift the raw data by 4 bits (to
                % get rid of the channel number and put the data value in the proper 
                % location).  After this conversion, you must still add or subtract
                % 2048, since otherwise the value is not right.  (I think that this
                % is because of the way that matlab handles negative values during
                % the bitwise operations.)
                % These calculations cause the results of ctx2txt.m to be the same as
                % for cortview.exe for the EOG and EPP values.
                
                eppdata = bitshift(epp_arr(i, trialcount+1), -4);
                
                if (eppdata < 0)
                    eppdata = eppdata  + 2047;
                else
                    eppdata = eppdata - 2048;
                end;
                
                epp_arr(i, trialcount+1) = eppdata;
                
                
                
            end;
            epp_lengths(trialcount+1) = hd(1,8);
            
            
            eog_arr(1:(hd(1,7)),trialcount+1)     = (fread (fid,(hd(1,7)), 'short'));
            eog_lengths(trialcount+1) = hd(1,7);
            
            % put this trial's header in the header_array
            header(1:13,trialcount+1)=hd(1,1:13)';
            trialcount = trialcount+1;
        catch
            break;
        end;
    end; 
end;

fclose(fid);
time_arr(:,[trialcount+1:end]) = [];
event_arr(:,[trialcount+1:end]) = []; 
eog_arr(:,[trialcount+1:end]) = []; 
epp_arr(:,[trialcount+1:end]) = []; 
header(:,[trialcount+1:end]) = []; 

if (size(eog_arr,1) == 1)
    eog_arr = [];
else
    % 'nan' padding the eog_ary
    for i = 1:trialcount
        %i
        %eog_lengths(i)
        %size(eog_arr)
        if (eog_lengths(i) < size(eog_arr,1))
            eog_arr([eog_lengths(i)+1:end],i) = nan;
        end
    end
end

if (size(epp_arr,1) == 1)
    epp_arr = [];
else
    % 'nan' padding the epp_arr
    for i = 1:trialcount
        if (epp_lengths(i) < size(epp_arr,1))
            epp_arr([epp_lengths(i)+1:end],i) = nan;   
        end
    end
end

%%%%% Added by MAS to decode the special write_header() info %%%%%
if (nargout > 6) % only run this if the user specifies they want "header2"
    first_trial = event_arr(:,1);
    i = find (first_trial < 256);
    if (~isempty(i) && (first_trial(1) == 65535))
        % If the first code sent is 65535, that's a marker
        % to indicate there is write_header() data
        t = first_trial(1:min(i)-1);
        for I=1:length(t)
            t2(2*I) = floor(t(I)/256);
            t2(2*I-1) = mod(t(I),256);
        end
        % add a trailing 255 if necessary to help with parsing the header
        if (t2(length(t2)) ~= 255)
            t2(length(t2)+1) = 255;
        end
        % 255 is used to space out the data in the header
        j = find(t2 == 255);
        % if the header starts with 3 255's, cut it down to 2.
        if (sum(t2(1:3)) == 765)
            j(1) = [];
        end
        % Get the required header data
        header2.data_file = char(t2(j(2)+1:j(3)-1));
        header2.cnd_file = char(t2(j(3)+1:j(4)-1));
        header2.ext_file = char(t2(j(4)+1:j(5)-1));
        header2.item_file = char(t2(j(5)+1:j(6)-1));
        header2.css_file = char(t2(j(6)+1:j(7)-1));
        header2.xdim = char(t2(j(7)+1:j(8)-1));
        header2.ydim = char(t2(j(8)+1:j(9)-1));
        header2.fps = char(t2(j(9)+1:j(10)-1));
        header2.hpix = char(t2(j(10)+1:j(11)-1));
        header2.vpix = char(t2(j(11)+1:j(12)-1));
        header2.bpp = char(t2(j(12)+1:j(13)-1));
        % Get the extern header data (if it's present)
        num_externs = ceil((length(j) - 13 - 1)/2);
        if (num_externs > 0)
            header2.ext_name = cell(num_externs,1);
            header2.ext_val = cell(num_externs,1);
            for I=1:(num_externs*2)
                if (mod(I,2) == 1)
                    namestart = j(13+I-1)+1;
                    namestop = j(13+I)-1;
                    header2.ext_name{floor(I/2)+1} = char(t2(namestart:namestop));
                end
                if (mod(I,2) == 0)
                    valstart = j(13+I-1)+1;
                    valstop = j(13+I)-1;
                    header2.ext_val{I/2} = char(t2(valstart:valstop));
                end    
            end
        end
    end
end