function list = ctx2mat(fname)
% function list = ctx2mat(fname)
% Given a string fname, read in that Cortex data file and produce a full
% representation of that information in a Matlab list.
%
% The top-level list structure is interpretable as:
%   { trial1, trial2, ..., trialn }
% 
% Each trial is itself a list containing:
%   { header, encode_times, encode_number, eog_values, epp_values }
% 
% The header is a vector of:
%   [ cond_no, reapeat_no, block_no, trial_no, isi_size, code_size, ...
%     eog_size, epp_size, khz_res, eye_storage_rate, expected, response,...
%     response_err ]
% For an interpreation of these fields, refer to the Cortex documentation.
% These variables are shown in the same order as they appear in the Cortex
% header.
%
% Version 1.0
% For additional code, updated versions, questions or comments, please refer
% to the Active Perception Lab home page
%            http://www.cnbc.cmu.edu/~tai/lab.html

% Copyright 1998-1999
% Rick Romero
% rickr+@cmu.edu
% Permission to use and modify is granted,
% but not to redistribute original or modified code.

fid = fopen(fname, 'r');
if (fid < 1)
  sprintf('Problem with opening file %s', fname)
  return
end
shift1 = 256;
shift2 = shift1 * shift1;
shift3 = shift1 * shift2;
entry = 1;
list = {};
[header,c] = fread(fid, [26,1], 'uchar');

while (c == 26)
  i = 1;
  length = header(i) + header(i+1)*shift1; i = i + 2;
  cond_no = header(i) + header(i+1)*shift1; i = i + 2;
  repeat_no = header(i) + header(i+1)*shift1; i = i + 2;
  block_no = header(i) + header(i+1)*shift1; i = i + 2;
  trial_no = header(i) + header(i+1)*shift1; i = i + 2;
  isi_size = header(i) + header(i+1)*shift1; i = i + 2;
  isi_size = isi_size / 4;
  code_size = header(i) + header(i+1)*shift1; i = i + 2;
  code_size = code_size / 2;
  eog_size = header(i) + header(i+1)*shift1; i = i + 2;
  eog_size = eog_size / 2;
  epp_size = header(i) + header(i+1)*shift1; i = i + 2;
  epp_size = epp_size / 2;
  khz_res = header(i); i = i + 1;
  eye_storage_rate = header(i); i = i + 1;
  expected = header(i) + header(i+1)*shift1; i = i + 2;
  response = header(i) + header(i+1)*shift1; i = i + 2;
  response_err = header(i) + header(i+1)*shift1;

  curEntry = {[cond_no,repeat_no,block_no,trial_no,isi_size,code_size,eog_size,epp_size,khz_res,eye_storage_rate,expected,response,response_err],[],[],[],[]};
  [curEntry{1}, ftell(fid)];
  if (isi_size > 0)
    [curEnc,cnt] = fread(fid, [4,isi_size], 'uchar');
    if (cnt ~= 4*isi_size)
      error(sprintf('Problem reading ISI codes:%d', ftell(fid)));
    end
    curEnc = curEnc(1,:) + curEnc(2,:) * shift1 + curEnc(3,:) * shift2 + ...
             curEnc(4,:) * shift3;
    curEntry{2} = curEnc;
  end
  if (code_size > 0)
    [curCodes,cnt] = fread(fid, [2, code_size], 'uchar');
    if (cnt ~= 2*code_size)
      error(sprintf('Problem reading Encodes:%d', ftell(fid)));
    end
    curCodes = curCodes(1,:) + curCodes(2,:) * shift1;
    curCodes = curCodes - (shift2 * (curCodes >= (shift2 / 2)));
    curEntry{3} = curCodes;
  end
  if (eog_size > 0)
    [curEOG,cnt] = fread(fid, [2, eog_size], 'uchar');
    if (cnt ~= 2*eog_size)
      error(sprintf('Problem reading EOG codes:%d', ftell(fid)));
    end
    curEOG = curEOG(1,:) + curEOG(2,:) * shift1;
    curEOG = curEOG - (shift2 * (curEOG >= (shift2 / 2)));
    curEntry{4} = curEOG;
  end
  if (epp_size > 0)
    [curEPP,cnt] = fread(fid, [2, epp_size], 'uchar');
    if (cnt ~= 2*epp_size)
      error(sprintf('Problem reading EPP codes:%d', ftell(fid)));
    end
    curEPP = curEPP(1,:) + curEPP(2,:) * shift1;
    curEPP = curEPP - (shift2 * (curEPP >= (shift2 / 2)));
    curEntry{5} = curEPP;
  end
  list{entry} = curEntry;
  entry = entry + 1;
  [header,c] = fread(fid, [26,1], 'uchar');
end


fclose(fid);