% extractpar - Extraction of data in .par and .rep file to Matlab/Octave environment
%
% Input: filename, a string variable in the current workspace
%        with the path to the .par and .rep files without the
%        extensions, e.g. use filename = '../../cod' to indicate
%        ../../cod.par and ../../cod.rep.
%
% Output: N, matrix with population trajectory, read from .rep file.
%
%         The variables in the .par file, with the same names as in the 
%         .par file.
%
% NOTE: The .par file must be EXACTLY on the form provided by ADMB.
%       The .rep file must contain only numbers (defining N) first.
%
% Written by Lennart Frimannslund, April 2010.
%

if (exist('filename','var') == 0),

  fprintf(1,'%s: No filename specified!\n',mfilename);
  return;

end;


% Get the .par file
fid = fopen([filename '.par'],'r');

% Discard first line, which contains information about the objective function, etc.
l = fgetl(fid);
l = 0;

% Process remaining lines, in pairs. The first line of the pair has the name, the second the value.
while (l ~= -1),

  l = fgetl(fid);
  if (l == -1),
    break;
  end;
  varname = strip_hash_and_colon(l);
  l = fgetl(fid); 

  % Send the variable name and values to the command line
  eval(sprintf('%s = [ %s ];',varname,l));
  %sprintf('%s = [ %s ];',varname,l)
end;


fclose(fid);

% Get the .rep file

% Number of lines in the rep file
n_lines = length(N0);

N_cell = cell(n_lines,1);
max_width_so_far = 0;

fid = fopen([filename '.rep']);

% Get one line at a time
for (i=1:n_lines),

  output = fgetl(fid);
  N_cell{i} = str2num(output);  
  max_width_so_far = max(max_width_so_far,length(N_cell{i}));

end;

fclose(fid);

N = zeros(n_lines,max_width_so_far);

for (i=1:n_lines),
  N(i,1:length(N_cell{i})) = N_cell{i}(:)';
end;


% ...and clean up our temporary variables
clear N_cell output max_width_so_far n_lines i

return;