function ctxanim(fname, data, varargin)
% function ctxanim(fname, data, mincolor, maxcolor, mask)
% 
% Create a Cortex animation or bitmap out of a data matrix.
% Writes the Cortex file to the string in fname.
% 
% The data matrix is rescaled so that the global minimum and maximum
% map to the range defined by mincolor and maxcolor. mincolor defaults to
% 128 and maxcolor defaults to 255. Cortex typically uses the lower portion
% of the colormap for default colors, so it is recommended that you specify
% a higher value than zero.
%
% The optional mask argument can be passed as a multiplicative factor to
% apply to each individual re-scaled frame. One reason you may want to use
% this feature is to create a region of the bitmap which will correspond
% to whatever the background color is. By setting the mask to zero
% in the areas that correspond to background and one in the areas that
% will be foreground, you can achieve this effect. The default mask is
% all ones.
%
% Note that this function requires Matlab 5 to work properly, as it
% uses multi-dimensional arrays and Endian options for file writing,
% both not available in Matlab 4.
%
% 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
% Rick Romero
% rickr+@cmu.edu
% Permission to use and modify is granted,
% but not to redistribute original or modified code.

xsize = size(data,2);
ysize = size(data,1);
frames = size(data,3);
if (length(varargin) < 3)
  mask = ones(xsize, ysize);
else
  mask = varargin{3};
end
if (length(varargin) < 2)
  maxcolor = 255;
else
  maxcolor = varargin{2};
end
if (length(varargin) < 1)
  mincolor = 128;
else
  mincolor = varargin{1};
end


fid = fopen(fname, 'w', 'ieee-le');
header = [0 0 0 0 0 0 xsize ysize (frames-1)];
if (frames > 1)
  minx = min(min(min(data,[],1),[],2),[],3);
  maxx = max(max(max(data,[],1),[],2),[],3);
else
  minx = min(min(data,[],1),[],2);
  maxx = max(max(data,[],1),[],2);
end  

if (maxx == minx)
  maxx = minx + 1;
end

for i = 1:frames
  data2 = mask .* round(((data(:,:,i) - minx) ./ (maxx - minx)) .* (maxcolor - mincolor) + mincolor)';
  fwrite(fid, header, 'int16');
  fwrite(fid, data2, 'uchar');
end

fclose(fid);