WiscPlan_olderMV/photonDoseCalc/scripts_m/label2short.m

function out_data = label2short(varargin)
%%%%%%%%%
%
%   The more non-zero elements your labelfield has, the longer this
%   function will take to run!!!
%
%   USAGE: (1) >> data = label2short;   <Enter>
%          (2) >> label2short('C:\Data\SU00x\Foo_label-field.am');  <Enter>
%   
%   Uncomment the last lines of text if you want to write new files!
%   Creates an additional file called xxx_short.am
%
%   Multi-file select works!!
%
%   This m-file decodes Amira's Run-Length Encoding that they use to save
%   space in their LabelFields.  As per usual, no documentation on their
%   compression algorithm, so I figured it out on my own.  
%
%   0 to 127 --> Copy the next value n times
%   -127 to -1 -->  Copy the next n values VERBATIM
%
%   The string:
%   00001111111000001010000001000
%   Saved in Amira's RLE as:
%   4 0 7 1 5 0 -125 1 0 1 6 0 -127 1 3 0
%
%   I never knew about RLE, this guy's site was fairly useful. His name is
%   dipperstein, I mean, come on!
%   http://michael.dipperstein.com/rle/index.html
%   last updated June 8, 2008 - viewed 3/18/09
%
%   DLB 3/18/09
%

%% multi file selector
switch nargin
    case 1
        filename = varargin{1};
        leng = 1;
    case 0
        [file, pathname] = uigetfile({'*.am'},'Please locate Amira LabelField(s).','Multiselect','on');
        if isequal(file,0)
            disp('User selected Cancel');
            fclose all;
            return
        else
            if isa(file,'cell')
                for k = 1:length(file)
                    filename{k} = fullfile(pathname,file{k});
                    disp(['User selected ' filename{k}]); 
                end
                leng = length(file);
            else
                filename = [pathname file];
                disp(['User selected ', fullfile(pathname, filename)]);
                leng = 1;
            end
        end
end

for n = 1:leng
    if isa(filename,'cell')
        fil = filename{n};
    else
        fil = filename;
    end

fid = fopen(fil,'r','ieee-be');
datachar = char(fread(fid,inf,'char'))';
switch isempty(findstr(datachar,'BINARY-LITTLE-ENDIAN'))
    case 1
        endianness = 'be';
    case 0
        endianness = 'le';
end
lattice = findstr(datachar,'define Lattice');
parameter = findstr(datachar,'Parameters');
boundingbox = findstr(datachar,'BoundingBox'); 
CoordType = findstr(datachar,'CoordType');
ByteRLE = findstr(datachar,'HxByteRLE,');
start_data_position = findstr(datachar,'@1');  % note there will be two @1, so take the second one!
DataSection = findstr(datachar,'# Data section follows');

%% get the dimensions from the amira header
fseek(fid,lattice+14,'bof');
dimensions = str2num(char(fread(fid,parameter-lattice-15,'char'))');

fseek(fid,ByteRLE+9,'bof');
byte_length = str2num(char(fread(fid,DataSection - ByteRLE-13,'char'))');


fseek(fid,boundingbox-1,'bof');
BB = char(fread(fid,CoordType - boundingbox-5,'char'))';

%% Switch endianess?
switch endianness
    case 'le'
        fclose(fid);
        fid = fopen(fil,'r',['ieee-' endianness]);
        fseek(fid,start_data_position(2)+2,'bof');
        data = fread(fid,byte_length,'int8');
    case 'be'
        fseek(fid,start_data_position(2)+2,'bof');
        data = fread(fid,byte_length,'int8');
end

%% This decodes Amira's RLE. I figured this out by trial and error, not
%  sure what algorithm they use.
 
% pre-allocate space for the output
out_line = zeros(dimensions(1)*dimensions(2)*dimensions(3),1);

% pre-compute the final offset due to -#'s
final_offset = sum(data(find(data<0))+127);

net_counter = 0;
offset = 0;
for i = 1:floor((byte_length-final_offset)/2) % 
%     disp(int2str(i));
    data_counter = 2*i+offset;
    if ((data(data_counter) == 0) && (data(data_counter-1) > 0))
        net_counter = data(data_counter-1)+net_counter;
    else
        if data(data_counter-1) < 0
            for j = 1:128+data(data_counter-1)
                out_line(j+net_counter) = data(data_counter+j-1);
%                 disp(['i = ' int2str(i) ', length = ' int2str(data(data_counter-1)) ', written value = ' int2str(data(data_counter+j-1)) ', offset = ' int2str(offset)]);
            end
            net_counter = 128+data(data_counter-1)+net_counter;
            offset = offset + 127+ data(data_counter-1);
        else
            for j = 1:data(data_counter-1)
                out_line(j+net_counter) = data(data_counter);
%                 disp(['i = ' int2str(i) ', length = ' int2str(data(data_counter-1)) ', written value = ' int2str(data(data_counter))]);
            end
            net_counter = data(data_counter-1)+net_counter;
        end
    end
end 

out_data = reshape(out_line,dimensions(1),dimensions(2),dimensions(3));

%% this is from my amiraCTWriter.m
% fid = fopen(strrep(fil,'.am','_short.am'),'w');
% switch endianness
%     case 'be'
%         fprintf(fid,'# AmiraMesh 3D BINARY 2.0\n\n');
%         fprintf(fid,['# CreationDate: ' datestr(now,'ddd mmm') datestr(now,' dd HH:MM:SS yyyy') '\n\n']);
%     case 'le'
%         fprintf(fid,'# AmiraMesh BINARY-LITTLE-ENDIAN 2.1\n\n');
% end
% fprintf(fid,'define Lattice %g %g %g\n\n',dimensions(1),dimensions(2),dimensions(3));
% fprintf(fid,'Parameters {\n');
% fprintf(fid,'    Content "%gx%gx%g %s, uniform coordinates",\n',dimensions(1),dimensions(2),dimensions(3),'short');
% fprintf(fid,'    %s\n',BB);
% fprintf(fid,'    CoordType "uniform"\n');
% fprintf(fid,'}\n\n');
% fprintf(fid,'Lattice { %s Data } @1\n\n','short');
% fprintf(fid,'# Data section follows\n');
% fprintf(fid,'@1\n');
% fclose(fid);  % close the text part of the file
% fid = fopen(strrep(fil,'.am','_short.am'),'ab',['ieee-' endianness]);
% fwrite(fid,out_data(:,:,:),'short');
% fclose(fid);
end