utilities_LW/mha_read_volume.m

   1 function V = mha_read_volume(info)
   2 % Function for reading the volume of a Insight Meta-Image (.mha, .mhd) file
   3 %
   4 % volume = tk_read_volume(file-header)
   5 %
   6 % examples:
   7 % 1: info = mha_read_header()
   8 %    V = mha_read_volume(info);
   9 %    imshow(squeeze(V(:,:,round(end/2))),[]);
  10 %
  11 % 2: V = mha_read_volume('test.mha');
  12
  13 if(~isstruct(info)), info=mha_read_header(info); end
  14
  15
  16 switch(lower(info.DataFile))
  17     case 'local'
  18     otherwise
  19     % Seperate file
  20     info.Filename=fullfile(fileparts(info.Filename),info.DataFile);
  21 end
  22
  23 % Open file
  24 switch(info.ByteOrder(1))
  25     case ('true')
  26         fid=fopen(info.Filename,'rb','ieee-be');
  27     otherwise
  28         fid=fopen(info.Filename,'rb','ieee-le');
  29 end
  30
  31 switch(lower(info.DataFile))
  32     case 'local'
  33         % Skip header
  34         fseek(fid,info.HeaderSize,'bof');
  35     otherwise
  36         fseek(fid,0,'bof');
  37 end
  38
  39 datasize=prod(info.Dimensions)*info.BitDepth/8; % in bytes
  40
  41 switch(info.CompressedData(1))
  42     case 'f'
  43         % Read the Data
  44         switch(info.DataType)
  45             case 'char'
  46                  V = int8(fread(fid,datasize,'char'));
  47             case 'uchar'
  48                 V = uint8(fread(fid,datasize,'uchar'));
  49             case 'short'
  50                 V = int16(fread(fid,datasize,'short'));
  51             case 'ushort'
  52                 V = uint16(fread(fid,datasize,'ushort'));
  53             case 'int'
  54                  V = int32(fread(fid,datasize,'int'));
  55             case 'uint'
  56                  V = uint32(fread(fid,datasize,'uint'));
  57             case 'float'
  58                  V = single(fread(fid,datasize,'float'));
  59             case 'double'
  60                 V = double(fread(fid,datasize,'double'));
  61         end
  62     case 't'
  63         switch(info.DataType)
  64             case 'char', DataType='int8';
  65             case 'uchar', DataType='uint8';
  66             case 'short', DataType='int16';
  67             case 'ushort', DataType='uint16';
  68             case 'int', DataType='int32';
  69             case 'uint', DataType='uint32';
  70             case 'float', DataType='single';
  71             case 'double', DataType='double';
  72         end
  73         Z  = fread(fid,inf,'uchar=>uint8');
  74         V = zlib_decompress(Z,DataType);
  75
  76 end
  77
  78 fclose(fid);
  79 V = reshape(V,info.Dimensions);
  80
  81 function M = zlib_decompress(Z,DataType)
  82 import com.mathworks.mlwidgets.io.InterruptibleStreamCopier
  83 a=java.io.ByteArrayInputStream(Z);
  84 b=java.util.zip.InflaterInputStream(a);
  85 isc = InterruptibleStreamCopier.getInterruptibleStreamCopier;
  86 c = java.io.ByteArrayOutputStream;
  87 isc.copyStream(b,c);
  88 M=typecast(c.toByteArray,DataType);