Useful functions for simulations (created by LW, free to use)

[CreaPhase.git] / utilities_LW / mha_read_volume.m

diff --git a/utilities_LW/mha_read_volume.m b/utilities_LW/mha_read_volume.m
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+++ b/utilities_LW/mha_read_volume.m
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+function V = mha_read_volume(info)
+% Function for reading the volume of a Insight Meta-Image (.mha, .mhd) file
+% 
+% volume = tk_read_volume(file-header)
+%
+% examples:
+% 1: info = mha_read_header()
+%    V = mha_read_volume(info);
+%    imshow(squeeze(V(:,:,round(end/2))),[]);
+%
+% 2: V = mha_read_volume('test.mha');
+
+if(~isstruct(info)), info=mha_read_header(info); end
+
+
+switch(lower(info.DataFile))
+    case 'local'
+    otherwise
+    % Seperate file
+    info.Filename=fullfile(fileparts(info.Filename),info.DataFile);
+end
+        
+% Open file
+switch(info.ByteOrder(1))
+    case ('true')
+        fid=fopen(info.Filename,'rb','ieee-be');
+    otherwise
+        fid=fopen(info.Filename,'rb','ieee-le');
+end
+
+switch(lower(info.DataFile))
+    case 'local'
+        % Skip header
+        fseek(fid,info.HeaderSize,'bof');
+    otherwise
+        fseek(fid,0,'bof');
+end
+
+datasize=prod(info.Dimensions)*info.BitDepth/8; % in bytes
+
+switch(info.CompressedData(1))
+    case 'f'
+        % Read the Data
+        switch(info.DataType)
+            case 'char'
+                 V = int8(fread(fid,datasize,'char')); 
+            case 'uchar'
+                V = uint8(fread(fid,datasize,'uchar')); 
+            case 'short'
+                V = int16(fread(fid,datasize,'short')); 
+            case 'ushort'
+                V = uint16(fread(fid,datasize,'ushort')); 
+            case 'int'
+                 V = int32(fread(fid,datasize,'int')); 
+            case 'uint'
+                 V = uint32(fread(fid,datasize,'uint')); 
+            case 'float'
+                 V = single(fread(fid,datasize,'float'));   
+            case 'double'
+                V = double(fread(fid,datasize,'double'));
+        end
+    case 't'
+        switch(info.DataType)
+            case 'char', DataType='int8';
+            case 'uchar', DataType='uint8';
+            case 'short', DataType='int16';
+            case 'ushort', DataType='uint16';
+            case 'int', DataType='int32';
+            case 'uint', DataType='uint32';
+            case 'float', DataType='single';
+            case 'double', DataType='double';
+        end
+        Z  = fread(fid,inf,'uchar=>uint8');
+        V = zlib_decompress(Z,DataType);
+
+end
+
+fclose(fid);
+V = reshape(V,info.Dimensions);
+
+function M = zlib_decompress(Z,DataType)
+import com.mathworks.mlwidgets.io.InterruptibleStreamCopier
+a=java.io.ByteArrayInputStream(Z);
+b=java.util.zip.InflaterInputStream(a);
+isc = InterruptibleStreamCopier.getInterruptibleStreamCopier;
+c = java.io.ByteArrayOutputStream;
+isc.copyStream(b,c);
+M=typecast(c.toByteArray,DataType);