avw_img_write.html

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0150 
0151 <span class="keyword">switch</span> double(avw.hdr.dime.datatype),
0152 <span class="keyword">case</span>   1,
0153     avw.hdr.dime.bitpix = int16( 1); precision = <span class="string">'bit1'</span>;
0154 <span class="keyword">case</span>   2,
0155     avw.hdr.dime.bitpix = int16( 8); precision = <span class="string">'uchar'</span>;
0156 <span class="keyword">case</span>   4,
0157     avw.hdr.dime.bitpix = int16(16); precision = <span class="string">'int16'</span>;
0158 <span class="keyword">case</span>   8,
0159     avw.hdr.dime.bitpix = int16(32); precision = <span class="string">'int32'</span>;
0160 <span class="keyword">case</span>  16,
0161     avw.hdr.dime.bitpix = int16(32); precision = <span class="string">'single'</span>;
0162 <span class="keyword">case</span>  32,
0163     error(<span class="string">'...complex datatype not yet supported.\n'</span>);
0164 <span class="keyword">case</span>  64,
0165     avw.hdr.dime.bitpix = int16(64); precision = <span class="string">'double'</span>;
0166 <span class="keyword">case</span> 128,
0167     error(<span class="string">'...RGB datatype not yet supported.\n'</span>);
0168 <span class="keyword">otherwise</span>
0169     fprintf(<span class="string">'...unknown datatype, using type 16 (32 bit floats).\n'</span>);
0170     avw.hdr.dime.datatype = int16(16);
0171     avw.hdr.dime.bitpix = int16(32); precision = <span class="string">'single'</span>;
0172 <span class="keyword">end</span>
0173 
0174 
0175 <span class="comment">% write the .img file, depending on the .img orientation</span>
0176 fprintf(<span class="string">'...writing %s precision Analyze image (%s).\n'</span>,precision,machine);
0177 
0178 fseek(fid,0,<span class="string">'bof'</span>);
0179 
0180 <span class="comment">% The standard image orientation is axial unflipped</span>
0181 <span class="keyword">if</span> isempty(avw.hdr.hist.orient),
0182     msg = [ <span class="string">'...WARNING: avw.hdr.hist.orient ~= 0.\n'</span>,<span class="keyword">...</span>
0183             <span class="string">'   This function assumes the input avw.img is\n'</span>,<span class="keyword">...</span>
0184             <span class="string">'   in axial unflipped orientation in memory.  This is\n'</span>,<span class="keyword">...</span>
0185             <span class="string">'   created by the avw_img_read function, which converts\n'</span>,<span class="keyword">...</span>
0186             <span class="string">'   any input file image to axial unflipped in memory.\n'</span>];
0187     fprintf(msg)
0188 <span class="keyword">end</span>
0189 
0190 <span class="keyword">if</span> isempty(IMGorient),
0191     fprintf(<span class="string">'...no IMGorient specified, using avw.hdr.hist.orient value.\n'</span>);
0192     IMGorient = double(avw.hdr.hist.orient);
0193 <span class="keyword">end</span>
0194 
0195 <span class="keyword">if</span> ~isfinite(IMGorient),
0196     fprintf(<span class="string">'...IMGorient is not finite!\n'</span>);
0197     IMGorient = 99;
0198 <span class="keyword">end</span>
0199 
0200 <span class="keyword">switch</span> IMGorient,
0201     
0202 <span class="keyword">case</span> 0, <span class="comment">% transverse/axial unflipped</span>
0203     
0204     <span class="comment">% For the 'transverse unflipped' type, the voxels are stored with</span>
0205     <span class="comment">% Pixels in 'x' axis (varies fastest) - from patient right to left</span>
0206     <span class="comment">% Rows in   'y' axis                  - from patient posterior to anterior</span>
0207     <span class="comment">% Slices in 'z' axis                  - from patient inferior to superior</span>
0208     
0209     fprintf(<span class="string">'...writing axial unflipped\n'</span>);
0210     
0211     avw.hdr.hist.orient = uint8(0);
0212     
0213     SliceDim = double(avw.hdr.dime.dim(4)); <span class="comment">% z</span>
0214     RowDim   = double(avw.hdr.dime.dim(3)); <span class="comment">% y</span>
0215     PixelDim = double(avw.hdr.dime.dim(2)); <span class="comment">% x</span>
0216     SliceSz  = double(avw.hdr.dime.pixdim(4));
0217     RowSz    = double(avw.hdr.dime.pixdim(3));
0218     PixelSz  = double(avw.hdr.dime.pixdim(2));
0219     
0220     x = 1:PixelDim;
0221     <span class="keyword">for</span> z = 1:SliceDim,
0222         <span class="keyword">for</span> y = 1:RowDim,
0223             fwrite(fid,avw.img(x,y,z),precision);
0224         <span class="keyword">end</span>
0225     <span class="keyword">end</span>
0226     
0227 <span class="keyword">case</span> 1, <span class="comment">% coronal unflipped</span>
0228     
0229     <span class="comment">% For the 'coronal unflipped' type, the voxels are stored with</span>
0230     <span class="comment">% Pixels in 'x' axis (varies fastest) - from patient right to left</span>
0231     <span class="comment">% Rows in   'z' axis                  - from patient inferior to superior</span>
0232     <span class="comment">% Slices in 'y' axis                  - from patient posterior to anterior</span>
0233     
0234     fprintf(<span class="string">'...writing coronal unflipped\n'</span>);
0235     
0236     avw.hdr.hist.orient = uint8(1);
0237     
0238     SliceDim = double(avw.hdr.dime.dim(3)); <span class="comment">% y</span>
0239     RowDim   = double(avw.hdr.dime.dim(4)); <span class="comment">% z</span>
0240     PixelDim = double(avw.hdr.dime.dim(2)); <span class="comment">% x</span>
0241     SliceSz  = double(avw.hdr.dime.pixdim(3));
0242     RowSz    = double(avw.hdr.dime.pixdim(4));
0243     PixelSz  = double(avw.hdr.dime.pixdim(2));
0244     
0245     x = 1:PixelDim;
0246     <span class="keyword">for</span> y = 1:SliceDim,
0247         <span class="keyword">for</span> z = 1:RowDim,
0248             fwrite(fid,avw.img(x,y,z),precision);
0249         <span class="keyword">end</span>
0250     <span class="keyword">end</span>
0251     
0252 <span class="keyword">case</span> 2, <span class="comment">% sagittal unflipped</span>
0253     
0254     <span class="comment">% For the 'sagittal unflipped' type, the voxels are stored with</span>
0255     <span class="comment">% Pixels in 'y' axis (varies fastest) - from patient posterior to anterior</span>
0256     <span class="comment">% Rows in   'z' axis                  - from patient inferior to superior</span>
0257     <span class="comment">% Slices in 'x' axis                  - from patient right to left</span>
0258     
0259     fprintf(<span class="string">'...writing sagittal unflipped\n'</span>);
0260     
0261     avw.hdr.hist.orient = uint8(2);
0262     
0263     SliceDim = double(avw.hdr.dime.dim(2)); <span class="comment">% x</span>
0264     RowDim   = double(avw.hdr.dime.dim(4)); <span class="comment">% z</span>
0265     PixelDim = double(avw.hdr.dime.dim(3)); <span class="comment">% y</span>
0266     SliceSz  = double(avw.hdr.dime.pixdim(2));
0267     RowSz    = double(avw.hdr.dime.pixdim(4));
0268     PixelSz  = double(avw.hdr.dime.pixdim(3));
0269     
0270     y = 1:PixelDim;
0271     <span class="keyword">for</span> x = 1:SliceDim,
0272         <span class="keyword">for</span> z = 1:RowDim,
0273             fwrite(fid,avw.img(x,y,z),precision);
0274         <span class="keyword">end</span>
0275     <span class="keyword">end</span>
0276     
0277 <span class="keyword">case</span> 3, <span class="comment">% transverse/axial flipped</span>
0278     
0279     <span class="comment">% For the 'transverse flipped' type, the voxels are stored with</span>
0280     <span class="comment">% Pixels in 'x' axis (varies fastest) - from patient right to left</span>
0281     <span class="comment">% Rows in   'y' axis                  - from patient anterior to posterior*</span>
0282     <span class="comment">% Slices in 'z' axis                  - from patient inferior to superior</span>
0283     
0284     fprintf(<span class="string">'...writing axial flipped (+Y from Anterior to Posterior)\n'</span>);
0285     
0286     avw.hdr.hist.orient = uint8(3);
0287     
0288     SliceDim = double(avw.hdr.dime.dim(4)); <span class="comment">% z</span>
0289     RowDim   = double(avw.hdr.dime.dim(3)); <span class="comment">% y</span>
0290     PixelDim = double(avw.hdr.dime.dim(2)); <span class="comment">% x</span>
0291     SliceSz  = double(avw.hdr.dime.pixdim(4));
0292     RowSz    = double(avw.hdr.dime.pixdim(3));
0293     PixelSz  = double(avw.hdr.dime.pixdim(2));
0294     
0295     x = 1:PixelDim;
0296     <span class="keyword">for</span> z = 1:SliceDim,
0297         <span class="keyword">for</span> y = RowDim:-1:1, <span class="comment">% flipped in Y</span>
0298             fwrite(fid,avw.img(x,y,z),precision);
0299         <span class="keyword">end</span>
0300     <span class="keyword">end</span>
0301     
0302 <span class="keyword">case</span> 4, <span class="comment">% coronal flipped</span>
0303     
0304     <span class="comment">% For the 'coronal flipped' type, the voxels are stored with</span>
0305     <span class="comment">% Pixels in 'x' axis (varies fastest) - from patient right to left</span>
0306     <span class="comment">% Rows in   'z' axis                  - from patient inferior to superior</span>
0307     <span class="comment">% Slices in 'y' axis                  - from patient anterior to posterior</span>
0308     
0309     fprintf(<span class="string">'...writing coronal flipped (+Z from Superior to Inferior)\n'</span>);
0310     
0311     avw.hdr.hist.orient = uint8(4);
0312     
0313     SliceDim = double(avw.hdr.dime.dim(3)); <span class="comment">% y</span>
0314     RowDim   = double(avw.hdr.dime.dim(4)); <span class="comment">% z</span>
0315     PixelDim = double(avw.hdr.dime.dim(2)); <span class="comment">% x</span>
0316     SliceSz  = double(avw.hdr.dime.pixdim(3));
0317     RowSz    = double(avw.hdr.dime.pixdim(4));
0318     PixelSz  = double(avw.hdr.dime.pixdim(2));
0319     
0320     x = 1:PixelDim;
0321     <span class="keyword">for</span> y = 1:SliceDim,
0322         <span class="keyword">for</span> z = RowDim:-1:1,
0323             fwrite(fid,avw.img(x,y,z),precision);
0324         <span class="keyword">end</span>
0325     <span class="keyword">end</span>
0326     
0327 <span class="keyword">case</span> 5, <span class="comment">% sagittal flipped</span>
0328     
0329     <span class="comment">% For the 'sagittal flipped' type, the voxels are stored with</span>
0330     <span class="comment">% Pixels in 'y' axis (varies fastest) - from patient posterior to anterior</span>
0331     <span class="comment">% Rows in   'z' axis                  - from patient superior to inferior</span>
0332     <span class="comment">% Slices in 'x' axis                  - from patient right to left</span>
0333     
0334     fprintf(<span class="string">'...writing sagittal flipped (+Z from Superior to Inferior)\n'</span>);
0335     
0336     avw.hdr.hist.orient = uint8(5);
0337     
0338     SliceDim = double(avw.hdr.dime.dim(2)); <span class="comment">% x</span>
0339     RowDim   = double(avw.hdr.dime.dim(4)); <span class="comment">% z</span>
0340     PixelDim = double(avw.hdr.dime.dim(3)); <span class="comment">% y</span>
0341     SliceSz  = double(avw.hdr.dime.pixdim(2));
0342     RowSz    = double(avw.hdr.dime.pixdim(4));
0343     PixelSz  = double(avw.hdr.dime.pixdim(3));
0344     
0345     y = 1:PixelDim;
0346     <span class="keyword">for</span> x = 1:SliceDim,
0347         <span class="keyword">for</span> z = RowDim:-1:1, <span class="comment">% superior to inferior</span>
0348             fwrite(fid,avw.img(x,y,z),precision);
0349         <span class="keyword">end</span>
0350     <span class="keyword">end</span>
0351     
0352 <span class="keyword">otherwise</span>, <span class="comment">% transverse/axial unflipped</span>
0353     
0354     <span class="comment">% For the 'transverse unflipped' type, the voxels are stored with</span>
0355     <span class="comment">% Pixels in 'x' axis (varies fastest) - from patient right to left</span>
0356     <span class="comment">% Rows in   'y' axis                  - from patient posterior to anterior</span>
0357     <span class="comment">% Slices in 'z' axis                  - from patient inferior to superior</span>
0358     
0359     fprintf(<span class="string">'...unknown orientation specified, assuming default axial unflipped\n'</span>);
0360     
0361     avw.hdr.hist.orient = uint8(0);
0362     
0363     SliceDim = double(avw.hdr.dime.dim(4)); <span class="comment">% z</span>
0364     RowDim   = double(avw.hdr.dime.dim(3)); <span class="comment">% y</span>
0365     PixelDim = double(avw.hdr.dime.dim(2)); <span class="comment">% x</span>
0366     SliceSz  = double(avw.hdr.dime.pixdim(4));
0367     RowSz    = double(avw.hdr.dime.pixdim(3));
0368     PixelSz  = double(avw.hdr.dime.pixdim(2));
0369     
0370     x = 1:PixelDim;
0371     <span class="keyword">for</span> z = 1:SliceDim,
0372         <span class="keyword">for</span> y = 1:RowDim,
0373             fwrite(fid,avw.img(x,y,z),precision);
0374         <span class="keyword">end</span>
0375     <span class="keyword">end</span>
0376     
0377 <span class="keyword">end</span>
0378 
0379 fclose(fid);
0380 
0381 <span class="comment">% Update the header</span>
0382 avw.hdr.dime.dim(2:4) = int16([PixelDim,RowDim,SliceDim]);
0383 avw.hdr.dime.pixdim(2:4) = single([PixelSz,RowSz,SliceSz]);
0384 
0385 <span class="keyword">return</span></pre></div>
<hr><address>Generated on Fri 21-May-2004 12:38:21 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/">m2html</a></strong> &copy; 2003</address>
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