ge_series_read.html

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0074 dirFiles = dir(seriesPath);
0075 n = 0;
0076 <span class="keyword">for</span> i = 1:length(dirFiles),
0077     <span class="comment">% check whether this file is a directory</span>
0078     <span class="keyword">if</span> ~ dirFiles(i).isdir,
0079         <span class="comment">% check whether it ends with .MR</span>
0080         <span class="keyword">if</span> findstr(dirFiles(i).name,<span class="string">'.MR'</span>),
0081             <span class="comment">%fprintf(sprintf('found *.MR file: %s\n',dirFiles(i).name));</span>
0082             n = n + 1;
0083             seriesFileNames{n} = dirFiles(i).name;
0084             imageFormat = <span class="string">'MR'</span>;
0085         <span class="keyword">elseif</span> findstr(dirFiles(i).name,<span class="string">'I.'</span>),
0086             <span class="comment">%fprintf(sprintf('found I. file: %s\n',dirFiles(i).name));</span>
0087             n = n + 1;
0088             seriesFileNames{n} = dirFiles(i).name;
0089             imageFormat = <span class="string">'I'</span>;
0090         <span class="keyword">end</span>
0091     <span class="keyword">end</span>
0092 <span class="keyword">end</span>
0093 
0094 <span class="keyword">if</span> n == 0,
0095     msg = sprintf(<span class="string">'...Found %d image files (I.* or *.MR)!\n'</span>,n);
0096     error(msg);
0097 <span class="keyword">else</span>
0098     fprintf(<span class="string">'...Found %d image files\n'</span>,n);
0099 <span class="keyword">end</span>
0100 
0101 <span class="keyword">if</span> isequal(imageFormat,<span class="string">'MR'</span>),
0102     
0103     fprintf(<span class="string">'...sorting *.MR image files into numerical order\n'</span>);
0104     
0105     <span class="comment">% extract exam/series/image numbers and sort into numerical order</span>
0106     fileName.position.exam   = findstr(seriesFileNames{1},<span class="string">'E'</span>);
0107     fileName.position.series = findstr(seriesFileNames{1},<span class="string">'S'</span>);
0108     fileName.position.image  = findstr(seriesFileNames{1},<span class="string">'I'</span>);
0109     
0110     range = [ (fileName.position.exam + 1) : (fileName.position.series - 1) ];
0111     examN = seriesFileNames{1}(range);
0112     
0113     range   = [ (fileName.position.series + 1) : (fileName.position.image - 1) ];
0114     seriesN = seriesFileNames{1}(range);
0115     
0116     <span class="keyword">for</span> i = 1:length(seriesFileNames),
0117         range = [ fileName.position.image + 1 ];
0118         imageNumbers{i} = seriesFileNames{i}(range:end);
0119         imageNumbers{i} = strrep(imageNumbers{i},<span class="string">'.MR'</span>,<span class="string">''</span>);
0120     <span class="keyword">end</span>
0121     imageNumbers = str2double(imageNumbers);
0122     [n,i] = sort(imageNumbers);
0123     
0124     sortedFileNames = seriesFileNames(i);
0125     
0126 <span class="keyword">elseif</span> isequal(imageFormat, <span class="string">'I'</span>),
0127     
0128     fprintf(<span class="string">'...sorting I.* image files into numerical order\n'</span>);
0129     
0130     <span class="comment">% extract image numbers, which might already be in numerical order</span>
0131     
0132     <span class="keyword">for</span> i = 1:length(seriesFileNames),
0133         imageNumbers{i} = seriesFileNames{i}(3:end);
0134     <span class="keyword">end</span>
0135     imageNumbers = str2double(imageNumbers);
0136     [n,i] = sort(imageNumbers);
0137     
0138     sortedFileNames = seriesFileNames(i);
0139     
0140 <span class="keyword">end</span>
0141 
0142 <span class="comment">% --- Create the name of the first file in examPath</span>
0143 firstfile = fullfile(seriesPath,sortedFileNames{1});
0144 
0145 
0146 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>
0147 <span class="comment">% --- Read the header from the first file in the series</span>
0148 ge = <a href="ge_hdr_read.html" class="code" title="function [ ge ] = ge_hdr_read(imageFileName)">ge_hdr_read</a>(firstfile);
0149 
0150 
0151 
0152 im_offset = ge.img.offset;  <span class="comment">% this is not so good, as the ge.img is replaced below!</span>
0153 
0154 
0155 
0156 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>
0157 <span class="comment">% --- Read the image data from the GE series files</span>
0158 
0159 version = <span class="string">'[$Revision: 1.4 $]'</span>;
0160 fprintf(<span class="string">'\nGE_SERIES_READ [v%s]\n'</span>,version(12:16));
0161 fprintf(<span class="string">'...reading image data\n'</span>);
0162 
0163 <span class="comment">% initialize some variables</span>
0164 nX = ge.hdr.image.imatrix_X; <span class="comment">% X Voxels</span>
0165 nY = ge.hdr.image.imatrix_Y; <span class="comment">% Y Voxels</span>
0166 nZ = ge.hdr.image.slquant;   <span class="comment">% Z Voxels (slice quantity)</span>
0167 
0168 sliceSize = nX*nY;
0169 ge.img = zeros(nX, nY, nZ);
0170 
0171 fprintf(<span class="string">'...reading '</span>);
0172 
0173 <span class="keyword">for</span> i = 1:nZ,
0174     
0175     imageFile = fullfile(seriesPath,sortedFileNames{i});
0176     
0177     <span class="comment">% output filename to indicate progress</span>
0178     <span class="keyword">if</span> i == 1,
0179         backspaces = <span class="string">''</span>;
0180     <span class="keyword">else</span>
0181         filePreviousLength = length(fullfile(seriesPath,sortedFileNames{i-1}));
0182         backspaces = repmat(<span class="string">'\b'</span>,1,filePreviousLength);
0183     <span class="keyword">end</span>
0184     fprintf([backspaces,<span class="string">'%s'</span>],imageFile);
0185     
0186     
0187     <span class="comment">% Open the file</span>
0188     [fid,message] = fopen(imageFile,<span class="string">'r'</span>,<span class="string">'b'</span>); <span class="comment">% big endian</span>
0189     <span class="keyword">if</span> (fid == -1)
0190         fprintf(<span class="string">'Cannot Open %s (big endian).\n'</span>,imageFile);
0191         
0192         <span class="comment">% Can try to read little endian (shouldn't be necessary!)</span>
0193         fprintf(<span class="string">'Trying to read little endian\n'</span>);
0194         [fid,message] = fopen(imageFile,<span class="string">'r'</span>,<span class="string">'l'</span>); <span class="comment">% little endian</span>
0195         <span class="keyword">if</span> (fid == -1),
0196             fprintf(<span class="string">'Cannot Open %s (little endian).\n'</span>,imageFile);
0197             <span class="keyword">break</span>
0198         <span class="keyword">end</span>
0199     <span class="keyword">end</span>
0200     
0201     <span class="comment">% Skip the header, goto the data</span>
0202     fseek(fid,im_offset,-1);
0203     <span class="comment">% Read the slice data</span>
0204     buffer = fread(fid,sliceSize,sprintf(<span class="string">'int%d'</span>,ge.hdr.image.screenformat));
0205     <span class="comment">% append the slice to the imageSet</span>
0206     ge.img(:,:,i) = reshape(buffer, nX, nY);
0207     
0208     <span class="comment">% Close the file</span>
0209     status = fclose(fid);
0210     
0211     <span class="comment">% Set the lastfile</span>
0212     lastfile = imageFile;
0213 <span class="keyword">end</span>
0214 
0215 t=toc; fprintf(<span class="string">'\n...done (%5.2f sec).\n'</span>,t);
0216 
0217 <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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