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<!-- HTML header for doxygen 1.8.17-->
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml">
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<meta name="generator" content="Doxygen 1.13.2"/>
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<title>SimpleITK: AdvancedImageReading/AdvancedImageReading.R</title>
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<div id="projectname">SimpleITK
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<!-- Generated by Doxygen 1.13.2 -->
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/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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$(function() { codefold.init(0); });
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/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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/* @license-end */
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</script>
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<div class="header">
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<div class="headertitle"><div class="title">AdvancedImageReading/AdvancedImageReading.R</div></div>
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</div><!--header-->
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<div class="contents">
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<div class="fragment"><div class="line">#=========================================================================</div>
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<div class="line">#</div>
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<div class="line"># Copyright NumFOCUS</div>
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<div class="line">#</div>
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<div class="line"># Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</div>
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<div class="line"># you may not use this file except in compliance with the License.</div>
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<div class="line"># You may obtain a copy of the License at</div>
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<div class="line">#</div>
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<div class="line"># http://www.apache.org/licenses/LICENSE-2.0.txt</div>
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<div class="line">#</div>
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<div class="line"># Unless required by applicable law or agreed to in writing, software</div>
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<div class="line"># distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</div>
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<div class="line"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</div>
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<div class="line"># See the License for the specific language governing permissions and</div>
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<div class="line"># limitations under the License.</div>
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<div class="line">#</div>
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<div class="line">#=========================================================================</div>
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<div class="line"># Run with:</div>
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<div class="line">#</div>
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<div class="line"># Rscript --vanilla AdvancedImageReading.R</div>
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<div class="line">#</div>
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<div class="line"> </div>
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<div class="line">library(SimpleITK)</div>
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<div class="line"> </div>
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<div class="line">args &lt;- commandArgs( TRUE )</div>
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<div class="line"> </div>
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<div class="line">if (length(args) &lt; 1) {</div>
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<div class="line"> write(&#39;Usage arguments: &lt;image_file_name&gt;&#39;, stderr())</div>
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<div class="line"> quit(save=&quot;no&quot;, status=1)</div>
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<div class="line">}</div>
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<div class="line"> </div>
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<div class="line"># Read image information without reading the bulk data.</div>
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<div class="line">file_reader &lt;- ImageFileReader()</div>
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<div class="line">file_reader$SetFileName(args[1])</div>
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<div class="line">file_reader$ReadImageInformation()</div>
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<div class="line">cat(&#39;image size:&#39;, file_reader$GetSize(), &#39;\n&#39;)</div>
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<div class="line">cat(&#39;image spacing:&#39;, file_reader$GetSpacing(), &#39;\n&#39;)</div>
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<div class="line"># Some files have a rich meta-data dictionary (e.g. DICOM)</div>
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<div class="line">for(key in file_reader$GetMetaDataKeys())</div>
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<div class="line">{</div>
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<div class="line"> cat(paste0(key, &#39;: &#39;, file_reader$GetMetaData(key), &#39;\n&#39;))</div>
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<div class="line">}</div>
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<div class="line">cat(rep(&#39;-&#39;,20),&#39;\n&#39;, sep=&#39;&#39;)</div>
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<div class="line"> </div>
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<div class="line"># When low on memory, we can incrementally work on sub-images. The following</div>
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<div class="line"># subtracts two images (ok, the same image) by reading them as multiple sub-images.</div>
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<div class="line"> </div>
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<div class="line">image1_file_name &lt;- args[1]</div>
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<div class="line">image2_file_name &lt;- args[1]</div>
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<div class="line"> </div>
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<div class="line">parts &lt;- 5 # Number of sub-regions we use</div>
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<div class="line"> </div>
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<div class="line">file_reader &lt;- ImageFileReader()</div>
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<div class="line">file_reader$SetFileName(image1_file_name)</div>
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<div class="line">file_reader$ReadImageInformation()</div>
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<div class="line">image_size &lt;- file_reader$GetSize()</div>
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<div class="line"> </div>
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<div class="line">result_img &lt;- Image(file_reader$GetSize(), file_reader$GetPixelID(), file_reader$GetNumberOfComponents())</div>
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<div class="line">result_img$SetSpacing(file_reader$GetSpacing())</div>
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<div class="line">result_img$SetOrigin(file_reader$GetOrigin())</div>
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<div class="line">result_img$SetDirection(file_reader$GetDirection())</div>
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<div class="line"> </div>
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<div class="line">extract_size &lt;- file_reader$GetSize()</div>
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<div class="line">extract_size[-1] &lt;- extract_size[-1]%/%parts</div>
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<div class="line">current_index &lt;- rep(0,file_reader$GetDimension())</div>
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<div class="line">for(i in 1:parts)</div>
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<div class="line">{</div>
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<div class="line"> if(i == parts)</div>
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<div class="line"> {</div>
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<div class="line"> extract_size[-1] &lt;- image_size[-1] - current_index[-1]</div>
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<div class="line"> }</div>
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<div class="line"> file_reader$SetFileName(image1_file_name)</div>
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<div class="line"> file_reader$SetExtractIndex(current_index)</div>
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<div class="line"> file_reader$SetExtractSize(extract_size)</div>
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<div class="line"> sub_image1 &lt;- file_reader$Execute()</div>
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<div class="line"> </div>
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<div class="line"> file_reader$SetFileName(image2_file_name)</div>
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<div class="line"> file_reader$SetExtractIndex(current_index)</div>
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<div class="line"> file_reader$SetExtractSize(extract_size)</div>
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<div class="line"> sub_image2 &lt;- file_reader$Execute()</div>
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<div class="line"> result_img &lt;- Paste(result_img, sub_image1 - sub_image2, extract_size, rep(0,file_reader$GetDimension()), current_index)</div>
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<div class="line"> current_index[-1] &lt;- current_index[-1] + extract_size[-1]</div>
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<div class="line">}</div>
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<div class="line"> </div>
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<div class="line">rm(sub_image1, sub_image2)</div>
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<div class="line"> </div>
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<div class="line"># Check that our iterative approach is equivalent to reading the whole images.</div>
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<div class="line">if(any(as.array(result_img - ReadImage(image1_file_name) + ReadImage(image2_file_name))!=0))</div>
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<div class="line">{</div>
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<div class="line"> cat(&#39;Subtraction error.\n&#39;)</div>
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<div class="line"> quit(save=&quot;no&quot;, status=1)</div>
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<div class="line">}</div>
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<div class="line">quit(save=&quot;no&quot;, status=0)</div>
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</div><!-- fragment --> </div><!-- contents -->
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<!-- HTML footer for doxygen 1.8.17-->
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<hr class="footer"/><address class="footer"><small>
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Generated on <span id="datetime">unknown</span> for SimpleITK by &#160;
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