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<div id="projectname">SimpleITK
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<div class="header">
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<div class="headertitle"><div class="title">LandmarkRegistration/LandmarkRegistration.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"> </div>
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<div class="line"># A SimpleITK example demonstrating landmark registration.</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"># Black image with a small white square in it.</div>
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<div class="line">fixedImage &lt;- Image(100, 100, &#39;sitkUInt8&#39;)</div>
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<div class="line"># Set pixels in rectangle [11:20, 11:20] to 200</div>
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<div class="line">for (x in 11:19) {</div>
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<div class="line"> for (y in 11:19) {</div>
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<div class="line"> fixedImage$SetPixel(c(x, y), 200)</div>
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<div class="line"> }</div>
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<div class="line">}</div>
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<div class="line"> </div>
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<div class="line"># Black image with a small grey square at a different location.</div>
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<div class="line">movingImage &lt;- Image(100, 100, &#39;sitkUInt8&#39;)</div>
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<div class="line"># Set pixels in rectangle [51:60, 51:60] to 69</div>
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<div class="line">for (x in 51:59) {</div>
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<div class="line"> for (y in 51:59) {</div>
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<div class="line"> movingImage$SetPixel(c(x, y), 69)</div>
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<div class="line"> }</div>
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<div class="line">}</div>
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<div class="line"> </div>
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<div class="line"># Landmarks are 3 corners of the squares.</div>
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<div class="line"># 3 (X, Y) pairs are flattened into 1-d lists.</div>
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<div class="line">fixedLandmarks &lt;- c(10, 10, 20, 10, 20, 20)</div>
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<div class="line">movingLandmarks &lt;- c(50, 50, 60, 50, 60, 60)</div>
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<div class="line"> </div>
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<div class="line"># Set up the LandmarkBasedTransformInitializerFilter.</div>
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<div class="line">landmarkInitializer &lt;- LandmarkBasedTransformInitializerFilter()</div>
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<div class="line"> </div>
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<div class="line">landmarkInitializer$SetFixedLandmarks(fixedLandmarks)</div>
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<div class="line">landmarkInitializer$SetMovingLandmarks(movingLandmarks)</div>
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<div class="line"> </div>
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<div class="line">transform &lt;- Euler2DTransform()</div>
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<div class="line"> </div>
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<div class="line"># Compute the transform.</div>
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<div class="line">outputTransform &lt;- landmarkInitializer$Execute(transform)</div>
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<div class="line"> </div>
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<div class="line">cat(outputTransform$ToString())</div>
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<div class="line"> </div>
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<div class="line"># Resample the transformed moving image onto the fixed image.</div>
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<div class="line">outputImage &lt;- Resample(movingImage, fixedImage, outputTransform, &#39;sitkLinear&#39;, 150)</div>
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<div class="line"> </div>
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<div class="line"># Write the resampled image.</div>
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<div class="line">WriteImage(outputImage, &quot;landmark_example.png&quot;)</div>
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<div class="line"> </div>
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<div class="line"># Write the transform.</div>
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<div class="line">if (length(args) &gt; 0) {</div>
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<div class="line"> outName &lt;- args[1]</div>
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<div class="line">} else {</div>
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<div class="line"> outName &lt;- &quot;landmark_transform.tfm&quot;</div>
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<div class="line">}</div>
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<div class="line"> </div>
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<div class="line">WriteTransform(outputTransform, outName)</div>
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