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<div class="header">
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<div class="headertitle"><div class="title">ImageRegistrationMethodBSpline3/ImageRegistrationMethodBSpline3.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 ImageRegistrationMethodBSpline3.R fixedImageFilter movingImageFile outputTransformFile</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"># Callback invoked each iteration</div>
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<div class="line">command_iteration &lt;- function(method, bspline_transform) {</div>
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<div class="line"> if (method$GetOptimizerIteration() == 0) {</div>
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<div class="line"> # The BSpline is resized before the first optimizer</div>
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<div class="line"> # iteration is completed per level. Print the transform object</div>
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<div class="line"> # to show the adapted BSpline transform.</div>
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<div class="line"> cat(bspline_transform$ToString(), &quot;\n&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"> cat(sprintf(&quot;%3d = %10.5f\n&quot;,</div>
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<div class="line"> method$GetOptimizerIteration(),</div>
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<div class="line"> method$GetMetricValue()))</div>
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<div class="line">}</div>
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<div class="line"> </div>
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<div class="line"># Callback invoked before starting a multi-resolution level.</div>
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<div class="line">command_multi_iteration &lt;- function(method) {</div>
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<div class="line"> if (method$GetCurrentLevel() &gt; 0) {</div>
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<div class="line"> cat(sprintf(&quot;Optimizer stop condition: %s\n&quot;,</div>
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<div class="line"> method$GetOptimizerStopConditionDescription()))</div>
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<div class="line"> cat(sprintf(&quot; Iteration: %d\n&quot;, method$GetOptimizerIteration()))</div>
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<div class="line"> cat(sprintf(&quot; Metric value: %f\n&quot;, method$GetMetricValue()))</div>
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<div class="line"> }</div>
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<div class="line"> </div>
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<div class="line"> cat(&quot;--------- Resolution Changing ---------\n&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">args &lt;- commandArgs( TRUE )</div>
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<div class="line"> </div>
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<div class="line">if (length(args) &lt; 3) {</div>
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<div class="line"> stop(&quot;Usage: fixedImageFilter movingImageFile outputTransformFile&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">fixed &lt;- ReadImage(args[1], &#39;sitkFloat32&#39;)</div>
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<div class="line">moving &lt;- ReadImage(args[2], &#39;sitkFloat32&#39;)</div>
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<div class="line"> </div>
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<div class="line">transformDomainMeshSize &lt;- rep(2, fixed$GetDimension())</div>
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<div class="line">tx &lt;- BSplineTransformInitializer(fixed, transformDomainMeshSize)</div>
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<div class="line"> </div>
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<div class="line">cat(sprintf(&quot;Initial Number of Parameters: %d\n&quot;, tx$GetNumberOfParameters()))</div>
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<div class="line"> </div>
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<div class="line">R &lt;- ImageRegistrationMethod()</div>
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<div class="line">R$SetMetricAsJointHistogramMutualInformation()</div>
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<div class="line"> </div>
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<div class="line">learningRate &lt;- 5.0</div>
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<div class="line">numberOfIterations &lt;- 100</div>
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<div class="line">convergenceMinimumValue &lt;- 1e-4</div>
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<div class="line">convergenceWindowSize &lt;- 5</div>
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<div class="line">R$SetOptimizerAsGradientDescentLineSearch(learningRate, numberOfIterations,</div>
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<div class="line"> convergenceMinimumValue, convergenceWindowSize)</div>
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<div class="line"> </div>
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<div class="line">R$SetInterpolator(&#39;sitkLinear&#39;)</div>
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<div class="line"> </div>
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<div class="line">R$SetInitialTransformAsBSpline(tx, inPlace=TRUE, scaleFactors=c(1, 2, 5))</div>
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<div class="line">R$SetShrinkFactorsPerLevel(c(4, 2, 1))</div>
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<div class="line">R$SetSmoothingSigmasPerLevel(c(4, 2, 1))</div>
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<div class="line"> </div>
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<div class="line">R$AddCommand(&#39;sitkIterationEvent&#39;, function() command_iteration(R, tx))</div>
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<div class="line">R$AddCommand(&#39;sitkMultiResolutionIterationEvent&#39;, function() command_multi_iteration(R))</div>
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<div class="line"> </div>
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<div class="line">outTx &lt;- R$Execute(fixed, moving)</div>
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<div class="line"> </div>
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<div class="line">cat(&quot;-------\n&quot;)</div>
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<div class="line">cat(tx$ToString(), &quot;\n&quot;)</div>
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<div class="line">cat(outTx$ToString(), &quot;\n&quot;)</div>
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<div class="line">cat(sprintf(&quot;Optimizer stop condition: %s\n&quot;, R$GetOptimizerStopConditionDescription()))</div>
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<div class="line">cat(sprintf(&quot; Iteration: %d\n&quot;, R$GetOptimizerIteration()))</div>
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<div class="line">cat(sprintf(&quot; Metric value: %f\n&quot;, R$GetMetricValue()))</div>
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<div class="line"> </div>
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<div class="line">WriteTransform(outTx, args[3])</div>
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<div class="line"> </div>
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<div class="line">if (Sys.getenv(&quot;SITK_NOSHOW&quot;) == &quot;&quot;) {</div>
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<div class="line"> resampler &lt;- ResampleImageFilter()</div>
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<div class="line"> resampler$SetReferenceImage(fixed)</div>
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<div class="line"> resampler$SetInterpolator(&#39;sitkLinear&#39;)</div>
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<div class="line"> resampler$SetDefaultPixelValue(100)</div>
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<div class="line"> resampler$SetTransform(outTx)</div>
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<div class="line"> </div>
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<div class="line"> out &lt;- resampler$Execute(moving)</div>
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<div class="line"> simg1 &lt;- Cast(RescaleIntensity(fixed), &#39;sitkUInt8&#39;)</div>
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<div class="line"> simg2 &lt;- Cast(RescaleIntensity(out), &#39;sitkUInt8&#39;)</div>
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<div class="line"> cimg &lt;- Compose(simg1, simg2, simg1 %/% 2.0 + simg2 %/% 2.0)</div>
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<div class="line"> Show(cimg, &quot;Image Registration Composition&quot;)</div>
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<div class="line">}</div>
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