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<h1><a href="https://neurita.github.io/how_to_interact_with_mitk_images_from_python"> How to interact with <span class="caps">MITK</span> images from Python </a></h1>
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<h4>Contents</h4>
<div class="toc">
<ul>
<li><a href="#extending-your-mitk-plugin">Extending your <span class="caps">MITK</span> plugin</a><ul>
<li><a href="#method-1-simpleitk">Method 1: SimpleITK</a></li>
<li><a href="#method-2-other-process-an-image-from-path">Method 2: Other (process an image from path)</a></li>
</ul>
</li>
</ul>
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<div class="span8 article-content">
<h2 id="extending-your-mitk-plugin">Extending your <span class="caps">MITK</span> plugin<a class="headerlink" href="#extending-your-mitk-plugin" title="Permanent link">¶</a></h2>
<ul>
<li>
<p>I recommend that you build <span class="caps">MITK</span> with Boost enabled, also adding <code>filesystem</code> to the variable <code>MITK_USE_Boost_LIBRARIES</code>. It is not strictly necessary, but recommended for this example.</p>
</li>
<li>
<p>Following the previous recommendation, you will need to modify your plugin <code>CMakeLists.txt</code>.</p>
</li>
</ul>
<div class="highlight"><pre><span></span><span class="nb">project</span><span class="p">(</span><span class="s">com_company_example_python</span><span class="p">)</span>
<span class="nb">mitk_create_plugin</span><span class="p">(</span>
<span class="s">EXPORT_DIRECTIVE</span> <span class="s">EXAMPLE_PYTHON_EXPORT</span>
<span class="s">EXPORTED_INCLUDE_SUFFIXES</span> <span class="s">src</span>
<span class="s">MODULE_DEPENDS</span> <span class="s">MitkQtWidgetsExt</span> <span class="s">MitkPython</span>
<span class="s">PACKAGE_DEPENDS</span> <span class="s">Boost</span> <span class="c">#Add this line</span>
<span class="p">)</span>
</pre></div>
<ul>
<li>Boost in your plugin view file <code>MyView.cpp</code>.</li>
</ul>
<div class="highlight"><pre><span></span><span class="c1">// Boost</span>
<span class="cp">#include</span> <span class="cpf"><boost/filesystem.hpp></span><span class="cp"></span>
<span class="k">namespace</span> <span class="n">fs</span> <span class="o">=</span> <span class="n">boost</span><span class="o">::</span><span class="n">filesystem</span><span class="p">;</span>
<span class="k">using</span> <span class="n">fs</span><span class="o">::</span><span class="n">path</span><span class="p">;</span>
</pre></div>
<ul>
<li>
<p>In order to follow this tutorial you will probably need the plugin source code. You can found it in my repository @ljsalvatierra.</p>
<ul>
<li><a href="https://github.com/ljsalvatierra/mitk-projects/blob/master/LJSProject/Plugins/com.ljsalvatierra.example_python/src/internal/LJSView.cpp" target="_blank">LJSView.cpp</a></li>
<li><a href="https://github.com/ljsalvatierra/mitk-projects/blob/master/python/mitk_python_images/mitk_python_images/raw_images.py" target="_blank">Python module</a> </li>
</ul>
</li>
</ul>
<h3 id="method-1-simpleitk">Method 1: SimpleITK<a class="headerlink" href="#method-1-simpleitk" title="Permanent link">¶</a></h3>
<ul>
<li>Process a SimpleItk image and load it in the <span class="caps">MITK</span> Viewer.</li>
</ul>
<div class="highlight"><pre><span></span><span class="c1">//DoImageProcessing()</span>
<span class="n">mitk</span><span class="o">::</span><span class="n">Image</span><span class="o">::</span><span class="n">Pointer</span> <span class="n">postProcessedImage</span> <span class="o">=</span> <span class="k">this</span><span class="o">-></span><span class="n">ProcessSimpleItkImageInPython</span><span class="p">(</span><span class="n">image</span><span class="p">);</span>
<span class="k">this</span><span class="o">-></span><span class="n">LoadImage</span><span class="p">(</span><span class="n">node</span><span class="p">,</span> <span class="n">postProcessedImage</span><span class="p">,</span> <span class="n">name</span><span class="p">);</span>
</pre></div>
<p>Where <code>node</code> is a <code>mitk::DataNode</code> that contains the image. And <code>name</code> is one of the properties of the <code>node</code>.</p>
<p>I have successfully tested the plugin with Raw <code>.nrrd</code> and Dicom <code>.dcm</code> images. The Dicom images must be loaded with the <code>Open Dicom tool</code>, once that is loaded in the <code>DataStorage</code> you can get the image from the <code>node</code>.</p>
<p><img alt="Mitk Dicom Plugin" src="images/MITK_dicom_plugin_001.png"/></p>
<p><img alt="Mitk Dicom Plugin" src="images/MITK_dicom_plugin_002.png"/></p>
<p><img alt="Mitk Dicom Plugin" src="images/MITK_dicom_plugin_003.png"/></p>
<p>How do we send the image to our Python module?</p>
<ul>
<li>Import the module.</li>
</ul>
<div class="highlight"><pre><span></span><span class="n">StringList</span> <span class="n">code</span> <span class="o">=</span> <span class="n">QStringList</span><span class="p">()</span>
<span class="o"><<</span> <span class="s">"import sys"</span>
<span class="o"><<</span> <span class="s">"try:"</span>
<span class="o"><<</span> <span class="s">" sys.path.append('"</span> <span class="o">+</span> <span class="n">pythonScriptsPath</span> <span class="o">+</span> <span class="s">"')"</span>
<span class="o"><<</span> <span class="s">" import "</span> <span class="o">+</span> <span class="n">pythonPluginName</span> <span class="o">+</span> <span class="s">" as "</span> <span class="o">+</span> <span class="n">pythonPluginNameAlias</span>
<span class="o"><<</span> <span class="s">" plugin_available = True"</span>
<span class="o"><<</span> <span class="s">"except ImportError:"</span>
<span class="o"><<</span> <span class="s">" plugin_available = False"</span>
<span class="o"><<</span> <span class="s">" raise ImportError('No module named "</span> <span class="o">+</span> <span class="n">pythonPluginName</span> <span class="o">+</span> <span class="s">"')"</span>
</pre></div>
<ul>
<li>If we successfully import the module, call an example function.</li>
</ul>
<div class="highlight"><pre><span></span> <span class="o"><<</span> <span class="s">"if plugin_available:"</span>
<span class="o"><<</span> <span class="s">" try:"</span>
<span class="o"><<</span> <span class="s">" "</span> <span class="o">+</span> <span class="n">pythonOutputImage</span> <span class="o">+</span> <span class="s">" = "</span>
<span class="o">+</span> <span class="n">pythonPluginNameAlias</span> <span class="o">+</span> <span class="s">"."</span> <span class="o">+</span> <span class="n">pythonPluginFunction</span>
<span class="o">+</span> <span class="s">"("</span> <span class="o">+</span> <span class="n">pythonInputImage</span> <span class="o">+</span> <span class="s">")"</span>
<span class="o"><<</span> <span class="s">" except TypeError:"</span>
<span class="o"><<</span> <span class="s">" raise TypeError('Image Type Error')"</span><span class="p">;</span>
</pre></div>
<ul>
<li>Run the script.</li>
</ul>
<div class="highlight"><pre><span></span><span class="k">const</span> <span class="n">std</span><span class="o">::</span><span class="n">string</span> <span class="n">command</span> <span class="o">=</span> <span class="n">code</span><span class="p">.</span><span class="n">join</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">).</span><span class="n">toStdString</span><span class="p">();</span>
<span class="n">m_PythonService</span><span class="o">-></span><span class="n">Execute</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="n">mitk</span><span class="o">::</span><span class="n">PythonService</span><span class="o">::</span><span class="n">MULTI_LINE_COMMAND</span><span class="p">);</span>
</pre></div>
<p>Ok, but where is <code>pythonOutputImage</code>?</p>
<ul>
<li>Thanks to <code>PythonService</code> we can get all the variables saved in the stack.</li>
</ul>
<div class="highlight"><pre><span></span><span class="n">std</span><span class="o">::</span><span class="n">vector</span><span class="o"><</span><span class="n">mitk</span><span class="o">::</span><span class="n">PythonVariable</span><span class="o">></span> <span class="n">list</span> <span class="o">=</span> <span class="n">m_PythonService</span><span class="o">-></span><span class="n">GetVariableStack</span><span class="p">();</span>
<span class="n">mitk</span><span class="o">::</span><span class="n">Image</span><span class="o">::</span><span class="n">Pointer</span> <span class="n">outputImage</span><span class="p">;</span>
<span class="k">if</span> <span class="p">(</span> <span class="n">m_PythonService</span><span class="o">-></span><span class="n">DoesVariableExist</span><span class="p">(</span><span class="n">pythonOutputImage</span><span class="p">.</span><span class="n">toStdString</span><span class="p">())</span> <span class="p">)</span>
<span class="p">{</span>
<span class="n">outputImage</span> <span class="o">=</span> <span class="n">m_PythonService</span><span class="o">-></span><span class="n">CopySimpleItkImageFromPython</span><span class="p">(</span><span class="n">pythonOutputImage</span><span class="p">.</span><span class="n">toStdString</span><span class="p">());</span>
<span class="p">}</span>
</pre></div>
<p>Now that we have the image, how do we load it in the Workbench Viewer?</p>
<ul>
<li>Create a new node and populate it.</li>
</ul>
<div class="highlight"><pre><span></span><span class="n">mitk</span><span class="o">::</span><span class="n">DataNode</span><span class="o">::</span><span class="n">Pointer</span> <span class="n">ds</span> <span class="o">=</span> <span class="n">mitk</span><span class="o">::</span><span class="n">DataNode</span><span class="o">::</span><span class="n">New</span><span class="p">();</span>
<span class="n">ds</span><span class="o">-></span><span class="n">SetData</span><span class="p">(</span><span class="n">image</span><span class="p">);</span>
<span class="n">ds</span><span class="o">-></span><span class="n">SetProperty</span><span class="p">(</span><span class="s">"name"</span><span class="p">,</span> <span class="n">mitk</span><span class="o">::</span><span class="n">StringProperty</span><span class="o">::</span><span class="n">New</span><span class="p">(</span><span class="n">name</span> <span class="o">+</span> <span class="s">"_postProcessedImage"</span><span class="p">));</span>
</pre></div>
<ul>
<li>Add the new node to the <code>DataStorage</code> with the original image as <code>Parent node</code>.</li>
</ul>
<div class="highlight"><pre><span></span><span class="k">this</span><span class="o">-></span><span class="n">GetDataStorage</span><span class="p">()</span><span class="o">-></span><span class="n">Add</span><span class="p">(</span><span class="n">ds</span><span class="p">,</span><span class="n">originalImageNode</span><span class="p">);</span>
</pre></div>
<ul>
<li>Update the <code>RenderingManager</code>.</li>
</ul>
<div class="highlight"><pre><span></span><span class="n">mitk</span><span class="o">::</span><span class="n">RenderingManager</span><span class="o">::</span><span class="n">GetInstance</span><span class="p">()</span><span class="o">-></span><span class="n">RequestUpdateAll</span><span class="p">();</span>
</pre></div>
<p>And that’s it, you should see the processed image like this.</p>
<p><img alt="Mitk Processed image" src="images/MITK_processed_image_001.png"/></p>
<h3 id="method-2-other-process-an-image-from-path">Method 2: Other (process an image from path)<a class="headerlink" href="#method-2-other-process-an-image-from-path" title="Permanent link">¶</a></h3>
<p><code>This example doesn't work for dicom images.</code></p>
<ul>
<li>Process an image from path.</li>
</ul>
<div class="highlight"><pre><span></span><span class="n">std</span><span class="o">::</span><span class="n">string</span> <span class="n">imagePath</span> <span class="o">=</span> <span class="k">this</span><span class="o">-></span><span class="n">GetDataPath</span><span class="p">(</span><span class="n">data</span><span class="p">);</span>
<span class="n">path</span> <span class="n">p</span> <span class="o">=</span> <span class="n">path</span><span class="p">(</span><span class="n">imagePath</span><span class="p">);</span>
<span class="n">std</span><span class="o">::</span><span class="n">string</span> <span class="n">filename</span> <span class="o">=</span> <span class="n">p</span><span class="p">.</span><span class="n">filename</span><span class="p">().</span><span class="n">string</span><span class="p">();</span>
<span class="n">std</span><span class="o">::</span><span class="n">string</span> <span class="n">postProcessedImagePath</span> <span class="o">=</span> <span class="s">"/tmp/postProcessed_"</span> <span class="o">+</span> <span class="n">filename</span><span class="p">;</span>
<span class="k">this</span><span class="o">-></span><span class="n">ProcessImageInPython</span><span class="p">(</span><span class="n">imagePath</span><span class="p">,</span> <span class="n">postProcessedImagePath</span><span class="p">);</span>
<span class="k">this</span><span class="o">-></span><span class="n">LoadImageFromPath</span><span class="p">(</span><span class="n">node</span><span class="p">,</span> <span class="n">postProcessedImagePath</span><span class="p">,</span> <span class="n">filename</span><span class="p">);</span>
</pre></div>
<p>Where <code>GetDataPath()</code> is a function to get the image path inside <code>mitk::BaseData</code>.</p>
<div class="highlight"><pre><span></span><span class="n">std</span><span class="o">::</span><span class="n">string</span> <span class="n">imagePath</span> <span class="o">=</span> <span class="p">(</span><span class="n">data</span><span class="o">-></span><span class="n">GetProperty</span><span class="p">(</span><span class="s">"path"</span><span class="p">))</span><span class="o">-></span><span class="n">GetValueAsString</span><span class="p">();</span>
</pre></div>
<p>How do we send the image path to our Python module?</p>
<ul>
<li>Import the module, as in the first method (SimpleITK).</li>
</ul>
<div class="highlight"><pre><span></span><span class="n">QStringList</span> <span class="n">code</span> <span class="o">=</span> <span class="n">QStringList</span><span class="p">()</span>
<span class="o"><<</span> <span class="s">"import sys"</span>
<span class="o"><<</span> <span class="s">"try:"</span>
<span class="o"><<</span> <span class="s">" sys.path.append('"</span> <span class="o">+</span> <span class="n">pythonScriptsPath</span> <span class="o">+</span> <span class="s">"')"</span>
<span class="o"><<</span> <span class="s">" import "</span> <span class="o">+</span> <span class="n">pythonPluginName</span> <span class="o">+</span> <span class="s">" as "</span> <span class="o">+</span> <span class="n">pythonPluginNameAlias</span>
<span class="o"><<</span> <span class="s">" plugin_available = True"</span>
<span class="o"><<</span> <span class="s">"except ImportError:"</span>
<span class="o"><<</span> <span class="s">" plugin_available = False"</span>
<span class="o"><<</span> <span class="s">" raise ImportError('No module named "</span> <span class="o">+</span> <span class="n">pythonPluginName</span> <span class="o">+</span> <span class="s">"')"</span>
</pre></div>
<ul>
<li>If we successfully import the module, call and example function.</li>
</ul>
<div class="highlight"><pre><span></span> <span class="o"><<</span> <span class="s">"if plugin_available:"</span>
<span class="o"><<</span> <span class="s">" try:"</span>
<span class="o"><<</span> <span class="s">" "</span> <span class="o">+</span> <span class="n">pythonPluginNameAlias</span> <span class="o">+</span> <span class="s">"."</span> <span class="o">+</span> <span class="n">pythonPluginFunction</span>
<span class="o">+</span> <span class="s">"('"</span> <span class="o">+</span> <span class="n">pythonInputImage</span> <span class="o">+</span> <span class="s">"','"</span> <span class="o">+</span> <span class="n">pythonOutputImage</span> <span class="o">+</span> <span class="s">"')"</span>
<span class="o"><<</span> <span class="s">" except TypeError:"</span>
<span class="o"><<</span> <span class="s">" raise TypeError('Image Type Error')"</span><span class="p">;</span>
</pre></div>
<ul>
<li>Run the script.</li>
</ul>
<div class="highlight"><pre><span></span><span class="k">const</span> <span class="n">std</span><span class="o">::</span><span class="n">string</span> <span class="n">command</span> <span class="o">=</span> <span class="n">code</span><span class="p">.</span><span class="n">join</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">).</span><span class="n">toStdString</span><span class="p">();</span>
<span class="n">m_PythonService</span><span class="o">-></span><span class="n">Execute</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="n">mitk</span><span class="o">::</span><span class="n">PythonService</span><span class="o">::</span><span class="n">MULTI_LINE_COMMAND</span><span class="p">);</span>
</pre></div>
<p>Now we need to get the output image path.</p>
<ul>
<li>Get the path from the variable stack.</li>
</ul>
<div class="highlight"><pre><span></span><span class="n">std</span><span class="o">::</span><span class="n">string</span> <span class="n">outputImage</span><span class="p">;</span>
<span class="n">std</span><span class="o">::</span><span class="n">vector</span><span class="o"><</span><span class="n">mitk</span><span class="o">::</span><span class="n">PythonVariable</span><span class="o">></span> <span class="n">list</span> <span class="o">=</span> <span class="n">m_PythonService</span><span class="o">-></span><span class="n">GetVariableStack</span><span class="p">();</span>
<span class="k">for</span> <span class="p">(</span><span class="k">auto</span> <span class="o">&</span><span class="nl">i</span> <span class="p">:</span> <span class="n">list</span><span class="p">){</span>
<span class="k">if</span> <span class="p">(</span> <span class="n">i</span><span class="p">.</span><span class="n">m_Name</span> <span class="o">==</span> <span class="n">pythonOutputImage</span><span class="p">.</span><span class="n">toStdString</span><span class="p">()</span> <span class="p">)</span>
<span class="p">{</span>
<span class="n">outputImage</span> <span class="o">=</span> <span class="n">i</span><span class="p">.</span><span class="n">m_Value</span><span class="p">;</span>
<span class="k">break</span><span class="p">;</span>
<span class="p">}</span>
<span class="p">}</span>
</pre></div>
<p>Load the image in the Workbench Viewer.</p>
<ul>
<li>Create a new node and load the image from path.</li>
</ul>
<div class="highlight"><pre><span></span><span class="n">mitk</span><span class="o">::</span><span class="n">StandaloneDataStorage</span><span class="o">::</span><span class="n">Pointer</span> <span class="n">ds</span> <span class="o">=</span> <span class="n">mitk</span><span class="o">::</span><span class="n">StandaloneDataStorage</span><span class="o">::</span><span class="n">New</span><span class="p">();</span>
<span class="n">mitk</span><span class="o">::</span><span class="n">StandaloneDataStorage</span><span class="o">::</span><span class="n">SetOfObjects</span><span class="o">::</span><span class="n">Pointer</span> <span class="n">dataNodes</span> <span class="o">=</span> <span class="n">mitk</span><span class="o">::</span><span class="n">IOUtil</span><span class="o">::</span><span class="n">Load</span><span class="p">(</span><span class="n">processedImage</span><span class="p">,</span> <span class="o">*</span><span class="n">ds</span><span class="p">);</span>
<span class="n">mitk</span><span class="o">::</span><span class="n">DataNode</span><span class="o">::</span><span class="n">Pointer</span> <span class="n">node</span> <span class="o">=</span> <span class="n">dataNodes</span><span class="o">-></span><span class="n">at</span><span class="p">(</span><span class="mi">0</span><span class="p">);</span>
</pre></div>
<ul>
<li>Add the new node to the <code>DataStorage</code> with the original image as <code>Parent node</code>.</li>
</ul>
<div class="highlight"><pre><span></span><span class="k">this</span><span class="o">-></span><span class="n">GetDataStorage</span><span class="p">()</span><span class="o">-></span><span class="n">Add</span><span class="p">(</span><span class="n">node</span><span class="p">,</span><span class="n">originalImageNode</span><span class="p">);</span>
</pre></div>
<ul>
<li>Update the <code>RenderingManager</code>.</li>
</ul>
<div class="highlight"><pre><span></span><span class="n">mitk</span><span class="o">::</span><span class="n">RenderingManager</span><span class="o">::</span><span class="n">GetInstance</span><span class="p">()</span><span class="o">-></span><span class="n">RequestUpdateAll</span><span class="p">();</span>
</pre></div>
<p>The result, as before, should look like this.</p>
<p><img alt="Mitk Processed image" src="images/MITK_processed_image_002.png"/></p>
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<h4>Author</h4>
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