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<section id="plot-3d-images">
<h1>Plot 3D images<a class="headerlink" href="#plot-3d-images" title="Permalink to this heading"></a></h1>
<p>You can plot surfaces from freesurfer:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span> <span class="n">surf</span> <span class="o">=</span> <span class="n">Surf</span><span class="p">(</span><span class="n">surf_path</span><span class="p">)</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">Viz3</span><span class="p">()</span>
<span class="n">v</span><span class="o">.</span><span class="n">add_surf</span><span class="p">(</span><span class="n">surf</span><span class="p">)</span>
</pre></div>
</div>
<img alt="../_images/viz3_01_surf.png" src="../_images/viz3_01_surf.png" />
<p>and you can plot the color for the whole surface:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span> <span class="n">surf</span> <span class="o">=</span> <span class="n">Surf</span><span class="p">(</span><span class="n">surf_path</span><span class="p">)</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">Viz3</span><span class="p">()</span>
<span class="n">v</span><span class="o">.</span><span class="n">add_surf</span><span class="p">(</span><span class="n">surf</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="p">(</span><span class="mf">.5</span><span class="p">,</span> <span class="mf">.5</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
</pre></div>
</div>
<img alt="../_images/viz3_02_surf_color.png" src="../_images/viz3_02_surf_color.png" />
<p>or you can give the value for each vertex.
You can specify the min and max limits with <code class="docutils literal notranslate"><span class="pre">limits_c</span></code>.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span> <span class="n">surf</span> <span class="o">=</span> <span class="n">Surf</span><span class="p">(</span><span class="n">surf_path</span><span class="p">)</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">Viz3</span><span class="p">()</span>
<span class="n">v</span><span class="o">.</span><span class="n">add_surf</span><span class="p">(</span><span class="n">surf</span><span class="p">,</span> <span class="n">values</span><span class="o">=</span><span class="n">surf</span><span class="o">.</span><span class="n">vert</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">],</span> <span class="n">limits_c</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">50</span><span class="p">))</span>
</pre></div>
</div>
<img alt="../_images/viz3_03_surf_values.png" src="../_images/viz3_03_surf_values.png" />
<p>You can add a colorbar at the back of the head (you might need to zoom out to see it):</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span> <span class="n">surf</span> <span class="o">=</span> <span class="n">Surf</span><span class="p">(</span><span class="n">surf_path</span><span class="p">)</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">Viz3</span><span class="p">()</span>
<span class="n">v</span><span class="o">.</span><span class="n">add_surf</span><span class="p">(</span><span class="n">surf</span><span class="p">,</span> <span class="n">values</span><span class="o">=</span><span class="n">surf</span><span class="o">.</span><span class="n">vert</span><span class="p">[:,</span> <span class="mi">2</span><span class="p">],</span> <span class="n">limits_c</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">50</span><span class="p">),</span> <span class="n">colorbar</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
</pre></div>
</div>
<img alt="../_images/viz3_04_surf_colorbar.png" src="../_images/viz3_04_surf_colorbar.png" />
<p>You can then add channel positions, such ECoG on the surface:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span> <span class="n">surf</span> <span class="o">=</span> <span class="n">Surf</span><span class="p">(</span><span class="n">surf_path</span><span class="p">)</span>
<span class="n">channels</span> <span class="o">=</span> <span class="n">Channels</span><span class="p">(</span><span class="n">chan_path</span><span class="p">)</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">Viz3</span><span class="p">()</span>
<span class="n">v</span><span class="o">.</span><span class="n">add_chan</span><span class="p">(</span><span class="n">channels</span><span class="p">)</span>
<span class="n">v</span><span class="o">.</span><span class="n">add_surf</span><span class="p">(</span><span class="n">surf</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">.8</span><span class="p">)</span>
</pre></div>
</div>
<img alt="../_images/viz3_05_surf_chan.png" src="../_images/viz3_05_surf_chan.png" />
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>Note how the channel groups had different colors.
This is based on the channel labels.</p>
</div>
<p>You can also specify one color (in RGB, values between 0 and 1) to use the same color for all the channels:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span> <span class="n">surf</span> <span class="o">=</span> <span class="n">Surf</span><span class="p">(</span><span class="n">surf_path</span><span class="p">)</span>
<span class="n">channels</span> <span class="o">=</span> <span class="n">Channels</span><span class="p">(</span><span class="n">chan_path</span><span class="p">)</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">Viz3</span><span class="p">()</span>
<span class="n">v</span><span class="o">.</span><span class="n">add_chan</span><span class="p">(</span><span class="n">channels</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
<span class="n">v</span><span class="o">.</span><span class="n">add_surf</span><span class="p">(</span><span class="n">surf</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">.5</span><span class="p">)</span>
</pre></div>
</div>
<img alt="../_images/viz3_06_surf_chan_color_one.png" src="../_images/viz3_06_surf_chan_color_one.png" />
<p>To specify the transparency, enter the keyword <code class="docutils literal notranslate"><span class="pre">alpha</span></code> (0: transparent, 1: opaque).</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span> <span class="n">surf</span> <span class="o">=</span> <span class="n">Surf</span><span class="p">(</span><span class="n">surf_path</span><span class="p">)</span>
<span class="n">channels</span> <span class="o">=</span> <span class="n">Channels</span><span class="p">(</span><span class="n">chan_path</span><span class="p">)</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">Viz3</span><span class="p">()</span>
<span class="n">v</span><span class="o">.</span><span class="n">add_chan</span><span class="p">(</span><span class="n">channels</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.5</span><span class="p">)</span>
<span class="n">v</span><span class="o">.</span><span class="n">add_surf</span><span class="p">(</span><span class="n">surf</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">.5</span><span class="p">)</span>
</pre></div>
</div>
<img alt="../_images/viz3_07_surf_chan_color_one_alpha.png" src="../_images/viz3_07_surf_chan_color_one_alpha.png" />
<p>You can also specify the color for each channel (in this example, we alternate red and blue channels).</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span> <span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">tile</span>
<span class="n">surf</span> <span class="o">=</span> <span class="n">Surf</span><span class="p">(</span><span class="n">surf_path</span><span class="p">)</span>
<span class="n">channels</span> <span class="o">=</span> <span class="n">Channels</span><span class="p">(</span><span class="n">chan_path</span><span class="p">)</span>
<span class="n">color_everyother</span> <span class="o">=</span> <span class="n">tile</span><span class="p">([[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">]],</span> <span class="p">(</span><span class="mi">14</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">Viz3</span><span class="p">()</span>
<span class="n">v</span><span class="o">.</span><span class="n">add_chan</span><span class="p">(</span><span class="n">channels</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">color_everyother</span><span class="p">)</span>
<span class="n">v</span><span class="o">.</span><span class="n">add_surf</span><span class="p">(</span><span class="n">surf</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">.5</span><span class="p">)</span>
</pre></div>
</div>
<img alt="../_images/viz3_08_surf_chan_color_everyother.png" src="../_images/viz3_08_surf_chan_color_everyother.png" />
<p>Finally, you can specify the values for each channels (and add a colorbar).</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span> <span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">arange</span>
<span class="n">surf</span> <span class="o">=</span> <span class="n">Surf</span><span class="p">(</span><span class="n">surf_path</span><span class="p">)</span>
<span class="n">channels</span> <span class="o">=</span> <span class="n">Channels</span><span class="p">(</span><span class="n">chan_path</span><span class="p">)</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">Viz3</span><span class="p">()</span>
<span class="n">v</span><span class="o">.</span><span class="n">add_chan</span><span class="p">(</span><span class="n">channels</span><span class="p">,</span> <span class="n">values</span><span class="o">=</span><span class="n">arange</span><span class="p">(</span><span class="n">channels</span><span class="o">.</span><span class="n">n_chan</span><span class="p">),</span> <span class="n">colorbar</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">v</span><span class="o">.</span><span class="n">add_surf</span><span class="p">(</span><span class="n">surf</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">.5</span><span class="p">)</span>
</pre></div>
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