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Deployed 36bab7b to dev with MkDocs 1.6.1 and mike 2.1.3
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github-actions[bot] committed Dec 5, 2024
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2 changes: 1 addition & 1 deletion dev/search/search_index.json
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10 changes: 5 additions & 5 deletions dev/tutorial/08_importing_morphologies/index.html
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Expand Up @@ -1264,7 +1264,7 @@ <h1 id="working-with-morphologies">Working with morphologies<a class="headerlink
<span class="c1"># define colorwheel with 10 colors</span>
<span class="n">colors</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">cm</span><span class="o">.</span><span class="n">tab10</span><span class="o">.</span><span class="n">colors</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">branch</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">cell</span><span class="o">.</span><span class="n">branches</span><span class="p">):</span>
<span class="n">branch</span><span class="o">.</span><span class="n">vis</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span> <span class="n">col</span><span class="o">=</span><span class="n">colors</span><span class="p">[</span><span class="n">i</span> <span class="o">%</span> <span class="mi">10</span><span class="p">])</span>
<span class="n">branch</span><span class="o">.</span><span class="n">vis</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colors</span><span class="p">[</span><span class="n">i</span> <span class="o">%</span> <span class="mi">10</span><span class="p">])</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axis</span><span class="p">(</span><span class="s2">&quot;off&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s2">&quot;Branches&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
Expand All @@ -1277,7 +1277,7 @@ <h1 id="working-with-morphologies">Working with morphologies<a class="headerlink
<span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="n">layout</span><span class="o">=</span><span class="s2">&quot;constrained&quot;</span><span class="p">,</span> <span class="n">sharex</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">sharey</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">cell</span><span class="o">.</span><span class="n">vis</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="nb">type</span><span class="o">=</span><span class="s2">&quot;morph&quot;</span><span class="p">,</span> <span class="n">dims</span><span class="o">=</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="n">cell</span><span class="o">.</span><span class="n">vis</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="nb">type</span><span class="o">=</span><span class="s2">&quot;comp&quot;</span><span class="p">,</span> <span class="n">dims</span><span class="o">=</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="n">cell</span><span class="o">.</span><span class="n">vis</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="nb">type</span><span class="o">=</span><span class="s2">&quot;scatter&quot;</span><span class="p">,</span> <span class="n">dims</span><span class="o">=</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="n">morph_plot_kwargs</span><span class="o">=</span><span class="p">{</span><span class="s2">&quot;s&quot;</span><span class="p">:</span> <span class="mi">1</span><span class="p">})</span>
<span class="n">cell</span><span class="o">.</span><span class="n">vis</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="nb">type</span><span class="o">=</span><span class="s2">&quot;scatter&quot;</span><span class="p">,</span> <span class="n">dims</span><span class="o">=</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="n">s</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">cell</span><span class="o">.</span><span class="n">vis</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="nb">type</span><span class="o">=</span><span class="s2">&quot;line&quot;</span><span class="p">,</span> <span class="n">dims</span><span class="o">=</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="n">fig</span><span class="o">.</span><span class="n">suptitle</span><span class="p">(</span><span class="s2">&quot;Comparison of plot types&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
Expand All @@ -1299,9 +1299,9 @@ <h1 id="working-with-morphologies">Working with morphologies<a class="headerlink

<span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="mi">5</span><span class="p">))</span>
<span class="n">colors</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">cm</span><span class="o">.</span><span class="n">tab10</span><span class="o">.</span><span class="n">colors</span>
<span class="n">cell</span><span class="o">.</span><span class="n">basal</span><span class="o">.</span><span class="n">vis</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span> <span class="n">col</span><span class="o">=</span><span class="n">colors</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
<span class="n">cell</span><span class="o">.</span><span class="n">soma</span><span class="o">.</span><span class="n">vis</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span> <span class="n">col</span><span class="o">=</span><span class="n">colors</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="n">cell</span><span class="o">.</span><span class="n">apical</span><span class="o">.</span><span class="n">vis</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span> <span class="n">col</span><span class="o">=</span><span class="n">colors</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">cell</span><span class="o">.</span><span class="n">basal</span><span class="o">.</span><span class="n">vis</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colors</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
<span class="n">cell</span><span class="o">.</span><span class="n">soma</span><span class="o">.</span><span class="n">vis</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colors</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="n">cell</span><span class="o">.</span><span class="n">apical</span><span class="o">.</span><span class="n">vis</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">colors</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axis</span><span class="p">(</span><span class="s2">&quot;off&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s2">&quot;Groups&quot;</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
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