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76 changes: 40 additions & 36 deletions dev/reference/utils/index.html
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Expand Up @@ -1557,12 +1557,7 @@ <h3 id="jaxley.utils.cell_utils.compute_morphology_indices_in_levels" class="doc

<details class="quote">
<summary>Source code in <code>jaxley/utils/cell_utils.py</code></summary>
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<span class="n">num_branchpoints</span><span class="p">,</span>
<span class="n">child_belongs_to_branchpoint</span><span class="p">,</span>
<span class="n">par_inds</span><span class="p">,</span>
Expand Down Expand Up @@ -1678,12 +1678,7 @@ <h3 id="jaxley.utils.cell_utils.convert_point_process_to_distributed" class="doc
</details>
<details class="quote">
<summary>Source code in <code>jaxley/utils/cell_utils.py</code></summary>
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<span class="n">current</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="n">radius</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="n">length</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span>
<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Convert current point process (nA) to distributed current (uA/cm2).</span>
Expand Down Expand Up @@ -1852,12 +1852,7 @@ <h3 id="jaxley.utils.cell_utils.group_and_sum" class="doc doc-heading">

<details class="quote">
<summary>Source code in <code>jaxley/utils/cell_utils.py</code></summary>
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<span class="n">values_to_sum</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="n">inds_to_group_by</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="n">num_branchpoints</span><span class="p">:</span> <span class="nb">int</span>
<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Group values by whether they have the same integer and sum values within group.</span>
Expand Down Expand Up @@ -2094,10 +2094,7 @@ <h3 id="jaxley.utils.cell_utils.interpolate_xyz" class="doc doc-heading">
</details>
<details class="quote">
<summary>Source code in <code>jaxley/utils/cell_utils.py</code></summary>
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<span class="w"> </span><span class="sd">&quot;&quot;&quot;Perform a linear interpolation between xyz-coordinates.</span>

<span class="sd"> Args:</span>
Expand All @@ -2116,9 +2118,11 @@ <h3 id="jaxley.utils.cell_utils.interpolate_xyz" class="doc doc-heading">
<span class="sd"> Return:</span>
<span class="sd"> Interpolated xyz coordinate at `loc`, shape `(3,).</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="n">vmap</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">jnp</span><span class="o">.</span><span class="n">interp</span><span class="p">(</span><span class="n">loc</span><span class="p">,</span> <span class="n">jnp</span><span class="o">.</span><span class="n">linspace</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="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">)),</span> <span class="n">x</span><span class="p">),</span> <span class="n">in_axes</span><span class="o">=</span><span class="p">(</span><span class="mi">1</span><span class="p">,))(</span>
<span class="n">coords</span><span class="p">[:,</span> <span class="p">:</span><span class="mi">3</span><span class="p">]</span>
<span class="p">)</span>
<span class="n">dl</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">diff</span><span class="p">(</span><span class="n">coords</span><span class="p">[:,</span> <span class="p">:</span><span class="mi">3</span><span class="p">],</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">**</span> <span class="mi">2</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">))</span>
<span class="n">pathlens</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">cumsum</span><span class="p">(</span><span class="n">dl</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="c1"># cummulative length of sections</span>
<span class="n">norm_pathlens</span> <span class="o">=</span> <span class="n">pathlens</span> <span class="o">/</span> <span class="n">pathlens</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="c1"># path lengths normalized to [0,1]</span>

<span class="k">return</span> <span class="n">v_interp</span><span class="p">(</span><span class="n">loc</span><span class="p">,</span> <span class="n">norm_pathlens</span><span class="p">,</span> <span class="n">coords</span><span class="p">[:,</span> <span class="p">:</span><span class="mi">3</span><span class="p">])</span>
</code></pre></div></td></tr></table></div>
</details>
</div>
Expand Down Expand Up @@ -2500,12 +2504,7 @@ <h3 id="jaxley.utils.cell_utils.params_to_pstate" class="doc doc-heading">

<details class="quote">
<summary>Source code in <code>jaxley/utils/cell_utils.py</code></summary>
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<span class="n">params</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">]],</span>
<span class="n">indices_set_by_trainables</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">jnp</span><span class="o">.</span><span class="n">ndarray</span><span class="p">],</span>
<span class="p">):</span>
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