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jonescompneurolab · Jul 31, 2024 · 7904cf3 · 7904cf3
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diff --git a/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip
diff --git a/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip b/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip
diff --git a/dev/_downloads/9575eddd15339b520cfc58b84c61894f/optimize_evoked.zip b/dev/_downloads/9575eddd15339b520cfc58b84c61894f/optimize_evoked.zip
diff --git a/dev/_downloads/b52c981e7b898beab8949a80ade71521/optimize_rhythmic.zip b/dev/_downloads/b52c981e7b898beab8949a80ade71521/optimize_rhythmic.zip
diff --git a/dev/_modules/hnn_core/cell_response.html b/dev/_modules/hnn_core/cell_response.html
diff --git a/dev/_modules/hnn_core/viz.html b/dev/_modules/hnn_core/viz.html
@@ -599,7 +599,10 @@ <h1>Source code for hnn_core.viz</h1><div class="highlight"><pre>
     <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">color</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
         <span class="n">color_cycle</span> <span class="o">=</span> <span class="n">cycle</span><span class="p">(</span><span class="n">color</span><span class="p">)</span>
 
-    <span class="n">bins</span> <span class="o">=</span> <span class="n">np</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="n">spike_times</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="mi">50</span><span class="p">)</span>
+    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">cell_response</span><span class="o">.</span><span class="n">times</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+        <span class="n">bins</span> <span class="o">=</span> <span class="n">np</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="n">cell_response</span><span class="o">.</span><span class="n">times</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="mi">50</span><span class="p">)</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">bins</span> <span class="o">=</span> <span class="n">np</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="n">spike_times</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="mi">50</span><span class="p">)</span>
 
     <span class="c1"># Create dictionary to aggregate spike times that have the same spike_label</span>
     <span class="n">spike_type_times</span> <span class="o">=</span> <span class="p">{</span><span class="n">spike_label</span><span class="p">:</span> <span class="nb">list</span><span class="p">()</span> <span class="k">for</span>

diff --git a/dev/_sources/whats_new.rst.txt b/dev/_sources/whats_new.rst.txt
@@ -92,6 +92,9 @@ Changelog
   and interpolation method to smoothen CSD plot,
   by `Katharina Duecker`_ in :gh:`815`
 
+- Cleaned up internal logic in :class:`~hnn_core.CellResponse`,
+  by `Nick Tolley`_ in :gh:`647`.
+
 Bug
 ~~~
 - Fix inconsistent connection mapping from drive gids to cell gids, by

diff --git a/dev/generated/hnn_core.CellResponse.html b/dev/generated/hnn_core.CellResponse.html
@@ -89,7 +89,6 @@
       aria-labelledby="dLabelLocalToc"><ul>
 <li><a class="reference internal" href="#">hnn_core.CellResponse</a><ul>
 <li><a class="reference internal" href="#hnn_core.CellResponse"><code class="docutils literal notranslate"><span class="pre">CellResponse</span></code></a><ul>
-<li><a class="reference internal" href="#hnn_core.CellResponse.__getitem__"><code class="docutils literal notranslate"><span class="pre">CellResponse.__getitem__()</span></code></a></li>
 <li><a class="reference internal" href="#hnn_core.CellResponse.__repr__"><code class="docutils literal notranslate"><span class="pre">CellResponse.__repr__()</span></code></a></li>
 <li><a class="reference internal" href="#hnn_core.CellResponse.mean_rates"><code class="docutils literal notranslate"><span class="pre">CellResponse.mean_rates()</span></code></a></li>
 <li><a class="reference internal" href="#hnn_core.CellResponse.plot_spikes_hist"><code class="docutils literal notranslate"><span class="pre">CellResponse.plot_spikes_hist()</span></code></a></li>
@@ -161,14 +160,14 @@ <h1>hnn_core.CellResponse<a class="headerlink" href="#hnn-core-cellresponse" tit
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><dl class="simple">
-<dt><strong>spike_times</strong><span class="classifier">list (n_trials,) of list (n_spikes,) of float, shape | None</span></dt><dd><p>Each element of the outer list is a trial.
+<dt><strong>spike_times</strong><span class="classifier">list (n_trials,) of list (n_spikes,) of float | None</span></dt><dd><p>Each element of the outer list is a trial.
 The inner list contains the time stamps of spikes.</p>
 </dd>
-<dt><strong>spike_gids</strong><span class="classifier">list (n_trials,) of list (n_spikes,) of float, shape | None</span></dt><dd><p>Each element of the outer list is a trial.
+<dt><strong>spike_gids</strong><span class="classifier">list (n_trials,) of list (n_spikes,) of float | None</span></dt><dd><p>Each element of the outer list is a trial.
 The inner list contains the cell IDs of neurons that
 spiked.</p>
 </dd>
-<dt><strong>spike_types</strong><span class="classifier">list (n_trials,) of list (n_spikes,) of float, shape | None</span></dt><dd><p>Each element of the outer list is a trial.
+<dt><strong>spike_types</strong><span class="classifier">list (n_trials,) of list (n_spikes,) of float | None</span></dt><dd><p>Each element of the outer list is a trial.
 The inner list contains the type of spike (e.g., evprox1
 or L2_pyramidal) that occurred at the corresponding time stamp.
 Each gid corresponds to a type via Network().gid_ranges.</p>
@@ -183,22 +182,22 @@ <h1>hnn_core.CellResponse<a class="headerlink" href="#hnn-core-cellresponse" tit
 </dd>
 <dt class="field-even">Attributes<span class="colon">:</span></dt>
 <dd class="field-even"><dl class="simple">
-<dt><strong>spike_times</strong><span class="classifier">list (n_trials,) of list (n_spikes,) of float, shape</span></dt><dd><p>Each element of the outer list is a trial.
+<dt><strong>spike_times</strong><span class="classifier">list (n_trials,) of list (n_spikes,) of float</span></dt><dd><p>Each element of the outer list is a trial.
 The inner list contains the time stamps of spikes.</p>
 </dd>
-<dt><strong>spike_gids</strong><span class="classifier">list (n_trials,) of list (n_spikes,) of float, shape</span></dt><dd><p>Each element of the outer list is a trial.
+<dt><strong>spike_gids</strong><span class="classifier">list (n_trials,) of list (n_spikes,) of float</span></dt><dd><p>Each element of the outer list is a trial.
 The inner list contains the cell IDs of neurons that
 spiked.</p>
 </dd>
-<dt><strong>spike_types</strong><span class="classifier">list (n_trials,) of list (n_spikes,) of float, shape</span></dt><dd><p>Each element of the outer list is a trial.
+<dt><strong>spike_types</strong><span class="classifier">list (n_trials,) of list (n_spikes,) of float</span></dt><dd><p>Each element of the outer list is a trial.
 The inner list contains the type of spike (e.g., evprox1
 or L2_pyramidal) that occurred at the corresponding time stamp.
 Each gid corresponds to a type via Network::gid_ranges.</p>
 </dd>
-<dt><strong>vsec</strong><span class="classifier">list (n_trials,) of dict, shape</span></dt><dd><p>Each element of the outer list is a trial.
+<dt><strong>vsec</strong><span class="classifier">list (n_trials,) of dict</span></dt><dd><p>Each element of the outer list is a trial.
 Dictionary indexed by gids containing voltages for cell sections.</p>
 </dd>
-<dt><strong>isec</strong><span class="classifier">list (n_trials,) of dict, shape</span></dt><dd><p>Each element of the outer list is a trial.
+<dt><strong>isec</strong><span class="classifier">list (n_trials,) of dict</span></dt><dd><p>Each element of the outer list is a trial.
 Dictionary indexed by gids containing currents for cell sections.</p>
 </dd>
 <dt><strong>ca</strong><span class="classifier">list (n_trials,) of dict, shape</span></dt><dd><p>Each element of the outer list is a trial.
@@ -231,26 +230,6 @@ <h1>hnn_core.CellResponse<a class="headerlink" href="#hnn-core-cellresponse" tit
 </tr>
 </tbody>
 </table>
-<dl class="py method">
-<dt class="sig sig-object py" id="hnn_core.CellResponse.__getitem__">
-<span class="sig-name descname"><span class="pre">__getitem__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gid_item</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/hnn_core/cell_response.html#CellResponse.__getitem__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hnn_core.CellResponse.__getitem__" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns a CellResponse object with a copied subset filtered by gid.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><dl class="simple">
-<dt><strong>gid_item</strong><span class="classifier">int | slice</span></dt><dd><p>Subset of gids .</p>
-</dd>
-</dl>
-</dd>
-<dt class="field-even">Returns<span class="colon">:</span></dt>
-<dd class="field-even"><dl class="simple">
-<dt><strong>cell_response</strong><span class="classifier">instance of CellResponse</span></dt><dd><p>See below for use cases.</p>
-</dd>
-</dl>
-</dd>
-</dl>
-</dd></dl>
-
 <dl class="py method">
 <dt class="sig sig-object py" id="hnn_core.CellResponse.__repr__">
 <span class="sig-name descname"><span class="pre">__repr__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/hnn_core/cell_response.html#CellResponse.__repr__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hnn_core.CellResponse.__repr__" title="Permalink to this definition">¶</a></dt>

diff --git a/dev/genindex.html b/dev/genindex.html
@@ -160,8 +160,6 @@ <h1 id="index">Index</h1>
 <h2 id="_">_</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="generated/hnn_core.CellResponse.html#hnn_core.CellResponse.__getitem__">__getitem__() (hnn_core.CellResponse method)</a>
-</li>
       <li><a href="generated/hnn_core.Cell.html#hnn_core.Cell.__repr__">__repr__() (hnn_core.Cell method)</a>
 
       <ul>

diff --git a/dev/objects.inv b/dev/objects.inv
diff --git a/dev/searchindex.js b/dev/searchindex.js
diff --git a/dev/whats_new.html b/dev/whats_new.html
@@ -231,6 +231,8 @@ <h3>Changelog<a class="headerlink" href="#changelog" title="Permalink to this he
 <li><p>Added features to <code class="xref py py-func docutils literal notranslate"><span class="pre">plot_csd()</span></code>: to set color of sinks and sources, range of the colormap,
 and interpolation method to smoothen CSD plot,
 by <a class="reference external" href="https://github.com/katduecker">Katharina Duecker</a> in <a class="reference external" href="https://github.com/jonescompneurolab/hnn-core/issues/815">#815</a></p></li>
+<li><p>Cleaned up internal logic in <a class="reference internal" href="generated/hnn_core.CellResponse.html#hnn_core.CellResponse" title="hnn_core.CellResponse"><code class="xref py py-class docutils literal notranslate"><span class="pre">CellResponse</span></code></a>,
+by <a class="reference external" href="https://github.com/ntolley">Nick Tolley</a> in <a class="reference external" href="https://github.com/jonescompneurolab/hnn-core/issues/647">#647</a>.</p></li>
 </ul>
 </section>
 <section id="bug">