updating with auditory filternet tutorial

AllenInstitute · Apr 24, 2024 · b051e78 · b051e78
1 parent bf6ebc8
commit b051e78
Show file tree

Hide file tree

Showing 388 changed files with 92,698 additions and 6,313 deletions.
diff --git a/_images/Filters_sp_t_mod.png b/_images/Filters_sp_t_mod.png
diff --git a/_images/Responses_to_diff_scales_and_orientations.png b/_images/Responses_to_diff_scales_and_orientations.png
diff --git a/_images/tutorial_auditory_filternet_2_1.png b/_images/tutorial_auditory_filternet_2_1.png
diff --git a/_images/tutorial_auditory_filternet_2_2.png b/_images/tutorial_auditory_filternet_2_2.png
diff --git a/_images/tutorial_auditory_filternet_7_1.png b/_images/tutorial_auditory_filternet_7_1.png
diff --git a/_images/tutorial_auditory_filternet_7_2.png b/_images/tutorial_auditory_filternet_7_2.png
diff --git a/_modules/bmtk/analyzer.html b/_modules/bmtk/analyzer.html
@@ -1,17 +1,15 @@
-
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>bmtk.analyzer &#8212; Brain Modeling Toolkit 0.0.6 documentation</title>
+    <title>bmtk.analyzer &#8212; Brain Modeling Toolkit 1.0.8 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../_static/aibs_sphinx.css" />
     <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
-    <script src="../../_static/jquery.js"></script>
-    <script src="../../_static/underscore.js"></script>
     <script src="../../_static/doctools.js"></script>
+    <script src="../../_static/sphinx_highlight.js"></script>
     <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -772,7 +770,7 @@ <h1>Source code for bmtk.analyzer</h1><div class="highlight"><pre>
     <span class="n">spikes_file</span> <span class="o">=</span> <span class="n">config</span><span class="p">[</span><span class="s1">&#39;output&#39;</span><span class="p">][</span><span class="s1">&#39;spikes_file&#39;</span><span class="p">]</span>
     <span class="n">spikes_h5</span> <span class="o">=</span> <span class="n">h5py</span><span class="o">.</span><span class="n">File</span><span class="p">(</span><span class="n">spikes_file</span><span class="p">,</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span>
     <span class="n">gids</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">spikes_h5</span><span class="p">[</span><span class="s1">&#39;/spikes/gids&#39;</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">uint</span><span class="p">)</span>
-    <span class="n">times</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">spikes_h5</span><span class="p">[</span><span class="s1">&#39;/spikes/timestamps&#39;</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">float</span><span class="p">)</span>
+    <span class="n">times</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">spikes_h5</span><span class="p">[</span><span class="s1">&#39;/spikes/timestamps&#39;</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">float</span><span class="p">)</span>
     <span class="k">return</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;gid&#39;</span><span class="p">:</span> <span class="n">gids</span><span class="p">,</span> <span class="s1">&#39;spike time (ms)&#39;</span><span class="p">:</span> <span class="n">times</span><span class="p">})</span></div>
     <span class="c1">#return pd.read_csv(spikes_ascii, names=[&#39;time (ms)&#39;, &#39;cell gid&#39;], sep=&#39; &#39;)</span>
 
@@ -828,12 +826,30 @@ <h3><a href="../../index.html">Contents</a></h3>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../../analyzer.html">Analyzing the Results</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../tutorials.html">Tutorials</a><ul class="simple">
+<li class="toctree-l1"><a class="reference internal" href="../../tutorials.html">Main Tutorials</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../tutorial_NetworkBuilder_Intro.html">Builder: Using the Network Builder</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../tutorial_single_cell_clamped.html">BioNet: Single cell with current injection</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../tutorial_single_cell_syn.html">BioNet: Single with with synaptic input</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../tutorial_single_pop.html">BioNet: Multiple Nodes with single cell-type</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../tutorial_multi_pop.html">BioNet: Heterogeneous network</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../tutorial_pointnet_modeling.html">PointNet: Point-neuron modeling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../tutorial_population_modeling.html">PopNet: Population-based firing rate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../tutorial_filter_models.html">FilterNet: Full-field flashing movie</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../../ad_tutorials.html">Additional Tutorials</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../tutorial_cell_placement.html">Cell placement: Functions for spatially distributing units</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../tutorial_dynamic_synapses.html">Accessing synapse models in NEST to model dynamic synapses</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../tutorial_spike_trains_refractory.html">Creating spike trains with refractory periods</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../tutorial_bionet_disconnected_sims.html">Replaying disconnected simulations in BioNet</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../../examples.html">Example Networks</a></li>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/AllenInstitute/bmtk.git">Github Profile</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../workshop.html">Annual Modeling Software Workshop</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../registration.html">Registration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../contributors.html">Contributors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../how_to_cite.html">How to Cite</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../bmtk/bmtk.html">Source Documentation</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="../../bmtk/bmtk.analyzer.html">bmtk.analyzer package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../bmtk/bmtk.builder.html">bmtk.builder package</a></li>
@@ -853,7 +869,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
       <div class="clearer"></div>

diff --git a/_modules/bmtk/analyzer/compartment.html b/_modules/bmtk/analyzer/compartment.html
@@ -1,17 +1,15 @@
-
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>bmtk.analyzer.compartment &#8212; Brain Modeling Toolkit 1.0.7 documentation</title>
+    <title>bmtk.analyzer.compartment &#8212; Brain Modeling Toolkit 1.0.8 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/aibs_sphinx.css" />
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
-    <script src="../../../_static/jquery.js"></script>
-    <script src="../../../_static/underscore.js"></script>
     <script src="../../../_static/doctools.js"></script>
+    <script src="../../../_static/sphinx_highlight.js"></script>
     <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
@@ -687,7 +685,7 @@ <h1>Source code for bmtk.analyzer.compartment</h1><div class="highlight"><pre>
                 <span class="n">group_excludes</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">nodes_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">node_types_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
                 <span class="n">node_ids</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">sections</span><span class="o">=</span><span class="s1">&#39;origin&#39;</span><span class="p">,</span> <span class="n">average</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">times</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">title</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
                 <span class="n">show_legend</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">show</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">save_as</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">plt_style</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Plot compartment variables (eg Membrane Voltage, Calcium conc.) traces from the output of simulation. Will</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Plot compartment variables (eg Membrane Voltage, Calcium conc.) traces from the output of simulation. Will</span>
 <span class="sd">    attempt to look in the SONATA simulation configuration json &quot;reports&quot; sections for any matching &quot;membrane_report&quot;</span>
 <span class="sd">    outputs with a matching report_name::</span>
 
@@ -866,7 +864,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
       <div class="clearer"></div>

diff --git a/_modules/bmtk/analyzer/ecp.html b/_modules/bmtk/analyzer/ecp.html
@@ -4,15 +4,18 @@
 <html>
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>bmtk.analyzer.ecp &#8212; Brain Modeling Toolkit 0.0.6 documentation</title>
-    <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="../../../_static/aibs_sphinx.css" />
-    <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>bmtk.analyzer.ecp &#8212; Brain Modeling Toolkit 1.0.7 documentation</title>
+    <link rel="stylesheet" href="../../../_static/aibs_sphinx.css" type="text/css" />
+    <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
+    <script id="documentation_options" data-url_root="../../../" src="../../../_static/documentation_options.js"></script>
     <script src="../../../_static/jquery.js"></script>
     <script src="../../../_static/underscore.js"></script>
     <script src="../../../_static/doctools.js"></script>
+    <script src="../../../_static/language_data.js"></script>
     <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
+    <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <script type="text/x-mathjax-config">MathJax.Hub.Config({"tex2jax": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true, "ignoreClass": "document", "processClass": "math|output_area"}})</script>
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
   </head><body>
@@ -726,12 +729,29 @@ <h3><a href="../../../index.html">Contents</a></h3>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../../../analyzer.html">Analyzing the Results</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../tutorials.html">Tutorials</a><ul class="simple">
+<li class="toctree-l1"><a class="reference internal" href="../../../tutorials.html">Main Tutorials</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../../tutorial_NetworkBuilder_Intro.html">Builder: Using the Network Builder</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../../tutorial_single_cell_clamped.html">BioNet: Single cell with current injection</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../../tutorial_single_cell_syn.html">BioNet: Single with with synaptic input</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../../tutorial_single_pop.html">BioNet: Multiple Nodes with single cell-type</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../../tutorial_multi_pop.html">BioNet: Heterogeneous network</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../../tutorial_pointnet_modeling.html">PointNet: Point-neuron modeling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../../tutorial_population_modeling.html">PopNet: Population-based firing rate models</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../../tutorial_filter_models.html">FilterNet: Full-field flashing movie</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../../../ad_tutorials.html">Additional Tutorials</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../../tutorial_cell_placement.html">Cell placement: Functions for spatially distributing units</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../../tutorial_dynamic_synapses.html">Accessing synapse models in NEST to model dynamic synapses</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../../../tutorial_spike_trains_refractory.html">Creating spike trains with refractory periods</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../../../examples.html">Example Networks</a></li>
 <li class="toctree-l1"><a class="reference external" href="https://github.com/AllenInstitute/bmtk.git">Github Profile</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../workshop.html">Annual Modeling Software Workshop</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../registration.html">Registration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../contributors.html">Contributors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../how_to_cite.html">How to Cite</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../bmtk/bmtk.html">Source Documentation</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="../../../bmtk/bmtk.analyzer.html">bmtk.analyzer package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="../../../bmtk/bmtk.builder.html">bmtk.builder package</a></li>
@@ -746,7 +766,7 @@ <h3><a href="../../../index.html">Contents</a></h3>
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../../../search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+      <input type="text" name="q" aria-labelledby="searchlabel" />
       <input type="submit" value="Go" />
     </form>
     </div>