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api/bAnalysis/index.html

@@ -4384,7 +4384,8 @@ <h1>bAnalysis</h1>
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-<span class="normal">2763</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">bAnalysis</span><span class="p">:</span>
+<span class="normal">2763</span>
+<span class="normal">2764</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">bAnalysis</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    The bAnalysis class represents a whole-cell recording and provides functions for analysis.</span>
 
@@ -6465,7 +6466,8 @@ <h1>bAnalysis</h1>
             <span class="bp">self</span><span class="o">.</span><span class="n">_dfReportForScatter</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dfReportForScatter</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s1">&#39;include&#39;</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="bp">self</span><span class="o">.</span><span class="n">_dfReportForScatter</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dfReportForScatter</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s1">&#39;cellType&#39;</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="bp">self</span><span class="o">.</span><span class="n">_dfReportForScatter</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dfReportForScatter</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s1">&#39;sex&#39;</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="bp">self</span><span class="o">.</span><span class="n">_dfReportForScatter</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dfReportForScatter</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s1">&#39;condition&#39;</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="c1"># 202401 removed</span>
+            <span class="c1"># self._dfReportForScatter = self._dfReportForScatter.drop(&#39;condition&#39;, axis=1)</span>
 
             <span class="c1"># add all file meta data to df</span>
             <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">metaData</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
@@ -7742,8 +7744,7 @@ <h3 id="sanpy.bAnalysis.getErrorReport" class="doc doc-heading">
 
           <details class="quote">
             <summary>Source code in <code>sanpy/bAnalysis_.py</code></summary>
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@@ -7796,7 +7797,8 @@ <h3 id="sanpy.bAnalysis.getErrorReport" class="doc doc-heading">
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-<span class="normal">2530</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">getErrorReport</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="normal">2530</span>
+<span class="normal">2531</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">getErrorReport</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Generate an error report, one row per error.</span>
 
 <span class="sd">    Spikes can have more than one error.</span>
@@ -7924,8 +7926,7 @@ <h3 id="sanpy.bAnalysis.getSpikeClips" class="doc doc-heading">
 
           <details class="quote">
             <summary>Source code in <code>sanpy/bAnalysis_.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">2382</span>
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@@ -8010,7 +8011,8 @@ <h3 id="sanpy.bAnalysis.getSpikeClips" class="doc doc-heading">
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-<span class="normal">2468</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">getSpikeClips</span><span class="p">(</span>
+<span class="normal">2468</span>
+<span class="normal">2469</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">getSpikeClips</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">,</span>
     <span class="n">theMin</span><span class="p">,</span>
     <span class="n">theMax</span><span class="p">,</span>
@@ -8890,8 +8892,7 @@ <h3 id="sanpy.bAnalysis.printSpike" class="doc doc-heading">
 
           <details class="quote">
             <summary>Source code in <code>sanpy/bAnalysis_.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">2242</span>
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+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">2243</span>
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@@ -8907,7 +8908,8 @@ <h3 id="sanpy.bAnalysis.printSpike" class="doc doc-heading">
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-<span class="normal">2259</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">printSpike</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">idx</span><span class="p">):</span>
+<span class="normal">2259</span>
+<span class="normal">2260</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">printSpike</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">idx</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Print values in one spike analysis using self.spikeDict (sanpy.bAnalysisResults).</span>
 <span class="sd">    &quot;&quot;&quot;</span>
@@ -8950,8 +8952,7 @@ <h3 id="sanpy.bAnalysis.saveAnalysis" class="doc doc-heading">
 
           <details class="quote">
             <summary>Source code in <code>sanpy/bAnalysis_.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">2616</span>
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+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">2617</span>
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@@ -8985,7 +8986,8 @@ <h3 id="sanpy.bAnalysis.saveAnalysis" class="doc doc-heading">
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-<span class="normal">2651</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">saveAnalysis</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">forceSave</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+<span class="normal">2651</span>
+<span class="normal">2652</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">saveAnalysis</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">forceSave</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Not used.</span>
 
 <span class="sd">    Save detection parameters and analysis results as json.</span>
@@ -9076,8 +9078,7 @@ <h3 id="sanpy.bAnalysis.saveAnalysis_tocsv" class="doc doc-heading">
 
           <details class="quote">
             <summary>Source code in <code>sanpy/bAnalysis_.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">2579</span>
-<span class="normal">2580</span>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">2580</span>
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@@ -9107,7 +9108,8 @@ <h3 id="sanpy.bAnalysis.saveAnalysis_tocsv" class="doc doc-heading">
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-<span class="normal">2610</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">saveAnalysis_tocsv</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span> <span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+<span class="normal">2610</span>
+<span class="normal">2611</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">saveAnalysis_tocsv</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span> <span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Save analysis to csv.</span>
 
 <span class="sd">    CSV starts with one </span>

api/bAnalysisUtil/index.html

@@ -1690,7 +1690,15 @@ <h1>bAnalysisUtil</h1>
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-<span class="normal">586</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">bAnalysisUtil</span><span class="p">:</span>
+<span class="normal">586</span>
+<span class="normal">587</span>
+<span class="normal">588</span>
+<span class="normal">589</span>
+<span class="normal">590</span>
+<span class="normal">591</span>
+<span class="normal">592</span>
+<span class="normal">593</span>
+<span class="normal">594</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">bAnalysisUtil</span><span class="p">:</span>
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 
         <span class="c1"># built in analysis results</span>
@@ -2095,6 +2103,14 @@ <h1>bAnalysisUtil</h1>
             <span class="s2">&quot;xStatUnits&quot;</span><span class="p">:</span> <span class="s2">&quot;&quot;</span><span class="p">,</span>
         <span class="p">}</span>
 
+        <span class="n">statList</span><span class="p">[</span><span class="s2">&quot;Condition&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s2">&quot;name&quot;</span><span class="p">:</span> <span class="s2">&quot;condition&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;yStat&quot;</span><span class="p">:</span> <span class="s2">&quot;condition&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;yStatUnits&quot;</span><span class="p">:</span> <span class="s2">&quot;&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;xStat&quot;</span><span class="p">:</span> <span class="s2">&quot;&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;xStatUnits&quot;</span><span class="p">:</span> <span class="s2">&quot;&quot;</span><span class="p">,</span>
+        <span class="p">}</span>
+
         <span class="c1"># sa node specific</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        statList[&#39;Region&#39;] = {</span>

getting-started-gui/index.html

@@ -338,6 +338,15 @@
     </span>
   </a>
 
+</li>
+
+        <li class="md-nav__item">
+  <a href="#load-a-file-detect-spikes-set-spike-conditions-and-plot-with-plot-tool-plugin" class="md-nav__link">
+    <span class="md-ellipsis">
+      Load a file, detect spikes, set spike conditions and plot with Plot Tool plugin
+    </span>
+  </a>
+
 </li>
 
     </ul>
@@ -1067,6 +1076,15 @@
     </span>
   </a>
 
+</li>
+
+        <li class="md-nav__item">
+  <a href="#load-a-file-detect-spikes-set-spike-conditions-and-plot-with-plot-tool-plugin" class="md-nav__link">
+    <span class="md-ellipsis">
+      Load a file, detect spikes, set spike conditions and plot with Plot Tool plugin
+    </span>
+  </a>
+
 </li>
 
     </ul>
@@ -1084,8 +1102,6 @@
 
 
 
-  <h1>Getting Started With The GUI</h1>
-
 <p>These are tutorials to get started using the SanPy desktop GUI.</p>
 <p>Please watch the videos as you follow along with a recipes.</p>
 <h2 id="load-a-file-detect-spikes-and-run-some-plugins">Load a file, detect spikes, and run some plugins<a class="headerlink" href="#load-a-file-detect-spikes-and-run-some-plugins" title="Permanent link">¤</a></h2>
@@ -1140,6 +1156,12 @@ <h2 id="loading-a-folder-detect-spikes-in-multiple-files-and-run-the-plot-tool-p
 <p>The step above can be repeated for any <code>Y-Stat</code> such as <code>Take Off Potential (mV)</code> or other.</p>
 <p>Likewise, a scatter plot is easily created by selecting Plot Type <code>Scatter Plot</code> and choosing the desired X-Stat and Y-Stat.</p>
 <p><IMG SRC="../img/figure-4/scatter-spike-freq.png" width=200></p>
+<h1 id="load-a-file-detect-spikes-set-spike-conditions-and-plot-with-plot-tool-plugin">Load a file, detect spikes, set spike conditions and plot with Plot Tool plugin<a class="headerlink" href="#load-a-file-detect-spikes-set-spike-conditions-and-plot-with-plot-tool-plugin" title="Permanent link">¤</a></h1>
+<p><strong>Recipe</strong> for remaking the SanPy manuscript Figure 6 from the GUI.</p>
+<p>Please note, this will not be the same exact data but the plots will be similar.</p>
+<iframe width="560" height="315" src="https://www.youtube.com/embed/jaiFOsq3kGM?si=3DyejqH8C2wieaNp" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+<p>We are working on a recipe, check back soon!</p>