v 0.0.9.3

- Added support for extraction of phasic and tonic components in EDA. Users can now run getPhasicAndTonic() to separate the two components. - Fixed a typo within the documentation for the phasicFilter Function
Gabrock94 · Apr 3, 2019 · 359eeca · 359eeca
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diff --git a/docs/html/_modules/electrocardiography.html b/docs/html/_modules/electrocardiography.html
@@ -4,19 +4,28 @@
 
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@@ -89,7 +98,7 @@ <h1>Source code for electrocardiography</h1><div class="highlight"><pre>
 <span class="sd">        </span>
 <span class="sd">        SDNN reflects all the cyclic components responsible for variability in the period of recording, therefore it represents total variability</span>
 <span class="sd">        </span>
-<span class="sd">        SDNN = sqrt((1/N-1) * sum(i=1 --&gt; N)(rri - rrmean)^2</span>
+<span class="sd">        SDNN = sqrt((1/N-1) * sum(i=1 --&gt; N)(rri - rrmean)^2)</span>
 <span class="sd">        </span>
 <span class="sd">        Input: peaks of the ECG signal,samplerate of the signal</span>
 <span class="sd">        </span>
@@ -458,14 +467,12 @@ <h1>Source code for electrocardiography</h1><div class="highlight"><pre>
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diff --git a/docs/html/_modules/electrodermalactivity.html b/docs/html/_modules/electrodermalactivity.html
@@ -4,19 +4,28 @@
 
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@@ -50,14 +59,14 @@ <h1>Source code for electrodermalactivity</h1><div class="highlight"><pre>
 <span class="c1">###############################################################################</span>
 
 <div class="viewcode-block" id="phasicGSRFilter"><a class="viewcode-back" href="../electrodermalactivity.html#electrodermalactivity.phasicGSRFilter">[docs]</a><span class="k">def</span> <span class="nf">phasicGSRFilter</span><span class="p">(</span><span class="n">rawGSRSignal</span><span class="p">,</span><span class="n">samplerate</span><span class="p">,</span><span class="n">seconds</span><span class="o">=</span><span class="mi">4</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot; Apply a phasic filter to the signal, with +- X seconds from each sample. Default is 10 seconds</span>
+    <span class="sd">&quot;&quot;&quot; Apply a phasic filter to the signal, with +- X seconds from each sample. Default is 4 seconds</span>
 <span class="sd">    </span>
 <span class="sd">        * Input:</span>
 <span class="sd">            * rawGSRSignal = gsr signal as list</span>
 <span class="sd">            * samplerate = samplerate of the signal    </span>
 <span class="sd">            * seconds = number of seconds before and after each timepoint to use in order to compute the filtered value</span>
 <span class="sd">        * Output:</span>
-<span class="sd">            * phasic filtered signal            </span>
+<span class="sd">            * phasic signal            </span>
 <span class="sd">        </span>
 <span class="sd">        :param rawGSRSignal: raw GSR Signal</span>
 <span class="sd">        :type rawGSRSignal: list</span>
@@ -67,6 +76,7 @@ <h1>Source code for electrodermalactivity</h1><div class="highlight"><pre>
 <span class="sd">        :param seconds: int</span>
 <span class="sd">        :return: filtered signal</span>
 <span class="sd">        :rtype: list</span>
+<span class="sd">        </span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="n">phasicSignal</span> <span class="o">=</span> <span class="p">[]</span>    
@@ -84,6 +94,68 @@ <h1>Source code for electrodermalactivity</h1><div class="highlight"><pre>
         <span class="n">phasicSignal</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">newsample</span><span class="p">)</span>
     <span class="k">return</span><span class="p">(</span><span class="n">phasicSignal</span><span class="p">)</span></div>
 
+
+<div class="viewcode-block" id="tonicGSRFilter"><a class="viewcode-back" href="../electrodermalactivity.html#electrodermalactivity.tonicGSRFilter">[docs]</a><span class="k">def</span> <span class="nf">tonicGSRFilter</span><span class="p">(</span><span class="n">rawGSRSignal</span><span class="p">,</span><span class="n">samplerate</span><span class="p">,</span><span class="n">seconds</span><span class="o">=</span><span class="mi">4</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot; Apply a modified filter to the signal, with +- X seconds from each sample, in order to extract the tonic component. Default is 4 seconds</span>
+<span class="sd">    </span>
+<span class="sd">        * Input:</span>
+<span class="sd">            * rawGSRSignal = gsr signal as list</span>
+<span class="sd">            * samplerate = samplerate of the signal    </span>
+<span class="sd">            * seconds = number of seconds before and after each timepoint to use in order to compute the filtered value</span>
+<span class="sd">        * Output:</span>
+<span class="sd">            * tonic signal            </span>
+<span class="sd">        </span>
+<span class="sd">        :param rawGSRSignal: raw GSR Signal</span>
+<span class="sd">        :type rawGSRSignal: list</span>
+<span class="sd">        :param samplerate: samplerate of the GSR signal in Hz</span>
+<span class="sd">        :type samplerate: int</span>
+<span class="sd">        :param seconds: seconds to use to apply the phasic filter</span>
+<span class="sd">        :param seconds: int</span>
+<span class="sd">        :return: filtered signal</span>
+<span class="sd">        :rtype: list</span>
+<span class="sd">        </span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">tonicSignal</span> <span class="o">=</span> <span class="p">[]</span>    
+    <span class="k">for</span> <span class="n">sample</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="nb">len</span><span class="p">(</span><span class="n">rawGSRSignal</span><span class="p">)):</span>
+        <span class="n">smin</span> <span class="o">=</span> <span class="n">sample</span> <span class="o">-</span> <span class="n">seconds</span> <span class="o">*</span> <span class="n">samplerate</span> <span class="c1">#min sample index</span>
+        <span class="n">smax</span> <span class="o">=</span> <span class="n">sample</span> <span class="o">+</span> <span class="n">seconds</span> <span class="o">*</span> <span class="n">samplerate</span> <span class="c1">#max sample index</span>
+        <span class="c1">#is smin is &lt; 0 or smax &gt; signal length, fix it to the closest real sample</span>
+        <span class="k">if</span><span class="p">(</span><span class="n">smin</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">):</span> 
+            <span class="n">smin</span> <span class="o">=</span> <span class="n">sample</span>
+        <span class="k">if</span><span class="p">(</span><span class="n">smax</span> <span class="o">&gt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">rawGSRSignal</span><span class="p">)):</span>
+            <span class="n">smax</span> <span class="o">=</span> <span class="n">sample</span>
+        <span class="c1">#substract the mean of the segment</span>
+        <span class="n">newsample</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">rawGSRSignal</span><span class="p">[</span><span class="n">smin</span><span class="p">:</span><span class="n">smax</span><span class="p">])</span>
+        <span class="c1">#move to th</span>
+        <span class="n">tonicSignal</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">newsample</span><span class="p">)</span>
+    <span class="k">return</span><span class="p">(</span><span class="n">tonicSignal</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="getPhasicAndTonic"><a class="viewcode-back" href="../electrodermalactivity.html#electrodermalactivity.getPhasicAndTonic">[docs]</a><span class="k">def</span> <span class="nf">getPhasicAndTonic</span><span class="p">(</span><span class="n">rawGSRSignal</span><span class="p">,</span> <span class="n">samplerate</span><span class="p">,</span> <span class="n">seconds</span> <span class="o">=</span> <span class="mi">4</span><span class="p">):</span>
+    <span class="sd">&quot;&quot;&quot; This function returns the phasic and tonic components of a singnal.</span>
+<span class="sd">    </span>
+<span class="sd">        * Input: </span>
+<span class="sd">            * rawGSRSignal = gsr signal as list</span>
+<span class="sd">            * samplerate = samplerate of the signal    </span>
+<span class="sd">            * seconds = number of seconds before and after each timepoint to use in order to compute the filtered value</span>
+<span class="sd">        * Output:</span>
+<span class="sd">            * List containing the phasic and tonic components</span>
+<span class="sd">            </span>
+<span class="sd">        :param rawGSRSignal: raw GSR Signal</span>
+<span class="sd">        :type rawGSRSignal: list</span>
+<span class="sd">        :param samplerate: samplerate of the GSR signal in Hz</span>
+<span class="sd">        :type samplerate: int</span>
+<span class="sd">        :param seconds: seconds to use to apply the phasic filter</span>
+<span class="sd">        :param seconds: int</span>
+<span class="sd">        :return: phasic and tonic signals</span>
+<span class="sd">        :rtype: list</span>
+<span class="sd">        </span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">phasic</span> <span class="o">=</span> <span class="n">phasicGSRFilter</span><span class="p">(</span><span class="n">rawGSRSignal</span><span class="p">,</span> <span class="n">samplerate</span><span class="p">,</span> <span class="n">seconds</span><span class="p">)</span>
+    <span class="n">tonic</span> <span class="o">=</span> <span class="n">tonicGSRFilter</span><span class="p">(</span><span class="n">rawGSRSignal</span><span class="p">,</span> <span class="n">samplerate</span><span class="p">,</span> <span class="n">seconds</span><span class="p">)</span>
+    <span class="k">return</span><span class="p">(</span><span class="n">phasic</span><span class="p">,</span> <span class="n">tonic</span><span class="p">)</span></div>
+
 <div class="viewcode-block" id="findPeakOnsetAndOffset"><a class="viewcode-back" href="../electrodermalactivity.html#electrodermalactivity.findPeakOnsetAndOffset">[docs]</a><span class="k">def</span> <span class="nf">findPeakOnsetAndOffset</span><span class="p">(</span><span class="n">rawGSRSignal</span><span class="p">,</span><span class="n">onset</span><span class="o">=</span><span class="mf">0.01</span><span class="p">,</span><span class="n">offset</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot; This functions finds the peaks of a GSR signal</span>
 <span class="sd">    </span>
@@ -279,7 +351,6 @@ <h1>Source code for electrodermalactivity</h1><div class="highlight"><pre>
     <span class="n">y</span> <span class="o">=</span> <span class="n">lfilter</span><span class="p">(</span><span class="n">b</span><span class="p">,</span> <span class="n">a</span><span class="p">,</span> <span class="n">data</span><span class="p">)</span>
     <span class="k">return</span><span class="p">(</span><span class="n">y</span><span class="p">)</span></div>
 
-
 <span class="c1">###############################################################################</span>
 <span class="c1">#                                                                             #</span>
 <span class="c1">#                                  DEBUG                                      #</span>
@@ -292,7 +363,8 @@ <h1>Source code for electrodermalactivity</h1><div class="highlight"><pre>
     <span class="kn">import</span> <span class="nn">os</span>
     <span class="kn">import</span> <span class="nn">pprint</span>
     <span class="kn">import</span> <span class="nn">sampledata</span>
-    <span class="n">fakesignal</span> <span class="o">=</span><span class="n">sampledata</span><span class="o">.</span><span class="n">loadsampleEDA</span><span class="p">()</span> <span class="c1">#load the sample GSR Signal</span>
+    <span class="n">fakesignal</span> <span class="o">=</span> <span class="s1">&#39;/home/giulio/Desktop/EDAPhasic/convertedEDA.pkl&#39;</span>
+    <span class="n">fakesignal</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">fakesignal</span><span class="p">,</span><span class="s1">&#39;rb&#39;</span><span class="p">))</span>
     <span class="n">GSRResults</span> <span class="o">=</span> <span class="n">analyzeGSR</span><span class="p">(</span><span class="n">fakesignal</span><span class="p">[</span><span class="mi">1500</span><span class="p">:</span><span class="mi">9500</span><span class="p">],</span><span class="mi">1000</span><span class="p">,</span><span class="n">preprocessing</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span><span class="n">phasic_seconds</span><span class="o">=</span><span class="mi">8</span><span class="p">)</span> <span class="c1">#analyze it</span>
     <span class="n">pprint</span><span class="o">.</span><span class="n">pprint</span><span class="p">(</span><span class="n">GSRResults</span><span class="p">)</span> <span class="c1">#print the results for each peak found</span>
 </pre></div>
@@ -304,14 +376,12 @@ <h1>Source code for electrodermalactivity</h1><div class="highlight"><pre>
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@@ -333,7 +403,7 @@ <h3>Navigation</h3>
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