Rebuild documentation

pennmem · Jul 6, 2018 · 0e75d6b · 0e75d6b
1 parent 90f1ed2
commit 0e75d6b
Show file tree

Hide file tree

Showing 20 changed files with 832 additions and 323 deletions.
diff --git a/docs/html/_modules/cmlreaders/cmlreader.html b/docs/html/_modules/cmlreaders/cmlreader.html
diff --git a/docs/html/_modules/cmlreaders/convert.html b/docs/html/_modules/cmlreaders/convert.html
@@ -0,0 +1,316 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+  <title>cmlreaders.convert &mdash; CML Data Readers 0.7.0 documentation</title>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+    <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
+  <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
+  <link rel="stylesheet" href="../../_static/theme_overrides.css" type="text/css" />
+    <link rel="index" title="Index" href="../../genindex.html" />
+    <link rel="search" title="Search" href="../../search.html" /> 
+
+
+  <script src="../../_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav">
+
+
+  <div class="wy-grid-for-nav">
+
+
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search">
+
+
+
+            <a href="../../index.html" class="icon icon-home"> CML Data Readers
+
+
+
+          </a>
+
+
+
+
+              <div class="version">
+                0.7
+              </div>
+
+
+
+
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
+
+        </div>
+
+        <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+
+
+
+
+
+
+              <p class="caption"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../../intro.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../data_guide.html">Data Guide</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../getting_started.html">Getting Started with CML Readers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../api.html">API</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../dev.html">Developer’s Guide</a></li>
+</ul>
+
+
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+
+      <nav class="wy-nav-top" aria-label="top navigation">
+
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../../index.html">CML Data Readers</a>
+
+      </nav>
+
+
+      <div class="wy-nav-content">
+
+        <div class="rst-content">
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+<div role="navigation" aria-label="breadcrumbs navigation">
+
+  <ul class="wy-breadcrumbs">
+
+      <li><a href="../../index.html">Docs</a> &raquo;</li>
+
+          <li><a href="../index.html">Module code</a> &raquo;</li>
+
+      <li>cmlreaders.convert</li>
+
+
+      <li class="wy-breadcrumbs-aside">
+
+      </li>
+
+  </ul>
+
+
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <h1>Source code for cmlreaders.convert</h1><div class="highlight"><pre>
+<span></span><span class="kn">from</span> <span class="nn">typing</span> <span class="k">import</span> <span class="n">List</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Tuple</span><span class="p">,</span> <span class="n">Union</span>
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+
+
+<div class="viewcode-block" id="milliseconds_to_samples"><a class="viewcode-back" href="../../api.html#cmlreaders.convert.milliseconds_to_samples">[docs]</a><span class="k">def</span> <span class="nf">milliseconds_to_samples</span><span class="p">(</span><span class="n">millis</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span>
+                            <span class="n">sample_rate</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
+    <span class="sd">&quot;&quot;&quot;Covert times in milliseconds to number of samples.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    millis</span>
+<span class="sd">        Time in ms.</span>
+<span class="sd">    sample_rate</span>
+<span class="sd">        Sample rate in samples per second.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    Number of samples.</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">sample_rate</span> <span class="o">*</span> <span class="n">millis</span> <span class="o">/</span> <span class="mf">1000.</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="samples_to_milliseconds"><a class="viewcode-back" href="../../api.html#cmlreaders.convert.samples_to_milliseconds">[docs]</a><span class="k">def</span> <span class="nf">samples_to_milliseconds</span><span class="p">(</span><span class="n">samples</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
+                            <span class="n">sample_rate</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">]:</span>
+    <span class="sd">&quot;&quot;&quot;Convert samples to milliseconds.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    samples</span>
+<span class="sd">        Number of samples.</span>
+<span class="sd">    sample_rate</span>
+<span class="sd">        Sample rate in samples per second.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    Samples converted to milliseconds.</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">return</span> <span class="mi">1000</span> <span class="o">*</span> <span class="n">samples</span> <span class="o">/</span> <span class="n">sample_rate</span></div>
+
+
+<div class="viewcode-block" id="milliseconds_to_events"><a class="viewcode-back" href="../../api.html#cmlreaders.convert.milliseconds_to_events">[docs]</a><span class="k">def</span> <span class="nf">milliseconds_to_events</span><span class="p">(</span><span class="n">onsets</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">]],</span>
+                           <span class="n">sample_rate</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+    <span class="sd">&quot;&quot;&quot;Take times and produce a minimal events :class:`pd.DataFrame` to load</span>
+<span class="sd">    EEG data with.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    onsets</span>
+<span class="sd">        Onset times in ms.</span>
+<span class="sd">    sample_rate</span>
+<span class="sd">        Sample rate in samples per second.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    events</span>
+<span class="sd">        A :class:`pd.DataFrame` with ``eegoffset`` as the only column.</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">samples</span> <span class="o">=</span> <span class="p">[</span><span class="n">milliseconds_to_samples</span><span class="p">(</span><span class="n">onset</span><span class="p">,</span> <span class="n">sample_rate</span><span class="p">)</span> <span class="k">for</span> <span class="n">onset</span> <span class="ow">in</span> <span class="n">onsets</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="s2">&quot;eegoffset&quot;</span><span class="p">:</span> <span class="n">samples</span><span class="p">})</span></div>
+
+
+<div class="viewcode-block" id="events_to_epochs"><a class="viewcode-back" href="../../api.html#cmlreaders.convert.events_to_epochs">[docs]</a><span class="k">def</span> <span class="nf">events_to_epochs</span><span class="p">(</span><span class="n">events</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">rel_start</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">rel_stop</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
+                     <span class="n">sample_rate</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">],</span>
+                     <span class="n">basenames</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">]]</span> <span class="o">=</span> <span class="kc">None</span>
+                     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">List</span><span class="p">[</span><span class="n">Tuple</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">]]:</span>
+    <span class="sd">&quot;&quot;&quot;Convert events to epochs.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    events</span>
+<span class="sd">        Events to read.</span>
+<span class="sd">    rel_start</span>
+<span class="sd">        Start time relative to events in ms.</span>
+<span class="sd">    rel_stop</span>
+<span class="sd">        Stop time relative to events in ms.</span>
+<span class="sd">    sample_rate</span>
+<span class="sd">        Sample rate in Hz.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">    -------</span>
+<span class="sd">    epochs</span>
+<span class="sd">        A list of tuples giving absolute start and stop times in number of</span>
+<span class="sd">        samples.</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">rel_start</span> <span class="o">=</span> <span class="n">milliseconds_to_samples</span><span class="p">(</span><span class="n">rel_start</span><span class="p">,</span> <span class="n">sample_rate</span><span class="p">)</span>
+    <span class="n">rel_stop</span> <span class="o">=</span> <span class="n">milliseconds_to_samples</span><span class="p">(</span><span class="n">rel_stop</span><span class="p">,</span> <span class="n">sample_rate</span><span class="p">)</span>
+    <span class="n">offsets</span> <span class="o">=</span> <span class="n">events</span><span class="o">.</span><span class="n">eegoffset</span><span class="o">.</span><span class="n">values</span>
+    <span class="k">if</span> <span class="n">basenames</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="n">eegfiles</span> <span class="o">=</span> <span class="n">events</span><span class="o">.</span><span class="n">eegfile</span><span class="o">.</span><span class="n">values</span>
+        <span class="n">epochs</span> <span class="o">=</span> <span class="p">[(</span><span class="n">offset</span> <span class="o">+</span> <span class="n">rel_start</span><span class="p">,</span> <span class="n">offset</span> <span class="o">+</span> <span class="n">rel_stop</span><span class="p">,</span>
+                   <span class="n">basenames</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">eegfile</span><span class="p">))</span>
+                  <span class="k">for</span> <span class="p">(</span><span class="n">offset</span><span class="p">,</span> <span class="n">eegfile</span><span class="p">)</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">offsets</span><span class="p">,</span> <span class="n">eegfiles</span><span class="p">)]</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">epochs</span> <span class="o">=</span> <span class="p">[(</span><span class="n">offset</span> <span class="o">+</span> <span class="n">rel_start</span><span class="p">,</span> <span class="n">offset</span> <span class="o">+</span> <span class="n">rel_stop</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
+                  <span class="k">for</span> <span class="n">offset</span> <span class="ow">in</span> <span class="n">offsets</span><span class="p">]</span>
+    <span class="k">return</span> <span class="n">epochs</span></div>
+</pre></div>
+
+           </div>
+
+          </div>
+          <footer>
+
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2018.
+
+    </p>
+  </div>
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 
+
+</footer>
+
+        </div>
+      </div>
+
+    </section>
+
+  </div>
+
+
+
+
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'../../',
+            VERSION:'0.7.0',
+            LANGUAGE:'None',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true,
+            SOURCELINK_SUFFIX: '.txt'
+        };
+    </script>
+      <script type="text/javascript" src="../../_static/jquery.js"></script>
+      <script type="text/javascript" src="../../_static/underscore.js"></script>
+      <script type="text/javascript" src="../../_static/doctools.js"></script>
+      <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+
+
+
+
+    <script type="text/javascript" src="../../_static/js/theme.js"></script>
+
+
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>
diff --git a/docs/html/_modules/cmlreaders/path_finder.html b/docs/html/_modules/cmlreaders/path_finder.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>cmlreaders.path_finder &mdash; CML Data Readers 0.6.0 documentation</title>
+  <title>cmlreaders.path_finder &mdash; CML Data Readers 0.7.0 documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                0.6
+                0.7
               </div>
 
 
@@ -212,7 +212,13 @@ <h1>Source code for cmlreaders.path_finder</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">experiment</span> <span class="o">=</span> <span class="n">experiment</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">session</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">session</span><span class="p">)</span>
 
-        <span class="c1"># Stringify localization and montage only if they are given</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">subject</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">protocol</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">subject</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;R1&quot;</span><span class="p">):</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">protocol</span> <span class="o">=</span> <span class="s2">&quot;r1&quot;</span>
+        <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">subject</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;LTP&quot;</span><span class="p">):</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">protocol</span> <span class="o">=</span> <span class="s2">&quot;ltp&quot;</span>
+
         <span class="bp">self</span><span class="o">.</span><span class="n">localization</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">localization</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">montage</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">montage</span><span class="p">)</span>
 
@@ -300,6 +306,7 @@ <h1>Source code for cmlreaders.path_finder</h1><div class="highlight"><pre>
                 <span class="k">return</span> <span class="n">ramulator_session_folder</span>
 
         <span class="n">expected_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_find_single_path</span><span class="p">(</span><span class="n">paths_to_check</span><span class="p">,</span>
+                                               <span class="n">protocol</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">protocol</span><span class="p">,</span>
                                                <span class="n">subject</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">subject</span><span class="p">,</span>
                                                <span class="n">subject_montage</span><span class="o">=</span><span class="n">subject_montage</span><span class="p">,</span>
                                                <span class="n">timestamped_dir</span><span class="o">=</span><span class="n">timestamped_dir</span><span class="p">,</span>
@@ -397,7 +404,7 @@ <h1>Source code for cmlreaders.path_finder</h1><div class="highlight"><pre>
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'../../',
-            VERSION:'0.6.0',
+            VERSION:'0.7.0',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',