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<section id="module-wonambi.ioeeg.edf">
<span id="wonambi-ioeeg-edf-module"></span><h1>wonambi.ioeeg.edf module<a class="headerlink" href="#module-wonambi.ioeeg.edf" title="Permalink to this heading"></a></h1>
<p>Module reads and writes header and data for EDF data.</p>
<dl class="py class">
<dt class="sig sig-object py" id="wonambi.ioeeg.edf.Edf">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">wonambi.ioeeg.edf.</span></span><span class="sig-name descname"><span class="pre">Edf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">edffile</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/ioeeg/edf.html#Edf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.ioeeg.edf.Edf" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Provide class EDF, which can be used to read the header and the data.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>edffile</strong> (<em>str</em>) – Full path for the EDF file</p>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="wonambi.ioeeg.edf.Edf.hdr">
<span class="sig-name descname"><span class="pre">hdr</span></span><a class="headerlink" href="#wonambi.ioeeg.edf.Edf.hdr" title="Permalink to this definition"></a></dt>
<dd><p>header taken from EDF file</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="wonambi.ioeeg.edf.Edf.return_dat">
<span class="sig-name descname"><span class="pre">return_dat</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chan</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">begsam</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">endsam</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/ioeeg/edf.html#Edf.return_dat"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.ioeeg.edf.Edf.return_dat" title="Permalink to this definition"></a></dt>
<dd><p>Read data from an EDF file.</p>
<p>Reads channel by channel, and adjusts the values by calibration.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>chan</strong> (<em>list</em><em> of </em><em>int</em>) – index (indices) of the channels to read</p></li>
<li><p><strong>begsam</strong> (<em>int</em>) – index of the first sample</p></li>
<li><p><strong>endsam</strong> (<em>int</em>) – index of the last sample</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><em>numpy.ndarray</em> – A 2d matrix, where the first dimension is the channels and the
second dimension are the samples.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="wonambi.ioeeg.edf.Edf.return_hdr">
<span class="sig-name descname"><span class="pre">return_hdr</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/ioeeg/edf.html#Edf.return_hdr"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.ioeeg.edf.Edf.return_hdr" title="Permalink to this definition"></a></dt>
<dd><p>Return the header for further use.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><ul class="simple">
<li><p><strong>subj_id</strong> (<em>str</em>) – subject identification code</p></li>
<li><p><strong>start_time</strong> (<em>datetime</em>) – start time of the dataset</p></li>
<li><p><strong>s_freq</strong> (<em>float</em>) – sampling frequency</p></li>
<li><p><strong>chan_name</strong> (<em>list of str</em>) – list of all the channels</p></li>
<li><p><strong>n_samples</strong> (<em>int</em>) – number of samples in the dataset</p></li>
<li><p><strong>orig</strong> (<em>dict</em>) – additional information taken directly from the header</p></li>
</ul>
</p>
</dd>
</dl>
<p class="rubric">Notes</p>
<p>EDF+ accepts multiple frequency rates for different channels. Here, we
use only the highest sampling frequency (normally used for EEG and MEG
signals), and we UPSAMPLE all the other channels.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="wonambi.ioeeg.edf.Edf.return_markers">
<span class="sig-name descname"><span class="pre">return_markers</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/ioeeg/edf.html#Edf.return_markers"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.ioeeg.edf.Edf.return_markers" title="Permalink to this definition"></a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="wonambi.ioeeg.edf.remove_datetime">
<span class="sig-prename descclassname"><span class="pre">wonambi.ioeeg.edf.</span></span><span class="sig-name descname"><span class="pre">remove_datetime</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/ioeeg/edf.html#remove_datetime"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.ioeeg.edf.remove_datetime" title="Permalink to this definition"></a></dt>
<dd><p>Remove datetime from filename by overwriting the date / time info.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>filename</strong> (<a class="reference internal" href="wonambi.widgets.utils.html#wonambi.widgets.utils.Path" title="wonambi.widgets.utils.Path"><em>Path</em></a>) – path to edf file</p>
</dd>
</dl>
<p class="rubric">Notes</p>
<p>It modifies the file.</p>
<div class="admonition-todo admonition" id="id1">
<p class="admonition-title">Todo</p>
<p>This function might be part of a large anonymization procedure for edf</p>
</div>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="wonambi.ioeeg.edf.write_edf">
<span class="sig-prename descclassname"><span class="pre">wonambi.ioeeg.edf.</span></span><span class="sig-name descname"><span class="pre">write_edf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">subj_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'X</span> <span class="pre">X</span> <span class="pre">X</span> <span class="pre">X'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">physical_max</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">physical_min</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/ioeeg/edf.html#write_edf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.ioeeg.edf.write_edf" title="Permalink to this definition"></a></dt>
<dd><p>Export data to FieldTrip.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data</strong> (<em>instance</em><em> of </em><a class="reference internal" href="wonambi.datatype.html#wonambi.datatype.ChanTime" title="wonambi.datatype.ChanTime"><em>ChanTime</em></a>) – data with only one trial</p></li>
<li><p><strong>filename</strong> (<em>path to file</em>) – file to export to (include ‘.mat’)</p></li>
<li><p><strong>subj_id</strong> (<em>str</em>) – subject id</p></li>
<li><p><strong>physical_max</strong> (<em>int</em>) – values above this parameter will be considered saturated (and also
those that are too negative). This parameter defines the precision.</p></li>
</ul>
</dd>
</dl>
<p class="rubric">Notes</p>
<p>Data is always recorded as 2 Byte int (which is ‘int16’), so precision is
limited. You can control the precision with physical_max. To get the
precision:</p>
<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">precision</span> <span class="o">=</span> <span class="n">physical_max</span> <span class="o">/</span> <span class="n">DIGITAL_MAX</span>
</pre></div>
</div>
<p>where DIGITAL_MAX is 32767.</p>
</dd></dl>
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