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introduction.html
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<section id="wonambi">
<h1>WONAMBI<a class="headerlink" href="#wonambi" title="Permalink to this heading"></a></h1>
<p>Package for the analysis of EEG, ECoG and other electrophysiology modalities.
Allows for visualization of the data and sleep stage scoring in a GUI.
Provides automatic detectors for spindles and slow waves.</p>
<section id="features">
<h2>Features<a class="headerlink" href="#features" title="Permalink to this heading"></a></h2>
<ul class="simple">
<li><p>Can read files of format:</p>
<ul>
<li><p>Axon (.abf, ABF2 only)</p></li>
<li><p>BCI2000 (.dat)</p></li>
<li><p>Blackrock (.nev, .ns2, .ns3, .ns5)</p></li>
<li><p>Brain Vision (.vhdr, .vmrk, .eeg / .dat)</p></li>
<li><p>EEGLAB (.set, .set / .fdt)</p></li>
<li><p>European Data Format (.edf)</p></li>
<li><p>EGI MFF (.mff)</p></li>
<li><p>Fieldtrip (.mat)</p></li>
<li><p>mne FIFF (.fiff)</p></li>
<li><p>SystemPlus Micromed (.trc)</p></li>
<li><p>Moberg (“EEG,Composite,SampleSeries,Composite,MRIAmp,data”)</p></li>
<li><p>openephys (.continuous, .openephys)</p></li>
<li><p>BIDS-formatted data file</p></li>
</ul>
</li>
<li><p>Interface for Sleep Scoring</p></li>
<li><p>Computes frequency analysis (spectrogram), time-frequency analysis (short-time spectrogram, Morlet wavelet)</p></li>
<li><p>Detection of spindles and slow waves</p></li>
<li><p>Pure Python</p></li>
</ul>
</section>
<section id="installation">
<h2>Installation<a class="headerlink" href="#installation" title="Permalink to this heading"></a></h2>
<p>Install wonambi by running:</p>
<blockquote>
<div><p>pip3 install wonambi</p>
</div></blockquote>
<p>See <a class="reference external" href="http://wonambi-python.github.io/installation.html">Installation for details</a></p>
<p>If you want to scroll recordings and do some sleep scoring (requires PyQt5)</p>
<blockquote>
<div><p>wonambi</p>
</div></blockquote>
</section>
<section id="run-it">
<h2>Run it!<a class="headerlink" href="#run-it" title="Permalink to this heading"></a></h2>
<p>From the command line, simply type:</p>
<blockquote>
<div><p>wonambi</p>
</div></blockquote>
<p>To open a dataset directly, add the full path to the file you want to open:</p>
<blockquote>
<div><p>wonambi /home/me/sleep_recordings.edf</p>
</div></blockquote>
</section>
<section id="documentation">
<h2>Documentation<a class="headerlink" href="#documentation" title="Permalink to this heading"></a></h2>
<p>See <a class="reference external" href="http://wonambi-python.github.io/">Documentation</a></p>
</section>
<section id="change-log">
<h2>Change Log<a class="headerlink" href="#change-log" title="Permalink to this heading"></a></h2>
<p>See <a class="reference external" href="http://wonambi-python.github.io/changelog.html">Change Log</a></p>
</section>
<section id="requirements">
<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this heading"></a></h2>
<ul class="simple">
<li><p>Python 3.6 or later</p></li>
<li><p>numpy</p></li>
<li><p>scipy</p></li>
</ul>
</section>
<section id="optional-requirements">
<h2>Optional Requirements<a class="headerlink" href="#optional-requirements" title="Permalink to this heading"></a></h2>
<ul class="simple">
<li><p>PyQt5 (optional for sleep scoring GUI)</p></li>
<li><p>python-vlc (optional, to watch embedded movies)</p></li>
<li><p>vispy (optional to plot 3D brain surfaces and electrodes)</p></li>
<li><p>h5py (optional to read FieldTrip Matlab files)</p></li>
<li><p>mne (optional, to export to mne FIFF files)</p></li>
<li><p>nibabel (optional to read freesurfer)</p></li>
<li><p>tensorpac (optional to run phase-amplitude analysis, tensorpac version should be 0.5.6)</p></li>
<li><p>fooof 1.0 (optional to run parametrization of power spectra)</p></li>
</ul>
</section>
<section id="status">
<h2>Status<a class="headerlink" href="#status" title="Permalink to this heading"></a></h2>
<a class="reference external image-reference" href="https://travis-ci.com/wonambi-python/wonambi"><img alt="https://travis-ci.com/wonambi-python/wonambi.svg?branch=master" src="https://travis-ci.com/wonambi-python/wonambi.svg?branch=master" /></a>
<a class="reference external image-reference" href="https://codecov.io/gh/wonambi-python/wonambi"><img alt="https://codecov.io/gh/wonambi-python/wonambi/branch/master/graph/badge.svg" src="https://codecov.io/gh/wonambi-python/wonambi/branch/master/graph/badge.svg" /></a>
</section>
<section id="license">
<h2>License<a class="headerlink" href="#license" title="Permalink to this heading"></a></h2>
<p>The project is licensed under the 3-clause BSD license.</p>
</section>
</section>
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