wonambi

WONAMBI

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.

Features

• Can read files of format:

  • Axon (.abf, ABF2 only)
  • BCI2000 (.dat)
  • Blackrock (.nev, .ns2, .ns3, .ns5)
  • Brain Vision (.vhdr, .vmrk, .eeg / .dat)
  • EEGLAB (.set, .set / .fdt)
  • European Data Format (.edf)
  • EGI MFF (.mff)
  • Fieldtrip (.mat)
  • mne FIFF (.fiff)
  • SystemPlus Micromed (.trc)
  • Moberg ("EEG,Composite,SampleSeries,Composite,MRIAmp,data")
  • openephys (.continuous, .openephys)
  • BIDS-formatted data file

• Interface for Sleep Scoring

• Computes frequency analysis (spectrogram), time-frequency analysis (short-time spectrogram, Morlet wavelet)

• Detection of spindles and slow waves

• Pure Python

Installation

Install wonambi by running:

pip3 install wonambi

See Installation for details <http://wonambi-python.github.io/installation.html>_

If you want to scroll recordings and do some sleep scoring (requires PyQt5)

wonambi

Run it!

From the command line, simply type:

wonambi

To open a dataset directly, add the full path to the file you want to open:

wonambi /home/me/sleep_recordings.edf

Documentation

See Documentation <http://wonambi-python.github.io/>_

Change Log

See Change Log <http://wonambi-python.github.io/changelog.html>_

Requirements

• Python 3.6 or later
• numpy
• scipy

Optional Requirements

• PyQt5 (optional for sleep scoring GUI)
• python-vlc (optional, to watch embedded movies)
• vispy (optional to plot 3D brain surfaces and electrodes)
• h5py (optional to read FieldTrip Matlab files)
• mne (optional, to export to mne FIFF files)
• nibabel (optional to read freesurfer)
• tensorpac (optional to run phase-amplitude analysis, tensorpac version should be 0.5.6)
• fooof 1.0 (optional to run parametrization of power spectra)

Status

.. image:: https://travis-ci.com/wonambi-python/wonambi.svg?branch=master :target: https://travis-ci.com/wonambi-python/wonambi

.. image:: https://codecov.io/gh/wonambi-python/wonambi/branch/master/graph/badge.svg :target: https://codecov.io/gh/wonambi-python/wonambi

License

The project is licensed under the 3-clause BSD license.