pyEDFlib

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What is pyEDFlib

pyEDFlib is a python library to read/write EDF+/BDF+ files based on EDFlib.

EDF means European Data Format_ and was firstly published Kemp1992. In 2003, an improved version of the file protocol named EDF+ has been published and can be found at Kemp2003.

The EDF/EDF+ format saves all data with 16 Bit. A version which saves all data with 24 Bit, was introduces by the company BioSemi_.

The definition of the EDF/EDF+/BDF/BDF+ format can be found under edfplus.info_.

This Python toolbox is a fork of the toolbox from Christopher Lee-Messer_ and uses the EDFlib_ from Teunis van Beelen. The EDFlib is able to read and write EDF/EDF+/BDF/BDF+ files.

Documentation

Documentation is available online at http://pyedflib.readthedocs.org.

Installation

pyEDFlib can be used with Python_ >=3.5. It depends on the Numpy_ package. To use the newest source code from git, you have to download the source code. You need a C compiler and a recent version of Cython_. Go then to the source directory and type::

python setup.py build
python setup.py install

There are binary wheels which can be installed by (use pip3 when available)::

pip install pyEDFlib

Users of the Anaconda_ Python distribution can directly obtain pre-built Windows, Intel Linux or macOS / OSX binaries from the conda-forge channel. This can be done via::

conda install -c conda-forge pyedflib

The most recent development version can be found on GitHub at https://github.com/holgern/pyedflib.

The latest release, including source and binary packages for Linux, macOS and Windows, is available for download from the Python Package Index. You can find source releases at the Releases Page.

Highlevel interface

pyEDFlib includes an highlevel interface for easy access to read and write edf files. Additionally functionality as anonymizing, dropping or renaming channels can be found there.

.. code-block:: Python

from pyedflib import highlevel

# write an edf file
signals = np.random.rand(5, 256*300)*200 # 5 minutes of random signal
channel_names = ['ch1', 'ch2', 'ch3', 'ch4', 'ch5']
signal_headers = highlevel.make_signal_headers(channel_names, sample_frequency=256)
header = highlevel.make_header(patientname='patient_x', gender='Female')
highlevel.write_edf('edf_file.edf', signals, signal_headers, header)

# read an edf file
signals, signal_headers, header = highlevel.read_edf('edf_file.edf', ch_names=['ch1', 'ch2'])
print(signal_headers[0]['sample_frequency']) # prints 256

# drop a channel from the file or anonymize edf
highlevel.drop_channels('edf_file.edf', to_drop=['ch2', 'ch4'])
highlevel.anonymize_edf('edf_file.edf', new_file='anonymized.edf'
                         to_remove=['patientname', 'birthdate'],
                         new_values=['anonymized', ''])
# check if the two files have the same content
highlevel.compare_edf('edf_file.edf', 'anonymized.edf')
# change polarity of certain channels 
highlevel.change_polarity('file.edf', channels=[1,3])
# rename channels within a file
highlevel.rename_channels('file.edf', mapping={'C3-M1':'C3'})

License

pyEDFlib is a free Open Source software released under the BSD 2-clause license.

Releases can be cited via Zenodo.

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5678481.svg :target: https://doi.org/10.5281/zenodo.5678481

.. _Cython: http://cython.org/ .. _Anaconda: https://www.continuum.io .. _GitHub: https://github.com/holgern/pyedflib .. _GitHub Issues: https://github.com/holgern/pyedflib/issues .. _Numpy: http://www.numpy.org .. _Python: http://python.org/ .. _Python Package Index: http://pypi.python.org/pypi/pyEDFlib/ .. _Releases Page: https://github.com/holgern/pyedflib/releases .. _edfplus.info: http://www.edfplus.info/ .. _European Data Format: http://www.edfplus.info/ .. _Kemp2003: https://www.ncbi.nlm.nih.gov/pubmed/12948806?dopt=Citation .. _Kemp1992: https://www.ncbi.nlm.nih.gov/pubmed/1374708?dopt=Abstract .. _BioSemi: http://www.biosemi.com/faq/file_format.htm .. _toolbox from Christopher Lee-Messer: https://github.com/cleemesser/python-edf .. _EDFlib: http://www.teuniz.net/edflib/