This directory contains code to wrap Teunis van Beelen's edflib for python.

It provides access to EDF files, the european data format---commonly used for EEG and other biosignal recordings.

python-edf/

src/ -> holds the a version of edflib from Teunis's web site edflib/ -> holds the python/cython code to wrap edflib tests/ -> tests examples/ -> example code and short samples

Almost all of the low-level C functions in Teunis's edflib are wrapped in edflib._edflib which is created in cython. I have started creating more pythonic wrappers.

License

This code is licensed under the same BSD-style license that Teunis released edflib under and with the same disclaimer. (See src/edflib.c and README-edflib.txt)

Authors/Contributors

• Chris Lee-Messer
• Sharif Olorin <sio@tesser.org>
• backports from https://github.com/holgern/pyedflib

Status

This is currently "research quality" code. I initially developed it for my limited purposes to read a few dozen EEGs for a research project. It is inching towards respectability as it is being updated as we have project that needs it to process through tens of thousands of edf files.

It still more needs tests, more refractoring to make a real pythonic api before heading to towards a polished package.

I am currently updating edfwriter for 0.8 as I will be needing to use this functionality again.

edfreader - now has tests - needs more edfwriter likely needs re-writing

I continue to make it available in the hopes that it may be useful for others. As I need to use it, I may continue to improve and update it, but I can make no promises.

installation

the most reliable way to install edflib currently is to download the source (or git clone it). After unpacking the source, from the command line change to the directory:

python setup.py install

Or, if you are doing development, you can do:

pip install -r requirements-dev.txt
python setup.py develop

This requires a working C compiler on your machine as well as the other build requirements such as cython, setuptools and numpy.

python 3 compatibility

The package is now compatible with python 3. The distinction between bytes and strings is now clear. For clarity all the cython and C code uses bytes only. The python code deals with decoding and encoding to either ascii or UTF-8 (for annotations) as described in the spec. In addition, I will accept UTF-8 on reading though it is outside of spec.

Functions and properties with an 'underscore b' (_b) deal with bytes representation, while unadorned python functions return native python strings or numbers.

The goal is such that one can always get full access to the raw C functions and bytes from python, but provide pleasant to use python interfaces via the reader and writer classes.

Related Projects

• pyedf is a fork of this project with some nice work and documentation.
• Robert Oostenveld wrote bids-standard/pyedf, which is a pure python implementation of the standard.
• Teuniz wrote his own python library as well at https://gitlab.com/Teuniz/EDFlib-Python

Change list

2020-05-11 0.82 fix missing edf.pxi file in MANIFEST.in 2020-05-11 0.81 transition to github given sunsetting of mercurial support on bithbucket 2018-10-08 created mirror of code on github at https://github.com/cleemesser/python-edf 2018-10-08 added wraps for writing shorts, bump edflib version to 116 2018-02-15 noted that edflib.h not included in source package added to extension file list for 0.74 2017-03-22 added bitbucket-piplines.yml and got integration tests running 2017-03-22 update properties to modern (python 3) syntax in _edflib. Make distinction clear. Add tests. 2017-03 tweaks to api, python 3 working: will try for dual compatible code python 2.7 + python 3.5+ support 2015-06 update to edflib 1.11

packaging

I am currently working on using setuptools and the pyproject.toml file to make it so that you can at least do a pip install of the source distribution.

Install/Packing Status:

On ubuntu 20.04 with gcc installed: - pip install <path-to-cloned-git-repo> # works with setuptools branch

• with pip 21.2.2 python=3.7; pip 21.2.4 python=3.8, python=3.9, python=3.10

  pip install edflib # works to install edflib 0.84.1 from source distribution

• windows install worked

To upload to pypi:

python setup.py sdist
twine upload -r legacypypi dist/*

Todo:

::

• [ ] fix examples to be compatible with changes in api
• [x] basic tests with py.test
• [ ] test opening two files at once
• [/] test, tests, tests !!!
• [x] inital port to python 3 (tested with 3.5)
• [ ] add new functions from version 1.10 of edflibX
• [ ] update cython interface to use typed memory views. This will be required for cython 3.0
• [x] set up continuous build/integration if possible - done on bitbucket for py 3.5 but not yet for github
• [x] incorporate edflib code for utf-8 and short (int16) vs int (int32) digital writes
• [ ] test edflib code for utf-8 and short (int16) vs int (int32) digital writes
• [x] create mirror on github
• [ ] investigate manylinux solution to wheels. [PEP 513](https://www.python.org/dev/peps/pep-0513/) and

• [/] fix python packaging problems so that pip installs work again

  • progress: as of 0.84 have sdist installs working on linux