pyEDFlib
========
.. contents::
.. image:: https://codecov.io/gh/holgern/pyedflib/branch/master/graph/badge.svg
:target: https://codecov.io/gh/holgern/pyedflib
:alt: Test Coverage
.. image:: https://readthedocs.org/projects/pyedflib/badge/?version=latest
:target: https://pyedflib.readthedocs.io/en/latest/?badge=latest
:alt: Docs Build
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:target: https://badge.fury.io/py/pyEDFlib
:alt: PyPI Version
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:target: https://anaconda.org/conda-forge/pyedflib
:alt: Conda Version
.. image:: https://anaconda.org/conda-forge/pyedflib/badges/downloads.svg
:target: https://anaconda.org/conda-forge/pyedflib
:alt: Conda Downloads
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. The company `BioSemi`_
introduced a version which saves all data with 24 Bit.
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 https://pyedflib.readthedocs.io.
Installation
------------
pyEDFlib can be used with `Python`_ >=3.7. 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: https://cython.org/
.. _Anaconda: https://www.anaconda.com/
.. _GitHub: https://github.com/holgern/pyedflib
.. _GitHub Issues: https://github.com/holgern/pyedflib/issues
.. _Numpy: https://numpy.org/
.. _Python: https://www.python.org/
.. _Python Package Index: https://pypi.org/project/pyEDFlib/
.. _Releases Page: https://github.com/holgern/pyedflib/releases
.. _edfplus.info: https://www.edfplus.info/
.. _European Data Format: https://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: https://www.biosemi.com/faq/file_format.htm
.. _toolbox from Christopher Lee-Messer: https://github.com/cleemesser/python-edf
.. _EDFlib: https://www.teuniz.net/edflib/
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"description": "pyEDFlib\n========\n\n.. contents::\n\n.. image:: https://codecov.io/gh/holgern/pyedflib/branch/master/graph/badge.svg\n :target: https://codecov.io/gh/holgern/pyedflib\n :alt: Test Coverage\n\n.. image:: https://readthedocs.org/projects/pyedflib/badge/?version=latest\n :target: https://pyedflib.readthedocs.io/en/latest/?badge=latest\n :alt: Docs Build\n\n.. image:: https://badge.fury.io/py/pyEDFlib.svg\n :target: https://badge.fury.io/py/pyEDFlib\n :alt: PyPI Version\n\n.. image:: https://img.shields.io/conda/vn/conda-forge/pyedflib.svg\n :target: https://anaconda.org/conda-forge/pyedflib\n :alt: Conda Version\n\n.. image:: https://anaconda.org/conda-forge/pyedflib/badges/downloads.svg\n :target: https://anaconda.org/conda-forge/pyedflib\n :alt: Conda Downloads\n\nWhat is pyEDFlib\n----------------\npyEDFlib is a python library to read/write EDF+/BDF+ files based on EDFlib.\n\nEDF means `European Data Format`_ and was firstly published `Kemp1992`_.\nIn 2003, an improved version of the file protocol named EDF+ has been published and can be found at `Kemp2003`_.\n\nThe EDF/EDF+ format saves all data with 16 Bit. The company `BioSemi`_\nintroduced a version which saves all data with 24 Bit.\n\nThe definition of the EDF/EDF+/BDF/BDF+ format can be found under `edfplus.info`_.\n\nThis Python toolbox is a fork of the `toolbox from Christopher Lee-Messer`_\nand uses the `EDFlib`_ from Teunis van Beelen.\nThe EDFlib is able to read and write EDF/EDF+/BDF/BDF+ files.\n\nDocumentation\n-------------\n\nDocumentation is available online at https://pyedflib.readthedocs.io.\n\nInstallation\n------------\n\npyEDFlib can be used with `Python`_ >=3.7. It depends on the `Numpy`_ package.\nTo use the newest source code from git, you have to download the source code.\nYou need a C compiler and a recent version of `Cython`_. Go then to the source directory and type::\n\n python setup.py build\n python setup.py install\n\nThere are binary wheels which can be installed by (use pip3 when available)::\n\n pip install pyEDFlib\n\nUsers of the Anaconda_ Python distribution can directly obtain pre-built\nWindows, Intel Linux or macOS / OSX binaries from the conda-forge channel.\nThis can be done via::\n\n conda install -c conda-forge pyedflib\n\n\nThe most recent *development* version can be found on GitHub at\nhttps://github.com/holgern/pyedflib.\n\nThe latest release, including source and binary packages for Linux,\nmacOS and Windows, is available for download from the `Python Package Index`_.\nYou can find source releases at the `Releases Page`_.\n\n\nHighlevel interface\n-------------------\n\npyEDFlib includes an highlevel interface for easy access to read and write edf files.\nAdditionally functionality as anonymizing, dropping or renaming channels can be found there.\n\n.. code-block:: Python\n\n from pyedflib import highlevel\n\n # write an edf file\n signals = np.random.rand(5, 256*300)*200 # 5 minutes of random signal\n channel_names = ['ch1', 'ch2', 'ch3', 'ch4', 'ch5']\n signal_headers = highlevel.make_signal_headers(channel_names, sample_frequency=256)\n header = highlevel.make_header(patientname='patient_x', gender='Female')\n highlevel.write_edf('edf_file.edf', signals, signal_headers, header)\n\n # read an edf file\n signals, signal_headers, header = highlevel.read_edf('edf_file.edf', ch_names=['ch1', 'ch2'])\n print(signal_headers[0]['sample_frequency']) # prints 256\n\n # drop a channel from the file or anonymize edf\n highlevel.drop_channels('edf_file.edf', to_drop=['ch2', 'ch4'])\n highlevel.anonymize_edf('edf_file.edf', new_file='anonymized.edf'\n to_remove=['patientname', 'birthdate'],\n new_values=['anonymized', ''])\n # check if the two files have the same content\n highlevel.compare_edf('edf_file.edf', 'anonymized.edf')\n # change polarity of certain channels\n highlevel.change_polarity('file.edf', channels=[1,3])\n # rename channels within a file\n highlevel.rename_channels('file.edf', mapping={'C3-M1':'C3'})\n\n\nLicense\n-------\n\npyEDFlib is a free Open Source software released under the BSD 2-clause license.\n\n\nReleases can be cited via Zenodo.\n\n.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5678481.svg\n :target: https://doi.org/10.5281/zenodo.5678481\n\n.. _Cython: https://cython.org/\n.. _Anaconda: https://www.anaconda.com/\n.. _GitHub: https://github.com/holgern/pyedflib\n.. _GitHub Issues: https://github.com/holgern/pyedflib/issues\n.. _Numpy: https://numpy.org/\n.. _Python: https://www.python.org/\n.. _Python Package Index: https://pypi.org/project/pyEDFlib/\n.. _Releases Page: https://github.com/holgern/pyedflib/releases\n.. _edfplus.info: https://www.edfplus.info/\n.. _European Data Format: https://www.edfplus.info/\n.. _Kemp2003: https://www.ncbi.nlm.nih.gov/pubmed/12948806?dopt=Citation\n.. _Kemp1992: https://www.ncbi.nlm.nih.gov/pubmed/1374708?dopt=Abstract\n.. _BioSemi: https://www.biosemi.com/faq/file_format.htm\n.. _toolbox from Christopher Lee-Messer: https://github.com/cleemesser/python-edf\n.. _EDFlib: https://www.teuniz.net/edflib/\n",
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