biobabel 0.5

Python wrapper for reading major bio/physiology data formats (e.g. ECG, PPG, EDA) into a unified accessible interface

Biobabel : a unified interface for reading a plethora of physiology file formats

Many different file formats exist for physiology signals such as cardiac (ECG, PPG) or respiratory data. Many packages exist in Python to read these formats but they load into different data structures. This package is a wrapper of sorts for already existing tools providing a unified easy-to-use interface.

Installation

python -m pip install "biobabel @ git+https://github.com/florisvanvugt/biobabel"

Usage

Command line

To preview a file, use the provided script from the command line:

biobabel <FILENAME>

You can leave <FILENAME> blank in which case you will be prompted to select a file you want to preview.

Python

Simple usage example in Python:

import biobabel
bio = biobabel.load('filename.txt')
bio.print()
bio.plot()
bio.save('new_filename.hdf5')

More complete overview of functionality in Jupyter notebook.

Requirements

Physiology dialects

Currently supported dialects are:

• hdphysio5 thanks to hdphysio5
• labstreaminglayer (LSL) XDF (rudimentary) thanks to pyxdf
• BioPAC Acknowledge (acq) thanks to bioread
• opensignals ("OpenSignals (r)evolution" thanks to opensignalsreader
• Brams-Bio-Box (custom)
• TeensyECG (custom)

Wish-list:

• EDF
• Biosemi BDF https://pypi.org/project/pybdf/

Development

Install locally:

pip install .

and editable:

pip install -e .

Create wheels with:

python3 -m build