biobabel 1.0.4

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

python3 -m pip install biobabel

Install latest development version from Github:

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

Usage

Command line

From the terminal or command prompt, you can use the following commands. To show basic info about a file, use:

bioinfo <FILENAME>

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

bioview <FILENAME>

Or, for a simpler lightweight viewer:

biobabel <FILENAME>

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

To turn one or multiple files into an HTML rendition:

biohtml <FILENAME(s)>

To split a file into multiple files along the marker time series (this will create <FILENAME_001>, <FILENAME_002> etc.:

biosplit <FILENAME>

To merge multiple files into a single output file (assuming that all channels have the same time onset):

biomerge <FILE1> <FILE2> ... <OUTPUT_FILE>

To convert a file to HDF5:

tohdf5 <FILENAME>

Python

Simple usage example in Python:

import biobabel
bio = biobabel.load('tests/example.hdf5')
bio.print()
bio.plot()
bio.save('new_filename.hdf5')

More complete overview of functionality in Jupyter notebook.

Requirements

Physiology dialects

Currently supported dialects are:

• EDF through PyEDFlib
• labstreaminglayer (LSL) XDF (alpha) thanks to pyxdf
• BioPAC Acknowledge (acq) thanks to bioread
• opensignals ("OpenSignals (r)evolution" thanks to opensignalsreader
• Biosemi BDF thanks to pybdf
• Generic CSV (where CSV delimiter is automatically inferred and the time column is guessed as well)
• Brams-Bio-Box (in-house format, even though the Generic-CSV functionality should take care of this now)
• hdphysio5 thanks to hdphysio5
• TeensyECG (in-house format)

Development

Install locally:

pip install .

and editable:

pip install -e .