Metadata-Version: 2.4
Name: biobabel
Version: 1.1.0
Summary: Python wrapper for reading major bio/physiology data formats (e.g. ECG, PPG, EDA) into a unified accessible interface
Author-email: Floris van Vugt <ftvanvugt@gmail.com>
Project-URL: Homepage, https://github.com/florisvanvugt/biobabel
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: h5py
Requires-Dist: numpy
Requires-Dist: pyxdf
Requires-Dist: matplotlib
Requires-Dist: bioread
Requires-Dist: opensignalsreader
Requires-Dist: pandas
Requires-Dist: pyedflib
Requires-Dist: scipy
Provides-Extra: bdf
Requires-Dist: pybdf; extra == "bdf"
Provides-Extra: neurokit
Requires-Dist: neurokit2; extra == "neurokit"
Dynamic: license-file



# Biobabel : a unified interface for reading diverse physiology file formats

[![DOI](https://zenodo.org/badge/660740111.svg)](https://zenodo.org/badge/latestdoi/660740111)


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"
```



# Documentation

https://biobabel.readthedocs.io/




# Physiology dialects

Currently supported dialects for reading are:
* EDF through [PyEDFlib](https://pyedflib.readthedocs.io/en/latest/)
* labstreaminglayer (LSL) XDF (alpha) thanks to [pyxdf](https://pypi.org/project/pyxdf/)
* BioPAC Acknowledge (acq) thanks to [bioread](https://pypi.org/project/bioread/)
* opensignals ("OpenSignals (r)evolution" thanks to [opensignalsreader](https://github.com/PGomes92/opensignalsreader)
* Biosemi BDF thanks to [pybdf](https://pypi.org/project/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](https://github.com/florisvanvugt/hdphysio5)
* TeensyECG (in-house format)



# Development version

Install locally:

```
pip install .
```

and editable:

```
pip install -e .
```


# Testing

To run the included tests, simply install the package and then run the following command from the root:

```
pytest
```


# Support

If you have a question or would like to contribute, please see the [Contributing to biobabel](CONTRIBUTING.md) section.



# Citation

Please cite this work if you use it:

  * van Vugt, F.T. (2025). Biobabel: Python package for reading major bio/physiology data formats. https://doi.org/10.5281/zenodo.15453402
  
Thank you!
