Biotuner

Python toolbox that incorporates tools from biological signal processing and musical theory to extract harmonic structures from biosignals.

Installation

1. Install using PyPI (Recommended)

To install the latest stable version of Biotuner from PyPI, run:

pip install biotuner

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2. Install from the GitHub Repository (Development Version)

If you want the latest development version or contribute to the code, follow these steps:

2.1. Automatically Setup the Environment (Recommended)

The easiest way to set up a development environment is by using invoke, which will:

✅ Create a Conda environment
✅ Install dependencies
✅ Install Biotuner in editable mode

# Clone the repository
git clone https://github.com/AntoineBellemare/biotuner.git
cd biotuner

# Install Invoke (if not already installed)
pip install invoke

# Automatically create a Conda environment and install Biotuner
invoke setup

👉 This will create a Conda environment named biotuner_env and install all dependencies.

To activate the Conda environment manually:

conda activate biotuner_env

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2.2. Manual Setup (Alternative)

If you prefer to set up the environment manually, follow these steps:

1️⃣ Create a Conda environment

conda create --name biotuner_env python=3.11 -y
conda activate biotuner_env

2️⃣ Install dependencies

pip install -r requirements.txt
pip install -e .

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3. Verify Installation by Running Tests

To confirm that Biotuner is installed correctly, run the test suite:

invoke test

or manually using:

pytest tests/

If all tests pass ✅, your installation is complete!

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🎯 Summary

• For general users: Install via pip install biotuner
• For development: Clone the repo and run invoke setup
• To verify installation: Run invoke test

Simple use case

biotuning = biotuner(sf = 1000) #initialize the object
biotuning.peaks_extraction(data, peaks_function='FOOOF') #extract spectral peaks
biotuning.compute_peaks_metrics() #get consonance metrics for spectral peaks

Running the Biotuner GUI

You can run the Biotuner graphical interface using Invoke or Streamlit.

Option 1: Run via Invoke (Recommended)

If you have invoke installed and set up, simply run:

invoke gui

This command will ensure all dependencies are installed before launching the GUI.

Option 2: Run via Streamlit

If you prefer to start the GUI manually, run:

streamlit run gui.py

Note: If you use this option, you must first install the GUI dependencies. You can install them using:

pip install ".[gui]"

Access the Interface

Once the GUI starts, you should see a local URL in the terminal, such as:

http://localhost:8501/

Multimodal Harmonic Analysis

The figure above illustrates Biotuner's ability to extract harmonic structures across different biological and physical systems. It showcases harmonic ratios detected in biosignals from the brain, heart, and plants, as well as their correspondence with audio signals. By analyzing the fundamental frequency relationships in these diverse modalities, Biotuner enables a cross-domain exploration of resonance and tuning in biological and artificial systems.

Peaks extraction methods