somnopy 0.0.9

PSG Power for Python

Sleep Spindle-Slow Oscillation Coupling Analysis

Overview

This package provides tools for analyzing sleep EEG data, focusing on Sleep Spindles (SPs) and Slow Oscillations (SOs) and their coupling interactions. The package includes functionalities for:

• EEG Preprocessing
• Slow Oscillation (SO) Detection
• Sleep Spindle (SP) Detection
• Phase-Amplitude Coupling (PAC) Analysis
• Peri-Event Time Histogram (PETH) Analysis
• Data Visualization for SOs and SPs

Features

• Multi-method SO and SP Detection: Choose from various published detection methods.
• Coupling Analysis: Computes phase-amplitude coupling between SOs and SPs.
• Batch Processing: Analyze multiple EEG recordings efficiently.
• Interactive and Static Plotting: Visualize SO and SP events using topomaps and time-series plots.

Installation

Ensure you have Python installed. Then, install dependencies using:

pip install -r requirements.txt

Usage

1️⃣ Load EEG & Hypnogram Data

from polysomnography import PolySomnoGraphy

psg = PolySomnoGraphy(
    eeg_path="subject1.edf",
    hypnogram_path="subject1.txt",
    hypnogram_type="RemLogic"
)

# Access raw EEG data
raw = psg.get_raw()
# Access hypnogram data
hypnogram = psg.get_hypnogram()

2️⃣ Detect Sleep Spindles & Slow Oscillations

so_results = psg.detect_slow_oscillations(method="Staresina")
spindle_results = psg.detect_spindles(method="Hahn2020")

3️⃣ Compute Phase-Amplitude Coupling (PAC)

pac_results = psg.pac()

4️⃣ Batch Processing for Multiple EEG Files

from somno import get_sosp_for_folder

event_summary, coupling_events, so_waveforms = get_sosp_for_folder(
    raw_folder="EEG_data",
    stage_folder="Hypnogram_data"
)

5️⃣ Visualizations

from metrics import plot_SO, plot_SP

# Plot Slow Oscillation Events
plot_SO(so_results, raw)

# Plot Spindle Events
plot_SP(spindle_results, raw)

Supported File Formats

• EEG Files: .edf, .vhdr, .set, .fif, .bdf, .cnt
• Hypnogram Files:
  • RemLogic (.txt)
  • Hume (.mat)

License

MIT License

Contributors

• Roger Balcells Sanchez
• Thea Ng
• Atif Abedeen
• Lindsey Mooney

Acknowledgments

This package integrates various methods from published research on sleep spindles and slow oscillations.

Issues & Support

For bug reports and feature requests, please open an issue on GitHub.

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📌 Want to contribute? Feel free to submit a pull request! 🚀