sleep-utils

A python toolbox for sleep researchers. Plot hypnograms, spectrograms, confusion matrices, PSG summaries

Hypnogram summary
{'TRT': 460.5,
 'TST': 444.5,
 'WASO': 16.0,
 'lat_REM': 65.0,
 'lat_N1': 0.0,
 'lat_N2': 2.0,
 'lat_SWS': 9.0,
 'min_REM': 109.5,
 'min_N1': 13.5,
 'min_N2': 214.0,
 'min_SWS': 107.5,
 'perc_REM': 0.24634420697412823,
 'perc_N1': 0.030371203599550055,
 'perc_N2': 0.4814398200224972,
 'perc_SWS': 0.24184476940382452,
 'perc_W': 0.03474484256243214,
 'recording_length': 547.0,
 'sleep_offset_after_rec_start': 534.0,
 'sleep_onset_after_rec_start': 73.5}

Install

pip install sleep-utils

or

pip install git+https://github.com/skjerns/sleep-utils

Modules

The sleep-utils package is organized into several modules, each providing specific functionalities for sleep data analysis.

sleep_utils.gui

This module provides graphical user interface (GUI) components built with tkinter. It simplifies tasks like selecting files and folders, and getting user input, making your scripts more interactive.

sleep_utils.plotting

A comprehensive module for creating various plots related to sleep analysis. You can use it to:

• Plot hypnograms
• Generate spectrograms of EEG data
• Visualize confusion matrices for inter-rater reliability
• Plot noise characteristics of your signals

sleep_utils.sigproc

This module contains a collection of functions for signal processing of physiological data. Key features include:

• Filtering and resampling signals
• Detecting artifacts in your data
• Heuristics for spindle detection and other sleep-related events.

sleep_utils.tools

A set of utility functions that make working with sleep data easier. This module provides tools for:

• Reading and writing hypnograms in various formats
• Calculating and summarizing sleep statistics (e.g., TST, WASO, sleep efficiency) based on AASM guidelines.
• Inferring relationships between PSG and hypnogram files.

sleep_utils.usleep_utils

This module provides a convenient wrapper around the U-Sleep API for automatic sleep staging. You can use it to:

• Predict sleep stages from EEG/EOG data using the U-Sleep model
• Manage prediction sessions with the API
• It supports both mne.io.Raw objects and EDF files as input.

By default requests go to the public service at https://sleep.ai.ku.dk. If you run your own U-Sleep server, point the functions at it with url=:

hypno = predict_usleep(edf_file, api_token, eeg_chs=..., eog_chs=...,
                       url="http://my-usleep-server:8887")

Alternatively set the USLEEP_API_URL environment variable to redirect every call without touching any code. predict_usleep, predict_usleep_raw and delete_all_sessions all accept url=; omitting it keeps the previous behaviour.