hypnospy 0.0.2

A Device-Agnostic, Open-Source Python Software for Wearable Circadian Rhythm and Sleep Analysis and Visualization

HypnosPy :sleeping_bed:

A Device-Agnostic, Open-Source Python Software for Wearable Circadian Rhythm and Sleep Analysis and Visualization

Installation :computer:

You can install HypnosPy with pip in a (bash) shell environment, type:

pip install hypnospy

To update HypnosPy type:

pip install -U hypnospy

Dependencies include python 3.7 and the following packages:

Usage :bulb:

Here is a simple example of how you can use HypnosPy in your research:

from hypnospy import Wearable
from hypnospy.data import MESAPreProcessing
from hypnospy.analysis import SleepWakeAnalysis, Viewer, NonWearingDetector

# MESAPreProcessing is a specialized class to preprocess csv files from Philips Actiwatch Spectrum devices used in the MESA Sleep experiment
# MESA Sleep dataset can be found here: https://sleepdata.org/datasets/mesa/
preprocessed = MESAPreProcessing("../data/examples_mesa/mesa-sample.csv")

# Wearable is the main object in HypnosPy.
w = Wearable(preprocessed)

# In HypnosPy, we have the concept of ``experiment day'' which by default starts at midnight (00 hours).
# We can easily change it to any other time we wish. For example, lets run this script with experiment days
# that start at 3pm (15h)
w.change_start_hour_for_experiment_day(15)

# Sleep Wake Analysis module
sw = SleepWakeAnalysis(w)
sw.run_sleep_algorithm("ScrippsClinic", inplace=True) # runs alg and creates new col named 'ScrippsClinic'
sw.run_sleep_algorithm("Cole-Kripke", inplace=True)   # runs alg and creates new col named 'Cole-Kripke'

# View results
v = Viewer(w)
v.view_signals(signal_categories=["activity"], signal_as_area=["ScrippsClinic", "Cole-Kripke", "Oakley"],
               colors={"area": ["green", "red", "blue"]}, alphas={"area": 0.6})

# Easily remove non-wearing epochs/days.
nwd = NonWearingDetector(w)
nwd.detect_non_wear(strategy="choi")
nwd.check_valid_days(max_non_wear_minutes_per_day=180)
nwd.drop_invalid_days()

Some of the amazing features of HypnosPy are shown in the here. Try it out! :test_tube:

Under the hood :mag_right:

Here we'll iput a breakdown of the software architecture

Ignacio to provide a breakdown of the main software functionalities here

Circadian

HR algorithm (update)

We found that HR quantiles offered a personalized method to direct our sleeping window search as observed in the figure bellow:

Example

Cite our work! :memo::pencil:

Contributing :handshake:

We are very keen on having other colleagues contribute to our work and to make this as generalizable as possible of a package. This project came about due to the frustration of not having a centralized analysis tool that worked across devices, so if you find our project interesting or think you can improve it, please contribute by:

• reporting bugs (how you got it and if possible, how to solve it)
• adding new tools- if you are interested on this please email one of the main developers, we'd love to hear from you
• adding pre-processing pipelines for new devices. The more, the merrier.
• sharing our work with your colleagues, this will allow the project to improve and not die in this corner of the interweb.
• reaching out!- we are always keen on learning more of how you are using/want to use hypnospy

License :clipboard:

This project is released under a BSD 2-Clause Licence (see LICENCE file)

Contributions :man_technologist: :woman_technologist:

• João Palotti (MIT) @joaopalotti main developer
• Marius Posa (Cambridge) @marius-posa main developer
• Ignacio Perez-Pozuelo (Cambridge) @ippozuelo main developer

Research that uses HypnosPy :rocket:

• Perez-Pozuelo, I., Posa, M., Spathis, D., Westgate, K., Wareham, N., Mascolo, C., ... & Palotti, J. (2020). Detecting sleep in free-living conditions without sleep-diaries: a device-agnostic, wearable heart rate sensing approach. medRxiv.

Acknowledgements :pray:

• We thank the MRC Epidemiology Unit at Cambridge for supporting some of the research associated to this work as well as QCRI and MIT.