wristpy 0.0.1a0

A beautiful description.

Wristpy: Wrist-Worn Accelerometer Data Processing

Welcome to wristpy, a Python library designed for processing and analyzing wrist-worn accelerometer data. This library provides a set of tools for calibrating raw accelerometer data, calculating physical activity metrics (ENMO derived) and sleep metrics (angle-Z derived), finding non-wear periods, and detecing sleep periods (onset and wakeup times). Additionally, we provide access to other sensor dat that may be recorded by the watch, including; temperature, luminosity, capacitive sensing, battery voltage, and all metadata.

Supported formats & devices

The package currently supports the following formats:

Format	Manufacturer	Device	Implementation status
GT3X	Actigraph	wGT3X-BT	✅
BIN	GENEActiv	GENEActiv	✅

Features

• GGIR Calibration: Applies the GGIR calibration procedure to raw accelerometer data.
• Metrics Calculation: Calculates various metrics on the calibrated data, namely ENMO (euclidean norm , minus one) and angle-Z (angle of acceleration relative to the x-y axis).
• Physical activity levels: Using the enmo data (aggreagated into epoch 1 time bins, 5 second default) we compute activity levels into the following categories: inactivity, light activity, moderate activity, vigorous activity.
• Non-wear detection: We find periods of non-wear based on the acceleration data.
• Sleep Detection: Using the HDCZ¹ and HSPT² algorithms to analyze changes in arm angle to find periods of sleep. We find the sleep onset-wakeup times for all sleep windows detected.

Installation

Install this package via :

pip install wristpy

Or get the newest development version via:

pip install git+https://github.com/childmindresearch/wristpy

Quick start

Here is a sample script that goes through the various functions that are built into wristpy.

#loading the prerequisite modules
import wristpy
from wristpy.core import computations
from wristpy.io.readers import readers
from wristpy.processing import metrics, analytics

#set the paths to the raw data and the desired output path
file_path = '/path/to/your/file.gt3x'

#load the acceleration data
test_data = readers.read_watch_data(file_path)

#calibrate the data
calibrator = calibration.Calibration()
calibrated_data = calibrator.run(test_data.acceleration)

#Compute some metrics and get epoch1 data
enmo = metrics.euclidean_norm_minus_one(calibrated_data)
anglez = metrics.angle_relative_to_horizontal(calibrated_data)

enmo_epoch1 = computations.moving_mean(enmo)
anglez_epoch1 = computations.moving_mean(anglez)

#Find sleep windows
sleep_detector_class = analytics.GGIRSleepDetection(anglez)
sleep_windows = sleep_detector_class.run_sleep_detection()

#Find non-wear periods
non_wear_array =  metrics.detect_nonwear(calibrated_data, 900,4, 0.1,0.5)

#Get activity levels
activity_measurement = analytics.compute_physical_activty_categories(enmo_epoch1)

References

1. van Hees, V.T., Sabia, S., Jones, S.E. et al. Estimating sleep parameters using an accelerometer without sleep diary. Sci Rep 8, 12975 (2018). https://doi.org/10.1038/s41598-018-31266-z
2. van Hees, V. T. et al. A Novel, Open Access Method to Assess Sleep Duration Using a Wrist-Worn Accelerometer. PLoS One 10, e0142533 (2015). https://doi.org/10.1371/journal.pone.0142533