_images/accelerometerLogo.png

A tool to extract meaningful health information from large accelerometer datasets. The software generates time-series and summary metrics useful for answering key questions such as how much time is spent in sleep, sedentary behaviour, or doing physical activity.

Installation

Dependencies include: unix, java 8 ([Java 8 JDK](http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html)) and python 3.7 ([Anaconda’s Python 3](https://www.anaconda.com/download/) or installation via [Brew](https://docs.python-guide.org/starting/install3/osx/) should do the trick).

$ git clone https://github.com/activityMonitoring/biobankAccelerometerAnalysis.git
$ cd biobankAccelerometerAnalysis
$ bash utilities/downloadDataModels.sh # Downloads example data and models for behaviour classification
$ pip install --upgrade pip # Upgrades pip version if required
$ pip3 install --upgrade -r requirements.txt # Installs a known working set of dependencies, other package versions may also work
$ javac -cp java/JTransforms-3.1-with-dependencies.jar java/*.java # Compiles Java code
$
$ # Now to install the package, run:
$ pip3 install --user .

Note for developers: If you are actively developing the package, you may wish to skip the installation step.

Keeping up to date

biobankAccelerometerAnalysis is regularly updated (e.g. a new dependency was introduced in January 2021, making the models compatible with the newest versions of dependency packages). To install the most recent version with the most recent set of dependencies, run (from within the folder):

$ git pull # Pulls any changes
$ bash utilities/downloadDataModels.sh # Downloads example data and models for behaviour classification
$ pip install --upgrade pip # Upgrades pip version if required
$ pip3 install --upgrade -r requirements.txt # Installs a known working set of dependencies, other package versions may also work
$ javac -cp java/JTransforms-3.1-with-dependencies.jar java/*.java # Compiles Java code
$
$ # Now to install the package, run:
$ pip3 install --user .

Getting started

To extract a summary of movement (average sample vector magnitude) and (non)wear time from raw Axivity .CWA (or gzipped .cwa.gz) accelerometer files:

$ python3 accProcess.py data/sample.cwa.gz
<output written to data/sample-outputSummary.json>
<time series output written to data/sample-timeSeries.csv.gz>

The main output JSON will look like:

{
    file-name: "sample.cwa.gz",
    file-startTime: "2014-05-07 13:29:50",
    file-endTime: "2014-05-13 09:49:50",
    acc-overall-avg(mg): 32.78149,
    wearTime-overall(days): 5.8,
    nonWearTime-overall(days): 0.04,
    quality-goodWearTime: 1
}

To visualise the time series and activity classification output:

python3 accPlot.py data/sample-timeSeries.csv.gz data/sample-plot.png
  <output plot written to data/sample-plot.png>
_images/samplePlot.png

Output plot of overall activity and class predictions for each 30sec time window

The underlying modules can also be called in custom python scripts:

from accelerometer import summariseEpoch
summary = {}
epochData, labels = summariseEpoch.getActivitySummary("sample-epoch.csv.gz",
        "sample-nonWear.csv.gz", summary)
# <nonWear file written to "sample-nonWear.csv.gz" and dict "summary" updated
# with outcomes>

Citing our work

When describing or using the UK Biobank accelerometer dataset, or using this tool to extract overall activity from your accelerometer data, please cite [Doherty2017].

When using this tool to extract sleep duration and physical activity behaviours from your accelerometer data, please cite [Willetts2018] [Doherty2018] and [Walmsley2020].

Doherty2017

Doherty A, Jackson D, Hammerla N, et al. (2017) Large scale population assessment of physical activity using wrist worn accelerometers: the UK Biobank study. PLOS ONE. 12(2):e0169649

Willetts2018

Willetts M, Hollowell S, Aslett L, Holmes C, Doherty A. (2018) Statistical machine learning of sleep and physical activity phenotypes from sensor data in 96,220 UK Biobank participants. Scientific Reports. 8(1):7961

Doherty2018

Doherty A, Smith-Bryne K, Ferreira T, et al. (2018) GWAS identifies 14 loci for device-measured physical activity and sleep duration. Nature Communications. 9(1):5257

Walmsley2020

Walmsley R, Chan S, et al. (2020) Reallocating time from machine-learned sleep, sedentary behaviour or light physical activity to moderate-to-vigorous physical activity is associated with lower cardiovascular disease risk (preprint https://doi.org/10.1101/2020.11.10.20227769)

Licence

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

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