![Accelerometer data processing overview](docs/source/accelerometerLogo.png)

[![Github all releases](https://img.shields.io/github/release/activityMonitoring/biobankAccelerometerAnalysis.svg)](https://github.com/activityMonitoring/biobankAccelerometerAnalysis/releases/)
![Build](https://github.com/activityMonitoring/biobankAccelerometerAnalysis/workflows/build/badge.svg)
![Gt3X](https://github.com/activityMonitoring/biobankAccelerometerAnalysis/workflows/gt3x/badge.svg)
![CWA](https://github.com/activityMonitoring/biobankAccelerometerAnalysis/workflows/cwa_regression/badge.svg)

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

```bash
pip install accelerometer
```

You also need Java 8 (1.8.0) or greater. Check with the following:

```bash
java -version
```

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

```bash
$ accProcess data/sample.cwa.gz

 <output written to data/sample-outputSummary.json>
 <time series output written to data/sample-timeSeries.csv.gz>
```

The main JSON output 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:
```
$ accPlot data/sample-timeSeries.csv.gz
 <output plot written to data/sample-timeSeries-plot.png>
```
![Time series plot](docs/source/samplePlot.png)

You can also import the underlying modules to use in your custom python scripts:
```Python
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>
```

## Under the hood
Interpreted levels of physical activity can vary, as many approaches can be
taken to extract summary physical activity information from raw accelerometer
data. To minimise error and bias, our tool uses published methods to calibrate,
resample, and summarise the accelerometer data. [Click here for detailed
information on the
data processing methods on our wiki.](https://biobankaccanalysis.readthedocs.io/en/latest/methods.html)

![Accelerometer data processing overview](docs/source/accMethodsOverview.png)
![Activity classification](docs/source/accClassification.png)



## 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
[Walmsley2021]

```
[Doherty2017] Doherty A, Jackson D, 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, et al. (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-Byrne K, et al. (2018)
GWAS identifies 14 loci for device-measured physical activity and sleep
duration. Nature Communications. 9(1):5257

[Walmsley2021] Walmsley R, Chan S, Smith-Byrne K, et al. (2021)
Reallocation of time between device-measured movement behaviours and risk
of incident cardiovascular disease. British Journal of Sports Medicine.
Published Online First. doi: 10.1136/bjsports-2021-104050
```

###### Licence
This project is released under a [BSD 2-Clause Licence](http://opensource.org/licenses/BSD-2-Clause) (see LICENCE file)
