# actipy
A Python package to process accelerometer data.
Axivity3 and Axivity6 (`.cwa`), Actigraph (`.gt3x`), and GENEActiv (`.bin`) files are supported,
as well as custom CSV files.
Axivity3 is the activity tracker watch used in the large-scale
[UK-Biobank accelerometer study](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0169649).
## Getting started
### Prerequisite
- Python 3.8 or greater
```console
$ python --version # or python3 --version
```
- Java 8 (1.8.0) or greater
```console
$ java -version
```
### Install
```bash
$ pip install actipy
```
<!-- With Conda:
```bash
$ conda install -c oxwear actipy
``` -->
## Usage
```python
import actipy
data, info = actipy.read_device("sample.cwa.gz", # or "sample.gt3x.gz" or "sample.bin.gz"
lowpass_hz=20,
calibrate_gravity=True,
detect_nonwear=True,
resample_hz=50)
```
Output:
```console
data [pandas.DataFrame]
x y z temperature light
time
2014-05-07 13:29:50.430 -0.513990 0.070390 1.671922 20.000000 78.420235
2014-05-07 13:29:50.440 -0.233940 -0.586568 0.082067 20.000000 78.420235
2014-05-07 13:29:50.450 -0.080319 -0.950817 -0.810613 20.000000 78.420235
2014-05-07 13:29:50.460 -0.067236 -0.975886 -0.865132 20.000000 78.420235
2014-05-07 13:29:50.470 -0.109636 -0.857004 -0.508666 20.000000 78.420235
... ... ... ... ... ...
info [dict]
Filename : data/sample.cwa.gz
Filesize(MB) : 69.4
Device : Axivity
DeviceID : 13110
ReadErrors : 0
SampleRate : 100.0
ReadOK : 1
StartTime : 2014-05-07 13:29:50
EndTime : 2014-05-13 09:50:33
NumTicks : 51391800
WearTime(days) : 5.847725231481482
NumInterrupts : 1
ResampleRate : 100.0
NumTicksAfterResample : 25262174
LowpassOK : 1
LowpassCutoff(Hz) : 20.0
CalibErrorBefore(mg) : 82.95806873592024
CalibErrorAfter(mg) : 4.434966371604519
CalibOK : 1
NonwearTime(days) : 0.0
NumNonwearEpisodes : 0
...
```
Refer to the [Data Dictionary](data-dictionary.md) for a comprehensive list of outputs.
### Processing a custom CSV file
You can also use the routines in `actipy.processing` to process custom CSV files, or for more fine-grained control:
```python
import actipy.processing as P
data, info_lowpass = P.lowpass(data, 100, 20)
data, info_calib = P.calibrate_gravity(data)
data, info_nonwear = P.flag_nonwear(data)
data, info_resample = P.resample(data, sample_rate)
```
See the [documentation](https://actipy.readthedocs.io/en/latest/) for more.
### Processing from the command line
We also provide a command-line tool to process a device file (currently, only AX3 and AX6 are supported) and output to CSV:
```bash
$ read_cwa sample.cwa.gz -o outputs --lowpass-hz 20 --resample-hz 50 --calibrate-gravity --detect-nonwear
```
Outputs:
- "outputs/sample/sample.csv.gz"
- "outputs/sample/sample-Info.json"
## Contributing
If you would like to contribute to this repository, please check out [CONTRIBUTING.md](https://github.com/OxWearables/actipy/blob/main/CONTRIBUTING.md).
We welcome contributions in the form of bug reports, feature requests, and pull requests.
## License
See [LICENSE.md](LICENSE.md).
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