# actipy
[](https://github.com/OxWearables/actipy/releases/)
[](https://doi.org/10.5281/zenodo.14514488)
A Python package to process accelerometer data.
Axivity3 and Axivity6 (.cwa), Actigraph (.gt3x), GENEActiv (.bin), and Matrix (.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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"description": "# actipy\n\n[](https://github.com/OxWearables/actipy/releases/)\n[](https://doi.org/10.5281/zenodo.14514488)\n\nA Python package to process accelerometer data.\n\nAxivity3 and Axivity6 (.cwa), Actigraph (.gt3x), GENEActiv (.bin), and Matrix (.bin) files are supported,\nas well as custom CSV files.\n\nAxivity3 is the activity tracker watch used in the large-scale\n[UK-Biobank accelerometer study](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0169649).\n\n## Getting started\n\n### Prerequisite\n\n- Python 3.8 or greater\n ```console\n $ python --version # or python3 --version\n ```\n\n- Java 8 (1.8.0) or greater\n ```console\n $ java -version\n ```\n\n### Install\n\n```bash\n$ pip install actipy\n```\n\n<!-- With Conda:\n```bash\n$ conda install -c oxwear actipy\n``` -->\n\n## Usage\n\n```python\nimport actipy\n\ndata, info = actipy.read_device(\"sample.cwa.gz\", # or \"sample.gt3x.gz\" or \"sample.bin.gz\"\n lowpass_hz=20,\n calibrate_gravity=True,\n detect_nonwear=True,\n resample_hz=50)\n```\n\nOutput:\n```console\ndata [pandas.DataFrame]\n x y z temperature light\n time\n 2014-05-07 13:29:50.430 -0.513990 0.070390 1.671922 20.000000 78.420235\n 2014-05-07 13:29:50.440 -0.233940 -0.586568 0.082067 20.000000 78.420235\n 2014-05-07 13:29:50.450 -0.080319 -0.950817 -0.810613 20.000000 78.420235\n 2014-05-07 13:29:50.460 -0.067236 -0.975886 -0.865132 20.000000 78.420235\n 2014-05-07 13:29:50.470 -0.109636 -0.857004 -0.508666 20.000000 78.420235\n ... ... ... ... ... ...\n\ninfo [dict]\n Filename : data/sample.cwa.gz\n Filesize(MB) : 69.4\n Device : Axivity\n DeviceID : 13110\n ReadErrors : 0\n SampleRate : 100.0\n ReadOK : 1\n StartTime : 2014-05-07 13:29:50\n EndTime : 2014-05-13 09:50:33\n NumTicks : 51391800\n WearTime(days) : 5.847725231481482\n NumInterrupts : 1\n ResampleRate : 100.0\n NumTicksAfterResample : 25262174\n LowpassOK : 1\n LowpassCutoff(Hz) : 20.0\n CalibErrorBefore(mg) : 82.95806873592024\n CalibErrorAfter(mg) : 4.434966371604519\n CalibOK : 1\n NonwearTime(days) : 0.0\n NumNonwearEpisodes : 0\n ...\n\n```\nRefer to the [Data Dictionary](data-dictionary.md) for a comprehensive list of outputs.\n\n### Processing a custom CSV file\nYou can also use the routines in `actipy.processing` to process custom CSV files, or for more fine-grained control:\n\n```python\nimport actipy.processing as P\n\ndata, info_lowpass = P.lowpass(data, 100, 20)\ndata, info_calib = P.calibrate_gravity(data)\ndata, info_nonwear = P.flag_nonwear(data)\ndata, info_resample = P.resample(data, sample_rate)\n```\n\nSee the [documentation](https://actipy.readthedocs.io/en/latest/) for more.\n\n### Processing from the command line\nWe also provide a command-line tool to process a device file (currently, only AX3 and AX6 are supported) and output to CSV:\n```bash\n$ read_cwa sample.cwa.gz -o outputs --lowpass-hz 20 --resample-hz 50 --calibrate-gravity --detect-nonwear\n```\n\nOutputs:\n - \"outputs/sample/sample.csv.gz\"\n - \"outputs/sample/sample-Info.json\"\n\n\n## Contributing\nIf you would like to contribute to this repository, please check out [CONTRIBUTING.md](https://github.com/OxWearables/actipy/blob/main/CONTRIBUTING.md).\nWe welcome contributions in the form of bug reports, feature requests, and pull requests. \n\n## License\nSee [LICENSE.md](LICENSE.md).\n",
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