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Python Software Development Kit (SDK) to process wearable sensor data
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OxWearables/actipy
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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-scaleUK-Biobank accelerometer study.
Python 3.8 or greater
$python --version# or python3 --versionJava 8 (1.8.0) or greater
$java -version
$ pip install actipy
importactipydata,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:
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 theData Dictionary for a comprehensive list of outputs.
You can also use the routines inactipy.processing to process custom CSV files, or for more fine-grained control:
importactipy.processingasPdata,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 thedocumentation for more.
We also provide a command-line tool to process a device file (currently, only AX3 and AX6 are supported) and output to CSV:
$ 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"
If you would like to contribute to this repository, please check outCONTRIBUTING.md.We welcome contributions in the form of bug reports, feature requests, and pull requests.
SeeLICENSE.md.
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Python Software Development Kit (SDK) to process wearable sensor data