Python package to process wearable accelerometer data
Project description
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.
Getting started
Prerequisite
-
Python 3.8 or greater
$ python --version # or python3 --version
-
Java 8 (1.8.0) or greater
$ java -version
Install
$ pip install actipy
Usage
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:
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 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:
import actipy.processing as P
data, info_lowpass = P.lowpass(data, 100, 20)
data, info_calib = P.calibrate_gravity(data)
data, info_nonwear = P.detect_nonwear(data)
data, info_resample = P.resample(data, sample_rate)
See the documentation 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:
$ 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. We welcome contributions in the form of bug reports, feature requests, and pull requests.
License
See LICENSE.md.
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