actipy 1.0.1

Python package to process wearable accelerometer data

actipy

A Python package to process accelerometer data.

Axivity3 (.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.

Installation

Getting started

Prerequisite

• Python 3.7 or greater

  $ python --version  # or python3 --version
  

• Java 8 (1.8.0) or greater

  $ java -version
  

Install

With Pip:

pip install actipy

With Conda:

conda install -c oxwear actipy

Usage

Process an Axivity3 (.cwa) file:

import actipy

data, info = actipy.read_device("sample.cwa.gz",
                                 lowpass_hz=20,
                                 calibrate_gravity=True,
                                 detect_nonwear=True,
                                 resample_hz=50)

Output:

data [pandas.DataFrame]
                                 x         y         z  temperature
 time
 2014-05-07 13:29:50.430 -0.513936  0.070043  1.671264    20.000000
 2014-05-07 13:29:50.440 -0.233910 -0.586894  0.081946    20.000000
 2014-05-07 13:29:50.450 -0.080303 -0.951132 -0.810433    20.000000
 2014-05-07 13:29:50.460 -0.067221 -0.976200 -0.864934    20.000000
 2014-05-07 13:29:50.470 -0.109617 -0.857322 -0.508587    20.000000
 ...                           ...       ...       ...          ...

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
 ...

If you have a CSV file that you want to process, you can also use the data processing routines from actipy.processing:

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.

License

See LICENSE.md.