Open Movement Python Code

This repository contains the Python code for the Open Movement project.

Install the current build from the repository:

python -m pip install "git+https://github.com/digitalinteraction/openmovement-python.git#egg=openmovement"

cwa_load - .CWA file loader

Load .CWA files directly into Python (requires numpy and pandas).

from openmovement.load import CwaData

filename = 'cwa-data.cwa'
with CwaData(filename, include_gyro=False, include_temperature=True) as cwa_data:
    # As an ndarray of [time,accel_x,accel_y,accel_z,temperature]
    sample_values = cwa_data.get_sample_values()
    # As a pandas DataFrame
    samples = cwa_data.get_samples()

You can also use MultiData instead of CwaData, which supports .CWA files, .WAV accelerometer files and timeseries .CSV files (all of which could be inside a .ZIP file).

omconvert - wrapper for omconvert binary executable

(omconvert.py) is a Python wrapper for the omconvert executable, which processes .cwa and .omx binary files and produce calculated outputs, such as SVM (signal vector magnitude) and WTV (wear-time validation). It can also be used to output raw accelerometer .csv files (these can be very large).

The example code, run_omconvert.py, exports the SVM and WTV files. A basic usage example is:

import os
from openmovement.process import OmConvert

source_file = 'CWA-DATA.CWA'

base_name = os.path.splitext(source_file)[0]
options = {}

# Nearest-point sampling
options['interpolate_mode'] = 1

# Optionally export accelerometer CSV file (can take a long time)
#options['csv_file'] = base_name + '.csv'

# SVM (no filter)
options['svm_filter'] = 0
options['svm_file'] = base_name + '.svm.csv'

# Wear-time validation
options['wtv_file'] = base_name + '.wtv.csv'

# Run the processing
om = OmConvert()
result = om.execute(source_file, options)

Note: You will need the omconvert binary either in your PATH, in the current working directory, or in the same directory as the omconvert.py file (or, on Windows, if you have OmGui installed in the default location). On Windows you can use the bin/build-omconvert.bat script to fetch the source and build the binary, or on macOS/Linux you can use the bin/build-omconvert.sh script.

zip_helper - "potentially zipped" file helper

Handles a "potentially zipped" file: one that may be inside a .ZIP archive but, if so, you need the extracted file on a drive and it can't be a stream from a compressed file. For example, when you need to memory-map the file (e.g. with cwa_load), or use it with an external process (e.g. with omconvert).

Offers a convenient with syntax:

• If the file extension is not '.zip', the original filename is passed through via the with syntax.

• Otherwise, the file is opened as a .ZIP archive, and it is searched for exactly one matching filename (by default, a single-file archive). The matching file is extracted to a temporary location, and that location is passed through the with syntax as the filename to use. At the end of the with block, the temporary file is automatically removed.

from openmovement.load import PotentiallyZippedFile

filename = 'example.zip'
with PotentiallyZippedFile(filename, ['*.cwa', '*.omx']) as file:
    print('Using: ' + file)
    pass

Algorithms

SVM - Signal Vector Magnitude

Calculates the mean abs(SVM-1) value (otherwise known as the Euclidean Norm Minus One) for timestamped accelerometer data (default 60 seconds).

from openmovement.load import MultiData
from openmovement.process import calc_svm

filename = 'cwa-data.cwa'
with MultiData(filename) as data:
    samples = data.get_sample_values()

svm_calc = calc_svm.calculate_svm(samples)

WTV - Wear-Time Validation

Calculates the wear-time validation value in 30 minute epochs for timestamped accelerometer data.

This is an implementation of the algorithm described in: van Hees et al. (2011). Estimation of daily energy expenditure in pregnant and non-pregnant women using a wrist-worn tri-axial accelerometer. PloS one, 6(7), e22922.

from openmovement.load import MultiData
from openmovement.process import calc_wtv

filename = 'cwa-data.cwa'
with MultiData(filename) as data:
    samples = data.get_sample_values()

wtv_calc = calc_wtv.calculate_wtv(samples)