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Introduction
The Parkinsons Disease Digital Markers (ParaDigMa) toolbox is a Python software package designed for processing passively collected wrist sensor data to extract digital measures of motor and non-motor signs of Parkinson’s disease (PD).
Specifically, the toolbox contains three data processing pipelines: (1) arm swing during gait, (2) tremor, and (3) heart rate analysis. Furthermore, the toolbox contains general functionalities for signal processing and feature extraction, such as filtering, peak detection, and spectral analysis. The toolbox is designed to be user-friendly and modular, enabling researchers to easily extend the toolbox with new algorithms and functionalities. The toolbox is accompanied by a set of example scripts and notebooks for each domain that demonstrate how to use the toolbox for processing sensor data and extracting digital measures.
It contains functionalities for processing the following sensor types:
Inertial Measurement Units (accelerometer, gyroscope)
Photoplethysmogram (PPG)
More about ParaDigMa
The components of ParaDigMa are visually shown in the diagram below.
Processes
ParaDigMa can best be understood by categorizing the sequential processes:
Process |
Description |
|---|---|
Preprocessing |
Ensuring that the sensor data is ready for further processing |
Feature extraction |
Creating features based on windowed views of the timestamps |
Classification |
Making predictions using developed and validated classifiers |
Quantification |
Selecting specific features of interest |
Aggregation |
Aggregating the features at a specified time-level |
Domain requirements
ParaDigMa can be used to extract aggregations related to a single or multiple domain(s). Each domain has its specific data requirements. Strict requirements for the domain are marked by X, soft requirements (for some additional functionalities) are marked by O.
Gait |
Tremor |
Heart Rate |
|
|---|---|---|---|
Accelerometer |
X |
O |
|
Gyroscope |
X |
X |
|
PPG |
X |
Installation
The package is available in PyPi and requires Python 3.10 or higher. It can be installed using:
pip install paradigma
Usage
See our extended documentation.
Development
Installation
The package requires Python 3.11 or higher. Use Poetry to set up the environment and install the dependencies:
poetry install
Testing
poetry run pytest
Type checking
poetry run pytype .
Building documentation
poetry run make html --directory docs/
Contributing
Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.
License
The core team of ParaDigMa consists of Erik Post, Kars Veldkamp, Nienke Timmermans, Diogo Coutinho Soriano, Luc Evers, Peter Kok and Vedran Kasalica. Advisors to the project are Max Little, Jordan Raykov, Twan van Laarhoven, Hayriye Cagnan, and Bas Bloem. It is licensed under the terms of the Apache License 2.0 license.
Credits
ParaDigMa was created with cookiecutter and the py-pkgs-cookiecutter template.
Contact
For more information or questions about ParaDigMa, please reach out to erik.post@radboudumc.nl.
User guides
API