paradigma 1.0.4__py3-none-any.whl → 1.1.0__py3-none-any.whl

paradigma-1.1.0.dist-info/RECORD

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{paradigma-1.0.4.dist-info → paradigma-1.1.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.2.1
+Generator: poetry-core 2.3.1
 Root-Is-Purelib: true
 Tag: py3-none-any

paradigma-1.0.4.dist-info/METADATA

@@ -1,140 +0,0 @@
-Metadata-Version: 2.4
-Name: paradigma
-Version: 1.0.4
-Summary: ParaDigMa - A toolbox for deriving Parkinson's disease Digital Markers from real-life wrist sensor data
-License: Apache-2.0
-License-File: LICENSE
-Author: Erik Post
-Author-email: erik.post@radboudumc.nl
-Requires-Python: >=3.11,<4.0
-Classifier: License :: OSI Approved :: Apache Software License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Classifier: Programming Language :: Python :: 3.14
-Requires-Dist: nbconvert (>=7.16.6,<8.0.0)
-Requires-Dist: pandas (>=2.1.4,<3.0.0)
-Requires-Dist: python-dateutil (>=2.9.0.post0,<3.0.0)
-Requires-Dist: pytype (>=2024.4.11,<2025.0.0)
-Requires-Dist: scikit-learn (>=1.3.2,<1.6.1)
-Requires-Dist: tsdf (>=0.5.2,<0.6.0)
-Description-Content-Type: text/markdown
-
-<p align="center">
-  <img src="https://raw.githubusercontent.com/biomarkersParkinson/paradigma/main/docs/source/_static/img/paradigma-logo-banner.png" alt="ParaDigMa logo"/>
-</p>
-
-| Badges | |
-|:----:|----|
-| **Packages and Releases** | [![Latest release](https://img.shields.io/github/release/biomarkersparkinson/paradigma.svg)](https://github.com/biomarkersparkinson/paradigma/releases/latest) [![PyPI](https://img.shields.io/pypi/v/paradigma.svg)](https://pypi.python.org/pypi/paradigma/)  [![Static Badge](https://img.shields.io/badge/RSD-paradigma-lib)](https://research-software-directory.org/software/paradigma) |
-| **DOI** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13838392.svg)](https://doi.org/10.5281/zenodo.13838392) |
-| **Build Status** | [![](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/) [![Build and test](https://github.com/biomarkersParkinson/paradigma/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/biomarkersParkinson/paradigma/actions/workflows/build-and-test.yml) [![pages-build-deployment](https://github.com/biomarkersParkinson/paradigma/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/biomarkersParkinson/paradigma/actions/workflows/pages/pages-build-deployment) |
-| **License** |  [![GitHub license](https://img.shields.io/github/license/biomarkersParkinson/paradigma)](https://github.com/biomarkersparkinson/paradigma/blob/main/LICENSE) |
-<!-- | **Fairness** |  [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) [![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/8083/badge)](https://www.bestpractices.dev/projects/8083) | -->
-
-## Overview
-The Parkinson's disease Digital Markers (ParaDigMa) toolbox is a Python
-software package designed for processing real-life wrist sensor data
-to extract digital measures of motor and non-motor signs of Parkinson's disease (PD).
-
-Specifically, the toolbox is designed to process accelerometer, gyroscope and
-photoplethysmography (PPG) signals, collected during passive monitoring in daily life.
-It contains three data processing pipelines: (1) arm swing during gait, (2) tremor,
-and (3) pulse rate. These pipelines are scientifically validated for their
-use in persons with PD. Furthermore, the toolbox contains general functionalities for
-signal processing and feature extraction, such as filtering, peak detection, and
-spectral analysis.
-
-The toolbox is accompanied by a set of example scripts and notebooks for
-each processing pipeline that demonstrate how to use the toolbox for extracting
-digital measures. In addition, the toolbox is designed to be modular, enabling
-researchers to easily extend the toolbox with new algorithms and functionalities.
-
-## Features
-The components of ParaDigMa are shown in the diagram below.
-
-<p align="center">
-  <img src="https://raw.githubusercontent.com/biomarkersParkinson/paradigma/main/docs/source/_static/img/pipeline-architecture.png" alt="Pipeline architeecture"/>
-</p>
-The three colored, shaded columns represent the individual pipelines. Processes of the pipelines are represented by blue ellipses, and input/output data by rectangular boxes. The input/output of each step is indicated by yellow horizontal bars denoting the type of data (e.g., 3. Extracted features). Arrows indicate the sequential order of the processes of the pipeline. <br/> <br/>
-ParaDigMa can best be understood by categorizing the sequential processes:
-
-| Process | Description |
-| ---- | ---- |
-| Preprocessing | Preparing raw sensor signals for further processing |
-| Feature extraction | Extracting features based on windowed sensor signals |
-| Classification | Detecting segments of interest using validated classifiers (e.g., gait segments) |
-| Quantification | Extracting specific measures from the detected segments (e.g., arm swing measures) |
-| Aggregation | Aggregating the measures over a specific time period (e.g., week-level aggregates) |
-
-<br/>
-ParaDigMa contains the following validated processing pipelines (each using the processes described above):
-
-| Pipeline | Input | Output classification | Output quantification | Output week-level aggregation |
-| ---- | ---- | ---- | ---- | ---- |
-| **Arm swing during gait** | Wrist accelerometer and gyroscope data | Gait probability, gait without other arm activities probability | Arm swing range of motion (RoM) | Typical & maximum arm swing RoM |
-| **Tremor** | Wrist gyroscope data | Tremor probability | Tremor power | % tremor time, typical & maximum tremor power |
-| **Pulse rate** | Wrist PPG and accelerometer data | PPG signal quality | Pulse rate | Resting & maximum pulse rate |
-
-## Installation
-
-The package is available in PyPI and requires [Python 3.11](https://www.python.org/downloads/) or higher. It can be installed using:
-
-```bash
-pip install paradigma
-```
-
-## Usage
-
-### Tutorials & documentation
-See our tutorials for example scripts on how to use the toolbox to extract digital measures from wrist sensor signals.
-The API reference contains detailed documentation of all toolbox modules and functions.
-The user guides provide additional information about specific topics (e.g. the required orientation of the wrist sensor).
-
-### Sensor data requirements
-The ParaDigMa toolbox is designed for the analysis of passive monitoring data collected using a wrist sensor in persons with PD.
-
-Specific requirements include:
-| Pipeline               | Sensor Configuration                                                                                                       | Context of Use                                                                                             |
-|------------------------|--------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------|
-| **All**               | - Sensor position: wrist-band on most or least affected side (validated for both, but different sensitivity for measuring disease progression for tremor and arm swing during gait).  <br> - Sensor orientation: orientation as described in [Coordinate System](https://biomarkersparkinson.github.io/paradigma/guides/coordinate_system.html). <br> - Timeframe: contiguous, strictly increasing timestamps. | - Population: persons with PD. <br> - Data collection protocol: passive monitoring in daily life. |
-| **Arm swing during gait** | - Accelerometer: minimum sampling rate of 100 Hz, minimum range of ± 4 g. <br> - Gyroscope: minimum sampling rate of 100 Hz, minimum range of ± 1000 degrees/sec. | - Population: no walking aid, no severe dyskinesia in the watch-sided arm. <br> - Compliance: for weekly measures: at least three compliant days (with ≥10 hours of data between 8 am and 10 pm), and at least 2 minutes of arm swing. |
-| **Tremor**            | - Gyroscope: minimum sampling rate of 100 Hz, minimum range of ± 1000 degrees/sec. | - Compliance: for weekly measures: at least three compliant days (with ≥10 hours of data between 8 am and 10 pm). |
-| **Pulse rate**        | - PPG*: minimum sampling rate of 30 Hz, green LED. <br> - Accelerometer: minimum sampling rate of 100 Hz, minimum range of ± 4 g. | - Population: no rhythm disorders (e.g. atrial fibrillation, atrial flutter). <br> - Compliance: for weekly measures: minimum average of 12 hours of data per day. |
-
-\* The processing of PPG signals is currently based on the blood volume pulse (arbitrary units) obtained from the Verily Study Watch. [This](https://biomarkersparkinson.github.io/paradigma/tutorials/_static/pulse_rate_analysis.html#step-3-signal-quality-classification) part of the PPG tutorial provides code and documentation on how to use the pipeline with other PPG devices.
-
-> [!WARNING]
-> While the toolbox is designed to work on any wrist sensor device which fulfills the requirements,
-we have currently verified its performance on data from the Gait-up Physilog 4 (arm swing during gait & tremor) and the Verily Study Watch (all pipelines). Furthermore, the specifications above are the minimally validated requirements. For example, while ParaDigMa works with accelerometer and gyroscope data sampled at 50 Hz, its effect on subsequent processes has not been empirically validated.
-<br/>
-
-We have included support for [TSDF](https://biomarkersparkinson.github.io/tsdf/) as format for loading and storing sensor data. TSDF enables efficient data storage with added metadata. However, ParaDigMa does not require a particular method of data storage and retrieval. Please see our tutorial [Data preparation](https://biomarkersparkinson.github.io/paradigma/tutorials/data_preparation.html) for examples of loading TSDF and other data formats into memory, and for preparing raw sensor data as input for the processing pipelines.
-
-## Scientific validation
-
-The pipelines were developed and validated using data from the Parkinson@Home Validation study [[Evers et al. (2020)]](https://pmc.ncbi.nlm.nih.gov/articles/PMC7584982/) and the Personalized Parkinson Project [[Bloem et al. (2019)]](https://pubmed.ncbi.nlm.nih.gov/31315608/). The following publications contain details and validation of the pipelines:
-* [Post, E. et al. (2025) - Quantifying arm swing in Parkinson's disease: a method account for arm activities during free-living gait](https://doi.org/10.1186/s12984-025-01578-z)
-* [Timmermans, N.A. et al. (2025) - A generalizable and open-source algorithm for real-life monitoring of tremor in Parkinson's disease](https://doi.org/10.1038/s41531-025-01056-2)
-* [Veldkamp, K.I. et al. (2025) - Heart rate monitoring using wrist photoplethysmography in Parkinson disease: feasibility and relation with autonomic dysfunction](https://doi.org/10.1101/2025.08.15.25333751)
-
-## Contributing
-
-We welcome contributions! Please check out our [contributing guidelines](https://biomarkersparkinson.github.io/paradigma/contributing.html).
-Please note that this project is released with a [Code of Conduct](https://biomarkersparkinson.github.io/paradigma/conduct.html). By contributing to this project, you agree to abide by its terms.
-
-## License
-
-It is licensed under the terms of the Apache License 2.0 license. See [License](https://biomarkersparkinson.github.io/paradigma/license.html) for more details.
-
-## Acknowledgements
-
-The core team of ParaDigMa consists of Erik Post, Kars Veldkamp, Nienke Timmermans, Diogo Coutinho Soriano, Peter Kok, Vedran Kasalica and Luc Evers.
-Advisors to the project are Max Little, Jordan Raykov, Twan van Laarhoven, Hayriye Cagnan, and Bas Bloem.
-The initial release of ParaDigMa was funded by the Michael J Fox Foundation (grant #020425) and the Dutch Research Council (grant #ASDI.2020.060 & grant #2023.010).
-ParaDigMa was created with [`cookiecutter`](https://cookiecutter.readthedocs.io/en/latest/) and the `py-pkgs-cookiecutter` [template](https://github.com/py-pkgs/py-pkgs-cookiecutter).
-
-## Contact
-Questions, issues or suggestions about ParaDigMa? Please reach out to paradigma@radboudumc.nl, or open an issue in the GitHub repository.
-

paradigma-1.0.4.dist-info/RECORD

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