paradigma 0.4.0__tar.gz → 0.4.2__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (22) hide show
  1. {paradigma-0.4.0 → paradigma-0.4.2}/PKG-INFO +31 -16
  2. {paradigma-0.4.0 → paradigma-0.4.2}/README.md +28 -11
  3. {paradigma-0.4.0 → paradigma-0.4.2}/pyproject.toml +10 -10
  4. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/pipelines/gait_pipeline.py +1 -1
  5. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/pipelines/tremor_pipeline.py +1 -1
  6. {paradigma-0.4.0 → paradigma-0.4.2}/LICENSE +0 -0
  7. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/__init__.py +0 -0
  8. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/assets/gait_detection_clf_package.pkl +0 -0
  9. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/assets/gait_filtering_clf_package.pkl +0 -0
  10. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/assets/ppg_quality_clf_package.pkl +0 -0
  11. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/assets/tremor_detection_clf_package.pkl +0 -0
  12. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/classification.py +0 -0
  13. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/config.py +0 -0
  14. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/constants.py +0 -0
  15. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/feature_extraction.py +0 -0
  16. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/pipelines/__init__.py +0 -0
  17. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/pipelines/heart_rate_pipeline.py +0 -0
  18. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/pipelines/heart_rate_utils.py +0 -0
  19. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/preprocessing.py +0 -0
  20. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/segmenting.py +0 -0
  21. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/testing.py +0 -0
  22. {paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/util.py +0 -0
{paradigma-0.4.0 → paradigma-0.4.2}/PKG-INFO RENAMED
@@ -1,48 +1,62 @@
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  Metadata-Version: 2.3
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  Name: paradigma
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- Version: 0.4.0
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+ Version: 0.4.2
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  Summary: Paradigma - a toolbox for Digital Biomarkers for Parkinson's Disease
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  License: Apache-2.0
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- Author: Peter Kok
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- Author-email: p.kok@esciencecenter.nl
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+ Author: Erik Post
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+ Author-email: erik.post@radboudumc.nl
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  Requires-Python: >=3.11,<4.0
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  Classifier: License :: OSI Approved :: Apache Software License
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  Classifier: Programming Language :: Python :: 3
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  Classifier: Programming Language :: Python :: 3.11
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  Classifier: Programming Language :: Python :: 3.12
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  Classifier: Programming Language :: Python :: 3.13
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- Requires-Dist: nbsphinx (>=0.9.6,<0.10.0)
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  Requires-Dist: pandas (>=2.1.4,<3.0.0)
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  Requires-Dist: python-dateutil (>=2.9.0.post0,<3.0.0)
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  Requires-Dist: pytype (>=2024.4.11,<2025.0.0)
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  Requires-Dist: scikit-learn (>=1.3.2,<1.6.1)
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- Requires-Dist: sphinx-autoapi (>=3.4.0,<4.0.0)
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  Requires-Dist: tsdf (>=0.5.2,<0.6.0)
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  Description-Content-Type: text/markdown
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- ![ParaDigMa logo](https://raw.githubusercontent.com/biomarkersParkinson/paradigma/update-readme/docs/source/_static/img/paradigma-logo-banner.png)
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+ <p align="center">
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+ <img src="https://raw.githubusercontent.com/biomarkersParkinson/paradigma/main/docs/source/_static/img/paradigma-logo-banner.png" alt="ParaDigMa logo"/>
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+ </p>
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  | Badges | |
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  |:----:|----|
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  | **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) |
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- | **DOI** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13838393.svg)](https://doi.org/10.5281/zenodo.13838393) |
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+ | **DOI** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13838392.svg)](https://doi.org/10.5281/zenodo.13838392) |
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  | **Build Status** | [![](https://img.shields.io/badge/python-3.10+-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) |
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  | **License** | [![GitHub license](https://img.shields.io/github/license/biomarkersParkinson/paradigma)](https://github.com/biomarkersparkinson/paradigma/blob/main/LICENSE) |
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  <!-- | **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) | -->
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- ParaDigMa is a Python package for processing time series data of wrist-worn sensors to quantify signs of Parkinson’s disease (PD). It contains functionalities for processing the following sensor types:
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- * Inertial Measurement Units (accelerometer, gyroscope)
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- * Photoplethysmogram (PPG)
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+ ## Introduction
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+ The Parkinsons Disease Digital Markers (ParaDigMa) toolbox is a Python
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+ software package designed for processing passively collected wrist
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+ sensor data to extract digital measures of motor and non-motor signs
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+ of Parkinson's disease (PD).
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38
 
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- And analyses of the following motor and non-motor domains:
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- * Gait
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- * Tremor
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- * Heart Rate
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+ Specifically, the toolbox contains three data processing pipelines:
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+ (1) arm swing during gait, (2) tremor, and (3) heart rate analysis.
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+ Furthermore, the toolbox contains general functionalities for signal
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+ processing and feature extraction, such as filtering, peak detection,
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+ and spectral analysis. The toolbox is designed to be user-friendly and
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+ modular, enabling researchers to easily extend the toolbox with new
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+ algorithms and functionalities. The toolbox is accompanied by a set of
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+ example scripts and notebooks for each domain that demonstrate how to use
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+ the toolbox for processing sensor data and extracting digital measures.
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+
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+ It contains functionalities for processing the following sensor types:
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+
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+ - Inertial Measurement Units (accelerometer, gyroscope)
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+ - Photoplethysmogram (PPG)
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53
 
42
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  ## More about ParaDigMa
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  The components of ParaDigMa are visually shown in the diagram below.
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- ![Pipeline Architecture](docs/source/_static/img/pipeline-architecture.png)
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+ <p align="center">
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+ <img src="https://raw.githubusercontent.com/biomarkersParkinson/paradigma/main/docs/source/_static/img/pipeline-architecture.png" alt="Pipeline architeecture"/>
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+ </p>
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  #### Processes
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  ParaDigMa can best be understood by categorizing the sequential processes:
@@ -112,7 +126,8 @@ Interested in contributing? Check out the contributing guidelines. Please note t
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  ## License
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- ParaDigMa was created by Peter Kok, Vedran Kasalica, Erik Post, Kars Veldkamp, Nienke Timmermans, Diogo Coutinho Soriano, Luc Evers. It is licensed under the terms of the Apache License 2.0 license.
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+ The core team of ParaDigMa consists of Erik Post, Kars Veldkamp, Nienke Timmermans, Diogo Coutinho Soriano, Luc Evers,
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+ 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.
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117
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  ## Credits
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{paradigma-0.4.0 → paradigma-0.4.2}/README.md RENAMED
@@ -1,26 +1,42 @@
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- ![ParaDigMa logo](https://raw.githubusercontent.com/biomarkersParkinson/paradigma/update-readme/docs/source/_static/img/paradigma-logo-banner.png)
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+ <p align="center">
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+ <img src="https://raw.githubusercontent.com/biomarkersParkinson/paradigma/main/docs/source/_static/img/paradigma-logo-banner.png" alt="ParaDigMa logo"/>
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+ </p>
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  | Badges | |
4
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  |:----:|----|
5
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  | **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) |
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- | **DOI** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13838393.svg)](https://doi.org/10.5281/zenodo.13838393) |
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+ | **DOI** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13838392.svg)](https://doi.org/10.5281/zenodo.13838392) |
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  | **Build Status** | [![](https://img.shields.io/badge/python-3.10+-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) |
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  | **License** | [![GitHub license](https://img.shields.io/github/license/biomarkersParkinson/paradigma)](https://github.com/biomarkersparkinson/paradigma/blob/main/LICENSE) |
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  <!-- | **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) | -->
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11
- ParaDigMa is a Python package for processing time series data of wrist-worn sensors to quantify signs of Parkinson’s disease (PD). It contains functionalities for processing the following sensor types:
12
- * Inertial Measurement Units (accelerometer, gyroscope)
13
- * Photoplethysmogram (PPG)
13
+ ## Introduction
14
+ The Parkinsons Disease Digital Markers (ParaDigMa) toolbox is a Python
15
+ software package designed for processing passively collected wrist
16
+ sensor data to extract digital measures of motor and non-motor signs
17
+ of Parkinson's disease (PD).
14
18
 
15
- And analyses of the following motor and non-motor domains:
16
- * Gait
17
- * Tremor
18
- * Heart Rate
19
+ Specifically, the toolbox contains three data processing pipelines:
20
+ (1) arm swing during gait, (2) tremor, and (3) heart rate analysis.
21
+ Furthermore, the toolbox contains general functionalities for signal
22
+ processing and feature extraction, such as filtering, peak detection,
23
+ and spectral analysis. The toolbox is designed to be user-friendly and
24
+ modular, enabling researchers to easily extend the toolbox with new
25
+ algorithms and functionalities. The toolbox is accompanied by a set of
26
+ example scripts and notebooks for each domain that demonstrate how to use
27
+ the toolbox for processing sensor data and extracting digital measures.
28
+
29
+ It contains functionalities for processing the following sensor types:
30
+
31
+ - Inertial Measurement Units (accelerometer, gyroscope)
32
+ - Photoplethysmogram (PPG)
19
33
 
20
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  ## More about ParaDigMa
21
35
  The components of ParaDigMa are visually shown in the diagram below.
22
36
 
23
- ![Pipeline Architecture](docs/source/_static/img/pipeline-architecture.png)
37
+ <p align="center">
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+ <img src="https://raw.githubusercontent.com/biomarkersParkinson/paradigma/main/docs/source/_static/img/pipeline-architecture.png" alt="Pipeline architeecture"/>
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+ </p>
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25
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  #### Processes
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  ParaDigMa can best be understood by categorizing the sequential processes:
@@ -90,7 +106,8 @@ Interested in contributing? Check out the contributing guidelines. Please note t
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91
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  ## License
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93
- ParaDigMa was created by Peter Kok, Vedran Kasalica, Erik Post, Kars Veldkamp, Nienke Timmermans, Diogo Coutinho Soriano, Luc Evers. It is licensed under the terms of the Apache License 2.0 license.
109
+ The core team of ParaDigMa consists of Erik Post, Kars Veldkamp, Nienke Timmermans, Diogo Coutinho Soriano, Luc Evers,
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+ 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.
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  ## Credits
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{paradigma-0.4.0 → paradigma-0.4.2}/pyproject.toml RENAMED
@@ -1,14 +1,15 @@
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  [tool.poetry]
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  name = "paradigma"
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- version = "0.4.0"
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+ version = "0.4.2"
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  description = "Paradigma - a toolbox for Digital Biomarkers for Parkinson's Disease"
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- authors = [ "Peter Kok <p.kok@esciencecenter.nl>",
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+ authors = [ "Erik Post <erik.post@radboudumc.nl>",
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+ "Kars Veldkamp <kars.veldkamp@radboudumc.nl>",
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+ "Nienke Timmermans <nienke.timmermans@radboudumc.nl>",
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+ "Diogo Soriano",
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  "Vedran Kasalica <v.kaslica@esciencecenter.nl>",
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- "Erik Post",
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- "Kars Veldkamp",
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- "Nienke Timmermans",
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- "Diogo Coutinho Soriano",
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- "Luc Evers" ]
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+ "Peter Kok <p.kok@esciencecenter.nl>",
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+ "Luc Evers <luc.evers@radboudumc.nl>",
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+ ]
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  license = "Apache License 2.0"
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  readme = "README.md"
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@@ -21,8 +22,6 @@ pytype = "^2024.4.11"
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  # for the record: pytype was installed directly with pip (in the poetry environment),
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  # because poetry didn't handle the install for different CPU architectures
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  python-dateutil = "^2.9.0.post0"
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- sphinx-autoapi = "^3.4.0"
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- nbsphinx = "^0.9.6"
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  [tool.poetry.group.testing.dependencies]
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  ipykernel = "^6.27.1"
@@ -37,7 +36,8 @@ myst-nb = "^1.1.0"
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  sphinx-autoapi = "^3.0.0"
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  sphinx-rtd-theme = "^2.0.0"
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  sphinx-serve = "^1.0.1"
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-
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+ myst-parser = "^4.0.0"
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+ nbsphinx = "^0.9.6"
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  [tool.poetry.group.dev.dependencies]
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  pytype = "^2024.10.11"
{paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/pipelines/gait_pipeline.py RENAMED
@@ -479,7 +479,7 @@ def quantify_arm_swing(
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  # Group consecutive timestamps into segments, with new segments starting after a pre-specified gap
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  # Now segments are based on predicted gait without other arm activity for subsequent processes
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  df_focus[DataColumns.SEGMENT_NR] = create_segments(
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- time_array=df[DataColumns.TIME],
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+ time_array=df_focus[DataColumns.TIME],
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  max_segment_gap_s=max_segment_gap_s
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  )
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  else:
{paradigma-0.4.0 → paradigma-0.4.2}/src/paradigma/pipelines/tremor_pipeline.py RENAMED
@@ -79,7 +79,7 @@ def detect_tremor(df: pd.DataFrame, config: TremorConfig, full_path_to_classifie
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  2. Scales the relevant features in the input DataFrame (`df`) using the loaded scaling parameters.
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  3. Makes predictions using the classifier to estimate the probability of tremor.
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  4. Applies a threshold to the predicted probabilities to classify whether tremor is detected or not.
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- 5. Checks for rest tremor by verifying the frequency of the peak and low-frequency power.
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+ 5. Checks for rest tremor by verifying the frequency of the peak and below tremor power.
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  6. Adds the predicted probabilities and the classification result to the DataFrame.
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  Parameters
{paradigma-0.4.0 → paradigma-0.4.2}/LICENSE RENAMED
File without changes