paradigma 0.3.2__tar.gz → 0.4.1__tar.gz

paradigma-0.4.1/PKG-INFO

@@ -0,0 +1,138 @@
+Metadata-Version: 2.3
+Name: paradigma
+Version: 0.4.1
+Summary: Paradigma - a toolbox for Digital Biomarkers for Parkinson's Disease
+License: Apache-2.0
+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
+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-3.10+-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) |
+| **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) | --> 
+
+## 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.
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/biomarkersParkinson/paradigma/main/docs/source/_static/img/pipeline-architecture.png" alt="Pipeline architeecture"/>
+</p>
+
+#### 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](https://www.python.org/downloads/) or higher. It can be installed using:
+
+```bash
+pip install paradigma
+```
+
+## Usage
+
+See our [extended documentation](https://biomarkersparkinson.github.io/paradigma/).
+
+## Development
+
+### Installation
+
+The package requires Python 3.11 or higher. Use [Poetry](https://python-poetry.org/docs/#installation) to set up the environment and install the dependencies:
+
+```bash
+poetry install
+```
+
+### Testing
+
+```bash
+poetry run pytest
+```
+
+### Type checking
+
+```bash
+poetry run pytype .
+```
+
+### Building documentation
+
+```bash
+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`](https://cookiecutter.readthedocs.io/en/latest/) and the `py-pkgs-cookiecutter` [template](https://github.com/py-pkgs/py-pkgs-cookiecutter).
+
+## Contact
+
+For more information or questions about ParaDigMa, please reach out to erik.post@radboudumc.nl.

paradigma-0.4.1/README.md

@@ -0,0 +1,118 @@
+<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-3.10+-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) |
+| **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) | --> 
+
+## 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.
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/biomarkersParkinson/paradigma/main/docs/source/_static/img/pipeline-architecture.png" alt="Pipeline architeecture"/>
+</p>
+
+#### 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](https://www.python.org/downloads/) or higher. It can be installed using:
+
+```bash
+pip install paradigma
+```
+
+## Usage
+
+See our [extended documentation](https://biomarkersparkinson.github.io/paradigma/).
+
+## Development
+
+### Installation
+
+The package requires Python 3.11 or higher. Use [Poetry](https://python-poetry.org/docs/#installation) to set up the environment and install the dependencies:
+
+```bash
+poetry install
+```
+
+### Testing
+
+```bash
+poetry run pytest
+```
+
+### Type checking
+
+```bash
+poetry run pytype .
+```
+
+### Building documentation
+
+```bash
+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`](https://cookiecutter.readthedocs.io/en/latest/) and the `py-pkgs-cookiecutter` [template](https://github.com/py-pkgs/py-pkgs-cookiecutter).
+
+## Contact
+
+For more information or questions about ParaDigMa, please reach out to erik.post@radboudumc.nl.

{paradigma-0.3.2 → paradigma-0.4.1}/pyproject.toml

@@ -1,25 +1,27 @@
 [tool.poetry]
 name = "paradigma"
-version = "0.3.2"
+version = "0.4.1"
 description = "Paradigma - a toolbox for Digital Biomarkers for Parkinson's Disease"
-authors = [ "Peter Kok <p.kok@esciencecenter.nl>",
+authors = [ "Erik Post <erik.post@radboudumc.nl>",
+            "Kars Veldkamp <kars.veldkamp@radboudumc.nl>",
+            "Nienke Timmermans <nienke.timmermans@radboudumc.nl>",
+            "Diogo Soriano",
             "Vedran Kasalica <v.kaslica@esciencecenter.nl>",
-            "Erik Post",
-            "Kars Veldkamp",
-            "Nienke Timmermans",
-            "Diogo Coutinho Soriano",
-            "Luc Evers" ]
+            "Peter Kok <p.kok@esciencecenter.nl>",
+            "Luc Evers <luc.evers@radboudumc.nl>",
+            ]
 license = "Apache License 2.0"
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = "^3.10"
+python = "^3.11"
 pandas = "^2.1.4"
-scikit-learn = "^1.3.2"
+scikit-learn = ">=1.3.2,<1.6.1"
 tsdf = "^0.5.2"
 pytype = "^2024.4.11"
 # for the record: pytype was installed directly with pip (in the poetry environment),
 # because poetry didn't handle the install for different CPU architectures
+python-dateutil = "^2.9.0.post0"
 
 [tool.poetry.group.testing.dependencies]
 ipykernel = "^6.27.1"
@@ -34,6 +36,11 @@ myst-nb = "^1.1.0"
 sphinx-autoapi = "^3.0.0"
 sphinx-rtd-theme = "^2.0.0"
 sphinx-serve = "^1.0.1"
+myst-parser = "^4.0.0"
+nbsphinx = "^0.9.6"
+
+[tool.poetry.group.dev.dependencies]
+pytype = "^2024.10.11"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

paradigma-0.4.1/src/paradigma/classification.py

@@ -0,0 +1,115 @@
+import numpy as np
+import pickle
+
+from pathlib import Path
+from sklearn.base import BaseEstimator
+from typing import Any, Optional
+
+class ClassifierPackage:
+    def __init__(self, classifier: Optional[BaseEstimator] = None, 
+                 threshold: Optional[float] = None, 
+                 scaler: Optional[Any] = None):
+        """
+        Initialize the ClassifierPackage with a classifier, threshold, and scaler.
+
+        Parameters
+        ----------
+        classifier
+            The trained classifier.
+        threshold : float
+            The classification threshold.
+        scaler
+            The trained scaler (e.g., StandardScaler or MinMaxScaler).
+        """
+        self.classifier = classifier
+        self.threshold = threshold
+        self.scaler = scaler
+
+    def transform_features(self, X) -> np.ndarray:
+        """
+        Transform the input features using the scaler.
+
+        Parameters
+        ----------
+        X : np.ndarray
+            The input features.
+
+        Return
+        ------
+        np.ndarray
+            The transformed features.
+        """
+        if not self.scaler:
+            return X
+        return self.scaler.transform(X)
+
+    def predict_proba(self, X) -> float:
+        """
+        Make predictions using the classifier and apply the threshold.
+
+        Parameters
+        ----------
+        X : np.ndarray
+            The input features.
+
+        Return
+        ------
+        float
+            The predicted probability.
+
+        """
+        if not self.classifier:
+            raise ValueError("Classifier is not loaded.")
+        return self.classifier.predict_proba(X)[:, 1]
+    
+    def predict(self, X) -> int:
+        """
+        Make predictions using the classifier and apply the threshold.
+
+        Parameters
+        ----------
+        X : np.ndarray
+            The input features.
+
+        Return
+        ------
+        int
+            The predicted class.
+
+        """
+        if not self.classifier:
+            raise ValueError("Classifier is not loaded.")
+        return int(self.predict_proba(X) >= self.threshold)
+    
+    def save(self, filepath: str | Path) -> None:
+        """
+        Save the ClassifierPackage to a file.
+
+        Parameters
+        ----------
+        filepath : str
+            The path to the file.
+        """
+        with open(filepath, 'wb') as f:
+            pickle.dump(self, f)
+
+    @classmethod
+    def load(cls, filepath: str | Path):
+        """
+        Load a ClassifierPackage from a file.
+
+        Parameters
+        ----------
+        filepath : str
+            The path to the file.
+
+        Return
+        ------
+        ClassifierPackage
+            The loaded classifier package.
+        """
+        try:
+            with open(filepath, 'rb') as f:
+                return pickle.load(f)
+        except Exception as e:
+            raise ValueError(f"Failed to load classifier package: {e}") from e