https://github.com/manuelmariscal/biomedical_workshops
This repo is focused on movement analysis workshops, mainly using computational vision and AI, repo is still a work in progress.
https://github.com/manuelmariscal/biomedical_workshops
biomedical-engineering computational-vision movement-analysis
Last synced: 5 months ago
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This repo is focused on movement analysis workshops, mainly using computational vision and AI, repo is still a work in progress.
- Host: GitHub
- URL: https://github.com/manuelmariscal/biomedical_workshops
- Owner: manuelmariscal
- Created: 2024-07-08T23:44:59.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-08-12T23:25:24.000Z (about 1 year ago)
- Last Synced: 2024-08-13T01:58:59.964Z (about 1 year ago)
- Topics: biomedical-engineering, computational-vision, movement-analysis
- Language: Python
- Homepage:
- Size: 317 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Biomedical Workshops
## Real-time Movement Analysis for Biomedical Engineers
This repository contains a real-time movement analysis tool using video capture and Mediapipe's pose estimation. The tool is designed to help biomedical engineering students track and analyze movements using a laptop camera or a connected mobile phone camera. The analysis can be performed in real-time or on recorded data, and various metrics and visualizations are provided.
### Features
- **Real-time movement tracking** using Mediapipe and OpenCV.
- **Capture video** from a laptop camera or a mobile phone camera.
- **Extract and track key points** of interest (e.g., ankles, knees, hips, shoulders, elbows, wrists, and center of gravity).
- **Save tracked data** to CSV files for further analysis.
- **Analyze movement data** with various analytical tools.
- **Calculate correlations** between movements.
- **Visualize correlation matrices** and skeleton heatmaps.
- **Multiple modes of operation**:
- **track**: Capture and track movements in real-time.
- **analyze**: Analyze saved movement data.
- **corr**: Compute and visualize correlations between movement datasets.
### Repository Structure
```bash
biomedical_workshops/
├── main.py
├── README.md
├── requirements.txt
└── src/
├── tracking.py
├── corr.py
└── analysis.py
```
### Installation
1. **Clone the repository**:
```bash
git clone https://github.com/manuelmariscal/biomedical_workshops.git
cd biomedical_workshops
```
2. **Create a virtual environment** and activate it:
```bash
python -m venv bioworkshops
# On Windows:
bioworkshops\Scripts\activate
# On Unix or MacOS:
source bioworkshops/bin/activate
```
3. **Install the required dependencies**:
```bash
pip install -r requirements.txt
```
### Usage
The tool operates in different modes: `track`, `analyze`, and `corr`. You can specify the mode using the `--mode` argument.
#### Tracking Mode (`track`)
To run the real-time movement tracking:
```bash
python main.py --mode track --source 0
```
Where `0` is the default source for the laptop camera. You can also use a URL or another device index for a mobile phone camera or an external camera.
#### Analysis Mode (`analyze`)
To analyze saved movement data:
```bash
python main.py --mode analyze --data_folder data
```
This mode processes the CSV files in the specified `data_folder` and performs analysis, including plotting movements and calculating metrics.
#### Correlation Mode (`corr`)
To compute and visualize correlations between movement datasets:
```bash
python main.py --mode corr --data_folder data
```
This mode processes the CSV files in the specified `data_folder`, computes correlation matrices between pairs of datasets, and visualizes the results, including skeleton heatmaps.
#### Arguments
- `--mode`: Mode of operation (`track`, `analyze`, or `corr`).
- `--source`: Video source (e.g., `0` for laptop camera, URL for mobile camera). Used only in `track` mode.
- `--data_folder`: Folder where CSV data files are stored. Used in `analyze` and `corr` modes.
### Data Analysis
The tool captures video data and extracts key points of interest, saving the results in CSV files within the specified `data_folder`. It provides various visualizations and analyses, depending on the mode:
1. **Tracking Mode (`track`)**:
- **Real-time skeleton movement**: Displays the real-time movement of the skeleton with tracked key points and lines connecting them.
- **Data Saving**: Saves the tracked data to CSV files for later analysis.
2. **Analysis Mode (`analyze`)**:
- **Movement Plots**: Visualizes the movements from the saved data.
- **Animations**: Creates animations comparing valid and invalid movements.
- **Correlation Calculations**: Computes correlations between movements.
3. **Correlation Mode (`corr`)**:
- **Correlation Matrices**: Generates and displays correlation matrices for each pair of movement datasets.
- **Skeleton Heatmaps**: Plots the skeleton with a heatmap based on average keypoint correlations.
- **Correct Orientation**: The skeleton is displayed with the correct orientation.
- **Enhanced Visualization**: Thicker lines and larger keypoints are used for better visibility.
- **Blue Color Map**: A blue color map is used for the heatmap.
- **Visualization of Results**: Both the correlation matrices and the skeleton heatmap are displayed simultaneously with appropriate titles.
### Example
To run the tool in `corr` mode and analyze data in the `data` folder:
```bash
python main.py --mode corr --data_folder data
```
### Contributing
Feel free to contribute to this project by opening issues or submitting pull requests. Please ensure your code follows the coding standards and includes tests where applicable.
### License
This project is licensed under the MIT License.
### Acknowledgments
This project uses the following libraries:
- [Mediapipe](https://google.github.io/mediapipe/)
- [OpenCV](https://opencv.org/)
- [NumPy](https://numpy.org/)
- [Pandas](https://pandas.pydata.org/)
- [Matplotlib](https://matplotlib.org/)
- [SciPy](https://www.scipy.org/)
---
For more information, please visit the [project repository](https://github.com/manuelmariscal/biomedical_workshops).