Rx2Gantt

Rx2Gantt is a Python-based project designed to streamline the process of extracting, processing, and visualizing medication-related data from PDF files. It processes medical prescription records from Taipei Veterans General Hospital to generate structured summaries and visual Gantt charts for clear, timeline-based insights into medication usage.

Features

• PDF Data Extraction: Extracts prescription details from PDF files.
• Data Cleaning and Processing: Cleans and preprocesses extracted data, including handling dates, merging rows, and standardizing drug names.
• Drug Classification: Enriches the data with drug classifications such as MOA (Mechanism of Action), EPC (Established Pharmacologic Class), and PE (Physiologic Effect) via the RxNav API.
• Gantt Chart Visualization: Creates a detailed Gantt chart showing medication timelines, dosages, and frequencies.

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Installation

1. Clone the repository:

   git clone https://github.com/jimchen1551/Rx2Gantt.git
   cd Rx2Gantt

2. Install the required dependencies:

   pip install -r requirements.txt

3. Update the configuration:

   • Open config.py and update the INPUT_FOLDER variable to point to the directory containing your PDF files.

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Usage

1. Place your PDF files in the folder specified in the INPUT_FOLDER variable.

2. Run the project:

   python main.py

3. Outputs:

   • CSV File: A summary CSV file for each PDF, saved in the summary folder within the same directory as the input PDF.
   • Gantt Chart: A visual representation of the medication timeline, saved as a PNG file in the gantt folder.

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File Structure

Rx2Gantt/
├── examples              # Examples for ouput files
├── config.py             # Configuration settings
├── main.py               # Main entry point for the program
├── pdf_processor.py      # PDF extraction logic
├── data_cleaner.py       # Data cleaning and preprocessing logic
├── drug_classifier.py    # Drug classification using RxNav API
├── gantt_visualizer.py   # Gantt chart visualization logic
├── requirements.txt      # Python dependencies
└── README.md             # Project documentation

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Configuration

The config.py file contains customizable settings, including:

• Input Folder: The directory containing PDF files to process.
• Column Boundaries: x-coordinate boundaries for column detection in PDFs.
• RxNav API URL: Base URL for drug classification.
• Logging Level: Adjust logging verbosity (default: INFO).
• Chart Color Scheme: Matplotlib color scheme for the Gantt chart.

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Dependencies

• Python 3.8 or higher
• fitz (PyMuPDF) for PDF processing
• pandas for data handling
• matplotlib for Gantt chart visualization
• requests for RxNav API calls

Install dependencies with:

pip install -r requirements.txt

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Example Output

CSV Summary

A sample CSV output includes enriched data with classifications:

Drug name, EPC, MOA, PE, DDI, SE
Aspirin, Cyclooxygenase Inhibitor, Platelet Aggregation Inhibition, Analgesic Effect, , 

Gantt Chart

The Gantt chart visually displays medication timelines, highlighting:

• Start and stop dates of each medication
• Dosage and frequency annotations

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Contributing

We welcome contributions! To contribute:

1. Fork the repository.
2. Create a feature branch: git checkout -b feature-name.
3. Commit your changes: git commit -m "Add new feature".
4. Push to the branch: git push origin feature-name.
5. Open a pull request.

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License

This project is licensed under the MIT License. See the LICENSE file for details.

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Acknowledgments

• RxNav API: https://rxnav.nlm.nih.gov
• Matplotlib for charting

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Contact

For questions or feedback, please open an issue on the repository or contact the project maintainer.