open-kbp

This repository provides the code for the PyTorch implementation of the open-kbp, and here is the original paper.

Data

The details of the provided data are available in the paper OpenKBP: The open-access knowledge-based planning grand challenge and dataset. In short, it provides data for 340 patients who were treated for head-and-neck cancer with intensity modulated radiation therapy. The data is split into training (n=200), validation (n=40), and testing (n=100) sets. Every patient in these datasets has a dose distribution, CT images, structure masks, a feasible dose mask (i.e., mask of where dose can be non-zero), and voxel dimensions.

For running on a local machine

• Linux
• Python 3.10.9, Torch 2.7.1
• Nvidia GeForce RTX 3090 GPU

Created folder structure

This repository will create a file structure that branches from a directory called open-kbp. The file structure will keep information about predictions from a model (called baseline in this example) and the model itself in the results directory. All the data from the OpenKBP competition (with the original train/validation/test splits) is available under the directory called provided-data. This code will also make a directory called submissions to house the zip files that can be submitted to the leader boards on CodaLab. Use this folder tree as a reference (it will more or less build itself).

open-kbp
├── provided-data
│   ├── train-pats
│   │   ├── pt_*
│   │       ├── *.csv
│   ├── valid-pats
│   │   ├── pt_*
│   │       ├── *.csv
│   └── test-pats
│       ├── pt_*
│           ├── *.csv
├── results
│   ├── baseline
│   │   ├── models
│   │   │   ├── epoch_*.pt
│   │   ├── validation-predictions
│   │   │   ├── pt_*.csv
│   │   └── test-predictions
│   │       ├── pt_*.csv
│   ├── **Structure repeats when new model is made**
└── submissions
    ├── baseline.zip
    ├── **Structure repeats when new model is made**   

Creating the virtual environment

conda create -n open-kbp python=3.10.9
conda activate open-kbp

Getting the code

git clone https://github.com/bravePinocchio/open-kbp
cd open-kbp
pip install -r requirements.txt

Running the code

CUDA_VISIBLE_DEVICES=0 python main.py