- CUDA>=11.0
- PyTorch>=2.0
For other system requirements please follow
pip install -r requirements.txt
cd ./models/ops
python setup.py install
Please download Synthetic Vessel dataset and organize them as following:
code_root/
└── data/
└── vessel_data/
├── raw/
├── seg/
└── vtk/
After downloading the dataset run the following script to preprocess and prepare the data for training
python generate_data.py
The config file can be found at .configs/synth_3D.yaml
. Make custom changes if necessary.
For example, the command for training VesselFormer is following:
python train.py --config configs/synth_3D.yaml --cuda_visible_device 0 1 2 --nproc_per_node 3
Once you have the config file and trained model, run following command to evaluate it on test set:
python vesselformer_inference.py --config configs/synth_3D.yaml --model ./trained_weights/last_checkpoint.pt --eval
Please find the vesselmerger_inference.ipynb
for interactive visualization for vesselmerger algorithm