- python 3.7 virtual environment https://docs.hpc.ut.ee/cluster/python_envs/. Install all requirements
pip install -r requirements.txt
- Running HPC with gpu: Use
TransUNet/start_*.sh
scripts. - To execute job in HPC:
sbatch start_*.sh
. To monitor the executiontail -f slurm-*.out
- Testing logs (and performance measures DICE/pixel-wise F1, HD95) available in
TransUNet/test_log
.
Branches:
- master - Initial model with cropping
- additional_CNN - additional CNN or ResNet to bottleneck changes
- resnet_skip - additional skip-connection from ResNet hidden features to bottleneck
- transformer-to-skip - moving transformers from encoder to skip-connection.
Initial architecture source code repo: https://github.com/Beckschen/TransUNet