Training code for PGPS/PGPS+/RPSS can be found in directory:
- ./training/nnUNetTrainer/variants/sampling/nnUNetTrainer_PGPS.py
- ./training/nnUNetTrainer/variants/sampling/nnUNetTrainer_PGPS+.py
- ./training/nnUNetTrainer/variants/sampling/nnUNetTrainer_RPSS.py
For using the code, please install nnUNet from https://github.com/MIC-DKFZ/nnUNet according to their documentation. After that you can copy the training code plus a plans handler file from THIS github repo into the python site-package nnUNetv2 installation folder:
- ./training/nnUNetTrainer/variants/sampling/nnUNetTrainer_PGPS.py
- ./training/nnUNetTrainer/variants/sampling/nnUNetTrainer_PGPS+.py
- ./training/nnUNetTrainer/variants/sampling/nnUNetTrainer_RPSS.py
- ./utilities/plans_handling/plans_handler.py
Do training as standard nnUNet as specified here: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/how_to_use_nnunet.md The only difference is to specifiy the PGPS/PGPS+/RPSS trainer:
# for PGPS
nnUNetv2_train DATASET_NAME_OR_ID 3d_fullres FOLD -tr nnUNetTrainer_PGPS
# for PGPS+
nnUNetv2_train DATASET_NAME_OR_ID 3d_fullres FOLD -tr nnUNetTrainer_PGPS+
# for RPSS
nnUNetv2_train DATASET_NAME_OR_ID 3d_fullres FOLD -tr nnUNetTrainer_RPSS
uncomment codecarbon parts if you do not want to track C02-equivalents! \ For more information about codecarbon check their website: https://mlco2.github.io/codecarbon/installation.html