| # Preprocess pannuke fold02 (d11) + fold03 (d12) for BOTH nnU-Net and U-Mamba | |
| # (separate preprocessed dirs, separate envs), CPU-only, thread-capped. Copies the | |
| # fixed splits into each preprocessed dataset. | |
| set -u | |
| cd /home/wzhang/LSC/Code/NPJ | |
| source /opt/anaconda3/etc/profile.d/conda.sh | |
| RAW=/home/wzhang/LSC/Code/NPJ/nnunet_workspace/raw | |
| export OMP_NUM_THREADS=4 MKL_NUM_THREADS=4 OPENBLAS_NUM_THREADS=4 | |
| ( conda activate nnunet | |
| export nnUNet_raw=$RAW | |
| export nnUNet_preprocessed=/home/wzhang/LSC/Code/NPJ/nnunet_workspace/preprocessed_nnunet | |
| export nnUNet_results=/home/wzhang/LSC/Code/NPJ/nnunet_workspace/results_nnunet | |
| for id in 11 12; do | |
| nnUNetv2_plan_and_preprocess -d "$id" -c 2d -np 12 > "nnunet_workspace/pp_nnunet_d${id}.log" 2>&1 | |
| name=$(basename "$(ls -d $RAW/Dataset0${id}_*)") | |
| cp "$RAW/$name/splits_final.json" "$nnUNet_preprocessed/$name/splits_final.json" | |
| echo "nnunet d$id preprocessed ($name)" | |
| done ) & | |
| ( conda activate umamba | |
| export nnUNet_raw=$RAW | |
| export nnUNet_preprocessed=/home/wzhang/LSC/Code/NPJ/nnunet_workspace/preprocessed_umamba | |
| export nnUNet_results=/home/wzhang/LSC/Code/NPJ/nnunet_workspace/results_umamba | |
| for id in 11 12; do | |
| nnUNetv2_plan_and_preprocess -d "$id" -c 2d -np 12 > "nnunet_workspace/pp_umamba_d${id}.log" 2>&1 | |
| name=$(basename "$(ls -d $RAW/Dataset0${id}_*)") | |
| cp "$RAW/$name/splits_final.json" "$nnUNet_preprocessed/$name/splits_final.json" | |
| echo "umamba d$id preprocessed ($name)" | |
| done ) & | |
| wait | |
| echo PANNUKE_PP_DONE | |