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057ec4b | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | #!/bin/bash
# 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
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