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hg_pancreas_eval_5_folds.sh
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hg_pancreas_eval_5_folds.sh
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#!/bin/bash
#SBATCH --job-name=pixel2cancer_pancreas
#SBATCH -N 1
#SBATCH -n 12
#SBATCH -G a100:2
##SBATCH --exclusive
#SBATCH --mem=150G
#SBATCH -p general
#SBATCH -t 7-00:00:00
#SBATCH -q public
#SBATCH -o %x_slurm_%j.out/pancreas
#SBATCH -e %xslurm_%j.err
#SBATCH --mail-type=ALL
#SBATCH [email protected]
module load mamba/latest
source activate pixel2cancer
# pip install torch==1.11.0+cu113 torchvision==0.12.0+cu113 torchaudio==0.11.0 --extra-index-url https://download.pytorch.org/whl/cu113
# pip install -r requirements.txt
# cd ./surface-distance
# pip install .
# cd ..
# cd ./Tumor_Synthesis/cellular
# python setup.py install
dist=$((RANDOM % 99999 + 10000))
datapath=/data/jliang12/zzhou82/datasets/PublicAbdominalData/
#pancreas Real
#pancreas Synthesis
if [ $1 == 'eval.synt.pancreas.fold0.no_pretrain.unet' ]; then
python -W ignore validation.py --model=unet --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_0.json --log_dir runs_pancreas/synt.pancreas.fold0.no_pretrain.unet --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold0.pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_0.json --log_dir runs_pancreas/synt.pancreas.fold0.pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold0.no_pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_0.json --log_dir runs_pancreas/synt.pancreas.fold0.no_pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold0.no_pretrain.swin_unetrv2_small' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=small --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_0.json --log_dir runs_pancreas/synt.pancreas.fold0.no_pretrain.swin_unetrv2_small --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold0.no_pretrain.swin_unetrv2_tiny' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=tiny --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_0.json --log_dir runs_pancreas/synt.pancreas.fold0.no_pretrain.swin_unetrv2_tiny --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold1.no_pretrain.unet' ]; then
python -W ignore validation.py --model=unet --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_1.json --log_dir runs_pancreas/synt.pancreas.fold1.no_pretrain.unet --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold1.pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_1.json --log_dir runs_pancreas/synt.pancreas.fold1.pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold1.no_pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_1.json --log_dir runs_pancreas/synt.pancreas.fold1.no_pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold1.no_pretrain.swin_unetrv2_small' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=small --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_1.json --log_dir runs_pancreas/synt.pancreas.fold1.no_pretrain.swin_unetrv2_small --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold1.no_pretrain.swin_unetrv2_tiny' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=tiny --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_1.json --log_dir runs_pancreas/synt.pancreas.fold1.no_pretrain.swin_unetrv2_tiny --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold2.no_pretrain.unet' ]; then
python -W ignore validation.py --model=unet --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_2.json --log_dir runs_pancreas/synt.pancreas.fold2.no_pretrain.unet --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold2.pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_2.json --log_dir runs_pancreas/synt.pancreas.fold2.pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold2.no_pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_2.json --log_dir runs_pancreas/synt.pancreas.fold2.no_pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold2.no_pretrain.swin_unetrv2_small' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=small --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_2.json --log_dir runs_pancreas/synt.pancreas.fold2.no_pretrain.swin_unetrv2_small --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold2.no_pretrain.swin_unetrv2_tiny' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=tiny --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_2.json --log_dir runs_pancreas/synt.pancreas.fold2.no_pretrain.swin_unetrv2_tiny --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold3.no_pretrain.unet' ]; then
python -W ignore validation.py --model=unet --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_3.json --log_dir runs_pancreas/synt.pancreas.fold3.no_pretrain.unet --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold3.pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_3.json --log_dir runs_pancreas/synt.pancreas.fold3.pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold3.no_pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_3.json --log_dir runs_pancreas/synt.pancreas.fold3.no_pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold3.no_pretrain.swin_unetrv2_small' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=small --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_3.json --log_dir runs_pancreas/synt.pancreas.fold3.no_pretrain.swin_unetrv2_small --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold3.no_pretrain.swin_unetrv2_tiny' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=tiny --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_3.json --log_dir runs_pancreas/synt.pancreas.fold3.no_pretrain.swin_unetrv2_tiny --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold4.no_pretrain.unet' ]; then
python -W ignore validation.py --model=unet --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_4.json --log_dir runs_pancreas/synt.pancreas.fold4.no_pretrain.unet --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold4.pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_4.json --log_dir runs_pancreas/synt.pancreas.fold4.pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold4.no_pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_4.json --log_dir runs_pancreas/synt.pancreas.fold4.no_pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold4.no_pretrain.swin_unetrv2_small' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=small --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_4.json --log_dir runs_pancreas/synt.pancreas.fold4.no_pretrain.swin_unetrv2_small --save_dir out/pancreas
elif [ $1 == 'eval.synt.pancreas.fold4.no_pretrain.swin_unetrv2_tiny' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=tiny --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_4.json --log_dir runs_pancreas/synt.pancreas.fold4.no_pretrain.swin_unetrv2_tiny --save_dir out/pancreas
fi
# real
if [ $1 == 'eval.real.pancreas.fold0.no_pretrain.unet' ]; then
python -W ignore validation.py --model=unet --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_0.json --log_dir runs_pancreas/real.pancreas.fold0.no_pretrain.unet --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold0.pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_0.json --log_dir runs_pancreas/real.pancreas.fold0.pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold0.no_pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_0.json --log_dir runs_pancreas/real.pancreas.fold0.no_pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold0.no_pretrain.swin_unetrv2_small' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=small --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_0.json --log_dir runs_pancreas/real.pancreas.fold0.no_pretrain.swin_unetrv2_small --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold0.no_pretrain.swin_unetrv2_tiny' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=tiny --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_0.json --log_dir runs_pancreas/real.pancreas.fold0.no_pretrain.swin_unetrv2_tiny --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold1.no_pretrain.unet' ]; then
python -W ignore validation.py --model=unet --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_1.json --log_dir runs_pancreas/real.pancreas.fold1.no_pretrain.unet --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold1.pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_1.json --log_dir runs_pancreas/real.pancreas.fold1.pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold1.no_pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_1.json --log_dir runs_pancreas/real.pancreas.fold1.no_pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold1.no_pretrain.swin_unetrv2_small' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=small --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_1.json --log_dir runs_pancreas/real.pancreas.fold1.no_pretrain.swin_unetrv2_small --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold1.no_pretrain.swin_unetrv2_tiny' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=tiny --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_1.json --log_dir runs_pancreas/real.pancreas.fold1.no_pretrain.swin_unetrv2_tiny --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold2.no_pretrain.unet' ]; then
python -W ignore validation.py --model=unet --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_2.json --log_dir runs_pancreas/real.pancreas.fold2.no_pretrain.unet --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold2.pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_2.json --log_dir runs_pancreas/real.pancreas.fold2.pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold2.no_pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_2.json --log_dir runs_pancreas/real.pancreas.fold2.no_pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold2.no_pretrain.swin_unetrv2_small' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=small --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_2.json --log_dir runs_pancreas/real.pancreas.fold2.no_pretrain.swin_unetrv2_small --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold2.no_pretrain.swin_unetrv2_tiny' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=tiny --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_2.json --log_dir runs_pancreas/real.pancreas.fold2.no_pretrain.swin_unetrv2_tiny --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold3.no_pretrain.unet' ]; then
python -W ignore validation.py --model=unet --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_3.json --log_dir runs_pancreas/real.pancreas.fold3.no_pretrain.unet --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold3.pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_3.json --log_dir runs_pancreas/real.pancreas.fold3.pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold3.no_pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_3.json --log_dir runs_pancreas/real.pancreas.fold3.no_pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold3.no_pretrain.swin_unetrv2_small' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=small --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_3.json --log_dir runs_pancreas/real.pancreas.fold3.no_pretrain.swin_unetrv2_small --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold3.no_pretrain.swin_unetrv2_tiny' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=tiny --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_3.json --log_dir runs_pancreas/real.pancreas.fold3.no_pretrain.swin_unetrv2_tiny --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold4.no_pretrain.unet' ]; then
python -W ignore validation.py --model=unet --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_4.json --log_dir runs_pancreas/real.pancreas.fold4.no_pretrain.unet --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold4.pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_4.json --log_dir runs_pancreas/real.pancreas.fold4.pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold4.no_pretrain.swin_unetrv2_base' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=base --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_4.json --log_dir runs_pancreas/real.pancreas.fold4.no_pretrain.swin_unetrv2_base --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold4.no_pretrain.swin_unetrv2_small' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=small --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_4.json --log_dir runs_pancreas/real.pancreas.fold4.no_pretrain.swin_unetrv2_small --save_dir out/pancreas
elif [ $1 == 'eval.real.pancreas.fold4.no_pretrain.swin_unetrv2_tiny' ]; then
python -W ignore validation.py --model=swin_unetrv2 --swin_type=tiny --val_overlap=0.75 --val_dir $datapath --json_dir datafolds/5_fold/pancreas/pancreas_tumor_4.json --log_dir runs_pancreas/real.pancreas.fold4.no_pretrain.swin_unetrv2_tiny --save_dir out/pancreas
fi