set -e

echo "Start post-process masks"
python p_processing.py \
    --input_dir ./nnUNet_predictions \
    --output_dir ./nnUNet_predictions \
    --rules "6:1,7:2|3,8:4,9:5" \
    --keep_mode any \
    --target_labels "6,7,8,9" \
    --min_size 25 \
    --dilation_iters 1 \
    --connectivity 26 \
    --num_workers 16
echo "Post-processing finished"

echo "Start organize into BDMAP format"
python masks_BDMAP.py \
    --source_dir ./nnUNet_predictions \
    --output_dir ./nnUNet_predictions_BDMAP

echo "Organization finished"