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#!/bin/bash -l |
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while getopts ":m:d:" opt; do |
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case $opt in |
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m) model="$OPTARG";; |
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d) data="$OPTARG";; |
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*) echo "Unknown error occurred." |
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exit 1;; |
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esac |
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done |
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export data_raw=$data |
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export nnUNet_raw_data_base=$data_raw'/data_nnUNet_preprocessed/NIFTI/' |
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export nnUNet_preprocessed=$data_raw'/data_nnUNet_preprocessed/' |
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export RESULTS_FOLDER=$data_raw'/calvingfronts/' |
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python3 nnunet/dataset_conversion/Task500_Glacier_inference.py -data_percentage 100 -base $data_raw |
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python3 nnunet/inference/predict_simple.py -i $nnUNet_raw_data_base'nnUNet_raw_data/Task500_Glacier_zonefronts/imagesTs/' -o $RESULTS_FOLDER/fold_0 -t 500 -m 2d -f 0 -p nnUNetPlansv2.1 -tr nnUNetTrainerV2 -model_folder_name $model |
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python3 nnunet/dataset_conversion/Task500_Glacier_reverse.py -i $RESULTS_FOLDER'fold_0/' |
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