| imports: | |
| - "$import glob" | |
| - "$import json" | |
| - "$import os" | |
| - "$from scripts.compute_metric import compute_abdominal_ct_metrics" | |
| - "$from scripts.compute_metric import compute" | |
| workflow_type: evaluate | |
| spatial_dims: "$len(@spatial_size)" | |
| bundle_root: "." | |
| output_dir: "$@bundle_root + '/eval/dynunet_FT_trt_32'" | |
| dataset_dir: "/processed/Public/CT_TotalSegmentator/TS_split/test/" | |
| data_list_file_path: "$@bundle_root + '/configs/TS_test.json'" | |
| datalist: "$monai.data.load_decathlon_datalist(@data_list_file_path, data_list_key='validation')" | |
| datalist_pred: "$[{**d, 'pred': os.path.join(@output_dir, d['label'].split('/')[-1].split('.')[0] + '_trans.nii.gz')} for d in @datalist]" | |
| run: | |
| #- "$compute_abdominal_ct_metrics(@datalist_pred, @output_dir)" | |
| - "$compute(@datalist_pred, @output_dir)" | |