| from nnunetv2.nnsyn.nnsyn_preprocessing import nnsyn_plan_and_preprocess |
| from nnunetv2.nnsyn.nnsyn_preprocessing_seg import nnsyn_plan_and_preprocess_seg |
|
|
| def nnsyn_plan_and_preprocess_entry(): |
| import argparse |
| parser = argparse.ArgumentParser(description="nnUNet preprocessing for nnSyn") |
| parser.add_argument('-d', '--dataset_id', type=int, required=True, help="Dataset ID (will create DatasetXXX_<name> and DatasetXXX+1_<name> in nnUNet_raw and nnUNet_preprocessed)") |
| parser.add_argument('-c', '--configuration', type=str, default='3d_fullres', help="Configuration to preprocess (default: 3d_fullres)") |
| parser.add_argument('-pl', '--planner_class', type=str, default='ExperimentPlanner', help="Experiment planner class (default: nnUNetExperimentPlanner3D_v2)") |
| parser.add_argument('-p', '--plan', type=str, default='nnUNetPlans', help="Plan identifier (default: nnUNetPlans)") |
| parser.add_argument('--data_origin_path', type=str, required=True, help="Root path for nnUNet_raw and nnUNet_preprocessed (default: uses environment variables)") |
| parser.add_argument('--preprocessing_input', type=str, required=True, help="Preprocessing for input data (e.g., CT, MR, synthrad, etc.)") |
| parser.add_argument('--preprocessing_target', type=str, required=True, help="Preprocessing for target data (e.g., CT, MR, synthrad, etc.)") |
| parser.add_argument('--dataset_name', type=str, default=None, required=False, help="Name for input dataset (e.g., CT, MR, synthrad, etc.)") |
| parser.add_argument('--use_mask', action='store_true', default=False, help="Whether to use masks (default: False)") |
|
|
| args = parser.parse_args() |
|
|
| nnsyn_plan_and_preprocess( |
| data_origin_path=args.data_origin_path, |
| dataset_id=args.dataset_id, |
| dataset_name=args.dataset_name, |
| preprocessing_input=args.preprocessing_input, |
| preprocessing_target=args.preprocessing_target, |
| use_mask=args.use_mask, |
| configuration=args.configuration, |
| planner_class=args.planner_class, |
| plan=args.plan, |
| ) |
| |
| def nnsyn_plan_and_preprocess_seg_entry(): |
| import argparse |
| parser = argparse.ArgumentParser(description="nnUNet preprocessing for nnSyn") |
| parser.add_argument('-d', '--dataset_id', type=int, required=True, help="Dataset ID (will create DatasetXXX_<name> and DatasetXXX+1_<name> in nnUNet_raw and nnUNet_preprocessed)") |
| parser.add_argument('-ds', '--dataset_id_src', type=int, required=True, help="Source Dataset ID (will create DatasetXXX_<name> and DatasetXXX+1_<name> in nnUNet_raw and nnUNet_preprocessed)") |
| parser.add_argument('-c', '--configuration', type=str, default='3d_fullres', help="Configuration to preprocess (default: 3d_fullres)") |
| parser.add_argument('-p', '--plan', type=str, default='nnUNetPlans', help="Plan identifier (default: nnUNetPlans)") |
| parser.add_argument('--data_origin_path', type=str, required=True, help="Root path for nnUNet_raw and nnUNet_preprocessed (default: uses environment variables)") |
| parser.add_argument('--preprocessing_target', type=str, required=True, help="Preprocessing for target data (e.g., CT, MR, synthrad, etc.)") |
| parser.add_argument('--dataset_name', type=str, default=None, required=False, help="Name for input dataset (e.g., CT, MR, synthrad, etc.)") |
|
|
| args = parser.parse_args() |
|
|
| nnsyn_plan_and_preprocess_seg(data_origin_path='/datasets/work/hb-synthrad2023/work/synthrad2025/bw_workplace/data/nnunet_struct/ORIGIN/synthrad2025_task1_mri2ct_AB', |
| dataset_id=961, dataset_id_src=960, |
| preprocessing_target='CT', |
| configuration='3d_fullres', plan='nnUNetResEncUNetLPlans') |
| |
| |
| nnsyn_plan_and_preprocess_seg( |
| data_origin_path=args.data_origin_path, |
| dataset_id=args.dataset_id, |
| dataset_id_src=args.dataset_id_src, |
| dataset_name=args.dataset_name, |
| preprocessing_target=args.preprocessing_target, |
| configuration=args.configuration, |
| plan=args.plan, |
| ) |
| |
| |
| |
| |
| if __name__ == '__main__': |
| nnsyn_plan_and_preprocess_entry() |
|
|
| |
| |
