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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,
)
# example usage:
# python -m nnsyn_plan_and_preprocess_entry -d 982 -c 3d_fullres -pl nnUNetPlannerResEncL -p nnUNetResEncUNetLPlans --data_origin_path '/datasets/work/hb-synthrad2023/work/synthrad2025/bw_workplace/data/nnunet_struct/ORIGIN/Synthrad2025_MRI2CT_AB' --preprocessing_input MR --preprocessing_target CT
# nnsyn_plan_and_preprocess -d 960 -c 3d_fullres -pl nnUNetPlannerResEncL -p nnUNetResEncUNetLPlans --data_origin_path '/datasets/work/hb-synthrad2023/work/synthrad2025/bw_workplace/data/nnunet_struct/ORIGIN/Synthrad2025_MRI2CT_AB' --preprocessing_input MR --preprocessing_target CT
if __name__ == '__main__':
nnsyn_plan_and_preprocess_entry()
# example usage:
# python -m nnsyn_plan_and_preprocess_seg_entry -d 961 -ds 960 -c 3d_fullres -p nnUNetResEncUNetLPlans --data_origin_path '/datasets/work/hb-synthrad2023/work/synthrad2025/bw_workplace/data/nnunet_struct/ORIGIN/synthrad2025_task1_mri2ct_AB' --preprocessing_target CT |