move itk to io

nndet/inference/predictor.py

@@ -29,7 +29,7 @@ from nndet.io.load import save_pickle
 from nndet.arch.abstract import AbstractModel
 from nndet.io.transforms import NoOp
 from nndet.io.transforms.base import AbstractTransform
-from nndet.inference.patching import save_get_crop, create_grid
+from nndet.io.patching import save_get_crop, create_grid
 from nndet.utils import to_device, maybe_verbose_iterable
 
 

nndet/io/datamodule/bg_loader.py

@@ -25,7 +25,7 @@ from batchgenerators.dataloading import SlimDataLoaderBase
 
 from nndet.io.datamodule import DATALOADER_REGISTRY
 from nndet.io.load import load_pickle
-from nndet.inference.patching import save_get_crop
+from nndet.io.patching import save_get_crop
 from nndet.utils.info import maybe_verbose_iterable
 from nndet.core.boxes.ops_np import box_size_np
 

nndet/utils/itk.py → nndet/io/itk.py

@@ -84,6 +84,7 @@ def copy_meta_data_itk(source: sitk.Image, target: sitk.Image) -> sitk.Image:
     """
     # for i in source.GetMetaDataKeys():
     #     target.SetMetaData(i, source.GetMetaData(i))
+    raise NotImplementedError("Does not work!")
     target.SetOrigin(source.GetOrigin())
     target.SetDirection(source.GetDirection())
     target.SetSpacing(source.GetSpacing())

nndet/planning/experiment/utils.py

@@ -7,7 +7,7 @@ from itertools import repeat
 from multiprocessing import Pool
 from typing import Dict
 
-from nndet.utils.itk import load_sitk_as_array
+from nndet.io.itk import load_sitk_as_array
 from nndet.io.load import load_json, load_pickle
 from nndet.io.paths import get_case_ids_from_dir
 from nndet.io.transforms.instances import (

nndet/utils/nnunet.py

@@ -21,11 +21,11 @@ from multiprocessing import Pool
 
 import SimpleITK as sitk
 import numpy as np
-from nndet.utils.itk import load_sitk_as_array, load_sitk
 from loguru import logger
 from pathlib import Path
 from typing import Sequence, Union
 
+from nndet.io.itk import load_sitk_as_array, load_sitk
 from nndet.io.load import save_json, load_json
 from nndet.io.paths import get_case_ids_from_dir
 from nndet.io.prepare import sitk_copy_metadata

scripts/convert_seg2det.py

@@ -33,8 +33,8 @@ from tqdm import tqdm
 from nndet.core.boxes import box_size_np
 from nndet.io import get_case_ids_from_dir, load_json, save_json
 from nndet.io.transforms.instances import get_bbox_np
+from nndet.io.itk import copy_meta_data_itk, load_sitk, load_sitk_as_array
 from nndet.utils.config import compose
-from nndet.utils.itk import copy_meta_data_itk, load_sitk, load_sitk_as_array
 
 
 def prepare_detection_label(case_id: str,