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| import shutil | |
| from batchgenerators.utilities.file_and_folder_operations import * | |
| from nnunetv2.paths import nnUNet_raw | |
| from nnunetv2.dataset_conversion.generate_dataset_json import generate_dataset_json | |
| if __name__ == '__main__': | |
| downloaded_amos_dir = '/home/isensee/amos22/amos22' # downloaded and extracted from https://zenodo.org/record/7155725#.Y0OOCOxBztM | |
| target_dataset_id = 223 | |
| target_dataset_name = f'Dataset{target_dataset_id:3.0f}_AMOS2022postChallenge' | |
| maybe_mkdir_p(join(nnUNet_raw, target_dataset_name)) | |
| imagesTr = join(nnUNet_raw, target_dataset_name, 'imagesTr') | |
| imagesTs = join(nnUNet_raw, target_dataset_name, 'imagesTs') | |
| labelsTr = join(nnUNet_raw, target_dataset_name, 'labelsTr') | |
| maybe_mkdir_p(imagesTr) | |
| maybe_mkdir_p(imagesTs) | |
| maybe_mkdir_p(labelsTr) | |
| train_identifiers = [] | |
| # copy images | |
| source = join(downloaded_amos_dir, 'imagesTr') | |
| source_files = nifti_files(source, join=False) | |
| train_identifiers += source_files | |
| for s in source_files: | |
| shutil.copy(join(source, s), join(imagesTr, s[:-7] + '_0000.nii.gz')) | |
| source = join(downloaded_amos_dir, 'imagesVa') | |
| source_files = nifti_files(source, join=False) | |
| train_identifiers += source_files | |
| for s in source_files: | |
| shutil.copy(join(source, s), join(imagesTr, s[:-7] + '_0000.nii.gz')) | |
| source = join(downloaded_amos_dir, 'imagesTs') | |
| source_files = nifti_files(source, join=False) | |
| for s in source_files: | |
| shutil.copy(join(source, s), join(imagesTs, s[:-7] + '_0000.nii.gz')) | |
| # copy labels | |
| source = join(downloaded_amos_dir, 'labelsTr') | |
| source_files = nifti_files(source, join=False) | |
| for s in source_files: | |
| shutil.copy(join(source, s), join(labelsTr, s)) | |
| source = join(downloaded_amos_dir, 'labelsVa') | |
| source_files = nifti_files(source, join=False) | |
| for s in source_files: | |
| shutil.copy(join(source, s), join(labelsTr, s)) | |
| old_dataset_json = load_json(join(downloaded_amos_dir, 'dataset.json')) | |
| new_labels = {v: k for k, v in old_dataset_json['labels'].items()} | |
| generate_dataset_json(join(nnUNet_raw, target_dataset_name), {0: 'nonCT'}, new_labels, | |
| num_training_cases=len(train_identifiers), file_ending='.nii.gz', regions_class_order=None, | |
| dataset_name=target_dataset_name, reference='https://zenodo.org/record/7155725#.Y0OOCOxBztM', | |
| license=old_dataset_json['licence'], # typo in OG dataset.json | |
| description=old_dataset_json['description'], | |
| release=old_dataset_json['release']) | |