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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'])
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