diff --git a/nnunetv2/dataset_conversion/Dataset021_CTAAorta.py b/nnunetv2/dataset_conversion/Dataset021_CTAAorta.py new file mode 100644 index 000000000..3fa581f31 --- /dev/null +++ b/nnunetv2/dataset_conversion/Dataset021_CTAAorta.py @@ -0,0 +1,71 @@ +from batchgenerators.utilities.file_and_folder_operations import * +import shutil +from nnunetv2.dataset_conversion.generate_dataset_json import generate_dataset_json +from nnunetv2.paths import nnUNet_raw +import SimpleITK as sitk + + +if __name__ == '__main__': + """ + + """ + # extracted traiing.zip file is here + base = '/home/isensee/Downloads/' + target_dataset_id = 21 + target_dataset_name = f'Dataset{target_dataset_id:03.0f}_CTAAorta' + + maybe_mkdir_p(join(nnUNet_raw, target_dataset_name)) + imagesTr = join(nnUNet_raw, target_dataset_name, 'imagesTr') + labelsTr = join(nnUNet_raw, target_dataset_name, 'labelsTr') + maybe_mkdir_p(imagesTr) + maybe_mkdir_p(labelsTr) + + cases = subfiles(join(base, 'images'), join=False, prefix='subject') + for case in cases: + outname = case.replace('_CTA.mha', '') + im = sitk.ReadImage(join(base, 'images', case)) + sitk.WriteImage(im, join(imagesTr, outname + '_0000.nii.gz')) + + seg = sitk.ReadImage(join(base, 'masks', case.replace('_CTA.mha', '_label.mha'))) + sitk.WriteImage(seg, join(labelsTr, outname + '.nii.gz')) + + labels = { + "background": 0, + "Zone_0": 1, + "Innominate": 2, + "Zone_1": 3, + "Left_Common_Carotid": 4, + "Zone_2": 5, + "Left_Subclavian_Artery": 6, + "Zone_3": 7, + "Zone_4": 8, + "Zone_5": 9, + "Zone_6": 10, + "Celiac_Artery": 11, + "Zone_7": 12, + "SMA": 13, + "Zone_8": 14, + "Right_Renal_Artery": 15, + "Left_Renal_Artery": 16, + "Zone_9": 17, + "Zone_10_R_(Right_Common_Iliac_Artery)": 18, + "Zone_10_L_(Left_Common_Iliac_Artery)": 19, + "Right_Internal_Iliac_Artery_Dice_Score": 20, + "Left_Internal_Iliac_Artery_Dice_Score": 21, + "Zone_11_R_(Right_External_Iliac_Artery)": 22, + "Zone_11_L_(Left_External_Iliac_Artery)": 23 + } + + + generate_dataset_json( + join(nnUNet_raw, target_dataset_name), + {0: 'CT'}, + labels, + len(cases), + '.nii.gz', + None, + target_dataset_name, + overwrite_image_reader_writer='NibabelIOWithReorient', + reference='https://aortaseg24.grand-challenge.org/', + license='see ref' + ) \ No newline at end of file