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import shutil |
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from batchgenerators.utilities.file_and_folder_operations import * |
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from nnunet.paths import nnUNet_raw_data |
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if __name__ == "__main__": |
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""" |
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Nick asked me to rerun the training with other labels (the Kidney region is defined differently). |
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These labels operate in interpolated spacing. I don't like that but that's how it is |
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""" |
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base = "/media/fabian/My Book/datasets/KiTS_NicksLabels/kits19/data" |
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labelsdir = "/media/fabian/My Book/datasets/KiTS_NicksLabels/filled_labels" |
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task_id = 65 |
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task_name = "KiTS_NicksLabels" |
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foldername = "Task%03.0d_%s" % (task_id, task_name) |
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out_base = join(nnUNet_raw_data, foldername) |
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imagestr = join(out_base, "imagesTr") |
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imagests = join(out_base, "imagesTs") |
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labelstr = join(out_base, "labelsTr") |
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maybe_mkdir_p(imagestr) |
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maybe_mkdir_p(imagests) |
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maybe_mkdir_p(labelstr) |
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train_patient_names = [] |
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test_patient_names = [] |
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all_cases = subfolders(base, join=False) |
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train_patients = all_cases[:210] |
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test_patients = all_cases[210:] |
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for p in train_patients: |
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curr = join(base, p) |
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label_file = join(labelsdir, p + ".nii.gz") |
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image_file = join(curr, "imaging.nii.gz") |
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shutil.copy(image_file, join(imagestr, p + "_0000.nii.gz")) |
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shutil.copy(label_file, join(labelstr, p + ".nii.gz")) |
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train_patient_names.append(p) |
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for p in test_patients: |
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curr = join(base, p) |
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image_file = join(curr, "imaging.nii.gz") |
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shutil.copy(image_file, join(imagests, p + "_0000.nii.gz")) |
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test_patient_names.append(p) |
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json_dict = {} |
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json_dict['name'] = "KiTS" |
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json_dict['description'] = "kidney and kidney tumor segmentation" |
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json_dict['tensorImageSize'] = "4D" |
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json_dict['reference'] = "KiTS data for nnunet" |
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json_dict['licence'] = "" |
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json_dict['release'] = "0.0" |
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json_dict['modality'] = { |
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"0": "CT", |
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} |
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json_dict['labels'] = { |
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"0": "background", |
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"1": "Kidney", |
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"2": "Tumor" |
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} |
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json_dict['numTraining'] = len(train_patient_names) |
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json_dict['numTest'] = len(test_patient_names) |
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json_dict['training'] = [{'image': "./imagesTr/%s.nii.gz" % i.split("/")[-1], "label": "./labelsTr/%s.nii.gz" % i.split("/")[-1]} for i in |
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train_patient_names] |
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json_dict['test'] = ["./imagesTs/%s.nii.gz" % i.split("/")[-1] for i in test_patient_names] |
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save_json(json_dict, os.path.join(out_base, "dataset.json")) |
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