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- import os
- import shutil
-
-
- origin_path = "/home/data2/wan/prostate158_resampled"
- nnUNet_raw_data_path = "/home/data2/wan/picai_nnunetv2/nnUNet_raw"
- os.makedirs(nnUNet_raw_data_path, exist_ok=True)
- task_path = os.path.join(nnUNet_raw_data_path, "Dataset610_Prostate158")
- os.makedirs(task_path, exist_ok=True)
- dst_imagesTr_path = os.path.join(task_path, "imagesTr")
- os.makedirs(dst_imagesTr_path, exist_ok=True)
- dst_labelsTr_path = os.path.join(task_path, "labelsTr")
- os.makedirs(dst_labelsTr_path, exist_ok=True)
- dst_imagesTs_path = os.path.join(task_path, "imagesTs")
- os.makedirs(dst_imagesTs_path, exist_ok=True)
- dst_labelsTs_path = os.path.join(task_path, "labelsTs")
- os.makedirs(dst_labelsTs_path, exist_ok=True)
-
- count = 0
- for case_id in sorted(os.listdir(origin_path)):
- origin_case_dir = os.path.join(origin_path, case_id)
- if "empty.nii.gz" in os.listdir(origin_case_dir):
- continue
- else:
- count += 1
- for modality in sorted(os.listdir(origin_case_dir)):
- if modality == "t2.nii.gz":
- origin_image_path = os.path.join(origin_case_dir, modality)
- dst_image_name = "Prostate158_" + case_id + "_" + "0000.nii.gz"
- dst_image_path = os.path.join(dst_imagesTr_path, dst_image_name)
- shutil.copy(origin_image_path, dst_image_path)
- elif modality == "adc.nii.gz":
- origin_image_path = os.path.join(origin_case_dir, modality)
- dst_image_name = "Prostate158_" + case_id + "_" + "0001.nii.gz"
- dst_image_path = os.path.join(dst_imagesTr_path, dst_image_name)
- shutil.copy(origin_image_path, dst_image_path)
- elif modality == "dwi.nii.gz":
- origin_image_path = os.path.join(origin_case_dir, modality)
- dst_image_name = "Prostate158_" + case_id + "_" + "0002.nii.gz"
- dst_image_path = os.path.join(dst_imagesTr_path, dst_image_name)
- shutil.copy(origin_image_path, dst_image_path)
- elif modality == "adc_tumor_reader1.nii.gz":
- origin_label_path = os.path.join(origin_case_dir, modality)
- dst_label_name = "Prostate158_" + case_id + ".nii.gz"
- dst_label_path = os.path.join(dst_labelsTr_path, dst_label_name)
- shutil.copy(origin_label_path, dst_label_path)
-
- print(count)
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