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| import os | |
| import numpy as np | |
| import nrrd | |
| from image_function_save_png_hist import load_volume, save_volume, pad_image, pad_image_3D | |
| import re | |
| def load_nrrd_file(nrrd_path): | |
| data, header = nrrd.read(nrrd_path) | |
| return data, header | |
| def save_nrrd_file(data, header, save_path): | |
| nrrd.write(save_path, data, header) | |
| def extract_liver_region(nrrd_path1, save_path): | |
| data1, headeroraffine = load_volume(nrrd_path1) | |
| # 将灰度值为5的部分保留并设为1，其他部分设为0，假设5为肝脏区域的标签 | |
| data1 = np.where(np.isclose(data1, 5, atol=1e-6), 1, 0).astype(np.uint8) | |
| #print(data1.shape) | |
| data1 = pad_image_3D(data1, [512,512, None], 0) | |
| #print(data1.shape) | |
| save_volume(data1, save_path, output_format='nii.gz', affine=headeroraffine) | |
| def main(folder1, output_folder): | |
| if not os.path.exists(output_folder): | |
| os.makedirs(output_folder) | |
| files1 = set(os.listdir(folder1)) | |
| for filename in files1: | |
| if filename.endswith(".nrrd") or filename.endswith(".nii.gz") or filename.endswith(".nii") : | |
| nrrd_path1 = os.path.join(folder1, filename) | |
| # Define the pattern for the patient ID | |
| pattern = r"ct-volume-(\d+).*? - (\d+)_seg" | |
| # Use re.search to find the patient ID | |
| match = re.search(pattern, filename) | |
| if match: | |
| # Extract patient ID components | |
| patient_id = f"{match.group(1)}_{match.group(2)}" | |
| print("Extracted Patient ID:", patient_id) | |
| else: | |
| print("No match found!") | |
| output_file_name = f"{patient_id}_liver_mask_volume.nii.gz" | |
| final_save_path = os.path.join(output_folder, output_file_name) | |
| print(f"Processing {nrrd_path1}, saving to {final_save_path}") | |
| extract_liver_region(nrrd_path1, final_save_path) | |
| if __name__ == "__main__": | |
| folder1 = r'D:\Project\seg2med_Project\synthrad_results\results_all_eval\phase1_ct_anika_4_models\Infer_ddpm2d_seg2med_anika_512_all\saved_outputs\volume_output\seg' | |
| output_folder = r'D:\Project\seg2med_Project\synthrad_results\results_all_eval\phase1_ct_anika_4_models\Infer_ddpm2d_seg2med_anika_512_all\saved_outputs\volume_output\Liver_masks' | |
| main(folder1, output_folder) |