| import SimpleITK as sitk | |
| import argparse | |
| import imageio | |
| import numpy as np | |
| import torch | |
| import os | |
| from batchgenerators.utilities.file_and_folder_operations import join, isdir, maybe_mkdir_p | |
| from data_processing.data_postprocessing import extract_front_from_zones | |
| from PIL import Image | |
| import cv2 | |
| def main(input_folder): | |
| files = os.listdir(input_folder) | |
| output_folder = join(input_folder, '../tifs') | |
| maybe_mkdir_p(output_folder) | |
| os.rmdir(os.path.join(input_folder,'../nnUNet')) | |
| kernel = np.ones((7, 7), np.uint8) | |
| for file in files: | |
| if file.endswith('.gz'): | |
| print(file) | |
| file_path = join(input_folder, file) | |
| image = sitk.ReadImage(file_path) | |
| image = sitk.GetArrayFromImage(image) | |
| image = image[0] | |
| color_zone = np.zeros_like(image) | |
| color_zone[image == 0] = 0 | |
| color_zone[image == 1] = 64 | |
| color_zone[image == 2] = 127 | |
| color_zone[image == 3] = 254 | |
| color_zone[image == 4] = 254 | |
| glacier = np.zeros_like(image) | |
| glacier[image == 2] = 1 | |
| glacier_dil = cv2.dilate(glacier, kernel, iterations=1) | |
| color_zone[glacier_dil == 1] = 127 | |
| color_front = extract_front_from_zones(color_zone, 10) | |
| color_front[color_front==255] =1 | |
| output_path_zone = join(output_folder, file[:-len('.nii.gz')] + '_zone.png') | |
| output_path_front = join(output_folder, file[:-len('.nii.gz')] + '_front.png') | |
| imageio.imwrite(output_path_zone, color_zone) | |
| imageio.imwrite(output_path_front, color_front) | |
| """ | |
| img_zone = Image.fromarray(color_zone) | |
| img_front = Image.fromarray(color_front) | |
| img_zone.save(output_path_zone) | |
| img_front.save(output_path_front) | |
| """ | |
| if __name__ == '__main__': | |
| parser = argparse.ArgumentParser() | |
| parser.add_argument("-i", '--input_folder', help="Folder with NIfTI files") | |
| args = parser.parse_args() | |
| input_folder = args.input_folder | |
| main(input_folder) | |