| import SimpleITK as sitk | |
| import argparse | |
| import numpy as np | |
| import torch | |
| import os | |
| from batchgenerators.utilities.file_and_folder_operations import join, isdir, maybe_mkdir_p | |
| import matplotlib.image as pltimage | |
| def main(input_folder): | |
| files = os.listdir(input_folder) | |
| output_folder = join(input_folder, 'pngs') | |
| maybe_mkdir_p(output_folder) | |
| for file in files: | |
| if file.endswith('.gz'): | |
| file_path = join(input_folder, file) | |
| image = sitk.ReadImage(file_path) | |
| image = sitk.GetArrayFromImage(image) | |
| front = image[0] | |
| zones = image[1] | |
| boundary = image[2] | |
| color_zones = np.zeros_like(zones) | |
| color_zones[zones == 0] = 0 | |
| color_zones[zones == 1] = 64 | |
| color_zones[zones == 2] = 127 | |
| color_zones[zones == 3] = 254 | |
| color_fronts = np.zeros_like(front) | |
| color_fronts[front == 0] = 0 | |
| color_fronts[front == 1] = 255 | |
| color_boundary = np.zeros_like(boundary) | |
| color_boundary[boundary == 0] =0 | |
| color_boundary[boundary == 1] = 255 | |
| output_path_zone = join(output_folder, file[:-len('.nii.gz')] + '_zone.png') | |
| pltimage.imsave(output_path_zone, color_zones, cmap='gray', vmax=255) | |
| output_path_front = join(output_folder, file[:-len('.nii.gz')] + '_front.png') | |
| pltimage.imsave(output_path_front, color_fronts, cmap='gray', vmax=255) | |
| output_path_recon = join(output_folder, file[:-len('.nii.gz')] + '_boundary.png') | |
| pltimage.imsave(output_path_recon, color_boundary, cmap='gray', vmax=255) | |
| 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) |