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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]
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
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)
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) |