File size: 2,111 Bytes
ecf08bc 84f0951 ecf08bc 84f0951 ecf08bc 84f0951 ecf08bc 84f0951 ecf08bc |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 |
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)
|