preprocessing_scripts/preprocess_nuclick.py

import os
import numpy as np
from PIL import Image

data_directory = "/vol/data/histo_datasets/NuClick/IHC_nuclick/IHC/"

splits = ["Train", "Validation"]
for s in splits:
    masks_list = os.listdir(data_directory + "masks/" + s)
    for m in masks_list:
        mask = np.load(data_directory + "masks/" + s + "/" + m)
        mask = mask.astype(np.uint8)
        Image.fromarray(mask).save(data_directory + "masks_png/" + s + "/" + m[:-4] + ".png")