to_nrrd.py

to_nrrd.py

"""
dependencies: numpy pillow pynrrd tqdm
"""

from PIL import Image
from pathlib import Path
from tqdm import tqdm
import nrrd
import numpy as np

input_folder = Path.home() / ("Desktop/20240927 boxes/ARPAM123924_PLA_box")
image_name = "USradial.tiff"

output_file = input_folder / Path(image_name).with_suffix(".nrrd")
print(output_file)


def load_images(folder: Path) -> np.ndarray:
    """Load images from a folder and return a 3D np.ndarray"""
    dtype = np.uint8

    image_files = sorted(folder.glob("**/" + image_name))
    if not image_files:
        raise ValueError(f"No TIFF files found in folder {folder}")

    first_image = Image.open(image_files[0])
    width, height = first_image.size
    width //= 2
    height //= 2

    image_stack = np.zeros((len(image_files), height, width), dtype=dtype)

    for i, image_file in enumerate(tqdm(image_files)):
        image = Image.open(image_file)
        image = image.resize((width, height))
        image_stack[i] = np.array(image)

    return image_stack


def main():
    image_stack = load_images(input_folder)

    nrrd.write(str(output_file), image_stack)
    print(f"NRRD file saved as {output_file}")


if __name__ == "__main__":
    main()