Convert a numpy array (.npz) to TIFF

convert_npz_to_tiff.py

#!/usr/bin/env python3

import click
import tifffile
import numpy as np


def convert_npz_to_tiff(input_file, output_file, pixelsize=0.05):
    data = np.load(input_file)

    # Convert the float64 to uint16 by dividing the float64 by the maximum value for each channel and multiplying by 65535
    img = np.zeros((data["img"].shape[0], data["img"].shape[1], data["img"].shape[2]), dtype='uint16')
    for i in range(data["img"].shape[2]):
        img[:, :, i] = (data["img"][:, :, i] / np.max(data["img"][:, :, i]) * 65535).astype('uint16')

    # Move the last dimension to the first dimension
    img = np.moveaxis(img, -1, 0)

    tifffile.imwrite(
        output_file,
        img,
        shape=img.shape,
        dtype='uint16',
        # photometric='minisblack',
        metadata={'axes': 'CYX', "Channel": {"Name": data["ch"].tolist()}},
    )

@click.command()
@click.argument('input_file', type=click.Path(exists=True))
@click.argument('output_file', type=click.Path())
def main(input_file, output_file):
    convert_npz_to_tiff(input_file, output_file)


if __name__ == '__main__':
    main()