convert dicom images

convert-dicom-images.py

#!/usr/bin/env python3.9
# -*- coding: utf-8 -*-

"""
Do What the Fuck You Want To Public License - Use at your own risk, no warranty!
"""

import os
import sys
import argparse
import traceback

import matplotlib.pyplot as plt
import pydicom
import pydicom.data


def main() -> None:
    parser = argparse.ArgumentParser(description="convert a dicom img to another img format")

    parser.add_argument('-f', '--file', type=str, nargs=1, default=None)
    parser.add_argument('-o', '--out', type=str, nargs=1, default=None)
    parser.add_argument('-r'. '--root', type=str, nargs=1, default=None)

    args = parser.parse_args()

    if not args.file or not args.out:
        raise SystemError('MISSING ARGUMENT ERROR')

    dicom_file_name: str = args.file[0]
    img_out_file_name: str = args.out[0]

    try:
        base = args.root[0]  # path of project root

        filename = pydicom.data.data_manager.get_files(base, dicom_file_name)[0]

        ds = pydicom.dcmread(filename)

        my_img = plt.imshow(ds.pixel_array, cmap=plt.cm.bone)
        # plt.show()

        plt.imsave(img_out_file_name, my_img[1])

    except Exception as err:
        traceback.print_exc(file=sys.stdout)
        sys.exit(f'\033[1;31m \n\nError: {err.__class__.__name__}\nMessage: {str(err)}')


if __name__ == "__main__":
    main()

requirements.txt

matplotlib
pydicom