file-setup/setup_files

#!/usr/bin/env python3.5
# coding=utf-8


"""
merge_images

Usage:  For usage instructions run with option --help
Author: Stephan Porada <sporada@uni-bielefeld.de>

"""

import argparse
import os
import subprocess


def parse_arguments():
    parser = argparse.ArgumentParser(description='Merges given input images '
                                                 'into one multipage tiff.')
    parser.add_argument('-i',
                        dest='input_dir',
                        required=True,
                        type=os.path.abspath)
    parser.add_argument('-o',
                        dest='output_dir',
                        required=True,
                        type=os.path.abspath)
    parser.add_argument('--zip',
                        default='combines-pictures',
                        dest='zip',
                        type=str,
                        help='''package result files in zip bundles and set a
                                filename prefix as a string.''',
                        required=False)
    return parser.parse_args()


def merge_images(input_dir, output_dir, zip):
    try:
        os.mkdir(output_dir)
    except FileExistsError:
        pass
    cmd = 'ls -Q -v {i}/*.* > {i}/file_list.txt'.format(i=input_dir)
    subprocess.run(cmd, shell=True)
    cmd = 'convert @{i}/file_list.txt {o}/combined.tif'.format(i=input_dir, o=output_dir)
    subprocess.run(cmd, shell=True)
    cmd = 'rm {i}/file_list.txt'.format(i=input_dir)
    subprocess.run(cmd, shell=True)
    if zip:
        cmd = 'cd {o} && zip -m {f}-combined.zip combined.tif && cd -'.format(o=output_dir, f=zip)
        subprocess.run(cmd, shell=True)


def main():
    args = parse_arguments()
    merge_images(args.input_dir, args.output_dir, args.zip)


if __name__ == '__main__':
    main()