Update after renaming

setup_files

@@ -0,0 +1,53 @@
+#!/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', action='store_true', default=False,
+                        dest='zip', help='package result files in zip bundles',
+                        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 combined.zip combined.tif && cd -'.format(o=output_dir)
+        subprocess.run(cmd, shell=True)
+
+
+def main():
+    args = parse_arguments()
+    merge_images(args.input_dir, args.output_dir, args.zip)
+
+
+if __name__ == '__main__':
+    main()