Update file_setup Pipeline

file_setup

@@ -0,0 +1,57 @@
+#!/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>
+
+"""
+
+from argparse import ArgumentParser
+import os
+import subprocess
+
+
+def parse_arguments():
+    parser = ArgumentParser(description='Merges images into one .pdf file.')
+    parser.add_argument('i', metavar='input directory')
+    parser.add_argument('o', metavar='output directory')
+    parser.add_argument('f', metavar='output file base')
+    parser.add_argument('--log-dir')
+    parser.add_argument('--zip')
+    return parser.parse_args()
+
+
+def merge_images(input_dir, output_dir, output_file_base, 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 @"{}"/file_list.txt "{}"/"{}".pdf'.format(input_dir, output_dir, output_file_base)  # noqa
+    subprocess.run(cmd, shell=True)
+    cmd = 'rm "{}"/file_list.txt'.format(input_dir)
+    subprocess.run(cmd, shell=True)
+    if zip is not None:
+        cmd = 'cd "{}"'.format(output_dir)
+        cmd += ' && '
+        cmd += 'zip'
+        cmd += ' -m'
+        cmd += ' "{}"_-_pdf "{}".pdf'.format(zip, output_file_base)
+        cmd += ' && '
+        cmd += 'cd -'
+        subprocess.run(cmd, shell=True)
+
+
+def main():
+    args = parse_arguments()
+    print(args)
+    merge_images(args.i, args.o, args.f, args.zip)
+
+
+if __name__ == '__main__':
+    main()