From dba21fbfd732150f2053b012c8d98a8186b3c2e5 Mon Sep 17 00:00:00 2001
From: Patrick Jentsch <p.jentsch@uni-bielefeld.de>
Date: Mon, 27 Jan 2020 15:52:20 +0100
Subject: [PATCH] Fix path problems

---
 merge_images | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/merge_images b/merge_images
index b8c9e88..6045fec 100755
--- a/merge_images
+++ b/merge_images
@@ -10,23 +10,33 @@ Author: Stephan Porada <sporada@uni-bielefeld.de>
 
 """
 
-import os
 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)
-    parser.add_argument('-o', dest='output_dir', required=True)
+    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)
     return parser.parse_args()
 
 
 def merge_images(input_dir, output_dir):
-    os.makedirs(output_dir, exist_ok=True)
-    os.system('ls -v {i}/*.* >> {i}/file_list.txt'.format(i=input_dir))
-    os.system('convert @{i}/file_list.txt {o}/combined.tiff'.format(i=input_dir,
-                                                                    o=output_dir))
+    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)
 
 
 def main():