--- a/imagecoordinates_flipaxis.py	Wed Mar 20 12:06:07 2019 -0400
+++ b/imagecoordinates_flipaxis.py	Mon Mar 25 11:15:54 2019 -0400
@@ -2,12 +2,12 @@
 import pandas as pd
 
 
-def imagecoordinates_flipyaxis(input_file, output_file, image_height):
+def imagecoordinates_flipyaxis(input_file, output_file, image_height, offset=[0,0]):
     df = pd.read_csv(input_file, sep='\t')
 
     x = df.copy().y # create copy instead of view
-    df.y = image_height-(df.x + 1) # since maximal y index = height-1 
-    df.x = x
+    df.y = image_height-(df.x + 1) + offset[1] # since maximal y index = height-1 
+    df.x = x + offset[0]
     df.to_csv(output_file, sep="\t", index=False)
 
 
@@ -16,8 +16,9 @@
     parser = argparse.ArgumentParser()
     parser.add_argument('input_file', type=argparse.FileType('r'), help='original file')
     parser.add_argument('out_file_str', type=str, help='string of output file name')
-    # parser.add_argument('image_height', help='height of image')
     parser.add_argument('image_height', type=int, help='height of image')
+    parser.add_argument('offset_x', type=int, help='offset in x direction (width)', default=0)
+    parser.add_argument('offset_y', type=int, help='offset in y direction (height)', default=0)
     args = parser.parse_args()
-    imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, args.image_height)
+    imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, args.image_height, [args.offset_x, args.offset_y])
     # imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, int(args.image_height))