--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagecoordinates_flipaxis.py	Wed Mar 20 12:06:07 2019 -0400
@@ -0,0 +1,23 @@
+import argparse
+import pandas as pd
+
+
+def imagecoordinates_flipyaxis(input_file, output_file, image_height):
+    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.to_csv(output_file, sep="\t", index=False)
+
+
+
+if __name__ == "__main__":
+    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')
+    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, int(args.image_height))