--- a/tomo_reduce.py	Mon Mar 20 17:30:24 2023 +0000
+++ b/tomo_reduce.py	Tue Mar 21 17:40:03 2023 +0000
@@ -15,30 +15,30 @@
     # Parse command line arguments
     parser = argparse.ArgumentParser(
             description='Reduce tomography data')
-#    parser.add_argument('-i', '--input_file',
-#            required=True,
-#            type=pathlib.Path,
-#            help='''Full or relative path to the input file (in yaml or nxs format).''')
-#    parser.add_argument('-o', '--output_file',
-#            required=True,
-#            type=pathlib.Path,
-#            help='''Full or relative path to the output file (in Nexus format).''')
-#    parser.add_argument('--galaxy_flag',
-#            action='store_true',
-#            help='''Use this flag to run the scripts as a galaxy tool.''')
-#    parser.add_argument('--img_x_bounds',
-#            required=False,
-#            nargs=2,
-#            type=int,
-#            help='Vertical data reduction image range')
+    parser.add_argument('-i', '--input_file',
+            required=True,
+            type=pathlib.Path,
+            help='''Full or relative path to the input file (in yaml or nxs format).''')
+    parser.add_argument('-o', '--output_file',
+            required=True,
+            type=pathlib.Path,
+            help='''Full or relative path to the output file (in Nexus format).''')
+    parser.add_argument('--galaxy_flag',
+            action='store_true',
+            help='''Use this flag to run the scripts as a galaxy tool.''')
+    parser.add_argument('--img_x_bounds',
+            required=False,
+            nargs=2,
+            type=int,
+            help='Vertical data reduction image range')
     parser.add_argument('-l', '--log',
 #            type=argparse.FileType('w'),
             default=sys.stdout,
             help='Logging stream or filename')
-#    parser.add_argument('--log_level',
-#            choices=logging._nameToLevel.keys(),
-#            default='INFO',
-#            help='''Specify a preferred logging level.''')
+    parser.add_argument('--log_level',
+            choices=logging._nameToLevel.keys(),
+            default='INFO',
+            help='''Specify a preferred logging level.''')
     args = parser.parse_args()
 
     # Set log configuration
@@ -66,28 +66,25 @@
 #    tracemalloc.start()
 
     # Log command line arguments
-#    logging.info(f'input_file = {args.input_file}')
-#    logging.info(f'output_file = {args.output_file}')
-#    logging.info(f'galaxy_flag = {args.galaxy_flag}')
-#    logging.info(f'img_x_bounds = {args.img_x_bounds}')
-#    logging.debug(f'log = {args.log}')
-#    logging.debug(f'is log stdout? {args.log is sys.stdout}')
-#    logging.debug(f'log_level = {args.log_level}')
-    logging.info(f'log = {args.log}')
-    logging.info(f'is log stdout? {args.log is sys.stdout}')
-    print('Done')
+    logging.info(f'input_file = {args.input_file}')
+    logging.info(f'output_file = {args.output_file}')
+    logging.info(f'galaxy_flag = {args.galaxy_flag}')
+    logging.info(f'img_x_bounds = {args.img_x_bounds}')
+    logging.debug(f'log = {args.log}')
+    logging.debug(f'is log stdout? {args.log is sys.stdout}')
+    logging.debug(f'log_level = {args.log_level}')
 
     # Instantiate Tomo object
-#    tomo = Tomo(galaxy_flag=args.galaxy_flag)
+    tomo = Tomo(galaxy_flag=args.galaxy_flag)
 
     # Read input file
-#    data = tomo.read(args.input_file)
+    data = tomo.read(args.input_file)
 
     # Generate reduced tomography images
-#    data = tomo.gen_reduced_data(data, img_x_bounds=args.img_x_bounds)
+    data = tomo.gen_reduced_data(data, img_x_bounds=args.img_x_bounds)
 
     # Write output file
-#    data = tomo.write(data, args.output_file)
+    data = tomo.write(data, args.output_file)
 
     # Displaying memory usage
 #    logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')