--- a/tomo_reduce.py	Mon Mar 20 17:08:28 2023 +0000
+++ b/tomo_reduce.py	Mon Mar 20 17:30:24 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
@@ -66,25 +66,28 @@
 #    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'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')
 
     # 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()}')