--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo_combine.py	Wed Apr 27 17:28:26 2022 +0000
@@ -0,0 +1,82 @@
+#!/usr/bin/env python3
+
+import logging
+
+import sys
+import argparse
+import tracemalloc
+
+from tomo import Tomo
+
+def __main__():
+
+    # Parse command line arguments
+    parser = argparse.ArgumentParser(
+            description='Combine reconstructed tomography stacks')
+    parser.add_argument('-i', '--input_stacks',
+            help='Reconstructed image file stacks')
+    parser.add_argument('-c', '--config',
+            help='Input config')
+    parser.add_argument('--x_bounds',
+            required=True, nargs=2, type=int, help='Reconstructed range in x direction')
+    parser.add_argument('--y_bounds',
+            required=True, nargs=2, type=int, help='Reconstructed range in y direction')
+    parser.add_argument('--z_bounds',
+            required=True, nargs=2, type=int, help='Reconstructed range in z direction')
+    parser.add_argument('--output_config',
+            help='Output config')
+    parser.add_argument('--output_data',
+            help='Combined tomography stacks')
+    parser.add_argument('-l', '--log', 
+            type=argparse.FileType('w'),
+            default=sys.stdout,
+            help='Log file')
+    args = parser.parse_args()
+
+    # Starting memory monitoring
+    tracemalloc.start()
+
+    # Set basic log configuration
+    logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
+    log_level = 'INFO'
+    level = getattr(logging, log_level.upper(), None)
+    if not isinstance(level, int):
+        raise ValueError(f'Invalid log_level: {log_level}')
+    logging.basicConfig(format=logging_format, level=level, force=True,
+            handlers=[logging.StreamHandler()])
+
+    logging.debug(f'input_stacks = {args.input_stacks}')
+    logging.debug(f'config = {args.config}')
+    logging.debug(f'x_bounds = {args.x_bounds} {type(args.x_bounds)}')
+    logging.debug(f'y_bounds = {args.y_bounds} {type(args.y_bounds)}')
+    logging.debug(f'z_bounds = {args.z_bounds} {type(args.z_bounds)}')
+    logging.debug(f'output_config = {args.output_config}')
+    logging.debug(f'output_data = {args.output_data}')
+    logging.debug(f'log = {args.log}')
+    logging.debug(f'is log stdout? {args.log is sys.stdout}')
+
+    # Instantiate Tomo object
+    tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
+            log_stream=args.log, galaxy_flag=True)
+    if not tomo.is_valid:
+        raise ValueError('Invalid config file provided.')
+    logging.debug(f'config:\n{tomo.config}')
+
+    # Load reconstructed image files
+    tomo.loadTomoStacks(args.input_stacks, recon_flag=True)
+
+    # Combined reconstructed tomography stacks
+    galaxy_param = {'x_bounds' : args.x_bounds, 'y_bounds' : args.y_bounds,
+            'z_bounds' : args.z_bounds, 'output_name' : args.output_data}
+    logging.info(f'galaxy_param = {galaxy_param}')
+    tomo.combineTomoStacks(galaxy_param)
+
+    # Displaying memory usage
+    logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
+
+    # stopping memory monitoring
+    tracemalloc.stop()
+
+if __name__ == "__main__":
+    __main__()
+