--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo_find_center.py	Tue Apr 05 18:23:54 2022 +0000
@@ -0,0 +1,74 @@
+#!/usr/bin/env python3
+
+import logging
+
+import sys
+import re
+import argparse
+
+from tomo import Tomo
+
+def __main__():
+
+    # Parse command line arguments
+    parser = argparse.ArgumentParser(
+            description='Find the center axis for a tomography reconstruction')
+    parser.add_argument('-i', '--input_stacks',
+            help='Preprocessed image file stacks')
+    parser.add_argument('-c', '--config',
+            help='Input config')
+    parser.add_argument('--row_bounds',
+            help='Reconstruction row bounds')
+    parser.add_argument('--center_rows',
+            help='Center finding rows')
+    parser.add_argument('--output_config',
+            help='Output config')
+    parser.add_argument('--recon_center_low',
+            help='Lower reconstructed slice center')
+    parser.add_argument('--recon_center_upp',
+            help='Upper reconstructed slice center')
+    parser.add_argument('-l', '--log', 
+            type=argparse.FileType('w'),
+            default=sys.stdout,
+            help='Log file')
+    args = parser.parse_args()
+
+    indexRegex = re.compile(r'\d+')
+    row_bounds = [int(i) for i in indexRegex.findall(args.row_bounds)]
+    center_rows = [int(i) for i in indexRegex.findall(args.center_rows)]
+
+    # 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'row_bounds = {args.row_bounds} {row_bounds}')
+    logging.debug(f'center_rows = {args.center_rows} {center_rows}')
+    logging.debug(f'output_config = {args.output_config}')
+    logging.debug(f'recon_center_low = {args.recon_center_low}')
+    logging.debug(f'recon_center_uppm = {args.recon_center_upp}')
+    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 preprocessed image files
+    tomo.loadTomoStacks(args.input_stacks)
+
+    # Find centers
+    tomo.findCenters(row_bounds, center_rows, args.recon_center_low, args.recon_center_upp)
+
+if __name__ == "__main__":
+    __main__()
+