--- a/tomo_find_center.py	Fri Aug 19 20:16:56 2022 +0000
+++ b/tomo_find_center.py	Fri Mar 10 16:02:04 2023 +0000
@@ -2,85 +2,95 @@
 
 import logging
 
+import argparse
+import pathlib
 import sys
-import argparse
-import tracemalloc
+#import tracemalloc
 
-from tomo import Tomo
+from workflow.run_tomo import Tomo
 
+#from memory_profiler import profile
+#@profile
 def __main__():
-
     # Parse command line arguments
     parser = argparse.ArgumentParser(
-            description='Find the center axis for a tomography reconstruction')
-    parser.add_argument('-i', '--input_stacks',
-            required=True, help='Preprocessed image file stacks')
-    parser.add_argument('-c', '--config',
-            required=True, help='Input config')
-    parser.add_argument('--row_bounds',
-            required=True, nargs=2, type=int, help='Reconstruction row bounds')
+            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 Nexus format).''')
+    parser.add_argument('-o', '--output_file',
+            required=False,
+            type=pathlib.Path,
+            help='''Full or relative path to the output file (in yaml format).''')
     parser.add_argument('--center_rows',
-            required=True, nargs=2, type=int, help='Center finding rows')
-    parser.add_argument('--center_type_selector',
-            help='Reconstruct slices for a set of center positions?')
-    parser.add_argument('--set_center',
-            type=int, help='Set center ')
-    parser.add_argument('--set_range',
-            type=float, help='Set range')
-    parser.add_argument('--set_step',
-            type=float, help='Set step')
-    parser.add_argument('--output_config',
-            required=True, help='Output config')
-    parser.add_argument('-l', '--log', 
-            type=argparse.FileType('w'), default=sys.stdout, help='Log file')
+            required=True,
+            nargs=2,
+            type=int,
+            help='''Center finding rows.''')
+    parser.add_argument('--galaxy_flag',
+            action='store_true',
+            help='''Use this flag to run the scripts as a galaxy tool.''')
+    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.''')
     args = parser.parse_args()
 
+    # Set log configuration
+    # When logging to file, the stdout log level defaults to WARNING
+    logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
+    level = logging.getLevelName(args.log_level)
+    if args.log is sys.stdout:
+        logging.basicConfig(format=logging_format, level=level, force=True,
+                handlers=[logging.StreamHandler()])
+    else:
+        if isinstance(args.log, str):
+            logging.basicConfig(filename=f'{args.log}', filemode='w',
+                    format=logging_format, level=level, force=True)
+        elif isinstance(args.log, io.TextIOWrapper):
+            logging.basicConfig(filemode='w', format=logging_format, level=level,
+                    stream=args.log, force=True)
+        else:
+            raise(ValueError(f'Invalid argument --log: {args.log}'))
+        stream_handler = logging.StreamHandler()
+        logging.getLogger().addHandler(stream_handler)
+        stream_handler.setLevel(logging.WARNING)
+        stream_handler.setFormatter(logging.Formatter(logging_format))
+
     # Starting memory monitoring
-    tracemalloc.start()
+#    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'config = {args.config}')
-    logging.debug(f'input_stacks = {args.input_stacks}')
-    logging.debug(f'row_bounds = {args.row_bounds} {type(args.row_bounds)}')
-    logging.debug(f'center_rows = {args.center_rows} {type(args.center_rows)}')
-    logging.debug(f'center_type_selector = {args.center_type_selector}')
-    logging.debug(f'set_center = {args.set_center}')
-    logging.debug(f'set_range = {args.set_range}')
-    logging.debug(f'set_step = {args.set_step}')
-    logging.debug(f'output_config = {args.output_config}')
+    # Log command line arguments
+    logging.info(f'input_file = {args.input_file}')
+    logging.info(f'output_file = {args.output_file}')
+    logging.info(f'center_rows = {args.center_rows}')
+    logging.info(f'galaxy_flag = {args.galaxy_flag}')
     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(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}')
+    tomo = Tomo(galaxy_flag=args.galaxy_flag)
+
+    # Read input file
+    data = tomo.read(args.input_file)
 
-    # Load preprocessed image files
-    tomo.loadTomoStacks(args.input_stacks)
+    # Find the calibrated center axis info
+    data = tomo.find_centers(data, center_rows=tuple(args.center_rows))
 
-    # Find centers
-    galaxy_param = {'row_bounds' : args.row_bounds, 'center_rows' : args.center_rows,
-            'center_type_selector' : args.center_type_selector, 'set_center' : args.set_center, 
-            'set_range' : args.set_range, 'set_step' : args.set_step}
-    tomo.findCenters(galaxy_param)
+    # Write output file
+    data = tomo.write(data, args.output_file)
 
     # Displaying memory usage
-    logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
-
+#    logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
+ 
     # stopping memory monitoring
-    tracemalloc.stop()
+#    tracemalloc.stop()
 
 if __name__ == "__main__":
     __main__()
-