diff tomo_find_center.py @ 13:40395e60d2be draft

"planemo upload for repository https://github.com/rolfverberg/galaxytools commit e61a62f5b5950b3142fedad2c0e49a00f66f9980"
author rv43
date Fri, 08 Apr 2022 17:49:28 +0000
parents 845270a96464
children 1bcca1f2adb4
line wrap: on
line diff
--- a/tomo_find_center.py	Fri Apr 08 16:56:53 2022 +0000
+++ b/tomo_find_center.py	Fri Apr 08 17:49:28 2022 +0000
@@ -30,10 +30,6 @@
             type=float, help='Set step')
     parser.add_argument('--output_config',
             required=True, help='Output config')
-    parser.add_argument('--recon_center_low',
-            help='Lower reconstructed slice center image name')
-    parser.add_argument('--recon_center_upp',
-            help='Upper reconstructed slice center image name')
     parser.add_argument('-l', '--log', 
             type=argparse.FileType('w'), default=sys.stdout, help='Log file')
     args = parser.parse_args()
@@ -56,8 +52,6 @@
     logging.debug(f'set_range = {args.set_range}')
     logging.debug(f'set_step = {args.set_step}')
     logging.debug(f'output_config = {args.output_config}')
-    logging.debug(f'recon_center_low = {args.recon_center_low}')
-    logging.debug(f'recon_center_upp = {args.recon_center_upp}')
     logging.debug(f'log = {args.log}')
     logging.debug(f'is log stdout? {args.log is sys.stdout}')
 
@@ -74,8 +68,7 @@
     # 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, 
-            'recon_center_low' : args.recon_center_low, 'recon_center_upp' : args.recon_center_upp}
+            'set_range' : args.set_range, 'set_step' : args.set_step}
     tomo.findCenters(galaxy_param)
 
 if __name__ == "__main__":