Mercurial > repos > rv43 > tomo

comparison tomo_combine.py @ 68:ba5866d0251d draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 3fde3e85030608a8a4d8e59308353b0144314dfe"
author rv43
date Fri, 19 Aug 2022 20:16:56 +0000
parents 059819ea1f0e
children fba792d5f83b
comparison
equal deleted inserted replaced
67:87a4acead65c 68:ba5866d0251d
43 if not isinstance(level, int): 43 if not isinstance(level, int):
44 raise ValueError(f'Invalid log_level: {log_level}') 44 raise ValueError(f'Invalid log_level: {log_level}')
45 logging.basicConfig(format=logging_format, level=level, force=True, 45 logging.basicConfig(format=logging_format, level=level, force=True,
46 handlers=[logging.StreamHandler()]) 46 handlers=[logging.StreamHandler()])
47 47
48 logging.debug(f'config = {args.config}')
48 logging.debug(f'input_stacks = {args.input_stacks}') 49 logging.debug(f'input_stacks = {args.input_stacks}')
49 logging.debug(f'config = {args.config}')
50 logging.debug(f'x_bounds = {args.x_bounds} {type(args.x_bounds)}') 50 logging.debug(f'x_bounds = {args.x_bounds} {type(args.x_bounds)}')
51 logging.debug(f'y_bounds = {args.y_bounds} {type(args.y_bounds)}') 51 logging.debug(f'y_bounds = {args.y_bounds} {type(args.y_bounds)}')
52 logging.debug(f'z_bounds = {args.z_bounds} {type(args.z_bounds)}') 52 logging.debug(f'z_bounds = {args.z_bounds} {type(args.z_bounds)}')
53 logging.debug(f'output_config = {args.output_config}') 53 logging.debug(f'output_config = {args.output_config}')
54 logging.debug(f'output_data = {args.output_data}') 54 logging.debug(f'output_data = {args.output_data}')
66 tomo.loadTomoStacks(args.input_stacks, recon_flag=True) 66 tomo.loadTomoStacks(args.input_stacks, recon_flag=True)
67 67
68 # Combined reconstructed tomography stacks 68 # Combined reconstructed tomography stacks
69 galaxy_param = {'x_bounds' : args.x_bounds, 'y_bounds' : args.y_bounds, 69 galaxy_param = {'x_bounds' : args.x_bounds, 'y_bounds' : args.y_bounds,
70 'z_bounds' : args.z_bounds, 'output_name' : args.output_data} 70 'z_bounds' : args.z_bounds, 'output_name' : args.output_data}
71 logging.info(f'galaxy_param = {galaxy_param}') 71 logging.debug(f'galaxy_param = {galaxy_param}')
72 tomo.combineTomoStacks(galaxy_param) 72 tomo.combineTomoStacks(galaxy_param)
73 73
74 # Displaying memory usage 74 # Displaying memory usage
75 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}') 75 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
76 76