Mercurial > repos > rv43 > tomo

comparison tomo_reconstruct.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 3caba2116858
children fba792d5f83b
comparison
equal deleted inserted replaced
67:87a4acead65c 68:ba5866d0251d
16 parser.add_argument('-i', '--input_stacks', 16 parser.add_argument('-i', '--input_stacks',
17 help='Preprocessed image file stacks') 17 help='Preprocessed image file stacks')
18 parser.add_argument('-c', '--config', 18 parser.add_argument('-c', '--config',
19 help='Input config') 19 help='Input config')
20 parser.add_argument('--center_offsets', 20 parser.add_argument('--center_offsets',
21 required=True, nargs=2, type=float, help='Reconstruction center axis offsets') 21 nargs=2, type=float, help='Reconstruction center axis offsets')
22 parser.add_argument('--output_config', 22 parser.add_argument('--output_config',
23 help='Output config') 23 help='Output config')
24 parser.add_argument('--output_data', 24 parser.add_argument('--output_data',
25 help='Reconstructed tomography data') 25 help='Reconstructed tomography data')
26 parser.add_argument('-l', '--log', 26 parser.add_argument('-l', '--log',
39 if not isinstance(level, int): 39 if not isinstance(level, int):
40 raise ValueError(f'Invalid log_level: {log_level}') 40 raise ValueError(f'Invalid log_level: {log_level}')
41 logging.basicConfig(format=logging_format, level=level, force=True, 41 logging.basicConfig(format=logging_format, level=level, force=True,
42 handlers=[logging.StreamHandler()]) 42 handlers=[logging.StreamHandler()])
43 43
44 logging.debug(f'config = {args.config}')
44 logging.debug(f'input_stacks = {args.input_stacks}') 45 logging.debug(f'input_stacks = {args.input_stacks}')
45 logging.debug(f'config = {args.config}')
46 logging.debug(f'center_offsets = {args.center_offsets} {type(args.center_offsets)}') 46 logging.debug(f'center_offsets = {args.center_offsets} {type(args.center_offsets)}')
47 logging.debug(f'output_config = {args.output_config}') 47 logging.debug(f'output_config = {args.output_config}')
48 logging.debug(f'output_data = {args.output_data}') 48 logging.debug(f'output_data = {args.output_data}')
49 logging.debug(f'log = {args.log}') 49 logging.debug(f'log = {args.log}')
50 logging.debug(f'is log stdout? {args.log is sys.stdout}') 50 logging.debug(f'is log stdout? {args.log is sys.stdout}')
54 log_stream=args.log, galaxy_flag=True) 54 log_stream=args.log, galaxy_flag=True)
55 if not tomo.is_valid: 55 if not tomo.is_valid:
56 raise ValueError('Invalid config file provided.') 56 raise ValueError('Invalid config file provided.')
57 logging.debug(f'config:\n{tomo.config}') 57 logging.debug(f'config:\n{tomo.config}')
58 58
59 # Set reconstruction center axis offsets
60 if args.center_offsets is None:
61 find_center = tomo.config.get('find_center')
62 if find_center is None:
63 raise ValueError('Invalid config file provided (missing find_center).')
64 center_offsets = [float(find_center.get('lower_center_offset')),
65 float(find_center.get('upper_center_offset'))]
66 else:
67 center_offsets = args.center_offsets
68
59 # Load preprocessed image files 69 # Load preprocessed image files
60 tomo.loadTomoStacks(args.input_stacks) 70 tomo.loadTomoStacks(args.input_stacks)
61 71
62 # Reconstruct tomography stacks 72 # Reconstruct tomography stacks
63 galaxy_param = {'center_offsets' : args.center_offsets, 'output_name' : args.output_data} 73 galaxy_param = {'center_offsets' : center_offsets, 'output_name' : args.output_data}
64 logging.info(f'galaxy_param = {galaxy_param}') 74 logging.debug(f'galaxy_param = {galaxy_param}')
65 tomo.reconstructTomoStacks(galaxy_param) 75 tomo.reconstructTomoStacks(galaxy_param)
66 76
67 # Displaying memory usage 77 # Displaying memory usage
68 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}') 78 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
69 79