Mercurial > repos > rv43 > tomo

comparison tomo_find_center.py @ 13:40395e60d2be draft

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"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
comparison
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12:27d4a36a8c4a 13:40395e60d2be
28 type=float, help='Set range') 28 type=float, help='Set range')
29 parser.add_argument('--set_step', 29 parser.add_argument('--set_step',
30 type=float, help='Set step') 30 type=float, help='Set step')
31 parser.add_argument('--output_config', 31 parser.add_argument('--output_config',
32 required=True, help='Output config') 32 required=True, help='Output config')
33 parser.add_argument('--recon_center_low',
34 help='Lower reconstructed slice center image name')
35 parser.add_argument('--recon_center_upp',
36 help='Upper reconstructed slice center image name')
37 parser.add_argument('-l', '--log', 33 parser.add_argument('-l', '--log',
38 type=argparse.FileType('w'), default=sys.stdout, help='Log file') 34 type=argparse.FileType('w'), default=sys.stdout, help='Log file')
39 args = parser.parse_args() 35 args = parser.parse_args()
40 36
41 # Set basic log configuration 37 # Set basic log configuration
54 logging.debug(f'center_type_selector = {args.center_type_selector}') 50 logging.debug(f'center_type_selector = {args.center_type_selector}')
55 logging.debug(f'set_center = {args.set_center}') 51 logging.debug(f'set_center = {args.set_center}')
56 logging.debug(f'set_range = {args.set_range}') 52 logging.debug(f'set_range = {args.set_range}')
57 logging.debug(f'set_step = {args.set_step}') 53 logging.debug(f'set_step = {args.set_step}')
58 logging.debug(f'output_config = {args.output_config}') 54 logging.debug(f'output_config = {args.output_config}')
59 logging.debug(f'recon_center_low = {args.recon_center_low}')
60 logging.debug(f'recon_center_upp = {args.recon_center_upp}')
61 logging.debug(f'log = {args.log}') 55 logging.debug(f'log = {args.log}')
62 logging.debug(f'is log stdout? {args.log is sys.stdout}') 56 logging.debug(f'is log stdout? {args.log is sys.stdout}')
63 57
64 # Instantiate Tomo object 58 # Instantiate Tomo object
65 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level, 59 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
72 tomo.loadTomoStacks(args.input_stacks) 66 tomo.loadTomoStacks(args.input_stacks)
73 67
74 # Find centers 68 # Find centers
75 galaxy_param = {'row_bounds' : args.row_bounds, 'center_rows' : args.center_rows, 69 galaxy_param = {'row_bounds' : args.row_bounds, 'center_rows' : args.center_rows,
76 'center_type_selector' : args.center_type_selector, 'set_center' : args.set_center, 70 'center_type_selector' : args.center_type_selector, 'set_center' : args.set_center,
77 'set_range' : args.set_range, 'set_step' : args.set_step, 71 'set_range' : args.set_range, 'set_step' : args.set_step}
78 'recon_center_low' : args.recon_center_low, 'recon_center_upp' : args.recon_center_upp}
79 tomo.findCenters(galaxy_param) 72 tomo.findCenters(galaxy_param)
80 73
81 if __name__ == "__main__": 74 if __name__ == "__main__":
82 __main__() 75 __main__()
83 76