Mercurial > repos > rv43 > tomo

comparison tomo_setup.py @ 41:ef5c2f7b49ec draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
author rv43
date Thu, 21 Apr 2022 14:21:38 +0000
parents 1bcca1f2adb4
children 26f99fdd8d61
comparison
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40:fa94fe25ca46 41:ef5c2f7b49ec
25 help='Input file collections') 25 help='Input file collections')
26 parser.add_argument('-c', '--config', 26 parser.add_argument('-c', '--config',
27 help='Input config') 27 help='Input config')
28 parser.add_argument('--theta_range', 28 parser.add_argument('--theta_range',
29 help='Theta range (lower bound, upper bound, number of angles)') 29 help='Theta range (lower bound, upper bound, number of angles)')
30 parser.add_argument('--dark',
31 help='Dark field')
32 parser.add_argument('--bright',
33 help='Bright field')
34 parser.add_argument('--tomo',
35 help='First tomography image')
36 parser.add_argument('--detectorbounds',
37 help='Detector bounds')
38 parser.add_argument('--output_config', 30 parser.add_argument('--output_config',
39 help='Output config') 31 help='Output config')
40 parser.add_argument('--output_data', 32 parser.add_argument('--output_data',
41 help='Preprocessed tomography data') 33 help='Preprocessed tomography data')
42 parser.add_argument('-l', '--log', 34 parser.add_argument('-l', '--log',
58 logging.basicConfig(format=logging_format, level=level, force=True, 50 logging.basicConfig(format=logging_format, level=level, force=True,
59 handlers=[logging.StreamHandler()]) 51 handlers=[logging.StreamHandler()])
60 52
61 logging.debug(f'config = {args.config}') 53 logging.debug(f'config = {args.config}')
62 logging.debug(f'theta_range = {args.theta_range.split()}') 54 logging.debug(f'theta_range = {args.theta_range.split()}')
63 logging.debug(f'dark = {args.dark}')
64 logging.debug(f'bright = {args.bright}')
65 logging.debug(f'tomo = {args.tomo}')
66 logging.debug(f'detectorbounds = {args.detectorbounds}')
67 logging.debug(f'output_config = {args.output_config}') 55 logging.debug(f'output_config = {args.output_config}')
68 logging.debug(f'output_data = {args.output_data}') 56 logging.debug(f'output_data = {args.output_data}')
69 logging.debug(f'log = {args.log}') 57 logging.debug(f'log = {args.log}')
70 logging.debug(f'is log stdout? {args.log is sys.stdout}') 58 logging.debug(f'is log stdout? {args.log is sys.stdout}')
71 logging.debug(f'tomoranges = {args.tomo_ranges}') 59 logging.debug(f'tomoranges = {args.tomo_ranges}')
160 tomo_stack_files.append(tomo_files[0]) 148 tomo_stack_files.append(tomo_files[0])
161 num_collections += 1 149 num_collections += 1
162 150
163 # Preprocess the image files 151 # Preprocess the image files
164 galaxy_param = {'tdf_files' : tdf_files[0], 'tbf_files' : tbf_files[0], 152 galaxy_param = {'tdf_files' : tdf_files[0], 'tbf_files' : tbf_files[0],
165 'tomo_stack_files' : tomo_stack_files, 'dark_field_pngname' : args.dark, 153 'tomo_stack_files' : tomo_stack_files, 'output_name' : args.output_data}
166 'bright_field_pngname' : args.bright, 'tomo_field_pngname' : args.tomo,
167 'detectorbounds_pngname' : args.detectorbounds, 'output_name' : args.output_data}
168 tomo.genTomoStacks(galaxy_param) 154 tomo.genTomoStacks(galaxy_param)
169 if not tomo.is_valid: 155 if not tomo.is_valid:
170 IOError('Unable to load all required image files.') 156 IOError('Unable to load all required image files.')
171 157
172 # Displaying memory usage 158 # Displaying memory usage