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comparison tomo_combine.py @ 71:1cf15b61cd83 draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213
author rv43
date Mon, 20 Mar 2023 13:56:57 +0000
parents fba792d5f83b
children
comparison
equal deleted inserted replaced
70:97c4e2cbbad9 71:1cf15b61cd83
21 help='''Full or relative path to the input file (in Nexus format).''') 21 help='''Full or relative path to the input file (in Nexus format).''')
22 parser.add_argument('-o', '--output_file', 22 parser.add_argument('-o', '--output_file',
23 required=False, 23 required=False,
24 type=pathlib.Path, 24 type=pathlib.Path,
25 help='''Full or relative path to the output file (in yaml format).''') 25 help='''Full or relative path to the output file (in yaml format).''')
26 parser.add_argument('--galaxy_flag',
27 action='store_true',
28 help='''Use this flag to run the scripts as a galaxy tool.''')
26 parser.add_argument('-l', '--log', 29 parser.add_argument('-l', '--log',
27 # type=argparse.FileType('w'), 30 # type=argparse.FileType('w'),
28 default=sys.stdout, 31 default=sys.stdout,
29 help='Logging stream or filename') 32 help='Logging stream or filename')
30 parser.add_argument('--log_level', 33 parser.add_argument('--log_level',
31 choices=logging._nameToLevel.keys(), 34 choices=logging._nameToLevel.keys(),
32 default='INFO', 35 default='INFO',
33 help='''Specify a preferred logging level.''') 36 help='''Specify a preferred logging level.''')
37 parser.add_argument('--x_bounds',
38 required=False,
39 nargs=2,
40 type=int,
41 help='''Boundaries of reconstructed images in x-direction.''')
42 parser.add_argument('--y_bounds',
43 required=False,
44 nargs=2,
45 type=int,
46 help='''Boundaries of reconstructed images in y-direction.''')
34 args = parser.parse_args() 47 args = parser.parse_args()
35 48
36 # Set log configuration 49 # Set log configuration
37 # When logging to file, the stdout log level defaults to WARNING 50 # When logging to file, the stdout log level defaults to WARNING
38 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s' 51 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
61 logging.info(f'input_file = {args.input_file}') 74 logging.info(f'input_file = {args.input_file}')
62 logging.info(f'output_file = {args.output_file}') 75 logging.info(f'output_file = {args.output_file}')
63 logging.debug(f'log = {args.log}') 76 logging.debug(f'log = {args.log}')
64 logging.debug(f'is log stdout? {args.log is sys.stdout}') 77 logging.debug(f'is log stdout? {args.log is sys.stdout}')
65 logging.debug(f'log_level = {args.log_level}') 78 logging.debug(f'log_level = {args.log_level}')
79 logging.info(f'x_bounds = {args.x_bounds}')
80 logging.info(f'y_bounds = {args.y_bounds}')
66 81
67 # Instantiate Tomo object 82 # Instantiate Tomo object
68 tomo = Tomo() 83 tomo = Tomo(galaxy_flag=args.galaxy_flag)
69 84
70 # Read input file 85 # Read input file
71 data = tomo.read(args.input_file) 86 data = tomo.read(args.input_file)
72 87
73 # Combine the reconstructed tomography stacks 88 # Combine the reconstructed tomography stacks
74 data = tomo.combine_data(data) 89 data = tomo.combine_data(data, x_bounds=args.x_bounds, y_bounds=args.y_bounds)
75 90
76 # Write output file 91 # Write output file
77 data = tomo.write(data, args.output_file) 92 if data is not None:
93 data = tomo.write(data, args.output_file)
78 94
79 # Displaying memory usage 95 # Displaying memory usage
80 # logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}') 96 # logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
81 97
82 # stopping memory monitoring 98 # stopping memory monitoring