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comparison tomo_reduce.py @ 73:adb84c450789 draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213-dirty
author rv43
date Mon, 20 Mar 2023 17:30:24 +0000
parents 1cf15b61cd83
children 4f4ee8db5f67
comparison
equal deleted inserted replaced
72:d5329ca0210d 73:adb84c450789
13 #@profile 13 #@profile
14 def __main__(): 14 def __main__():
15 # Parse command line arguments 15 # Parse command line arguments
16 parser = argparse.ArgumentParser( 16 parser = argparse.ArgumentParser(
17 description='Reduce tomography data') 17 description='Reduce tomography data')
18 parser.add_argument('-i', '--input_file', 18 # parser.add_argument('-i', '--input_file',
19 required=True, 19 # required=True,
20 type=pathlib.Path, 20 # type=pathlib.Path,
21 help='''Full or relative path to the input file (in yaml or nxs format).''') 21 # help='''Full or relative path to the input file (in yaml or nxs format).''')
22 parser.add_argument('-o', '--output_file', 22 # parser.add_argument('-o', '--output_file',
23 required=True, 23 # required=True,
24 type=pathlib.Path, 24 # type=pathlib.Path,
25 help='''Full or relative path to the output file (in Nexus format).''') 25 # help='''Full or relative path to the output file (in Nexus format).''')
26 parser.add_argument('--galaxy_flag', 26 # parser.add_argument('--galaxy_flag',
27 action='store_true', 27 # action='store_true',
28 help='''Use this flag to run the scripts as a galaxy tool.''') 28 # help='''Use this flag to run the scripts as a galaxy tool.''')
29 parser.add_argument('--img_x_bounds', 29 # parser.add_argument('--img_x_bounds',
30 required=False, 30 # required=False,
31 nargs=2, 31 # nargs=2,
32 type=int, 32 # type=int,
33 help='Vertical data reduction image range') 33 # help='Vertical data reduction image range')
34 parser.add_argument('-l', '--log', 34 parser.add_argument('-l', '--log',
35 # type=argparse.FileType('w'), 35 # type=argparse.FileType('w'),
36 default=sys.stdout, 36 default=sys.stdout,
37 help='Logging stream or filename') 37 help='Logging stream or filename')
38 parser.add_argument('--log_level', 38 # parser.add_argument('--log_level',
39 choices=logging._nameToLevel.keys(), 39 # choices=logging._nameToLevel.keys(),
40 default='INFO', 40 # default='INFO',
41 help='''Specify a preferred logging level.''') 41 # help='''Specify a preferred logging level.''')
42 args = parser.parse_args() 42 args = parser.parse_args()
43 43
44 # Set log configuration 44 # Set log configuration
45 # When logging to file, the stdout log level defaults to WARNING 45 # When logging to file, the stdout log level defaults to WARNING
46 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s' 46 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
64 64
65 # Start memory monitoring 65 # Start memory monitoring
66 # tracemalloc.start() 66 # tracemalloc.start()
67 67
68 # Log command line arguments 68 # Log command line arguments
69 logging.info(f'input_file = {args.input_file}') 69 # logging.info(f'input_file = {args.input_file}')
70 logging.info(f'output_file = {args.output_file}') 70 # logging.info(f'output_file = {args.output_file}')
71 logging.info(f'galaxy_flag = {args.galaxy_flag}') 71 # logging.info(f'galaxy_flag = {args.galaxy_flag}')
72 logging.info(f'img_x_bounds = {args.img_x_bounds}') 72 # logging.info(f'img_x_bounds = {args.img_x_bounds}')
73 logging.debug(f'log = {args.log}') 73 # logging.debug(f'log = {args.log}')
74 logging.debug(f'is log stdout? {args.log is sys.stdout}') 74 # logging.debug(f'is log stdout? {args.log is sys.stdout}')
75 logging.debug(f'log_level = {args.log_level}') 75 # logging.debug(f'log_level = {args.log_level}')
76 logging.info(f'log = {args.log}')
77 logging.info(f'is log stdout? {args.log is sys.stdout}')
78 print('Done')
76 79
77 # Instantiate Tomo object 80 # Instantiate Tomo object
78 tomo = Tomo(galaxy_flag=args.galaxy_flag) 81 # tomo = Tomo(galaxy_flag=args.galaxy_flag)
79 82
80 # Read input file 83 # Read input file
81 data = tomo.read(args.input_file) 84 # data = tomo.read(args.input_file)
82 85
83 # Generate reduced tomography images 86 # Generate reduced tomography images
84 data = tomo.gen_reduced_data(data, img_x_bounds=args.img_x_bounds) 87 # data = tomo.gen_reduced_data(data, img_x_bounds=args.img_x_bounds)
85 88
86 # Write output file 89 # Write output file
87 data = tomo.write(data, args.output_file) 90 # data = tomo.write(data, args.output_file)
88 91
89 # Displaying memory usage 92 # Displaying memory usage
90 # logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}') 93 # logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
91 94
92 # Stop memory monitoring 95 # Stop memory monitoring