Mercurial > repos > rv43 > chess_tomo

comparison tomo_combine.py @ 30:3342c0518d4c draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
author rv43
date Wed, 22 Mar 2023 12:52:20 +0000
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29:551d1ea2416d 30:3342c0518d4c
1 #!/usr/bin/env python3
2
3 import logging
4
5 import argparse
6 import pathlib
7 import sys
8 #import tracemalloc
9
10 from workflow.run_tomo import Tomo
11
12 #from memory_profiler import profile
13 #@profile
14 def __main__():
15 # Parse command line arguments
16 parser = argparse.ArgumentParser(
17 description='Reduce tomography data')
18 parser.add_argument('-i', '--input_file',
19 required=True,
20 type=pathlib.Path,
21 help='''Full or relative path to the input file (in Nexus format).''')
22 parser.add_argument('-o', '--output_file',
23 required=False,
24 type=pathlib.Path,
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.''')
29 parser.add_argument('-l', '--log',
30 # type=argparse.FileType('w'),
31 default=sys.stdout,
32 help='Logging stream or filename')
33 parser.add_argument('--log_level',
34 choices=logging._nameToLevel.keys(),
35 default='INFO',
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.''')
47 args = parser.parse_args()
48
49 # Set log configuration
50 # When logging to file, the stdout log level defaults to WARNING
51 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
52 level = logging.getLevelName(args.log_level)
53 if args.log is sys.stdout:
54 logging.basicConfig(format=logging_format, level=level, force=True,
55 handlers=[logging.StreamHandler()])
56 else:
57 if isinstance(args.log, str):
58 logging.basicConfig(filename=f'{args.log}', filemode='w',
59 format=logging_format, level=level, force=True)
60 elif isinstance(args.log, io.TextIOWrapper):
61 logging.basicConfig(filemode='w', format=logging_format, level=level,
62 stream=args.log, force=True)
63 else:
64 raise(ValueError(f'Invalid argument --log: {args.log}'))
65 stream_handler = logging.StreamHandler()
66 logging.getLogger().addHandler(stream_handler)
67 stream_handler.setLevel(logging.WARNING)
68 stream_handler.setFormatter(logging.Formatter(logging_format))
69
70 # Starting memory monitoring
71 # tracemalloc.start()
72
73 # Log command line arguments
74 logging.info(f'input_file = {args.input_file}')
75 logging.info(f'output_file = {args.output_file}')
76 logging.debug(f'log = {args.log}')
77 logging.debug(f'is log stdout? {args.log is sys.stdout}')
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}')
81
82 # Instantiate Tomo object
83 tomo = Tomo(galaxy_flag=args.galaxy_flag)
84
85 # Read input file
86 data = tomo.read(args.input_file)
87
88 # Combine the reconstructed tomography stacks
89 data = tomo.combine_data(data, x_bounds=args.x_bounds, y_bounds=args.y_bounds)
90
91 # Write output file
92 if data is not None:
93 data = tomo.write(data, args.output_file)
94
95 # Displaying memory usage
96 # logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
97
98 # stopping memory monitoring
99 # tracemalloc.stop()
100
101 if __name__ == "__main__":
102 __main__()