Mercurial > repos > rv43 > chess_tomo

comparison tomo_reconstruct.py @ 18:dee0b25fcabe draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
author rv43
date Tue, 21 Mar 2023 15:35:48 +0000
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17:e89919e468cd 18:dee0b25fcabe
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='Perform a tomography reconstruction')
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('-c', '--center_file',
23 required=True,
24 type=pathlib.Path,
25 help='''Full or relative path to the center info file (in yaml format).''')
26 parser.add_argument('-o', '--output_file',
27 required=False,
28 type=pathlib.Path,
29 help='''Full or relative path to the output file (in Nexus format).''')
30 parser.add_argument('--galaxy_flag',
31 action='store_true',
32 help='''Use this flag to run the scripts as a galaxy tool.''')
33 parser.add_argument('-l', '--log',
34 # type=argparse.FileType('w'),
35 default=sys.stdout,
36 help='Logging stream or filename')
37 parser.add_argument('--log_level',
38 choices=logging._nameToLevel.keys(),
39 default='INFO',
40 help='''Specify a preferred logging level.''')
41 parser.add_argument('--x_bounds',
42 required=False,
43 nargs=2,
44 type=int,
45 help='''Boundaries of reconstructed images in x-direction.''')
46 parser.add_argument('--y_bounds',
47 required=False,
48 nargs=2,
49 type=int,
50 help='''Boundaries of reconstructed images in y-direction.''')
51 args = parser.parse_args()
52
53 # Set log configuration
54 # When logging to file, the stdout log level defaults to WARNING
55 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
56 level = logging.getLevelName(args.log_level)
57 if args.log is sys.stdout:
58 logging.basicConfig(format=logging_format, level=level, force=True,
59 handlers=[logging.StreamHandler()])
60 else:
61 if isinstance(args.log, str):
62 logging.basicConfig(filename=f'{args.log}', filemode='w',
63 format=logging_format, level=level, force=True)
64 elif isinstance(args.log, io.TextIOWrapper):
65 logging.basicConfig(filemode='w', format=logging_format, level=level,
66 stream=args.log, force=True)
67 else:
68 raise(ValueError(f'Invalid argument --log: {args.log}'))
69 stream_handler = logging.StreamHandler()
70 logging.getLogger().addHandler(stream_handler)
71 stream_handler.setLevel(logging.WARNING)
72 stream_handler.setFormatter(logging.Formatter(logging_format))
73
74 # Starting memory monitoring
75 # tracemalloc.start()
76
77 # Log command line arguments
78 logging.info(f'input_file = {args.input_file}')
79 logging.info(f'center_file = {args.center_file}')
80 logging.info(f'output_file = {args.output_file}')
81 logging.info(f'galaxy_flag = {args.galaxy_flag}')
82 logging.debug(f'log = {args.log}')
83 logging.debug(f'is log stdout? {args.log is sys.stdout}')
84 logging.debug(f'log_level = {args.log_level}')
85 logging.info(f'x_bounds = {args.x_bounds}')
86 logging.info(f'y_bounds = {args.y_bounds}')
87
88 # Instantiate Tomo object
89 tomo = Tomo(galaxy_flag=args.galaxy_flag)
90
91 # Read input file
92 data = tomo.read(args.input_file)
93
94 # Read center data
95 center_data = tomo.read(args.center_file)
96
97 # Find the calibrated center axis info
98 data = tomo.reconstruct_data(data, center_data, x_bounds=args.x_bounds, y_bounds=args.y_bounds)
99
100 # Write output file
101 data = tomo.write(data, args.output_file)
102
103 # Displaying memory usage
104 # logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
105
106 # stopping memory monitoring
107 # tracemalloc.stop()
108
109 logging.info('Completed tomography reconstruction')
110
111
112 if __name__ == "__main__":
113 __main__()