Mercurial > repos > rv43 > tomo

comparison tomo_reconstruct.py @ 3:f9c52762c32c draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
author rv43
date Tue, 05 Apr 2022 18:23:54 +0000
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children 1bcca1f2adb4
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2:b8977c98800b 3:f9c52762c32c
1 #!/usr/bin/env python3
2
3 import logging
4
5 import sys
6 import argparse
7
8 from tomo import Tomo
9
10 def __main__():
11
12 # Parse command line arguments
13 parser = argparse.ArgumentParser(
14 description='Perfrom a tomography reconstruction')
15 parser.add_argument('-i', '--input_stacks',
16 help='Preprocessed image file stacks')
17 parser.add_argument('-c', '--config',
18 help='Input config')
19 parser.add_argument('--output_config',
20 help='Output config')
21 parser.add_argument('--output_data',
22 help='Reconstructed tomography data')
23 parser.add_argument('-l', '--log',
24 type=argparse.FileType('w'),
25 default=sys.stdout,
26 help='Log file')
27 args = parser.parse_args()
28
29 # Set basic log configuration
30 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
31 log_level = 'INFO'
32 level = getattr(logging, log_level.upper(), None)
33 if not isinstance(level, int):
34 raise ValueError(f'Invalid log_level: {log_level}')
35 logging.basicConfig(format=logging_format, level=level, force=True,
36 handlers=[logging.StreamHandler()])
37
38 logging.debug(f'input_stacks = {args.input_stacks}')
39 logging.debug(f'config = {args.config}')
40 logging.debug(f'output_config = {args.output_config}')
41 logging.debug(f'output_data = {args.output_data}')
42 logging.debug(f'log = {args.log}')
43 logging.debug(f'is log stdout? {args.log is sys.stdout}')
44
45 # Instantiate Tomo object
46 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
47 log_stream=args.log, galaxy_flag=True)
48 if not tomo.is_valid:
49 raise ValueError('Invalid config file provided.')
50 logging.debug(f'config:\n{tomo.config}')
51
52 # Load preprocessed image files
53 tomo.loadTomoStacks(args.input_stacks)
54
55 # Reconstruct tomography stacks
56 tomo.reconstructTomoStacks(args.output_data)
57
58 if __name__ == "__main__":
59 __main__()
60