Mercurial > repos > rv43 > tomo

comparison tomo_combine.py @ 48:059819ea1f0e draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit b97c6a8f181dea6d2f9cfa2069b86d30dcc47b4d"
author rv43
date Wed, 27 Apr 2022 17:28:26 +0000
parents
children ba5866d0251d
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47:c693117d01e9 48:059819ea1f0e
1 #!/usr/bin/env python3
2
3 import logging
4
5 import sys
6 import argparse
7 import tracemalloc
8
9 from tomo import Tomo
10
11 def __main__():
12
13 # Parse command line arguments
14 parser = argparse.ArgumentParser(
15 description='Combine reconstructed tomography stacks')
16 parser.add_argument('-i', '--input_stacks',
17 help='Reconstructed image file stacks')
18 parser.add_argument('-c', '--config',
19 help='Input config')
20 parser.add_argument('--x_bounds',
21 required=True, nargs=2, type=int, help='Reconstructed range in x direction')
22 parser.add_argument('--y_bounds',
23 required=True, nargs=2, type=int, help='Reconstructed range in y direction')
24 parser.add_argument('--z_bounds',
25 required=True, nargs=2, type=int, help='Reconstructed range in z direction')
26 parser.add_argument('--output_config',
27 help='Output config')
28 parser.add_argument('--output_data',
29 help='Combined tomography stacks')
30 parser.add_argument('-l', '--log',
31 type=argparse.FileType('w'),
32 default=sys.stdout,
33 help='Log file')
34 args = parser.parse_args()
35
36 # Starting memory monitoring
37 tracemalloc.start()
38
39 # Set basic log configuration
40 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
41 log_level = 'INFO'
42 level = getattr(logging, log_level.upper(), None)
43 if not isinstance(level, int):
44 raise ValueError(f'Invalid log_level: {log_level}')
45 logging.basicConfig(format=logging_format, level=level, force=True,
46 handlers=[logging.StreamHandler()])
47
48 logging.debug(f'input_stacks = {args.input_stacks}')
49 logging.debug(f'config = {args.config}')
50 logging.debug(f'x_bounds = {args.x_bounds} {type(args.x_bounds)}')
51 logging.debug(f'y_bounds = {args.y_bounds} {type(args.y_bounds)}')
52 logging.debug(f'z_bounds = {args.z_bounds} {type(args.z_bounds)}')
53 logging.debug(f'output_config = {args.output_config}')
54 logging.debug(f'output_data = {args.output_data}')
55 logging.debug(f'log = {args.log}')
56 logging.debug(f'is log stdout? {args.log is sys.stdout}')
57
58 # Instantiate Tomo object
59 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
60 log_stream=args.log, galaxy_flag=True)
61 if not tomo.is_valid:
62 raise ValueError('Invalid config file provided.')
63 logging.debug(f'config:\n{tomo.config}')
64
65 # Load reconstructed image files
66 tomo.loadTomoStacks(args.input_stacks, recon_flag=True)
67
68 # Combined reconstructed tomography stacks
69 galaxy_param = {'x_bounds' : args.x_bounds, 'y_bounds' : args.y_bounds,
70 'z_bounds' : args.z_bounds, 'output_name' : args.output_data}
71 logging.info(f'galaxy_param = {galaxy_param}')
72 tomo.combineTomoStacks(galaxy_param)
73
74 # Displaying memory usage
75 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
76
77 # stopping memory monitoring
78 tracemalloc.stop()
79
80 if __name__ == "__main__":
81 __main__()
82