Mercurial > repos > rv43 > tomo

comparison tomo_find_center.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
parents
children 845270a96464
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2:b8977c98800b 3:f9c52762c32c
1 #!/usr/bin/env python3
2
3 import logging
4
5 import sys
6 import re
7 import argparse
8
9 from tomo import Tomo
10
11 def __main__():
12
13 # Parse command line arguments
14 parser = argparse.ArgumentParser(
15 description='Find the center axis for a tomography reconstruction')
16 parser.add_argument('-i', '--input_stacks',
17 help='Preprocessed image file stacks')
18 parser.add_argument('-c', '--config',
19 help='Input config')
20 parser.add_argument('--row_bounds',
21 help='Reconstruction row bounds')
22 parser.add_argument('--center_rows',
23 help='Center finding rows')
24 parser.add_argument('--output_config',
25 help='Output config')
26 parser.add_argument('--recon_center_low',
27 help='Lower reconstructed slice center')
28 parser.add_argument('--recon_center_upp',
29 help='Upper reconstructed slice center')
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 indexRegex = re.compile(r'\d+')
37 row_bounds = [int(i) for i in indexRegex.findall(args.row_bounds)]
38 center_rows = [int(i) for i in indexRegex.findall(args.center_rows)]
39
40 # Set basic log configuration
41 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
42 log_level = 'INFO'
43 level = getattr(logging, log_level.upper(), None)
44 if not isinstance(level, int):
45 raise ValueError(f'Invalid log_level: {log_level}')
46 logging.basicConfig(format=logging_format, level=level, force=True,
47 handlers=[logging.StreamHandler()])
48
49 logging.debug(f'input_stacks = {args.input_stacks}')
50 logging.debug(f'config = {args.config}')
51 logging.debug(f'row_bounds = {args.row_bounds} {row_bounds}')
52 logging.debug(f'center_rows = {args.center_rows} {center_rows}')
53 logging.debug(f'output_config = {args.output_config}')
54 logging.debug(f'recon_center_low = {args.recon_center_low}')
55 logging.debug(f'recon_center_uppm = {args.recon_center_upp}')
56 logging.debug(f'log = {args.log}')
57 logging.debug(f'is log stdout? {args.log is sys.stdout}')
58
59 # Instantiate Tomo object
60 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
61 log_stream=args.log, galaxy_flag=True)
62 if not tomo.is_valid:
63 raise ValueError('Invalid config file provided.')
64 logging.debug(f'config:\n{tomo.config}')
65
66 # Load preprocessed image files
67 tomo.loadTomoStacks(args.input_stacks)
68
69 # Find centers
70 tomo.findCenters(row_bounds, center_rows, args.recon_center_low, args.recon_center_upp)
71
72 if __name__ == "__main__":
73 __main__()
74