Mercurial > repos > rv43 > tomo

annotate tomo_find_center.py @ 8:9cabd6e746d3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/rolfverberg/galaxytools commit f4ed0a752072e2bebb1604a44e2d9843f1552817"
author rv43
date Thu, 07 Apr 2022 21:17:32 +0000
parents 845270a96464
children 40395e60d2be
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
1 #!/usr/bin/env python3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
2
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
3 import logging
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
4
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
5 import sys
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
6 import argparse
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
7
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
8 from tomo import Tomo
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
9
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
10 def __main__():
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
11
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
12 # Parse command line arguments
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
13 parser = argparse.ArgumentParser(
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
14 description='Find the center axis for a tomography reconstruction')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
15 parser.add_argument('-i', '--input_stacks',
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
16 required=True, help='Preprocessed image file stacks')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
17 parser.add_argument('-c', '--config',
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
18 required=True, help='Input config')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
19 parser.add_argument('--row_bounds',
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
20 required=True, nargs=2, type=int, help='Reconstruction row bounds')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
21 parser.add_argument('--center_rows',
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
22 required=True, nargs=2, type=int, help='Center finding rows')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
23 parser.add_argument('--center_type_selector',
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
24 help='Reconstruct slices for a set of center positions?')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
25 parser.add_argument('--set_center',
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
26 type=int, help='Set center ')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
27 parser.add_argument('--set_range',
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
28 type=float, help='Set range')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
29 parser.add_argument('--set_step',
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
30 type=float, help='Set step')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
31 parser.add_argument('--output_config',
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
32 required=True, help='Output config')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
33 parser.add_argument('--recon_center_low',
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
34 help='Lower reconstructed slice center image name')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
35 parser.add_argument('--recon_center_upp',
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
36 help='Upper reconstructed slice center image name')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
37 parser.add_argument('-l', '--log',
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
38 type=argparse.FileType('w'), default=sys.stdout, help='Log file')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
39 args = parser.parse_args()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
40
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
41 # Set basic log configuration
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
42 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
43 log_level = 'INFO'
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
44 level = getattr(logging, log_level.upper(), None)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
45 if not isinstance(level, int):
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
46 raise ValueError(f'Invalid log_level: {log_level}')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
47 logging.basicConfig(format=logging_format, level=level, force=True,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
48 handlers=[logging.StreamHandler()])
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
49
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
50 logging.debug(f'input_stacks = {args.input_stacks}')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
51 logging.debug(f'config = {args.config}')
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
52 logging.debug(f'row_bounds = {args.row_bounds} {type(args.row_bounds)}')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
53 logging.debug(f'center_rows = {args.center_rows} {type(args.center_rows)}')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
54 logging.debug(f'center_type_selector = {args.center_type_selector}')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
55 logging.debug(f'set_center = {args.set_center}')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
56 logging.debug(f'set_range = {args.set_range}')
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
57 logging.debug(f'set_step = {args.set_step}')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
58 logging.debug(f'output_config = {args.output_config}')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
59 logging.debug(f'recon_center_low = {args.recon_center_low}')
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
60 logging.debug(f'recon_center_upp = {args.recon_center_upp}')
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
61 logging.debug(f'log = {args.log}')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
62 logging.debug(f'is log stdout? {args.log is sys.stdout}')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
63
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
64 # Instantiate Tomo object
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
65 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
66 log_stream=args.log, galaxy_flag=True)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
67 if not tomo.is_valid:
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
68 raise ValueError('Invalid config file provided.')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
69 logging.debug(f'config:\n{tomo.config}')
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
70
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
71 # Load preprocessed image files
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
72 tomo.loadTomoStacks(args.input_stacks)
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
73
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
74 # Find centers
7
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
75 galaxy_param = {'row_bounds' : args.row_bounds, 'center_rows' : args.center_rows,
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
76 'center_type_selector' : args.center_type_selector, 'set_center' : args.set_center,
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
77 'set_range' : args.set_range, 'set_step' : args.set_step,
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
78 'recon_center_low' : args.recon_center_low, 'recon_center_upp' : args.recon_center_upp}
845270a96464 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit a08ed1264ea7b7c878ba96801e4b27ef621fb6be"
rv43
parents: 3
diff changeset
79 tomo.findCenters(galaxy_param)
3
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
80
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
81 if __name__ == "__main__":
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
82 __main__()
f9c52762c32c "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
rv43
parents:
diff changeset
83