Mercurial > repos > rv43 > tomo

comparison tomo_reconstruct.py @ 15:1bcca1f2adb4 draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
author rv43
date Wed, 13 Apr 2022 16:02:44 +0000
parents f9c52762c32c
children 7f723407beb3
comparison
equal deleted inserted replaced
14:50c8d19d5f89 15:1bcca1f2adb4
2 2
3 import logging 3 import logging
4 4
5 import sys 5 import sys
6 import argparse 6 import argparse
7 import tracemalloc
7 8
8 from tomo import Tomo 9 from tomo import Tomo
9 10
10 def __main__(): 11 def __main__():
11 12
14 description='Perfrom a tomography reconstruction') 15 description='Perfrom a tomography reconstruction')
15 parser.add_argument('-i', '--input_stacks', 16 parser.add_argument('-i', '--input_stacks',
16 help='Preprocessed image file stacks') 17 help='Preprocessed image file stacks')
17 parser.add_argument('-c', '--config', 18 parser.add_argument('-c', '--config',
18 help='Input config') 19 help='Input config')
20 parser.add_argument('--center_offsets',
21 required=True, nargs=2, type=float, help='Reconstruction center axis offsets')
19 parser.add_argument('--output_config', 22 parser.add_argument('--output_config',
20 help='Output config') 23 help='Output config')
21 parser.add_argument('--output_data', 24 parser.add_argument('--output_data',
22 help='Reconstructed tomography data') 25 help='Reconstructed tomography data')
23 parser.add_argument('-l', '--log', 26 parser.add_argument('-l', '--log',
24 type=argparse.FileType('w'), 27 type=argparse.FileType('w'),
25 default=sys.stdout, 28 default=sys.stdout,
26 help='Log file') 29 help='Log file')
27 args = parser.parse_args() 30 args = parser.parse_args()
31
32 # Starting memory monitoring
33 tracemalloc.start()
28 34
29 # Set basic log configuration 35 # Set basic log configuration
30 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s' 36 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
31 log_level = 'INFO' 37 log_level = 'INFO'
32 level = getattr(logging, log_level.upper(), None) 38 level = getattr(logging, log_level.upper(), None)
35 logging.basicConfig(format=logging_format, level=level, force=True, 41 logging.basicConfig(format=logging_format, level=level, force=True,
36 handlers=[logging.StreamHandler()]) 42 handlers=[logging.StreamHandler()])
37 43
38 logging.debug(f'input_stacks = {args.input_stacks}') 44 logging.debug(f'input_stacks = {args.input_stacks}')
39 logging.debug(f'config = {args.config}') 45 logging.debug(f'config = {args.config}')
46 logging.debug(f'center_offsets = {args.center_offsets} {type(args.center_offsets)}')
40 logging.debug(f'output_config = {args.output_config}') 47 logging.debug(f'output_config = {args.output_config}')
41 logging.debug(f'output_data = {args.output_data}') 48 logging.debug(f'output_data = {args.output_data}')
42 logging.debug(f'log = {args.log}') 49 logging.debug(f'log = {args.log}')
43 logging.debug(f'is log stdout? {args.log is sys.stdout}') 50 logging.debug(f'is log stdout? {args.log is sys.stdout}')
44 51
51 58
52 # Load preprocessed image files 59 # Load preprocessed image files
53 tomo.loadTomoStacks(args.input_stacks) 60 tomo.loadTomoStacks(args.input_stacks)
54 61
55 # Reconstruct tomography stacks 62 # Reconstruct tomography stacks
56 tomo.reconstructTomoStacks(args.output_data) 63 galaxy_param = {'center_offsets' : args.center_offsets, 'output_name' : args.output_data}
64 tomo.reconstructTomoStacks(galaxy_param)
65
66 # Displaying memory usage
67 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
68
69 # stopping memory monitoring
70 tracemalloc.stop()
57 71
58 if __name__ == "__main__": 72 if __name__ == "__main__":
59 __main__() 73 __main__()
60 74