Mercurial > repos > rv43 > tomo

comparison tomo_find_center.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 40395e60d2be
children ba5866d0251d
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
31 parser.add_argument('--output_config', 32 parser.add_argument('--output_config',
32 required=True, help='Output config') 33 required=True, help='Output config')
33 parser.add_argument('-l', '--log', 34 parser.add_argument('-l', '--log',
34 type=argparse.FileType('w'), default=sys.stdout, help='Log file') 35 type=argparse.FileType('w'), default=sys.stdout, help='Log file')
35 args = parser.parse_args() 36 args = parser.parse_args()
37
38 # Starting memory monitoring
39 tracemalloc.start()
36 40
37 # Set basic log configuration 41 # Set basic log configuration
38 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s' 42 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
39 log_level = 'INFO' 43 log_level = 'INFO'
40 level = getattr(logging, log_level.upper(), None) 44 level = getattr(logging, log_level.upper(), None)
69 galaxy_param = {'row_bounds' : args.row_bounds, 'center_rows' : args.center_rows, 73 galaxy_param = {'row_bounds' : args.row_bounds, 'center_rows' : args.center_rows,
70 'center_type_selector' : args.center_type_selector, 'set_center' : args.set_center, 74 'center_type_selector' : args.center_type_selector, 'set_center' : args.set_center,
71 'set_range' : args.set_range, 'set_step' : args.set_step} 75 'set_range' : args.set_range, 'set_step' : args.set_step}
72 tomo.findCenters(galaxy_param) 76 tomo.findCenters(galaxy_param)
73 77
78 # Displaying memory usage
79 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
80
81 # stopping memory monitoring
82 tracemalloc.stop()
83
74 if __name__ == "__main__": 84 if __name__ == "__main__":
75 __main__() 85 __main__()
76 86