Mercurial > repos > rv43 > tomo

comparison tomo_find_center.py @ 69:fba792d5f83b draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
author rv43
date Fri, 10 Mar 2023 16:02:04 +0000
parents ba5866d0251d
children 1cf15b61cd83
comparison
equal deleted inserted replaced
68:ba5866d0251d 69:fba792d5f83b
1 #!/usr/bin/env python3 1 #!/usr/bin/env python3
2 2
3 import logging 3 import logging
4 4
5 import argparse
6 import pathlib
5 import sys 7 import sys
6 import argparse 8 #import tracemalloc
7 import tracemalloc
8 9
9 from tomo import Tomo 10 from workflow.run_tomo import Tomo
10 11
12 #from memory_profiler import profile
13 #@profile
11 def __main__(): 14 def __main__():
12
13 # Parse command line arguments 15 # Parse command line arguments
14 parser = argparse.ArgumentParser( 16 parser = argparse.ArgumentParser(
15 description='Find the center axis for a tomography reconstruction') 17 description='Reduce tomography data')
16 parser.add_argument('-i', '--input_stacks', 18 parser.add_argument('-i', '--input_file',
17 required=True, help='Preprocessed image file stacks') 19 required=True,
18 parser.add_argument('-c', '--config', 20 type=pathlib.Path,
19 required=True, help='Input config') 21 help='''Full or relative path to the input file (in Nexus format).''')
20 parser.add_argument('--row_bounds', 22 parser.add_argument('-o', '--output_file',
21 required=True, nargs=2, type=int, help='Reconstruction row bounds') 23 required=False,
24 type=pathlib.Path,
25 help='''Full or relative path to the output file (in yaml format).''')
22 parser.add_argument('--center_rows', 26 parser.add_argument('--center_rows',
23 required=True, nargs=2, type=int, help='Center finding rows') 27 required=True,
24 parser.add_argument('--center_type_selector', 28 nargs=2,
25 help='Reconstruct slices for a set of center positions?') 29 type=int,
26 parser.add_argument('--set_center', 30 help='''Center finding rows.''')
27 type=int, help='Set center ') 31 parser.add_argument('--galaxy_flag',
28 parser.add_argument('--set_range', 32 action='store_true',
29 type=float, help='Set range') 33 help='''Use this flag to run the scripts as a galaxy tool.''')
30 parser.add_argument('--set_step', 34 parser.add_argument('-l', '--log',
31 type=float, help='Set step') 35 # type=argparse.FileType('w'),
32 parser.add_argument('--output_config', 36 default=sys.stdout,
33 required=True, help='Output config') 37 help='Logging stream or filename')
34 parser.add_argument('-l', '--log', 38 parser.add_argument('--log_level',
35 type=argparse.FileType('w'), default=sys.stdout, help='Log file') 39 choices=logging._nameToLevel.keys(),
40 default='INFO',
41 help='''Specify a preferred logging level.''')
36 args = parser.parse_args() 42 args = parser.parse_args()
37 43
44 # Set log configuration
45 # When logging to file, the stdout log level defaults to WARNING
46 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
47 level = logging.getLevelName(args.log_level)
48 if args.log is sys.stdout:
49 logging.basicConfig(format=logging_format, level=level, force=True,
50 handlers=[logging.StreamHandler()])
51 else:
52 if isinstance(args.log, str):
53 logging.basicConfig(filename=f'{args.log}', filemode='w',
54 format=logging_format, level=level, force=True)
55 elif isinstance(args.log, io.TextIOWrapper):
56 logging.basicConfig(filemode='w', format=logging_format, level=level,
57 stream=args.log, force=True)
58 else:
59 raise(ValueError(f'Invalid argument --log: {args.log}'))
60 stream_handler = logging.StreamHandler()
61 logging.getLogger().addHandler(stream_handler)
62 stream_handler.setLevel(logging.WARNING)
63 stream_handler.setFormatter(logging.Formatter(logging_format))
64
38 # Starting memory monitoring 65 # Starting memory monitoring
39 tracemalloc.start() 66 # tracemalloc.start()
40 67
41 # Set basic log configuration 68 # Log command line arguments
42 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s' 69 logging.info(f'input_file = {args.input_file}')
43 log_level = 'INFO' 70 logging.info(f'output_file = {args.output_file}')
44 level = getattr(logging, log_level.upper(), None) 71 logging.info(f'center_rows = {args.center_rows}')
45 if not isinstance(level, int): 72 logging.info(f'galaxy_flag = {args.galaxy_flag}')
46 raise ValueError(f'Invalid log_level: {log_level}')
47 logging.basicConfig(format=logging_format, level=level, force=True,
48 handlers=[logging.StreamHandler()])
49
50 logging.debug(f'config = {args.config}')
51 logging.debug(f'input_stacks = {args.input_stacks}')
52 logging.debug(f'row_bounds = {args.row_bounds} {type(args.row_bounds)}')
53 logging.debug(f'center_rows = {args.center_rows} {type(args.center_rows)}')
54 logging.debug(f'center_type_selector = {args.center_type_selector}')
55 logging.debug(f'set_center = {args.set_center}')
56 logging.debug(f'set_range = {args.set_range}')
57 logging.debug(f'set_step = {args.set_step}')
58 logging.debug(f'output_config = {args.output_config}')
59 logging.debug(f'log = {args.log}') 73 logging.debug(f'log = {args.log}')
60 logging.debug(f'is log stdout? {args.log is sys.stdout}') 74 logging.debug(f'is log stdout? {args.log is sys.stdout}')
75 logging.debug(f'log_level = {args.log_level}')
61 76
62 # Instantiate Tomo object 77 # Instantiate Tomo object
63 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level, 78 tomo = Tomo(galaxy_flag=args.galaxy_flag)
64 log_stream=args.log, galaxy_flag=True)
65 if not tomo.is_valid:
66 raise ValueError('Invalid config file provided.')
67 logging.debug(f'config:\n{tomo.config}')
68 79
69 # Load preprocessed image files 80 # Read input file
70 tomo.loadTomoStacks(args.input_stacks) 81 data = tomo.read(args.input_file)
71 82
72 # Find centers 83 # Find the calibrated center axis info
73 galaxy_param = {'row_bounds' : args.row_bounds, 'center_rows' : args.center_rows, 84 data = tomo.find_centers(data, center_rows=tuple(args.center_rows))
74 'center_type_selector' : args.center_type_selector, 'set_center' : args.set_center, 85
75 'set_range' : args.set_range, 'set_step' : args.set_step} 86 # Write output file
76 tomo.findCenters(galaxy_param) 87 data = tomo.write(data, args.output_file)
77 88
78 # Displaying memory usage 89 # Displaying memory usage
79 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}') 90 # logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
80 91
81 # stopping memory monitoring 92 # stopping memory monitoring
82 tracemalloc.stop() 93 # tracemalloc.stop()
83 94
84 if __name__ == "__main__": 95 if __name__ == "__main__":
85 __main__() 96 __main__()
86