Mercurial > repos > rv43 > tomo

comparison tomo_reconstruct.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='Perfrom a tomography reconstruction') 17 description='Reduce tomography data')
16 parser.add_argument('-i', '--input_stacks', 18 parser.add_argument('-i', '--input_file',
17 help='Preprocessed image file stacks') 19 required=True,
18 parser.add_argument('-c', '--config', 20 type=pathlib.Path,
19 help='Input config') 21 help='''Full or relative path to the input file (in Nexus format).''')
20 parser.add_argument('--center_offsets', 22 parser.add_argument('-c', '--center_file',
21 nargs=2, type=float, help='Reconstruction center axis offsets') 23 required=True,
22 parser.add_argument('--output_config', 24 type=pathlib.Path,
23 help='Output config') 25 help='''Full or relative path to the center info file (in Nexus format).''')
24 parser.add_argument('--output_data', 26 parser.add_argument('-o', '--output_file',
25 help='Reconstructed tomography data') 27 required=False,
26 parser.add_argument('-l', '--log', 28 type=pathlib.Path,
27 type=argparse.FileType('w'), 29 help='''Full or relative path to the output file (in yaml format).''')
30 parser.add_argument('--galaxy_flag',
31 action='store_true',
32 help='''Use this flag to run the scripts as a galaxy tool.''')
33 parser.add_argument('-l', '--log',
34 # type=argparse.FileType('w'),
28 default=sys.stdout, 35 default=sys.stdout,
29 help='Log file') 36 help='Logging stream or filename')
37 parser.add_argument('--log_level',
38 choices=logging._nameToLevel.keys(),
39 default='INFO',
40 help='''Specify a preferred logging level.''')
41 parser.add_argument('--x_bounds',
42 required=False,
43 nargs=2,
44 type=int,
45 help='''Boundaries of reconstructed images in x-direction.''')
46 parser.add_argument('--y_bounds',
47 required=False,
48 nargs=2,
49 type=int,
50 help='''Boundaries of reconstructed images in y-direction.''')
30 args = parser.parse_args() 51 args = parser.parse_args()
31 52
53 # Set log configuration
54 # When logging to file, the stdout log level defaults to WARNING
55 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
56 level = logging.getLevelName(args.log_level)
57 if args.log is sys.stdout:
58 logging.basicConfig(format=logging_format, level=level, force=True,
59 handlers=[logging.StreamHandler()])
60 else:
61 if isinstance(args.log, str):
62 logging.basicConfig(filename=f'{args.log}', filemode='w',
63 format=logging_format, level=level, force=True)
64 elif isinstance(args.log, io.TextIOWrapper):
65 logging.basicConfig(filemode='w', format=logging_format, level=level,
66 stream=args.log, force=True)
67 else:
68 raise(ValueError(f'Invalid argument --log: {args.log}'))
69 stream_handler = logging.StreamHandler()
70 logging.getLogger().addHandler(stream_handler)
71 stream_handler.setLevel(logging.WARNING)
72 stream_handler.setFormatter(logging.Formatter(logging_format))
73
32 # Starting memory monitoring 74 # Starting memory monitoring
33 tracemalloc.start() 75 # tracemalloc.start()
34 76
35 # Set basic log configuration 77 # Log command line arguments
36 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s' 78 logging.info(f'input_file = {args.input_file}')
37 log_level = 'INFO' 79 logging.info(f'center_file = {args.center_file}')
38 level = getattr(logging, log_level.upper(), None) 80 logging.info(f'output_file = {args.output_file}')
39 if not isinstance(level, int): 81 logging.info(f'galaxy_flag = {args.galaxy_flag}')
40 raise ValueError(f'Invalid log_level: {log_level}')
41 logging.basicConfig(format=logging_format, level=level, force=True,
42 handlers=[logging.StreamHandler()])
43
44 logging.debug(f'config = {args.config}')
45 logging.debug(f'input_stacks = {args.input_stacks}')
46 logging.debug(f'center_offsets = {args.center_offsets} {type(args.center_offsets)}')
47 logging.debug(f'output_config = {args.output_config}')
48 logging.debug(f'output_data = {args.output_data}')
49 logging.debug(f'log = {args.log}') 82 logging.debug(f'log = {args.log}')
50 logging.debug(f'is log stdout? {args.log is sys.stdout}') 83 logging.debug(f'is log stdout? {args.log is sys.stdout}')
84 logging.debug(f'log_level = {args.log_level}')
85 logging.info(f'x_bounds = {args.x_bounds}')
86 logging.info(f'y_bounds = {args.y_bounds}')
51 87
52 # Instantiate Tomo object 88 # Instantiate Tomo object
53 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level, 89 tomo = Tomo(galaxy_flag=args.galaxy_flag)
54 log_stream=args.log, galaxy_flag=True)
55 if not tomo.is_valid:
56 raise ValueError('Invalid config file provided.')
57 logging.debug(f'config:\n{tomo.config}')
58 90
59 # Set reconstruction center axis offsets 91 # Read input file
60 if args.center_offsets is None: 92 data = tomo.read(args.input_file)
61 find_center = tomo.config.get('find_center')
62 if find_center is None:
63 raise ValueError('Invalid config file provided (missing find_center).')
64 center_offsets = [float(find_center.get('lower_center_offset')),
65 float(find_center.get('upper_center_offset'))]
66 else:
67 center_offsets = args.center_offsets
68 93
69 # Load preprocessed image files 94 # Read center data
70 tomo.loadTomoStacks(args.input_stacks) 95 center_data = tomo.read(args.center_file)
71 96
72 # Reconstruct tomography stacks 97 # Find the calibrated center axis info
73 galaxy_param = {'center_offsets' : center_offsets, 'output_name' : args.output_data} 98 data = tomo.reconstruct_data(data, center_data, x_bounds=args.x_bounds, y_bounds=args.y_bounds)
74 logging.debug(f'galaxy_param = {galaxy_param}') 99
75 tomo.reconstructTomoStacks(galaxy_param) 100 # Write output file
101 data = tomo.write(data, args.output_file)
76 102
77 # Displaying memory usage 103 # Displaying memory usage
78 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}') 104 # logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
79 105
80 # stopping memory monitoring 106 # stopping memory monitoring
81 tracemalloc.stop() 107 # tracemalloc.stop()
82 108
83 if __name__ == "__main__": 109 if __name__ == "__main__":
84 __main__() 110 __main__()
85