Mercurial > repos > rv43 > tomo

comparison tomo_combine.py @ 69:fba792d5f83b 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 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='Combine reconstructed tomography stacks') 17 description='Reduce tomography data')
16 parser.add_argument('-i', '--input_stacks', 18 parser.add_argument('-i', '--input_file',
17 help='Reconstructed 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('--x_bounds', 22 parser.add_argument('-o', '--output_file',
21 required=True, nargs=2, type=int, help='Reconstructed range in x direction') 23 required=False,
22 parser.add_argument('--y_bounds', 24 type=pathlib.Path,
23 required=True, nargs=2, type=int, help='Reconstructed range in y direction') 25 help='''Full or relative path to the output file (in yaml format).''')
24 parser.add_argument('--z_bounds', 26 parser.add_argument('-l', '--log',
25 required=True, nargs=2, type=int, help='Reconstructed range in z direction') 27 # type=argparse.FileType('w'),
26 parser.add_argument('--output_config',
27 help='Output config')
28 parser.add_argument('--output_data',
29 help='Combined tomography stacks')
30 parser.add_argument('-l', '--log',
31 type=argparse.FileType('w'),
32 default=sys.stdout, 28 default=sys.stdout,
33 help='Log file') 29 help='Logging stream or filename')
30 parser.add_argument('--log_level',
31 choices=logging._nameToLevel.keys(),
32 default='INFO',
33 help='''Specify a preferred logging level.''')
34 args = parser.parse_args() 34 args = parser.parse_args()
35 35
36 # Set log configuration
37 # When logging to file, the stdout log level defaults to WARNING
38 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
39 level = logging.getLevelName(args.log_level)
40 if args.log is sys.stdout:
41 logging.basicConfig(format=logging_format, level=level, force=True,
42 handlers=[logging.StreamHandler()])
43 else:
44 if isinstance(args.log, str):
45 logging.basicConfig(filename=f'{args.log}', filemode='w',
46 format=logging_format, level=level, force=True)
47 elif isinstance(args.log, io.TextIOWrapper):
48 logging.basicConfig(filemode='w', format=logging_format, level=level,
49 stream=args.log, force=True)
50 else:
51 raise(ValueError(f'Invalid argument --log: {args.log}'))
52 stream_handler = logging.StreamHandler()
53 logging.getLogger().addHandler(stream_handler)
54 stream_handler.setLevel(logging.WARNING)
55 stream_handler.setFormatter(logging.Formatter(logging_format))
56
36 # Starting memory monitoring 57 # Starting memory monitoring
37 tracemalloc.start() 58 # tracemalloc.start()
38 59
39 # Set basic log configuration 60 # Log command line arguments
40 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s' 61 logging.info(f'input_file = {args.input_file}')
41 log_level = 'INFO' 62 logging.info(f'output_file = {args.output_file}')
42 level = getattr(logging, log_level.upper(), None)
43 if not isinstance(level, int):
44 raise ValueError(f'Invalid log_level: {log_level}')
45 logging.basicConfig(format=logging_format, level=level, force=True,
46 handlers=[logging.StreamHandler()])
47
48 logging.debug(f'config = {args.config}')
49 logging.debug(f'input_stacks = {args.input_stacks}')
50 logging.debug(f'x_bounds = {args.x_bounds} {type(args.x_bounds)}')
51 logging.debug(f'y_bounds = {args.y_bounds} {type(args.y_bounds)}')
52 logging.debug(f'z_bounds = {args.z_bounds} {type(args.z_bounds)}')
53 logging.debug(f'output_config = {args.output_config}')
54 logging.debug(f'output_data = {args.output_data}')
55 logging.debug(f'log = {args.log}') 63 logging.debug(f'log = {args.log}')
56 logging.debug(f'is log stdout? {args.log is sys.stdout}') 64 logging.debug(f'is log stdout? {args.log is sys.stdout}')
65 logging.debug(f'log_level = {args.log_level}')
57 66
58 # Instantiate Tomo object 67 # Instantiate Tomo object
59 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level, 68 tomo = Tomo()
60 log_stream=args.log, galaxy_flag=True)
61 if not tomo.is_valid:
62 raise ValueError('Invalid config file provided.')
63 logging.debug(f'config:\n{tomo.config}')
64 69
65 # Load reconstructed image files 70 # Read input file
66 tomo.loadTomoStacks(args.input_stacks, recon_flag=True) 71 data = tomo.read(args.input_file)
67 72
68 # Combined reconstructed tomography stacks 73 # Combine the reconstructed tomography stacks
69 galaxy_param = {'x_bounds' : args.x_bounds, 'y_bounds' : args.y_bounds, 74 data = tomo.combine_data(data)
70 'z_bounds' : args.z_bounds, 'output_name' : args.output_data} 75
71 logging.debug(f'galaxy_param = {galaxy_param}') 76 # Write output file
72 tomo.combineTomoStacks(galaxy_param) 77 data = tomo.write(data, args.output_file)
73 78
74 # Displaying memory usage 79 # Displaying memory usage
75 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}') 80 # logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
76 81
77 # stopping memory monitoring 82 # stopping memory monitoring
78 tracemalloc.stop() 83 # tracemalloc.stop()
79 84
80 if __name__ == "__main__": 85 if __name__ == "__main__":
81 __main__() 86 __main__()
82