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comparison tomo_reduce.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
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children 97c4e2cbbad9
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68:ba5866d0251d 69:fba792d5f83b
1 #!/usr/bin/env python3
2
3 import logging
4
5 import argparse
6 import pathlib
7 import sys
8 #import tracemalloc
9
10 from workflow.run_tomo import Tomo
11
12 #from memory_profiler import profile
13 #@profile
14 def __main__():
15 # Parse command line arguments
16 parser = argparse.ArgumentParser(
17 description='Reduce tomography data')
18 parser.add_argument('-i', '--input_file',
19 required=True,
20 type=pathlib.Path,
21 help='''Full or relative path to the input file (in yaml format).''')
22 parser.add_argument('-o', '--output_file',
23 required=False,
24 type=pathlib.Path,
25 help='''Full or relative path to the output file (in Nexus format).''')
26 parser.add_argument('--galaxy_flag',
27 action='store_true',
28 help='''Use this flag to run the scripts as a galaxy tool.''')
29 parser.add_argument('--img_x_bounds',
30 required=False,
31 nargs=2,
32 type=int,
33 help='Vertical data reduction image range')
34 parser.add_argument('-l', '--log',
35 # type=argparse.FileType('w'),
36 default=sys.stdout,
37 help='Logging stream or filename')
38 parser.add_argument('--log_level',
39 choices=logging._nameToLevel.keys(),
40 default='INFO',
41 help='''Specify a preferred logging level.''')
42 args = parser.parse_args()
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
65 # Start memory monitoring
66 # tracemalloc.start()
67
68 # Log command line arguments
69 logging.info(f'input_file = {args.input_file}')
70 logging.info(f'output_file = {args.output_file}')
71 logging.info(f'galaxy_flag = {args.galaxy_flag}')
72 logging.info(f'img_x_bounds = {args.img_x_bounds}')
73 logging.debug(f'log = {args.log}')
74 logging.debug(f'is log stdout? {args.log is sys.stdout}')
75 logging.debug(f'log_level = {args.log_level}')
76
77 # Instantiate Tomo object
78 tomo = Tomo(galaxy_flag=args.galaxy_flag)
79
80 # Read input file
81 data = tomo.read(args.input_file)
82
83 # Generate reduced tomography images
84 data = tomo.gen_reduced_data(data, img_x_bounds=args.img_x_bounds)
85
86 # Write output file
87 data = tomo.write(data, args.output_file)
88
89 # Displaying memory usage
90 # logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
91
92 # Stop memory monitoring
93 # tracemalloc.stop()
94
95 if __name__ == "__main__":
96 __main__()