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comparison read_image.py @ 70:97c4e2cbbad9 draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit b891edb4a5881959112ff276f7696bbc36dcea33
author rv43
date Fri, 10 Mar 2023 16:39:22 +0000
parents 26f99fdd8d61
children
comparison
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69:fba792d5f83b 70:97c4e2cbbad9
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
7 import numpy as np
8 8
9 def __main__(): 9 def __main__():
10 10
11 # Parse command line arguments 11 # Parse command line arguments
12 parser = argparse.ArgumentParser( 12 parser = argparse.ArgumentParser(
13 description='Read a reconstructed image') 13 description='Read a raw or reconstructed image')
14 parser.add_argument('-i', '--input_image', 14 parser.add_argument('-i', '--input_file',
15 help='Reconstructed image file') 15 required=True,
16 parser.add_argument('-l', '--log', 16 type=pathlib.Path,
17 type=argparse.FileType('w'), 17 help='''Full or relative path to the input file (in yaml or nxs format).''')
18 parser.add_argument('--image_type',
19 required=False,
20 help='Image type (dark, bright, tomo_raw, tomo_reduced, or reconstructed')
21 parser.add_argument('--image_index',
22 required=False,
23 type=int,
24 help='Image index (only for raw or reduced images')
25 parser.add_argument('-l', '--log',
26 # type=argparse.FileType('w'),
18 default=sys.stdout, 27 default=sys.stdout,
19 help='Log file') 28 help='Logging stream or filename')
29 parser.add_argument('--log_level',
30 choices=logging._nameToLevel.keys(),
31 default='INFO',
32 help='''Specify a preferred logging level.''')
20 args = parser.parse_args() 33 args = parser.parse_args()
21 34
22 # Set basic log configuration 35 # Set log configuration
36 # When logging to file, the stdout log level defaults to WARNING
23 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s' 37 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
24 log_level = 'INFO' 38 level = logging.getLevelName(args.log_level)
25 level = getattr(logging, log_level.upper(), None) 39 if args.log is sys.stdout:
26 if not isinstance(level, int): 40 logging.basicConfig(format=logging_format, level=level, force=True,
27 raise ValueError(f'Invalid log_level: {log_level}') 41 handlers=[logging.StreamHandler()])
28 logging.basicConfig(format=logging_format, level=level, force=True, 42 else:
29 handlers=[logging.StreamHandler()]) 43 if isinstance(args.log, str):
44 logging.basicConfig(filename=f'{args.log}', filemode='w',
45 format=logging_format, level=level, force=True)
46 elif isinstance(args.log, io.TextIOWrapper):
47 logging.basicConfig(filemode='w', format=logging_format, level=level,
48 stream=args.log, force=True)
49 else:
50 raise(ValueError(f'Invalid argument --log: {args.log}'))
51 stream_handler = logging.StreamHandler()
52 logging.getLogger().addHandler(stream_handler)
53 stream_handler.setLevel(logging.WARNING)
54 stream_handler.setFormatter(logging.Formatter(logging_format))
30 55
31 logging.info(f'input_image = {args.input_image}') 56 # Log command line arguments
57 logging.info(f'input_file = {args.input_file}')
58 logging.info(f'image_type = {args.image_type}')
59 logging.info(f'image_index = {args.image_index}')
32 logging.debug(f'log = {args.log}') 60 logging.debug(f'log = {args.log}')
33 logging.debug(f'is log stdout? {args.log is sys.stdout}') 61 logging.debug(f'is log stdout? {args.log is sys.stdout}')
34 62
35 # Load image 63 # Instantiate Tomo object
36 f = np.load(args.input_image) 64 tomo = Tomo(galaxy_flag=args.galaxy_flag)
37 logging.info(f'f shape = {f.shape}') 65
66 # Read input file
67 data = tomo.read(args.input_file)
68 print(f'data:\n{data}')
38 69
39 if __name__ == "__main__": 70 if __name__ == "__main__":
40 __main__() 71 __main__()
41 72