Mercurial > repos > rv43 > tomo

comparison read_image.py @ 49:26f99fdd8d61 draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
author rv43
date Thu, 28 Jul 2022 16:05:24 +0000
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children 97c4e2cbbad9
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48:059819ea1f0e 49:26f99fdd8d61
1 #!/usr/bin/env python3
2
3 import logging
4
5 import sys
6 import argparse
7 import numpy as np
8
9 def __main__():
10
11 # Parse command line arguments
12 parser = argparse.ArgumentParser(
13 description='Read a reconstructed image')
14 parser.add_argument('-i', '--input_image',
15 help='Reconstructed image file')
16 parser.add_argument('-l', '--log',
17 type=argparse.FileType('w'),
18 default=sys.stdout,
19 help='Log file')
20 args = parser.parse_args()
21
22 # Set basic log configuration
23 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
24 log_level = 'INFO'
25 level = getattr(logging, log_level.upper(), None)
26 if not isinstance(level, int):
27 raise ValueError(f'Invalid log_level: {log_level}')
28 logging.basicConfig(format=logging_format, level=level, force=True,
29 handlers=[logging.StreamHandler()])
30
31 logging.info(f'input_image = {args.input_image}')
32 logging.debug(f'log = {args.log}')
33 logging.debug(f'is log stdout? {args.log is sys.stdout}')
34
35 # Load image
36 f = np.load(args.input_image)
37 logging.info(f'f shape = {f.shape}')
38
39 if __name__ == "__main__":
40 __main__()
41