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annotate read_image.py @ 63:98a83f03d91b draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit a9ebbfca439737ae17ddcb0df84408155f964877"
author rv43
date Thu, 18 Aug 2022 14:36:46 +0000
parents 26f99fdd8d61
children 97c4e2cbbad9
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26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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1 #!/usr/bin/env python3
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3 import logging
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5 import sys
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6 import argparse
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7 import numpy as np
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9 def __main__():
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11 # Parse command line arguments
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12 parser = argparse.ArgumentParser(
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13 description='Read a reconstructed image')
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14 parser.add_argument('-i', '--input_image',
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15 help='Reconstructed image file')
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16 parser.add_argument('-l', '--log',
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17 type=argparse.FileType('w'),
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18 default=sys.stdout,
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19 help='Log file')
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20 args = parser.parse_args()
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22 # Set basic log configuration
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23 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
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24 log_level = 'INFO'
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25 level = getattr(logging, log_level.upper(), None)
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26 if not isinstance(level, int):
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27 raise ValueError(f'Invalid log_level: {log_level}')
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28 logging.basicConfig(format=logging_format, level=level, force=True,
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29 handlers=[logging.StreamHandler()])
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31 logging.info(f'input_image = {args.input_image}')
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32 logging.debug(f'log = {args.log}')
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33 logging.debug(f'is log stdout? {args.log is sys.stdout}')
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35 # Load image
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36 f = np.load(args.input_image)
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37 logging.info(f'f shape = {f.shape}')
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39 if __name__ == "__main__":
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40 __main__()
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