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annotate 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
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1 #!/usr/bin/env python3
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3 import logging
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5 import argparse
97c4e2cbbad9 planemo upload for repository https://github.com/rolfverberg/galaxytools commit b891edb4a5881959112ff276f7696bbc36dcea33
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6 import pathlib
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7 import sys
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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 raw or reconstructed image')
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14 parser.add_argument('-i', '--input_file',
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15 required=True,
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16 type=pathlib.Path,
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17 help='''Full or relative path to the input file (in yaml or nxs format).''')
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18 parser.add_argument('--image_type',
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19 required=False,
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20 help='Image type (dark, bright, tomo_raw, tomo_reduced, or reconstructed')
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21 parser.add_argument('--image_index',
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22 required=False,
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23 type=int,
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24 help='Image index (only for raw or reduced images')
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25 parser.add_argument('-l', '--log',
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26 # type=argparse.FileType('w'),
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27 default=sys.stdout,
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28 help='Logging stream or filename')
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29 parser.add_argument('--log_level',
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30 choices=logging._nameToLevel.keys(),
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31 default='INFO',
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32 help='''Specify a preferred logging level.''')
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33 args = parser.parse_args()
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35 # Set log configuration
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36 # When logging to file, the stdout log level defaults to WARNING
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37 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
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38 level = logging.getLevelName(args.log_level)
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39 if args.log is sys.stdout:
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40 logging.basicConfig(format=logging_format, level=level, force=True,
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41 handlers=[logging.StreamHandler()])
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42 else:
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43 if isinstance(args.log, str):
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44 logging.basicConfig(filename=f'{args.log}', filemode='w',
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45 format=logging_format, level=level, force=True)
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46 elif isinstance(args.log, io.TextIOWrapper):
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47 logging.basicConfig(filemode='w', format=logging_format, level=level,
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48 stream=args.log, force=True)
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49 else:
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50 raise(ValueError(f'Invalid argument --log: {args.log}'))
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51 stream_handler = logging.StreamHandler()
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52 logging.getLogger().addHandler(stream_handler)
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53 stream_handler.setLevel(logging.WARNING)
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54 stream_handler.setFormatter(logging.Formatter(logging_format))
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56 # Log command line arguments
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57 logging.info(f'input_file = {args.input_file}')
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58 logging.info(f'image_type = {args.image_type}')
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59 logging.info(f'image_index = {args.image_index}')
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60 logging.debug(f'log = {args.log}')
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61 logging.debug(f'is log stdout? {args.log is sys.stdout}')
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63 # Instantiate Tomo object
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64 tomo = Tomo(galaxy_flag=args.galaxy_flag)
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66 # Read input file
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67 data = tomo.read(args.input_file)
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68 print(f'data:\n{data}')
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70 if __name__ == "__main__":
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71 __main__()
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