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annotate tomo_reconstruct.py @ 3:f9c52762c32c draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
author rv43
date Tue, 05 Apr 2022 18:23:54 +0000
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children 1bcca1f2adb4
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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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8 from tomo import Tomo
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10 def __main__():
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12 # Parse command line arguments
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13 parser = argparse.ArgumentParser(
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14 description='Perfrom a tomography reconstruction')
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15 parser.add_argument('-i', '--input_stacks',
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16 help='Preprocessed image file stacks')
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17 parser.add_argument('-c', '--config',
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18 help='Input config')
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19 parser.add_argument('--output_config',
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20 help='Output config')
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21 parser.add_argument('--output_data',
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22 help='Reconstructed tomography data')
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23 parser.add_argument('-l', '--log',
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24 type=argparse.FileType('w'),
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25 default=sys.stdout,
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26 help='Log file')
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27 args = parser.parse_args()
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29 # Set basic log configuration
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30 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
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31 log_level = 'INFO'
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32 level = getattr(logging, log_level.upper(), None)
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33 if not isinstance(level, int):
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34 raise ValueError(f'Invalid log_level: {log_level}')
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35 logging.basicConfig(format=logging_format, level=level, force=True,
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36 handlers=[logging.StreamHandler()])
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38 logging.debug(f'input_stacks = {args.input_stacks}')
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39 logging.debug(f'config = {args.config}')
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40 logging.debug(f'output_config = {args.output_config}')
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41 logging.debug(f'output_data = {args.output_data}')
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42 logging.debug(f'log = {args.log}')
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43 logging.debug(f'is log stdout? {args.log is sys.stdout}')
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45 # Instantiate Tomo object
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46 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
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47 log_stream=args.log, galaxy_flag=True)
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48 if not tomo.is_valid:
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49 raise ValueError('Invalid config file provided.')
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50 logging.debug(f'config:\n{tomo.config}')
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52 # Load preprocessed image files
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53 tomo.loadTomoStacks(args.input_stacks)
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55 # Reconstruct tomography stacks
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56 tomo.reconstructTomoStacks(args.output_data)
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58 if __name__ == "__main__":
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59 __main__()
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