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annotate tomo_combine.py @ 69:fba792d5f83b draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
author rv43
date Fri, 10 Mar 2023 16:02:04 +0000
parents ba5866d0251d
children 1cf15b61cd83
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1 #!/usr/bin/env python3
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3 import logging
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5 import argparse
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6 import pathlib
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7 import sys
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8 #import tracemalloc
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9
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10 from workflow.run_tomo import Tomo
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12 #from memory_profiler import profile
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13 #@profile
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14 def __main__():
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15 # Parse command line arguments
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16 parser = argparse.ArgumentParser(
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17 description='Reduce tomography data')
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18 parser.add_argument('-i', '--input_file',
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19 required=True,
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20 type=pathlib.Path,
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21 help='''Full or relative path to the input file (in Nexus format).''')
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22 parser.add_argument('-o', '--output_file',
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23 required=False,
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24 type=pathlib.Path,
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25 help='''Full or relative path to the output file (in yaml format).''')
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26 parser.add_argument('-l', '--log',
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27 # type=argparse.FileType('w'),
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28 default=sys.stdout,
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29 help='Logging stream or filename')
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30 parser.add_argument('--log_level',
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31 choices=logging._nameToLevel.keys(),
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32 default='INFO',
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33 help='''Specify a preferred logging level.''')
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34 args = parser.parse_args()
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36 # Set log configuration
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37 # When logging to file, the stdout log level defaults to WARNING
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38 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
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39 level = logging.getLevelName(args.log_level)
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40 if args.log is sys.stdout:
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41 logging.basicConfig(format=logging_format, level=level, force=True,
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42 handlers=[logging.StreamHandler()])
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43 else:
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44 if isinstance(args.log, str):
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45 logging.basicConfig(filename=f'{args.log}', filemode='w',
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46 format=logging_format, level=level, force=True)
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47 elif isinstance(args.log, io.TextIOWrapper):
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48 logging.basicConfig(filemode='w', format=logging_format, level=level,
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49 stream=args.log, force=True)
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50 else:
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51 raise(ValueError(f'Invalid argument --log: {args.log}'))
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52 stream_handler = logging.StreamHandler()
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53 logging.getLogger().addHandler(stream_handler)
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54 stream_handler.setLevel(logging.WARNING)
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55 stream_handler.setFormatter(logging.Formatter(logging_format))
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56
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57 # Starting memory monitoring
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58 # tracemalloc.start()
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60 # Log command line arguments
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61 logging.info(f'input_file = {args.input_file}')
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62 logging.info(f'output_file = {args.output_file}')
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63 logging.debug(f'log = {args.log}')
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64 logging.debug(f'is log stdout? {args.log is sys.stdout}')
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65 logging.debug(f'log_level = {args.log_level}')
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67 # Instantiate Tomo object
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68 tomo = Tomo()
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70 # Read input file
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71 data = tomo.read(args.input_file)
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72
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73 # Combine the reconstructed tomography stacks
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74 data = tomo.combine_data(data)
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75
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76 # Write output file
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77 data = tomo.write(data, args.output_file)
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79 # Displaying memory usage
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80 # logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
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81
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82 # stopping memory monitoring
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83 # tracemalloc.stop()
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85 if __name__ == "__main__":
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86 __main__()