Mercurial > repos > rv43 > chess_tomo

annotate tomo_find_center.py @ 28:562fc79de827 draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
author rv43
date Tue, 21 Mar 2023 17:59:41 +0000
parents e89919e468cd
children
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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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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='Find the center axis for a tomography reconstruction')
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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('--center_rows',
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27 nargs=2,
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28 type=int,
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29 help='''Center finding rows.''')
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30 parser.add_argument('--galaxy_flag',
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31 action='store_true',
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32 help='''Use this flag to run the scripts as a galaxy tool.''')
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33 parser.add_argument('-l', '--log',
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34 # type=argparse.FileType('w'),
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35 default=sys.stdout,
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36 help='Logging stream or filename')
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37 parser.add_argument('--log_level',
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38 choices=logging._nameToLevel.keys(),
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39 default='INFO',
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40 help='''Specify a preferred logging level.''')
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41 args = parser.parse_args()
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42
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43 # Set log configuration
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44 # When logging to file, the stdout log level defaults to WARNING
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45 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
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46 level = logging.getLevelName(args.log_level)
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47 if args.log is sys.stdout:
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48 logging.basicConfig(format=logging_format, level=level, force=True,
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49 handlers=[logging.StreamHandler()])
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50 else:
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51 if isinstance(args.log, str):
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52 logging.basicConfig(filename=f'{args.log}', filemode='w',
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53 format=logging_format, level=level, force=True)
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54 elif isinstance(args.log, io.TextIOWrapper):
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55 logging.basicConfig(filemode='w', format=logging_format, level=level,
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56 stream=args.log, force=True)
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57 else:
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58 raise(ValueError(f'Invalid argument --log: {args.log}'))
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59 stream_handler = logging.StreamHandler()
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60 logging.getLogger().addHandler(stream_handler)
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61 stream_handler.setLevel(logging.WARNING)
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62 stream_handler.setFormatter(logging.Formatter(logging_format))
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63
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64 # Starting memory monitoring
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65 # tracemalloc.start()
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66
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67 # Log command line arguments
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68 logging.info(f'input_file = {args.input_file}')
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69 logging.info(f'output_file = {args.output_file}')
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70 logging.info(f'center_rows = {args.center_rows}')
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71 logging.info(f'galaxy_flag = {args.galaxy_flag}')
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72 logging.debug(f'log = {args.log}')
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73 logging.debug(f'is log stdout? {args.log is sys.stdout}')
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74 logging.debug(f'log_level = {args.log_level}')
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75
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76 # Instantiate Tomo object
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77 tomo = Tomo(galaxy_flag=args.galaxy_flag)
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78
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79 # Read input file
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80 data = tomo.read(args.input_file)
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81
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82 # Find the calibrated center axis info
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83 data = tomo.find_centers(data, center_rows=args.center_rows)
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84
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85 # Write output file
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86 data = tomo.write(data, args.output_file)
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87
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88 # Displaying memory usage
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89 # logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
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90
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91 # stopping memory monitoring
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92 # tracemalloc.stop()
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93
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94 logging.info('Completed find center axis')
13
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95
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96
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97 if __name__ == "__main__":
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98 __main__()