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planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
author rv43
date Thu, 23 Mar 2023 13:39:14 +0000
parents 1cf15b61cd83
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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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('--galaxy_flag',
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27 action='store_true',
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28 help='''Use this flag to run the scripts as a galaxy tool.''')
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29 parser.add_argument('-l', '--log',
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30 # type=argparse.FileType('w'),
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31 default=sys.stdout,
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32 help='Logging stream or filename')
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33 parser.add_argument('--log_level',
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34 choices=logging._nameToLevel.keys(),
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35 default='INFO',
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36 help='''Specify a preferred logging level.''')
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37 parser.add_argument('--x_bounds',
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38 required=False,
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39 nargs=2,
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40 type=int,
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41 help='''Boundaries of reconstructed images in x-direction.''')
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42 parser.add_argument('--y_bounds',
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43 required=False,
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44 nargs=2,
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45 type=int,
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46 help='''Boundaries of reconstructed images in y-direction.''')
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47 args = parser.parse_args()
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49 # Set log configuration
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50 # When logging to file, the stdout log level defaults to WARNING
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51 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
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52 level = logging.getLevelName(args.log_level)
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53 if args.log is sys.stdout:
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54 logging.basicConfig(format=logging_format, level=level, force=True,
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55 handlers=[logging.StreamHandler()])
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56 else:
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57 if isinstance(args.log, str):
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58 logging.basicConfig(filename=f'{args.log}', filemode='w',
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59 format=logging_format, level=level, force=True)
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60 elif isinstance(args.log, io.TextIOWrapper):
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61 logging.basicConfig(filemode='w', format=logging_format, level=level,
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62 stream=args.log, force=True)
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63 else:
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64 raise(ValueError(f'Invalid argument --log: {args.log}'))
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65 stream_handler = logging.StreamHandler()
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66 logging.getLogger().addHandler(stream_handler)
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67 stream_handler.setLevel(logging.WARNING)
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68 stream_handler.setFormatter(logging.Formatter(logging_format))
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69
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70 # Starting memory monitoring
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71 # tracemalloc.start()
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72
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73 # Log command line arguments
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74 logging.info(f'input_file = {args.input_file}')
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75 logging.info(f'output_file = {args.output_file}')
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76 logging.debug(f'log = {args.log}')
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77 logging.debug(f'is log stdout? {args.log is sys.stdout}')
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78 logging.debug(f'log_level = {args.log_level}')
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79 logging.info(f'x_bounds = {args.x_bounds}')
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80 logging.info(f'y_bounds = {args.y_bounds}')
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82 # Instantiate Tomo object
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83 tomo = Tomo(galaxy_flag=args.galaxy_flag)
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84
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85 # Read input file
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86 data = tomo.read(args.input_file)
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87
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88 # Combine the reconstructed tomography stacks
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89 data = tomo.combine_data(data, x_bounds=args.x_bounds, y_bounds=args.y_bounds)
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90
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91 # Write output file
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92 if data is not None:
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93 data = tomo.write(data, args.output_file)
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95 # Displaying memory usage
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96 # logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
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97
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98 # stopping memory monitoring
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99 # tracemalloc.stop()
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101 if __name__ == "__main__":
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102 __main__()