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annotate tomo_find_center.py @ 34:63de912323e5 draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit c81dfe083e164b51b3688e512f2a0b00b953851c"
author rv43
date Tue, 19 Apr 2022 16:40:34 +0000
parents 1bcca1f2adb4
children ba5866d0251d
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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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7 import tracemalloc
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9 from tomo import Tomo
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11 def __main__():
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13 # Parse command line arguments
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14 parser = argparse.ArgumentParser(
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15 description='Find the center axis for a tomography reconstruction')
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16 parser.add_argument('-i', '--input_stacks',
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17 required=True, help='Preprocessed image file stacks')
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18 parser.add_argument('-c', '--config',
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19 required=True, help='Input config')
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20 parser.add_argument('--row_bounds',
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21 required=True, nargs=2, type=int, help='Reconstruction row bounds')
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22 parser.add_argument('--center_rows',
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23 required=True, nargs=2, type=int, help='Center finding rows')
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24 parser.add_argument('--center_type_selector',
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25 help='Reconstruct slices for a set of center positions?')
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26 parser.add_argument('--set_center',
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27 type=int, help='Set center ')
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28 parser.add_argument('--set_range',
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29 type=float, help='Set range')
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30 parser.add_argument('--set_step',
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31 type=float, help='Set step')
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32 parser.add_argument('--output_config',
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33 required=True, help='Output config')
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34 parser.add_argument('-l', '--log',
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35 type=argparse.FileType('w'), default=sys.stdout, help='Log file')
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36 args = parser.parse_args()
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37
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38 # Starting memory monitoring
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39 tracemalloc.start()
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41 # Set basic log configuration
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42 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
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43 log_level = 'INFO'
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44 level = getattr(logging, log_level.upper(), None)
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45 if not isinstance(level, int):
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46 raise ValueError(f'Invalid log_level: {log_level}')
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47 logging.basicConfig(format=logging_format, level=level, force=True,
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48 handlers=[logging.StreamHandler()])
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50 logging.debug(f'input_stacks = {args.input_stacks}')
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51 logging.debug(f'config = {args.config}')
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52 logging.debug(f'row_bounds = {args.row_bounds} {type(args.row_bounds)}')
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53 logging.debug(f'center_rows = {args.center_rows} {type(args.center_rows)}')
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54 logging.debug(f'center_type_selector = {args.center_type_selector}')
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55 logging.debug(f'set_center = {args.set_center}')
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56 logging.debug(f'set_range = {args.set_range}')
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57 logging.debug(f'set_step = {args.set_step}')
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58 logging.debug(f'output_config = {args.output_config}')
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59 logging.debug(f'log = {args.log}')
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60 logging.debug(f'is log stdout? {args.log is sys.stdout}')
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62 # Instantiate Tomo object
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63 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
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64 log_stream=args.log, galaxy_flag=True)
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65 if not tomo.is_valid:
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66 raise ValueError('Invalid config file provided.')
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67 logging.debug(f'config:\n{tomo.config}')
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69 # Load preprocessed image files
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70 tomo.loadTomoStacks(args.input_stacks)
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72 # Find centers
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73 galaxy_param = {'row_bounds' : args.row_bounds, 'center_rows' : args.center_rows,
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74 'center_type_selector' : args.center_type_selector, 'set_center' : args.set_center,
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75 'set_range' : args.set_range, 'set_step' : args.set_step}
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76 tomo.findCenters(galaxy_param)
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78 # Displaying memory usage
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79 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
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81 # stopping memory monitoring
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82 tracemalloc.stop()
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84 if __name__ == "__main__":
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85 __main__()
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