Mercurial > repos > rv43 > tomo

annotate tomo_reconstruct.py @ 68:ba5866d0251d draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 3fde3e85030608a8a4d8e59308353b0144314dfe"
author rv43
date Fri, 19 Aug 2022 20:16:56 +0000
parents 3caba2116858
children fba792d5f83b
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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='Perfrom a tomography reconstruction')
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16 parser.add_argument('-i', '--input_stacks',
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17 help='Preprocessed image file stacks')
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18 parser.add_argument('-c', '--config',
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19 help='Input config')
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20 parser.add_argument('--center_offsets',
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21 nargs=2, type=float, help='Reconstruction center axis offsets')
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22 parser.add_argument('--output_config',
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23 help='Output config')
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24 parser.add_argument('--output_data',
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25 help='Reconstructed tomography data')
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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='Log file')
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30 args = parser.parse_args()
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32 # Starting memory monitoring
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33 tracemalloc.start()
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35 # Set basic log configuration
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36 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
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37 log_level = 'INFO'
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38 level = getattr(logging, log_level.upper(), None)
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39 if not isinstance(level, int):
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40 raise ValueError(f'Invalid log_level: {log_level}')
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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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44 logging.debug(f'config = {args.config}')
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45 logging.debug(f'input_stacks = {args.input_stacks}')
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46 logging.debug(f'center_offsets = {args.center_offsets} {type(args.center_offsets)}')
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47 logging.debug(f'output_config = {args.output_config}')
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48 logging.debug(f'output_data = {args.output_data}')
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49 logging.debug(f'log = {args.log}')
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50 logging.debug(f'is log stdout? {args.log is sys.stdout}')
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52 # Instantiate Tomo object
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53 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
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54 log_stream=args.log, galaxy_flag=True)
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55 if not tomo.is_valid:
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56 raise ValueError('Invalid config file provided.')
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57 logging.debug(f'config:\n{tomo.config}')
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59 # Set reconstruction center axis offsets
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60 if args.center_offsets is None:
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61 find_center = tomo.config.get('find_center')
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62 if find_center is None:
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63 raise ValueError('Invalid config file provided (missing find_center).')
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64 center_offsets = [float(find_center.get('lower_center_offset')),
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65 float(find_center.get('upper_center_offset'))]
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66 else:
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67 center_offsets = args.center_offsets
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69 # Load preprocessed image files
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70 tomo.loadTomoStacks(args.input_stacks)
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72 # Reconstruct tomography stacks
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73 galaxy_param = {'center_offsets' : center_offsets, 'output_name' : args.output_data}
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74 logging.debug(f'galaxy_param = {galaxy_param}')
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75 tomo.reconstructTomoStacks(galaxy_param)
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77 # Displaying memory usage
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78 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
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80 # stopping memory monitoring
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81 tracemalloc.stop()
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83 if __name__ == "__main__":
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84 __main__()
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