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annotate tomo_combine.py @ 64:15288e9746e0 draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 53d0c2b812d01f0567eceb476375444802ed70cf"
author rv43
date Thu, 18 Aug 2022 14:49:16 +0000
parents 059819ea1f0e
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='Combine reconstructed tomography stacks')
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16 parser.add_argument('-i', '--input_stacks',
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17 help='Reconstructed 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('--x_bounds',
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21 required=True, nargs=2, type=int, help='Reconstructed range in x direction')
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22 parser.add_argument('--y_bounds',
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23 required=True, nargs=2, type=int, help='Reconstructed range in y direction')
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24 parser.add_argument('--z_bounds',
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25 required=True, nargs=2, type=int, help='Reconstructed range in z direction')
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26 parser.add_argument('--output_config',
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27 help='Output config')
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28 parser.add_argument('--output_data',
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29 help='Combined tomography stacks')
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30 parser.add_argument('-l', '--log',
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31 type=argparse.FileType('w'),
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32 default=sys.stdout,
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33 help='Log file')
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34 args = parser.parse_args()
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36 # Starting memory monitoring
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37 tracemalloc.start()
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38
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39 # Set basic log configuration
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40 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
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41 log_level = 'INFO'
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42 level = getattr(logging, log_level.upper(), None)
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43 if not isinstance(level, int):
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44 raise ValueError(f'Invalid log_level: {log_level}')
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45 logging.basicConfig(format=logging_format, level=level, force=True,
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46 handlers=[logging.StreamHandler()])
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47
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48 logging.debug(f'input_stacks = {args.input_stacks}')
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49 logging.debug(f'config = {args.config}')
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50 logging.debug(f'x_bounds = {args.x_bounds} {type(args.x_bounds)}')
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51 logging.debug(f'y_bounds = {args.y_bounds} {type(args.y_bounds)}')
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52 logging.debug(f'z_bounds = {args.z_bounds} {type(args.z_bounds)}')
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53 logging.debug(f'output_config = {args.output_config}')
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54 logging.debug(f'output_data = {args.output_data}')
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55 logging.debug(f'log = {args.log}')
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56 logging.debug(f'is log stdout? {args.log is sys.stdout}')
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58 # Instantiate Tomo object
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59 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
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60 log_stream=args.log, galaxy_flag=True)
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61 if not tomo.is_valid:
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62 raise ValueError('Invalid config file provided.')
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63 logging.debug(f'config:\n{tomo.config}')
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65 # Load reconstructed image files
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66 tomo.loadTomoStacks(args.input_stacks, recon_flag=True)
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68 # Combined reconstructed tomography stacks
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69 galaxy_param = {'x_bounds' : args.x_bounds, 'y_bounds' : args.y_bounds,
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70 'z_bounds' : args.z_bounds, 'output_name' : args.output_data}
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71 logging.info(f'galaxy_param = {galaxy_param}')
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72 tomo.combineTomoStacks(galaxy_param)
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73
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74 # Displaying memory usage
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75 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
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77 # stopping memory monitoring
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78 tracemalloc.stop()
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79
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80 if __name__ == "__main__":
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81 __main__()
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