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annotate tomo_find_center.py @ 3:f9c52762c32c draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 7dce44d576e4149f31bdc2ee4dce0bb6962badb6"
author rv43
date Tue, 05 Apr 2022 18:23:54 +0000
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children 845270a96464
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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 re
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7 import argparse
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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 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('--row_bounds',
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21 help='Reconstruction row bounds')
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22 parser.add_argument('--center_rows',
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23 help='Center finding rows')
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24 parser.add_argument('--output_config',
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25 help='Output config')
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26 parser.add_argument('--recon_center_low',
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27 help='Lower reconstructed slice center')
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28 parser.add_argument('--recon_center_upp',
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29 help='Upper reconstructed slice center')
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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 indexRegex = re.compile(r'\d+')
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37 row_bounds = [int(i) for i in indexRegex.findall(args.row_bounds)]
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38 center_rows = [int(i) for i in indexRegex.findall(args.center_rows)]
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40 # Set basic log configuration
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41 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
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42 log_level = 'INFO'
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43 level = getattr(logging, log_level.upper(), None)
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44 if not isinstance(level, int):
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45 raise ValueError(f'Invalid log_level: {log_level}')
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46 logging.basicConfig(format=logging_format, level=level, force=True,
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47 handlers=[logging.StreamHandler()])
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49 logging.debug(f'input_stacks = {args.input_stacks}')
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50 logging.debug(f'config = {args.config}')
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51 logging.debug(f'row_bounds = {args.row_bounds} {row_bounds}')
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52 logging.debug(f'center_rows = {args.center_rows} {center_rows}')
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53 logging.debug(f'output_config = {args.output_config}')
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54 logging.debug(f'recon_center_low = {args.recon_center_low}')
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55 logging.debug(f'recon_center_uppm = {args.recon_center_upp}')
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56 logging.debug(f'log = {args.log}')
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57 logging.debug(f'is log stdout? {args.log is sys.stdout}')
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59 # Instantiate Tomo object
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60 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
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61 log_stream=args.log, galaxy_flag=True)
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62 if not tomo.is_valid:
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63 raise ValueError('Invalid config file provided.')
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64 logging.debug(f'config:\n{tomo.config}')
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66 # Load preprocessed image files
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67 tomo.loadTomoStacks(args.input_stacks)
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69 # Find centers
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70 tomo.findCenters(row_bounds, center_rows, args.recon_center_low, args.recon_center_upp)
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72 if __name__ == "__main__":
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73 __main__()
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