Mercurial > repos > rv43 > tomo
annotate tomo_reduce.py @ 75:d5e1d4ea2b7e draft default tip
planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
author | rv43 |
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date | Thu, 23 Mar 2023 13:39:14 +0000 |
parents | 4f4ee8db5f67 |
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fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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1 #!/usr/bin/env python3 |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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2 |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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3 import logging |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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4 |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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5 import argparse |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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6 import pathlib |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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7 import sys |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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8 #import tracemalloc |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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9 |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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10 from workflow.run_tomo import Tomo |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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11 |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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12 #from memory_profiler import profile |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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13 #@profile |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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14 def __main__(): |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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15 # Parse command line arguments |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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16 parser = argparse.ArgumentParser( |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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17 description='Reduce tomography data') |
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4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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18 parser.add_argument('-i', '--input_file', |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
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19 required=True, |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
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20 type=pathlib.Path, |
75
d5e1d4ea2b7e
planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
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21 help='''Full or relative path to the input file (in yaml or Nexus format).''') |
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4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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22 parser.add_argument('-o', '--output_file', |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
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23 required=True, |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
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24 type=pathlib.Path, |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
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25 help='''Full or relative path to the output file (in Nexus format).''') |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
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26 parser.add_argument('--galaxy_flag', |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
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27 action='store_true', |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
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28 help='''Use this flag to run the scripts as a galaxy tool.''') |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
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29 parser.add_argument('--img_x_bounds', |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
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30 required=False, |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
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31 nargs=2, |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
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32 type=int, |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
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33 help='Vertical data reduction image range') |
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fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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34 parser.add_argument('-l', '--log', |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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35 # type=argparse.FileType('w'), |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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36 default=sys.stdout, |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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37 help='Logging stream or filename') |
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4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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38 parser.add_argument('--log_level', |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
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39 choices=logging._nameToLevel.keys(), |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
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40 default='INFO', |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
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41 help='''Specify a preferred logging level.''') |
69
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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42 args = parser.parse_args() |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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43 |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
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44 # Set log configuration |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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45 # When logging to file, the stdout log level defaults to WARNING |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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46 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s' |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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47 level = logging.getLevelName(args.log_level) |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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48 if args.log is sys.stdout: |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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49 logging.basicConfig(format=logging_format, level=level, force=True, |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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50 handlers=[logging.StreamHandler()]) |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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51 else: |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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52 if isinstance(args.log, str): |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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53 logging.basicConfig(filename=f'{args.log}', filemode='w', |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
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54 format=logging_format, level=level, force=True) |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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55 elif isinstance(args.log, io.TextIOWrapper): |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
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56 logging.basicConfig(filemode='w', format=logging_format, level=level, |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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57 stream=args.log, force=True) |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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58 else: |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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59 raise(ValueError(f'Invalid argument --log: {args.log}')) |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
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60 stream_handler = logging.StreamHandler() |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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61 logging.getLogger().addHandler(stream_handler) |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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62 stream_handler.setLevel(logging.WARNING) |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
parents:
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63 stream_handler.setFormatter(logging.Formatter(logging_format)) |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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64 |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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65 # Start memory monitoring |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
rv43
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66 # tracemalloc.start() |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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67 |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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68 # Log command line arguments |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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69 logging.info(f'input_file = {args.input_file}') |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
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70 logging.info(f'output_file = {args.output_file}') |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
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71 logging.info(f'galaxy_flag = {args.galaxy_flag}') |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
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72 logging.info(f'img_x_bounds = {args.img_x_bounds}') |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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parents:
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73 logging.debug(f'log = {args.log}') |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
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74 logging.debug(f'is log stdout? {args.log is sys.stdout}') |
4f4ee8db5f67
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
rv43
parents:
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75 logging.debug(f'log_level = {args.log_level}') |
69
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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76 |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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77 # Instantiate Tomo object |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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78 tomo = Tomo(galaxy_flag=args.galaxy_flag) |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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79 |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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80 # Read input file |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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81 data = tomo.read(args.input_file) |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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82 |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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83 # Generate reduced tomography images |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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84 data = tomo.gen_reduced_data(data, img_x_bounds=args.img_x_bounds) |
69
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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85 |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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86 # Write output file |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
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87 data = tomo.write(data, args.output_file) |
69
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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88 |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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89 # Displaying memory usage |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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90 # logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}') |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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91 |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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92 # Stop memory monitoring |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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93 # tracemalloc.stop() |
fba792d5f83b
planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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94 |
75
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
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95 logging.info('Completed tomography data reduction') |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
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96 |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69
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97 |
69
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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98 if __name__ == "__main__": |
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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
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99 __main__() |