Mercurial > repos > rv43 > tomo

comparison tomo_setup.py @ 15:1bcca1f2adb4 draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
author rv43
date Wed, 13 Apr 2022 16:02:44 +0000
parents b8977c98800b
children ef5c2f7b49ec
comparison
equal deleted inserted replaced
14:50c8d19d5f89 15:1bcca1f2adb4
6 import sys 6 import sys
7 import re 7 import re
8 import yaml 8 import yaml
9 import argparse 9 import argparse
10 import numpy as np 10 import numpy as np
11 import tracemalloc
11 12
12 from tomo import Tomo 13 from tomo import Tomo
13 import msnc_tools as msnc 14 import msnc_tools as msnc
14 15
16 #from memory_profiler import profile
17 #@profile
15 def __main__(): 18 def __main__():
16 19
17 # Parse command line arguments 20 # Parse command line arguments
18 parser = argparse.ArgumentParser( 21 parser = argparse.ArgumentParser(
19 description='Setup tomography reconstruction') 22 description='Setup tomography reconstruction')
40 type=argparse.FileType('w'), 43 type=argparse.FileType('w'),
41 default=sys.stdout, 44 default=sys.stdout,
42 help='Log file') 45 help='Log file')
43 parser.add_argument('tomo_ranges', metavar='N', type=int, nargs='+') 46 parser.add_argument('tomo_ranges', metavar='N', type=int, nargs='+')
44 args = parser.parse_args() 47 args = parser.parse_args()
48
49 # Starting memory monitoring
50 tracemalloc.start()
45 51
46 # Set basic log configuration 52 # Set basic log configuration
47 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s' 53 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
48 log_level = 'INFO' 54 log_level = 'INFO'
49 level = getattr(logging, log_level.upper(), None) 55 level = getattr(logging, log_level.upper(), None)
153 exit(f'Unable to obtain tomography images for set {stack["index"]}') 159 exit(f'Unable to obtain tomography images for set {stack["index"]}')
154 tomo_stack_files.append(tomo_files[0]) 160 tomo_stack_files.append(tomo_files[0])
155 num_collections += 1 161 num_collections += 1
156 162
157 # Preprocess the image files 163 # Preprocess the image files
158 tomo.genTomoStacks(tdf_files[0], tbf_files[0], tomo_stack_files, args.dark, args.bright, 164 galaxy_param = {'tdf_files' : tdf_files[0], 'tbf_files' : tbf_files[0],
159 args.tomo, args.detectorbounds, args.output_data) 165 'tomo_stack_files' : tomo_stack_files, 'dark_field_pngname' : args.dark,
166 'bright_field_pngname' : args.bright, 'tomo_field_pngname' : args.tomo,
167 'detectorbounds_pngname' : args.detectorbounds, 'output_name' : args.output_data}
168 tomo.genTomoStacks(galaxy_param)
160 if not tomo.is_valid: 169 if not tomo.is_valid:
161 IOError('Unable to load all required image files.') 170 IOError('Unable to load all required image files.')
171
172 # Displaying memory usage
173 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
174
175 # stopping memory monitoring
176 tracemalloc.stop()
162 177
163 if __name__ == "__main__": 178 if __name__ == "__main__":
164 __main__() 179 __main__()
165 180