Mercurial > repos > rv43 > tomo
diff tomo_setup.py @ 41:ef5c2f7b49ec draft
"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0d207c80e38a6019595ebe178f5678372b75f3e7"
| author | rv43 |
|---|---|
| date | Thu, 21 Apr 2022 14:21:38 +0000 |
| parents | 1bcca1f2adb4 |
| children | 26f99fdd8d61 |
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--- a/tomo_setup.py Tue Apr 19 19:11:59 2022 +0000 +++ b/tomo_setup.py Thu Apr 21 14:21:38 2022 +0000 @@ -27,14 +27,6 @@ help='Input config') parser.add_argument('--theta_range', help='Theta range (lower bound, upper bound, number of angles)') - parser.add_argument('--dark', - help='Dark field') - parser.add_argument('--bright', - help='Bright field') - parser.add_argument('--tomo', - help='First tomography image') - parser.add_argument('--detectorbounds', - help='Detector bounds') parser.add_argument('--output_config', help='Output config') parser.add_argument('--output_data', @@ -60,10 +52,6 @@ logging.debug(f'config = {args.config}') logging.debug(f'theta_range = {args.theta_range.split()}') - logging.debug(f'dark = {args.dark}') - logging.debug(f'bright = {args.bright}') - logging.debug(f'tomo = {args.tomo}') - logging.debug(f'detectorbounds = {args.detectorbounds}') logging.debug(f'output_config = {args.output_config}') logging.debug(f'output_data = {args.output_data}') logging.debug(f'log = {args.log}') @@ -162,9 +150,7 @@ # Preprocess the image files galaxy_param = {'tdf_files' : tdf_files[0], 'tbf_files' : tbf_files[0], - 'tomo_stack_files' : tomo_stack_files, 'dark_field_pngname' : args.dark, - 'bright_field_pngname' : args.bright, 'tomo_field_pngname' : args.tomo, - 'detectorbounds_pngname' : args.detectorbounds, 'output_name' : args.output_data} + 'tomo_stack_files' : tomo_stack_files, 'output_name' : args.output_data} tomo.genTomoStacks(galaxy_param) if not tomo.is_valid: IOError('Unable to load all required image files.')