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comparison tomo_setup.py @ 68:ba5866d0251d draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 3fde3e85030608a8a4d8e59308353b0144314dfe"
author rv43
date Fri, 19 Aug 2022 20:16:56 +0000
parents 98a83f03d91b
children
comparison
equal deleted inserted replaced
67:87a4acead65c 68:ba5866d0251d
55 raise ValueError(f'Invalid log_level: {log_level}') 55 raise ValueError(f'Invalid log_level: {log_level}')
56 logging.basicConfig(format=logging_format, level=level, force=True, 56 logging.basicConfig(format=logging_format, level=level, force=True,
57 handlers=[logging.StreamHandler()]) 57 handlers=[logging.StreamHandler()])
58 58
59 # Check command line arguments 59 # Check command line arguments
60 logging.info(f'config = {args.config}') 60 logging.debug(f'config = {args.config}')
61 if args.detector is None: 61 if args.detector is None:
62 logging.info(f'detector = {args.detector}') 62 logging.debug(f'detector = {args.detector}')
63 else: 63 else:
64 logging.info(f'detector = {args.detector.split()}') 64 logging.debug(f'detector = {args.detector.split()}')
65 logging.info(f'num_theta = {args.num_theta}') 65 logging.debug(f'num_theta = {args.num_theta}')
66 if args.theta_range is None: 66 if args.theta_range is None:
67 logging.info(f'theta_range = {args.theta_range}') 67 logging.debug(f'theta_range = {args.theta_range}')
68 else: 68 else:
69 logging.info(f'theta_range = {args.theta_range.split()}') 69 logging.debug(f'theta_range = {args.theta_range.split()}')
70 logging.info(f'output_config = {args.output_config}') 70 logging.debug(f'output_config = {args.output_config}')
71 logging.info(f'output_data = {args.output_data}') 71 logging.debug(f'output_data = {args.output_data}')
72 logging.info(f'log = {args.log}') 72 logging.debug(f'log = {args.log}')
73 logging.debug(f'is log stdout? {args.log is sys.stdout}') 73 logging.debug(f'is log stdout? {args.log is sys.stdout}')
74 if args.detector is not None and len(args.detector.split()) != 3: 74 if args.detector is not None and len(args.detector.split()) != 3:
75 raise ValueError(f'Invalid detector: {args.detector}') 75 raise ValueError(f'Invalid detector: {args.detector}')
76 if args.num_theta is None or int(args.num_theta) < 1: 76 if args.num_theta is None or int(args.num_theta) < 1:
77 raise ValueError(f'Invalid num_theta: {args.num_theta}') 77 raise ValueError(f'Invalid num_theta: {args.num_theta}')
95 ref_heights = [float(x.strip()) for x in inputconfig[6].split()] 95 ref_heights = [float(x.strip()) for x in inputconfig[6].split()]
96 assert(args.detector is not None) 96 assert(args.detector is not None)
97 assert(args.theta_range is not None) 97 assert(args.theta_range is not None)
98 else: 98 else:
99 ref_heights = None 99 ref_heights = None
100 logging.info(f'config_type = {config_type} {type(config_type)}') 100 logging.debug(f'config_type = {config_type} {type(config_type)}')
101 logging.info(f'input_type = {input_type} {type(input_type)}') 101 logging.debug(f'input_type = {input_type} {type(input_type)}')
102 logging.info(f'num_stack = {num_stack} {type(num_stack)}') 102 logging.debug(f'num_stack = {num_stack} {type(num_stack)}')
103 logging.info(f'stack_types = {stack_types} {type(stack_types)}') 103 logging.debug(f'stack_types = {stack_types} {type(stack_types)}')
104 logging.info(f'num_imgs = {num_imgs} {type(num_imgs)}') 104 logging.debug(f'num_imgs = {num_imgs} {type(num_imgs)}')
105 logging.info(f'img_offsets = {img_offsets} {type(img_offsets)}') 105 logging.debug(f'img_offsets = {img_offsets} {type(img_offsets)}')
106 logging.info(f'ref_heights = {ref_heights} {type(ref_heights)}') 106 logging.debug(f'ref_heights = {ref_heights} {type(ref_heights)}')
107 if config_type != 'config_file' and config_type != 'config_manual': 107 if config_type != 'config_file' and config_type != 'config_manual':
108 raise ValueError('Invalid input config provided.') 108 raise ValueError('Invalid input config provided.')
109 if input_type != 'collections' and input_type != 'files': 109 if input_type != 'collections' and input_type != 'files':
110 raise ValueError('Invalid input config provided.') 110 raise ValueError('Invalid input config provided.')
111 if len(stack_types) != num_stack: 111 if len(stack_types) != num_stack:
196 if len(tdf_files) != 1 or len(tdf_files[0]) < 1: 196 if len(tdf_files) != 1 or len(tdf_files[0]) < 1:
197 logging.warning('Unable to obtain dark field files') 197 logging.warning('Unable to obtain dark field files')
198 if config_type == 'config_file': 198 if config_type == 'config_file':
199 assert(dark_field is not None) 199 assert(dark_field is not None)
200 assert(dark_field['data_path'] is None) 200 assert(dark_field['data_path'] is None)
201 assert(dark_field['img_start'] == -1) 201 if dark_field.get('img_start') is None or dark_field['img_start'] != -1:
202 assert(not dark_field['num']) 202 dark_field['img_start'] = -1
203 if dark_field.get('num') is None or dark_field['num'] != 0:
204 dark_field['num'] = 0
203 else: 205 else:
204 tomo.config['dark_field'] = {'data_path' : None, 'img_start' : -1, 'num' : 0} 206 tomo.config['dark_field'] = {'data_path' : None, 'img_start' : -1, 'num' : 0}
205 tdf_files = [None] 207 tdf_files = [None]
206 num_collections = 0 208 num_collections = 0
207 else: 209 else:
208 if config_type == 'config_file': 210 if config_type == 'config_file':
209 assert(dark_field is not None) 211 assert(dark_field is not None)
210 assert(dark_field['data_path'] is not None) 212 assert(dark_field['data_path'] is not None)
211 assert(dark_field.get('img_start') is not None) 213 if dark_field.get('img_start') is None:
214 dark_field['img_start'] = 0
212 else: 215 else:
213 tomo.config['dark_field'] = {'data_path' : tdf_files[0], 'img_start' : 0} 216 tomo.config['dark_field'] = {'data_path' : tdf_files[0], 'img_start' : 0}
214 dark_field = tomo.config['dark_field'] 217 dark_field = tomo.config['dark_field']
215 tdf_index = [i for i,c in enumerate(collections) if c['name'] == 'tdf'] 218 tdf_index = [i for i,c in enumerate(collections) if c['name'] == 'tdf']
216 tdf_index_check = [i for i,s in enumerate(stack_types) if s == 'tdf'] 219 tdf_index_check = [i for i,s in enumerate(stack_types) if s == 'tdf']
227 if len(tbf_files) != 1 or len(tbf_files[0]) < 1: 230 if len(tbf_files) != 1 or len(tbf_files[0]) < 1:
228 exit('Unable to obtain bright field files') 231 exit('Unable to obtain bright field files')
229 if config_type == 'config_file': 232 if config_type == 'config_file':
230 assert(bright_field is not None) 233 assert(bright_field is not None)
231 assert(bright_field['data_path'] is not None) 234 assert(bright_field['data_path'] is not None)
232 assert(bright_field.get('img_start') is not None) 235 if bright_field.get('img_start') is None:
236 bright_field['img_start'] = 0
233 else: 237 else:
234 tomo.config['bright_field'] = {'data_path' : tbf_files[0], 'img_start' : 0} 238 tomo.config['bright_field'] = {'data_path' : tbf_files[0], 'img_start' : 0}
235 bright_field = tomo.config['bright_field'] 239 bright_field = tomo.config['bright_field']
236 tbf_index = [i for i,c in enumerate(collections) if c['name'] == 'tbf'] 240 tbf_index = [i for i,c in enumerate(collections) if c['name'] == 'tbf']
237 tbf_index_check = [i for i,s in enumerate(stack_types) if s == 'tbf'] 241 tbf_index_check = [i for i,s in enumerate(stack_types) if s == 'tbf']
249 if stack_info['num'] != len(collections) - num_collections: 253 if stack_info['num'] != len(collections) - num_collections:
250 raise ValueError('Inconsistent number of tomography data image sets') 254 raise ValueError('Inconsistent number of tomography data image sets')
251 assert(stack_info.get('stacks') is not None) 255 assert(stack_info.get('stacks') is not None)
252 for stack in stack_info['stacks']: 256 for stack in stack_info['stacks']:
253 assert(stack['data_path'] is not None) 257 assert(stack['data_path'] is not None)
254 assert(stack.get('img_start') is not None) 258 if stack.get('img_start') is None:
259 stack['img_start'] = 0
255 assert(stack.get('index') is not None) 260 assert(stack.get('index') is not None)
256 assert(stack.get('ref_height') is not None) 261 assert(stack.get('ref_height') is not None)
257 else: 262 else:
258 tomo.config['stack_info'] = {'num' : len(collections) - num_collections, 'stacks' : []} 263 tomo.config['stack_info'] = {'num' : len(collections) - num_collections, 'stacks' : []}
259 stack_info = tomo.config['stack_info'] 264 stack_info = tomo.config['stack_info']