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comparison tomo_setup.py @ 2:d13fd27cb206 draft

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author rv43
date Thu, 24 Mar 2022 16:57:45 +0000
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1:2718cbde04fe 2:d13fd27cb206
1 #!/usr/bin/env python3
2
3 import logging
4
5 import os
6 import sys
7 import re
8 import yaml
9 import argparse
10 import numpy as np
11
12 from tomo import Tomo
13 import msnc_tools as msnc
14
15 def __main__():
16
17 # Parse command line arguments
18 parser = argparse.ArgumentParser(
19 description='Setup tomography reconstruction')
20 parser.add_argument('-i', '--inputfiles',
21 default='inputfiles.txt',
22 help='Input file collections')
23 parser.add_argument('-c', '--config',
24 help='Input config')
25 parser.add_argument('--theta_range',
26 help='Theta range (lower bound, upper bound, number of angles)')
27 parser.add_argument('--dark',
28 help='Dark field')
29 parser.add_argument('--bright',
30 help='Bright field')
31 parser.add_argument('--tomo',
32 help='First tomography image')
33 parser.add_argument('--detectorbounds',
34 help='Detector bounds')
35 parser.add_argument('--output_config',
36 help='Output config')
37 parser.add_argument('--output_data',
38 help='Preprocessed tomography data')
39 parser.add_argument('-l', '--log',
40 type=argparse.FileType('w'),
41 default=sys.stdout,
42 help='Log file')
43 parser.add_argument('tomo_ranges', metavar='N', type=int, nargs='+')
44 args = parser.parse_args()
45
46 # Set basic log configuration
47 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
48 log_level = 'INFO'
49 level = getattr(logging, log_level.upper(), None)
50 if not isinstance(level, int):
51 raise ValueError(f'Invalid log_level: {log_level}')
52 logging.basicConfig(format=logging_format, level=level, force=True,
53 handlers=[logging.StreamHandler()])
54
55 logging.info(f'config = {args.config}\n')
56 logging.info(f'theta_range = {args.theta_range.split()}\n')
57 logging.info(f'dark = {args.dark}\n')
58 logging.info(f'bright = {args.bright}\n')
59 logging.info(f'tomo = {args.tomo}\n')
60 logging.info(f'detectorbounds = {args.detectorbounds}\n')
61 logging.info(f'output_config = {args.output_config}\n')
62 logging.info(f'output_data = {args.output_data}\n')
63 logging.info(f'log = {args.log}')
64 logging.info(f'is log stdout? {args.log == sys.stdout}')
65 logging.info(f'tomoranges = {args.tomo_ranges}\n\n')
66
67 # Read input files and collect data files info
68 logging.debug('data files:\n')
69 datasets = []
70 with open(args.inputfiles) as cf:
71 for line in cf:
72 if not line.strip() or line.startswith('#'):
73 continue
74 fields = [x.strip() for x in line.split('\t')]
75 filepath = fields[0]
76 element_identifier = fields[1] if len(fields) > 1 else fields[0].split('/')[-1]
77 datasets.append({'element_identifier' : fields[1], 'filepath' : filepath})
78 logging.debug(f'\ndatasets: {datasets}\n')
79
80 # Read and sort data files
81 collections = []
82 for dataset in datasets:
83 element_identifier = [x.strip() for x in dataset['element_identifier'].split('_')]
84 if len(element_identifier) > 1:
85 name = element_identifier[0]
86 else:
87 name = 'other'
88 filepath = dataset['filepath']
89 if not len(collections):
90 collections = [{'name' : name, 'filepaths' : [filepath]}]
91 else:
92 collection = [c for c in collections if c['name'] == name]
93 if len(collection):
94 collection[0]['filepaths'].append(filepath)
95 else:
96 collection = {'name' : name, 'filepaths' : [filepath]}
97 collections.append(collection)
98 logging.debug(f'\ncollections:\n{collections}\n\n')
99 if len(args.tomo_ranges) != 2*len(collections):
100 raise ValueError('Inconsistent tomo ranges size.')
101
102 # Instantiate Tomo object
103 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
104 log_stream=args.log, galaxy_flag=True)
105 if not tomo.is_valid:
106 raise ValueError('Invalid config file provided.')
107 logging.debug(f'config:\n{tomo.config}\n\n')
108
109 # Set theta inputs
110 theta_range = args.theta_range.split()
111 config_theta_range = tomo.config.get('theta_range')
112 if config_theta_range is None:
113 config_tomo.config['theta_range'] = {'start' : float(theta_range[0]),
114 'end' : float(theta_range[1]), 'num' : int(theta_range[2])}
115 else:
116 config_theta_range['start'] = float(theta_range[0])
117 config_theta_range['end'] = float(theta_range[1])
118 config_theta_range['num'] = int(theta_range[2])
119 tomo.cf.saveFile(args.output_config)
120
121 # Find dark field files
122 dark_field = tomo.config['dark_field']
123 tdf_files = [c['filepaths'] for c in collections if c['name'] == 'tdf']
124 if len(tdf_files) != 1 or len(tdf_files[0]) < 1:
125 logging.warning('Unable to obtain dark field files')
126 assert(dark_field['data_path'] is None)
127 assert(dark_field['img_start'] == -1)
128 assert(not dark_field['num'])
129 tdf_files = [None]
130 num_collections = 0
131 else:
132 dark_field['img_offset'] = args.tomo_ranges[0]
133 dark_field['num'] = args.tomo_ranges[1]
134 num_collections = 1
135
136 # Find bright field files
137 bright_field = tomo.config['bright_field']
138 bright_field['img_offset'] = args.tomo_ranges[2*num_collections]
139 bright_field['num'] = args.tomo_ranges[2*num_collections+1]
140 tbf_files = [c['filepaths'] for c in collections if c['name'] == 'tbf']
141 if len(tbf_files) != 1 or len(tbf_files[0]) < 1:
142 exit('Unable to obtain bright field files')
143 num_collections += 1
144
145 # Find tomography files
146 stack_info = tomo.config['stack_info']
147 if stack_info['num'] != len(collections) - num_collections:
148 raise ValueError('Inconsistent number of tomography data image sets')
149 tomo_stack_files = []
150 for stack in stack_info['stacks']:
151 stack['img_offset'] = args.tomo_ranges[2*num_collections]
152 stack['num'] = args.tomo_ranges[2*num_collections+1]
153 tomo_files = [c['filepaths'] for c in collections if c['name'] == f'set{stack["index"]}']
154 if len(tomo_files) != 1 or len(tomo_files[0]) < 1:
155 exit(f'Unable to obtain tomography images for set {stack["index"]}\n')
156 tomo_stack_files.append(tomo_files[0])
157 num_collections += 1
158
159 # Preprocess the image files
160 tomo.genTomoStacks(tdf_files[0], tbf_files[0], tomo_stack_files, args.dark, args.bright,
161 args.tomo, args.detectorbounds, args.output_data)
162 if not tomo.is_valid:
163 IOError('Unable to load all required image files.')
164
165 #RV make start_theta, end_theta and num_theta inputs
166
167 if __name__ == "__main__":
168 __main__()
169