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annotate tomo_setup.py @ 2:b8977c98800b draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0c40fb274acc13ebf7054379bb49ed13acec918e"
author rv43
date Thu, 31 Mar 2022 20:48:17 +0000
parents cb1b0d757704
children 1bcca1f2adb4
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1 #!/usr/bin/env python3
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3 import logging
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5 import os
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6 import sys
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7 import re
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8 import yaml
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9 import argparse
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10 import numpy as np
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11
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12 from tomo import Tomo
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13 import msnc_tools as msnc
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15 def __main__():
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16
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17 # Parse command line arguments
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18 parser = argparse.ArgumentParser(
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19 description='Setup tomography reconstruction')
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20 parser.add_argument('-i', '--inputfiles',
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21 default='inputfiles.txt',
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22 help='Input file collections')
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23 parser.add_argument('-c', '--config',
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24 help='Input config')
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25 parser.add_argument('--theta_range',
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26 help='Theta range (lower bound, upper bound, number of angles)')
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27 parser.add_argument('--dark',
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28 help='Dark field')
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29 parser.add_argument('--bright',
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30 help='Bright field')
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31 parser.add_argument('--tomo',
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32 help='First tomography image')
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33 parser.add_argument('--detectorbounds',
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34 help='Detector bounds')
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35 parser.add_argument('--output_config',
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36 help='Output config')
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37 parser.add_argument('--output_data',
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38 help='Preprocessed tomography data')
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39 parser.add_argument('-l', '--log',
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40 type=argparse.FileType('w'),
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41 default=sys.stdout,
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42 help='Log file')
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43 parser.add_argument('tomo_ranges', metavar='N', type=int, nargs='+')
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44 args = parser.parse_args()
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45
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46 # Set basic log configuration
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47 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
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48 log_level = 'INFO'
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49 level = getattr(logging, log_level.upper(), None)
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50 if not isinstance(level, int):
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51 raise ValueError(f'Invalid log_level: {log_level}')
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52 logging.basicConfig(format=logging_format, level=level, force=True,
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53 handlers=[logging.StreamHandler()])
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54
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55 logging.debug(f'config = {args.config}')
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56 logging.debug(f'theta_range = {args.theta_range.split()}')
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57 logging.debug(f'dark = {args.dark}')
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58 logging.debug(f'bright = {args.bright}')
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59 logging.debug(f'tomo = {args.tomo}')
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60 logging.debug(f'detectorbounds = {args.detectorbounds}')
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61 logging.debug(f'output_config = {args.output_config}')
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62 logging.debug(f'output_data = {args.output_data}')
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63 logging.debug(f'log = {args.log}')
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64 logging.debug(f'is log stdout? {args.log is sys.stdout}')
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65 logging.debug(f'tomoranges = {args.tomo_ranges}')
0
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66
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67 # Read input files and collect data files info
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68 datasets = []
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69 with open(args.inputfiles) as cf:
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70 for line in cf:
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71 if not line.strip() or line.startswith('#'):
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72 continue
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73 fields = [x.strip() for x in line.split('\t')]
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74 filepath = fields[0]
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75 element_identifier = fields[1] if len(fields) > 1 else fields[0].split('/')[-1]
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76 datasets.append({'element_identifier' : fields[1], 'filepath' : filepath})
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77 logging.debug(f'datasets:\n{datasets}')
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78
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79 # Read and sort data files
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80 collections = []
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81 for dataset in datasets:
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82 element_identifier = [x.strip() for x in dataset['element_identifier'].split('_')]
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83 if len(element_identifier) > 1:
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84 name = element_identifier[0]
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85 else:
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86 name = 'other'
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87 filepath = dataset['filepath']
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88 if not len(collections):
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89 collections = [{'name' : name, 'filepaths' : [filepath]}]
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90 else:
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91 collection = [c for c in collections if c['name'] == name]
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92 if len(collection):
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93 collection[0]['filepaths'].append(filepath)
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94 else:
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95 collection = {'name' : name, 'filepaths' : [filepath]}
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96 collections.append(collection)
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97 logging.debug(f'collections:\n{collections}')
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98 if len(args.tomo_ranges) != 2*len(collections):
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99 raise ValueError('Inconsistent tomo ranges size.')
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100
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101 # Instantiate Tomo object
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102 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
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103 log_stream=args.log, galaxy_flag=True)
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104 if not tomo.is_valid:
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105 raise ValueError('Invalid config file provided.')
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106 logging.debug(f'config:\n{tomo.config}')
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107
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108 # Set theta inputs
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109 theta_range = args.theta_range.split()
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110 config_theta_range = tomo.config.get('theta_range')
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111 if config_theta_range is None:
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112 config_tomo.config['theta_range'] = {'start' : float(theta_range[0]),
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113 'end' : float(theta_range[1]), 'num' : int(theta_range[2])}
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114 else:
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115 config_theta_range['start'] = float(theta_range[0])
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116 config_theta_range['end'] = float(theta_range[1])
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117 config_theta_range['num'] = int(theta_range[2])
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118
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119 # Find dark field files
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120 dark_field = tomo.config['dark_field']
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121 tdf_files = [c['filepaths'] for c in collections if c['name'] == 'tdf']
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122 if len(tdf_files) != 1 or len(tdf_files[0]) < 1:
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123 logging.warning('Unable to obtain dark field files')
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124 assert(dark_field['data_path'] is None)
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125 assert(dark_field['img_start'] == -1)
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126 assert(not dark_field['num'])
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127 tdf_files = [None]
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128 num_collections = 0
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129 else:
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130 dark_field['img_offset'] = args.tomo_ranges[0]
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131 dark_field['num'] = args.tomo_ranges[1]
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132 num_collections = 1
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133
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134 # Find bright field files
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135 bright_field = tomo.config['bright_field']
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136 bright_field['img_offset'] = args.tomo_ranges[2*num_collections]
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137 bright_field['num'] = args.tomo_ranges[2*num_collections+1]
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138 tbf_files = [c['filepaths'] for c in collections if c['name'] == 'tbf']
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139 if len(tbf_files) != 1 or len(tbf_files[0]) < 1:
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140 exit('Unable to obtain bright field files')
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141 num_collections += 1
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142
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143 # Find tomography files
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144 stack_info = tomo.config['stack_info']
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145 if stack_info['num'] != len(collections) - num_collections:
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146 raise ValueError('Inconsistent number of tomography data image sets')
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147 tomo_stack_files = []
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148 for stack in stack_info['stacks']:
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149 stack['img_offset'] = args.tomo_ranges[2*num_collections]
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150 stack['num'] = args.tomo_ranges[2*num_collections+1]
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151 tomo_files = [c['filepaths'] for c in collections if c['name'] == f'set{stack["index"]}']
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152 if len(tomo_files) != 1 or len(tomo_files[0]) < 1:
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153 exit(f'Unable to obtain tomography images for set {stack["index"]}')
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154 tomo_stack_files.append(tomo_files[0])
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155 num_collections += 1
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156
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157 # Preprocess the image files
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158 tomo.genTomoStacks(tdf_files[0], tbf_files[0], tomo_stack_files, args.dark, args.bright,
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159 args.tomo, args.detectorbounds, args.output_data)
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160 if not tomo.is_valid:
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161 IOError('Unable to load all required image files.')
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162
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163 if __name__ == "__main__":
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164 __main__()
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165