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annotate tomo_setup.py @ 59:feb2a5fc7c76 draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 9a07ab3099737ee0d99e82739b55048f89c36bc6"
author rv43
date Tue, 16 Aug 2022 16:55:50 +0000
parents bead50a4eadc
children 52db7707ff48
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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 import tracemalloc
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13 from tomo import Tomo
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14
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15 #from memory_profiler import profile
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16 #@profile
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17 def __main__():
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19 # Parse command line arguments
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20 parser = argparse.ArgumentParser(
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21 description='Setup tomography reconstruction')
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22 parser.add_argument('--inputconfig',
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23 default='inputconfig.txt',
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24 help='Input config from tool form')
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25 parser.add_argument('--inputfiles',
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26 default='inputfiles.txt',
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27 help='Input file collections')
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28 parser.add_argument('-c', '--config',
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29 help='Input config file')
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30 parser.add_argument('--num_theta',
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31 help='Number of theta angles')
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32 parser.add_argument('--theta_range',
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33 help='Theta range (lower bound, upper bound)')
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34 parser.add_argument('--output_config',
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35 help='Output config')
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36 parser.add_argument('--output_data',
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37 help='Preprocessed tomography data')
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38 parser.add_argument('-l', '--log',
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39 type=argparse.FileType('w'),
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40 default=sys.stdout,
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41 help='Log file')
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42 args = parser.parse_args()
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44 # Starting memory monitoring
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45 tracemalloc.start()
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46
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47 # Set basic log configuration
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48 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
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49 log_level = 'INFO'
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50 level = getattr(logging, log_level.upper(), None)
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51 if not isinstance(level, int):
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52 raise ValueError(f'Invalid log_level: {log_level}')
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53 logging.basicConfig(format=logging_format, level=level, force=True,
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54 handlers=[logging.StreamHandler()])
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55
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56 logging.info(f'config = {args.config}')
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57 logging.info(f'num_theta = {args.num_theta}')
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58 if args.theta_range is None:
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59 logging.info(f'theta_range = {args.theta_range}')
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60 else:
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61 logging.info(f'theta_range = {args.theta_range.split()}')
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62 logging.info(f'output_config = {args.output_config}')
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63 logging.info(f'output_data = {args.output_data}')
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64 logging.info(f'log = {args.log}')
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65 logging.debug(f'is log stdout? {args.log is sys.stdout}')
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66
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67 # Read tool config input
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68 inputconfig = []
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69 with open(args.inputconfig) as f:
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70 inputconfig = [line.strip() for line in f if line.strip() and not line.startswith('#')]
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71 assert(len(inputconfig) >= 6)
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72 config_type = inputconfig[0]
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73 input_type = inputconfig[1]
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74 num_stack = int(inputconfig[2])
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75 stack_types = [x.strip() for x in inputconfig[3].split()]
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76 num_imgs = [int(x.strip()) for x in inputconfig[4].split()]
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77 img_offsets = [int(x.strip()) for x in inputconfig[5].split()]
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78 if config_type == 'config_manual':
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79 assert(len(inputconfig) == 7)
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80 ref_heights = [float(x.strip()) for x in inputconfig[6].split()]
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81 else:
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82 ref_heights = None
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83 logging.info(f'config_type = {config_type} {type(config_type)}')
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84 logging.info(f'input_type = {input_type} {type(input_type)}')
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85 logging.info(f'num_stack = {num_stack} {type(num_stack)}')
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86 logging.info(f'stack_types = {stack_types} {type(stack_types)}')
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87 logging.info(f'num_imgs = {num_imgs} {type(num_imgs)}')
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88 logging.info(f'img_offsets = {img_offsets} {type(img_offsets)}')
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89 logging.info(f'ref_heights = {ref_heights} {type(ref_heights)}')
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90
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91 # Read input files and collect data files info
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92 datasets = []
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93 with open(args.inputfiles) as f:
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94 for line in f:
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95 if not line.strip() or line.startswith('#'):
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96 continue
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97 fields = [x.strip() for x in line.split('\t')]
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98 filepath = fields[0]
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99 element_identifier = fields[1] if len(fields) > 1 else fields[0].split('/')[-1]
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100 datasets.append({'element_identifier' : fields[1], 'filepath' : filepath})
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101 logging.debug(f'datasets:\n{datasets}')
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102 print(f'datasets:\n{datasets}')
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103
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104 # Read and sort data files
0
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105 collections = []
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106 for dataset in datasets:
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107 element_identifier = [x.strip() for x in dataset['element_identifier'].split('_')]
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108 if len(element_identifier) > 1:
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109 name = element_identifier[0]
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110 else:
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111 name = 'other'
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112 filepath = dataset['filepath']
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113 print(f'element_identifier = {element_identifier} {len(element_identifier)}')
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114 print(f'name = {name}')
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115 print(f'filepath = {filepath}')
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116 if not len(collections):
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117 collections = [{'name' : name, 'filepaths' : [filepath]}]
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118 else:
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119 collection = [c for c in collections if c['name'] == name]
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120 if len(collection):
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121 collection[0]['filepaths'].append(filepath)
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122 else:
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123 collection = {'name' : name, 'filepaths' : [filepath]}
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124 collections.append(collection)
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125 logging.debug(f'collections:\n{collections}')
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126 print(f'collections:\n{collections}')
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127 return
0
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128
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129 # Instantiate Tomo object
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130 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
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131 log_stream=args.log, galaxy_flag=True)
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132 if not tomo.is_valid:
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133 raise ValueError('Invalid config file provided.')
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134 logging.debug(f'config:\n{tomo.config}')
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135
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136 # Set theta inputs
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137 theta_range = args.theta_range.split()
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138 config_theta_range = tomo.config.get('theta_range')
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139 if config_theta_range is None:
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140 config_tomo.config['theta_range'] = {'start' : float(theta_range[0]),
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141 'end' : float(theta_range[1]), 'num' : int(theta_range[2])}
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142 else:
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143 config_theta_range['start'] = float(theta_range[0])
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144 config_theta_range['end'] = float(theta_range[1])
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145 config_theta_range['num'] = int(theta_range[2])
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146
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147 # Find dark field files
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148 dark_field = tomo.config['dark_field']
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149 tdf_files = [c['filepaths'] for c in collections if c['name'] == 'tdf']
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150 if len(tdf_files) != 1 or len(tdf_files[0]) < 1:
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151 logging.warning('Unable to obtain dark field files')
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152 assert(dark_field['data_path'] is None)
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153 assert(dark_field['img_start'] == -1)
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154 assert(not dark_field['num'])
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155 tdf_files = [None]
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156 num_collections = 0
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157 else:
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158 dark_field['img_offset'] = args.tomo_ranges[0]
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159 dark_field['num'] = args.tomo_ranges[1]
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160 num_collections = 1
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161
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162 # Find bright field files
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163 bright_field = tomo.config['bright_field']
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164 bright_field['img_offset'] = args.tomo_ranges[2*num_collections]
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165 bright_field['num'] = args.tomo_ranges[2*num_collections+1]
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166 tbf_files = [c['filepaths'] for c in collections if c['name'] == 'tbf']
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167 if len(tbf_files) != 1 or len(tbf_files[0]) < 1:
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168 exit('Unable to obtain bright field files')
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169 num_collections += 1
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170
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171 # Find tomography files
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172 stack_info = tomo.config['stack_info']
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173 if stack_info['num'] != len(collections) - num_collections:
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174 raise ValueError('Inconsistent number of tomography data image sets')
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175 tomo_stack_files = []
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176 for stack in stack_info['stacks']:
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177 stack['img_offset'] = args.tomo_ranges[2*num_collections]
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178 stack['num'] = args.tomo_ranges[2*num_collections+1]
59
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179 tomo_files = [c['filepaths'] for c in collections if c['name'] == f'set{stack["index"]}']
0
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180 if len(tomo_files) != 1 or len(tomo_files[0]) < 1:
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181 exit(f'Unable to obtain tomography images for set {stack["index"]}')
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182 tomo_stack_files.append(tomo_files[0])
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183 num_collections += 1
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184
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185 # Preprocess the image files
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186 galaxy_param = {'tdf_files' : tdf_files[0], 'tbf_files' : tbf_files[0],
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187 'tomo_stack_files' : tomo_stack_files, 'output_name' : args.output_data}
15
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188 tomo.genTomoStacks(galaxy_param)
0
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189 if not tomo.is_valid:
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190 IOError('Unable to load all required image files.')
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191
15
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192 # Displaying memory usage
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
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193 logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
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194
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
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195 # stopping memory monitoring
1bcca1f2adb4 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 38c19bf5addbc46f45d598f981bb1a48f7bca691"
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196 tracemalloc.stop()
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197
0
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198 if __name__ == "__main__":
cb1b0d757704 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 2da52c7db6def807073a1d437a00e0e2a8e7e72e"
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199 __main__()
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200