Mercurial > repos > rv43 > tomo

annotate detector.py @ 63:98a83f03d91b draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit a9ebbfca439737ae17ddcb0df84408155f964877"
author rv43
date Thu, 18 Aug 2022 14:36:46 +0000
parents 26f99fdd8d61
children 15288e9746e0
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1 import logging
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2 import os
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3 import yaml
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4 from functools import cache
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5 from copy import deepcopy
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6
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7 from .general import *
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9 #from hexrd.instrument import HEDMInstrument, PlanarDetector
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11 class DetectorConfig:
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12 def __init__(self, config_source):
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13
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14 self._config_source = config_source
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15
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16 if isinstance(self._config_source, ((str, bytes, os.PathLike, int))):
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17 self._config_file = self._config_source
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18 self._config = self._load_config_file()
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19 elif isinstance(self._config_source, dict):
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20 self._config_file = None
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21 self._config = self._config_source
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22 else:
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23 self._config_file = None
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24 self._config = False
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26 self._valid = self._validate()
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28 if not self.valid:
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29 logging.error(f'Cannot create a valid instance of {self.__class__.__name__} from {self._config_source}')
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31 def __repr__(self):
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32 return(f'{self.__class__.__name__}({self._config_source.__repr__()})')
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33 def __str__(self):
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34 return(f'{self.__class__.__name__} generated from {self._config_source}')
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35
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36 @property
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37 def config_file(self):
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38 return(self._config_file)
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39 @property
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40 def config(self):
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41 return(deepcopy(self._config))
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42 @property
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43 def valid(self):
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44 return(self._valid)
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46 def load_config_file(self):
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47 raise(NotImplementedError)
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48 def validate(self):
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49 raise(NotImplementedError)
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51 def _load_config_file(self):
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52 if not os.path.isfile(self.config_file):
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53 logging.error(f'{self.config_file} is not a file.')
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54 return(False)
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55 else:
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56 return(self.load_config_file())
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57 def _validate(self):
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58 if not self.config:
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59 logging.error('A configuration must be loaded prior to calling Detector._validate')
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60 return(False)
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61 else:
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62 return(self.validate())
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63 def _write_to_file(self, out_file):
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64 out_file = os.path.abspath(out_file)
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66 current_config_valid = self.validate()
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67 if not current_config_valid:
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68 write_invalid_config = input_yesno(s=f'This {self.__class__.__name__} is not currently valid. Write the configuration to {out_file} anyways?', default='no')
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69 if not write_invalid_config:
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70 logging.info(f'In accordance with user input, the invalid configuration will not be written to {out_file}')
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71 return
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73 if os.access(out_file, os.W_OK):
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74 if os.path.exists(out_file):
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75 overwrite = input_yesno(s=f'{out_file} already exists. Overwrite?', default='no')
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76 if overwrite:
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77 self.write_to_file(out_file)
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78 else:
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79 logging.info(f'In accordance with user input, {out_file} will not be overwritten')
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80 else:
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81 self.write_to_file(out_file)
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82 else:
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83 logging.error(f'Insufficient permissions to write to {out_file}')
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84
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85 def write_to_file(self, out_file):
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86 raise(NotImplementedError)
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87
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88 class YamlDetectorConfig(DetectorConfig):
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89 def __init__(self, config_source, validate_yaml_pars=[]):
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90 self._validate_yaml_pars = validate_yaml_pars
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91 super().__init__(config_source)
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92
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93 def load_config_file(self):
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94 with open(self.config_file, 'r') as infile:
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95 config = yaml.safe_load(infile)
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96 if isinstance(config, dict):
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97 return(config)
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98 else:
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diff changeset
99 logging.error(f'Unable to load {self.config_file} as a dictionary')
49
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100 return(False)
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101
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102 def validate(self):
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103 if not self._validate_yaml_pars:
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diff changeset
104 logging.warning('There are no required parameters provided for this detector configuration.')
49
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105 return(True)
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106
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107 def validate_nested_pars(config, validate_yaml_par):
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diff changeset
108
49
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109 yaml_par_levels = validate_yaml_par.split(':')
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110 first_level_par = yaml_par_levels[0]
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diff changeset
111 try:
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112 first_level_par = int(first_level_par)
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113 except:
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diff changeset
114 pass
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diff changeset
115 try:
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116 next_level_config = config[first_level_par]
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117 if len(yaml_par_levels) > 1:
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118 next_level_pars = ':'.join(yaml_par_levels[1:])
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119 return(validate_nested_pars(next_level_config, next_level_pars))
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120 else:
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121 return(True)
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122 except:
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123 return(False)
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124
63
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diff changeset
125 pars_missing = [p for p in self._validate_yaml_pars if not validate_nested_pars(self.config, p)]
49
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126 if len(pars_missing) > 0:
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127 logging.error(f'Missing item(s) in configuration: {", ".join(pars_missing)}')
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128 return(False)
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129 else:
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130 return(True)
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131
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132 def write_to_file(self, out_file):
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133 with open(out_file, 'w') as outf:
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134 yaml.dump(self.config, outf)
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135
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136
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137 class TomoDetectorConfig(YamlDetectorConfig):
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138 def __init__(self, config_source):
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139 validate_yaml_pars = ['detector',
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140 'lens_magnification',
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141 'detector:pixels:rows',
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142 'detector:pixels:columns',
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143 *[f'detector:pixels:size:{i}' for i in range(2)]]
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144 super().__init__(config_source, validate_yaml_pars=validate_yaml_pars)
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145
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146 @property
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147 @cache
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148 def lens_magnification(self):
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149 lens_magnification = self.config.get('lens_magnification')
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150 if not isinstance(lens_magnification, (int, float)) or lens_magnification <= 0.:
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diff changeset
151 illegal_value(lens_magnification, 'lens_magnification', 'detector file')
63
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diff changeset
152 logging.warning('Using default lens_magnification value of 1.0.')
49
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153 return(1.0)
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154 else:
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diff changeset
155 return(lens_magnification)
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diff changeset
156
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diff changeset
157 @property
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diff changeset
158 @cache
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diff changeset
159 def pixel_size(self):
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diff changeset
160 pixel_size = self.config['detector'].get('pixels').get('size')
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diff changeset
161 if isinstance(pixel_size, (int, float)):
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diff changeset
162 if pixel_size <= 0.:
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diff changeset
163 illegal_value(pixel_size, 'pixel_size', 'detector file')
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diff changeset
164 return(None)
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diff changeset
165 pixel_size /= self.lens_magnification
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diff changeset
166 elif isinstance(pixel_size, list):
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diff changeset
167 if ((len(pixel_size) > 2) or
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parents:
diff changeset
168 (len(pixel_size) == 2 and pixel_size[0] != pixel_size[1])):
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diff changeset
169 illegal_value(pixel_size, 'pixel size', 'detector file')
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diff changeset
170 return(None)
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diff changeset
171 elif not is_num(pixel_size[0], 0.):
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diff changeset
172 illegal_value(pixel_size, 'pixel size', 'detector file')
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diff changeset
173 return(None)
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diff changeset
174 else:
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diff changeset
175 pixel_size = pixel_size[0]/self.lens_magnification
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diff changeset
176 else:
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diff changeset
177 illegal_value(pixel_size, 'pixel size', 'detector file')
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diff changeset
178 return(None)
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179
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diff changeset
180 return(pixel_size)
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181
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diff changeset
182 @property
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diff changeset
183 @cache
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184 def dimensions(self):
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185 pixels = self.config['detector'].get('pixels')
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diff changeset
186 num_rows = pixels.get('rows')
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187 if not is_int(num_rows, 1):
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diff changeset
188 illegal_value(num_rows, 'rows', 'detector file')
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diff changeset
189 return(None)
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190 num_columns = pixels.get('columns')
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191 if not is_int(num_columns, 1):
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diff changeset
192 illegal_value(num_columns, 'columns', 'detector file')
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diff changeset
193 return(None)
63
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diff changeset
194
49
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diff changeset
195 return(num_rows, num_columns)
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196
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diff changeset
197
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diff changeset
198 class EDDDetectorConfig(YamlDetectorConfig):
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199 def __init__(self, config_source):
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200 validate_yaml_pars = ['num_bins',
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201 'max_E',
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202 # 'angle', # KLS leave this out for now -- I think it has to do with the relative geometry of sample, beam, and detector (not a property of the detector on its own), so may not belong here in the DetectorConfig object?
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203 'tth_angle',
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204 'slope',
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205 'intercept']
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206 super().__init__(config_source, validate_yaml_pars=validate_yaml_pars)
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207
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208 @property
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209 @cache
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210 def num_bins(self):
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211 try:
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212 num_bins = int(self.config['num_bins'])
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213 if num_bins <= 0:
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214 raise(ValueError)
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215 else:
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216 return(num_bins)
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217 except:
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218 illegal_value(self.config['num_bins'], 'num_bins')
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219 @property
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220 @cache
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221 def max_E(self):
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222 try:
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223 max_E = float(self.config['max_E'])
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224 if max_E <= 0:
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225 raise(ValueError)
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226 else:
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227 return(max_E)
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228 except:
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229 illegal_value(self.config['max_E'], 'max_E')
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230 return(None)
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231
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232 @property
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233 def bin_energies(self):
63
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diff changeset
234 return(self.slope * np.linspace(0, self.max_E, self.num_bins, endpoint=False) + self.intercept)
49
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235
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236 @property
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237 def tth_angle(self):
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238 try:
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239 return(float(self.config['tth_angle']))
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240 except:
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241 illegal_value(tth_angle, 'tth_angle')
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242 return(None)
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243 @tth_angle.setter
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244 def tth_angle(self, value):
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245 try:
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246 self._config['tth_angle'] = float(value)
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247 except:
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diff changeset
248 illegal_value(value, 'tth_angle')
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249
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250 @property
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251 def slope(self):
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252 try:
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253 return(float(self.config['slope']))
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254 except:
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diff changeset
255 illegal_value(slope, 'slope')
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diff changeset
256 return(None)
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257 @slope.setter
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258 def slope(self, value):
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diff changeset
259 try:
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260 self._config['slope'] = float(value)
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diff changeset
261 except:
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diff changeset
262 illegal_value(value, 'slope')
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diff changeset
263
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diff changeset
264 @property
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diff changeset
265 def intercept(self):
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diff changeset
266 try:
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267 return(float(self.config['intercept']))
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268 except:
26f99fdd8d61 "planemo upload for repository https://github.com/rolfverberg/galaxytools commit 4f7738d02f4a3fd91373f43937ed311b6fe11a12"
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diff changeset
269 illegal_value(intercept, 'intercept')
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diff changeset
270 return(None)
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diff changeset
271 @intercept.setter
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diff changeset
272 def intercept(self, value):
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diff changeset
273 try:
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diff changeset
274 self._config['intercept'] = float(value)
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diff changeset
275 except:
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diff changeset
276 illegal_value(value, 'intercept')
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diff changeset
277
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diff changeset
278
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279 # class HexrdDetectorConfig(YamlDetectorConfig):
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280 # def __init__(self, config_source, detector_names=[]):
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281 # self.detector_names = detector_names
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282 # validate_yaml_pars_each_detector = [*[f'buffer:{i}' for i in range(2)],
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283 # 'distortion:function_name',
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284 # *[f'distortion:parameters:{i}' for i in range(6)],
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285 # 'pixels:columns',
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286 # 'pixels:rows',
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287 # *['pixels:size:%i' % i for i in range(2)],
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288 # 'saturation_level',
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289 # *[f'transform:tilt:{i}' for i in range(3)],
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290 # *[f'transform:translation:{i}' for i in range(3)]]
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291 # validate_yaml_pars = []
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292 # for detector_name in self.detector_names:
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293 # validate_yaml_pars += [f'detectors:{detector_name}:{par}' for par in validate_yaml_pars_each_detector]
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294
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295 # super().__init__(config_source, validate_yaml_pars=validate_yaml_pars)
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296
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297 # def validate(self):
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298 # yaml_valid = YamlDetectorConfig.validate(self)
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299 # if not yaml_valid:
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300 # return(False)
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301 # else:
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302 # hedm_instrument = HEDMInstrument(instrument_config=self.config)
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303 # for detector_name in self.detector_names:
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304 # if detector_name in hedm_instrument.detectors:
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305 # if isinstance(hedm_instrument.detectors[detector_name], PlanarDetector):
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306 # continue
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307 # else:
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308 # return(False)
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309 # else:
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310 # return(False)
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311 # return(True)
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312
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313 # class SAXSWAXSDetectorConfig(DetectorConfig):
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314 # def __init__(self, config_source):
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315 # super().__init__(config_source)
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316
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317 # @property
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318 # def ai(self):
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319 # return(self.config)
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320 # @ai.setter
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321 # def ai(self, value):
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322 # if isinstance(value, pyFAI.azimuthalIntegrator.AzimuthalIntegrator):
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323 # self.config = ai
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324 # else:
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325 # illegal_value(value, 'azimuthal integrator')
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326
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327 # # pyFAI will perform its own error-checking for the mask attribute.
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328 # mask = property(self.ai.get_mask, self.ai,set_mask)
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329
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330
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331