1 | """ |
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2 | Convert models to and from sasview. |
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3 | """ |
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4 | from __future__ import print_function |
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5 | |
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6 | from os.path import join as joinpath, abspath, dirname |
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7 | import math |
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8 | import warnings |
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9 | |
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10 | from .conversion_table import CONVERSION_TABLE |
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11 | |
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12 | # List of models which SasView versions don't contain the explicit 'scale' argument. |
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13 | # When converting such a model, please update this list. |
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14 | MODELS_WITHOUT_SCALE = [ |
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15 | 'teubner_strey', |
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16 | 'broad_peak', |
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17 | 'two_lorentzian', |
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18 | "two_power_law", |
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19 | 'gel_fit', |
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20 | 'gauss_lorentz_gel', |
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21 | 'be_polyelectrolyte', |
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22 | 'correlation_length', |
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23 | 'fractal_core_shell', |
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24 | 'binary_hard_sphere', |
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25 | 'raspberry' |
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26 | ] |
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27 | |
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28 | # List of models which SasView versions don't contain the explicit 'background' argument. |
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29 | # When converting such a model, please update this list. |
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30 | MODELS_WITHOUT_BACKGROUND = [ |
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31 | 'guinier', |
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32 | ] |
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33 | |
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34 | MODELS_WITHOUT_VOLFRACTION = [ |
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35 | 'fractal', |
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36 | 'vesicle', |
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37 | 'multilayer_vesicle', |
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38 | ] |
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39 | |
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40 | MAGNETIC_SASVIEW_MODELS = [ |
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41 | 'core_shell', |
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42 | 'core_multi_shell', |
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43 | 'cylinder', |
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44 | 'parallelepiped', |
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45 | 'sphere', |
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46 | ] |
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47 | |
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48 | |
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49 | # Convert new style names for polydispersity info to old style names |
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50 | PD_DOT = [ |
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51 | ("", ""), |
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52 | ("_pd", ".width"), |
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53 | ("_pd_n", ".npts"), |
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54 | ("_pd_nsigma", ".nsigmas"), |
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55 | ("_pd_type", ".type"), |
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56 | ] |
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57 | |
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58 | def _convert_pars(pars, mapping): |
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59 | """ |
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60 | Rename the parameters and any associated polydispersity attributes. |
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61 | """ |
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62 | newpars = pars.copy() |
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63 | for new, old in mapping.items(): |
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64 | if old == new: continue |
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65 | for underscore, dot in PD_DOT: |
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66 | if old+dot in newpars: |
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67 | if new is not None: |
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68 | newpars[new+underscore] = pars[old+dot] |
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69 | del newpars[old+dot] |
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70 | return newpars |
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71 | |
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72 | def convert_model(name, pars): |
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73 | """ |
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74 | Convert model from old style parameter names to new style. |
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75 | """ |
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76 | _, _ = name, pars # lint |
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77 | raise NotImplementedError |
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78 | # need to load all new models in order to determine old=>new |
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79 | # model name mapping |
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80 | |
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81 | def _unscale(par, scale): |
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82 | return [pk*scale for pk in par] if isinstance(par, list) else par*scale |
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83 | |
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84 | def _is_sld(modelinfo, id): |
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85 | if id.startswith('M0:'): |
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86 | return True |
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87 | if (id.endswith('_pd') or id.endswith('_pd_n') or id.endswith('_pd_nsigma') |
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88 | or id.endswith('_pd_width') or id.endswith('_pd_type')): |
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89 | return False |
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90 | for p in modelinfo.parameters.call_parameters: |
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91 | if p.id == id: |
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92 | return p.type == 'sld' |
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93 | # check through kernel parameters in case it is a named as a vector |
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94 | for p in modelinfo.parameters.kernel_parameters: |
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95 | if p.id == id: |
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96 | return p.type == 'sld' |
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97 | raise ValueError("unknown parameter %r in conversion"%id) |
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98 | |
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99 | def _unscale_sld(modelinfo, pars): |
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100 | """ |
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101 | rescale all sld parameters in the new model definition by 1e6 so the |
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102 | numbers are nicer. Relies on the fact that all sld parameters in the |
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103 | new model definition end with sld. |
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104 | """ |
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105 | return dict((id, (_unscale(v, 1e-6) if _is_sld(modelinfo, id) else v)) |
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106 | for id, v in pars.items()) |
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107 | |
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108 | def _remove_pd(pars, key, name): |
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109 | """ |
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110 | Remove polydispersity from the parameter list. |
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111 | |
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112 | Note: operates in place |
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113 | """ |
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114 | # Bumps style parameter names |
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115 | width = pars.pop(key+".width", 0.0) |
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116 | n_points = pars.pop(key+".npts", 0) |
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117 | if width != 0.0 and n_points != 0: |
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118 | warnings.warn("parameter %s not polydisperse in sasview %s"%(key, name)) |
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119 | pars.pop(key+".nsigmas", None) |
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120 | pars.pop(key+".type", None) |
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121 | return pars |
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122 | |
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123 | def _revert_pars(pars, mapping): |
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124 | """ |
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125 | Rename the parameters and any associated polydispersity attributes. |
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126 | """ |
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127 | newpars = pars.copy() |
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128 | |
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129 | for new, old in mapping.items(): |
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130 | for underscore, dot in PD_DOT: |
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131 | if old and old+underscore == new+dot: |
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132 | continue |
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133 | if new+underscore in newpars: |
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134 | if old is not None: |
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135 | newpars[old+dot] = pars[new+underscore] |
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136 | del newpars[new+underscore] |
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137 | for k in list(newpars.keys()): |
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138 | for underscore, dot in PD_DOT[1:]: # skip "" => "" |
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139 | if k.endswith(underscore): |
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140 | newpars[k[:-len(underscore)]+dot] = newpars[k] |
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141 | del newpars[k] |
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142 | return newpars |
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143 | |
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144 | def revert_name(model_info): |
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145 | oldname, _ = CONVERSION_TABLE.get(model_info.id, [None, {}]) |
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146 | return oldname |
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147 | |
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148 | def _get_translation_table(model_info): |
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149 | _, translation = CONVERSION_TABLE.get(model_info.id, [None, {}]) |
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150 | translation = translation.copy() |
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151 | for p in model_info.parameters.kernel_parameters: |
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152 | if p.length > 1: |
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153 | newid = p.id |
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154 | oldid = translation.get(p.id, p.id) |
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155 | translation.pop(newid, None) |
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156 | for k in range(1, p.length+1): |
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157 | if newid+str(k) not in translation: |
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158 | translation[newid+str(k)] = oldid+str(k) |
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159 | # Remove control parameter from the result |
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160 | if model_info.control: |
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161 | translation[model_info.control] = "CONTROL" |
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162 | return translation |
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163 | |
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164 | def _trim_vectors(model_info, pars, oldpars): |
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165 | _, translation = CONVERSION_TABLE.get(model_info.id, [None, {}]) |
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166 | for p in model_info.parameters.kernel_parameters: |
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167 | if p.length_control is not None: |
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168 | n = int(pars[p.length_control]) |
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169 | oldname = translation.get(p.id, p.id) |
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170 | for k in range(n+1, p.length+1): |
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171 | for _, old in PD_DOT: |
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172 | oldpars.pop(oldname+str(k)+old, None) |
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173 | return oldpars |
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174 | |
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175 | def revert_pars(model_info, pars): |
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176 | """ |
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177 | Convert model from new style parameter names to old style. |
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178 | """ |
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179 | if model_info.composition is not None: |
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180 | composition_type, parts = model_info.composition |
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181 | if composition_type == 'product': |
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182 | translation = {'scale':'scale_factor'} |
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183 | translation.update(_get_translation_table(parts[0])) |
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184 | translation.update(_get_translation_table(parts[1])) |
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185 | else: |
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186 | raise NotImplementedError("cannot convert to sasview sum") |
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187 | else: |
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188 | translation = _get_translation_table(model_info) |
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189 | oldpars = _revert_pars(_unscale_sld(model_info, pars), translation) |
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190 | oldpars = _trim_vectors(model_info, pars, oldpars) |
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191 | |
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192 | # Make sure the control parameter is an integer |
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193 | if "CONTROL" in oldpars: |
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194 | oldpars["CONTROL"] = int(oldpars["CONTROL"]) |
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195 | |
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196 | # Note: update compare.constrain_pars to match |
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197 | name = model_info.id |
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198 | if name in MODELS_WITHOUT_SCALE or model_info.structure_factor: |
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199 | if oldpars.pop('scale', 1.0) != 1.0: |
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200 | warnings.warn("parameter scale not used in sasview %s"%name) |
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201 | if name in MODELS_WITHOUT_BACKGROUND or model_info.structure_factor: |
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202 | if oldpars.pop('background', 0.0) != 0.0: |
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203 | warnings.warn("parameter background not used in sasview %s"%name) |
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204 | |
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205 | # Remove magnetic parameters from non-magnetic sasview models |
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206 | if name not in MAGNETIC_SASVIEW_MODELS: |
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207 | oldpars = dict((k, v) for k, v in oldpars.items() if ':' not in k) |
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208 | |
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209 | # If it is a product model P*S, then check the individual forms for special |
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210 | # cases. Note: despite the structure factor alone not having scale or |
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211 | # background, the product model does, so this is below the test for |
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212 | # models without scale or background. |
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213 | namelist = name.split('*') if '*' in name else [name] |
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214 | for name in namelist: |
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215 | if name in MODELS_WITHOUT_VOLFRACTION: |
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216 | del oldpars['volfraction'] |
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217 | if name == 'stacked_disks': |
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218 | _remove_pd(oldpars, 'n_stacking', name) |
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219 | elif name == 'pearl_necklace': |
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220 | _remove_pd(oldpars, 'num_pearls', name) |
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221 | _remove_pd(oldpars, 'thick_string', name) |
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222 | elif name == 'core_shell_parallelepiped': |
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223 | _remove_pd(oldpars, 'rimA', name) |
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224 | _remove_pd(oldpars, 'rimB', name) |
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225 | _remove_pd(oldpars, 'rimC', name) |
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226 | elif name == 'polymer_micelle': |
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227 | if 'ndensity' in oldpars: |
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228 | oldpars['ndensity'] *= 1e15 |
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229 | elif name == 'spherical_sld': |
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230 | oldpars["CONTROL"] -= 1 |
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231 | # remove polydispersity from shells |
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232 | for k in range(1, 11): |
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233 | _remove_pd(oldpars, 'thick_flat'+str(k), 'thickness') |
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234 | _remove_pd(oldpars, 'thick_inter'+str(k), 'interface') |
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235 | # remove extra shells |
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236 | for k in range(int(pars['n_shells']), 11): |
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237 | oldpars.pop('sld_flat'+str(k), 0) |
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238 | oldpars.pop('thick_flat'+str(k), 0) |
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239 | oldpars.pop('thick_inter'+str(k), 0) |
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240 | oldpars.pop('func_inter'+str(k), 0) |
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241 | oldpars.pop('nu_inter'+str(k), 0) |
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242 | elif name == 'core_multi_shell': |
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243 | # kill extra shells |
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244 | for k in range(5, 11): |
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245 | oldpars.pop('sld_shell'+str(k), 0) |
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246 | oldpars.pop('thick_shell'+str(k), 0) |
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247 | oldpars.pop('mtheta:sld'+str(k), 0) |
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248 | oldpars.pop('mphi:sld'+str(k), 0) |
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249 | oldpars.pop('M0:sld'+str(k), 0) |
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250 | _remove_pd(oldpars, 'sld_shell'+str(k), 'sld') |
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251 | _remove_pd(oldpars, 'thick_shell'+str(k), 'thickness') |
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252 | elif name == 'core_shell_parallelepiped': |
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253 | _remove_pd(oldpars, 'rimA', name) |
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254 | elif name in ['mono_gauss_coil', 'poly_gauss_coil']: |
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255 | del oldpars['i_zero'] |
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256 | elif name == 'onion': |
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257 | oldpars.pop('n_shells', None) |
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258 | elif name == 'rpa': |
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259 | # convert scattering lengths from femtometers to centimeters |
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260 | for p in "L1", "L2", "L3", "L4": |
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261 | if p in oldpars: oldpars[p] *= 1e-13 |
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262 | if pars['case_num'] < 2: |
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263 | for k in ("a", "b"): |
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264 | for p in ("L", "N", "Phi", "b", "v"): |
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265 | oldpars.pop(p+k, None) |
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266 | for k in "Kab,Kac,Kad,Kbc,Kbd".split(','): |
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267 | oldpars.pop(k, None) |
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268 | elif pars['case_num'] < 5: |
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269 | for k in ("a",): |
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270 | for p in ("L", "N", "Phi", "b", "v"): |
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271 | oldpars.pop(p+k, None) |
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272 | for k in "Kab,Kac,Kad".split(','): |
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273 | oldpars.pop(k, None) |
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274 | |
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275 | #print("convert from",list(sorted(pars))) |
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276 | #print("convert to",list(sorted(oldpars.items()))) |
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277 | return oldpars |
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278 | |
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279 | def constrain_new_to_old(model_info, pars): |
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280 | """ |
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281 | Restrict parameter values to those that will match sasview. |
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282 | """ |
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283 | name = model_info.id |
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284 | # Note: update convert.revert_model to match |
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285 | if name in MODELS_WITHOUT_SCALE or model_info.structure_factor: |
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286 | pars['scale'] = 1 |
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287 | if name in MODELS_WITHOUT_BACKGROUND or model_info.structure_factor: |
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288 | pars['background'] = 0 |
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289 | # sasview multiplies background by structure factor |
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290 | if '*' in name: |
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291 | pars['background'] = 0 |
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292 | |
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293 | # Shut off magnetism when comparing non-magnetic sasview models |
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294 | if name not in MAGNETIC_SASVIEW_MODELS: |
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295 | suppress_magnetism = False |
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296 | for key in pars.keys(): |
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297 | if key.startswith("M0:"): |
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298 | suppress_magnetism = suppress_magnetism or (pars[key] != 0) |
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299 | pars[key] = 0 |
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300 | if suppress_magnetism: |
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301 | warnings.warn("suppressing magnetism for comparison with sasview") |
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302 | |
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303 | # Shut off theta polydispersity since algorithm has changed |
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304 | if 'theta_pd_n' in pars: |
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305 | if pars['theta_pd_n'] != 0: |
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306 | warnings.warn("suppressing theta polydispersity for comparison with sasview") |
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307 | pars['theta_pd_n'] = 0 |
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308 | |
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309 | # If it is a product model P*S, then check the individual forms for special |
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310 | # cases. Note: despite the structure factor alone not having scale or |
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311 | # background, the product model does, so this is below the test for |
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312 | # models without scale or background. |
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313 | namelist = name.split('*') if '*' in name else [name] |
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314 | for name in namelist: |
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315 | if name in MODELS_WITHOUT_VOLFRACTION: |
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316 | pars['volfraction'] = 1 |
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317 | if name == 'pearl_necklace': |
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318 | pars['string_thickness_pd_n'] = 0 |
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319 | pars['number_of_pearls_pd_n'] = 0 |
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320 | elif name == 'line': |
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321 | pars['scale'] = 1 |
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322 | pars['background'] = 0 |
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323 | elif name == 'rpa': |
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324 | pars['case_num'] = int(pars['case_num']) |
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325 | elif name == 'mono_gauss_coil': |
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326 | pars['i_zero'] = 1 |
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327 | elif name == 'poly_gauss_coil': |
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328 | pars['i_zero'] = 1 |
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329 | elif name == 'core_multi_shell': |
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330 | pars['n'] = min(math.ceil(pars['n']), 4) |
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331 | elif name == 'onion': |
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332 | pars['n_shells'] = math.ceil(pars['n_shells']) |
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333 | elif name == 'spherical_sld': |
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334 | pars['n_shells'] = math.ceil(pars['n_shells']) |
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335 | pars['n_steps'] = math.ceil(pars['n_steps']) |
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336 | for k in range(1, 11): |
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337 | pars['shape%d'%k] = math.trunc(pars['shape%d'%k]+0.5) |
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338 | for k in range(2, 11): |
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339 | pars['thickness%d_pd_n'%k] = 0 |
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340 | pars['interface%d_pd_n'%k] = 0 |
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341 | |
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