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51 | <h1>Source code for sas.models.ReflectivityIIModel</h1><div class="highlight"><pre> |
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52 | |
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53 | <span class="kn">from</span> <span class="nn">sas.models.BaseComponent</span> <span class="kn">import</span> <span class="n">BaseComponent</span> |
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54 | <span class="kn">from</span> <span class="nn">sas.models.ReflAdvModel</span> <span class="kn">import</span> <span class="n">ReflAdvModel</span> |
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55 | <span class="kn">from</span> <span class="nn">copy</span> <span class="kn">import</span> <span class="n">deepcopy</span> |
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56 | <span class="kn">from</span> <span class="nn">math</span> <span class="kn">import</span> <span class="n">floor</span> |
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57 | <span class="kn">from</span> <span class="nn">math</span> <span class="kn">import</span> <span class="n">fabs</span> |
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58 | <span class="n">func_list</span> <span class="o">=</span> <span class="p">{</span><span class="s">'Erf(|nu|*z)'</span><span class="p">:</span><span class="mi">0</span><span class="p">,</span> <span class="s">'RPower(z^|nu|)'</span><span class="p">:</span><span class="mi">1</span><span class="p">,</span> <span class="s">'LPower(z^|nu|)'</span><span class="p">:</span><span class="mi">2</span><span class="p">,</span> \ |
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59 | <span class="s">'RExp(-|nu|*z)'</span><span class="p">:</span><span class="mi">3</span><span class="p">,</span> <span class="s">'LExp(-|nu|*z)'</span><span class="p">:</span><span class="mi">4</span><span class="p">}</span> |
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60 | <span class="n">max_nshells</span> <span class="o">=</span> <span class="mi">10</span> |
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61 | <div class="viewcode-block" id="ReflectivityIIModel"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel">[docs]</a><span class="k">class</span> <span class="nc">ReflectivityIIModel</span><span class="p">(</span><span class="n">BaseComponent</span><span class="p">):</span> |
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62 | <span class="sd">"""</span> |
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63 | <span class="sd"> This multi-model is based on Parratt formalism and provides the capability</span> |
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64 | <span class="sd"> of changing the number of layers between 0 and 10.</span> |
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65 | <span class="sd"> """</span> |
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66 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">multfactor</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span> |
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67 | <span class="sd">"""</span> |
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68 | <span class="sd"> :param multfactor: number of layers in the model, </span> |
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69 | <span class="sd"> assumes 0<= n_layers <=10.</span> |
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70 | <span class="sd"> """</span> |
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71 | <span class="n">BaseComponent</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> |
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72 | |
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73 | <span class="c">## Setting model name model description</span> |
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74 | <span class="bp">self</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span> <span class="s">""</span> |
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75 | <span class="n">model</span> <span class="o">=</span> <span class="n">ReflAdvModel</span><span class="p">()</span> |
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76 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">model</span> |
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77 | <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">"ReflectivityIIModel"</span> |
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78 | <span class="bp">self</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">description</span> |
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79 | <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">multfactor</span><span class="p">)</span> |
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80 | <span class="c">## Define parameters</span> |
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81 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span> <span class="o">=</span> <span class="p">{}</span> |
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82 | |
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83 | <span class="c">## Parameter details [units, min, max]</span> |
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84 | <span class="bp">self</span><span class="o">.</span><span class="n">details</span> <span class="o">=</span> <span class="p">{}</span> |
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85 | |
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86 | <span class="c"># non-fittable parameters</span> |
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87 | <span class="bp">self</span><span class="o">.</span><span class="n">non_fittable</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">non_fittable</span> |
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88 | |
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89 | <span class="c"># list of function in order of the function number </span> |
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90 | <span class="bp">self</span><span class="o">.</span><span class="n">fun_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_func_list</span><span class="p">()</span> |
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91 | <span class="c">## dispersion</span> |
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92 | <span class="bp">self</span><span class="o">.</span><span class="n">_set_dispersion</span><span class="p">()</span> |
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93 | <span class="c">## Define parameters</span> |
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94 | <span class="bp">self</span><span class="o">.</span><span class="n">_set_params</span><span class="p">()</span> |
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95 | |
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96 | <span class="c">## Parameter details [units, min, max]</span> |
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97 | <span class="bp">self</span><span class="o">.</span><span class="n">_set_details</span><span class="p">()</span> |
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98 | |
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99 | <span class="c">#list of parameter that can be fitted</span> |
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100 | <span class="bp">self</span><span class="o">.</span><span class="n">_set_fixed_params</span><span class="p">()</span> |
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101 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'n_layers'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span> |
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102 | |
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103 | <span class="c">## functional multiplicity info of the model</span> |
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104 | <span class="c"># [int(maximum no. of functionality),"str(Titl),</span> |
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105 | <span class="c"># [str(name of function0),...], [str(x-asix name of sld),...]]</span> |
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106 | <span class="bp">self</span><span class="o">.</span><span class="n">multiplicity_info</span> <span class="o">=</span> <span class="p">[</span><span class="n">max_nshells</span><span class="p">,</span> <span class="s">"No. of Layers:"</span><span class="p">,</span> <span class="p">[],</span> <span class="p">[</span><span class="s">'Depth'</span><span class="p">]]</span> |
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107 | <span class="c">## independent parameter name and unit [string]</span> |
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108 | <span class="bp">self</span><span class="o">.</span><span class="n">input_name</span> <span class="o">=</span> <span class="s">"Q"</span> |
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109 | <span class="bp">self</span><span class="o">.</span><span class="n">input_unit</span> <span class="o">=</span> <span class="s">"A^{-1}"</span> |
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110 | <span class="c">## output name and unit [string]</span> |
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111 | <span class="bp">self</span><span class="o">.</span><span class="n">output_name</span> <span class="o">=</span> <span class="s">"Reflectivity"</span> |
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112 | <span class="bp">self</span><span class="o">.</span><span class="n">output_unit</span> <span class="o">=</span> <span class="s">""</span> |
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113 | |
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114 | |
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115 | <span class="k">def</span> <span class="nf">_clone</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">obj</span><span class="p">):</span> |
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116 | <span class="sd">"""</span> |
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117 | <span class="sd"> Internal utility function to copy the internal</span> |
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118 | <span class="sd"> data members to a fresh copy.</span> |
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119 | <span class="sd"> """</span> |
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120 | <span class="n">obj</span><span class="o">.</span><span class="n">params</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">)</span> |
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121 | <span class="n">obj</span><span class="o">.</span><span class="n">non_fittable</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">non_fittable</span><span class="p">)</span> |
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122 | <span class="n">obj</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">description</span><span class="p">)</span> |
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123 | <span class="n">obj</span><span class="o">.</span><span class="n">details</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">)</span> |
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124 | <span class="n">obj</span><span class="o">.</span><span class="n">dispersion</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dispersion</span><span class="p">)</span> |
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125 | <span class="n">obj</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">clone</span><span class="p">()</span> |
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126 | |
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127 | <span class="k">return</span> <span class="n">obj</span> |
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128 | |
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129 | |
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130 | <span class="k">def</span> <span class="nf">_set_dispersion</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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131 | <span class="sd">"""</span> |
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132 | <span class="sd"> model dispersions</span> |
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133 | <span class="sd"> """</span> |
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134 | <span class="c">##set dispersion from model </span> |
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135 | <span class="bp">self</span><span class="o">.</span><span class="n">dispersion</span> <span class="o">=</span> <span class="p">{}</span> |
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136 | |
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137 | |
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138 | <span class="k">def</span> <span class="nf">_set_params</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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139 | <span class="sd">"""</span> |
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140 | <span class="sd"> Concatenate the parameters of the model to create</span> |
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141 | <span class="sd"> this model parameters </span> |
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142 | <span class="sd"> """</span> |
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143 | <span class="c"># rearrange the parameters for the given # of shells</span> |
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144 | <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">iteritems</span><span class="p">():</span> |
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145 | <span class="n">n</span> <span class="o">=</span> <span class="mi">0</span> |
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146 | <span class="n">pos</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'_'</span><span class="p">))</span><span class="o">-</span><span class="mi">1</span> |
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147 | <span class="n">first_name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'_'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> |
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148 | <span class="n">last_name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'_'</span><span class="p">)[</span><span class="n">pos</span><span class="p">]</span> |
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149 | <span class="k">if</span> <span class="n">first_name</span> <span class="o">==</span> <span class="s">'npts'</span><span class="p">:</span> |
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150 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="n">name</span><span class="p">]</span><span class="o">=</span><span class="n">value</span> |
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151 | <span class="k">continue</span> |
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152 | <span class="k">elif</span> <span class="n">first_name</span> <span class="o">==</span> <span class="s">'sldIM'</span><span class="p">:</span> |
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153 | <span class="k">continue</span> |
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154 | <span class="k">elif</span> <span class="n">first_name</span> <span class="o">==</span> <span class="s">'func'</span><span class="p">:</span> |
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155 | <span class="n">n</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span> |
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156 | <span class="k">while</span> <span class="n">n</span> <span class="o"><</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span><span class="p">:</span> |
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157 | <span class="n">n</span> <span class="o">+=</span> <span class="mi">1</span> |
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158 | <span class="k">if</span> <span class="n">last_name</span> <span class="o">==</span> <span class="s">'inter</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">n</span><span class="p">):</span> |
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159 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span> |
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160 | <span class="k">continue</span> |
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161 | |
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162 | <span class="c">#continue</span> |
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163 | <span class="k">elif</span> <span class="n">last_name</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">5</span><span class="p">]</span> <span class="o">==</span> <span class="s">'inter'</span><span class="p">:</span> |
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164 | <span class="n">n</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span> |
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165 | <span class="k">while</span> <span class="n">n</span> <span class="o"><</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span><span class="p">:</span> |
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166 | <span class="n">n</span> <span class="o">+=</span> <span class="mi">1</span> |
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167 | <span class="k">if</span> <span class="n">last_name</span> <span class="o">==</span> <span class="s">'inter</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">n</span><span class="p">):</span> |
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168 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span> |
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169 | <span class="k">continue</span> |
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170 | <span class="k">elif</span> <span class="n">last_name</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">4</span><span class="p">]</span> <span class="o">==</span> <span class="s">'flat'</span><span class="p">:</span> |
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171 | <span class="k">while</span> <span class="n">n</span> <span class="o"><</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span><span class="p">:</span> |
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172 | <span class="n">n</span> <span class="o">+=</span> <span class="mi">1</span> |
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173 | <span class="k">if</span> <span class="n">last_name</span> <span class="o">==</span> <span class="s">'flat</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">n</span><span class="p">):</span> |
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174 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span> |
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175 | <span class="k">continue</span> |
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176 | <span class="k">elif</span> <span class="n">name</span> <span class="o">==</span> <span class="s">'n_layers'</span><span class="p">:</span> |
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177 | <span class="k">continue</span> |
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178 | <span class="k">else</span><span class="p">:</span> |
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179 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span> |
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180 | |
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181 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'n_layers'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span> |
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182 | |
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183 | <span class="c"># set constrained values for the original model params</span> |
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184 | <span class="bp">self</span><span class="o">.</span><span class="n">_set_xtra_model_param</span><span class="p">()</span> |
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185 | |
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186 | <span class="k">def</span> <span class="nf">_set_details</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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187 | <span class="sd">"""</span> |
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188 | <span class="sd"> Concatenate details of the original model to create</span> |
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189 | <span class="sd"> this model details </span> |
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190 | <span class="sd"> """</span> |
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191 | <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">detail</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">details</span><span class="o">.</span><span class="n">iteritems</span><span class="p">():</span> |
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192 | <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">iterkeys</span><span class="p">():</span> |
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193 | <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">detail</span> |
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194 | |
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195 | |
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196 | <span class="k">def</span> <span class="nf">_set_xtra_model_param</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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197 | <span class="sd">"""</span> |
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198 | <span class="sd"> Set params of original model that are hidden from this model</span> |
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199 | <span class="sd"> """</span> |
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200 | <span class="c"># look for the model parameters that are not in param list</span> |
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201 | <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">iterkeys</span><span class="p">():</span> |
---|
202 | <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span> |
---|
203 | <span class="k">if</span> <span class="n">key</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'_'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">'thick'</span><span class="p">:</span> |
---|
204 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> |
---|
205 | <span class="k">continue</span> |
---|
206 | <span class="k">if</span> <span class="n">key</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'_'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">'func'</span><span class="p">:</span> |
---|
207 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> |
---|
208 | <span class="k">continue</span> |
---|
209 | |
---|
210 | <span class="k">for</span> <span class="n">nshell</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span><span class="p">,</span><span class="n">max_nshells</span><span class="p">):</span> |
---|
211 | <span class="k">if</span> <span class="n">key</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'_'</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s">'flat</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">nshell</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span> |
---|
212 | <span class="k">try</span><span class="p">:</span> |
---|
213 | <span class="k">if</span> <span class="n">key</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'_'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">'sld'</span><span class="p">:</span> |
---|
214 | <span class="n">value</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'sld_medium'</span><span class="p">]</span> |
---|
215 | <span class="k">elif</span> <span class="n">key</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'_'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">'sldIM'</span><span class="p">:</span> |
---|
216 | <span class="n">value</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'sldIM_medium'</span><span class="p">]</span> |
---|
217 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span> |
---|
218 | <span class="k">except</span><span class="p">:</span> |
---|
219 | <span class="n">message</span> <span class="o">=</span> <span class="s">"ReflectivityIIModel evaluation problem"</span> |
---|
220 | <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="n">message</span> |
---|
221 | |
---|
222 | <span class="k">def</span> <span class="nf">_get_func_list</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
223 | <span class="sd">"""</span> |
---|
224 | <span class="sd"> Get the list of functions in each layer (shell) </span> |
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225 | <span class="sd"> """</span> |
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226 | <span class="k">return</span> <span class="n">func_list</span> |
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227 | |
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228 | <div class="viewcode-block" id="ReflectivityIIModel.getProfile"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel.getProfile">[docs]</a> <span class="k">def</span> <span class="nf">getProfile</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
229 | <span class="sd">"""</span> |
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230 | <span class="sd"> Get SLD profile </span> |
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231 | <span class="sd"> </span> |
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232 | <span class="sd"> : return: (z, beta) where z is a list of depth of the transition points</span> |
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233 | <span class="sd"> beta is a list of the corresponding SLD values </span> |
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234 | <span class="sd"> """</span> |
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235 | <span class="c"># max_pts for each layers</span> |
---|
236 | <span class="n">n_sub</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'npts_inter'</span><span class="p">])</span> |
---|
237 | <span class="n">z</span> <span class="o">=</span> <span class="p">[]</span> |
---|
238 | <span class="n">beta</span> <span class="o">=</span> <span class="p">[]</span> |
---|
239 | <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
---|
240 | <span class="n">beta</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'sld_bottom0'</span><span class="p">])</span> |
---|
241 | |
---|
242 | <span class="n">z0</span> <span class="o">=</span> <span class="mf">0.0</span> |
---|
243 | <span class="n">dz</span> <span class="o">=</span> <span class="mf">0.0</span> |
---|
244 | <span class="c"># for layers from the top</span> |
---|
245 | <span class="k">for</span> <span class="n">n_lyr</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span><span class="o">+</span><span class="mi">2</span><span class="p">):</span> |
---|
246 | <span class="n">i</span> <span class="o">=</span> <span class="n">n_lyr</span> |
---|
247 | <span class="c"># j=0 for interface, j=1 for flat layer </span> |
---|
248 | <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">):</span> |
---|
249 | <span class="c"># interation for sub-layers</span> |
---|
250 | <span class="k">for</span> <span class="n">n_s</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">n_sub</span><span class="p">):</span> |
---|
251 | <span class="c"># for flat layer</span> |
---|
252 | <span class="k">if</span> <span class="n">j</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span> |
---|
253 | <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span><span class="o">+</span><span class="mi">1</span><span class="p">:</span> |
---|
254 | <span class="k">break</span> |
---|
255 | <span class="c"># shift half sub thickness for the first point</span> |
---|
256 | <span class="n">z0</span> <span class="o">-=</span> <span class="n">dz</span><span class="o">/</span><span class="mf">2.0</span> |
---|
257 | <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">z0</span><span class="p">)</span> |
---|
258 | <span class="n">sld_i</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'sld_flat</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> |
---|
259 | <span class="n">beta</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sld_i</span><span class="p">)</span> |
---|
260 | <span class="n">dz</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'thick_flat</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> |
---|
261 | <span class="n">z0</span> <span class="o">+=</span> <span class="n">dz</span> |
---|
262 | <span class="k">else</span><span class="p">:</span> |
---|
263 | <span class="n">dz</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'thick_inter</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">)]</span><span class="o">/</span><span class="n">n_sub</span> |
---|
264 | <span class="n">nu</span> <span class="o">=</span> <span class="n">fabs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'nu_inter</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">)])</span> |
---|
265 | <span class="k">if</span> <span class="n">n_s</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> |
---|
266 | <span class="c"># shift half sub thickness for the point</span> |
---|
267 | <span class="n">z0</span> <span class="o">+=</span> <span class="n">dz</span><span class="o">/</span><span class="mf">2.0</span> |
---|
268 | <span class="c"># decide which sld is which, sld_r or sld_l</span> |
---|
269 | <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span> |
---|
270 | <span class="n">sld_l</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'sld_bottom0'</span><span class="p">]</span> |
---|
271 | <span class="k">else</span><span class="p">:</span> |
---|
272 | <span class="n">sld_l</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'sld_flat</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">)]</span> |
---|
273 | <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span><span class="o">+</span><span class="mi">1</span><span class="p">:</span> |
---|
274 | <span class="n">sld_r</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'sld_medium'</span><span class="p">]</span> |
---|
275 | <span class="k">else</span><span class="p">:</span> |
---|
276 | <span class="n">sld_r</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'sld_flat</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span> |
---|
277 | <span class="k">if</span> <span class="n">sld_r</span> <span class="o">==</span> <span class="n">sld_l</span><span class="p">:</span> |
---|
278 | <span class="n">sld_i</span> <span class="o">=</span> <span class="n">sld_r</span> |
---|
279 | <span class="k">else</span><span class="p">:</span> |
---|
280 | <span class="n">func_idx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'func_inter</span><span class="si">%s</span><span class="s">'</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">)]</span> |
---|
281 | <span class="c"># calculate the sld</span> |
---|
282 | <span class="n">sld_i</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_sld</span><span class="p">(</span><span class="n">func_idx</span><span class="p">,</span> <span class="n">n_sub</span><span class="p">,</span> <span class="n">n_s</span><span class="o">+</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">nu</span><span class="p">,</span> |
---|
283 | <span class="n">sld_l</span><span class="p">,</span> <span class="n">sld_r</span><span class="p">)</span> |
---|
284 | <span class="c"># append to the list</span> |
---|
285 | <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">z0</span><span class="p">)</span> |
---|
286 | <span class="n">beta</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sld_i</span><span class="p">)</span> |
---|
287 | <span class="k">if</span> <span class="n">j</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span> |
---|
288 | <span class="k">break</span> |
---|
289 | <span class="k">else</span><span class="p">:</span> |
---|
290 | <span class="n">z0</span> <span class="o">+=</span> <span class="n">dz</span> |
---|
291 | <span class="c"># put substrate and superstrate profile</span> |
---|
292 | <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">z0</span><span class="p">)</span> |
---|
293 | <span class="n">beta</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'sld_medium'</span><span class="p">])</span> |
---|
294 | <span class="n">z_ext</span> <span class="o">=</span> <span class="n">z0</span><span class="o">/</span><span class="mf">5.0</span> |
---|
295 | |
---|
296 | <span class="c"># put the extra points for the substrate </span> |
---|
297 | <span class="c"># and superstrate</span> |
---|
298 | <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">z0</span><span class="o">+</span><span class="n">z_ext</span><span class="p">)</span> |
---|
299 | <span class="n">beta</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'sld_medium'</span><span class="p">])</span> |
---|
300 | <span class="n">z</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="o">-</span><span class="n">z_ext</span><span class="p">)</span> |
---|
301 | <span class="n">beta</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">'sld_bottom0'</span><span class="p">])</span> |
---|
302 | <span class="c"># rearrange the profile for NR sld profile style</span> |
---|
303 | <span class="n">z</span> <span class="o">=</span> <span class="p">[</span><span class="n">z0</span> <span class="o">-</span> <span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">z</span><span class="p">]</span> |
---|
304 | <span class="n">z</span><span class="o">.</span><span class="n">reverse</span><span class="p">()</span> |
---|
305 | <span class="n">beta</span><span class="o">.</span><span class="n">reverse</span><span class="p">()</span> |
---|
306 | <span class="k">return</span> <span class="n">z</span><span class="p">,</span> <span class="n">beta</span> |
---|
307 | </div> |
---|
308 | <span class="k">def</span> <span class="nf">_get_sld</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">func_idx</span><span class="p">,</span> <span class="n">n_sub</span><span class="p">,</span> <span class="n">n_s</span><span class="p">,</span> <span class="n">nu</span><span class="p">,</span> <span class="n">sld_l</span><span class="p">,</span> <span class="n">sld_r</span><span class="p">):</span> |
---|
309 | <span class="sd">"""</span> |
---|
310 | <span class="sd"> Get the function asked to build sld profile</span> |
---|
311 | <span class="sd"> : param func_idx: func type number</span> |
---|
312 | <span class="sd"> : param n_sub: total number of sub_layer</span> |
---|
313 | <span class="sd"> : param n_s: index of sub_layer</span> |
---|
314 | <span class="sd"> : param nu: coefficient of the function</span> |
---|
315 | <span class="sd"> : param sld_l: sld on the left side</span> |
---|
316 | <span class="sd"> : param sld_r: sld on the right side</span> |
---|
317 | <span class="sd"> : return: sld value, float</span> |
---|
318 | <span class="sd"> """</span> |
---|
319 | <span class="kn">from</span> <span class="nn">sas.models.SLDCalFunc</span> <span class="kn">import</span> <span class="n">SLDCalFunc</span> |
---|
320 | <span class="c"># sld_cal init</span> |
---|
321 | <span class="n">sld_cal</span> <span class="o">=</span> <span class="n">SLDCalFunc</span><span class="p">()</span> |
---|
322 | <span class="c"># set params</span> |
---|
323 | <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">'fun_type'</span><span class="p">,</span> <span class="n">func_idx</span><span class="p">)</span> |
---|
324 | <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">'npts_inter'</span><span class="p">,</span> <span class="n">n_sub</span><span class="p">)</span> |
---|
325 | <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">'shell_num'</span><span class="p">,</span> <span class="n">n_s</span><span class="p">)</span> |
---|
326 | <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">'nu_inter'</span><span class="p">,</span> <span class="n">nu</span><span class="p">)</span> |
---|
327 | <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">'sld_left'</span><span class="p">,</span> <span class="n">sld_l</span><span class="p">)</span> |
---|
328 | <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">'sld_right'</span><span class="p">,</span> <span class="n">sld_r</span><span class="p">)</span> |
---|
329 | <span class="c"># return sld value</span> |
---|
330 | <span class="k">return</span> <span class="n">sld_cal</span><span class="o">.</span><span class="n">run</span><span class="p">()</span> |
---|
331 | |
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332 | <div class="viewcode-block" id="ReflectivityIIModel.setParam"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel.setParam">[docs]</a> <span class="k">def</span> <span class="nf">setParam</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span> |
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333 | <span class="sd">""" </span> |
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334 | <span class="sd"> Set the value of a model parameter</span> |
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335 | <span class="sd"> </span> |
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336 | <span class="sd"> : param name: name of the parameter</span> |
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337 | <span class="sd"> : param value: value of the parameter</span> |
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338 | <span class="sd"> """</span> |
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339 | <span class="c"># set param to new model</span> |
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340 | <span class="bp">self</span><span class="o">.</span><span class="n">_setParamHelper</span><span class="p">(</span> <span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span> |
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341 | |
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342 | <span class="c">## setParam to model </span> |
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343 | <span class="k">if</span> <span class="n">name</span> <span class="o">==</span> <span class="s">'sld_medium'</span><span class="p">:</span> |
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344 | <span class="c"># the sld_*** model.params not in params must set </span> |
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345 | <span class="c"># to value of sld_solv</span> |
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346 | <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">iterkeys</span><span class="p">():</span> |
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347 | <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span><span class="ow">and</span> <span class="n">key</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'_'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">'sld'</span><span class="p">:</span> |
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348 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span> |
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349 | |
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350 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span> <span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span> |
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351 | </div> |
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352 | <span class="k">def</span> <span class="nf">_setParamHelper</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span> |
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353 | <span class="sd">"""</span> |
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354 | <span class="sd"> Helper function to setParam</span> |
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355 | <span class="sd"> """</span> |
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356 | |
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357 | <span class="c"># Look for standard parameter</span> |
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358 | <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span> |
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359 | <span class="k">if</span> <span class="n">item</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">==</span><span class="n">name</span><span class="o">.</span><span class="n">lower</span><span class="p">():</span> |
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360 | <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="n">item</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span> |
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361 | <span class="k">return</span> |
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362 | |
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363 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="s">"Model does not contain parameter </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">name</span> |
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364 | |
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365 | |
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366 | <span class="k">def</span> <span class="nf">_set_fixed_params</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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367 | <span class="sd">"""</span> |
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368 | <span class="sd"> Fill the self.fixed list with the model fixed list</span> |
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369 | <span class="sd"> """</span> |
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370 | <span class="k">pass</span> |
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371 | |
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372 | <div class="viewcode-block" id="ReflectivityIIModel.run"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel.run">[docs]</a> <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span> <span class="o">=</span> <span class="mf">0.0</span><span class="p">):</span> |
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373 | <span class="sd">""" </span> |
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374 | <span class="sd"> Evaluate the model</span> |
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375 | <span class="sd"> </span> |
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376 | <span class="sd"> :param x: input q, or [q,phi]</span> |
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377 | <span class="sd"> </span> |
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378 | <span class="sd"> :return: scattering function P(q)</span> |
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379 | <span class="sd"> </span> |
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380 | <span class="sd"> """</span> |
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381 | |
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382 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> |
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383 | </div> |
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384 | <div class="viewcode-block" id="ReflectivityIIModel.runXY"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel.runXY">[docs]</a> <span class="k">def</span> <span class="nf">runXY</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span> <span class="o">=</span> <span class="mf">0.0</span><span class="p">):</span> |
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385 | <span class="sd">""" </span> |
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386 | <span class="sd"> Evaluate the model</span> |
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387 | <span class="sd"> </span> |
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388 | <span class="sd"> : param x: input q-value (float or [float, float] as [qx, qy])</span> |
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389 | <span class="sd"> : return: scattering function value</span> |
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390 | <span class="sd"> """</span> |
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391 | |
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392 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">runXY</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> |
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393 | |
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394 | <span class="c">## Now (May27,10) directly uses the model eval function </span> |
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395 | <span class="c">## instead of the for-loop in Base Component.</span></div> |
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396 | <div class="viewcode-block" id="ReflectivityIIModel.evalDistribution"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel.evalDistribution">[docs]</a> <span class="k">def</span> <span class="nf">evalDistribution</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span> |
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397 | <span class="sd">""" </span> |
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398 | <span class="sd"> Evaluate the model in cartesian coordinates</span> |
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399 | <span class="sd"> </span> |
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400 | <span class="sd"> : param x: input q[], or [qx[], qy[]]</span> |
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401 | <span class="sd"> : return: scattering function P(q[])</span> |
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402 | <span class="sd"> """</span> |
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403 | <span class="c"># set effective radius and scaling factor before run</span> |
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404 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">evalDistribution</span><span class="p">(</span><span class="n">x</span><span class="p">)</span></div> |
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405 | <div class="viewcode-block" id="ReflectivityIIModel.calculate_ER"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel.calculate_ER">[docs]</a> <span class="k">def</span> <span class="nf">calculate_ER</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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406 | <span class="sd">"""</span> |
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407 | <span class="sd"> """</span> |
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408 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">calculate_ER</span><span class="p">()</span></div> |
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409 | <div class="viewcode-block" id="ReflectivityIIModel.set_dispersion"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel.set_dispersion">[docs]</a> <span class="k">def</span> <span class="nf">set_dispersion</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parameter</span><span class="p">,</span> <span class="n">dispersion</span><span class="p">):</span> |
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410 | <span class="sd">"""</span> |
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411 | <span class="sd"> Set the dispersion object for a model parameter</span> |
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412 | <span class="sd"> </span> |
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413 | <span class="sd"> : param parameter: name of the parameter [string]</span> |
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414 | <span class="sd"> :dispersion: dispersion object of type DispersionModel</span> |
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415 | <span class="sd"> """</span> |
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416 | <span class="k">pass</span></div></div> |
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417 | </pre></div> |
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