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50 | <h1>Source code for sas.fit.ParkFitting</h1><div class="highlight"><pre> |
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51 | <span class="sd">"""</span> |
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52 | <span class="sd">ParkFitting module contains SasParameter,Model,Data</span> |
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53 | <span class="sd">FitArrange, ParkFit,Parameter classes.All listed classes work together</span> |
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54 | <span class="sd">to perform a simple fit with park optimizer.</span> |
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55 | <span class="sd">"""</span> |
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56 | <span class="c">#import time</span> |
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57 | <span class="kn">import</span> <span class="nn">numpy</span> |
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58 | <span class="kn">import</span> <span class="nn">math</span> |
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59 | <span class="kn">from</span> <span class="nn">numpy.linalg.linalg</span> <span class="kn">import</span> <span class="n">LinAlgError</span> |
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60 | <span class="c">#import park</span> |
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61 | <span class="kn">from</span> <span class="nn">park</span> <span class="kn">import</span> <span class="n">fit</span> |
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62 | <span class="kn">from</span> <span class="nn">park</span> <span class="kn">import</span> <span class="n">fitresult</span> |
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63 | <span class="kn">from</span> <span class="nn">park.fitresult</span> <span class="kn">import</span> <span class="n">FitParameter</span> |
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64 | <span class="kn">import</span> <span class="nn">park.simplex</span> |
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65 | <span class="kn">from</span> <span class="nn">park.assembly</span> <span class="kn">import</span> <span class="n">Assembly</span> |
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66 | <span class="kn">from</span> <span class="nn">park.assembly</span> <span class="kn">import</span> <span class="n">Part</span> |
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67 | <span class="kn">from</span> <span class="nn">park.fitmc</span> <span class="kn">import</span> <span class="n">FitSimplex</span> |
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68 | <span class="kn">import</span> <span class="nn">park.fitmc</span> |
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69 | <span class="kn">from</span> <span class="nn">park.fit</span> <span class="kn">import</span> <span class="n">Fitter</span> |
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70 | <span class="kn">from</span> <span class="nn">park.formatnum</span> <span class="kn">import</span> <span class="n">format_uncertainty</span> |
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71 | <span class="kn">from</span> <span class="nn">sas.fit.AbstractFitEngine</span> <span class="kn">import</span> <span class="n">FitEngine</span> |
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72 | <span class="kn">from</span> <span class="nn">sas.fit.AbstractFitEngine</span> <span class="kn">import</span> <span class="n">FResult</span> |
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73 | |
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74 | <span class="k">class</span> <span class="nc">SasParameter</span><span class="p">(</span><span class="n">park</span><span class="o">.</span><span class="n">Parameter</span><span class="p">):</span> |
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75 | <span class="sd">"""</span> |
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76 | <span class="sd"> SAS model parameters for use in the PARK fitting service.</span> |
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77 | <div class="viewcode-block" id="SasParameter"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasParameter">[docs]</a><span class="sd"> The parameter attribute value is redirected to the underlying</span> |
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78 | <span class="sd"> parameter value in the SAS model.</span> |
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79 | <span class="sd"> """</span> |
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80 | <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">name</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span> |
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81 | <span class="sd">"""</span> |
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82 | <span class="sd"> :param name: the name of the model parameter</span> |
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83 | <span class="sd"> :param model: the sas model to wrap as a park model</span> |
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84 | <span class="sd"> """</span> |
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85 | <span class="n">park</span><span class="o">.</span><span class="n">Parameter</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span> |
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86 | <span class="c">#self._model, self._name = model, name</span> |
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87 | <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">data</span> |
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88 | <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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89 | <span class="c">#set the value for the parameter of the given name</span> |
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90 | <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">getParam</span><span class="p">(</span><span class="n">name</span><span class="p">))</span> |
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91 | |
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92 | <span class="c"># TODO: model is missing parameter ranges for dispersion parameters</span> |
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93 | <span class="k">if</span> <span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">details</span><span class="p">:</span> |
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94 | <span class="c">#print "setting details for",name</span> |
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95 | <span class="n">model</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="p">[</span><span class="s">""</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span> |
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96 | |
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97 | <span class="k">def</span> <span class="nf">_getvalue</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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98 | <span class="sd">"""</span> |
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99 | <span class="sd"> override the _getvalue of park parameter</span> |
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100 | |
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101 | <span class="sd"> :return value the parameter associates with self.name</span> |
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102 | |
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103 | <span class="sd"> """</span> |
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104 | <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">getParam</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span> |
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105 | |
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106 | <span class="k">def</span> <span class="nf">_setvalue</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span> |
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107 | <span class="sd">"""</span> |
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108 | <span class="sd"> override the _setvalue pf park parameter</span> |
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109 | |
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110 | <span class="sd"> :param value: the value to set on a given parameter</span> |
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111 | |
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112 | <span class="sd"> """</span> |
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113 | <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="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span> |
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114 | |
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115 | <span class="n">value</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">_getvalue</span><span class="p">,</span> <span class="n">_setvalue</span><span class="p">)</span> |
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116 | |
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117 | <span class="k">def</span> <span class="nf">_getrange</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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118 | <span class="sd">"""</span> |
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119 | <span class="sd"> Override _getrange of park parameter</span> |
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120 | <span class="sd"> return the range of parameter</span> |
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121 | <span class="sd"> """</span> |
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122 | <span class="c">#if not self.name in self._model.getDispParamList():</span> |
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123 | <span class="n">lo</span><span class="p">,</span> <span class="n">hi</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">details</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">][</span><span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">]</span> |
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124 | <span class="k">if</span> <span class="n">lo</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> <span class="n">lo</span> <span class="o">=</span> <span class="o">-</span><span class="n">numpy</span><span class="o">.</span><span class="n">inf</span> |
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125 | <span class="k">if</span> <span class="n">hi</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> <span class="n">hi</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">inf</span> |
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126 | <span class="k">if</span> <span class="n">lo</span> <span class="o">></span> <span class="n">hi</span><span class="p">:</span> |
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127 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="s">"wrong fit range for parameters"</span> |
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128 | |
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129 | <span class="k">return</span> <span class="n">lo</span><span class="p">,</span> <span class="n">hi</span> |
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130 | |
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131 | <span class="k">def</span> <span class="nf">get_name</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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132 | <span class="sd">"""</span> |
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133 | <span class="sd"> """</span> |
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134 | <div class="viewcode-block" id="SasParameter.get_name"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasParameter.get_name">[docs]</a> <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getname</span><span class="p">()</span> |
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135 | |
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136 | <span class="k">def</span> <span class="nf">_setrange</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">r</span><span class="p">):</span> |
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137 | <span class="sd">"""</span> |
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138 | <span class="sd"> override _setrange of park parameter</span></div> |
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139 | |
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140 | <span class="sd"> :param r: the value of the range to set</span> |
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141 | |
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142 | <span class="sd"> """</span> |
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143 | <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="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">][</span><span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="n">r</span> |
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144 | <span class="nb">range</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">_getrange</span><span class="p">,</span> <span class="n">_setrange</span><span class="p">)</span> |
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145 | |
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146 | |
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147 | <span class="k">class</span> <span class="nc">ParkModel</span><span class="p">(</span><span class="n">park</span><span class="o">.</span><span class="n">Model</span><span class="p">):</span> |
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148 | <span class="sd">"""</span> |
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149 | <span class="sd"> PARK wrapper for SAS models.</span></div> |
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150 | <div class="viewcode-block" id="ParkModel"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkModel">[docs]</a><span class="sd"> """</span> |
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151 | <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">sas_model</span><span class="p">,</span> <span class="n">sas_data</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span> |
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152 | <span class="sd">"""</span> |
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153 | <span class="sd"> :param sas_model: the sas model to wrap using park interface</span> |
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154 | |
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155 | <span class="sd"> """</span> |
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156 | <span class="n">park</span><span class="o">.</span><span class="n">Model</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">)</span> |
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157 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">sas_model</span> |
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158 | <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">sas_model</span><span class="o">.</span><span class="n">name</span> |
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159 | <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">sas_data</span> |
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160 | <span class="c">#list of parameters names</span> |
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161 | <span class="bp">self</span><span class="o">.</span><span class="n">sasp</span> <span class="o">=</span> <span class="n">sas_model</span><span class="o">.</span><span class="n">getParamList</span><span class="p">()</span> |
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162 | <span class="c">#list of park parameter</span> |
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163 | <span class="bp">self</span><span class="o">.</span><span class="n">parkp</span> <span class="o">=</span> <span class="p">[</span><span class="n">SasParameter</span><span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="n">sas_model</span><span class="p">,</span> <span class="n">sas_data</span><span class="p">)</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">sasp</span><span class="p">]</span> |
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164 | <span class="c">#list of parameter set</span> |
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165 | <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span> <span class="o">=</span> <span class="n">park</span><span class="o">.</span><span class="n">ParameterSet</span><span class="p">(</span><span class="n">sas_model</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">pars</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">parkp</span><span class="p">)</span> |
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166 | <span class="bp">self</span><span class="o">.</span><span class="n">pars</span> <span class="o">=</span> <span class="p">[]</span> |
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167 | |
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168 | <span class="k">def</span> <span class="nf">get_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fitparams</span><span class="p">):</span> |
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169 | <span class="sd">"""</span> |
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170 | <span class="sd"> return a list of value of paramter to fit</span> |
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171 | <div class="viewcode-block" id="ParkModel.get_params"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkModel.get_params">[docs]</a> |
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172 | <span class="sd"> :param fitparams: list of paramaters name to fit</span> |
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173 | |
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174 | <span class="sd"> """</span> |
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175 | <span class="n">list_params</span> <span class="o">=</span> <span class="p">[]</span> |
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176 | <span class="bp">self</span><span class="o">.</span><span class="n">pars</span> <span class="o">=</span> <span class="n">fitparams</span> |
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177 | <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">fitparams</span><span class="p">:</span> |
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178 | <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parkp</span><span class="p">:</span> |
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179 | <span class="k">if</span> <span class="n">element</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">):</span> |
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180 | <span class="n">list_params</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">element</span><span class="o">.</span><span class="n">value</span><span class="p">)</span> |
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181 | <span class="k">return</span> <span class="n">list_params</span> |
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182 | |
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183 | <span class="k">def</span> <span class="nf">set_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">paramlist</span><span class="p">,</span> <span class="n">params</span><span class="p">):</span> |
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184 | <span class="sd">"""</span> |
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185 | <span class="sd"> Set value for parameters to fit</span></div> |
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186 | <div class="viewcode-block" id="ParkModel.set_params"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkModel.set_params">[docs]</a> |
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187 | <span class="sd"> :param params: list of value for parameters to fit</span> |
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188 | |
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189 | <span class="sd"> """</span> |
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190 | <span class="k">try</span><span class="p">:</span> |
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191 | <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parkp</span><span class="p">)):</span> |
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192 | <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="nb">len</span><span class="p">(</span><span class="n">paramlist</span><span class="p">)):</span> |
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193 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parkp</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">paramlist</span><span class="p">[</span><span class="n">j</span><span class="p">]:</span> |
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194 | <span class="bp">self</span><span class="o">.</span><span class="n">parkp</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">=</span> <span class="n">params</span><span class="p">[</span><span class="n">j</span><span class="p">]</span> |
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195 | <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="bp">self</span><span class="o">.</span><span class="n">parkp</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">params</span><span class="p">[</span><span class="n">j</span><span class="p">])</span> |
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196 | <span class="k">except</span><span class="p">:</span> |
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197 | <span class="k">raise</span> |
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198 | |
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199 | <span class="k">def</span> <span class="nf">eval</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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200 | <span class="sd">"""</span> |
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201 | <span class="sd"> Override eval method of park model.</span></div> |
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202 | <div class="viewcode-block" id="ParkModel.eval"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkModel.eval">[docs]</a> |
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203 | <span class="sd"> :param x: the x value used to compute a function</span> |
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204 | <span class="sd"> """</span> |
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205 | <span class="k">try</span><span class="p">:</span> |
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206 | <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> |
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207 | <span class="k">except</span><span class="p">:</span> |
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208 | <span class="k">raise</span> |
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209 | |
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210 | <span class="k">def</span> <span class="nf">eval_derivs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">pars</span><span class="o">=</span><span class="p">[]):</span> |
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211 | <span class="sd">"""</span> |
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212 | <span class="sd"> Evaluate the model and derivatives wrt pars at x.</span></div> |
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213 | <div class="viewcode-block" id="ParkModel.eval_derivs"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkModel.eval_derivs">[docs]</a> |
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214 | <span class="sd"> pars is a list of the names of the parameters for which derivatives</span> |
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215 | <span class="sd"> are desired.</span> |
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216 | |
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217 | <span class="sd"> This method needs to be specialized in the model to evaluate the</span> |
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218 | <span class="sd"> model function. Alternatively, the model can implement is own</span> |
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219 | <span class="sd"> version of residuals which calculates the residuals directly</span> |
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220 | <span class="sd"> instead of calling eval.</span> |
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221 | <span class="sd"> """</span> |
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222 | <span class="k">return</span> <span class="p">[]</span> |
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223 | |
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224 | |
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225 | <span class="k">class</span> <span class="nc">SasFitResult</span><span class="p">(</span><span class="n">fitresult</span><span class="o">.</span><span class="n">FitResult</span><span class="p">):</span> |
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226 | <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="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwrds</span><span class="p">):</span> |
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227 | <span class="n">fitresult</span><span class="o">.</span><span class="n">FitResult</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwrds</span><span class="p">)</span></div></div> |
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228 | <div class="viewcode-block" id="SasFitResult"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitResult">[docs]</a> <span class="bp">self</span><span class="o">.</span><span class="n">theory</span> <span class="o">=</span> <span class="bp">None</span> |
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229 | <span class="bp">self</span><span class="o">.</span><span class="n">inputs</span> <span class="o">=</span> <span class="p">[]</span> |
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230 | |
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231 | <span class="k">class</span> <span class="nc">SasFitSimplex</span><span class="p">(</span><span class="n">FitSimplex</span><span class="p">):</span> |
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232 | <span class="sd">"""</span> |
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233 | <span class="sd"> Local minimizer using Nelder-Mead simplex algorithm.</span></div> |
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234 | <div class="viewcode-block" id="SasFitSimplex"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitSimplex">[docs]</a> |
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235 | <span class="sd"> Simplex is robust and derivative free, though not very efficient.</span> |
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236 | |
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237 | <span class="sd"> This class wraps the bounds contrained Nelder-Mead simplex</span> |
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238 | <span class="sd"> implementation for `park.simplex.simplex`.</span> |
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239 | <span class="sd"> """</span> |
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240 | <span class="n">radius</span> <span class="o">=</span> <span class="mf">0.05</span> |
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241 | <span class="sd">"""Size of the initial simplex; this is a portion between 0 and 1"""</span> |
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242 | <span class="n">xtol</span> <span class="o">=</span> <span class="mi">1</span> |
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243 | <span class="c">#xtol = 1e-4</span> |
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244 | <span class="sd">"""Stop when simplex vertices are within xtol of each other"""</span> |
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245 | <span class="n">ftol</span> <span class="o">=</span> <span class="mf">5e-5</span> |
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246 | <span class="sd">"""Stop when vertex values are within ftol of each other"""</span> |
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247 | <span class="n">maxiter</span> <span class="o">=</span> <span class="bp">None</span> |
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248 | <span class="sd">"""Maximum number of iterations before fit terminates"""</span> |
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249 | <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">ftol</span><span class="o">=</span><span class="mf">5e-5</span><span class="p">):</span> |
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250 | <span class="bp">self</span><span class="o">.</span><span class="n">ftol</span> <span class="o">=</span> <span class="n">ftol</span> |
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251 | |
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252 | <span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fitness</span><span class="p">,</span> <span class="n">x0</span><span class="p">):</span> |
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253 | <span class="sd">"""Run the fit"""</span> |
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254 | <span class="bp">self</span><span class="o">.</span><span class="n">cancel</span> <span class="o">=</span> <span class="bp">False</span> |
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255 | <div class="viewcode-block" id="SasFitSimplex.fit"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitSimplex.fit">[docs]</a> <span class="n">pars</span> <span class="o">=</span> <span class="n">fitness</span><span class="o">.</span><span class="n">fit_parameters</span><span class="p">()</span> |
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256 | <span class="n">bounds</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">p</span><span class="o">.</span><span class="n">range</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pars</span><span class="p">])</span><span class="o">.</span><span class="n">T</span> |
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257 | <span class="n">result</span> <span class="o">=</span> <span class="n">park</span><span class="o">.</span><span class="n">simplex</span><span class="o">.</span><span class="n">simplex</span><span class="p">(</span><span class="n">fitness</span><span class="p">,</span> <span class="n">x0</span><span class="p">,</span> <span class="n">bounds</span><span class="o">=</span><span class="n">bounds</span><span class="p">,</span> |
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258 | <span class="n">radius</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">radius</span><span class="p">,</span> <span class="n">xtol</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">xtol</span><span class="p">,</span> |
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259 | <span class="n">ftol</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ftol</span><span class="p">,</span> <span class="n">maxiter</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">maxiter</span><span class="p">,</span> |
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260 | <span class="n">abort_test</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_iscancelled</span><span class="p">)</span> |
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261 | <span class="c">#print "calls:",result.calls</span> |
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262 | <span class="c">#print "simplex returned",result.x,result.fx</span> |
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263 | <span class="c"># Need to make our own copy of the fit results so that the</span> |
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264 | <span class="c"># values don't get stomped on by the next fit iteration.</span> |
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265 | <span class="n">fitpars</span> <span class="o">=</span> <span class="p">[</span><span class="n">SasFitParameter</span><span class="p">(</span><span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">name</span><span class="p">,</span><span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">range</span><span class="p">,</span><span class="n">v</span><span class="p">,</span> <span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">data</span><span class="p">)</span> |
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266 | <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">x</span><span class="p">)]</span> |
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267 | <span class="n">res</span> <span class="o">=</span> <span class="n">SasFitResult</span><span class="p">(</span><span class="n">fitpars</span><span class="p">,</span> <span class="n">result</span><span class="o">.</span><span class="n">calls</span><span class="p">,</span> <span class="n">result</span><span class="o">.</span><span class="n">fx</span><span class="p">)</span> |
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268 | <span class="n">res</span><span class="o">.</span><span class="n">inputs</span> <span class="o">=</span> <span class="p">[(</span><span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">data</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">x</span><span class="p">)]</span> |
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269 | <span class="c"># Compute the parameter uncertainties from the jacobian</span> |
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270 | <span class="n">res</span><span class="o">.</span><span class="n">calc_cov</span><span class="p">(</span><span class="n">fitness</span><span class="p">)</span> |
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271 | <span class="k">return</span> <span class="n">res</span> |
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272 | |
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273 | <span class="k">class</span> <span class="nc">SasFitter</span><span class="p">(</span><span class="n">Fitter</span><span class="p">):</span> |
---|
274 | <span class="sd">"""</span> |
---|
275 | <span class="sd"> """</span></div></div> |
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276 | <div class="viewcode-block" id="SasFitter"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitter">[docs]</a> <span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fitness</span><span class="p">,</span> <span class="n">handler</span><span class="p">):</span> |
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277 | <span class="sd">"""</span> |
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278 | <span class="sd"> Global optimizer.</span> |
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279 | <div class="viewcode-block" id="SasFitter.fit"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitter.fit">[docs]</a> |
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280 | <span class="sd"> This function should return immediately</span> |
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281 | <span class="sd"> """</span> |
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282 | <span class="c"># Determine initial value and bounds</span> |
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283 | <span class="n">pars</span> <span class="o">=</span> <span class="n">fitness</span><span class="o">.</span><span class="n">fit_parameters</span><span class="p">()</span> |
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284 | <span class="n">bounds</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">p</span><span class="o">.</span><span class="n">range</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pars</span><span class="p">])</span><span class="o">.</span><span class="n">T</span> |
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285 | <span class="n">x0</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pars</span><span class="p">]</span> |
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286 | |
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287 | <span class="c"># Initialize the monitor and results.</span> |
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288 | <span class="c"># Need to make our own copy of the fit results so that the</span> |
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289 | <span class="c"># values don't get stomped on by the next fit iteration.</span> |
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290 | <span class="n">handler</span><span class="o">.</span><span class="n">done</span> <span class="o">=</span> <span class="bp">False</span> |
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291 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span> <span class="o">=</span> <span class="n">handler</span> |
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292 | <span class="n">fitpars</span> <span class="o">=</span> <span class="p">[</span><span class="n">SasFitParameter</span><span class="p">(</span><span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">range</span><span class="p">,</span> <span class="n">v</span><span class="p">,</span> |
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293 | <span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">data</span><span class="p">)</span> |
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294 | <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">x0</span><span class="p">)]</span> |
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295 | <span class="n">handler</span><span class="o">.</span><span class="n">result</span> <span class="o">=</span> <span class="n">fitresult</span><span class="o">.</span><span class="n">FitResult</span><span class="p">(</span><span class="n">fitpars</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">numpy</span><span class="o">.</span><span class="n">NaN</span><span class="p">)</span> |
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296 | |
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297 | <span class="c"># Run the fit (fit should perform _progress and _improvement updates)</span> |
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298 | <span class="c"># This function may return before the fit is complete.</span> |
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299 | <span class="bp">self</span><span class="o">.</span><span class="n">_fit</span><span class="p">(</span><span class="n">fitness</span><span class="p">,</span> <span class="n">x0</span><span class="p">,</span> <span class="n">bounds</span><span class="p">)</span> |
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300 | |
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301 | <span class="k">class</span> <span class="nc">SasFitMC</span><span class="p">(</span><span class="n">SasFitter</span><span class="p">):</span> |
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302 | <span class="sd">"""</span> |
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303 | <span class="sd"> Monte Carlo optimizer.</span></div></div> |
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304 | <div class="viewcode-block" id="SasFitMC"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitMC">[docs]</a> |
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305 | <span class="sd"> This implements `park.fit.Fitter`.</span> |
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306 | <span class="sd"> """</span> |
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307 | <span class="n">localfit</span> <span class="o">=</span> <span class="n">SasFitSimplex</span><span class="p">()</span> |
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308 | <span class="n">start_points</span> <span class="o">=</span> <span class="mi">10</span> |
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309 | <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">localfit</span><span class="p">,</span> <span class="n">start_points</span><span class="o">=</span><span class="mi">10</span><span class="p">):</span> |
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310 | <span class="bp">self</span><span class="o">.</span><span class="n">localfit</span> <span class="o">=</span> <span class="n">localfit</span> |
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311 | <span class="bp">self</span><span class="o">.</span><span class="n">start_points</span> <span class="o">=</span> <span class="n">start_points</span> |
---|
312 | |
---|
313 | <span class="k">def</span> <span class="nf">_fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">objective</span><span class="p">,</span> <span class="n">x0</span><span class="p">,</span> <span class="n">bounds</span><span class="p">):</span> |
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314 | <span class="sd">"""</span> |
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315 | <span class="sd"> Run a monte carlo fit.</span> |
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316 | |
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317 | <span class="sd"> This procedure maps a local optimizer across a set of initial points.</span> |
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318 | <span class="sd"> """</span> |
---|
319 | <span class="k">try</span><span class="p">:</span> |
---|
320 | <span class="n">park</span><span class="o">.</span><span class="n">fitmc</span><span class="o">.</span><span class="n">fitmc</span><span class="p">(</span><span class="n">objective</span><span class="p">,</span> <span class="n">x0</span><span class="p">,</span> <span class="n">bounds</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">localfit</span><span class="p">,</span> |
---|
321 | <span class="bp">self</span><span class="o">.</span><span class="n">start_points</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="p">)</span> |
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322 | <span class="k">except</span><span class="p">:</span> |
---|
323 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="s">"Fit did not converge.</span><span class="se">\n</span><span class="s">"</span> |
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324 | |
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325 | <span class="k">class</span> <span class="nc">SasPart</span><span class="p">(</span><span class="n">Part</span><span class="p">):</span> |
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326 | <span class="sd">"""</span> |
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327 | <span class="sd"> Part of a fitting assembly. Part holds the model itself and</span></div> |
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328 | <div class="viewcode-block" id="SasPart"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasPart">[docs]</a><span class="sd"> associated data. The part can be initialized with a fitness</span> |
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329 | <span class="sd"> object or with a pair (model,data) for the default fitness function.</span> |
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330 | |
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331 | <span class="sd"> fitness (Fitness)</span> |
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332 | <span class="sd"> object implementing the `park.assembly.Fitness` interface. In</span> |
---|
333 | <span class="sd"> particular, fitness should provide a parameterset attribute</span> |
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334 | <span class="sd"> containing a ParameterSet and a residuals method returning a vector</span> |
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335 | <span class="sd"> of residuals.</span> |
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336 | <span class="sd"> weight (dimensionless)</span> |
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337 | <span class="sd"> weight for the model. See comments in assembly.py for details.</span> |
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338 | <span class="sd"> isfitted (boolean)</span> |
---|
339 | <span class="sd"> True if the model residuals should be included in the fit.</span> |
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340 | <span class="sd"> The model parameters may still be used in parameter</span> |
---|
341 | <span class="sd"> expressions, but there will be no comparison to the data.</span> |
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342 | <span class="sd"> residuals (vector)</span> |
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343 | <span class="sd"> Residuals for the model if they have been calculated, or None</span> |
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344 | <span class="sd"> degrees_of_freedom</span> |
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345 | <span class="sd"> Number of residuals minus number of fitted parameters.</span> |
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346 | <span class="sd"> Degrees of freedom for individual models does not make</span> |
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347 | <span class="sd"> sense in the presence of expressions combining models,</span> |
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348 | <span class="sd"> particularly in the case where a model has many parameters</span> |
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349 | <span class="sd"> but no data or many computed parameters. The degrees of</span> |
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350 | <span class="sd"> freedom for the model is set to be at least one.</span> |
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351 | <span class="sd"> chisq</span> |
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352 | <span class="sd"> sum(residuals**2); use chisq/degrees_of_freedom to</span> |
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353 | <span class="sd"> get the reduced chisq value.</span> |
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354 | |
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355 | <span class="sd"> Get/set the weight on the given model.</span> |
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356 | |
---|
357 | <span class="sd"> assembly.weight(3) returns the weight on model 3 (0-origin)</span> |
---|
358 | <span class="sd"> assembly.weight(3,0.5) sets the weight on model 3 (0-origin)</span> |
---|
359 | <span class="sd"> """</span> |
---|
360 | |
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361 | <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">fitness</span><span class="p">,</span> <span class="n">weight</span><span class="o">=</span><span class="mf">1.</span><span class="p">,</span> <span class="n">isfitted</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span> |
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362 | <span class="n">Part</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fitness</span><span class="o">=</span><span class="n">fitness</span><span class="p">,</span> <span class="n">weight</span><span class="o">=</span><span class="n">weight</span><span class="p">,</span> |
---|
363 | <span class="n">isfitted</span><span class="o">=</span><span class="n">isfitted</span><span class="p">)</span> |
---|
364 | |
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365 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">fitness</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">fitness</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> |
---|
366 | |
---|
367 | <span class="k">class</span> <span class="nc">SasFitParameter</span><span class="p">(</span><span class="n">FitParameter</span><span class="p">):</span> |
---|
368 | <span class="sd">"""</span> |
---|
369 | <span class="sd"> Fit result for an individual parameter.</span></div> |
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370 | <div class="viewcode-block" id="SasFitParameter"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitParameter">[docs]</a><span class="sd"> """</span> |
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371 | <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">name</span><span class="p">,</span> <span class="nb">range</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span> |
---|
372 | <span class="n">FitParameter</span><span class="o">.</span><span class="n">__init__</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="nb">range</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span> |
---|
373 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">model</span> |
---|
374 | <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">data</span> |
---|
375 | |
---|
376 | <span class="k">def</span> <span class="nf">summarize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
377 | <span class="sd">"""</span> |
---|
378 | <span class="sd"> Return parameter range string.</span> |
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379 | <div class="viewcode-block" id="SasFitParameter.summarize"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitParameter.summarize">[docs]</a> |
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380 | <span class="sd"> E.g., " Gold .....|.... 5.2043 in [2,7]"</span> |
---|
381 | <span class="sd"> """</span> |
---|
382 | <span class="n">bar</span> <span class="o">=</span> <span class="p">[</span><span class="s">'.'</span><span class="p">]</span><span class="o">*</span><span class="mi">10</span> |
---|
383 | <span class="n">lo</span><span class="p">,</span><span class="n">hi</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">range</span> |
---|
384 | <span class="k">if</span> <span class="n">numpy</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">lo</span><span class="p">)</span><span class="ow">and</span> <span class="n">numpy</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">hi</span><span class="p">):</span> |
---|
385 | <span class="n">portion</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">value</span><span class="o">-</span><span class="n">lo</span><span class="p">)</span><span class="o">/</span><span class="p">(</span><span class="n">hi</span><span class="o">-</span><span class="n">lo</span><span class="p">)</span> |
---|
386 | <span class="k">if</span> <span class="n">portion</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span> <span class="n">portion</span> <span class="o">=</span> <span class="mf">0.</span> |
---|
387 | <span class="k">elif</span> <span class="n">portion</span> <span class="o">>=</span> <span class="mi">1</span><span class="p">:</span> <span class="n">portion</span> <span class="o">=</span> <span class="mf">0.99999999</span> |
---|
388 | <span class="n">barpos</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">math</span><span class="o">.</span><span class="n">floor</span><span class="p">(</span><span class="n">portion</span><span class="o">*</span><span class="nb">len</span><span class="p">(</span><span class="n">bar</span><span class="p">)))</span> |
---|
389 | <span class="n">bar</span><span class="p">[</span><span class="n">barpos</span><span class="p">]</span> <span class="o">=</span> <span class="s">'|'</span> |
---|
390 | <span class="n">bar</span> <span class="o">=</span> <span class="s">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">bar</span><span class="p">)</span> |
---|
391 | <span class="n">lostr</span> <span class="o">=</span> <span class="s">"[</span><span class="si">%g</span><span class="s">"</span><span class="o">%</span><span class="n">lo</span> <span class="k">if</span> <span class="n">numpy</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">lo</span><span class="p">)</span> <span class="k">else</span> <span class="s">"(-inf"</span> |
---|
392 | <span class="n">histr</span> <span class="o">=</span> <span class="s">"</span><span class="si">%g</span><span class="s">]"</span><span class="o">%</span><span class="n">hi</span> <span class="k">if</span> <span class="n">numpy</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">hi</span><span class="p">)</span> <span class="k">else</span> <span class="s">"inf)"</span> |
---|
393 | <span class="n">valstr</span> <span class="o">=</span> <span class="n">format_uncertainty</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">value</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">stderr</span><span class="p">)</span> |
---|
394 | <span class="n">model_name</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="bp">None</span><span class="p">)</span> |
---|
395 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
396 | <span class="n">model_name</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">name</span> |
---|
397 | <span class="n">data_name</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="bp">None</span><span class="p">)</span> |
---|
398 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
399 | <span class="n">data_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">name</span> |
---|
400 | |
---|
401 | <span class="k">return</span> <span class="s">"</span><span class="si">%25s</span><span class="s"> </span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s"> in </span><span class="si">%s</span><span class="s">,</span><span class="si">%s</span><span class="s">, </span><span class="si">%s</span><span class="s">, </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span><span class="n">bar</span><span class="p">,</span><span class="n">valstr</span><span class="p">,</span><span class="n">lostr</span><span class="p">,</span><span class="n">histr</span><span class="p">,</span> |
---|
402 | <span class="n">model_name</span><span class="p">,</span> <span class="n">data_name</span><span class="p">)</span> |
---|
403 | <span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
404 | <span class="c">#return "FitParameter('%s')"%self.name</span> |
---|
405 | <span class="k">return</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">)</span></div> |
---|
406 | |
---|
407 | <span class="k">class</span> <span class="nc">MyAssembly</span><span class="p">(</span><span class="n">Assembly</span><span class="p">):</span> |
---|
408 | <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">models</span><span class="p">,</span> <span class="n">curr_thread</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
---|
409 | <span class="sd">"""Build an assembly from a list of models."""</span></div> |
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410 | <div class="viewcode-block" id="MyAssembly"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.MyAssembly">[docs]</a> <span class="bp">self</span><span class="o">.</span><span class="n">parts</span> <span class="o">=</span> <span class="p">[]</span> |
---|
411 | <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">models</span><span class="p">:</span> |
---|
412 | <span class="bp">self</span><span class="o">.</span><span class="n">parts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">SasPart</span><span class="p">(</span><span class="n">m</span><span class="p">))</span> |
---|
413 | <span class="bp">self</span><span class="o">.</span><span class="n">curr_thread</span> <span class="o">=</span> <span class="n">curr_thread</span> |
---|
414 | <span class="bp">self</span><span class="o">.</span><span class="n">chisq</span> <span class="o">=</span> <span class="bp">None</span> |
---|
415 | <span class="bp">self</span><span class="o">.</span><span class="n">_cancel</span> <span class="o">=</span> <span class="bp">False</span> |
---|
416 | <span class="bp">self</span><span class="o">.</span><span class="n">theory</span> <span class="o">=</span> <span class="bp">None</span> |
---|
417 | <span class="bp">self</span><span class="o">.</span><span class="n">_reset</span><span class="p">()</span> |
---|
418 | |
---|
419 | <span class="k">def</span> <span class="nf">fit_parameters</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
420 | <span class="sd">"""</span> |
---|
421 | <span class="sd"> Return an alphabetical list of the fitting parameters.</span> |
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422 | <div class="viewcode-block" id="MyAssembly.fit_parameters"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.MyAssembly.fit_parameters">[docs]</a> |
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423 | <span class="sd"> This function is called once at the beginning of a fit,</span> |
---|
424 | <span class="sd"> and serves as a convenient place to precalculate what</span> |
---|
425 | <span class="sd"> can be precalculated such as the set of fitting parameters</span> |
---|
426 | <span class="sd"> and the parameter expressions evaluator.</span> |
---|
427 | <span class="sd"> """</span> |
---|
428 | <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">setprefix</span><span class="p">()</span> |
---|
429 | <span class="bp">self</span><span class="o">.</span><span class="n">_fitparameters</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">fitted</span> |
---|
430 | <span class="bp">self</span><span class="o">.</span><span class="n">_restraints</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">restrained</span> |
---|
431 | <span class="n">pars</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">flatten</span><span class="p">()</span> |
---|
432 | <span class="n">context</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">gather_context</span><span class="p">()</span> |
---|
433 | <span class="bp">self</span><span class="o">.</span><span class="n">_fitexpression</span> <span class="o">=</span> <span class="n">park</span><span class="o">.</span><span class="n">expression</span><span class="o">.</span><span class="n">build_eval</span><span class="p">(</span><span class="n">pars</span><span class="p">,</span><span class="n">context</span><span class="p">)</span> |
---|
434 | <span class="c">#print "constraints",self._fitexpression.__doc__</span> |
---|
435 | |
---|
436 | <span class="bp">self</span><span class="o">.</span><span class="n">_fitparameters</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="k">lambda</span> <span class="n">a</span><span class="p">,</span><span class="n">b</span><span class="p">:</span> <span class="nb">cmp</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">path</span><span class="p">,</span><span class="n">b</span><span class="o">.</span><span class="n">path</span><span class="p">))</span> |
---|
437 | <span class="c"># Convert to fitparameter a object</span> |
---|
438 | |
---|
439 | <span class="n">fitpars</span> <span class="o">=</span> <span class="p">[</span><span class="n">SasFitParameter</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">path</span><span class="p">,</span><span class="n">p</span><span class="o">.</span><span class="n">range</span><span class="p">,</span><span class="n">p</span><span class="o">.</span><span class="n">value</span><span class="p">,</span> <span class="n">p</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">p</span><span class="o">.</span><span class="n">data</span><span class="p">)</span> |
---|
440 | <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_fitparameters</span><span class="p">]</span> |
---|
441 | <span class="c">#print "fitpars", fitpars</span> |
---|
442 | <span class="k">return</span> <span class="n">fitpars</span> |
---|
443 | |
---|
444 | <span class="k">def</span> <span class="nf">extend_results_with_calculated_parameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">result</span><span class="p">):</span> |
---|
445 | <span class="sd">"""</span> |
---|
446 | <span class="sd"> Extend result from the fit with the calculated parameters.</span></div> |
---|
447 | <div class="viewcode-block" id="MyAssembly.extend_results_with_calculated_parameters"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.MyAssembly.extend_results_with_calculated_parameters">[docs]</a><span class="sd"> """</span> |
---|
448 | <span class="n">calcpars</span> <span class="o">=</span> <span class="p">[</span><span class="n">SasFitParameter</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">path</span><span class="p">,</span><span class="n">p</span><span class="o">.</span><span class="n">range</span><span class="p">,</span><span class="n">p</span><span class="o">.</span><span class="n">value</span><span class="p">,</span> <span class="n">p</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">p</span><span class="o">.</span><span class="n">data</span><span class="p">)</span> |
---|
449 | <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">computed</span><span class="p">]</span> |
---|
450 | <span class="n">result</span><span class="o">.</span><span class="n">parameters</span> <span class="o">+=</span> <span class="n">calcpars</span> |
---|
451 | <span class="n">result</span><span class="o">.</span><span class="n">theory</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">theory</span> |
---|
452 | |
---|
453 | <span class="k">def</span> <span class="nf">eval</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
454 | <span class="sd">"""</span> |
---|
455 | <span class="sd"> Recalculate the theory functions, and from them, the</span></div> |
---|
456 | <div class="viewcode-block" id="MyAssembly.eval"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.MyAssembly.eval">[docs]</a><span class="sd"> residuals and chisq.</span> |
---|
457 | |
---|
458 | <span class="sd"> :note: Call this after the parameters have been updated.</span> |
---|
459 | <span class="sd"> """</span> |
---|
460 | <span class="c"># Handle abort from a separate thread.</span> |
---|
461 | <span class="bp">self</span><span class="o">.</span><span class="n">_cancel</span> <span class="o">=</span> <span class="bp">False</span> |
---|
462 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">curr_thread</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span> |
---|
463 | <span class="k">try</span><span class="p">:</span> |
---|
464 | <span class="bp">self</span><span class="o">.</span><span class="n">curr_thread</span><span class="o">.</span><span class="n">isquit</span><span class="p">()</span> |
---|
465 | <span class="k">except</span><span class="p">:</span> |
---|
466 | <span class="bp">self</span><span class="o">.</span><span class="n">_cancel</span> <span class="o">=</span> <span class="bp">True</span> |
---|
467 | |
---|
468 | <span class="c"># Evaluate the computed parameters</span> |
---|
469 | <span class="k">try</span><span class="p">:</span> |
---|
470 | <span class="bp">self</span><span class="o">.</span><span class="n">_fitexpression</span><span class="p">()</span> |
---|
471 | <span class="k">except</span> <span class="ne">NameError</span><span class="p">:</span> |
---|
472 | <span class="k">pass</span> |
---|
473 | |
---|
474 | <span class="c"># Check that the resulting parameters are in a feasible region.</span> |
---|
475 | <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">isfeasible</span><span class="p">():</span> <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">inf</span> |
---|
476 | |
---|
477 | <span class="n">resid</span> <span class="o">=</span> <span class="p">[]</span> |
---|
478 | <span class="n">k</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_fitparameters</span><span class="p">)</span> |
---|
479 | <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parts</span><span class="p">:</span> |
---|
480 | <span class="c"># In order to support abort, need to be able to propagate an</span> |
---|
481 | <span class="c"># external abort signal from self.abort() into an abort signal</span> |
---|
482 | <span class="c"># for the particular model. Can't see a way to do this which</span> |
---|
483 | <span class="c"># doesn't involve setting a state variable.</span> |
---|
484 | <span class="bp">self</span><span class="o">.</span><span class="n">_current_model</span> <span class="o">=</span> <span class="n">m</span> |
---|
485 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_cancel</span><span class="p">:</span> <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">inf</span> |
---|
486 | <span class="k">if</span> <span class="n">m</span><span class="o">.</span><span class="n">isfitted</span> <span class="ow">and</span> <span class="n">m</span><span class="o">.</span><span class="n">weight</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span> |
---|
487 | <span class="n">m</span><span class="o">.</span><span class="n">residuals</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">theory</span> <span class="o">=</span> <span class="n">m</span><span class="o">.</span><span class="n">fitness</span><span class="o">.</span><span class="n">residuals</span><span class="p">()</span> |
---|
488 | <span class="n">N</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">residuals</span><span class="p">)</span> |
---|
489 | <span class="n">m</span><span class="o">.</span><span class="n">degrees_of_freedom</span> <span class="o">=</span> <span class="n">N</span><span class="o">-</span><span class="n">k</span> <span class="k">if</span> <span class="n">N</span><span class="o">></span><span class="n">k</span> <span class="k">else</span> <span class="mi">1</span> |
---|
490 | <span class="c"># dividing residuals by N in order to be consistent with Scipy</span> |
---|
491 | <span class="n">m</span><span class="o">.</span><span class="n">chisq</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">residuals</span><span class="o">**</span><span class="mi">2</span><span class="o">/</span><span class="n">N</span><span class="p">)</span> |
---|
492 | <span class="n">resid</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">weight</span><span class="o">*</span><span class="n">m</span><span class="o">.</span><span class="n">residuals</span><span class="p">)</span> |
---|
493 | <span class="bp">self</span><span class="o">.</span><span class="n">residuals</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">hstack</span><span class="p">(</span><span class="n">resid</span><span class="p">)</span> |
---|
494 | <span class="n">N</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">residuals</span><span class="p">)</span> |
---|
495 | <span class="bp">self</span><span class="o">.</span><span class="n">degrees_of_freedom</span> <span class="o">=</span> <span class="n">N</span><span class="o">-</span><span class="n">k</span> <span class="k">if</span> <span class="n">N</span><span class="o">></span><span class="n">k</span> <span class="k">else</span> <span class="mi">1</span> |
---|
496 | <span class="bp">self</span><span class="o">.</span><span class="n">chisq</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">residuals</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span> |
---|
497 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">chisq</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">degrees_of_freedom</span> |
---|
498 | |
---|
499 | <span class="k">class</span> <span class="nc">ParkFit</span><span class="p">(</span><span class="n">FitEngine</span><span class="p">):</span> |
---|
500 | <span class="sd">""" </span> |
---|
501 | <span class="sd"> ParkFit performs the Fit.This class can be used as follow:</span></div></div> |
---|
502 | <div class="viewcode-block" id="ParkFit"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkFit">[docs]</a><span class="sd"> #Do the fit Park</span> |
---|
503 | <span class="sd"> create an engine: engine = ParkFit()</span> |
---|
504 | <span class="sd"> Use data must be of type plottable</span> |
---|
505 | <span class="sd"> Use a sas model</span> |
---|
506 | <span class="sd"> </span> |
---|
507 | <span class="sd"> Add data with a dictionnary of FitArrangeList where Uid is a key and data</span> |
---|
508 | <span class="sd"> is saved in FitArrange object.</span> |
---|
509 | <span class="sd"> engine.set_data(data,Uid)</span> |
---|
510 | <span class="sd"> </span> |
---|
511 | <span class="sd"> Set model parameter "M1"= model.name add {model.parameter.name:value}.</span> |
---|
512 | <span class="sd"> </span> |
---|
513 | <span class="sd"> ..note::</span> |
---|
514 | |
---|
515 | <span class="sd"> Set_param() if used must always preceded set_model() for the fit to be performed. ``engine.set_param( model,"M1", {'A':2,'B':4})``</span> |
---|
516 | <span class="sd"> </span> |
---|
517 | <span class="sd"> Add model with a dictionnary of FitArrangeList{} where Uid is a key</span> |
---|
518 | <span class="sd"> and model</span> |
---|
519 | <span class="sd"> is save in FitArrange object.</span> |
---|
520 | <span class="sd"> engine.set_model(model,Uid)</span> |
---|
521 | <span class="sd"> </span> |
---|
522 | <span class="sd"> engine.fit return chisqr,[model.parameter 1,2,..],[[err1....][..err2...]]</span> |
---|
523 | <span class="sd"> chisqr1, out1, cov1=engine.fit({model.parameter.name:value},qmin,qmax)</span> |
---|
524 | <span class="sd"> </span> |
---|
525 | <span class="sd"> ..note::</span> |
---|
526 | |
---|
527 | <span class="sd"> {model.parameter.name:value} is ignored in fit function since </span> |
---|
528 | <span class="sd"> the user should make sure to call set_param himself.</span> |
---|
529 | <span class="sd"> </span> |
---|
530 | <span class="sd"> """</span> |
---|
531 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
532 | <span class="sd">"""</span> |
---|
533 | <span class="sd"> Creates a dictionary (self.fitArrangeList={})of FitArrange elements</span> |
---|
534 | <span class="sd"> with Uid as keys</span> |
---|
535 | <span class="sd"> """</span> |
---|
536 | <span class="n">FitEngine</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> |
---|
537 | <span class="bp">self</span><span class="o">.</span><span class="n">fit_arrange_dict</span> <span class="o">=</span> <span class="p">{}</span> |
---|
538 | <span class="bp">self</span><span class="o">.</span><span class="n">param_list</span> <span class="o">=</span> <span class="p">[]</span> |
---|
539 | |
---|
540 | <span class="k">def</span> <span class="nf">create_assembly</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">curr_thread</span><span class="p">,</span> <span class="n">reset_flag</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span> |
---|
541 | <span class="sd">"""</span> |
---|
542 | <span class="sd"> Extract sasmodel and sasdata from </span> |
---|
543 | <div class="viewcode-block" id="ParkFit.create_assembly"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkFit.create_assembly">[docs]</a><span class="sd"> self.FitArrangelist ={Uid:FitArrange}</span> |
---|
544 | <span class="sd"> Create parkmodel and park data ,form a list couple of parkmodel </span> |
---|
545 | <span class="sd"> and parkdata</span> |
---|
546 | <span class="sd"> create an assembly self.problem= park.Assembly([(parkmodel,parkdata)])</span> |
---|
547 | <span class="sd"> """</span> |
---|
548 | <span class="n">mylist</span> <span class="o">=</span> <span class="p">[]</span> |
---|
549 | <span class="c">#listmodel = []</span> |
---|
550 | <span class="c">#i = 0</span> |
---|
551 | <span class="n">fitproblems</span> <span class="o">=</span> <span class="p">[]</span> |
---|
552 | <span class="k">for</span> <span class="n">fproblem</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">fit_arrange_dict</span><span class="o">.</span><span class="n">itervalues</span><span class="p">():</span> |
---|
553 | <span class="k">if</span> <span class="n">fproblem</span><span class="o">.</span><span class="n">get_to_fit</span><span class="p">()</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span> |
---|
554 | <span class="n">fitproblems</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">fproblem</span><span class="p">)</span> |
---|
555 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">fitproblems</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> |
---|
556 | <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="s">"No Assembly scheduled for Park fitting."</span> |
---|
557 | <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">fitproblems</span><span class="p">:</span> |
---|
558 | <span class="n">model</span> <span class="o">=</span> <span class="n">item</span><span class="o">.</span><span class="n">get_model</span><span class="p">()</span> |
---|
559 | <span class="n">parkmodel</span> <span class="o">=</span> <span class="n">ParkModel</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">model</span><span class="o">.</span><span class="n">data</span><span class="p">)</span> |
---|
560 | <span class="n">parkmodel</span><span class="o">.</span><span class="n">pars</span> <span class="o">=</span> <span class="n">item</span><span class="o">.</span><span class="n">pars</span> |
---|
561 | <span class="k">if</span> <span class="n">reset_flag</span><span class="p">:</span> |
---|
562 | <span class="c"># reset the initial value; useful for batch</span> |
---|
563 | <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">item</span><span class="o">.</span><span class="n">pars</span><span class="p">:</span> |
---|
564 | <span class="n">ind</span> <span class="o">=</span> <span class="n">item</span><span class="o">.</span><span class="n">pars</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">name</span><span class="p">)</span> |
---|
565 | <span class="n">parkmodel</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">item</span><span class="o">.</span><span class="n">vals</span><span class="p">[</span><span class="n">ind</span><span class="p">])</span> |
---|
566 | |
---|
567 | <span class="c"># set the constraints into the model</span> |
---|
568 | <span class="k">for</span> <span class="n">p</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="n">item</span><span class="o">.</span><span class="n">constraints</span><span class="p">:</span> |
---|
569 | <span class="n">parkmodel</span><span class="o">.</span><span class="n">parameterset</span><span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">p</span><span class="p">)]</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">v</span><span class="p">))</span> |
---|
570 | |
---|
571 | <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">parkmodel</span><span class="o">.</span><span class="n">parameterset</span><span class="p">:</span> |
---|
572 | <span class="c">## does not allow status change for constraint parameters</span> |
---|
573 | <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">status</span> <span class="o">!=</span> <span class="s">'computed'</span><span class="p">:</span> |
---|
574 | <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">get_name</span><span class="p">()</span> <span class="ow">in</span> <span class="n">item</span><span class="o">.</span><span class="n">pars</span><span class="p">:</span> |
---|
575 | <span class="c">## make parameters selected for </span> |
---|
576 | <span class="c">#fit will be between boundaries</span> |
---|
577 | <span class="n">p</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">range</span><span class="p">)</span> |
---|
578 | <span class="k">else</span><span class="p">:</span> |
---|
579 | <span class="n">p</span><span class="o">.</span><span class="n">status</span> <span class="o">=</span> <span class="s">'fixed'</span> |
---|
580 | <span class="n">data_list</span> <span class="o">=</span> <span class="n">item</span><span class="o">.</span><span class="n">get_data</span><span class="p">()</span> |
---|
581 | <span class="n">parkdata</span> <span class="o">=</span> <span class="n">data_list</span> |
---|
582 | <span class="n">fitness</span> <span class="o">=</span> <span class="p">(</span><span class="n">parkmodel</span><span class="p">,</span> <span class="n">parkdata</span><span class="p">)</span> |
---|
583 | <span class="n">mylist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">fitness</span><span class="p">)</span> |
---|
584 | <span class="bp">self</span><span class="o">.</span><span class="n">problem</span> <span class="o">=</span> <span class="n">MyAssembly</span><span class="p">(</span><span class="n">models</span><span class="o">=</span><span class="n">mylist</span><span class="p">,</span> <span class="n">curr_thread</span><span class="o">=</span><span class="n">curr_thread</span><span class="p">)</span> |
---|
585 | |
---|
586 | |
---|
587 | <span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">msg_q</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> |
---|
588 | <span class="n">q</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">handler</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">curr_thread</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> |
---|
589 | <span class="n">ftol</span><span class="o">=</span><span class="mf">1.49012e-8</span><span class="p">,</span> <span class="n">reset_flag</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span></div> |
---|
590 | <div class="viewcode-block" id="ParkFit.fit"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkFit.fit">[docs]</a> <span class="sd">"""</span> |
---|
591 | <span class="sd"> Performs fit with park.fit module.It can perform fit with one model</span> |
---|
592 | <span class="sd"> and a set of data, more than two fit of one model and sets of data or </span> |
---|
593 | <span class="sd"> fit with more than two model associated with their set of data and </span> |
---|
594 | <span class="sd"> constraints</span> |
---|
595 | <span class="sd"> </span> |
---|
596 | <span class="sd"> :param pars: Dictionary of parameter names for the model and their </span> |
---|
597 | <span class="sd"> values.</span> |
---|
598 | <span class="sd"> :param qmin: The minimum value of data's range to be fit</span> |
---|
599 | <span class="sd"> :param qmax: The maximum value of data's range to be fit</span> |
---|
600 | <span class="sd"> </span> |
---|
601 | <span class="sd"> :note: all parameter are ignored most of the time.Are just there </span> |
---|
602 | <span class="sd"> to keep ScipyFit and ParkFit interface the same.</span> |
---|
603 | <span class="sd"> </span> |
---|
604 | <span class="sd"> :return: result.fitness Value of the goodness of fit metric</span> |
---|
605 | <span class="sd"> :return: result.pvec list of parameter with the best value </span> |
---|
606 | <span class="sd"> found during fitting</span> |
---|
607 | <span class="sd"> :return: result.cov Covariance matrix</span> |
---|
608 | <span class="sd"> </span> |
---|
609 | <span class="sd"> """</span> |
---|
610 | <span class="bp">self</span><span class="o">.</span><span class="n">create_assembly</span><span class="p">(</span><span class="n">curr_thread</span><span class="o">=</span><span class="n">curr_thread</span><span class="p">,</span> <span class="n">reset_flag</span><span class="o">=</span><span class="n">reset_flag</span><span class="p">)</span> |
---|
611 | <span class="n">localfit</span> <span class="o">=</span> <span class="n">SasFitSimplex</span><span class="p">()</span> |
---|
612 | <span class="n">localfit</span><span class="o">.</span><span class="n">ftol</span> <span class="o">=</span> <span class="n">ftol</span> |
---|
613 | <span class="n">localfit</span><span class="o">.</span><span class="n">xtol</span> <span class="o">=</span> <span class="mf">1e-6</span> |
---|
614 | |
---|
615 | <span class="c"># See `park.fitresult.FitHandler` for details.</span> |
---|
616 | <span class="n">fitter</span> <span class="o">=</span> <span class="n">SasFitMC</span><span class="p">(</span><span class="n">localfit</span><span class="o">=</span><span class="n">localfit</span><span class="p">,</span> <span class="n">start_points</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> |
---|
617 | <span class="k">if</span> <span class="n">handler</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> |
---|
618 | <span class="n">handler</span> <span class="o">=</span> <span class="n">fitresult</span><span class="o">.</span><span class="n">ConsoleUpdate</span><span class="p">(</span><span class="n">improvement_delta</span><span class="o">=</span><span class="mf">0.1</span><span class="p">)</span> |
---|
619 | |
---|
620 | <span class="n">result_list</span> <span class="o">=</span> <span class="p">[]</span> |
---|
621 | <span class="k">try</span><span class="p">:</span> |
---|
622 | <span class="n">result</span> <span class="o">=</span> <span class="n">fit</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">problem</span><span class="p">,</span> <span class="n">fitter</span><span class="o">=</span><span class="n">fitter</span><span class="p">,</span> <span class="n">handler</span><span class="o">=</span><span class="n">handler</span><span class="p">)</span> |
---|
623 | <span class="bp">self</span><span class="o">.</span><span class="n">problem</span><span class="o">.</span><span class="n">extend_results_with_calculated_parameters</span><span class="p">(</span><span class="n">result</span><span class="p">)</span> |
---|
624 | |
---|
625 | <span class="k">except</span> <span class="n">LinAlgError</span><span class="p">:</span> |
---|
626 | <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="s">"SVD did not converge"</span> |
---|
627 | |
---|
628 | <span class="k">if</span> <span class="n">result</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> |
---|
629 | <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">"park did not return a fit result"</span><span class="p">)</span> |
---|
630 | |
---|
631 | <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">problem</span><span class="o">.</span><span class="n">parts</span><span class="p">:</span> |
---|
632 | <span class="n">residuals</span><span class="p">,</span> <span class="n">theory</span> <span class="o">=</span> <span class="n">m</span><span class="o">.</span><span class="n">fitness</span><span class="o">.</span><span class="n">residuals</span><span class="p">()</span> |
---|
633 | <span class="n">small_result</span> <span class="o">=</span> <span class="n">FResult</span><span class="p">(</span><span class="n">model</span><span class="o">=</span><span class="n">m</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">m</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">sas_data</span><span class="p">)</span> |
---|
634 | <span class="n">small_result</span><span class="o">.</span><span class="n">fitter_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">fitter_id</span> |
---|
635 | <span class="n">small_result</span><span class="o">.</span><span class="n">theory</span> <span class="o">=</span> <span class="n">theory</span> |
---|
636 | <span class="n">small_result</span><span class="o">.</span><span class="n">residuals</span> <span class="o">=</span> <span class="n">residuals</span> |
---|
637 | <span class="n">small_result</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">m</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">idx</span> |
---|
638 | <span class="n">small_result</span><span class="o">.</span><span class="n">fitness</span> <span class="o">=</span> <span class="n">result</span><span class="o">.</span><span class="n">fitness</span> |
---|
639 | |
---|
640 | <span class="c"># Extract the parameters that are part of this model; make sure</span> |
---|
641 | <span class="c"># they match the fitted parameters for this model, and place them</span> |
---|
642 | <span class="c"># in the same order as they occur in the model.</span> |
---|
643 | <span class="n">pars</span> <span class="o">=</span> <span class="p">{}</span> |
---|
644 | <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">result</span><span class="o">.</span><span class="n">parameters</span><span class="p">:</span> |
---|
645 | <span class="c">#if p.data.name == small_result.data.name and</span> |
---|
646 | <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">small_result</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">name</span><span class="p">:</span> |
---|
647 | <span class="n">model_name</span><span class="p">,</span> <span class="n">par_name</span> <span class="o">=</span> <span class="n">p</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">1</span><span class="p">)</span> |
---|
648 | <span class="n">pars</span><span class="p">[</span><span class="n">par_name</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">value</span><span class="p">,</span> <span class="n">p</span><span class="o">.</span><span class="n">stderr</span><span class="p">)</span> |
---|
649 | <span class="c">#assert len(pars.keys()) == len(m.model.pars)</span> |
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650 | <span class="n">v</span><span class="p">,</span><span class="n">dv</span> <span class="o">=</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span><span class="n">pars</span><span class="p">[</span><span class="n">p</span><span class="p">]</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">m</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">pars</span><span class="p">])</span> |
---|
651 | <span class="n">small_result</span><span class="o">.</span><span class="n">pvec</span> <span class="o">=</span> <span class="n">v</span> |
---|
652 | <span class="n">small_result</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="n">dv</span> |
---|
653 | <span class="n">small_result</span><span class="o">.</span><span class="n">param_list</span> <span class="o">=</span> <span class="n">m</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">pars</span> |
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654 | |
---|
655 | <span class="c"># normalize chisq by degrees of freedom</span> |
---|
656 | <span class="n">dof</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">small_result</span><span class="o">.</span><span class="n">residuals</span><span class="p">)</span><span class="o">-</span><span class="nb">len</span><span class="p">(</span><span class="n">small_result</span><span class="o">.</span><span class="n">pvec</span><span class="p">)</span> |
---|
657 | <span class="n">small_result</span><span class="o">.</span><span class="n">fitness</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">residuals</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span><span class="o">/</span><span class="n">dof</span> |
---|
658 | |
---|
659 | <span class="n">result_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">small_result</span><span class="p">)</span> |
---|
660 | <span class="k">if</span> <span class="n">q</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span> |
---|
661 | <span class="n">q</span><span class="o">.</span><span class="n">put</span><span class="p">(</span><span class="n">result_list</span><span class="p">)</span> |
---|
662 | <span class="k">return</span> <span class="n">q</span> |
---|
663 | <span class="k">return</span> <span class="n">result_list</span> |
---|
664 | |
---|
665 | </pre></div></div></div> |
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