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50 | <h1>Source code for sas.fit.ScipyFitting</h1><div class="highlight"><pre> |
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51 | <span class="sd">"""</span> |
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52 | <span class="sd">ScipyFitting module contains FitArrange , ScipyFit,</span> |
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53 | <span class="sd">Parameter classes.All listed classes work together to perform a </span> |
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54 | <span class="sd">simple fit with scipy optimizer.</span> |
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55 | <span class="sd">"""</span> |
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56 | <span class="kn">import</span> <span class="nn">sys</span> |
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57 | <span class="kn">import</span> <span class="nn">copy</span> |
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58 | |
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59 | <span class="kn">import</span> <span class="nn">numpy</span> |
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60 | |
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61 | <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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62 | <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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63 | |
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64 | <span class="n">_SMALLVALUE</span> <span class="o">=</span> <span class="mf">1.0e-10</span> |
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65 | |
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66 | <div class="viewcode-block" id="SasAssembly"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ScipyFitting.SasAssembly">[docs]</a><span class="k">class</span> <span class="nc">SasAssembly</span><span class="p">:</span> |
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67 | <span class="sd">"""</span> |
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68 | <span class="sd"> Sas Assembly class a class wrapper to be call in optimizer.leastsq method</span> |
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69 | <span class="sd"> """</span> |
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70 | <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">paramlist</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">fitresult</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> |
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71 | <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> <span class="n">msg_q</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
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72 | <span class="sd">"""</span> |
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73 | <span class="sd"> :param Model: the model wrapper fro sas -model</span> |
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74 | <span class="sd"> :param Data: the data wrapper for sas data</span> |
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75 | |
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76 | <span class="sd"> """</span> |
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77 | <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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78 | <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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79 | <span class="bp">self</span><span class="o">.</span><span class="n">paramlist</span> <span class="o">=</span> <span class="n">paramlist</span> |
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80 | <span class="bp">self</span><span class="o">.</span><span class="n">msg_q</span> <span class="o">=</span> <span class="n">msg_q</span> |
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81 | <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> |
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82 | <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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83 | <span class="bp">self</span><span class="o">.</span><span class="n">fitresult</span> <span class="o">=</span> <span class="n">fitresult</span> |
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84 | <span class="bp">self</span><span class="o">.</span><span class="n">res</span> <span class="o">=</span> <span class="p">[]</span> |
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85 | <span class="bp">self</span><span class="o">.</span><span class="n">true_res</span> <span class="o">=</span> <span class="p">[]</span> |
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86 | <span class="bp">self</span><span class="o">.</span><span class="n">func_name</span> <span class="o">=</span> <span class="s">"Functor"</span> |
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87 | <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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88 | |
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89 | <div class="viewcode-block" id="SasAssembly.chisq"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ScipyFitting.SasAssembly.chisq">[docs]</a> <span class="k">def</span> <span class="nf">chisq</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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90 | <span class="sd">"""</span> |
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91 | <span class="sd"> Calculates chi^2</span> |
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92 | |
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93 | <span class="sd"> :param params: list of parameter values</span> |
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94 | |
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95 | <span class="sd"> :return: chi^2</span> |
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96 | |
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97 | <span class="sd"> """</span> |
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98 | <span class="n">total</span> <span class="o">=</span> <span class="mi">0</span> |
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99 | <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">true_res</span><span class="p">:</span> |
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100 | <span class="n">total</span> <span class="o">+=</span> <span class="n">item</span> <span class="o">*</span> <span class="n">item</span> |
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101 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">true_res</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> |
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102 | <span class="k">return</span> <span class="bp">None</span> |
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103 | <span class="k">return</span> <span class="n">total</span> <span class="o">/</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">true_res</span><span class="p">)</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">paramlist</span><span class="p">))</span> |
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104 | </div> |
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105 | <span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">params</span><span class="p">):</span> |
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106 | <span class="sd">"""</span> |
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107 | <span class="sd"> Compute residuals</span> |
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108 | <span class="sd"> :param params: value of parameters to fit</span> |
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109 | <span class="sd"> """</span> |
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110 | <span class="c">#import thread</span> |
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111 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">set_params</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">paramlist</span><span class="p">,</span> <span class="n">params</span><span class="p">)</span> |
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112 | <span class="c">#print "params", params</span> |
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113 | <span class="bp">self</span><span class="o">.</span><span class="n">true_res</span><span class="p">,</span> <span class="n">theory</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">residuals</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">eval</span><span class="p">)</span> |
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114 | <span class="bp">self</span><span class="o">.</span><span class="n">theory</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">theory</span><span class="p">)</span> |
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115 | <span class="c"># check parameters range</span> |
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116 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">check_param_range</span><span class="p">():</span> |
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117 | <span class="c"># if the param value is outside of the bound</span> |
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118 | <span class="c"># just silent return res = inf</span> |
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119 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">res</span> |
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120 | <span class="bp">self</span><span class="o">.</span><span class="n">res</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">true_res</span> |
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121 | |
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122 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">fitresult</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
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123 | <span class="bp">self</span><span class="o">.</span><span class="n">fitresult</span><span class="o">.</span><span class="n">set_model</span><span class="p">(</span><span class="n">model</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="p">)</span> |
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124 | <span class="bp">self</span><span class="o">.</span><span class="n">fitresult</span><span class="o">.</span><span class="n">residuals</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">true_res</span> |
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125 | <span class="bp">self</span><span class="o">.</span><span class="n">fitresult</span><span class="o">.</span><span class="n">iterations</span> <span class="o">+=</span> <span class="mi">1</span> |
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126 | <span class="bp">self</span><span class="o">.</span><span class="n">fitresult</span><span class="o">.</span><span class="n">theory</span> <span class="o">=</span> <span class="n">theory</span> |
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127 | |
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128 | <span class="c">#fitness = self.chisq(params=params)</span> |
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129 | <span class="n">fitness</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">chisq</span><span class="p">()</span> |
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130 | <span class="bp">self</span><span class="o">.</span><span class="n">fitresult</span><span class="o">.</span><span class="n">pvec</span> <span class="o">=</span> <span class="n">params</span> |
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131 | <span class="bp">self</span><span class="o">.</span><span class="n">fitresult</span><span class="o">.</span><span class="n">set_fitness</span><span class="p">(</span><span class="n">fitness</span><span class="o">=</span><span class="n">fitness</span><span class="p">)</span> |
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132 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">msg_q</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
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133 | <span class="bp">self</span><span class="o">.</span><span class="n">msg_q</span><span class="o">.</span><span class="n">put</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">fitresult</span><span class="p">)</span> |
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134 | |
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135 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">handler</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
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136 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">set_result</span><span class="p">(</span><span class="n">result</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">fitresult</span><span class="p">)</span> |
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137 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">update_fit</span><span class="p">()</span> |
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138 | |
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139 | <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> |
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140 | <span class="k">try</span><span class="p">:</span> |
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141 | <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> |
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142 | <span class="k">except</span><span class="p">:</span> |
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143 | <span class="c">#msg = "Fitting: Terminated... Note: Forcing to stop "</span> |
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144 | <span class="c">#msg += "fitting may cause a 'Functor error message' "</span> |
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145 | <span class="c">#msg += "being recorded in the log file....."</span> |
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146 | <span class="c">#self.handler.stop(msg)</span> |
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147 | <span class="k">raise</span> |
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148 | |
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149 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">res</span> |
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150 | |
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151 | <div class="viewcode-block" id="SasAssembly.check_param_range"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ScipyFitting.SasAssembly.check_param_range">[docs]</a> <span class="k">def</span> <span class="nf">check_param_range</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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152 | <span class="sd">"""</span> |
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153 | <span class="sd"> Check the lower and upper bound of the parameter value</span> |
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154 | <span class="sd"> and set res to the inf if the value is outside of the</span> |
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155 | <span class="sd"> range</span> |
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156 | <span class="sd"> :limitation: the initial values must be within range.</span> |
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157 | <span class="sd"> """</span> |
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158 | |
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159 | <span class="c">#time.sleep(0.01)</span> |
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160 | <span class="n">is_outofbound</span> <span class="o">=</span> <span class="bp">False</span> |
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161 | <span class="c"># loop through the fit parameters</span> |
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162 | <span class="n">model</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">model</span> |
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163 | <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">paramlist</span><span class="p">:</span> |
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164 | <span class="n">value</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="n">p</span><span class="p">)</span> |
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165 | <span class="n">low</span><span class="p">,</span><span class="n">high</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="n">p</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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166 | <span class="k">if</span> <span class="n">low</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</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">low</span><span class="p">):</span> |
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167 | <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">value</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> |
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168 | <span class="c"># This value works on Scipy</span> |
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169 | <span class="c"># Do not change numbers below</span> |
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170 | <span class="n">value</span> <span class="o">=</span> <span class="n">_SMALLVALUE</span> |
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171 | <span class="c"># For leastsq, it needs a bit step back from the boundary</span> |
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172 | <span class="n">val</span> <span class="o">=</span> <span class="n">low</span> <span class="o">-</span> <span class="n">value</span> <span class="o">*</span> <span class="n">_SMALLVALUE</span> |
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173 | <span class="k">if</span> <span class="n">value</span> <span class="o"><</span> <span class="n">val</span><span class="p">:</span> |
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174 | <span class="bp">self</span><span class="o">.</span><span class="n">res</span> <span class="o">*=</span> <span class="mf">1e+6</span> |
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175 | <span class="n">is_outofbound</span> <span class="o">=</span> <span class="bp">True</span> |
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176 | <span class="k">break</span> |
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177 | <span class="k">if</span> <span class="n">high</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</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">high</span><span class="p">):</span> |
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178 | <span class="c"># This value works on Scipy</span> |
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179 | <span class="c"># Do not change numbers below</span> |
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180 | <span class="k">if</span> <span class="n">value</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> |
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181 | <span class="n">value</span> <span class="o">=</span> <span class="n">_SMALLVALUE</span> |
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182 | <span class="c"># For leastsq, it needs a bit step back from the boundary</span> |
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183 | <span class="n">val</span> <span class="o">=</span> <span class="n">high</span> <span class="o">+</span> <span class="n">value</span> <span class="o">*</span> <span class="n">_SMALLVALUE</span> |
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184 | <span class="k">if</span> <span class="n">value</span> <span class="o">></span> <span class="n">val</span><span class="p">:</span> |
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185 | <span class="bp">self</span><span class="o">.</span><span class="n">res</span> <span class="o">*=</span> <span class="mf">1e+6</span> |
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186 | <span class="n">is_outofbound</span> <span class="o">=</span> <span class="bp">True</span> |
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187 | <span class="k">break</span> |
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188 | |
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189 | <span class="k">return</span> <span class="n">is_outofbound</span> |
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190 | </div></div> |
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191 | <div class="viewcode-block" id="ScipyFit"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ScipyFitting.ScipyFit">[docs]</a><span class="k">class</span> <span class="nc">ScipyFit</span><span class="p">(</span><span class="n">FitEngine</span><span class="p">):</span> |
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192 | <span class="sd">""" </span> |
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193 | <span class="sd"> ScipyFit performs the Fit.This class can be used as follow:</span> |
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194 | <span class="sd"> #Do the fit SCIPY</span> |
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195 | <span class="sd"> create an engine: engine = ScipyFit()</span> |
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196 | <span class="sd"> Use data must be of type plottable</span> |
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197 | <span class="sd"> Use a sas model</span> |
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198 | <span class="sd"> </span> |
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199 | <span class="sd"> Add data with a dictionnary of FitArrangeDict where Uid is a key and data</span> |
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200 | <span class="sd"> is saved in FitArrange object.</span> |
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201 | <span class="sd"> engine.set_data(data,Uid)</span> |
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202 | <span class="sd"> </span> |
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203 | <span class="sd"> Set model parameter "M1"= model.name add {model.parameter.name:value}.</span> |
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204 | <span class="sd"> </span> |
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205 | <span class="sd"> :note: Set_param() if used must always preceded set_model()</span> |
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206 | <span class="sd"> for the fit to be performed.In case of Scipyfit set_param is called in</span> |
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207 | <span class="sd"> fit () automatically.</span> |
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208 | <span class="sd"> </span> |
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209 | <span class="sd"> engine.set_param( model,"M1", {'A':2,'B':4})</span> |
---|
210 | <span class="sd"> </span> |
---|
211 | <span class="sd"> Add model with a dictionnary of FitArrangeDict{} where Uid is a key and model</span> |
---|
212 | <span class="sd"> is save in FitArrange object.</span> |
---|
213 | <span class="sd"> engine.set_model(model,Uid)</span> |
---|
214 | <span class="sd"> </span> |
---|
215 | <span class="sd"> engine.fit return chisqr,[model.parameter 1,2,..],[[err1....][..err2...]]</span> |
---|
216 | <span class="sd"> chisqr1, out1, cov1=engine.fit({model.parameter.name:value},qmin,qmax)</span> |
---|
217 | <span class="sd"> """</span> |
---|
218 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
219 | <span class="sd">"""</span> |
---|
220 | <span class="sd"> Creates a dictionary (self.fit_arrange_dict={})of FitArrange elements</span> |
---|
221 | <span class="sd"> with Uid as keys</span> |
---|
222 | <span class="sd"> """</span> |
---|
223 | <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> |
---|
224 | <span class="bp">self</span><span class="o">.</span><span class="n">curr_thread</span> <span class="o">=</span> <span class="bp">None</span> |
---|
225 | <span class="c">#def fit(self, *args, **kw):</span> |
---|
226 | <span class="c"># return profile(self._fit, *args, **kw)</span> |
---|
227 | |
---|
228 | <div class="viewcode-block" id="ScipyFit.fit"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ScipyFitting.ScipyFit.fit">[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">msg_q</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> |
---|
229 | <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> |
---|
230 | <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> |
---|
231 | <span class="sd">"""</span> |
---|
232 | <span class="sd"> """</span> |
---|
233 | <span class="n">fitproblem</span> <span class="o">=</span> <span class="p">[]</span> |
---|
234 | <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> |
---|
235 | <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> |
---|
236 | <span class="n">fitproblem</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">fproblem</span><span class="p">)</span> |
---|
237 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">fitproblem</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span> <span class="p">:</span> |
---|
238 | <span class="n">msg</span> <span class="o">=</span> <span class="s">"Scipy can't fit more than a single fit problem at a time."</span> |
---|
239 | <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="n">msg</span> |
---|
240 | <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">fitproblem</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="p">:</span> |
---|
241 | <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="s">"No Assembly scheduled for Scipy fitting."</span> |
---|
242 | <span class="n">model</span> <span class="o">=</span> <span class="n">fitproblem</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">get_model</span><span class="p">()</span> |
---|
243 | <span class="n">pars</span> <span class="o">=</span> <span class="n">fitproblem</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">pars</span> |
---|
244 | <span class="k">if</span> <span class="n">reset_flag</span><span class="p">:</span> |
---|
245 | <span class="c"># reset the initial value; useful for batch</span> |
---|
246 | <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">fitproblem</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">pars</span><span class="p">:</span> |
---|
247 | <span class="n">ind</span> <span class="o">=</span> <span class="n">fitproblem</span><span class="p">[</span><span class="mi">0</span><span class="p">]</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> |
---|
248 | <span class="n">model</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">fitproblem</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">vals</span><span class="p">[</span><span class="n">ind</span><span class="p">])</span> |
---|
249 | <span class="n">listdata</span> <span class="o">=</span> <span class="p">[]</span> |
---|
250 | <span class="n">listdata</span> <span class="o">=</span> <span class="n">fitproblem</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">get_data</span><span class="p">()</span> |
---|
251 | <span class="c"># Concatenate dList set (contains one or more data)before fitting</span> |
---|
252 | <span class="n">data</span> <span class="o">=</span> <span class="n">listdata</span> |
---|
253 | |
---|
254 | <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> |
---|
255 | <span class="n">ftol</span> <span class="o">=</span> <span class="n">ftol</span> |
---|
256 | |
---|
257 | <span class="c"># Check the initial value if it is within range</span> |
---|
258 | <span class="n">_check_param_range</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">pars</span><span class="p">)</span> |
---|
259 | |
---|
260 | <span class="n">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">model</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">data</span><span class="p">,</span> <span class="n">param_list</span><span class="o">=</span><span class="n">pars</span><span class="p">)</span> |
---|
261 | <span class="n">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> |
---|
262 | <span class="k">if</span> <span class="n">handler</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
263 | <span class="n">handler</span><span class="o">.</span><span class="n">set_result</span><span class="p">(</span><span class="n">result</span><span class="o">=</span><span class="n">result</span><span class="p">)</span> |
---|
264 | <span class="n">functor</span> <span class="o">=</span> <span class="n">SasAssembly</span><span class="p">(</span><span class="n">paramlist</span><span class="o">=</span><span class="n">pars</span><span class="p">,</span> |
---|
265 | <span class="n">model</span><span class="o">=</span><span class="n">model</span><span class="p">,</span> |
---|
266 | <span class="n">data</span><span class="o">=</span><span class="n">data</span><span class="p">,</span> |
---|
267 | <span class="n">handler</span><span class="o">=</span><span class="n">handler</span><span class="p">,</span> |
---|
268 | <span class="n">fitresult</span><span class="o">=</span><span class="n">result</span><span class="p">,</span> |
---|
269 | <span class="n">curr_thread</span><span class="o">=</span><span class="n">curr_thread</span><span class="p">,</span> |
---|
270 | <span class="n">msg_q</span><span class="o">=</span><span class="n">msg_q</span><span class="p">)</span> |
---|
271 | <span class="k">try</span><span class="p">:</span> |
---|
272 | <span class="c"># This import must be here; otherwise it will be confused when more</span> |
---|
273 | <span class="c"># than one thread exist.</span> |
---|
274 | <span class="kn">from</span> <span class="nn">scipy</span> <span class="kn">import</span> <span class="n">optimize</span> |
---|
275 | |
---|
276 | <span class="n">out</span><span class="p">,</span> <span class="n">cov_x</span><span class="p">,</span> <span class="n">_</span><span class="p">,</span> <span class="n">mesg</span><span class="p">,</span> <span class="n">success</span> <span class="o">=</span> <span class="n">optimize</span><span class="o">.</span><span class="n">leastsq</span><span class="p">(</span><span class="n">functor</span><span class="p">,</span> |
---|
277 | <span class="n">model</span><span class="o">.</span><span class="n">get_params</span><span class="p">(</span><span class="n">pars</span><span class="p">),</span> |
---|
278 | <span class="n">ftol</span><span class="o">=</span><span class="n">ftol</span><span class="p">,</span> |
---|
279 | <span class="n">full_output</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> |
---|
280 | <span class="k">except</span><span class="p">:</span> |
---|
281 | <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">sys</span><span class="p">,</span> <span class="s">'last_type'</span><span class="p">)</span> <span class="ow">and</span> <span class="n">sys</span><span class="o">.</span><span class="n">last_type</span> <span class="o">==</span> <span class="ne">KeyboardInterrupt</span><span class="p">:</span> |
---|
282 | <span class="k">if</span> <span class="n">handler</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
283 | <span class="n">msg</span> <span class="o">=</span> <span class="s">"Fitting: Terminated!!!"</span> |
---|
284 | <span class="n">handler</span><span class="o">.</span><span class="n">stop</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span> |
---|
285 | <span class="k">raise</span> <span class="ne">KeyboardInterrupt</span><span class="p">,</span> <span class="n">msg</span> |
---|
286 | <span class="k">else</span><span class="p">:</span> |
---|
287 | <span class="k">raise</span> |
---|
288 | <span class="n">chisqr</span> <span class="o">=</span> <span class="n">functor</span><span class="o">.</span><span class="n">chisq</span><span class="p">()</span> |
---|
289 | |
---|
290 | <span class="k">if</span> <span class="n">cov_x</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</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">cov_x</span><span class="p">)</span><span class="o">.</span><span class="n">all</span><span class="p">():</span> |
---|
291 | <span class="n">stderr</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="n">cov_x</span><span class="p">))</span> |
---|
292 | <span class="k">else</span><span class="p">:</span> |
---|
293 | <span class="n">stderr</span> <span class="o">=</span> <span class="p">[]</span> |
---|
294 | |
---|
295 | <span class="n">result</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">idx</span> |
---|
296 | <span class="n">result</span><span class="o">.</span><span class="n">fitness</span> <span class="o">=</span> <span class="n">chisqr</span> |
---|
297 | <span class="n">result</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="n">stderr</span> |
---|
298 | <span class="n">result</span><span class="o">.</span><span class="n">pvec</span> <span class="o">=</span> <span class="n">out</span> |
---|
299 | <span class="n">result</span><span class="o">.</span><span class="n">success</span> <span class="o">=</span> <span class="n">success</span> |
---|
300 | <span class="n">result</span><span class="o">.</span><span class="n">theory</span> <span class="o">=</span> <span class="n">functor</span><span class="o">.</span><span class="n">theory</span> |
---|
301 | <span class="k">if</span> <span class="n">handler</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
302 | <span class="n">handler</span><span class="o">.</span><span class="n">set_result</span><span class="p">(</span><span class="n">result</span><span class="o">=</span><span class="n">result</span><span class="p">)</span> |
---|
303 | <span class="n">handler</span><span class="o">.</span><span class="n">update_fit</span><span class="p">(</span><span class="n">last</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span> |
---|
304 | <span class="k">if</span> <span class="n">q</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
305 | <span class="n">q</span><span class="o">.</span><span class="n">put</span><span class="p">(</span><span class="n">result</span><span class="p">)</span> |
---|
306 | <span class="k">return</span> <span class="n">q</span> |
---|
307 | <span class="k">if</span> <span class="n">success</span> <span class="o"><</span> <span class="mi">1</span> <span class="ow">or</span> <span class="n">success</span> <span class="o">></span> <span class="mi">5</span><span class="p">:</span> |
---|
308 | <span class="n">result</span><span class="o">.</span><span class="n">fitness</span> <span class="o">=</span> <span class="bp">None</span> |
---|
309 | <span class="k">return</span> <span class="p">[</span><span class="n">result</span><span class="p">]</span> |
---|
310 | |
---|
311 | </div></div> |
---|
312 | <span class="k">def</span> <span class="nf">_check_param_range</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">pars</span><span class="p">):</span> |
---|
313 | <span class="sd">"""</span> |
---|
314 | <span class="sd"> Check parameter range and set the initial value inside</span> |
---|
315 | <span class="sd"> if it is out of range.</span> |
---|
316 | |
---|
317 | <span class="sd"> : model: park model object</span> |
---|
318 | <span class="sd"> """</span> |
---|
319 | <span class="c"># loop through parameterset</span> |
---|
320 | <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pars</span><span class="p">:</span> |
---|
321 | <span class="n">value</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="n">p</span><span class="p">)</span> |
---|
322 | <span class="n">low</span><span class="p">,</span><span class="n">high</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">details</span><span class="o">.</span><span class="n">setdefault</span><span class="p">(</span><span class="n">p</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><span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">]</span> |
---|
323 | <span class="c"># if the range was defined, check the range</span> |
---|
324 | <span class="k">if</span> <span class="n">low</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">value</span> <span class="o"><=</span> <span class="n">low</span><span class="p">:</span> |
---|
325 | <span class="n">value</span> <span class="o">=</span> <span class="n">low</span> <span class="o">+</span> <span class="n">_get_zero_shift</span><span class="p">(</span><span class="n">low</span><span class="p">)</span> |
---|
326 | <span class="k">if</span> <span class="n">high</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">value</span> <span class="o">></span> <span class="n">high</span><span class="p">:</span> |
---|
327 | <span class="n">value</span> <span class="o">=</span> <span class="n">high</span> <span class="o">-</span> <span class="n">_get_zero_shift</span><span class="p">(</span><span class="n">high</span><span class="p">)</span> |
---|
328 | <span class="c"># Check one more time if the new value goes below</span> |
---|
329 | <span class="c"># the low bound, If so, re-evaluate the value</span> |
---|
330 | <span class="c"># with the mean of the range.</span> |
---|
331 | <span class="k">if</span> <span class="n">low</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">value</span> <span class="o"><</span> <span class="n">low</span><span class="p">:</span> |
---|
332 | <span class="n">value</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">low</span><span class="o">+</span><span class="n">high</span><span class="p">)</span> |
---|
333 | <span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span> |
---|
334 | |
---|
335 | <span class="k">def</span> <span class="nf">_get_zero_shift</span><span class="p">(</span><span class="n">limit</span><span class="p">):</span> |
---|
336 | <span class="sd">"""</span> |
---|
337 | <span class="sd"> Get 10% shift of the param value = 0 based on the range value</span> |
---|
338 | |
---|
339 | <span class="sd"> : param range: min or max value of the bounds</span> |
---|
340 | <span class="sd"> """</span> |
---|
341 | <span class="k">return</span> <span class="mf">0.1</span> <span class="o">*</span> <span class="p">(</span><span class="n">limit</span> <span class="k">if</span> <span class="n">limit</span> <span class="o">!=</span> <span class="mf">0.0</span> <span class="k">else</span> <span class="mf">1.0</span><span class="p">)</span> |
---|
342 | |
---|
343 | |
---|
344 | <span class="c">#def profile(fn, *args, **kw):</span> |
---|
345 | <span class="c"># import cProfile, pstats, os</span> |
---|
346 | <span class="c"># global call_result</span> |
---|
347 | <span class="c"># def call():</span> |
---|
348 | <span class="c"># global call_result</span> |
---|
349 | <span class="c"># call_result = fn(*args, **kw)</span> |
---|
350 | <span class="c"># cProfile.runctx('call()', dict(call=call), {}, 'profile.out')</span> |
---|
351 | <span class="c"># stats = pstats.Stats('profile.out')</span> |
---|
352 | <span class="c"># stats.sort_stats('time')</span> |
---|
353 | <span class="c"># stats.sort_stats('calls')</span> |
---|
354 | <span class="c"># stats.print_stats()</span> |
---|
355 | <span class="c"># os.unlink('profile.out')</span> |
---|
356 | <span class="c"># return call_result</span> |
---|
357 | |
---|
358 | |
---|
359 | </pre></div> |
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360 | |
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361 | </div> |
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362 | </div> |
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364 | <div class="sphinxsidebar"> |
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365 | <div class="sphinxsidebarwrapper"> |
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366 | <div id="searchbox" style="display: none"> |
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367 | <h3>Quick search</h3> |
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374 | <p class="searchtip" style="font-size: 90%"> |
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375 | Enter search terms or a module, class or function name. |
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383 | <div class="related"> |
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384 | <h3>Navigation</h3> |
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385 | <ul> |
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386 | <li class="right" style="margin-right: 10px"> |
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387 | <a href="../../../genindex.html" title="General Index" |
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388 | >index</a></li> |
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389 | <li class="right" > |
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390 | <a href="../../../py-modindex.html" title="Python Module Index" |
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391 | >modules</a> |</li> |
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392 | <li><a href="../../../index.html">SasView 3.0.0 documentation</a> »</li> |
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393 | <li><a href="../../index.html" >Module code</a> »</li> |
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394 | </ul> |
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395 | </div> |
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396 | <div class="footer"> |
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397 | © Copyright 2013, The SasView Project. |
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398 | Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. |
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399 | </div> |
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400 | </body> |
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401 | </html> |
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