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50 | <h1>Source code for park.fitresult</h1><div class="highlight"><pre> |
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51 | <span class="kn">import</span> <span class="nn">sys</span><span class="o">,</span> <span class="nn">math</span><span class="o">,</span> <span class="nn">time</span> |
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52 | <span class="kn">import</span> <span class="nn">numpy</span> |
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53 | |
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54 | <span class="kn">from</span> <span class="nn">formatnum</span> <span class="kn">import</span> <span class="n">format_uncertainty</span> |
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55 | |
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56 | <div class="viewcode-block" id="FitHandler"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitHandler">[docs]</a><span class="k">class</span> <span class="nc">FitHandler</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
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57 | <span class="sd">"""</span> |
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58 | <span class="sd"> Abstract interface for fit thread handler.</span> |
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59 | |
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60 | <span class="sd"> The methods in this class are called by the optimizer as the fit</span> |
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61 | <span class="sd"> progresses.</span> |
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62 | |
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63 | <span class="sd"> Note that it is up to the optimizer to call the fit handler correctly,</span> |
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64 | <span class="sd"> reporting all status changes and maintaining the 'done' flag.</span> |
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65 | <span class="sd"> """</span> |
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66 | <span class="n">done</span> <span class="o">=</span> <span class="bp">False</span> |
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67 | <span class="sd">"""True when the fit job is complete"""</span> |
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68 | <span class="n">result</span> <span class="o">=</span> <span class="bp">None</span> |
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69 | <span class="sd">"""The current best result of the fit"""</span> |
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70 | |
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71 | <div class="viewcode-block" id="FitHandler.improvement"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitHandler.improvement">[docs]</a> <span class="k">def</span> <span class="nf">improvement</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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72 | <span class="sd">"""</span> |
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73 | <span class="sd"> Called when a result is observed which is better than previous</span> |
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74 | <span class="sd"> results from the fit.</span> |
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75 | |
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76 | <span class="sd"> result is a FitResult object, with parameters, #calls and fitness.</span> |
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77 | <span class="sd"> """</span></div> |
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78 | <div class="viewcode-block" id="FitHandler.error"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitHandler.error">[docs]</a> <span class="k">def</span> <span class="nf">error</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">msg</span><span class="p">):</span> |
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79 | <span class="sd">"""</span> |
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80 | <span class="sd"> Model had an error; print traceback</span> |
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81 | <span class="sd"> """</span></div> |
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82 | <div class="viewcode-block" id="FitHandler.progress"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitHandler.progress">[docs]</a> <span class="k">def</span> <span class="nf">progress</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">current</span><span class="p">,</span> <span class="n">expected</span><span class="p">):</span> |
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83 | <span class="sd">"""</span> |
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84 | <span class="sd"> Called each cycle of the fit, reporting the current and the</span> |
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85 | <span class="sd"> expected amount of work. The meaning of these values is</span> |
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86 | <span class="sd"> optimizer dependent, but they can be converted into a percent</span> |
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87 | <span class="sd"> complete using (100*current)//expected.</span> |
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88 | |
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89 | <span class="sd"> Progress is updated each iteration of the fit, whatever that</span> |
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90 | <span class="sd"> means for the particular optimization algorithm. It is called</span> |
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91 | <span class="sd"> after any calls to improvement for the iteration so that the</span> |
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92 | <span class="sd"> update handler can control I/O bandwidth by suppressing</span> |
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93 | <span class="sd"> intermediate improvements until the fit is complete.</span> |
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94 | <span class="sd"> """</span></div> |
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95 | <div class="viewcode-block" id="FitHandler.finalize"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitHandler.finalize">[docs]</a> <span class="k">def</span> <span class="nf">finalize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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96 | <span class="sd">"""</span> |
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97 | <span class="sd"> Fit is complete; best results are reported</span> |
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98 | <span class="sd"> """</span></div> |
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99 | <div class="viewcode-block" id="FitHandler.abort"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitHandler.abort">[docs]</a> <span class="k">def</span> <span class="nf">abort</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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100 | <span class="sd">"""</span> |
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101 | <span class="sd"> Fit was aborted.</span> |
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102 | <span class="sd"> """</span> |
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103 | </div></div> |
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104 | <div class="viewcode-block" id="ConsoleUpdate"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.ConsoleUpdate">[docs]</a><span class="k">class</span> <span class="nc">ConsoleUpdate</span><span class="p">(</span><span class="n">FitHandler</span><span class="p">):</span> |
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105 | <span class="sd">"""</span> |
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106 | <span class="sd"> Print progress to the console.</span> |
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107 | <span class="sd"> """</span> |
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108 | <span class="n">isbetter</span> <span class="o">=</span> <span class="bp">False</span> |
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109 | <span class="sd">"""Record whether results improved since last update"""</span> |
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110 | <span class="n">progress_delta</span> <span class="o">=</span> <span class="mi">60</span> |
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111 | <span class="sd">"""Number of seconds between progress updates"""</span> |
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112 | <span class="n">improvement_delta</span> <span class="o">=</span> <span class="mi">5</span> |
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113 | <span class="sd">"""Number of seconds between improvement updates"""</span> |
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114 | <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">quiet</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span><span class="n">progress_delta</span><span class="o">=</span><span class="mi">60</span><span class="p">,</span><span class="n">improvement_delta</span><span class="o">=</span><span class="mi">5</span><span class="p">):</span> |
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115 | <span class="sd">"""</span> |
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116 | <span class="sd"> If quiet is true, only print out final summary, not progress and</span> |
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117 | <span class="sd"> improvements.</span> |
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118 | <span class="sd"> """</span> |
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119 | <span class="c">#import traceback; traceback.print_stack()</span> |
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120 | <span class="bp">self</span><span class="o">.</span><span class="n">progress_time</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span> |
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121 | <span class="bp">self</span><span class="o">.</span><span class="n">progress_percent</span> <span class="o">=</span> <span class="mi">0</span> |
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122 | <span class="bp">self</span><span class="o">.</span><span class="n">improvement_time</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">progress_time</span> |
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123 | <span class="bp">self</span><span class="o">.</span><span class="n">isbetter</span> <span class="o">=</span> <span class="bp">False</span> |
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124 | <span class="bp">self</span><span class="o">.</span><span class="n">quiet</span> <span class="o">=</span> <span class="n">quiet</span> |
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125 | <span class="bp">self</span><span class="o">.</span><span class="n">progress_delta</span> <span class="o">=</span> <span class="n">progress_delta</span> |
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126 | <span class="bp">self</span><span class="o">.</span><span class="n">improvement_delta</span> <span class="o">=</span> <span class="n">improvement_delta</span> |
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127 | |
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128 | <div class="viewcode-block" id="ConsoleUpdate.progress"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.ConsoleUpdate.progress">[docs]</a> <span class="k">def</span> <span class="nf">progress</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">n</span><span class="p">):</span> |
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129 | <span class="sd">"""</span> |
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130 | <span class="sd"> Report on progress.</span> |
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131 | <span class="sd"> """</span> |
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132 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">quiet</span><span class="p">:</span> <span class="k">return</span> |
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133 | <span class="n">t</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span> |
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134 | <span class="n">p</span> <span class="o">=</span> <span class="nb">int</span><span class="p">((</span><span class="mi">100</span><span class="o">*</span><span class="n">k</span><span class="p">)</span><span class="o">//</span><span class="n">n</span><span class="p">)</span> |
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135 | |
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136 | <span class="c"># Show improvements if there are any</span> |
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137 | <span class="n">dt</span> <span class="o">=</span> <span class="n">t</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">improvement_time</span> |
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138 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">isbetter</span> <span class="ow">and</span> <span class="n">dt</span> <span class="o">></span> <span class="bp">self</span><span class="o">.</span><span class="n">improvement_delta</span><span class="p">:</span> |
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139 | <span class="bp">self</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">print_summary</span><span class="p">()</span> |
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140 | <span class="bp">self</span><span class="o">.</span><span class="n">isbetter</span> <span class="o">=</span> <span class="bp">False</span> |
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141 | <span class="bp">self</span><span class="o">.</span><span class="n">improvement_time</span> <span class="o">=</span> <span class="n">t</span> |
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142 | |
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143 | <span class="c"># Update percent complete</span> |
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144 | <span class="n">dp</span> <span class="o">=</span> <span class="n">p</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">progress_percent</span> |
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145 | <span class="k">if</span> <span class="n">dp</span> <span class="o"><</span> <span class="mi">1</span><span class="p">:</span> <span class="k">return</span> |
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146 | <span class="n">dt</span> <span class="o">=</span> <span class="n">t</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">progress_time</span> |
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147 | <span class="k">if</span> <span class="n">dt</span> <span class="o">></span> <span class="bp">self</span><span class="o">.</span><span class="n">progress_delta</span><span class="p">:</span> |
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148 | <span class="k">if</span> <span class="mi">1</span> <span class="o"><=</span> <span class="n">dp</span> <span class="o"><=</span> <span class="mi">2</span><span class="p">:</span> |
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149 | <span class="k">print</span> <span class="s">"</span><span class="si">%d%%</span><span class="s"> complete"</span><span class="o">%</span><span class="n">p</span> |
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150 | <span class="bp">self</span><span class="o">.</span><span class="n">progress_percent</span> <span class="o">=</span> <span class="n">p</span> |
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151 | <span class="bp">self</span><span class="o">.</span><span class="n">progress_time</span> <span class="o">=</span> <span class="n">t</span> |
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152 | <span class="k">elif</span> <span class="mi">2</span> <span class="o"><</span> <span class="n">dp</span> <span class="o"><=</span> <span class="mi">5</span><span class="p">:</span> |
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153 | <span class="k">if</span> <span class="n">p</span><span class="o">//</span><span class="mi">5</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">progress_percent</span><span class="o">//</span><span class="mi">5</span><span class="p">:</span> |
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154 | <span class="k">print</span> <span class="s">"</span><span class="si">%d%%</span><span class="s"> complete"</span><span class="o">%</span><span class="p">(</span><span class="mi">5</span><span class="o">*</span><span class="p">(</span><span class="n">p</span><span class="o">//</span><span class="mi">5</span><span class="p">))</span> |
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155 | <span class="bp">self</span><span class="o">.</span><span class="n">progress_percent</span> <span class="o">=</span> <span class="n">p</span> |
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156 | <span class="bp">self</span><span class="o">.</span><span class="n">progress_time</span> <span class="o">=</span> <span class="n">t</span> |
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157 | <span class="k">else</span><span class="p">:</span> |
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158 | <span class="k">if</span> <span class="n">p</span><span class="o">//</span><span class="mi">10</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">progress_percent</span><span class="o">//</span><span class="mi">10</span><span class="p">:</span> |
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159 | <span class="k">print</span> <span class="s">"</span><span class="si">%d%%</span><span class="s"> complete"</span><span class="o">%</span><span class="p">(</span><span class="mi">10</span><span class="o">*</span><span class="p">(</span><span class="n">p</span><span class="o">//</span><span class="mi">10</span><span class="p">))</span> |
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160 | <span class="bp">self</span><span class="o">.</span><span class="n">progress_percent</span> <span class="o">=</span> <span class="n">p</span> |
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161 | <span class="bp">self</span><span class="o">.</span><span class="n">progress_time</span> <span class="o">=</span> <span class="n">t</span> |
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162 | </div> |
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163 | <div class="viewcode-block" id="ConsoleUpdate.improvement"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.ConsoleUpdate.improvement">[docs]</a> <span class="k">def</span> <span class="nf">improvement</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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164 | <span class="sd">"""</span> |
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165 | <span class="sd"> Called when a result is observed which is better than previous</span> |
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166 | <span class="sd"> results from the fit.</span> |
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167 | <span class="sd"> """</span> |
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168 | <span class="bp">self</span><span class="o">.</span><span class="n">isbetter</span> <span class="o">=</span> <span class="bp">True</span> |
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169 | </div> |
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170 | <div class="viewcode-block" id="ConsoleUpdate.error"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.ConsoleUpdate.error">[docs]</a> <span class="k">def</span> <span class="nf">error</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">msg</span><span class="p">):</span> |
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171 | <span class="sd">"""</span> |
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172 | <span class="sd"> Model had an error; print traceback</span> |
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173 | <span class="sd"> """</span> |
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174 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">isbetter</span><span class="p">:</span> |
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175 | <span class="bp">self</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">print_summary</span><span class="p">()</span> |
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176 | <span class="k">print</span> <span class="n">msg</span> |
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177 | </div> |
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178 | <div class="viewcode-block" id="ConsoleUpdate.finalize"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.ConsoleUpdate.finalize">[docs]</a> <span class="k">def</span> <span class="nf">finalize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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179 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">isbetter</span><span class="p">:</span> |
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180 | <span class="bp">self</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">print_summary</span><span class="p">()</span> |
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181 | <span class="k">print</span> <span class="s">"Total function calls:"</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">calls</span> |
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182 | </div> |
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183 | <div class="viewcode-block" id="ConsoleUpdate.abort"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.ConsoleUpdate.abort">[docs]</a> <span class="k">def</span> <span class="nf">abort</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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184 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">isbetter</span><span class="p">:</span> |
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185 | <span class="bp">self</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">print_summary</span><span class="p">()</span> |
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186 | |
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187 | </div></div> |
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188 | <div class="viewcode-block" id="FitParameter"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitParameter">[docs]</a><span class="k">class</span> <span class="nc">FitParameter</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
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189 | <span class="sd">"""</span> |
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190 | <span class="sd"> Fit result for an individual parameter.</span> |
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191 | <span class="sd"> """</span> |
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192 | <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> |
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193 | <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span> |
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194 | <span class="bp">self</span><span class="o">.</span><span class="n">range</span> <span class="o">=</span> <span class="nb">range</span> |
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195 | <span class="bp">self</span><span class="o">.</span><span class="n">value</span> <span class="o">=</span> <span class="n">value</span> |
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196 | <span class="bp">self</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="bp">None</span> |
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197 | <div class="viewcode-block" id="FitParameter.summarize"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitParameter.summarize">[docs]</a> <span class="k">def</span> <span class="nf">summarize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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198 | <span class="sd">"""</span> |
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199 | <span class="sd"> Return parameter range string.</span> |
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200 | |
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201 | <span class="sd"> E.g., " Gold .....|.... 5.2043 in [2,7]"</span> |
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202 | <span class="sd"> """</span> |
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203 | <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> |
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204 | <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> |
---|
205 | <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> |
---|
206 | <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> |
---|
207 | <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> |
---|
208 | <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> |
---|
209 | <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> |
---|
210 | <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> |
---|
211 | <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> |
---|
212 | <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> |
---|
213 | <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> |
---|
214 | <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> |
---|
215 | <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="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></div> |
---|
216 | <span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
217 | <span class="k">return</span> <span class="s">"FitParameter('</span><span class="si">%s</span><span class="s">')"</span><span class="o">%</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span> |
---|
218 | </div> |
---|
219 | <div class="viewcode-block" id="FitResult"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitResult">[docs]</a><span class="k">class</span> <span class="nc">FitResult</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
---|
220 | <span class="sd">"""</span> |
---|
221 | <span class="sd"> Container for reporting fit results.</span> |
---|
222 | <span class="sd"> """</span> |
---|
223 | <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">parameters</span><span class="p">,</span> <span class="n">calls</span><span class="p">,</span> <span class="n">fitness</span><span class="p">):</span> |
---|
224 | <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span> <span class="o">=</span> <span class="n">parameters</span> |
---|
225 | <span class="sd">"""Fit parameter list, each with name, range and value attributes."""</span> |
---|
226 | <span class="bp">self</span><span class="o">.</span><span class="n">calls</span> <span class="o">=</span> <span class="n">calls</span> |
---|
227 | <span class="sd">"""Number of function calls"""</span> |
---|
228 | <span class="bp">self</span><span class="o">.</span><span class="n">fitness</span> <span class="o">=</span> <span class="n">fitness</span> |
---|
229 | <span class="sd">"""Value of the goodness of fit metric"""</span> |
---|
230 | <span class="bp">self</span><span class="o">.</span><span class="n">pvec</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">value</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">parameters</span><span class="p">])</span> |
---|
231 | <span class="sd">"""Parameter vector"""</span> |
---|
232 | <span class="bp">self</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="bp">None</span> |
---|
233 | <span class="sd">"""Parameter uncertainties"""</span> |
---|
234 | <span class="bp">self</span><span class="o">.</span><span class="n">cov</span> <span class="o">=</span> <span class="bp">None</span> |
---|
235 | <span class="sd">"""Covariance matrix"""</span> |
---|
236 | |
---|
237 | <div class="viewcode-block" id="FitResult.update"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitResult.update">[docs]</a> <span class="k">def</span> <span class="nf">update</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pvec</span><span class="p">,</span> <span class="n">fitness</span><span class="p">,</span> <span class="n">calls</span><span class="p">):</span> |
---|
238 | <span class="bp">self</span><span class="o">.</span><span class="n">calls</span> <span class="o">=</span> <span class="n">calls</span> |
---|
239 | <span class="bp">self</span><span class="o">.</span><span class="n">fitness</span> <span class="o">=</span> <span class="n">fitness</span> |
---|
240 | <span class="bp">self</span><span class="o">.</span><span class="n">pvec</span> <span class="o">=</span> <span class="n">pvec</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span> |
---|
241 | <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">p</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">):</span> |
---|
242 | <span class="n">p</span><span class="o">.</span><span class="n">value</span> <span class="o">=</span> <span class="n">pvec</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> |
---|
243 | </div> |
---|
244 | <div class="viewcode-block" id="FitResult.calc_cov"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitResult.calc_cov">[docs]</a> <span class="k">def</span> <span class="nf">calc_cov</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fn</span><span class="p">):</span> |
---|
245 | <span class="sd">"""</span> |
---|
246 | <span class="sd"> Return the covariance matrix inv(J'J) at point p.</span> |
---|
247 | <span class="sd"> """</span> |
---|
248 | <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">fn</span><span class="p">,</span> <span class="s">'jacobian'</span><span class="p">):</span> |
---|
249 | <span class="c"># Find cov of f at p</span> |
---|
250 | <span class="c"># cov(f,p) = inv(J'J)</span> |
---|
251 | <span class="c"># Use SVD</span> |
---|
252 | <span class="c"># J = U S V'</span> |
---|
253 | <span class="c"># J'J = (U S V')' (U S V')</span> |
---|
254 | <span class="c"># = V S' U' U S V'</span> |
---|
255 | <span class="c"># = V S S V'</span> |
---|
256 | <span class="c"># inv(J'J) = inv(V S S V')</span> |
---|
257 | <span class="c"># = inv(V') inv(S S) inv(V)</span> |
---|
258 | <span class="c"># = V inv (S S) V'</span> |
---|
259 | <span class="n">J</span> <span class="o">=</span> <span class="n">fn</span><span class="o">.</span><span class="n">jacobian</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pvec</span><span class="p">)</span> |
---|
260 | <span class="n">u</span><span class="p">,</span><span class="n">s</span><span class="p">,</span><span class="n">vh</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">svd</span><span class="p">(</span><span class="n">J</span><span class="p">,</span><span class="mi">0</span><span class="p">)</span> |
---|
261 | <span class="n">JTJinv</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">vh</span><span class="o">.</span><span class="n">T</span><span class="o">.</span><span class="n">conj</span><span class="p">()</span><span class="o">/</span><span class="n">s</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="n">vh</span><span class="p">)</span> |
---|
262 | <span class="bp">self</span><span class="o">.</span><span class="n">set_cov</span><span class="p">(</span><span class="n">JTJinv</span><span class="p">)</span> |
---|
263 | </div> |
---|
264 | <div class="viewcode-block" id="FitResult.set_cov"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitResult.set_cov">[docs]</a> <span class="k">def</span> <span class="nf">set_cov</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cov</span><span class="p">):</span> |
---|
265 | <span class="sd">"""</span> |
---|
266 | <span class="sd"> Return the covariance matrix inv(J'J) at point p.</span> |
---|
267 | <span class="sd"> """</span> |
---|
268 | <span class="bp">self</span><span class="o">.</span><span class="n">cov</span> <span class="o">=</span> <span class="n">cov</span> |
---|
269 | <span class="k">if</span> <span class="n">cov</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> |
---|
270 | <span class="bp">self</span><span class="o">.</span><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="bp">self</span><span class="o">.</span><span class="n">cov</span><span class="p">))</span> |
---|
271 | <span class="c"># Set the uncertainties on the individual parameters</span> |
---|
272 | <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">p</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">):</span> |
---|
273 | <span class="n">p</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">stderr</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> |
---|
274 | <span class="k">else</span><span class="p">:</span> |
---|
275 | <span class="bp">self</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="bp">None</span> |
---|
276 | <span class="c"># Reset the uncertainties on the individual parameters</span> |
---|
277 | <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">p</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">):</span> |
---|
278 | <span class="n">p</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="bp">None</span> |
---|
279 | </div> |
---|
280 | <span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
281 | <span class="c">#import traceback; traceback.print_stack()</span> |
---|
282 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> <span class="k">return</span> <span class="s">"No results"</span> |
---|
283 | <span class="n">L</span> <span class="o">=</span> <span class="p">[</span><span class="s">"P</span><span class="si">%-3d</span><span class="s"> </span><span class="si">%s</span><span class="s">"</span><span class="o">%</span><span class="p">(</span><span class="n">n</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="n">p</span><span class="o">.</span><span class="n">summarize</span><span class="p">())</span> <span class="k">for</span> <span class="n">n</span><span class="p">,</span><span class="n">p</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">)]</span> |
---|
284 | <span class="n">L</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">"=== goodness of fit: </span><span class="si">%g</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">fitness</span><span class="p">))</span> |
---|
285 | <span class="k">return</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">L</span><span class="p">)</span> |
---|
286 | |
---|
287 | <div class="viewcode-block" id="FitResult.print_summary"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitResult.print_summary">[docs]</a> <span class="k">def</span> <span class="nf">print_summary</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fid</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">):</span> |
---|
288 | <span class="k">print</span> <span class="o">>></span><span class="n">fid</span><span class="p">,</span> <span class="bp">self</span> |
---|
289 | </pre></div></div></div> |
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290 | |
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