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| 59 | |
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| 60 | <div class="section" id="sas-fit-package"> |
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| 61 | <h1>sas.fit package</h1> |
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| 62 | <div class="section" id="submodules"> |
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| 63 | <h2>Submodules</h2> |
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| 64 | </div> |
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| 65 | <div class="section" id="module-sas.fit.AbstractFitEngine"> |
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| 66 | <span id="sas-fit-abstractfitengine-module"></span><h2>sas.fit.AbstractFitEngine module</h2> |
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| 67 | <dl class="class"> |
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| 68 | <dt id="sas.fit.AbstractFitEngine.FResult"> |
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| 69 | <em class="property">class </em><tt class="descclassname">sas.fit.AbstractFitEngine.</tt><tt class="descname">FResult</tt><big>(</big><em>model=None</em>, <em>param_list=None</em>, <em>data=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FResult"><span class="viewcode-link">[source]</span></a></dt> |
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| 70 | <dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">object</span></tt></p> |
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| 71 | <p>Storing fit result</p> |
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| 72 | <dl class="method"> |
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| 73 | <dt id="sas.fit.AbstractFitEngine.FResult.print_summary"> |
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| 74 | <tt class="descname">print_summary</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FResult.print_summary"><span class="viewcode-link">[source]</span></a></dt> |
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| 75 | <dd></dd></dl> |
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| 76 | |
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| 77 | <dl class="method"> |
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| 78 | <dt id="sas.fit.AbstractFitEngine.FResult.set_fitness"> |
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| 79 | <tt class="descname">set_fitness</tt><big>(</big><em>fitness</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FResult.set_fitness"><span class="viewcode-link">[source]</span></a></dt> |
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| 80 | <dd></dd></dl> |
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| 81 | |
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| 82 | <dl class="method"> |
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| 83 | <dt id="sas.fit.AbstractFitEngine.FResult.set_model"> |
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| 84 | <tt class="descname">set_model</tt><big>(</big><em>model</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FResult.set_model"><span class="viewcode-link">[source]</span></a></dt> |
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| 85 | <dd></dd></dl> |
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| 86 | |
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| 87 | </dd></dl> |
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| 88 | |
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| 89 | <dl class="exception"> |
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| 90 | <dt id="sas.fit.AbstractFitEngine.FitAbort"> |
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| 91 | <em class="property">exception </em><tt class="descclassname">sas.fit.AbstractFitEngine.</tt><tt class="descname">FitAbort</tt><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitAbort"><span class="viewcode-link">[source]</span></a></dt> |
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| 92 | <dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">exceptions.Exception</span></tt></p> |
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| 93 | <p>Exception raise to stop the fit</p> |
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| 94 | </dd></dl> |
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| 95 | |
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| 96 | <dl class="class"> |
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| 97 | <dt id="sas.fit.AbstractFitEngine.FitArrange"> |
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| 98 | <em class="property">class </em><tt class="descclassname">sas.fit.AbstractFitEngine.</tt><tt class="descname">FitArrange</tt><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitArrange"><span class="viewcode-link">[source]</span></a></dt> |
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| 99 | <dd><dl class="method"> |
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| 100 | <dt id="sas.fit.AbstractFitEngine.FitArrange.add_data"> |
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| 101 | <tt class="descname">add_data</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitArrange.add_data"><span class="viewcode-link">[source]</span></a></dt> |
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| 102 | <dd><p>add_data fill a self.data_list with data to fit</p> |
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| 103 | <table class="docutils field-list" frame="void" rules="none"> |
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| 104 | <col class="field-name" /> |
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| 105 | <col class="field-body" /> |
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| 106 | <tbody valign="top"> |
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| 107 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data</strong> – Data to add in the list</td> |
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| 108 | </tr> |
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| 109 | </tbody> |
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| 110 | </table> |
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| 111 | </dd></dl> |
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| 112 | |
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| 113 | <dl class="method"> |
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| 114 | <dt id="sas.fit.AbstractFitEngine.FitArrange.get_data"> |
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| 115 | <tt class="descname">get_data</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitArrange.get_data"><span class="viewcode-link">[source]</span></a></dt> |
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| 116 | <dd><table class="docutils field-list" frame="void" rules="none"> |
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| 117 | <col class="field-name" /> |
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| 118 | <col class="field-body" /> |
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| 119 | <tbody valign="top"> |
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| 120 | <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">list of data data_list</td> |
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| 121 | </tr> |
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| 122 | </tbody> |
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| 123 | </table> |
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| 124 | </dd></dl> |
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| 125 | |
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| 126 | <dl class="method"> |
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| 127 | <dt id="sas.fit.AbstractFitEngine.FitArrange.get_model"> |
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| 128 | <tt class="descname">get_model</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitArrange.get_model"><span class="viewcode-link">[source]</span></a></dt> |
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| 129 | <dd><table class="docutils field-list" frame="void" rules="none"> |
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| 130 | <col class="field-name" /> |
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| 131 | <col class="field-body" /> |
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| 132 | <tbody valign="top"> |
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| 133 | <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">saved model</td> |
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| 134 | </tr> |
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| 135 | </tbody> |
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| 136 | </table> |
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| 137 | </dd></dl> |
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| 138 | |
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| 139 | <dl class="method"> |
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| 140 | <dt id="sas.fit.AbstractFitEngine.FitArrange.get_to_fit"> |
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| 141 | <tt class="descname">get_to_fit</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitArrange.get_to_fit"><span class="viewcode-link">[source]</span></a></dt> |
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| 142 | <dd><p>return self.selected value</p> |
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| 143 | </dd></dl> |
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| 144 | |
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| 145 | <dl class="method"> |
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| 146 | <dt id="sas.fit.AbstractFitEngine.FitArrange.remove_data"> |
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| 147 | <tt class="descname">remove_data</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitArrange.remove_data"><span class="viewcode-link">[source]</span></a></dt> |
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| 148 | <dd><p>Remove one element from the list</p> |
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| 149 | <table class="docutils field-list" frame="void" rules="none"> |
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| 150 | <col class="field-name" /> |
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| 151 | <col class="field-body" /> |
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| 152 | <tbody valign="top"> |
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| 153 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data</strong> – Data to remove from data_list</td> |
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| 154 | </tr> |
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| 155 | </tbody> |
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| 156 | </table> |
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| 157 | </dd></dl> |
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| 158 | |
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| 159 | <dl class="method"> |
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| 160 | <dt id="sas.fit.AbstractFitEngine.FitArrange.set_model"> |
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| 161 | <tt class="descname">set_model</tt><big>(</big><em>model</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitArrange.set_model"><span class="viewcode-link">[source]</span></a></dt> |
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| 162 | <dd><p>set_model save a copy of the model</p> |
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| 163 | <table class="docutils field-list" frame="void" rules="none"> |
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| 164 | <col class="field-name" /> |
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| 165 | <col class="field-body" /> |
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| 166 | <tbody valign="top"> |
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| 167 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>model</strong> – the model being set</td> |
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| 168 | </tr> |
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| 169 | </tbody> |
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| 170 | </table> |
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| 171 | </dd></dl> |
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| 172 | |
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| 173 | <dl class="method"> |
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| 174 | <dt id="sas.fit.AbstractFitEngine.FitArrange.set_to_fit"> |
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| 175 | <tt class="descname">set_to_fit</tt><big>(</big><em>value=0</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitArrange.set_to_fit"><span class="viewcode-link">[source]</span></a></dt> |
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| 176 | <dd><p>set self.selected to 0 or 1 for other values raise an exception</p> |
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| 177 | <table class="docutils field-list" frame="void" rules="none"> |
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| 178 | <col class="field-name" /> |
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| 179 | <col class="field-body" /> |
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| 180 | <tbody valign="top"> |
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| 181 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>value</strong> – integer between 0 or 1</td> |
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| 182 | </tr> |
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| 183 | </tbody> |
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| 184 | </table> |
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| 185 | </dd></dl> |
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| 186 | |
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| 187 | </dd></dl> |
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| 188 | |
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| 189 | <dl class="class"> |
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| 190 | <dt id="sas.fit.AbstractFitEngine.FitData1D"> |
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| 191 | <em class="property">class </em><tt class="descclassname">sas.fit.AbstractFitEngine.</tt><tt class="descname">FitData1D</tt><big>(</big><em>x</em>, <em>y</em>, <em>dx=None</em>, <em>dy=None</em>, <em>smearer=None</em>, <em>data=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitData1D"><span class="viewcode-link">[source]</span></a></dt> |
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| 192 | <dd><p>Bases: <a class="reference internal" href="sas.dataloader.html#sas.dataloader.data_info.Data1D" title="sas.dataloader.data_info.Data1D"><tt class="xref py py-class docutils literal"><span class="pre">sas.dataloader.data_info.Data1D</span></tt></a></p> |
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| 193 | <p>Wrapper class for SAS data |
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| 194 | FitData1D inherits from DataLoader.data_info.Data1D. Implements |
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| 195 | a way to get residuals from data.</p> |
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| 196 | <dl class="method"> |
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| 197 | <dt id="sas.fit.AbstractFitEngine.FitData1D.get_fit_range"> |
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| 198 | <tt class="descname">get_fit_range</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitData1D.get_fit_range"><span class="viewcode-link">[source]</span></a></dt> |
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| 199 | <dd><p>Return the range of data.x to fit</p> |
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| 200 | </dd></dl> |
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| 201 | |
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| 202 | <dl class="method"> |
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| 203 | <dt id="sas.fit.AbstractFitEngine.FitData1D.residuals"> |
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| 204 | <tt class="descname">residuals</tt><big>(</big><em>fn</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitData1D.residuals"><span class="viewcode-link">[source]</span></a></dt> |
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| 205 | <dd><p>Compute residuals.</p> |
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| 206 | <p>If self.smearer has been set, use if to smear |
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| 207 | the data before computing chi squared.</p> |
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| 208 | <table class="docutils field-list" frame="void" rules="none"> |
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| 209 | <col class="field-name" /> |
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| 210 | <col class="field-body" /> |
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| 211 | <tbody valign="top"> |
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| 212 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fn</strong> – function that return model value</td> |
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| 213 | </tr> |
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| 214 | <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">residuals</td> |
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| 215 | </tr> |
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| 216 | </tbody> |
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| 217 | </table> |
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| 218 | </dd></dl> |
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| 219 | |
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| 220 | <dl class="method"> |
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| 221 | <dt id="sas.fit.AbstractFitEngine.FitData1D.residuals_deriv"> |
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| 222 | <tt class="descname">residuals_deriv</tt><big>(</big><em>model</em>, <em>pars=[]</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitData1D.residuals_deriv"><span class="viewcode-link">[source]</span></a></dt> |
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| 223 | <dd><table class="docutils field-list" frame="void" rules="none"> |
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| 224 | <col class="field-name" /> |
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| 225 | <col class="field-body" /> |
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| 226 | <tbody valign="top"> |
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| 227 | <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">residuals derivatives .</td> |
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| 228 | </tr> |
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| 229 | <tr class="field-even field"><th class="field-name">Note:</th><td class="field-body">in this case just return empty array</td> |
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| 230 | </tr> |
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| 231 | </tbody> |
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| 232 | </table> |
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| 233 | </dd></dl> |
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| 234 | |
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| 235 | <dl class="method"> |
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| 236 | <dt id="sas.fit.AbstractFitEngine.FitData1D.set_fit_range"> |
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| 237 | <tt class="descname">set_fit_range</tt><big>(</big><em>qmin=None</em>, <em>qmax=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitData1D.set_fit_range"><span class="viewcode-link">[source]</span></a></dt> |
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| 238 | <dd><p>to set the fit range</p> |
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| 239 | </dd></dl> |
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| 240 | |
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| 241 | <dl class="method"> |
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| 242 | <dt id="sas.fit.AbstractFitEngine.FitData1D.size"> |
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| 243 | <tt class="descname">size</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitData1D.size"><span class="viewcode-link">[source]</span></a></dt> |
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| 244 | <dd><p>Number of measurement points in data set after masking, etc.</p> |
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| 245 | </dd></dl> |
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| 246 | |
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| 247 | </dd></dl> |
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| 248 | |
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| 249 | <dl class="class"> |
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| 250 | <dt id="sas.fit.AbstractFitEngine.FitData2D"> |
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| 251 | <em class="property">class </em><tt class="descclassname">sas.fit.AbstractFitEngine.</tt><tt class="descname">FitData2D</tt><big>(</big><em>sas_data2d</em>, <em>data=None</em>, <em>err_data=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitData2D"><span class="viewcode-link">[source]</span></a></dt> |
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| 252 | <dd><p>Bases: <a class="reference internal" href="sas.dataloader.html#sas.dataloader.data_info.Data2D" title="sas.dataloader.data_info.Data2D"><tt class="xref py py-class docutils literal"><span class="pre">sas.dataloader.data_info.Data2D</span></tt></a></p> |
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| 253 | <p>Wrapper class for SAS data</p> |
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| 254 | <dl class="method"> |
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| 255 | <dt id="sas.fit.AbstractFitEngine.FitData2D.get_fit_range"> |
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| 256 | <tt class="descname">get_fit_range</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitData2D.get_fit_range"><span class="viewcode-link">[source]</span></a></dt> |
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| 257 | <dd><p>return the range of data.x to fit</p> |
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| 258 | </dd></dl> |
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| 259 | |
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| 260 | <dl class="method"> |
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| 261 | <dt id="sas.fit.AbstractFitEngine.FitData2D.residuals"> |
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| 262 | <tt class="descname">residuals</tt><big>(</big><em>fn</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitData2D.residuals"><span class="viewcode-link">[source]</span></a></dt> |
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| 263 | <dd><p>return the residuals</p> |
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| 264 | </dd></dl> |
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| 265 | |
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| 266 | <dl class="method"> |
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| 267 | <dt id="sas.fit.AbstractFitEngine.FitData2D.residuals_deriv"> |
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| 268 | <tt class="descname">residuals_deriv</tt><big>(</big><em>model</em>, <em>pars=[]</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitData2D.residuals_deriv"><span class="viewcode-link">[source]</span></a></dt> |
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| 269 | <dd><table class="docutils field-list" frame="void" rules="none"> |
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| 270 | <col class="field-name" /> |
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| 271 | <col class="field-body" /> |
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| 272 | <tbody valign="top"> |
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| 273 | <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">residuals derivatives .</td> |
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| 274 | </tr> |
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| 275 | <tr class="field-even field"><th class="field-name">Note:</th><td class="field-body">in this case just return empty array</td> |
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| 276 | </tr> |
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| 277 | </tbody> |
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| 278 | </table> |
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| 279 | </dd></dl> |
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| 280 | |
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| 281 | <dl class="method"> |
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| 282 | <dt id="sas.fit.AbstractFitEngine.FitData2D.set_data"> |
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| 283 | <tt class="descname">set_data</tt><big>(</big><em>sas_data2d</em>, <em>qmin=None</em>, <em>qmax=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitData2D.set_data"><span class="viewcode-link">[source]</span></a></dt> |
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| 284 | <dd><p>Determine the correct qx_data and qy_data within range to fit</p> |
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| 285 | </dd></dl> |
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| 286 | |
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| 287 | <dl class="method"> |
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| 288 | <dt id="sas.fit.AbstractFitEngine.FitData2D.set_fit_range"> |
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| 289 | <tt class="descname">set_fit_range</tt><big>(</big><em>qmin=None</em>, <em>qmax=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitData2D.set_fit_range"><span class="viewcode-link">[source]</span></a></dt> |
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| 290 | <dd><p>To set the fit range</p> |
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| 291 | </dd></dl> |
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| 292 | |
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| 293 | <dl class="method"> |
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| 294 | <dt id="sas.fit.AbstractFitEngine.FitData2D.set_smearer"> |
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| 295 | <tt class="descname">set_smearer</tt><big>(</big><em>smearer</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitData2D.set_smearer"><span class="viewcode-link">[source]</span></a></dt> |
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| 296 | <dd><p>Set smearer</p> |
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| 297 | </dd></dl> |
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| 298 | |
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| 299 | <dl class="method"> |
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| 300 | <dt id="sas.fit.AbstractFitEngine.FitData2D.size"> |
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| 301 | <tt class="descname">size</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitData2D.size"><span class="viewcode-link">[source]</span></a></dt> |
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| 302 | <dd><p>Number of measurement points in data set after masking, etc.</p> |
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| 303 | </dd></dl> |
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| 304 | |
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| 305 | </dd></dl> |
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| 306 | |
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| 307 | <dl class="class"> |
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| 308 | <dt id="sas.fit.AbstractFitEngine.FitEngine"> |
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| 309 | <em class="property">class </em><tt class="descclassname">sas.fit.AbstractFitEngine.</tt><tt class="descname">FitEngine</tt><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitEngine"><span class="viewcode-link">[source]</span></a></dt> |
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| 310 | <dd><dl class="method"> |
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| 311 | <dt id="sas.fit.AbstractFitEngine.FitEngine.get_model"> |
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| 312 | <tt class="descname">get_model</tt><big>(</big><em>id</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitEngine.get_model"><span class="viewcode-link">[source]</span></a></dt> |
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| 313 | <dd><table class="docutils field-list" frame="void" rules="none"> |
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| 314 | <col class="field-name" /> |
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| 315 | <col class="field-body" /> |
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| 316 | <tbody valign="top"> |
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| 317 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>id</strong> – id is key in the dictionary containing the model to return</td> |
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| 318 | </tr> |
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| 319 | <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">a model at this id or None if no FitArrange element was |
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| 320 | created with this id</td> |
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| 321 | </tr> |
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| 322 | </tbody> |
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| 323 | </table> |
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| 324 | </dd></dl> |
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| 325 | |
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| 326 | <dl class="method"> |
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| 327 | <dt id="sas.fit.AbstractFitEngine.FitEngine.get_problem_to_fit"> |
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| 328 | <tt class="descname">get_problem_to_fit</tt><big>(</big><em>id</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitEngine.get_problem_to_fit"><span class="viewcode-link">[source]</span></a></dt> |
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| 329 | <dd><p>return the self.selected value of the fit problem of id</p> |
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| 330 | <table class="docutils field-list" frame="void" rules="none"> |
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| 331 | <col class="field-name" /> |
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| 332 | <col class="field-body" /> |
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| 333 | <tbody valign="top"> |
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| 334 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>id</strong> – the id of the problem</td> |
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| 335 | </tr> |
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| 336 | </tbody> |
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| 337 | </table> |
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| 338 | </dd></dl> |
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| 339 | |
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| 340 | <dl class="method"> |
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| 341 | <dt id="sas.fit.AbstractFitEngine.FitEngine.remove_fit_problem"> |
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| 342 | <tt class="descname">remove_fit_problem</tt><big>(</big><em>id</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitEngine.remove_fit_problem"><span class="viewcode-link">[source]</span></a></dt> |
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| 343 | <dd><p>remove fitarrange in id</p> |
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| 344 | </dd></dl> |
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| 345 | |
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| 346 | <dl class="method"> |
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| 347 | <dt id="sas.fit.AbstractFitEngine.FitEngine.select_problem_for_fit"> |
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| 348 | <tt class="descname">select_problem_for_fit</tt><big>(</big><em>id</em>, <em>value</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitEngine.select_problem_for_fit"><span class="viewcode-link">[source]</span></a></dt> |
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| 349 | <dd><p>select a couple of model and data at the id position in dictionary |
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| 350 | and set in self.selected value to value</p> |
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| 351 | <table class="docutils field-list" frame="void" rules="none"> |
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| 352 | <col class="field-name" /> |
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| 353 | <col class="field-body" /> |
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| 354 | <tbody valign="top"> |
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| 355 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>value</strong> – the value to allow fitting. |
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| 356 | can only have the value one or zero</td> |
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| 357 | </tr> |
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| 358 | </tbody> |
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| 359 | </table> |
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| 360 | </dd></dl> |
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| 361 | |
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| 362 | <dl class="method"> |
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| 363 | <dt id="sas.fit.AbstractFitEngine.FitEngine.set_data"> |
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| 364 | <tt class="descname">set_data</tt><big>(</big><em>data</em>, <em>id</em>, <em>smearer=None</em>, <em>qmin=None</em>, <em>qmax=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitEngine.set_data"><span class="viewcode-link">[source]</span></a></dt> |
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| 365 | <dd><p>Receives plottable, creates a list of data to fit,set data |
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| 366 | in a FitArrange object and adds that object in a dictionary |
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| 367 | with key id.</p> |
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| 368 | <table class="docutils field-list" frame="void" rules="none"> |
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| 369 | <col class="field-name" /> |
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| 370 | <col class="field-body" /> |
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| 371 | <tbody valign="top"> |
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| 372 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> |
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| 373 | <li><strong>data</strong> – data added</li> |
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| 374 | <li><strong>id</strong> – unique key corresponding to a fitArrange object with data</li> |
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| 375 | </ul> |
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| 376 | </td> |
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| 377 | </tr> |
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| 378 | </tbody> |
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| 379 | </table> |
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| 380 | </dd></dl> |
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| 381 | |
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| 382 | <dl class="method"> |
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| 383 | <dt id="sas.fit.AbstractFitEngine.FitEngine.set_model"> |
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| 384 | <tt class="descname">set_model</tt><big>(</big><em>model</em>, <em>id</em>, <em>pars=[]</em>, <em>constraints=[]</em>, <em>data=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitEngine.set_model"><span class="viewcode-link">[source]</span></a></dt> |
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| 385 | <dd><p>set a model on a given in the fit engine.</p> |
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| 386 | <table class="docutils field-list" frame="void" rules="none"> |
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| 387 | <col class="field-name" /> |
---|
| 388 | <col class="field-body" /> |
---|
| 389 | <tbody valign="top"> |
---|
| 390 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> |
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| 391 | <li><strong>model</strong> – sas.models type</li> |
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| 392 | <li><strong>id</strong> – is the key of the fitArrange dictionary where model is saved as a value</li> |
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| 393 | <li><strong>pars</strong> – the list of parameters to fit</li> |
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| 394 | <li><strong>constraints</strong> – list of |
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| 395 | tuple (name of parameter, value of parameters) |
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| 396 | the value of parameter must be a string to constraint 2 different |
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| 397 | parameters. |
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| 398 | Example: |
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| 399 | we want to fit 2 model M1 and M2 both have parameters A and B. |
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| 400 | constraints can be <tt class="docutils literal"><span class="pre">constraints</span> <span class="pre">=</span> <span class="pre">[(M1.A,</span> <span class="pre">M2.B+2),</span> <span class="pre">(M1.B=</span> <span class="pre">M2.A</span> <span class="pre">*5),...,]</span></tt></li> |
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| 401 | </ul> |
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| 402 | </td> |
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| 403 | </tr> |
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| 404 | <tr class="field-even field"><th class="field-name">Note:</th><td class="field-body"><p class="first last">pars must contains only name of existing model’s parameters</p> |
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| 405 | </td> |
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| 406 | </tr> |
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| 407 | </tbody> |
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| 408 | </table> |
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| 409 | </dd></dl> |
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| 410 | |
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| 411 | </dd></dl> |
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| 412 | |
---|
| 413 | <dl class="class"> |
---|
| 414 | <dt id="sas.fit.AbstractFitEngine.FitHandler"> |
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| 415 | <em class="property">class </em><tt class="descclassname">sas.fit.AbstractFitEngine.</tt><tt class="descname">FitHandler</tt><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitHandler"><span class="viewcode-link">[source]</span></a></dt> |
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| 416 | <dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">object</span></tt></p> |
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| 417 | <p>Abstract interface for fit thread handler.</p> |
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| 418 | <p>The methods in this class are called by the optimizer as the fit |
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| 419 | progresses.</p> |
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| 420 | <p>Note that it is up to the optimizer to call the fit handler correctly, |
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| 421 | reporting all status changes and maintaining the ‘done’ flag.</p> |
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| 422 | <dl class="method"> |
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| 423 | <dt id="sas.fit.AbstractFitEngine.FitHandler.abort"> |
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| 424 | <tt class="descname">abort</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitHandler.abort"><span class="viewcode-link">[source]</span></a></dt> |
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| 425 | <dd><p>Fit was aborted.</p> |
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| 426 | </dd></dl> |
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| 427 | |
---|
| 428 | <dl class="attribute"> |
---|
| 429 | <dt id="sas.fit.AbstractFitEngine.FitHandler.done"> |
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| 430 | <tt class="descname">done</tt><em class="property"> = False</em></dt> |
---|
| 431 | <dd><p>True when the fit job is complete</p> |
---|
| 432 | </dd></dl> |
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| 433 | |
---|
| 434 | <dl class="method"> |
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| 435 | <dt id="sas.fit.AbstractFitEngine.FitHandler.error"> |
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| 436 | <tt class="descname">error</tt><big>(</big><em>msg</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitHandler.error"><span class="viewcode-link">[source]</span></a></dt> |
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| 437 | <dd><p>Model had an error; print traceback</p> |
---|
| 438 | </dd></dl> |
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| 439 | |
---|
| 440 | <dl class="method"> |
---|
| 441 | <dt id="sas.fit.AbstractFitEngine.FitHandler.finalize"> |
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| 442 | <tt class="descname">finalize</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitHandler.finalize"><span class="viewcode-link">[source]</span></a></dt> |
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| 443 | <dd><p>Fit is complete; best results are reported</p> |
---|
| 444 | </dd></dl> |
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| 445 | |
---|
| 446 | <dl class="method"> |
---|
| 447 | <dt id="sas.fit.AbstractFitEngine.FitHandler.improvement"> |
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| 448 | <tt class="descname">improvement</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitHandler.improvement"><span class="viewcode-link">[source]</span></a></dt> |
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| 449 | <dd><p>Called when a result is observed which is better than previous |
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| 450 | results from the fit.</p> |
---|
| 451 | <p>result is a FitResult object, with parameters, #calls and fitness.</p> |
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| 452 | </dd></dl> |
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| 453 | |
---|
| 454 | <dl class="method"> |
---|
| 455 | <dt id="sas.fit.AbstractFitEngine.FitHandler.progress"> |
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| 456 | <tt class="descname">progress</tt><big>(</big><em>current</em>, <em>expected</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitHandler.progress"><span class="viewcode-link">[source]</span></a></dt> |
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| 457 | <dd><p>Called each cycle of the fit, reporting the current and the |
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| 458 | expected amount of work. The meaning of these values is |
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| 459 | optimizer dependent, but they can be converted into a percent |
---|
| 460 | complete using (100*current)//expected.</p> |
---|
| 461 | <p>Progress is updated each iteration of the fit, whatever that |
---|
| 462 | means for the particular optimization algorithm. It is called |
---|
| 463 | after any calls to improvement for the iteration so that the |
---|
| 464 | update handler can control I/O bandwidth by suppressing |
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| 465 | intermediate improvements until the fit is complete.</p> |
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| 466 | </dd></dl> |
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| 467 | |
---|
| 468 | <dl class="attribute"> |
---|
| 469 | <dt id="sas.fit.AbstractFitEngine.FitHandler.result"> |
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| 470 | <tt class="descname">result</tt><em class="property"> = None</em></dt> |
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| 471 | <dd><p>The current best result of the fit</p> |
---|
| 472 | </dd></dl> |
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| 473 | |
---|
| 474 | <dl class="method"> |
---|
| 475 | <dt id="sas.fit.AbstractFitEngine.FitHandler.set_result"> |
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| 476 | <tt class="descname">set_result</tt><big>(</big><em>result=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitHandler.set_result"><span class="viewcode-link">[source]</span></a></dt> |
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| 477 | <dd></dd></dl> |
---|
| 478 | |
---|
| 479 | <dl class="method"> |
---|
| 480 | <dt id="sas.fit.AbstractFitEngine.FitHandler.update_fit"> |
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| 481 | <tt class="descname">update_fit</tt><big>(</big><em>last=False</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#FitHandler.update_fit"><span class="viewcode-link">[source]</span></a></dt> |
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| 482 | <dd></dd></dl> |
---|
| 483 | |
---|
| 484 | </dd></dl> |
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| 485 | |
---|
| 486 | <dl class="class"> |
---|
| 487 | <dt id="sas.fit.AbstractFitEngine.Model"> |
---|
| 488 | <em class="property">class </em><tt class="descclassname">sas.fit.AbstractFitEngine.</tt><tt class="descname">Model</tt><big>(</big><em>sas_model</em>, <em>sas_data=None</em>, <em>**kw</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#Model"><span class="viewcode-link">[source]</span></a></dt> |
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| 489 | <dd><p>Fit wrapper for SAS models.</p> |
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| 490 | <dl class="method"> |
---|
| 491 | <dt id="sas.fit.AbstractFitEngine.Model.eval"> |
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| 492 | <tt class="descname">eval</tt><big>(</big><em>x</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#Model.eval"><span class="viewcode-link">[source]</span></a></dt> |
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| 493 | <dd><p>Override eval method of park model.</p> |
---|
| 494 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 495 | <col class="field-name" /> |
---|
| 496 | <col class="field-body" /> |
---|
| 497 | <tbody valign="top"> |
---|
| 498 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>x</strong> – the x value used to compute a function</td> |
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| 499 | </tr> |
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| 500 | </tbody> |
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| 501 | </table> |
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| 502 | </dd></dl> |
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| 503 | |
---|
| 504 | <dl class="method"> |
---|
| 505 | <dt id="sas.fit.AbstractFitEngine.Model.eval_derivs"> |
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| 506 | <tt class="descname">eval_derivs</tt><big>(</big><em>x</em>, <em>pars=[]</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#Model.eval_derivs"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 507 | <dd><p>Evaluate the model and derivatives wrt pars at x.</p> |
---|
| 508 | <p>pars is a list of the names of the parameters for which derivatives |
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| 509 | are desired.</p> |
---|
| 510 | <p>This method needs to be specialized in the model to evaluate the |
---|
| 511 | model function. Alternatively, the model can implement is own |
---|
| 512 | version of residuals which calculates the residuals directly |
---|
| 513 | instead of calling eval.</p> |
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| 514 | </dd></dl> |
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| 515 | |
---|
| 516 | <dl class="method"> |
---|
| 517 | <dt id="sas.fit.AbstractFitEngine.Model.get_params"> |
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| 518 | <tt class="descname">get_params</tt><big>(</big><em>fitparams</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#Model.get_params"><span class="viewcode-link">[source]</span></a></dt> |
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| 519 | <dd><p>return a list of value of paramter to fit</p> |
---|
| 520 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 521 | <col class="field-name" /> |
---|
| 522 | <col class="field-body" /> |
---|
| 523 | <tbody valign="top"> |
---|
| 524 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fitparams</strong> – list of paramaters name to fit</td> |
---|
| 525 | </tr> |
---|
| 526 | </tbody> |
---|
| 527 | </table> |
---|
| 528 | </dd></dl> |
---|
| 529 | |
---|
| 530 | <dl class="method"> |
---|
| 531 | <dt id="sas.fit.AbstractFitEngine.Model.set"> |
---|
| 532 | <tt class="descname">set</tt><big>(</big><em>**kw</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#Model.set"><span class="viewcode-link">[source]</span></a></dt> |
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| 533 | <dd></dd></dl> |
---|
| 534 | |
---|
| 535 | <dl class="method"> |
---|
| 536 | <dt id="sas.fit.AbstractFitEngine.Model.set_params"> |
---|
| 537 | <tt class="descname">set_params</tt><big>(</big><em>paramlist</em>, <em>params</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/AbstractFitEngine.html#Model.set_params"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 538 | <dd><p>Set value for parameters to fit</p> |
---|
| 539 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 540 | <col class="field-name" /> |
---|
| 541 | <col class="field-body" /> |
---|
| 542 | <tbody valign="top"> |
---|
| 543 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>params</strong> – list of value for parameters to fit</td> |
---|
| 544 | </tr> |
---|
| 545 | </tbody> |
---|
| 546 | </table> |
---|
| 547 | </dd></dl> |
---|
| 548 | |
---|
| 549 | </dd></dl> |
---|
| 550 | |
---|
| 551 | </div> |
---|
| 552 | <div class="section" id="module-sas.fit.BumpsFitting"> |
---|
| 553 | <span id="sas-fit-bumpsfitting-module"></span><h2>sas.fit.BumpsFitting module</h2> |
---|
| 554 | <p>BumpsFitting module runs the bumps optimizer.</p> |
---|
| 555 | <dl class="class"> |
---|
| 556 | <dt id="sas.fit.BumpsFitting.BumpsFit"> |
---|
| 557 | <em class="property">class </em><tt class="descclassname">sas.fit.BumpsFitting.</tt><tt class="descname">BumpsFit</tt><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#BumpsFit"><span class="viewcode-link">[source]</span></a></dt> |
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| 558 | <dd><p>Bases: <a class="reference internal" href="#sas.fit.AbstractFitEngine.FitEngine" title="sas.fit.AbstractFitEngine.FitEngine"><tt class="xref py py-class docutils literal"><span class="pre">sas.fit.AbstractFitEngine.FitEngine</span></tt></a></p> |
---|
| 559 | <p>Fit a model using bumps.</p> |
---|
| 560 | <dl class="method"> |
---|
| 561 | <dt id="sas.fit.BumpsFitting.BumpsFit.fit"> |
---|
| 562 | <tt class="descname">fit</tt><big>(</big><em>msg_q=None</em>, <em>q=None</em>, <em>handler=None</em>, <em>curr_thread=None</em>, <em>ftol=1.49012e-08</em>, <em>reset_flag=False</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#BumpsFit.fit"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 563 | <dd></dd></dl> |
---|
| 564 | |
---|
| 565 | </dd></dl> |
---|
| 566 | |
---|
| 567 | <dl class="class"> |
---|
| 568 | <dt id="sas.fit.BumpsFitting.BumpsMonitor"> |
---|
| 569 | <em class="property">class </em><tt class="descclassname">sas.fit.BumpsFitting.</tt><tt class="descname">BumpsMonitor</tt><big>(</big><em>handler</em>, <em>max_step</em>, <em>pars</em>, <em>dof</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#BumpsMonitor"><span class="viewcode-link">[source]</span></a></dt> |
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| 570 | <dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">object</span></tt></p> |
---|
| 571 | <dl class="method"> |
---|
| 572 | <dt id="sas.fit.BumpsFitting.BumpsMonitor.config_history"> |
---|
| 573 | <tt class="descname">config_history</tt><big>(</big><em>history</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#BumpsMonitor.config_history"><span class="viewcode-link">[source]</span></a></dt> |
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| 574 | <dd></dd></dl> |
---|
| 575 | |
---|
| 576 | </dd></dl> |
---|
| 577 | |
---|
| 578 | <dl class="class"> |
---|
| 579 | <dt id="sas.fit.BumpsFitting.ConvergenceMonitor"> |
---|
| 580 | <em class="property">class </em><tt class="descclassname">sas.fit.BumpsFitting.</tt><tt class="descname">ConvergenceMonitor</tt><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#ConvergenceMonitor"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 581 | <dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">object</span></tt></p> |
---|
| 582 | <p>ConvergenceMonitor contains population summary statistics to show progress |
---|
| 583 | of the fit. This is a list [ (best, 0%, 25%, 50%, 75%, 100%) ] or |
---|
| 584 | just a list [ (best, ) ] if population size is 1.</p> |
---|
| 585 | <dl class="method"> |
---|
| 586 | <dt id="sas.fit.BumpsFitting.ConvergenceMonitor.config_history"> |
---|
| 587 | <tt class="descname">config_history</tt><big>(</big><em>history</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#ConvergenceMonitor.config_history"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 588 | <dd></dd></dl> |
---|
| 589 | |
---|
| 590 | </dd></dl> |
---|
| 591 | |
---|
| 592 | <dl class="class"> |
---|
| 593 | <dt id="sas.fit.BumpsFitting.ParameterExpressions"> |
---|
| 594 | <em class="property">class </em><tt class="descclassname">sas.fit.BumpsFitting.</tt><tt class="descname">ParameterExpressions</tt><big>(</big><em>models</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#ParameterExpressions"><span class="viewcode-link">[source]</span></a></dt> |
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| 595 | <dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">object</span></tt></p> |
---|
| 596 | </dd></dl> |
---|
| 597 | |
---|
| 598 | <dl class="class"> |
---|
| 599 | <dt id="sas.fit.BumpsFitting.Progress"> |
---|
| 600 | <em class="property">class </em><tt class="descclassname">sas.fit.BumpsFitting.</tt><tt class="descname">Progress</tt><big>(</big><em>history</em>, <em>max_step</em>, <em>pars</em>, <em>dof</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#Progress"><span class="viewcode-link">[source]</span></a></dt> |
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| 601 | <dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">object</span></tt></p> |
---|
| 602 | </dd></dl> |
---|
| 603 | |
---|
| 604 | <dl class="class"> |
---|
| 605 | <dt id="sas.fit.BumpsFitting.SasFitness"> |
---|
| 606 | <em class="property">class </em><tt class="descclassname">sas.fit.BumpsFitting.</tt><tt class="descname">SasFitness</tt><big>(</big><em>model</em>, <em>data</em>, <em>fitted=[]</em>, <em>constraints={}</em>, <em>initial_values=None</em>, <em>**kw</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#SasFitness"><span class="viewcode-link">[source]</span></a></dt> |
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| 607 | <dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">object</span></tt></p> |
---|
| 608 | <p>Wrap SAS model as a bumps fitness object</p> |
---|
| 609 | <dl class="method"> |
---|
| 610 | <dt id="sas.fit.BumpsFitting.SasFitness.nllf"> |
---|
| 611 | <tt class="descname">nllf</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#SasFitness.nllf"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 612 | <dd></dd></dl> |
---|
| 613 | |
---|
| 614 | <dl class="method"> |
---|
| 615 | <dt id="sas.fit.BumpsFitting.SasFitness.numpoints"> |
---|
| 616 | <tt class="descname">numpoints</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#SasFitness.numpoints"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 617 | <dd></dd></dl> |
---|
| 618 | |
---|
| 619 | <dl class="method"> |
---|
| 620 | <dt id="sas.fit.BumpsFitting.SasFitness.parameters"> |
---|
| 621 | <tt class="descname">parameters</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#SasFitness.parameters"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 622 | <dd></dd></dl> |
---|
| 623 | |
---|
| 624 | <dl class="method"> |
---|
| 625 | <dt id="sas.fit.BumpsFitting.SasFitness.residuals"> |
---|
| 626 | <tt class="descname">residuals</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#SasFitness.residuals"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 627 | <dd></dd></dl> |
---|
| 628 | |
---|
| 629 | <dl class="method"> |
---|
| 630 | <dt id="sas.fit.BumpsFitting.SasFitness.set_fitted"> |
---|
| 631 | <tt class="descname">set_fitted</tt><big>(</big><em>param_list</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#SasFitness.set_fitted"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 632 | <dd><p>Flag a set of parameters as fitted parameters.</p> |
---|
| 633 | </dd></dl> |
---|
| 634 | |
---|
| 635 | <dl class="method"> |
---|
| 636 | <dt id="sas.fit.BumpsFitting.SasFitness.theory"> |
---|
| 637 | <tt class="descname">theory</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#SasFitness.theory"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 638 | <dd></dd></dl> |
---|
| 639 | |
---|
| 640 | <dl class="method"> |
---|
| 641 | <dt id="sas.fit.BumpsFitting.SasFitness.update"> |
---|
| 642 | <tt class="descname">update</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#SasFitness.update"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 643 | <dd></dd></dl> |
---|
| 644 | |
---|
| 645 | </dd></dl> |
---|
| 646 | |
---|
| 647 | <dl class="function"> |
---|
| 648 | <dt id="sas.fit.BumpsFitting.run_bumps"> |
---|
| 649 | <tt class="descclassname">sas.fit.BumpsFitting.</tt><tt class="descname">run_bumps</tt><big>(</big><em>problem</em>, <em>handler</em>, <em>curr_thread</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/BumpsFitting.html#run_bumps"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 650 | <dd></dd></dl> |
---|
| 651 | |
---|
| 652 | </div> |
---|
| 653 | <div class="section" id="module-sas.fit.Fitting"> |
---|
| 654 | <span id="sas-fit-fitting-module"></span><h2>sas.fit.Fitting module</h2> |
---|
| 655 | <p>Class Fit contains ScipyFit and ParkFit methods declaration |
---|
| 656 | allows to create instance of type ScipyFit or ParkFit to perform either |
---|
| 657 | a park fit or a scipy fit.</p> |
---|
| 658 | <dl class="class"> |
---|
| 659 | <dt id="sas.fit.Fitting.Fit"> |
---|
| 660 | <em class="property">class </em><tt class="descclassname">sas.fit.Fitting.</tt><tt class="descname">Fit</tt><big>(</big><em>engine='scipy'</em>, <em>*args</em>, <em>**kw</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Fitting.html#Fit"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 661 | <dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">object</span></tt></p> |
---|
| 662 | <p>Wrap class that allows to select the fitting type.this class |
---|
| 663 | can be used as follow :</p> |
---|
| 664 | <div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">sas.fit.Fitting</span> <span class="kn">import</span> <span class="n">Fit</span> |
---|
| 665 | <span class="n">fitter</span><span class="o">=</span> <span class="n">Fit</span><span class="p">()</span> |
---|
| 666 | <span class="n">fitter</span><span class="o">.</span><span class="n">fit_engine</span><span class="p">(</span><span class="s">'scipy'</span><span class="p">)</span> <span class="ow">or</span> <span class="n">fitter</span><span class="o">.</span><span class="n">fit_engine</span><span class="p">(</span><span class="s">'park'</span><span class="p">)</span> |
---|
| 667 | <span class="n">engine</span> <span class="o">=</span> <span class="n">fitter</span><span class="o">.</span><span class="n">returnEngine</span><span class="p">()</span> |
---|
| 668 | <span class="n">engine</span><span class="o">.</span><span class="n">set_data</span><span class="p">(</span><span class="n">data</span><span class="p">,</span><span class="nb">id</span><span class="p">)</span> |
---|
| 669 | <span class="n">engine</span><span class="o">.</span><span class="n">set_param</span><span class="p">(</span> <span class="n">model</span><span class="p">,</span><span class="n">model</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">pars</span><span class="p">)</span> |
---|
| 670 | <span class="n">engine</span><span class="o">.</span><span class="n">set_model</span><span class="p">(</span><span class="n">model</span><span class="p">,</span><span class="nb">id</span><span class="p">)</span> |
---|
| 671 | |
---|
| 672 | <span class="n">chisqr1</span><span class="p">,</span> <span class="n">out1</span><span class="p">,</span> <span class="n">cov1</span><span class="o">=</span><span class="n">engine</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">pars</span><span class="p">,</span><span class="n">qmin</span><span class="p">,</span><span class="n">qmax</span><span class="p">)</span> |
---|
| 673 | </pre></div> |
---|
| 674 | </div> |
---|
| 675 | <dl class="method"> |
---|
| 676 | <dt id="sas.fit.Fitting.Fit.fit"> |
---|
| 677 | <tt class="descname">fit</tt><big>(</big><em>msg_q=None</em>, <em>q=None</em>, <em>handler=None</em>, <em>curr_thread=None</em>, <em>ftol=1.49012e-08</em>, <em>reset_flag=False</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Fitting.html#Fit.fit"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 678 | <dd><p>Perform the fit</p> |
---|
| 679 | </dd></dl> |
---|
| 680 | |
---|
| 681 | <dl class="method"> |
---|
| 682 | <dt id="sas.fit.Fitting.Fit.get_model"> |
---|
| 683 | <tt class="descname">get_model</tt><big>(</big><em>id</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Fitting.html#Fit.get_model"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 684 | <dd><p>return list of data</p> |
---|
| 685 | </dd></dl> |
---|
| 686 | |
---|
| 687 | <dl class="method"> |
---|
| 688 | <dt id="sas.fit.Fitting.Fit.get_problem_to_fit"> |
---|
| 689 | <tt class="descname">get_problem_to_fit</tt><big>(</big><em>id</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Fitting.html#Fit.get_problem_to_fit"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 690 | <dd><p>return the self.selected value of the fit problem of id</p> |
---|
| 691 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 692 | <col class="field-name" /> |
---|
| 693 | <col class="field-body" /> |
---|
| 694 | <tbody valign="top"> |
---|
| 695 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>id</strong> – the id of the problem</td> |
---|
| 696 | </tr> |
---|
| 697 | </tbody> |
---|
| 698 | </table> |
---|
| 699 | </dd></dl> |
---|
| 700 | |
---|
| 701 | <dl class="method"> |
---|
| 702 | <dt id="sas.fit.Fitting.Fit.remove_fit_problem"> |
---|
| 703 | <tt class="descname">remove_fit_problem</tt><big>(</big><em>id</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Fitting.html#Fit.remove_fit_problem"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 704 | <dd><p>remove fitarrange in id</p> |
---|
| 705 | </dd></dl> |
---|
| 706 | |
---|
| 707 | <dl class="method"> |
---|
| 708 | <dt id="sas.fit.Fitting.Fit.select_problem_for_fit"> |
---|
| 709 | <tt class="descname">select_problem_for_fit</tt><big>(</big><em>id</em>, <em>value</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Fitting.html#Fit.select_problem_for_fit"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 710 | <dd><p>select a couple of model and data at the id position in dictionary |
---|
| 711 | and set in self.selected value to value</p> |
---|
| 712 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 713 | <col class="field-name" /> |
---|
| 714 | <col class="field-body" /> |
---|
| 715 | <tbody valign="top"> |
---|
| 716 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>value</strong> – the value to allow fitting. |
---|
| 717 | can only have the value one or zero</td> |
---|
| 718 | </tr> |
---|
| 719 | </tbody> |
---|
| 720 | </table> |
---|
| 721 | </dd></dl> |
---|
| 722 | |
---|
| 723 | <dl class="method"> |
---|
| 724 | <dt id="sas.fit.Fitting.Fit.set_data"> |
---|
| 725 | <tt class="descname">set_data</tt><big>(</big><em>data</em>, <em>id</em>, <em>smearer=None</em>, <em>qmin=None</em>, <em>qmax=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Fitting.html#Fit.set_data"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 726 | <dd><p>Store data to fit at the psotion id of the fit engine</p> |
---|
| 727 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 728 | <col class="field-name" /> |
---|
| 729 | <col class="field-body" /> |
---|
| 730 | <tbody valign="top"> |
---|
| 731 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> |
---|
| 732 | <li><strong>data</strong> – data to fit</li> |
---|
| 733 | <li><strong>smearer</strong> – smearerobject to smear data</li> |
---|
| 734 | <li><strong>qmin</strong> – the minimum q range to fit</li> |
---|
| 735 | <li><strong>qmax</strong> – the minimum q range to fit</li> |
---|
| 736 | </ul> |
---|
| 737 | </td> |
---|
| 738 | </tr> |
---|
| 739 | </tbody> |
---|
| 740 | </table> |
---|
| 741 | </dd></dl> |
---|
| 742 | |
---|
| 743 | <dl class="method"> |
---|
| 744 | <dt id="sas.fit.Fitting.Fit.set_engine"> |
---|
| 745 | <tt class="descname">set_engine</tt><big>(</big><em>word</em>, <em>*args</em>, <em>**kw</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Fitting.html#Fit.set_engine"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 746 | <dd><p>Select the type of Fit</p> |
---|
| 747 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 748 | <col class="field-name" /> |
---|
| 749 | <col class="field-body" /> |
---|
| 750 | <tbody valign="top"> |
---|
| 751 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>word</strong> – the keyword to select the fit type</td> |
---|
| 752 | </tr> |
---|
| 753 | <tr class="field-even field"><th class="field-name">Raise:</th><td class="field-body">if the user does not enter ‘scipy’ or ‘park’, |
---|
| 754 | a valueError is raised</td> |
---|
| 755 | </tr> |
---|
| 756 | </tbody> |
---|
| 757 | </table> |
---|
| 758 | </dd></dl> |
---|
| 759 | |
---|
| 760 | <dl class="method"> |
---|
| 761 | <dt id="sas.fit.Fitting.Fit.set_model"> |
---|
| 762 | <tt class="descname">set_model</tt><big>(</big><em>model</em>, <em>id</em>, <em>pars=[]</em>, <em>constraints=[]</em>, <em>data=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Fitting.html#Fit.set_model"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 763 | <dd><p>store a model model to fit at the position id of the fit engine</p> |
---|
| 764 | </dd></dl> |
---|
| 765 | |
---|
| 766 | </dd></dl> |
---|
| 767 | |
---|
| 768 | </div> |
---|
| 769 | <div class="section" id="module-sas.fit.Loader"> |
---|
| 770 | <span id="sas-fit-loader-module"></span><h2>sas.fit.Loader module</h2> |
---|
| 771 | <dl class="class"> |
---|
| 772 | <dt id="sas.fit.Loader.Load"> |
---|
| 773 | <em class="property">class </em><tt class="descclassname">sas.fit.Loader.</tt><tt class="descname">Load</tt><big>(</big><em>x=None</em>, <em>y=None</em>, <em>dx=None</em>, <em>dy=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Loader.html#Load"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 774 | <dd><p>This class is loading values from given file or value giving by the user</p> |
---|
| 775 | <dl class="method"> |
---|
| 776 | <dt id="sas.fit.Loader.Load.get_filename"> |
---|
| 777 | <tt class="descname">get_filename</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Loader.html#Load.get_filename"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 778 | <dd><p>return the file’s path</p> |
---|
| 779 | </dd></dl> |
---|
| 780 | |
---|
| 781 | <dl class="method"> |
---|
| 782 | <dt id="sas.fit.Loader.Load.get_values"> |
---|
| 783 | <tt class="descname">get_values</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Loader.html#Load.get_values"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 784 | <dd><p>Return x, y, dx, dy</p> |
---|
| 785 | </dd></dl> |
---|
| 786 | |
---|
| 787 | <dl class="method"> |
---|
| 788 | <dt id="sas.fit.Loader.Load.load_data"> |
---|
| 789 | <tt class="descname">load_data</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Loader.html#Load.load_data"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 790 | <dd><p>Return plottable</p> |
---|
| 791 | </dd></dl> |
---|
| 792 | |
---|
| 793 | <dl class="method"> |
---|
| 794 | <dt id="sas.fit.Loader.Load.set_filename"> |
---|
| 795 | <tt class="descname">set_filename</tt><big>(</big><em>path=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Loader.html#Load.set_filename"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 796 | <dd><p>Store path into a variable.If the user doesn’t give |
---|
| 797 | a path as a parameter a pop-up |
---|
| 798 | window appears to select the file.</p> |
---|
| 799 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 800 | <col class="field-name" /> |
---|
| 801 | <col class="field-body" /> |
---|
| 802 | <tbody valign="top"> |
---|
| 803 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>path</strong> – the path given by the user</td> |
---|
| 804 | </tr> |
---|
| 805 | </tbody> |
---|
| 806 | </table> |
---|
| 807 | </dd></dl> |
---|
| 808 | |
---|
| 809 | <dl class="method"> |
---|
| 810 | <dt id="sas.fit.Loader.Load.set_values"> |
---|
| 811 | <tt class="descname">set_values</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/Loader.html#Load.set_values"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 812 | <dd><p>Store the values loaded from file in local variables</p> |
---|
| 813 | </dd></dl> |
---|
| 814 | |
---|
| 815 | </dd></dl> |
---|
| 816 | |
---|
| 817 | </div> |
---|
| 818 | <div class="section" id="module-sas.fit.ParkFitting"> |
---|
| 819 | <span id="sas-fit-parkfitting-module"></span><h2>sas.fit.ParkFitting module</h2> |
---|
| 820 | <p>ParkFitting module contains SasParameter,Model,Data |
---|
| 821 | FitArrange, ParkFit,Parameter classes.All listed classes work together |
---|
| 822 | to perform a simple fit with park optimizer.</p> |
---|
| 823 | <dl class="class"> |
---|
| 824 | <dt id="sas.fit.ParkFitting.MyAssembly"> |
---|
| 825 | <em class="property">class </em><tt class="descclassname">sas.fit.ParkFitting.</tt><tt class="descname">MyAssembly</tt><big>(</big><em>models</em>, <em>curr_thread=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#MyAssembly"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 826 | <dd><p>Bases: <a class="reference internal" href="park.html#park.assembly.Assembly" title="park.assembly.Assembly"><tt class="xref py py-class docutils literal"><span class="pre">park.assembly.Assembly</span></tt></a></p> |
---|
| 827 | <dl class="method"> |
---|
| 828 | <dt id="sas.fit.ParkFitting.MyAssembly.eval"> |
---|
| 829 | <tt class="descname">eval</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#MyAssembly.eval"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 830 | <dd><p>Recalculate the theory functions, and from them, the |
---|
| 831 | residuals and chisq.</p> |
---|
| 832 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 833 | <col class="field-name" /> |
---|
| 834 | <col class="field-body" /> |
---|
| 835 | <tbody valign="top"> |
---|
| 836 | <tr class="field-odd field"><th class="field-name">Note:</th><td class="field-body">Call this after the parameters have been updated.</td> |
---|
| 837 | </tr> |
---|
| 838 | </tbody> |
---|
| 839 | </table> |
---|
| 840 | </dd></dl> |
---|
| 841 | |
---|
| 842 | <dl class="method"> |
---|
| 843 | <dt id="sas.fit.ParkFitting.MyAssembly.extend_results_with_calculated_parameters"> |
---|
| 844 | <tt class="descname">extend_results_with_calculated_parameters</tt><big>(</big><em>result</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#MyAssembly.extend_results_with_calculated_parameters"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 845 | <dd><p>Extend result from the fit with the calculated parameters.</p> |
---|
| 846 | </dd></dl> |
---|
| 847 | |
---|
| 848 | <dl class="method"> |
---|
| 849 | <dt id="sas.fit.ParkFitting.MyAssembly.fit_parameters"> |
---|
| 850 | <tt class="descname">fit_parameters</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#MyAssembly.fit_parameters"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 851 | <dd><p>Return an alphabetical list of the fitting parameters.</p> |
---|
| 852 | <p>This function is called once at the beginning of a fit, |
---|
| 853 | and serves as a convenient place to precalculate what |
---|
| 854 | can be precalculated such as the set of fitting parameters |
---|
| 855 | and the parameter expressions evaluator.</p> |
---|
| 856 | </dd></dl> |
---|
| 857 | |
---|
| 858 | </dd></dl> |
---|
| 859 | |
---|
| 860 | <dl class="class"> |
---|
| 861 | <dt id="sas.fit.ParkFitting.ParkFit"> |
---|
| 862 | <em class="property">class </em><tt class="descclassname">sas.fit.ParkFitting.</tt><tt class="descname">ParkFit</tt><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#ParkFit"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 863 | <dd><p>Bases: <a class="reference internal" href="#sas.fit.AbstractFitEngine.FitEngine" title="sas.fit.AbstractFitEngine.FitEngine"><tt class="xref py py-class docutils literal"><span class="pre">sas.fit.AbstractFitEngine.FitEngine</span></tt></a></p> |
---|
| 864 | <p>ParkFit performs the Fit.This class can be used as follow: |
---|
| 865 | #Do the fit Park |
---|
| 866 | create an engine: engine = ParkFit() |
---|
| 867 | Use data must be of type plottable |
---|
| 868 | Use a sas model</p> |
---|
| 869 | <p>Add data with a dictionnary of FitArrangeList where Uid is a key and data |
---|
| 870 | is saved in FitArrange object. |
---|
| 871 | engine.set_data(data,Uid)</p> |
---|
| 872 | <p>Set model parameter “M1”= model.name add {model.parameter.name:value}.</p> |
---|
| 873 | <p>..note:</p> |
---|
| 874 | <div class="highlight-python"><div class="highlight"><pre>Set_param() if used must always preceded set_model() for the fit to be performed. ``engine.set_param( model,"M1", {'A':2,'B':4})`` |
---|
| 875 | </pre></div> |
---|
| 876 | </div> |
---|
| 877 | <p>Add model with a dictionnary of FitArrangeList{} where Uid is a key |
---|
| 878 | and model |
---|
| 879 | is save in FitArrange object. |
---|
| 880 | engine.set_model(model,Uid)</p> |
---|
| 881 | <p>engine.fit return chisqr,[model.parameter 1,2,..],[[err1....][..err2...]] |
---|
| 882 | chisqr1, out1, cov1=engine.fit({model.parameter.name:value},qmin,qmax)</p> |
---|
| 883 | <p>..note:</p> |
---|
| 884 | <div class="highlight-python"><div class="highlight"><pre>{model.parameter.name:value} is ignored in fit function since |
---|
| 885 | the user should make sure to call set_param himself. |
---|
| 886 | </pre></div> |
---|
| 887 | </div> |
---|
| 888 | <dl class="method"> |
---|
| 889 | <dt id="sas.fit.ParkFitting.ParkFit.create_assembly"> |
---|
| 890 | <tt class="descname">create_assembly</tt><big>(</big><em>curr_thread</em>, <em>reset_flag=False</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#ParkFit.create_assembly"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 891 | <dd><p>Extract sasmodel and sasdata from |
---|
| 892 | self.FitArrangelist ={Uid:FitArrange} |
---|
| 893 | Create parkmodel and park data ,form a list couple of parkmodel |
---|
| 894 | and parkdata |
---|
| 895 | create an assembly self.problem= park.Assembly([(parkmodel,parkdata)])</p> |
---|
| 896 | </dd></dl> |
---|
| 897 | |
---|
| 898 | <dl class="method"> |
---|
| 899 | <dt id="sas.fit.ParkFitting.ParkFit.fit"> |
---|
| 900 | <tt class="descname">fit</tt><big>(</big><em>msg_q=None</em>, <em>q=None</em>, <em>handler=None</em>, <em>curr_thread=None</em>, <em>ftol=1.49012e-08</em>, <em>reset_flag=False</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#ParkFit.fit"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 901 | <dd><p>Performs fit with park.fit module.It can perform fit with one model |
---|
| 902 | and a set of data, more than two fit of one model and sets of data or |
---|
| 903 | fit with more than two model associated with their set of data and |
---|
| 904 | constraints</p> |
---|
| 905 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 906 | <col class="field-name" /> |
---|
| 907 | <col class="field-body" /> |
---|
| 908 | <tbody valign="top"> |
---|
| 909 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> |
---|
| 910 | <li><strong>pars</strong> – Dictionary of parameter names for the model and their |
---|
| 911 | values.</li> |
---|
| 912 | <li><strong>qmin</strong> – The minimum value of data’s range to be fit</li> |
---|
| 913 | <li><strong>qmax</strong> – The maximum value of data’s range to be fit</li> |
---|
| 914 | </ul> |
---|
| 915 | </td> |
---|
| 916 | </tr> |
---|
| 917 | <tr class="field-even field"><th class="field-name">Note:</th><td class="field-body"><p class="first">all parameter are ignored most of the time.Are just there |
---|
| 918 | to keep ScipyFit and ParkFit interface the same.</p> |
---|
| 919 | </td> |
---|
| 920 | </tr> |
---|
| 921 | <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">result.fitness Value of the goodness of fit metric</p> |
---|
| 922 | </td> |
---|
| 923 | </tr> |
---|
| 924 | <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">result.pvec list of parameter with the best value |
---|
| 925 | found during fitting</p> |
---|
| 926 | </td> |
---|
| 927 | </tr> |
---|
| 928 | <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">result.cov Covariance matrix</p> |
---|
| 929 | </td> |
---|
| 930 | </tr> |
---|
| 931 | </tbody> |
---|
| 932 | </table> |
---|
| 933 | </dd></dl> |
---|
| 934 | |
---|
| 935 | </dd></dl> |
---|
| 936 | |
---|
| 937 | <dl class="class"> |
---|
| 938 | <dt id="sas.fit.ParkFitting.ParkModel"> |
---|
| 939 | <em class="property">class </em><tt class="descclassname">sas.fit.ParkFitting.</tt><tt class="descname">ParkModel</tt><big>(</big><em>sas_model</em>, <em>sas_data=None</em>, <em>**kw</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#ParkModel"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 940 | <dd><p>Bases: <a class="reference internal" href="park.html#park.model.Model" title="park.model.Model"><tt class="xref py py-class docutils literal"><span class="pre">park.model.Model</span></tt></a></p> |
---|
| 941 | <p>PARK wrapper for SAS models.</p> |
---|
| 942 | <dl class="method"> |
---|
| 943 | <dt id="sas.fit.ParkFitting.ParkModel.eval"> |
---|
| 944 | <tt class="descname">eval</tt><big>(</big><em>x</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#ParkModel.eval"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 945 | <dd><p>Override eval method of park model.</p> |
---|
| 946 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 947 | <col class="field-name" /> |
---|
| 948 | <col class="field-body" /> |
---|
| 949 | <tbody valign="top"> |
---|
| 950 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>x</strong> – the x value used to compute a function</td> |
---|
| 951 | </tr> |
---|
| 952 | </tbody> |
---|
| 953 | </table> |
---|
| 954 | </dd></dl> |
---|
| 955 | |
---|
| 956 | <dl class="method"> |
---|
| 957 | <dt id="sas.fit.ParkFitting.ParkModel.eval_derivs"> |
---|
| 958 | <tt class="descname">eval_derivs</tt><big>(</big><em>x</em>, <em>pars=[]</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#ParkModel.eval_derivs"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 959 | <dd><p>Evaluate the model and derivatives wrt pars at x.</p> |
---|
| 960 | <p>pars is a list of the names of the parameters for which derivatives |
---|
| 961 | are desired.</p> |
---|
| 962 | <p>This method needs to be specialized in the model to evaluate the |
---|
| 963 | model function. Alternatively, the model can implement is own |
---|
| 964 | version of residuals which calculates the residuals directly |
---|
| 965 | instead of calling eval.</p> |
---|
| 966 | </dd></dl> |
---|
| 967 | |
---|
| 968 | <dl class="method"> |
---|
| 969 | <dt id="sas.fit.ParkFitting.ParkModel.get_params"> |
---|
| 970 | <tt class="descname">get_params</tt><big>(</big><em>fitparams</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#ParkModel.get_params"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 971 | <dd><p>return a list of value of paramter to fit</p> |
---|
| 972 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 973 | <col class="field-name" /> |
---|
| 974 | <col class="field-body" /> |
---|
| 975 | <tbody valign="top"> |
---|
| 976 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fitparams</strong> – list of paramaters name to fit</td> |
---|
| 977 | </tr> |
---|
| 978 | </tbody> |
---|
| 979 | </table> |
---|
| 980 | </dd></dl> |
---|
| 981 | |
---|
| 982 | <dl class="attribute"> |
---|
| 983 | <dt id="sas.fit.ParkFitting.ParkModel.parameters"> |
---|
| 984 | <tt class="descname">parameters</tt><em class="property"> = []</em></dt> |
---|
| 985 | <dd></dd></dl> |
---|
| 986 | |
---|
| 987 | <dl class="attribute"> |
---|
| 988 | <dt id="sas.fit.ParkFitting.ParkModel.parameterset"> |
---|
| 989 | <tt class="descname">parameterset</tt><em class="property"> = []</em></dt> |
---|
| 990 | <dd></dd></dl> |
---|
| 991 | |
---|
| 992 | <dl class="method"> |
---|
| 993 | <dt id="sas.fit.ParkFitting.ParkModel.set_params"> |
---|
| 994 | <tt class="descname">set_params</tt><big>(</big><em>paramlist</em>, <em>params</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#ParkModel.set_params"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 995 | <dd><p>Set value for parameters to fit</p> |
---|
| 996 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 997 | <col class="field-name" /> |
---|
| 998 | <col class="field-body" /> |
---|
| 999 | <tbody valign="top"> |
---|
| 1000 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>params</strong> – list of value for parameters to fit</td> |
---|
| 1001 | </tr> |
---|
| 1002 | </tbody> |
---|
| 1003 | </table> |
---|
| 1004 | </dd></dl> |
---|
| 1005 | |
---|
| 1006 | </dd></dl> |
---|
| 1007 | |
---|
| 1008 | <dl class="class"> |
---|
| 1009 | <dt id="sas.fit.ParkFitting.SasFitMC"> |
---|
| 1010 | <em class="property">class </em><tt class="descclassname">sas.fit.ParkFitting.</tt><tt class="descname">SasFitMC</tt><big>(</big><em>localfit</em>, <em>start_points=10</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#SasFitMC"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1011 | <dd><p>Bases: <a class="reference internal" href="#sas.fit.ParkFitting.SasFitter" title="sas.fit.ParkFitting.SasFitter"><tt class="xref py py-class docutils literal"><span class="pre">sas.fit.ParkFitting.SasFitter</span></tt></a></p> |
---|
| 1012 | <p>Monte Carlo optimizer.</p> |
---|
| 1013 | <p>This implements <cite>park.fit.Fitter</cite>.</p> |
---|
| 1014 | <dl class="attribute"> |
---|
| 1015 | <dt id="sas.fit.ParkFitting.SasFitMC.localfit"> |
---|
| 1016 | <tt class="descname">localfit</tt><em class="property"> = <sas.fit.ParkFitting.SasFitSimplex object at 0x10ab534d0></em></dt> |
---|
| 1017 | <dd></dd></dl> |
---|
| 1018 | |
---|
| 1019 | <dl class="attribute"> |
---|
| 1020 | <dt id="sas.fit.ParkFitting.SasFitMC.start_points"> |
---|
| 1021 | <tt class="descname">start_points</tt><em class="property"> = 10</em></dt> |
---|
| 1022 | <dd></dd></dl> |
---|
| 1023 | |
---|
| 1024 | </dd></dl> |
---|
| 1025 | |
---|
| 1026 | <dl class="class"> |
---|
| 1027 | <dt id="sas.fit.ParkFitting.SasFitParameter"> |
---|
| 1028 | <em class="property">class </em><tt class="descclassname">sas.fit.ParkFitting.</tt><tt class="descname">SasFitParameter</tt><big>(</big><em>name</em>, <em>range</em>, <em>value</em>, <em>model</em>, <em>data</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#SasFitParameter"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1029 | <dd><p>Bases: <a class="reference internal" href="park.html#park.fitresult.FitParameter" title="park.fitresult.FitParameter"><tt class="xref py py-class docutils literal"><span class="pre">park.fitresult.FitParameter</span></tt></a></p> |
---|
| 1030 | <p>Fit result for an individual parameter.</p> |
---|
| 1031 | <dl class="method"> |
---|
| 1032 | <dt id="sas.fit.ParkFitting.SasFitParameter.summarize"> |
---|
| 1033 | <tt class="descname">summarize</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#SasFitParameter.summarize"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1034 | <dd><p>Return parameter range string.</p> |
---|
| 1035 | <p>E.g., ” Gold .....|.... 5.2043 in [2,7]”</p> |
---|
| 1036 | </dd></dl> |
---|
| 1037 | |
---|
| 1038 | </dd></dl> |
---|
| 1039 | |
---|
| 1040 | <dl class="class"> |
---|
| 1041 | <dt id="sas.fit.ParkFitting.SasFitResult"> |
---|
| 1042 | <em class="property">class </em><tt class="descclassname">sas.fit.ParkFitting.</tt><tt class="descname">SasFitResult</tt><big>(</big><em>*args</em>, <em>**kwrds</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#SasFitResult"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1043 | <dd><p>Bases: <a class="reference internal" href="park.html#park.fitresult.FitResult" title="park.fitresult.FitResult"><tt class="xref py py-class docutils literal"><span class="pre">park.fitresult.FitResult</span></tt></a></p> |
---|
| 1044 | </dd></dl> |
---|
| 1045 | |
---|
| 1046 | <dl class="class"> |
---|
| 1047 | <dt id="sas.fit.ParkFitting.SasFitSimplex"> |
---|
| 1048 | <em class="property">class </em><tt class="descclassname">sas.fit.ParkFitting.</tt><tt class="descname">SasFitSimplex</tt><big>(</big><em>ftol=5e-05</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#SasFitSimplex"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1049 | <dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">park.fitmc.FitSimplex</span></tt></p> |
---|
| 1050 | <p>Local minimizer using Nelder-Mead simplex algorithm.</p> |
---|
| 1051 | <p>Simplex is robust and derivative free, though not very efficient.</p> |
---|
| 1052 | <p>This class wraps the bounds contrained Nelder-Mead simplex |
---|
| 1053 | implementation for <cite>park.simplex.simplex</cite>.</p> |
---|
| 1054 | <dl class="method"> |
---|
| 1055 | <dt id="sas.fit.ParkFitting.SasFitSimplex.fit"> |
---|
| 1056 | <tt class="descname">fit</tt><big>(</big><em>fitness</em>, <em>x0</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#SasFitSimplex.fit"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1057 | <dd><p>Run the fit</p> |
---|
| 1058 | </dd></dl> |
---|
| 1059 | |
---|
| 1060 | <dl class="attribute"> |
---|
| 1061 | <dt id="sas.fit.ParkFitting.SasFitSimplex.ftol"> |
---|
| 1062 | <tt class="descname">ftol</tt><em class="property"> = 5e-05</em></dt> |
---|
| 1063 | <dd><p>Stop when vertex values are within ftol of each other</p> |
---|
| 1064 | </dd></dl> |
---|
| 1065 | |
---|
| 1066 | <dl class="attribute"> |
---|
| 1067 | <dt id="sas.fit.ParkFitting.SasFitSimplex.maxiter"> |
---|
| 1068 | <tt class="descname">maxiter</tt><em class="property"> = None</em></dt> |
---|
| 1069 | <dd><p>Maximum number of iterations before fit terminates</p> |
---|
| 1070 | </dd></dl> |
---|
| 1071 | |
---|
| 1072 | <dl class="attribute"> |
---|
| 1073 | <dt id="sas.fit.ParkFitting.SasFitSimplex.radius"> |
---|
| 1074 | <tt class="descname">radius</tt><em class="property"> = 0.05</em></dt> |
---|
| 1075 | <dd><p>Size of the initial simplex; this is a portion between 0 and 1</p> |
---|
| 1076 | </dd></dl> |
---|
| 1077 | |
---|
| 1078 | <dl class="attribute"> |
---|
| 1079 | <dt id="sas.fit.ParkFitting.SasFitSimplex.xtol"> |
---|
| 1080 | <tt class="descname">xtol</tt><em class="property"> = 1</em></dt> |
---|
| 1081 | <dd><p>Stop when simplex vertices are within xtol of each other</p> |
---|
| 1082 | </dd></dl> |
---|
| 1083 | |
---|
| 1084 | </dd></dl> |
---|
| 1085 | |
---|
| 1086 | <dl class="class"> |
---|
| 1087 | <dt id="sas.fit.ParkFitting.SasFitter"> |
---|
| 1088 | <em class="property">class </em><tt class="descclassname">sas.fit.ParkFitting.</tt><tt class="descname">SasFitter</tt><big>(</big><em>**kw</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#SasFitter"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1089 | <dd><p>Bases: <a class="reference internal" href="park.html#park.fit.Fitter" title="park.fit.Fitter"><tt class="xref py py-class docutils literal"><span class="pre">park.fit.Fitter</span></tt></a></p> |
---|
| 1090 | <dl class="method"> |
---|
| 1091 | <dt id="sas.fit.ParkFitting.SasFitter.fit"> |
---|
| 1092 | <tt class="descname">fit</tt><big>(</big><em>fitness</em>, <em>handler</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#SasFitter.fit"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1093 | <dd><p>Global optimizer.</p> |
---|
| 1094 | <p>This function should return immediately</p> |
---|
| 1095 | </dd></dl> |
---|
| 1096 | |
---|
| 1097 | </dd></dl> |
---|
| 1098 | |
---|
| 1099 | <dl class="class"> |
---|
| 1100 | <dt id="sas.fit.ParkFitting.SasParameter"> |
---|
| 1101 | <em class="property">class </em><tt class="descclassname">sas.fit.ParkFitting.</tt><tt class="descname">SasParameter</tt><big>(</big><em>name</em>, <em>model</em>, <em>data</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#SasParameter"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1102 | <dd><p>Bases: <a class="reference internal" href="park.html#park.parameter.Parameter" title="park.parameter.Parameter"><tt class="xref py py-class docutils literal"><span class="pre">park.parameter.Parameter</span></tt></a></p> |
---|
| 1103 | <p>SAS model parameters for use in the PARK fitting service. |
---|
| 1104 | The parameter attribute value is redirected to the underlying |
---|
| 1105 | parameter value in the SAS model.</p> |
---|
| 1106 | <dl class="method"> |
---|
| 1107 | <dt id="sas.fit.ParkFitting.SasParameter.get_name"> |
---|
| 1108 | <tt class="descname">get_name</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#SasParameter.get_name"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1109 | <dd></dd></dl> |
---|
| 1110 | |
---|
| 1111 | <dl class="attribute"> |
---|
| 1112 | <dt id="sas.fit.ParkFitting.SasParameter.range"> |
---|
| 1113 | <tt class="descname">range</tt></dt> |
---|
| 1114 | <dd><p>Override _getrange of park parameter |
---|
| 1115 | return the range of parameter</p> |
---|
| 1116 | </dd></dl> |
---|
| 1117 | |
---|
| 1118 | <dl class="attribute"> |
---|
| 1119 | <dt id="sas.fit.ParkFitting.SasParameter.value"> |
---|
| 1120 | <tt class="descname">value</tt></dt> |
---|
| 1121 | <dd><p>override the _getvalue of park parameter</p> |
---|
| 1122 | <p>:return value the parameter associates with self.name</p> |
---|
| 1123 | </dd></dl> |
---|
| 1124 | |
---|
| 1125 | </dd></dl> |
---|
| 1126 | |
---|
| 1127 | <dl class="class"> |
---|
| 1128 | <dt id="sas.fit.ParkFitting.SasPart"> |
---|
| 1129 | <em class="property">class </em><tt class="descclassname">sas.fit.ParkFitting.</tt><tt class="descname">SasPart</tt><big>(</big><em>fitness</em>, <em>weight=1.0</em>, <em>isfitted=True</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ParkFitting.html#SasPart"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1130 | <dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">park.assembly.Part</span></tt></p> |
---|
| 1131 | <p>Part of a fitting assembly. Part holds the model itself and |
---|
| 1132 | associated data. The part can be initialized with a fitness |
---|
| 1133 | object or with a pair (model,data) for the default fitness function.</p> |
---|
| 1134 | <dl class="docutils"> |
---|
| 1135 | <dt>fitness (Fitness)</dt> |
---|
| 1136 | <dd>object implementing the <cite>park.assembly.Fitness</cite> interface. In |
---|
| 1137 | particular, fitness should provide a parameterset attribute |
---|
| 1138 | containing a ParameterSet and a residuals method returning a vector |
---|
| 1139 | of residuals.</dd> |
---|
| 1140 | <dt>weight (dimensionless)</dt> |
---|
| 1141 | <dd>weight for the model. See comments in assembly.py for details.</dd> |
---|
| 1142 | <dt>isfitted (boolean)</dt> |
---|
| 1143 | <dd>True if the model residuals should be included in the fit. |
---|
| 1144 | The model parameters may still be used in parameter |
---|
| 1145 | expressions, but there will be no comparison to the data.</dd> |
---|
| 1146 | <dt>residuals (vector)</dt> |
---|
| 1147 | <dd>Residuals for the model if they have been calculated, or None</dd> |
---|
| 1148 | <dt>degrees_of_freedom</dt> |
---|
| 1149 | <dd>Number of residuals minus number of fitted parameters. |
---|
| 1150 | Degrees of freedom for individual models does not make |
---|
| 1151 | sense in the presence of expressions combining models, |
---|
| 1152 | particularly in the case where a model has many parameters |
---|
| 1153 | but no data or many computed parameters. The degrees of |
---|
| 1154 | freedom for the model is set to be at least one.</dd> |
---|
| 1155 | <dt>chisq</dt> |
---|
| 1156 | <dd><p class="first">sum(residuals**2); use chisq/degrees_of_freedom to |
---|
| 1157 | get the reduced chisq value.</p> |
---|
| 1158 | <p>Get/set the weight on the given model.</p> |
---|
| 1159 | <p class="last">assembly.weight(3) returns the weight on model 3 (0-origin) |
---|
| 1160 | assembly.weight(3,0.5) sets the weight on model 3 (0-origin)</p> |
---|
| 1161 | </dd> |
---|
| 1162 | </dl> |
---|
| 1163 | </dd></dl> |
---|
| 1164 | |
---|
| 1165 | </div> |
---|
| 1166 | <div class="section" id="module-sas.fit.ScipyFitting"> |
---|
| 1167 | <span id="sas-fit-scipyfitting-module"></span><h2>sas.fit.ScipyFitting module</h2> |
---|
| 1168 | <p>ScipyFitting module contains FitArrange , ScipyFit, |
---|
| 1169 | Parameter classes.All listed classes work together to perform a |
---|
| 1170 | simple fit with scipy optimizer.</p> |
---|
| 1171 | <dl class="class"> |
---|
| 1172 | <dt id="sas.fit.ScipyFitting.SasAssembly"> |
---|
| 1173 | <em class="property">class </em><tt class="descclassname">sas.fit.ScipyFitting.</tt><tt class="descname">SasAssembly</tt><big>(</big><em>paramlist</em>, <em>model=None</em>, <em>data=None</em>, <em>fitresult=None</em>, <em>handler=None</em>, <em>curr_thread=None</em>, <em>msg_q=None</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ScipyFitting.html#SasAssembly"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1174 | <dd><p>Sas Assembly class a class wrapper to be call in optimizer.leastsq method</p> |
---|
| 1175 | <dl class="method"> |
---|
| 1176 | <dt id="sas.fit.ScipyFitting.SasAssembly.check_param_range"> |
---|
| 1177 | <tt class="descname">check_param_range</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ScipyFitting.html#SasAssembly.check_param_range"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1178 | <dd><p>Check the lower and upper bound of the parameter value |
---|
| 1179 | and set res to the inf if the value is outside of the |
---|
| 1180 | range |
---|
| 1181 | :limitation: the initial values must be within range.</p> |
---|
| 1182 | </dd></dl> |
---|
| 1183 | |
---|
| 1184 | <dl class="method"> |
---|
| 1185 | <dt id="sas.fit.ScipyFitting.SasAssembly.chisq"> |
---|
| 1186 | <tt class="descname">chisq</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ScipyFitting.html#SasAssembly.chisq"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1187 | <dd><p>Calculates chi^2</p> |
---|
| 1188 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 1189 | <col class="field-name" /> |
---|
| 1190 | <col class="field-body" /> |
---|
| 1191 | <tbody valign="top"> |
---|
| 1192 | <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>params</strong> – list of parameter values</td> |
---|
| 1193 | </tr> |
---|
| 1194 | <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">chi^2</td> |
---|
| 1195 | </tr> |
---|
| 1196 | </tbody> |
---|
| 1197 | </table> |
---|
| 1198 | </dd></dl> |
---|
| 1199 | |
---|
| 1200 | </dd></dl> |
---|
| 1201 | |
---|
| 1202 | <dl class="class"> |
---|
| 1203 | <dt id="sas.fit.ScipyFitting.ScipyFit"> |
---|
| 1204 | <em class="property">class </em><tt class="descclassname">sas.fit.ScipyFitting.</tt><tt class="descname">ScipyFit</tt><a class="reference internal" href="../../_modules/sas/fit/ScipyFitting.html#ScipyFit"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1205 | <dd><p>Bases: <a class="reference internal" href="#sas.fit.AbstractFitEngine.FitEngine" title="sas.fit.AbstractFitEngine.FitEngine"><tt class="xref py py-class docutils literal"><span class="pre">sas.fit.AbstractFitEngine.FitEngine</span></tt></a></p> |
---|
| 1206 | <p>ScipyFit performs the Fit.This class can be used as follow: |
---|
| 1207 | #Do the fit SCIPY |
---|
| 1208 | create an engine: engine = ScipyFit() |
---|
| 1209 | Use data must be of type plottable |
---|
| 1210 | Use a sas model</p> |
---|
| 1211 | <p>Add data with a dictionnary of FitArrangeDict where Uid is a key and data |
---|
| 1212 | is saved in FitArrange object. |
---|
| 1213 | engine.set_data(data,Uid)</p> |
---|
| 1214 | <p>Set model parameter “M1”= model.name add {model.parameter.name:value}.</p> |
---|
| 1215 | <table class="docutils field-list" frame="void" rules="none"> |
---|
| 1216 | <col class="field-name" /> |
---|
| 1217 | <col class="field-body" /> |
---|
| 1218 | <tbody valign="top"> |
---|
| 1219 | <tr class="field-odd field"><th class="field-name">Note:</th><td class="field-body">Set_param() if used must always preceded set_model() |
---|
| 1220 | for the fit to be performed.In case of Scipyfit set_param is called in |
---|
| 1221 | fit () automatically.</td> |
---|
| 1222 | </tr> |
---|
| 1223 | </tbody> |
---|
| 1224 | </table> |
---|
| 1225 | <p>engine.set_param( model,”M1”, {‘A’:2,’B’:4})</p> |
---|
| 1226 | <p>Add model with a dictionnary of FitArrangeDict{} where Uid is a key and model |
---|
| 1227 | is save in FitArrange object. |
---|
| 1228 | engine.set_model(model,Uid)</p> |
---|
| 1229 | <p>engine.fit return chisqr,[model.parameter 1,2,..],[[err1....][..err2...]] |
---|
| 1230 | chisqr1, out1, cov1=engine.fit({model.parameter.name:value},qmin,qmax)</p> |
---|
| 1231 | <dl class="method"> |
---|
| 1232 | <dt id="sas.fit.ScipyFitting.ScipyFit.fit"> |
---|
| 1233 | <tt class="descname">fit</tt><big>(</big><em>msg_q=None</em>, <em>q=None</em>, <em>handler=None</em>, <em>curr_thread=None</em>, <em>ftol=1.49012e-08</em>, <em>reset_flag=False</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/ScipyFitting.html#ScipyFit.fit"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1234 | <dd></dd></dl> |
---|
| 1235 | |
---|
| 1236 | </dd></dl> |
---|
| 1237 | |
---|
| 1238 | </div> |
---|
| 1239 | <div class="section" id="module-sas.fit.expression"> |
---|
| 1240 | <span id="sas-fit-expression-module"></span><h2>sas.fit.expression module</h2> |
---|
| 1241 | <p>Parameter expression evaluator.</p> |
---|
| 1242 | <p>For systems in which constraints are expressed as string expressions rather |
---|
| 1243 | than python code, <a class="reference internal" href="#sas.fit.expression.compile_constraints" title="sas.fit.expression.compile_constraints"><tt class="xref py py-func docutils literal"><span class="pre">compile_constraints()</span></tt></a> can construct an expression |
---|
| 1244 | evaluator that substitutes the computed values of the expressions into the |
---|
| 1245 | parameters.</p> |
---|
| 1246 | <p>The compiler requires a symbol table, an expression set and a context. |
---|
| 1247 | The symbol table maps strings containing fully qualified names such as |
---|
| 1248 | ‘M1.c[3].full_width’ to parameter objects with a ‘value’ property that |
---|
| 1249 | can be queried and set. The expression set maps symbol names from the |
---|
| 1250 | symbol table to string expressions. The context provides additional symbols |
---|
| 1251 | for the expressions in addition to the usual mathematical functions and |
---|
| 1252 | constants.</p> |
---|
| 1253 | <p>The expressions are compiled and interpreted by python, with only minimal |
---|
| 1254 | effort to make sure that they don’t contain bad code. The resulting |
---|
| 1255 | constraints function returns 0 so it can be used directly in a fit problem |
---|
| 1256 | definition.</p> |
---|
| 1257 | <p>Extracting the symbol table from the model depends on the structure of the |
---|
| 1258 | model. If fitness.parameters() is set correctly, then this should simply |
---|
| 1259 | be a matter of walking the parameter data, remembering the path to each |
---|
| 1260 | parameter in the symbol table. For compactness, dictionary elements should |
---|
| 1261 | be referenced by .name rather than [“name”]. Model name can be used as the |
---|
| 1262 | top level.</p> |
---|
| 1263 | <p>Getting the parameter expressions applied correctly is challenging. |
---|
| 1264 | The following monkey patch works by overriding model_update in FitProblem |
---|
| 1265 | so that after setp(p) is called and, the constraints expression can be |
---|
| 1266 | applied before telling the underlying fitness function that the model |
---|
| 1267 | is out of date:</p> |
---|
| 1268 | <div class="highlight-python"><div class="highlight"><pre><span class="c"># Override model update so that parameter constraints are applied</span> |
---|
| 1269 | <span class="n">problem</span><span class="o">.</span><span class="n">_model_update</span> <span class="o">=</span> <span class="n">problem</span><span class="o">.</span><span class="n">model_update</span> |
---|
| 1270 | <span class="k">def</span> <span class="nf">model_update</span><span class="p">():</span> |
---|
| 1271 | <span class="n">constraints</span><span class="p">()</span> |
---|
| 1272 | <span class="n">problem</span><span class="o">.</span><span class="n">_model_update</span><span class="p">()</span> |
---|
| 1273 | <span class="n">problem</span><span class="o">.</span><span class="n">model_update</span> <span class="o">=</span> <span class="n">model_update</span> |
---|
| 1274 | </pre></div> |
---|
| 1275 | </div> |
---|
| 1276 | <p>Ideally, this interface will change</p> |
---|
| 1277 | <dl class="function"> |
---|
| 1278 | <dt id="sas.fit.expression.compile_constraints"> |
---|
| 1279 | <tt class="descclassname">sas.fit.expression.</tt><tt class="descname">compile_constraints</tt><big>(</big><em>symtab</em>, <em>exprs</em>, <em>context={}</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/expression.html#compile_constraints"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1280 | <dd><p>Build and return a function to evaluate all parameter expressions in |
---|
| 1281 | the proper order.</p> |
---|
| 1282 | <p>Input:</p> |
---|
| 1283 | <blockquote> |
---|
| 1284 | <div><p><em>symtab</em> is the symbol table for the model: { ‘name’: parameter }</p> |
---|
| 1285 | <p><em>exprs</em> is the set of computed symbols: { ‘name’: ‘expression’ }</p> |
---|
| 1286 | <p><em>context</em> is any additional context needed to evaluate the expression</p> |
---|
| 1287 | </div></blockquote> |
---|
| 1288 | <p>Return:</p> |
---|
| 1289 | <blockquote> |
---|
| 1290 | <div>updater function which sets parameter.value for each expression</div></blockquote> |
---|
| 1291 | <p>Raises:</p> |
---|
| 1292 | <blockquote> |
---|
| 1293 | <div><p>AssertionError - model, parameter or function is missing</p> |
---|
| 1294 | <p>SyntaxError - improper expression syntax</p> |
---|
| 1295 | <p>ValueError - expressions have circular dependencies</p> |
---|
| 1296 | </div></blockquote> |
---|
| 1297 | <p>This function is not terribly sophisticated, and it would be easy to |
---|
| 1298 | trick. However it handles the common cases cleanly and generates |
---|
| 1299 | reasonable messages for the common errors.</p> |
---|
| 1300 | <p>This code has not been fully audited for security. While we have |
---|
| 1301 | removed the builtins and the ability to import modules, there may |
---|
| 1302 | be other vectors for users to perform more than simple function |
---|
| 1303 | evaluations. Unauthenticated users should not be running this code.</p> |
---|
| 1304 | <p>Parameter names are assumed to contain only _.a-zA-Z0-9#[]</p> |
---|
| 1305 | <p>Both names are provided for inverse functions, e.g., acos and arccos.</p> |
---|
| 1306 | <p>Should try running the function to identify syntax errors before |
---|
| 1307 | running it in a fit.</p> |
---|
| 1308 | <p>Use help(fn) to see the code generated for the returned function fn. |
---|
| 1309 | dis.dis(fn) will show the corresponding python vm instructions.</p> |
---|
| 1310 | </dd></dl> |
---|
| 1311 | |
---|
| 1312 | <dl class="function"> |
---|
| 1313 | <dt id="sas.fit.expression.no_constraints"> |
---|
| 1314 | <tt class="descclassname">sas.fit.expression.</tt><tt class="descname">no_constraints</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/expression.html#no_constraints"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1315 | <dd><p>This parameter set has no constraints between the parameters.</p> |
---|
| 1316 | </dd></dl> |
---|
| 1317 | |
---|
| 1318 | <dl class="function"> |
---|
| 1319 | <dt id="sas.fit.expression.order_dependencies"> |
---|
| 1320 | <tt class="descclassname">sas.fit.expression.</tt><tt class="descname">order_dependencies</tt><big>(</big><em>pairs</em><big>)</big><a class="reference internal" href="../../_modules/sas/fit/expression.html#order_dependencies"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1321 | <dd><p>Order elements from pairs so that b comes before a in the |
---|
| 1322 | ordered list for all pairs (a,b).</p> |
---|
| 1323 | </dd></dl> |
---|
| 1324 | |
---|
| 1325 | <dl class="function"> |
---|
| 1326 | <dt id="sas.fit.expression.test_deps"> |
---|
| 1327 | <tt class="descclassname">sas.fit.expression.</tt><tt class="descname">test_deps</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/expression.html#test_deps"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1328 | <dd></dd></dl> |
---|
| 1329 | |
---|
| 1330 | <dl class="function"> |
---|
| 1331 | <dt id="sas.fit.expression.test_expr"> |
---|
| 1332 | <tt class="descclassname">sas.fit.expression.</tt><tt class="descname">test_expr</tt><big>(</big><big>)</big><a class="reference internal" href="../../_modules/sas/fit/expression.html#test_expr"><span class="viewcode-link">[source]</span></a></dt> |
---|
| 1333 | <dd></dd></dl> |
---|
| 1334 | |
---|
| 1335 | </div> |
---|
| 1336 | <div class="section" id="module-sas.fit"> |
---|
| 1337 | <span id="module-contents"></span><h2>Module contents</h2> |
---|
| 1338 | </div> |
---|
| 1339 | </div> |
---|
| 1340 | |
---|
| 1341 | |
---|
| 1342 | </div> |
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| 1343 | </div> |
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| 1344 | </div> |
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| 1345 | <div class="sphinxsidebar"> |
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| 1346 | <div class="sphinxsidebarwrapper"> |
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| 1347 | <h3><a href="../../index.html">Table Of Contents</a></h3> |
---|
| 1348 | <ul> |
---|
| 1349 | <li><a class="reference internal" href="#">sas.fit package</a><ul> |
---|
| 1350 | <li><a class="reference internal" href="#submodules">Submodules</a></li> |
---|
| 1351 | <li><a class="reference internal" href="#module-sas.fit.AbstractFitEngine">sas.fit.AbstractFitEngine module</a></li> |
---|
| 1352 | <li><a class="reference internal" href="#module-sas.fit.BumpsFitting">sas.fit.BumpsFitting module</a></li> |
---|
| 1353 | <li><a class="reference internal" href="#module-sas.fit.Fitting">sas.fit.Fitting module</a></li> |
---|
| 1354 | <li><a class="reference internal" href="#module-sas.fit.Loader">sas.fit.Loader module</a></li> |
---|
| 1355 | <li><a class="reference internal" href="#module-sas.fit.ParkFitting">sas.fit.ParkFitting module</a></li> |
---|
| 1356 | <li><a class="reference internal" href="#module-sas.fit.ScipyFitting">sas.fit.ScipyFitting module</a></li> |
---|
| 1357 | <li><a class="reference internal" href="#module-sas.fit.expression">sas.fit.expression module</a></li> |
---|
| 1358 | <li><a class="reference internal" href="#module-sas.fit">Module contents</a></li> |
---|
| 1359 | </ul> |
---|
| 1360 | </li> |
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| 1361 | </ul> |
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| 1362 | |
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| 1363 | <h4>Previous topic</h4> |
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| 1364 | <p class="topless"><a href="sas.dataloader.readers.html" |
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| 1365 | title="previous chapter">sas.dataloader.readers package</a></p> |
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| 1366 | <h4>Next topic</h4> |
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| 1367 | <p class="topless"><a href="sas.guiframe.html" |
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| 1368 | title="next chapter">sas.guiframe package</a></p> |
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| 1369 | <h3>This Page</h3> |
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