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| 50 | <h1>Source code for sas.plottools.fittings</h1><div class="highlight"><pre> |
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| 51 | <span class="sd">"""</span> |
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| 52 | <span class="sd">"""</span> |
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| 53 | <span class="kn">from</span> <span class="nn">scipy</span> <span class="kn">import</span> <span class="n">optimize</span> |
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| 54 | |
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| 55 | |
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| 56 | <div class="viewcode-block" id="Parameter"><a class="viewcode-back" href="../../../dev/api/sas.plottools.html#sas.plottools.fittings.Parameter">[docs]</a><span class="k">class</span> <span class="nc">Parameter</span><span class="p">:</span> |
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| 57 | <span class="sd">"""</span> |
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| 58 | <span class="sd"> Class to handle model parameters</span> |
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| 59 | <span class="sd"> """</span> |
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| 60 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
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| 61 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">model</span> |
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| 62 | <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span> |
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| 63 | <span class="k">if</span> <span class="ow">not</span> <span class="n">value</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> |
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| 64 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span> |
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| 65 | |
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| 66 | <div class="viewcode-block" id="Parameter.set"><a class="viewcode-back" href="../../../dev/api/sas.plottools.html#sas.plottools.fittings.Parameter.set">[docs]</a> <span class="k">def</span> <span class="nf">set</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span> |
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| 67 | <span class="sd">"""</span> |
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| 68 | <span class="sd"> Set the value of the parameter</span> |
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| 69 | <span class="sd"> """</span> |
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| 70 | <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span> |
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| 71 | </div> |
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| 72 | <span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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| 73 | <span class="sd">"""</span> |
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| 74 | <span class="sd"> Return the current value of the parameter</span> |
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| 75 | <span class="sd"> """</span> |
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| 76 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">getParam</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span> |
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| 77 | |
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| 78 | </div> |
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| 79 | <div class="viewcode-block" id="sasfit"><a class="viewcode-back" href="../../../dev/api/sas.plottools.html#sas.plottools.fittings.sasfit">[docs]</a><span class="k">def</span> <span class="nf">sasfit</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">pars</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">err_y</span> <span class="p">,</span> <span class="n">qmin</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">qmax</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
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| 80 | <span class="sd">"""</span> |
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| 81 | <span class="sd"> Fit function</span> |
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| 82 | <span class="sd"> </span> |
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| 83 | <span class="sd"> :param model: sas model object</span> |
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| 84 | <span class="sd"> :param pars: list of parameters</span> |
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| 85 | <span class="sd"> :param x: vector of x data</span> |
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| 86 | <span class="sd"> :param y: vector of y data</span> |
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| 87 | <span class="sd"> :param err_y: vector of y errors</span> |
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| 88 | <span class="sd"> """</span> |
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| 89 | <span class="k">def</span> <span class="nf">f</span><span class="p">(</span><span class="n">params</span><span class="p">):</span> |
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| 90 | <span class="sd">"""</span> |
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| 91 | <span class="sd"> Calculates the vector of residuals for each point</span> |
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| 92 | <span class="sd"> in y for a given set of input parameters.</span> |
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| 93 | <span class="sd"> </span> |
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| 94 | <span class="sd"> :param params: list of parameter values</span> |
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| 95 | <span class="sd"> :return: vector of residuals</span> |
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| 96 | <span class="sd"> """</span> |
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| 97 | <span class="n">i</span> <span class="o">=</span> <span class="mi">0</span> |
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| 98 | <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pars</span><span class="p">:</span> |
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| 99 | <span class="n">p</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">params</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> |
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| 100 | <span class="n">i</span> <span class="o">+=</span> <span class="mi">1</span> |
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| 101 | |
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| 102 | <span class="n">residuals</span> <span class="o">=</span> <span class="p">[]</span> |
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| 103 | <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">)):</span> |
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| 104 | <span class="k">if</span> <span class="n">x</span><span class="p">[</span><span class="n">j</span><span class="p">]</span> <span class="o">>=</span> <span class="n">qmin</span> <span class="ow">and</span> <span class="n">x</span><span class="p">[</span><span class="n">j</span><span class="p">]</span> <span class="o"><=</span> <span class="n">qmax</span><span class="p">:</span> |
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| 105 | <span class="n">residuals</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">y</span><span class="p">[</span><span class="n">j</span><span class="p">]</span> <span class="o">-</span> <span class="n">model</span><span class="o">.</span><span class="n">runXY</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="n">j</span><span class="p">]))</span> <span class="o">/</span> <span class="n">err_y</span><span class="p">[</span><span class="n">j</span><span class="p">])</span> |
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| 106 | <span class="k">return</span> <span class="n">residuals</span> |
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| 107 | |
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| 108 | <span class="k">def</span> <span class="nf">chi2</span><span class="p">(</span><span class="n">params</span><span class="p">):</span> |
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| 109 | <span class="sd">"""</span> |
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| 110 | <span class="sd"> Calculates chi^2</span> |
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| 111 | <span class="sd"> </span> |
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| 112 | <span class="sd"> :param params: list of parameter values</span> |
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| 113 | <span class="sd"> </span> |
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| 114 | <span class="sd"> :return: chi^2</span> |
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| 115 | <span class="sd"> </span> |
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| 116 | <span class="sd"> """</span> |
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| 117 | <span class="nb">sum</span> <span class="o">=</span> <span class="mi">0</span> |
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| 118 | <span class="n">res</span> <span class="o">=</span> <span class="n">f</span><span class="p">(</span><span class="n">params</span><span class="p">)</span> |
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| 119 | <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">res</span><span class="p">:</span> |
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| 120 | <span class="nb">sum</span> <span class="o">+=</span> <span class="n">item</span> <span class="o">*</span> <span class="n">item</span> |
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| 121 | <span class="k">return</span> <span class="nb">sum</span> |
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| 122 | |
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| 123 | <span class="n">p</span> <span class="o">=</span> <span class="p">[</span><span class="n">param</span><span class="p">()</span> <span class="k">for</span> <span class="n">param</span> <span class="ow">in</span> <span class="n">pars</span><span class="p">]</span> |
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| 124 | <span class="n">out</span><span class="p">,</span> <span class="n">cov_x</span><span class="p">,</span> <span class="n">info</span><span class="p">,</span> <span class="n">mesg</span><span class="p">,</span> <span class="n">success</span> <span class="o">=</span> <span class="n">optimize</span><span class="o">.</span><span class="n">leastsq</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">p</span><span class="p">,</span> <span class="n">full_output</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> |
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| 125 | <span class="c"># Calculate chi squared</span> |
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| 126 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pars</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span> |
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| 127 | <span class="n">chisqr</span> <span class="o">=</span> <span class="n">chi2</span><span class="p">(</span><span class="n">out</span><span class="p">)</span> |
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| 128 | <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">pars</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span> |
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| 129 | <span class="n">chisqr</span> <span class="o">=</span> <span class="n">chi2</span><span class="p">([</span><span class="n">out</span><span class="p">])</span> |
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| 130 | |
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| 131 | <span class="k">return</span> <span class="n">chisqr</span><span class="p">,</span> <span class="n">out</span><span class="p">,</span> <span class="n">cov_x</span> |
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| 132 | |
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| 133 | </div> |
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| 134 | <div class="viewcode-block" id="calcCommandline"><a class="viewcode-back" href="../../../dev/api/sas.plottools.html#sas.plottools.fittings.calcCommandline">[docs]</a><span class="k">def</span> <span class="nf">calcCommandline</span><span class="p">(</span><span class="n">event</span><span class="p">):</span> |
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| 135 | <span class="c">#Testing implementation</span> |
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| 136 | <span class="c"># Fit a Line model</span> |
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| 137 | <span class="kn">from</span> <span class="nn">LineModel</span> <span class="kn">import</span> <span class="n">LineModel</span> |
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| 138 | <span class="n">line</span> <span class="o">=</span> <span class="n">LineModel</span><span class="p">()</span> |
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| 139 | <span class="n">cstA</span> <span class="o">=</span> <span class="n">Parameter</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="s">'A'</span><span class="p">,</span> <span class="n">event</span><span class="o">.</span><span class="n">cstA</span><span class="p">)</span> |
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| 140 | <span class="n">cstB</span> <span class="o">=</span> <span class="n">Parameter</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="s">'B'</span><span class="p">,</span> <span class="n">event</span><span class="o">.</span><span class="n">cstB</span><span class="p">)</span> |
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| 141 | <span class="n">y</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">run</span><span class="p">()</span> |
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| 142 | <span class="n">chisqr</span><span class="p">,</span> <span class="n">out</span><span class="p">,</span> <span class="n">cov</span> <span class="o">=</span> <span class="n">sasfit</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="p">[</span><span class="n">cstA</span><span class="p">,</span> <span class="n">cstB</span><span class="p">],</span> <span class="n">event</span><span class="o">.</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> |
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| 143 | <span class="c"># print "Output parameters:", out</span> |
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| 144 | <span class="k">print</span> <span class="s">"The right answer is [70.0, 1.0]"</span> |
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| 145 | <span class="k">print</span> <span class="n">chisqr</span><span class="p">,</span> <span class="n">out</span><span class="p">,</span> <span class="n">cov</span></div> |
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| 146 | </pre></div> |
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