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50  <h1>Source code for sas.fit.ParkFitting</h1><div class="highlight"><pre>
51<span class="sd">&quot;&quot;&quot;</span>
52<span class="sd">ParkFitting module contains SasParameter,Model,Data</span>
53<span class="sd">FitArrange, ParkFit,Parameter classes.All listed classes work together</span>
54<span class="sd">to perform a simple fit with park optimizer.</span>
55<span class="sd">&quot;&quot;&quot;</span>
56<span class="c">#import time</span>
57<span class="kn">import</span> <span class="nn">numpy</span>
58<span class="kn">import</span> <span class="nn">math</span>
59<span class="kn">from</span>  <span class="nn">numpy.linalg.linalg</span> <span class="kn">import</span> <span class="n">LinAlgError</span>
60<span class="c">#import park</span>
61<span class="kn">from</span> <span class="nn">park</span> <span class="kn">import</span> <span class="n">fit</span>
62<span class="kn">from</span> <span class="nn">park</span> <span class="kn">import</span> <span class="n">fitresult</span>
63<span class="kn">from</span>  <span class="nn">park.fitresult</span> <span class="kn">import</span> <span class="n">FitParameter</span>
64<span class="kn">import</span> <span class="nn">park.simplex</span>
65<span class="kn">from</span> <span class="nn">park.assembly</span> <span class="kn">import</span> <span class="n">Assembly</span>
66<span class="kn">from</span> <span class="nn">park.assembly</span> <span class="kn">import</span> <span class="n">Part</span>
67<span class="kn">from</span> <span class="nn">park.fitmc</span> <span class="kn">import</span> <span class="n">FitSimplex</span> 
68<span class="kn">import</span> <span class="nn">park.fitmc</span>
69<span class="kn">from</span> <span class="nn">park.fit</span> <span class="kn">import</span> <span class="n">Fitter</span>
70<span class="kn">from</span> <span class="nn">park.formatnum</span> <span class="kn">import</span> <span class="n">format_uncertainty</span>
71<span class="kn">from</span> <span class="nn">sas.fit.AbstractFitEngine</span> <span class="kn">import</span> <span class="n">FitEngine</span>
72<span class="kn">from</span> <span class="nn">sas.fit.AbstractFitEngine</span> <span class="kn">import</span> <span class="n">FResult</span>
73
74<span class="k">class</span> <span class="nc">SasParameter</span><span class="p">(</span><span class="n">park</span><span class="o">.</span><span class="n">Parameter</span><span class="p">):</span>
75    <span class="sd">&quot;&quot;&quot;</span>
76<span class="sd">    SAS model parameters for use in the PARK fitting service.</span>
77<div class="viewcode-block" id="SasParameter"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasParameter">[docs]</a><span class="sd">    The parameter attribute value is redirected to the underlying</span>
78<span class="sd">    parameter value in the SAS model.</span>
79<span class="sd">    &quot;&quot;&quot;</span>
80    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span>
81        <span class="sd">&quot;&quot;&quot;</span>
82<span class="sd">            :param name: the name of the model parameter</span>
83<span class="sd">            :param model: the sas model to wrap as a park model</span>
84<span class="sd">        &quot;&quot;&quot;</span>
85        <span class="n">park</span><span class="o">.</span><span class="n">Parameter</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span>
86        <span class="c">#self._model, self._name = model, name</span>
87        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">data</span>
88        <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">model</span>
89        <span class="c">#set the value for the parameter of the given name</span>
90        <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">getParam</span><span class="p">(</span><span class="n">name</span><span class="p">))</span>
91
92        <span class="c"># TODO: model is missing parameter ranges for dispersion parameters</span>
93        <span class="k">if</span> <span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">details</span><span class="p">:</span>
94            <span class="c">#print &quot;setting details for&quot;,name</span>
95            <span class="n">model</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">&quot;&quot;</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span>
96
97    <span class="k">def</span> <span class="nf">_getvalue</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
98        <span class="sd">&quot;&quot;&quot;</span>
99<span class="sd">        override the _getvalue of park parameter</span>
100
101<span class="sd">        :return value the parameter associates with self.name</span>
102
103<span class="sd">        &quot;&quot;&quot;</span>
104        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">getParam</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
105
106    <span class="k">def</span> <span class="nf">_setvalue</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
107        <span class="sd">&quot;&quot;&quot;</span>
108<span class="sd">        override the _setvalue pf park parameter</span>
109
110<span class="sd">        :param value: the value to set on a given parameter</span>
111
112<span class="sd">        &quot;&quot;&quot;</span>
113        <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
114
115    <span class="n">value</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">_getvalue</span><span class="p">,</span> <span class="n">_setvalue</span><span class="p">)</span>
116
117    <span class="k">def</span> <span class="nf">_getrange</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
118        <span class="sd">&quot;&quot;&quot;</span>
119<span class="sd">        Override _getrange of park parameter</span>
120<span class="sd">        return the range of parameter</span>
121<span class="sd">        &quot;&quot;&quot;</span>
122        <span class="c">#if not  self.name in self._model.getDispParamList():</span>
123        <span class="n">lo</span><span class="p">,</span> <span class="n">hi</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">][</span><span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">]</span>
124        <span class="k">if</span> <span class="n">lo</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> <span class="n">lo</span> <span class="o">=</span> <span class="o">-</span><span class="n">numpy</span><span class="o">.</span><span class="n">inf</span>
125        <span class="k">if</span> <span class="n">hi</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> <span class="n">hi</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">inf</span>
126        <span class="k">if</span> <span class="n">lo</span> <span class="o">&gt;</span> <span class="n">hi</span><span class="p">:</span>
127            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="s">&quot;wrong fit range for parameters&quot;</span>
128
129        <span class="k">return</span> <span class="n">lo</span><span class="p">,</span> <span class="n">hi</span>
130
131    <span class="k">def</span> <span class="nf">get_name</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
132        <span class="sd">&quot;&quot;&quot;</span>
133<span class="sd">        &quot;&quot;&quot;</span>
134<div class="viewcode-block" id="SasParameter.get_name"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasParameter.get_name">[docs]</a>        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_getname</span><span class="p">()</span>
135
136    <span class="k">def</span> <span class="nf">_setrange</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">r</span><span class="p">):</span>
137        <span class="sd">&quot;&quot;&quot;</span>
138<span class="sd">        override _setrange of park parameter</span></div>
139
140<span class="sd">        :param r: the value of the range to set</span>
141
142<span class="sd">        &quot;&quot;&quot;</span>
143        <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">][</span><span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="n">r</span>
144    <span class="nb">range</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">_getrange</span><span class="p">,</span> <span class="n">_setrange</span><span class="p">)</span>
145
146
147<span class="k">class</span> <span class="nc">ParkModel</span><span class="p">(</span><span class="n">park</span><span class="o">.</span><span class="n">Model</span><span class="p">):</span>
148    <span class="sd">&quot;&quot;&quot;</span>
149<span class="sd">    PARK wrapper for SAS models.</span></div>
150<div class="viewcode-block" id="ParkModel"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkModel">[docs]</a><span class="sd">    &quot;&quot;&quot;</span>
151    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sas_model</span><span class="p">,</span> <span class="n">sas_data</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
152        <span class="sd">&quot;&quot;&quot;</span>
153<span class="sd">        :param sas_model: the sas model to wrap using park interface</span>
154
155<span class="sd">        &quot;&quot;&quot;</span>
156        <span class="n">park</span><span class="o">.</span><span class="n">Model</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">)</span>
157        <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">sas_model</span>
158        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">sas_model</span><span class="o">.</span><span class="n">name</span>
159        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">sas_data</span>
160        <span class="c">#list of parameters names</span>
161        <span class="bp">self</span><span class="o">.</span><span class="n">sasp</span> <span class="o">=</span> <span class="n">sas_model</span><span class="o">.</span><span class="n">getParamList</span><span class="p">()</span>
162        <span class="c">#list of park parameter</span>
163        <span class="bp">self</span><span class="o">.</span><span class="n">parkp</span> <span class="o">=</span> <span class="p">[</span><span class="n">SasParameter</span><span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="n">sas_model</span><span class="p">,</span> <span class="n">sas_data</span><span class="p">)</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">sasp</span><span class="p">]</span>
164        <span class="c">#list of parameter set</span>
165        <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span> <span class="o">=</span> <span class="n">park</span><span class="o">.</span><span class="n">ParameterSet</span><span class="p">(</span><span class="n">sas_model</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">pars</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">parkp</span><span class="p">)</span>
166        <span class="bp">self</span><span class="o">.</span><span class="n">pars</span> <span class="o">=</span> <span class="p">[]</span>
167
168    <span class="k">def</span> <span class="nf">get_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fitparams</span><span class="p">):</span>
169        <span class="sd">&quot;&quot;&quot;</span>
170<span class="sd">        return a list of value of paramter to fit</span>
171<div class="viewcode-block" id="ParkModel.get_params"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkModel.get_params">[docs]</a>
172<span class="sd">        :param fitparams: list of paramaters name to fit</span>
173
174<span class="sd">        &quot;&quot;&quot;</span>
175        <span class="n">list_params</span> <span class="o">=</span> <span class="p">[]</span>
176        <span class="bp">self</span><span class="o">.</span><span class="n">pars</span> <span class="o">=</span> <span class="n">fitparams</span>
177        <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">fitparams</span><span class="p">:</span>
178            <span class="k">for</span> <span class="n">element</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parkp</span><span class="p">:</span>
179                <span class="k">if</span> <span class="n">element</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="nb">str</span><span class="p">(</span><span class="n">item</span><span class="p">):</span>
180                    <span class="n">list_params</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">element</span><span class="o">.</span><span class="n">value</span><span class="p">)</span>
181        <span class="k">return</span> <span class="n">list_params</span>
182
183    <span class="k">def</span> <span class="nf">set_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">paramlist</span><span class="p">,</span> <span class="n">params</span><span class="p">):</span>
184        <span class="sd">&quot;&quot;&quot;</span>
185<span class="sd">        Set value for parameters to fit</span></div>
186<div class="viewcode-block" id="ParkModel.set_params"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkModel.set_params">[docs]</a>
187<span class="sd">        :param params: list of value for parameters to fit</span>
188
189<span class="sd">        &quot;&quot;&quot;</span>
190        <span class="k">try</span><span class="p">:</span>
191            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parkp</span><span class="p">)):</span>
192                <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">paramlist</span><span class="p">)):</span>
193                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parkp</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">paramlist</span><span class="p">[</span><span class="n">j</span><span class="p">]:</span>
194                        <span class="bp">self</span><span class="o">.</span><span class="n">parkp</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">=</span> <span class="n">params</span><span class="p">[</span><span class="n">j</span><span class="p">]</span>
195                        <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parkp</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">params</span><span class="p">[</span><span class="n">j</span><span class="p">])</span>
196        <span class="k">except</span><span class="p">:</span>
197            <span class="k">raise</span>
198
199    <span class="k">def</span> <span class="nf">eval</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span>
200        <span class="sd">&quot;&quot;&quot;</span>
201<span class="sd">            Override eval method of park model.</span></div>
202<div class="viewcode-block" id="ParkModel.eval"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkModel.eval">[docs]</a>
203<span class="sd">            :param x: the x value used to compute a function</span>
204<span class="sd">        &quot;&quot;&quot;</span>
205        <span class="k">try</span><span class="p">:</span>
206            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">evalDistribution</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
207        <span class="k">except</span><span class="p">:</span>
208            <span class="k">raise</span>
209
210    <span class="k">def</span> <span class="nf">eval_derivs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">pars</span><span class="o">=</span><span class="p">[]):</span>
211        <span class="sd">&quot;&quot;&quot;</span>
212<span class="sd">        Evaluate the model and derivatives wrt pars at x.</span></div>
213<div class="viewcode-block" id="ParkModel.eval_derivs"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkModel.eval_derivs">[docs]</a>
214<span class="sd">        pars is a list of the names of the parameters for which derivatives</span>
215<span class="sd">        are desired.</span>
216
217<span class="sd">        This method needs to be specialized in the model to evaluate the</span>
218<span class="sd">        model function.  Alternatively, the model can implement is own</span>
219<span class="sd">        version of residuals which calculates the residuals directly</span>
220<span class="sd">        instead of calling eval.</span>
221<span class="sd">        &quot;&quot;&quot;</span>
222        <span class="k">return</span> <span class="p">[]</span>
223
224
225<span class="k">class</span> <span class="nc">SasFitResult</span><span class="p">(</span><span class="n">fitresult</span><span class="o">.</span><span class="n">FitResult</span><span class="p">):</span>
226    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwrds</span><span class="p">):</span>
227        <span class="n">fitresult</span><span class="o">.</span><span class="n">FitResult</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwrds</span><span class="p">)</span></div></div>
228<div class="viewcode-block" id="SasFitResult"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitResult">[docs]</a>        <span class="bp">self</span><span class="o">.</span><span class="n">theory</span> <span class="o">=</span> <span class="bp">None</span>
229        <span class="bp">self</span><span class="o">.</span><span class="n">inputs</span> <span class="o">=</span> <span class="p">[]</span>
230       
231<span class="k">class</span> <span class="nc">SasFitSimplex</span><span class="p">(</span><span class="n">FitSimplex</span><span class="p">):</span>
232    <span class="sd">&quot;&quot;&quot;</span>
233<span class="sd">    Local minimizer using Nelder-Mead simplex algorithm.</span></div>
234<div class="viewcode-block" id="SasFitSimplex"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitSimplex">[docs]</a>
235<span class="sd">    Simplex is robust and derivative free, though not very efficient.</span>
236
237<span class="sd">    This class wraps the bounds contrained Nelder-Mead simplex</span>
238<span class="sd">    implementation for `park.simplex.simplex`.</span>
239<span class="sd">    &quot;&quot;&quot;</span>
240    <span class="n">radius</span> <span class="o">=</span> <span class="mf">0.05</span>
241    <span class="sd">&quot;&quot;&quot;Size of the initial simplex; this is a portion between 0 and 1&quot;&quot;&quot;</span>
242    <span class="n">xtol</span> <span class="o">=</span> <span class="mi">1</span>
243    <span class="c">#xtol = 1e-4</span>
244    <span class="sd">&quot;&quot;&quot;Stop when simplex vertices are within xtol of each other&quot;&quot;&quot;</span>
245    <span class="n">ftol</span> <span class="o">=</span> <span class="mf">5e-5</span>
246    <span class="sd">&quot;&quot;&quot;Stop when vertex values are within ftol of each other&quot;&quot;&quot;</span>
247    <span class="n">maxiter</span> <span class="o">=</span> <span class="bp">None</span>
248    <span class="sd">&quot;&quot;&quot;Maximum number of iterations before fit terminates&quot;&quot;&quot;</span>
249    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ftol</span><span class="o">=</span><span class="mf">5e-5</span><span class="p">):</span>
250        <span class="bp">self</span><span class="o">.</span><span class="n">ftol</span> <span class="o">=</span> <span class="n">ftol</span>
251       
252    <span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fitness</span><span class="p">,</span> <span class="n">x0</span><span class="p">):</span>
253        <span class="sd">&quot;&quot;&quot;Run the fit&quot;&quot;&quot;</span>
254        <span class="bp">self</span><span class="o">.</span><span class="n">cancel</span> <span class="o">=</span> <span class="bp">False</span>
255<div class="viewcode-block" id="SasFitSimplex.fit"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitSimplex.fit">[docs]</a>        <span class="n">pars</span> <span class="o">=</span> <span class="n">fitness</span><span class="o">.</span><span class="n">fit_parameters</span><span class="p">()</span>
256        <span class="n">bounds</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">p</span><span class="o">.</span><span class="n">range</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pars</span><span class="p">])</span><span class="o">.</span><span class="n">T</span>
257        <span class="n">result</span> <span class="o">=</span> <span class="n">park</span><span class="o">.</span><span class="n">simplex</span><span class="o">.</span><span class="n">simplex</span><span class="p">(</span><span class="n">fitness</span><span class="p">,</span> <span class="n">x0</span><span class="p">,</span> <span class="n">bounds</span><span class="o">=</span><span class="n">bounds</span><span class="p">,</span>
258                                 <span class="n">radius</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">radius</span><span class="p">,</span> <span class="n">xtol</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">xtol</span><span class="p">,</span>
259                                 <span class="n">ftol</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">ftol</span><span class="p">,</span> <span class="n">maxiter</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">maxiter</span><span class="p">,</span>
260                                 <span class="n">abort_test</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_iscancelled</span><span class="p">)</span>
261        <span class="c">#print &quot;calls:&quot;,result.calls</span>
262        <span class="c">#print &quot;simplex returned&quot;,result.x,result.fx</span>
263        <span class="c"># Need to make our own copy of the fit results so that the</span>
264        <span class="c"># values don&#39;t get stomped on by the next fit iteration.</span>
265        <span class="n">fitpars</span> <span class="o">=</span> <span class="p">[</span><span class="n">SasFitParameter</span><span class="p">(</span><span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">name</span><span class="p">,</span><span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">range</span><span class="p">,</span><span class="n">v</span><span class="p">,</span> <span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
266                   <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">x</span><span class="p">)]</span>
267        <span class="n">res</span> <span class="o">=</span> <span class="n">SasFitResult</span><span class="p">(</span><span class="n">fitpars</span><span class="p">,</span> <span class="n">result</span><span class="o">.</span><span class="n">calls</span><span class="p">,</span> <span class="n">result</span><span class="o">.</span><span class="n">fx</span><span class="p">)</span>
268        <span class="n">res</span><span class="o">.</span><span class="n">inputs</span> <span class="o">=</span> <span class="p">[(</span><span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">data</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">x</span><span class="p">)]</span>
269        <span class="c"># Compute the parameter uncertainties from the jacobian</span>
270        <span class="n">res</span><span class="o">.</span><span class="n">calc_cov</span><span class="p">(</span><span class="n">fitness</span><span class="p">)</span>
271        <span class="k">return</span> <span class="n">res</span>
272     
273<span class="k">class</span> <span class="nc">SasFitter</span><span class="p">(</span><span class="n">Fitter</span><span class="p">):</span>
274    <span class="sd">&quot;&quot;&quot;</span>
275<span class="sd">    &quot;&quot;&quot;</span></div></div>
276<div class="viewcode-block" id="SasFitter"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitter">[docs]</a>    <span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fitness</span><span class="p">,</span> <span class="n">handler</span><span class="p">):</span>
277        <span class="sd">&quot;&quot;&quot;</span>
278<span class="sd">        Global optimizer.</span>
279<div class="viewcode-block" id="SasFitter.fit"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitter.fit">[docs]</a>
280<span class="sd">        This function should return immediately</span>
281<span class="sd">        &quot;&quot;&quot;</span>
282        <span class="c"># Determine initial value and bounds</span>
283        <span class="n">pars</span> <span class="o">=</span> <span class="n">fitness</span><span class="o">.</span><span class="n">fit_parameters</span><span class="p">()</span>
284        <span class="n">bounds</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">p</span><span class="o">.</span><span class="n">range</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pars</span><span class="p">])</span><span class="o">.</span><span class="n">T</span>
285        <span class="n">x0</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pars</span><span class="p">]</span>
286
287        <span class="c"># Initialize the monitor and results.</span>
288        <span class="c"># Need to make our own copy of the fit results so that the</span>
289        <span class="c"># values don&#39;t get stomped on by the next fit iteration.</span>
290        <span class="n">handler</span><span class="o">.</span><span class="n">done</span> <span class="o">=</span> <span class="bp">False</span>
291        <span class="bp">self</span><span class="o">.</span><span class="n">handler</span> <span class="o">=</span> <span class="n">handler</span>
292        <span class="n">fitpars</span> <span class="o">=</span> <span class="p">[</span><span class="n">SasFitParameter</span><span class="p">(</span><span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">range</span><span class="p">,</span> <span class="n">v</span><span class="p">,</span>
293                                     <span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">pars</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
294                   <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">x0</span><span class="p">)]</span>
295        <span class="n">handler</span><span class="o">.</span><span class="n">result</span> <span class="o">=</span> <span class="n">fitresult</span><span class="o">.</span><span class="n">FitResult</span><span class="p">(</span><span class="n">fitpars</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">numpy</span><span class="o">.</span><span class="n">NaN</span><span class="p">)</span>
296
297        <span class="c"># Run the fit (fit should perform _progress and _improvement updates)</span>
298        <span class="c"># This function may return before the fit is complete.</span>
299        <span class="bp">self</span><span class="o">.</span><span class="n">_fit</span><span class="p">(</span><span class="n">fitness</span><span class="p">,</span> <span class="n">x0</span><span class="p">,</span> <span class="n">bounds</span><span class="p">)</span>
300       
301<span class="k">class</span> <span class="nc">SasFitMC</span><span class="p">(</span><span class="n">SasFitter</span><span class="p">):</span>
302    <span class="sd">&quot;&quot;&quot;</span>
303<span class="sd">    Monte Carlo optimizer.</span></div></div>
304<div class="viewcode-block" id="SasFitMC"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitMC">[docs]</a>
305<span class="sd">    This implements `park.fit.Fitter`.</span>
306<span class="sd">    &quot;&quot;&quot;</span>
307    <span class="n">localfit</span> <span class="o">=</span> <span class="n">SasFitSimplex</span><span class="p">()</span>
308    <span class="n">start_points</span> <span class="o">=</span> <span class="mi">10</span>
309    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">localfit</span><span class="p">,</span> <span class="n">start_points</span><span class="o">=</span><span class="mi">10</span><span class="p">):</span>
310        <span class="bp">self</span><span class="o">.</span><span class="n">localfit</span> <span class="o">=</span> <span class="n">localfit</span>
311        <span class="bp">self</span><span class="o">.</span><span class="n">start_points</span> <span class="o">=</span> <span class="n">start_points</span>
312       
313    <span class="k">def</span> <span class="nf">_fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">objective</span><span class="p">,</span> <span class="n">x0</span><span class="p">,</span> <span class="n">bounds</span><span class="p">):</span>
314        <span class="sd">&quot;&quot;&quot;</span>
315<span class="sd">        Run a monte carlo fit.</span>
316
317<span class="sd">        This procedure maps a local optimizer across a set of initial points.</span>
318<span class="sd">        &quot;&quot;&quot;</span>
319        <span class="k">try</span><span class="p">:</span>
320            <span class="n">park</span><span class="o">.</span><span class="n">fitmc</span><span class="o">.</span><span class="n">fitmc</span><span class="p">(</span><span class="n">objective</span><span class="p">,</span> <span class="n">x0</span><span class="p">,</span> <span class="n">bounds</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">localfit</span><span class="p">,</span>
321                             <span class="bp">self</span><span class="o">.</span><span class="n">start_points</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="p">)</span>
322        <span class="k">except</span><span class="p">:</span>
323            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="s">&quot;Fit did not converge.</span><span class="se">\n</span><span class="s">&quot;</span>
324       
325<span class="k">class</span> <span class="nc">SasPart</span><span class="p">(</span><span class="n">Part</span><span class="p">):</span>
326    <span class="sd">&quot;&quot;&quot;</span>
327<span class="sd">    Part of a fitting assembly.  Part holds the model itself and</span></div>
328<div class="viewcode-block" id="SasPart"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasPart">[docs]</a><span class="sd">    associated data.  The part can be initialized with a fitness</span>
329<span class="sd">    object or with a pair (model,data) for the default fitness function.</span>
330
331<span class="sd">    fitness (Fitness)</span>
332<span class="sd">        object implementing the `park.assembly.Fitness` interface.  In</span>
333<span class="sd">        particular, fitness should provide a parameterset attribute</span>
334<span class="sd">        containing a ParameterSet and a residuals method returning a vector</span>
335<span class="sd">        of residuals.</span>
336<span class="sd">    weight (dimensionless)</span>
337<span class="sd">        weight for the model.  See comments in assembly.py for details.</span>
338<span class="sd">    isfitted (boolean)</span>
339<span class="sd">        True if the model residuals should be included in the fit.</span>
340<span class="sd">        The model parameters may still be used in parameter</span>
341<span class="sd">        expressions, but there will be no comparison to the data.</span>
342<span class="sd">    residuals (vector)</span>
343<span class="sd">        Residuals for the model if they have been calculated, or None</span>
344<span class="sd">    degrees_of_freedom</span>
345<span class="sd">        Number of residuals minus number of fitted parameters.</span>
346<span class="sd">        Degrees of freedom for individual models does not make</span>
347<span class="sd">        sense in the presence of expressions combining models,</span>
348<span class="sd">        particularly in the case where a model has many parameters</span>
349<span class="sd">        but no data or many computed parameters.  The degrees of</span>
350<span class="sd">        freedom for the model is set to be at least one.</span>
351<span class="sd">    chisq</span>
352<span class="sd">        sum(residuals**2); use chisq/degrees_of_freedom to</span>
353<span class="sd">        get the reduced chisq value.</span>
354
355<span class="sd">        Get/set the weight on the given model.</span>
356
357<span class="sd">        assembly.weight(3) returns the weight on model 3 (0-origin)</span>
358<span class="sd">        assembly.weight(3,0.5) sets the weight on model 3 (0-origin)</span>
359<span class="sd">    &quot;&quot;&quot;</span>
360
361    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fitness</span><span class="p">,</span> <span class="n">weight</span><span class="o">=</span><span class="mf">1.</span><span class="p">,</span> <span class="n">isfitted</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
362        <span class="n">Part</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fitness</span><span class="o">=</span><span class="n">fitness</span><span class="p">,</span> <span class="n">weight</span><span class="o">=</span><span class="n">weight</span><span class="p">,</span>
363                       <span class="n">isfitted</span><span class="o">=</span><span class="n">isfitted</span><span class="p">)</span>
364       
365        <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">fitness</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">fitness</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
366
367<span class="k">class</span> <span class="nc">SasFitParameter</span><span class="p">(</span><span class="n">FitParameter</span><span class="p">):</span>
368    <span class="sd">&quot;&quot;&quot;</span>
369<span class="sd">    Fit result for an individual parameter.</span></div>
370<div class="viewcode-block" id="SasFitParameter"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitParameter">[docs]</a><span class="sd">    &quot;&quot;&quot;</span>
371    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="nb">range</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span>
372        <span class="n">FitParameter</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="nb">range</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
373        <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">model</span>
374        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">data</span>
375       
376    <span class="k">def</span> <span class="nf">summarize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
377        <span class="sd">&quot;&quot;&quot;</span>
378<span class="sd">        Return parameter range string.</span>
379<div class="viewcode-block" id="SasFitParameter.summarize"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.SasFitParameter.summarize">[docs]</a>
380<span class="sd">        E.g.,  &quot;       Gold .....|.... 5.2043 in [2,7]&quot;</span>
381<span class="sd">        &quot;&quot;&quot;</span>
382        <span class="n">bar</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;.&#39;</span><span class="p">]</span><span class="o">*</span><span class="mi">10</span>
383        <span class="n">lo</span><span class="p">,</span><span class="n">hi</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">range</span>
384        <span class="k">if</span> <span class="n">numpy</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">lo</span><span class="p">)</span><span class="ow">and</span> <span class="n">numpy</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">hi</span><span class="p">):</span>
385            <span class="n">portion</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">value</span><span class="o">-</span><span class="n">lo</span><span class="p">)</span><span class="o">/</span><span class="p">(</span><span class="n">hi</span><span class="o">-</span><span class="n">lo</span><span class="p">)</span>
386            <span class="k">if</span> <span class="n">portion</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">:</span> <span class="n">portion</span> <span class="o">=</span> <span class="mf">0.</span>
387            <span class="k">elif</span> <span class="n">portion</span> <span class="o">&gt;=</span> <span class="mi">1</span><span class="p">:</span> <span class="n">portion</span> <span class="o">=</span> <span class="mf">0.99999999</span>
388            <span class="n">barpos</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">math</span><span class="o">.</span><span class="n">floor</span><span class="p">(</span><span class="n">portion</span><span class="o">*</span><span class="nb">len</span><span class="p">(</span><span class="n">bar</span><span class="p">)))</span>
389            <span class="n">bar</span><span class="p">[</span><span class="n">barpos</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;|&#39;</span>
390        <span class="n">bar</span> <span class="o">=</span> <span class="s">&quot;&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">bar</span><span class="p">)</span>
391        <span class="n">lostr</span> <span class="o">=</span> <span class="s">&quot;[</span><span class="si">%g</span><span class="s">&quot;</span><span class="o">%</span><span class="n">lo</span> <span class="k">if</span> <span class="n">numpy</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">lo</span><span class="p">)</span> <span class="k">else</span> <span class="s">&quot;(-inf&quot;</span>
392        <span class="n">histr</span> <span class="o">=</span> <span class="s">&quot;</span><span class="si">%g</span><span class="s">]&quot;</span><span class="o">%</span><span class="n">hi</span> <span class="k">if</span> <span class="n">numpy</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">hi</span><span class="p">)</span> <span class="k">else</span> <span class="s">&quot;inf)&quot;</span>
393        <span class="n">valstr</span> <span class="o">=</span> <span class="n">format_uncertainty</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">value</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">stderr</span><span class="p">)</span>
394        <span class="n">model_name</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="bp">None</span><span class="p">)</span>
395        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
396            <span class="n">model_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">name</span>
397        <span class="n">data_name</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="bp">None</span><span class="p">)</span>
398        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
399            <span class="n">data_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">name</span>
400           
401        <span class="k">return</span> <span class="s">&quot;</span><span class="si">%25s</span><span class="s"> </span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s"> in </span><span class="si">%s</span><span class="s">,</span><span class="si">%s</span><span class="s">, </span><span class="si">%s</span><span class="s">, </span><span class="si">%s</span><span class="s">&quot;</span>  <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span><span class="n">bar</span><span class="p">,</span><span class="n">valstr</span><span class="p">,</span><span class="n">lostr</span><span class="p">,</span><span class="n">histr</span><span class="p">,</span> 
402                                                 <span class="n">model_name</span><span class="p">,</span> <span class="n">data_name</span><span class="p">)</span>
403    <span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
404        <span class="c">#return &quot;FitParameter(&#39;%s&#39;)&quot;%self.name</span>
405        <span class="k">return</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">)</span></div>
406   
407<span class="k">class</span> <span class="nc">MyAssembly</span><span class="p">(</span><span class="n">Assembly</span><span class="p">):</span>
408    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">models</span><span class="p">,</span> <span class="n">curr_thread</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
409        <span class="sd">&quot;&quot;&quot;Build an assembly from a list of models.&quot;&quot;&quot;</span></div>
410<div class="viewcode-block" id="MyAssembly"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.MyAssembly">[docs]</a>        <span class="bp">self</span><span class="o">.</span><span class="n">parts</span> <span class="o">=</span> <span class="p">[]</span>
411        <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">models</span><span class="p">:</span>
412            <span class="bp">self</span><span class="o">.</span><span class="n">parts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">SasPart</span><span class="p">(</span><span class="n">m</span><span class="p">))</span>
413        <span class="bp">self</span><span class="o">.</span><span class="n">curr_thread</span> <span class="o">=</span> <span class="n">curr_thread</span>
414        <span class="bp">self</span><span class="o">.</span><span class="n">chisq</span> <span class="o">=</span> <span class="bp">None</span>
415        <span class="bp">self</span><span class="o">.</span><span class="n">_cancel</span> <span class="o">=</span> <span class="bp">False</span>
416        <span class="bp">self</span><span class="o">.</span><span class="n">theory</span> <span class="o">=</span> <span class="bp">None</span>
417        <span class="bp">self</span><span class="o">.</span><span class="n">_reset</span><span class="p">()</span>
418       
419    <span class="k">def</span> <span class="nf">fit_parameters</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
420        <span class="sd">&quot;&quot;&quot;</span>
421<span class="sd">        Return an alphabetical list of the fitting parameters.</span>
422<div class="viewcode-block" id="MyAssembly.fit_parameters"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.MyAssembly.fit_parameters">[docs]</a>
423<span class="sd">        This function is called once at the beginning of a fit,</span>
424<span class="sd">        and serves as a convenient place to precalculate what</span>
425<span class="sd">        can be precalculated such as the set of fitting parameters</span>
426<span class="sd">        and the parameter expressions evaluator.</span>
427<span class="sd">        &quot;&quot;&quot;</span>
428        <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">setprefix</span><span class="p">()</span>
429        <span class="bp">self</span><span class="o">.</span><span class="n">_fitparameters</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">fitted</span>
430        <span class="bp">self</span><span class="o">.</span><span class="n">_restraints</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">restrained</span>
431        <span class="n">pars</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">flatten</span><span class="p">()</span>
432        <span class="n">context</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">gather_context</span><span class="p">()</span>
433        <span class="bp">self</span><span class="o">.</span><span class="n">_fitexpression</span> <span class="o">=</span> <span class="n">park</span><span class="o">.</span><span class="n">expression</span><span class="o">.</span><span class="n">build_eval</span><span class="p">(</span><span class="n">pars</span><span class="p">,</span><span class="n">context</span><span class="p">)</span>
434        <span class="c">#print &quot;constraints&quot;,self._fitexpression.__doc__</span>
435
436        <span class="bp">self</span><span class="o">.</span><span class="n">_fitparameters</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="k">lambda</span> <span class="n">a</span><span class="p">,</span><span class="n">b</span><span class="p">:</span> <span class="nb">cmp</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">path</span><span class="p">,</span><span class="n">b</span><span class="o">.</span><span class="n">path</span><span class="p">))</span>
437        <span class="c"># Convert to fitparameter a object</span>
438       
439        <span class="n">fitpars</span> <span class="o">=</span> <span class="p">[</span><span class="n">SasFitParameter</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">path</span><span class="p">,</span><span class="n">p</span><span class="o">.</span><span class="n">range</span><span class="p">,</span><span class="n">p</span><span class="o">.</span><span class="n">value</span><span class="p">,</span> <span class="n">p</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">p</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
440                   <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_fitparameters</span><span class="p">]</span>
441        <span class="c">#print &quot;fitpars&quot;, fitpars</span>
442        <span class="k">return</span> <span class="n">fitpars</span>
443   
444    <span class="k">def</span> <span class="nf">extend_results_with_calculated_parameters</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">result</span><span class="p">):</span>
445        <span class="sd">&quot;&quot;&quot;</span>
446<span class="sd">        Extend result from the fit with the calculated parameters.</span></div>
447<div class="viewcode-block" id="MyAssembly.extend_results_with_calculated_parameters"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.MyAssembly.extend_results_with_calculated_parameters">[docs]</a><span class="sd">        &quot;&quot;&quot;</span>
448        <span class="n">calcpars</span> <span class="o">=</span> <span class="p">[</span><span class="n">SasFitParameter</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">path</span><span class="p">,</span><span class="n">p</span><span class="o">.</span><span class="n">range</span><span class="p">,</span><span class="n">p</span><span class="o">.</span><span class="n">value</span><span class="p">,</span> <span class="n">p</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">p</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
449                    <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">computed</span><span class="p">]</span>
450        <span class="n">result</span><span class="o">.</span><span class="n">parameters</span> <span class="o">+=</span> <span class="n">calcpars</span>
451        <span class="n">result</span><span class="o">.</span><span class="n">theory</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">theory</span>
452
453    <span class="k">def</span> <span class="nf">eval</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
454        <span class="sd">&quot;&quot;&quot;</span>
455<span class="sd">        Recalculate the theory functions, and from them, the</span></div>
456<div class="viewcode-block" id="MyAssembly.eval"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.MyAssembly.eval">[docs]</a><span class="sd">        residuals and chisq.</span>
457
458<span class="sd">        :note: Call this after the parameters have been updated.</span>
459<span class="sd">        &quot;&quot;&quot;</span>
460        <span class="c"># Handle abort from a separate thread.</span>
461        <span class="bp">self</span><span class="o">.</span><span class="n">_cancel</span> <span class="o">=</span> <span class="bp">False</span>
462        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">curr_thread</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span>
463            <span class="k">try</span><span class="p">:</span>
464                <span class="bp">self</span><span class="o">.</span><span class="n">curr_thread</span><span class="o">.</span><span class="n">isquit</span><span class="p">()</span>
465            <span class="k">except</span><span class="p">:</span>
466                <span class="bp">self</span><span class="o">.</span><span class="n">_cancel</span> <span class="o">=</span> <span class="bp">True</span>
467
468        <span class="c"># Evaluate the computed parameters</span>
469        <span class="k">try</span><span class="p">:</span>
470            <span class="bp">self</span><span class="o">.</span><span class="n">_fitexpression</span><span class="p">()</span>
471        <span class="k">except</span> <span class="ne">NameError</span><span class="p">:</span>
472            <span class="k">pass</span>
473
474        <span class="c"># Check that the resulting parameters are in a feasible region.</span>
475        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">isfeasible</span><span class="p">():</span> <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">inf</span>
476
477        <span class="n">resid</span> <span class="o">=</span> <span class="p">[]</span>
478        <span class="n">k</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_fitparameters</span><span class="p">)</span>
479        <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parts</span><span class="p">:</span>
480            <span class="c"># In order to support abort, need to be able to propagate an</span>
481            <span class="c"># external abort signal from self.abort() into an abort signal</span>
482            <span class="c"># for the particular model.  Can&#39;t see a way to do this which</span>
483            <span class="c"># doesn&#39;t involve setting a state variable.</span>
484            <span class="bp">self</span><span class="o">.</span><span class="n">_current_model</span> <span class="o">=</span> <span class="n">m</span>
485            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_cancel</span><span class="p">:</span> <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">inf</span>
486            <span class="k">if</span> <span class="n">m</span><span class="o">.</span><span class="n">isfitted</span> <span class="ow">and</span> <span class="n">m</span><span class="o">.</span><span class="n">weight</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
487                <span class="n">m</span><span class="o">.</span><span class="n">residuals</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">theory</span> <span class="o">=</span> <span class="n">m</span><span class="o">.</span><span class="n">fitness</span><span class="o">.</span><span class="n">residuals</span><span class="p">()</span>
488                <span class="n">N</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">residuals</span><span class="p">)</span>
489                <span class="n">m</span><span class="o">.</span><span class="n">degrees_of_freedom</span> <span class="o">=</span> <span class="n">N</span><span class="o">-</span><span class="n">k</span> <span class="k">if</span> <span class="n">N</span><span class="o">&gt;</span><span class="n">k</span> <span class="k">else</span> <span class="mi">1</span>
490                <span class="c"># dividing residuals by N in order to be consistent with Scipy</span>
491                <span class="n">m</span><span class="o">.</span><span class="n">chisq</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">residuals</span><span class="o">**</span><span class="mi">2</span><span class="o">/</span><span class="n">N</span><span class="p">)</span> 
492                <span class="n">resid</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">weight</span><span class="o">*</span><span class="n">m</span><span class="o">.</span><span class="n">residuals</span><span class="p">)</span>
493        <span class="bp">self</span><span class="o">.</span><span class="n">residuals</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">hstack</span><span class="p">(</span><span class="n">resid</span><span class="p">)</span>
494        <span class="n">N</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">residuals</span><span class="p">)</span>
495        <span class="bp">self</span><span class="o">.</span><span class="n">degrees_of_freedom</span> <span class="o">=</span> <span class="n">N</span><span class="o">-</span><span class="n">k</span> <span class="k">if</span> <span class="n">N</span><span class="o">&gt;</span><span class="n">k</span> <span class="k">else</span> <span class="mi">1</span>
496        <span class="bp">self</span><span class="o">.</span><span class="n">chisq</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">residuals</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span>
497        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">chisq</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">degrees_of_freedom</span>
498   
499<span class="k">class</span> <span class="nc">ParkFit</span><span class="p">(</span><span class="n">FitEngine</span><span class="p">):</span>
500    <span class="sd">&quot;&quot;&quot; </span>
501<span class="sd">    ParkFit performs the Fit.This class can be used as follow:</span></div></div>
502<div class="viewcode-block" id="ParkFit"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkFit">[docs]</a><span class="sd">    #Do the fit Park</span>
503<span class="sd">    create an engine: engine = ParkFit()</span>
504<span class="sd">    Use data must be of type plottable</span>
505<span class="sd">    Use a sas model</span>
506<span class="sd">    </span>
507<span class="sd">    Add data with a dictionnary of FitArrangeList where Uid is a key and data</span>
508<span class="sd">    is saved in FitArrange object.</span>
509<span class="sd">    engine.set_data(data,Uid)</span>
510<span class="sd">    </span>
511<span class="sd">    Set model parameter &quot;M1&quot;= model.name add {model.parameter.name:value}.</span>
512<span class="sd">    </span>
513<span class="sd">    ..note::</span>
514
515<span class="sd">       Set_param() if used must always preceded set_model() for the fit to be performed. ``engine.set_param( model,&quot;M1&quot;, {&#39;A&#39;:2,&#39;B&#39;:4})``</span>
516<span class="sd">    </span>
517<span class="sd">    Add model with a dictionnary of FitArrangeList{} where Uid is a key</span>
518<span class="sd">    and model</span>
519<span class="sd">    is save in FitArrange object.</span>
520<span class="sd">    engine.set_model(model,Uid)</span>
521<span class="sd">    </span>
522<span class="sd">    engine.fit return chisqr,[model.parameter 1,2,..],[[err1....][..err2...]]</span>
523<span class="sd">    chisqr1, out1, cov1=engine.fit({model.parameter.name:value},qmin,qmax)</span>
524<span class="sd">    </span>
525<span class="sd">    ..note::</span>
526
527<span class="sd">        {model.parameter.name:value} is ignored in fit function since </span>
528<span class="sd">        the user should make sure to call set_param himself.</span>
529<span class="sd">        </span>
530<span class="sd">    &quot;&quot;&quot;</span>
531    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
532        <span class="sd">&quot;&quot;&quot;</span>
533<span class="sd">        Creates a dictionary (self.fitArrangeList={})of FitArrange elements</span>
534<span class="sd">        with Uid as keys</span>
535<span class="sd">        &quot;&quot;&quot;</span>
536        <span class="n">FitEngine</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
537        <span class="bp">self</span><span class="o">.</span><span class="n">fit_arrange_dict</span> <span class="o">=</span> <span class="p">{}</span>
538        <span class="bp">self</span><span class="o">.</span><span class="n">param_list</span> <span class="o">=</span> <span class="p">[]</span>
539       
540    <span class="k">def</span> <span class="nf">create_assembly</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">curr_thread</span><span class="p">,</span> <span class="n">reset_flag</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
541        <span class="sd">&quot;&quot;&quot;</span>
542<span class="sd">        Extract sasmodel and sasdata from </span>
543<div class="viewcode-block" id="ParkFit.create_assembly"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkFit.create_assembly">[docs]</a><span class="sd">        self.FitArrangelist ={Uid:FitArrange}</span>
544<span class="sd">        Create parkmodel and park data ,form a list couple of parkmodel </span>
545<span class="sd">        and parkdata</span>
546<span class="sd">        create an assembly self.problem=  park.Assembly([(parkmodel,parkdata)])</span>
547<span class="sd">        &quot;&quot;&quot;</span>
548        <span class="n">mylist</span> <span class="o">=</span> <span class="p">[]</span>
549        <span class="c">#listmodel = []</span>
550        <span class="c">#i = 0</span>
551        <span class="n">fitproblems</span> <span class="o">=</span> <span class="p">[]</span>
552        <span class="k">for</span> <span class="n">fproblem</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">fit_arrange_dict</span><span class="o">.</span><span class="n">itervalues</span><span class="p">():</span>
553            <span class="k">if</span> <span class="n">fproblem</span><span class="o">.</span><span class="n">get_to_fit</span><span class="p">()</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
554                <span class="n">fitproblems</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">fproblem</span><span class="p">)</span>
555        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">fitproblems</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
556            <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="s">&quot;No Assembly scheduled for Park fitting.&quot;</span>
557        <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">fitproblems</span><span class="p">:</span>
558            <span class="n">model</span> <span class="o">=</span> <span class="n">item</span><span class="o">.</span><span class="n">get_model</span><span class="p">()</span>
559            <span class="n">parkmodel</span> <span class="o">=</span> <span class="n">ParkModel</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">model</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
560            <span class="n">parkmodel</span><span class="o">.</span><span class="n">pars</span> <span class="o">=</span> <span class="n">item</span><span class="o">.</span><span class="n">pars</span>
561            <span class="k">if</span> <span class="n">reset_flag</span><span class="p">:</span>
562                <span class="c"># reset the initial value; useful for batch</span>
563                <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">item</span><span class="o">.</span><span class="n">pars</span><span class="p">:</span>
564                    <span class="n">ind</span> <span class="o">=</span> <span class="n">item</span><span class="o">.</span><span class="n">pars</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
565                    <span class="n">parkmodel</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">item</span><span class="o">.</span><span class="n">vals</span><span class="p">[</span><span class="n">ind</span><span class="p">])</span>
566
567            <span class="c"># set the constraints into the model</span>
568            <span class="k">for</span> <span class="n">p</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="n">item</span><span class="o">.</span><span class="n">constraints</span><span class="p">:</span>
569                <span class="n">parkmodel</span><span class="o">.</span><span class="n">parameterset</span><span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">p</span><span class="p">)]</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">v</span><span class="p">))</span>
570           
571            <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">parkmodel</span><span class="o">.</span><span class="n">parameterset</span><span class="p">:</span>
572                <span class="c">## does not allow status change for constraint parameters</span>
573                <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">status</span> <span class="o">!=</span> <span class="s">&#39;computed&#39;</span><span class="p">:</span>
574                    <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">get_name</span><span class="p">()</span> <span class="ow">in</span> <span class="n">item</span><span class="o">.</span><span class="n">pars</span><span class="p">:</span>
575                        <span class="c">## make parameters selected for </span>
576                        <span class="c">#fit will be between boundaries</span>
577                        <span class="n">p</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">range</span><span class="p">)</span>         
578                    <span class="k">else</span><span class="p">:</span>
579                        <span class="n">p</span><span class="o">.</span><span class="n">status</span> <span class="o">=</span> <span class="s">&#39;fixed&#39;</span>
580            <span class="n">data_list</span> <span class="o">=</span> <span class="n">item</span><span class="o">.</span><span class="n">get_data</span><span class="p">()</span>
581            <span class="n">parkdata</span> <span class="o">=</span> <span class="n">data_list</span>
582            <span class="n">fitness</span> <span class="o">=</span> <span class="p">(</span><span class="n">parkmodel</span><span class="p">,</span> <span class="n">parkdata</span><span class="p">)</span>
583            <span class="n">mylist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">fitness</span><span class="p">)</span>
584        <span class="bp">self</span><span class="o">.</span><span class="n">problem</span> <span class="o">=</span> <span class="n">MyAssembly</span><span class="p">(</span><span class="n">models</span><span class="o">=</span><span class="n">mylist</span><span class="p">,</span> <span class="n">curr_thread</span><span class="o">=</span><span class="n">curr_thread</span><span class="p">)</span>
585       
586 
587    <span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">msg_q</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> 
588            <span class="n">q</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">handler</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">curr_thread</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> 
589            <span class="n">ftol</span><span class="o">=</span><span class="mf">1.49012e-8</span><span class="p">,</span> <span class="n">reset_flag</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span></div>
590<div class="viewcode-block" id="ParkFit.fit"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.ParkFitting.ParkFit.fit">[docs]</a>        <span class="sd">&quot;&quot;&quot;</span>
591<span class="sd">        Performs fit with park.fit module.It can  perform fit with one model</span>
592<span class="sd">        and a set of data, more than two fit of  one model and sets of data or </span>
593<span class="sd">        fit with more than two model associated with their set of data and </span>
594<span class="sd">        constraints</span>
595<span class="sd">        </span>
596<span class="sd">        :param pars: Dictionary of parameter names for the model and their </span>
597<span class="sd">            values.</span>
598<span class="sd">        :param qmin: The minimum value of data&#39;s range to be fit</span>
599<span class="sd">        :param qmax: The maximum value of data&#39;s range to be fit</span>
600<span class="sd">        </span>
601<span class="sd">        :note: all parameter are ignored most of the time.Are just there </span>
602<span class="sd">            to keep ScipyFit and ParkFit interface the same.</span>
603<span class="sd">            </span>
604<span class="sd">        :return: result.fitness Value of the goodness of fit metric</span>
605<span class="sd">        :return: result.pvec list of parameter with the best value </span>
606<span class="sd">            found during fitting</span>
607<span class="sd">        :return: result.cov Covariance matrix</span>
608<span class="sd">        </span>
609<span class="sd">        &quot;&quot;&quot;</span>
610        <span class="bp">self</span><span class="o">.</span><span class="n">create_assembly</span><span class="p">(</span><span class="n">curr_thread</span><span class="o">=</span><span class="n">curr_thread</span><span class="p">,</span> <span class="n">reset_flag</span><span class="o">=</span><span class="n">reset_flag</span><span class="p">)</span>
611        <span class="n">localfit</span> <span class="o">=</span> <span class="n">SasFitSimplex</span><span class="p">()</span>
612        <span class="n">localfit</span><span class="o">.</span><span class="n">ftol</span> <span class="o">=</span> <span class="n">ftol</span>
613        <span class="n">localfit</span><span class="o">.</span><span class="n">xtol</span> <span class="o">=</span> <span class="mf">1e-6</span>
614
615        <span class="c"># See `park.fitresult.FitHandler` for details.</span>
616        <span class="n">fitter</span> <span class="o">=</span> <span class="n">SasFitMC</span><span class="p">(</span><span class="n">localfit</span><span class="o">=</span><span class="n">localfit</span><span class="p">,</span> <span class="n">start_points</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
617        <span class="k">if</span> <span class="n">handler</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
618            <span class="n">handler</span> <span class="o">=</span> <span class="n">fitresult</span><span class="o">.</span><span class="n">ConsoleUpdate</span><span class="p">(</span><span class="n">improvement_delta</span><span class="o">=</span><span class="mf">0.1</span><span class="p">)</span>
619       
620        <span class="n">result_list</span> <span class="o">=</span> <span class="p">[]</span>
621        <span class="k">try</span><span class="p">:</span>
622            <span class="n">result</span> <span class="o">=</span> <span class="n">fit</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">problem</span><span class="p">,</span> <span class="n">fitter</span><span class="o">=</span><span class="n">fitter</span><span class="p">,</span> <span class="n">handler</span><span class="o">=</span><span class="n">handler</span><span class="p">)</span>
623            <span class="bp">self</span><span class="o">.</span><span class="n">problem</span><span class="o">.</span><span class="n">extend_results_with_calculated_parameters</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
624           
625        <span class="k">except</span> <span class="n">LinAlgError</span><span class="p">:</span>
626            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="s">&quot;SVD did not converge&quot;</span>
627
628        <span class="k">if</span> <span class="n">result</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
629            <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">&quot;park did not return a fit result&quot;</span><span class="p">)</span>
630   
631        <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">problem</span><span class="o">.</span><span class="n">parts</span><span class="p">:</span>
632            <span class="n">residuals</span><span class="p">,</span> <span class="n">theory</span> <span class="o">=</span> <span class="n">m</span><span class="o">.</span><span class="n">fitness</span><span class="o">.</span><span class="n">residuals</span><span class="p">()</span>
633            <span class="n">small_result</span> <span class="o">=</span> <span class="n">FResult</span><span class="p">(</span><span class="n">model</span><span class="o">=</span><span class="n">m</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">m</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">sas_data</span><span class="p">)</span>
634            <span class="n">small_result</span><span class="o">.</span><span class="n">fitter_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">fitter_id</span>
635            <span class="n">small_result</span><span class="o">.</span><span class="n">theory</span> <span class="o">=</span> <span class="n">theory</span>
636            <span class="n">small_result</span><span class="o">.</span><span class="n">residuals</span> <span class="o">=</span> <span class="n">residuals</span>
637            <span class="n">small_result</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">m</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">idx</span>
638            <span class="n">small_result</span><span class="o">.</span><span class="n">fitness</span> <span class="o">=</span> <span class="n">result</span><span class="o">.</span><span class="n">fitness</span>
639
640            <span class="c"># Extract the parameters that are part of this model; make sure</span>
641            <span class="c"># they match the fitted parameters for this model, and place them</span>
642            <span class="c"># in the same order as they occur in the model.</span>
643            <span class="n">pars</span> <span class="o">=</span> <span class="p">{}</span>
644            <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">result</span><span class="o">.</span><span class="n">parameters</span><span class="p">:</span>
645                <span class="c">#if p.data.name == small_result.data.name and</span>
646                <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">small_result</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">name</span><span class="p">:</span>
647                    <span class="n">model_name</span><span class="p">,</span> <span class="n">par_name</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;.&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
648                    <span class="n">pars</span><span class="p">[</span><span class="n">par_name</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">p</span><span class="o">.</span><span class="n">value</span><span class="p">,</span> <span class="n">p</span><span class="o">.</span><span class="n">stderr</span><span class="p">)</span>
649            <span class="c">#assert len(pars.keys()) == len(m.model.pars)</span>
650            <span class="n">v</span><span class="p">,</span><span class="n">dv</span> <span class="o">=</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span><span class="n">pars</span><span class="p">[</span><span class="n">p</span><span class="p">]</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">m</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">pars</span><span class="p">])</span>
651            <span class="n">small_result</span><span class="o">.</span><span class="n">pvec</span> <span class="o">=</span> <span class="n">v</span>
652            <span class="n">small_result</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="n">dv</span>
653            <span class="n">small_result</span><span class="o">.</span><span class="n">param_list</span> <span class="o">=</span> <span class="n">m</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">pars</span>
654
655            <span class="c"># normalize chisq by degrees of freedom</span>
656            <span class="n">dof</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">small_result</span><span class="o">.</span><span class="n">residuals</span><span class="p">)</span><span class="o">-</span><span class="nb">len</span><span class="p">(</span><span class="n">small_result</span><span class="o">.</span><span class="n">pvec</span><span class="p">)</span>
657            <span class="n">small_result</span><span class="o">.</span><span class="n">fitness</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">residuals</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span><span class="o">/</span><span class="n">dof</span>
658
659            <span class="n">result_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">small_result</span><span class="p">)</span>   
660        <span class="k">if</span> <span class="n">q</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span>
661            <span class="n">q</span><span class="o">.</span><span class="n">put</span><span class="p">(</span><span class="n">result_list</span><span class="p">)</span>
662            <span class="k">return</span> <span class="n">q</span>
663        <span class="k">return</span> <span class="n">result_list</span>
664       
665</pre></div></div></div>
666
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