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50  <h1>Source code for sas.fit.BumpsFitting</h1><div class="highlight"><pre>
51<span class="sd">&quot;&quot;&quot;</span>
52<span class="sd">BumpsFitting module runs the bumps optimizer.</span>
53<span class="sd">&quot;&quot;&quot;</span>
54<span class="kn">import</span> <span class="nn">os</span>
55<span class="kn">from</span> <span class="nn">datetime</span> <span class="kn">import</span> <span class="n">timedelta</span><span class="p">,</span> <span class="n">datetime</span>
56
57<span class="kn">import</span> <span class="nn">numpy</span>
58
59<span class="kn">from</span> <span class="nn">bumps</span> <span class="kn">import</span> <span class="n">fitters</span>
60<span class="kn">from</span> <span class="nn">bumps.mapper</span> <span class="kn">import</span> <span class="n">SerialMapper</span><span class="p">,</span> <span class="n">MPMapper</span>
61<span class="kn">from</span> <span class="nn">bumps</span> <span class="kn">import</span> <span class="n">parameter</span>
62<span class="kn">from</span> <span class="nn">bumps.fitproblem</span> <span class="kn">import</span> <span class="n">FitProblem</span>
63
64<span class="kn">from</span> <span class="nn">sas.fit.AbstractFitEngine</span> <span class="kn">import</span> <span class="n">FitEngine</span>
65<span class="kn">from</span> <span class="nn">sas.fit.AbstractFitEngine</span> <span class="kn">import</span> <span class="n">FResult</span>
66<span class="kn">from</span> <span class="nn">sas.fit.expression</span> <span class="kn">import</span> <span class="n">compile_constraints</span>
67
68<div class="viewcode-block" id="Progress"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.Progress">[docs]</a><span class="k">class</span> <span class="nc">Progress</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
69    <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">history</span><span class="p">,</span> <span class="n">max_step</span><span class="p">,</span> <span class="n">pars</span><span class="p">,</span> <span class="n">dof</span><span class="p">):</span>
70        <span class="n">remaining_time</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">history</span><span class="o">.</span><span class="n">time</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">max_step</span><span class="p">)</span><span class="o">/</span><span class="n">history</span><span class="o">.</span><span class="n">step</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span>
71        <span class="c"># Depending on the time remaining, either display the expected</span>
72        <span class="c"># time of completion, or the amount of time remaining.  Use precision</span>
73        <span class="c"># appropriate for the duration.</span>
74        <span class="k">if</span> <span class="n">remaining_time</span> <span class="o">&gt;=</span> <span class="mi">1800</span><span class="p">:</span>
75            <span class="n">completion_time</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span> <span class="o">+</span> <span class="n">timedelta</span><span class="p">(</span><span class="n">seconds</span><span class="o">=</span><span class="n">remaining_time</span><span class="p">)</span>
76            <span class="k">if</span> <span class="n">remaining_time</span> <span class="o">&gt;=</span> <span class="mi">36000</span><span class="p">:</span>
77                <span class="n">time</span> <span class="o">=</span> <span class="n">completion_time</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s">&#39;%Y-%m-</span><span class="si">%d</span><span class="s"> %H:%M&#39;</span><span class="p">)</span>
78            <span class="k">else</span><span class="p">:</span>
79                <span class="n">time</span> <span class="o">=</span> <span class="n">completion_time</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s">&#39;%H:%M&#39;</span><span class="p">)</span>
80        <span class="k">else</span><span class="p">:</span>
81            <span class="k">if</span> <span class="n">remaining_time</span> <span class="o">&gt;=</span> <span class="mi">3600</span><span class="p">:</span>
82                <span class="n">time</span> <span class="o">=</span> <span class="s">&#39;</span><span class="si">%d</span><span class="s">h </span><span class="si">%d</span><span class="s">m&#39;</span><span class="o">%</span><span class="p">(</span><span class="n">remaining_time</span><span class="o">//</span><span class="mi">3600</span><span class="p">,</span> <span class="p">(</span><span class="n">remaining_time</span><span class="o">%</span><span class="mi">3600</span><span class="p">)</span><span class="o">//</span><span class="mi">60</span><span class="p">)</span>
83            <span class="k">elif</span> <span class="n">remaining_time</span> <span class="o">&gt;=</span> <span class="mi">60</span><span class="p">:</span>
84                <span class="n">time</span> <span class="o">=</span> <span class="s">&#39;</span><span class="si">%d</span><span class="s">m </span><span class="si">%d</span><span class="s">s&#39;</span><span class="o">%</span><span class="p">(</span><span class="n">remaining_time</span><span class="o">//</span><span class="mi">60</span><span class="p">,</span> <span class="n">remaining_time</span><span class="o">%</span><span class="mi">60</span><span class="p">)</span>
85            <span class="k">else</span><span class="p">:</span>
86                <span class="n">time</span> <span class="o">=</span> <span class="s">&#39;</span><span class="si">%d</span><span class="s">s&#39;</span><span class="o">%</span><span class="n">remaining_time</span>
87        <span class="n">chisq</span> <span class="o">=</span> <span class="s">&quot;</span><span class="si">%.3g</span><span class="s">&quot;</span><span class="o">%</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">history</span><span class="o">.</span><span class="n">value</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">/</span><span class="n">dof</span><span class="p">)</span>
88        <span class="n">step</span> <span class="o">=</span> <span class="s">&quot;</span><span class="si">%d</span><span class="s"> of </span><span class="si">%d</span><span class="s">&quot;</span><span class="o">%</span><span class="p">(</span><span class="n">history</span><span class="o">.</span><span class="n">step</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">max_step</span><span class="p">)</span>
89        <span class="n">header</span> <span class="o">=</span> <span class="s">&quot;=== Steps: </span><span class="si">%s</span><span class="s">  chisq: </span><span class="si">%s</span><span class="s">  ETA: </span><span class="si">%s</span><span class="se">\n</span><span class="s">&quot;</span><span class="o">%</span><span class="p">(</span><span class="n">step</span><span class="p">,</span> <span class="n">chisq</span><span class="p">,</span> <span class="n">time</span><span class="p">)</span>
90        <span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span><span class="s">&quot;</span><span class="si">%15s</span><span class="s">: </span><span class="si">%-10.3g%s</span><span class="s">&quot;</span><span class="o">%</span><span class="p">(</span><span class="n">k</span><span class="p">,</span><span class="n">v</span><span class="p">,(</span><span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span> <span class="k">if</span> <span class="n">i</span><span class="o">%</span><span class="mi">3</span><span class="o">==</span><span class="mi">2</span> <span class="k">else</span> <span class="s">&quot; | &quot;</span><span class="p">))</span>
91                      <span class="k">for</span> <span class="n">i</span><span class="p">,(</span><span class="n">k</span><span class="p">,</span><span class="n">v</span><span class="p">)</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">pars</span><span class="p">,</span><span class="n">history</span><span class="o">.</span><span class="n">point</span><span class="p">[</span><span class="mi">0</span><span class="p">]))]</span>
92        <span class="bp">self</span><span class="o">.</span><span class="n">msg</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">header</span><span class="p">]</span><span class="o">+</span><span class="n">parameters</span><span class="p">)</span>
93
94    <span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
95        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">msg</span>
96
97</div>
98<div class="viewcode-block" id="BumpsMonitor"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.BumpsMonitor">[docs]</a><span class="k">class</span> <span class="nc">BumpsMonitor</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
99    <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">handler</span><span class="p">,</span> <span class="n">max_step</span><span class="p">,</span> <span class="n">pars</span><span class="p">,</span> <span class="n">dof</span><span class="p">):</span>
100        <span class="bp">self</span><span class="o">.</span><span class="n">handler</span> <span class="o">=</span> <span class="n">handler</span>
101        <span class="bp">self</span><span class="o">.</span><span class="n">max_step</span> <span class="o">=</span> <span class="n">max_step</span>
102        <span class="bp">self</span><span class="o">.</span><span class="n">pars</span> <span class="o">=</span> <span class="n">pars</span>
103        <span class="bp">self</span><span class="o">.</span><span class="n">dof</span> <span class="o">=</span> <span class="n">dof</span>
104
105<div class="viewcode-block" id="BumpsMonitor.config_history"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.BumpsMonitor.config_history">[docs]</a>    <span class="k">def</span> <span class="nf">config_history</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">history</span><span class="p">):</span>
106        <span class="n">history</span><span class="o">.</span><span class="n">requires</span><span class="p">(</span><span class="n">time</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">point</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">step</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
107</div>
108    <span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">history</span><span class="p">):</span>
109        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">handler</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> <span class="k">return</span>
110        <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">set_result</span><span class="p">(</span><span class="n">Progress</span><span class="p">(</span><span class="n">history</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_step</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">pars</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dof</span><span class="p">))</span>
111        <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">progress</span><span class="p">(</span><span class="n">history</span><span class="o">.</span><span class="n">step</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_step</span><span class="p">)</span>
112        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">history</span><span class="o">.</span><span class="n">step</span><span class="p">)</span><span class="o">&gt;</span><span class="mi">1</span> <span class="ow">and</span> <span class="n">history</span><span class="o">.</span><span class="n">step</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">&gt;</span> <span class="n">history</span><span class="o">.</span><span class="n">step</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span>
113            <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">improvement</span><span class="p">()</span>
114        <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">update_fit</span><span class="p">()</span>
115</div>
116<div class="viewcode-block" id="ConvergenceMonitor"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.ConvergenceMonitor">[docs]</a><span class="k">class</span> <span class="nc">ConvergenceMonitor</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
117    <span class="sd">&quot;&quot;&quot;</span>
118<span class="sd">    ConvergenceMonitor contains population summary statistics to show progress</span>
119<span class="sd">    of the fit.  This is a list [ (best, 0%, 25%, 50%, 75%, 100%) ] or</span>
120<span class="sd">    just a list [ (best, ) ] if population size is 1.</span>
121<span class="sd">    &quot;&quot;&quot;</span>
122    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
123        <span class="bp">self</span><span class="o">.</span><span class="n">convergence</span> <span class="o">=</span> <span class="p">[]</span>
124
125<div class="viewcode-block" id="ConvergenceMonitor.config_history"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.ConvergenceMonitor.config_history">[docs]</a>    <span class="k">def</span> <span class="nf">config_history</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">history</span><span class="p">):</span>
126        <span class="n">history</span><span class="o">.</span><span class="n">requires</span><span class="p">(</span><span class="n">value</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">population_values</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
127</div>
128    <span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">history</span><span class="p">):</span>
129        <span class="n">best</span> <span class="o">=</span> <span class="n">history</span><span class="o">.</span><span class="n">value</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
130        <span class="k">try</span><span class="p">:</span>
131            <span class="n">p</span> <span class="o">=</span> <span class="n">history</span><span class="o">.</span><span class="n">population_values</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
132            <span class="n">n</span><span class="p">,</span><span class="n">p</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">p</span><span class="p">),</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
133            <span class="n">QI</span><span class="p">,</span><span class="n">Qmid</span><span class="p">,</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="mf">0.2</span><span class="o">*</span><span class="n">n</span><span class="p">),</span><span class="nb">int</span><span class="p">(</span><span class="mf">0.5</span><span class="o">*</span><span class="n">n</span><span class="p">)</span>
134            <span class="bp">self</span><span class="o">.</span><span class="n">convergence</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">best</span><span class="p">,</span> <span class="n">p</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">p</span><span class="p">[</span><span class="n">QI</span><span class="p">],</span><span class="n">p</span><span class="p">[</span><span class="n">Qmid</span><span class="p">],</span><span class="n">p</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="o">-</span><span class="n">QI</span><span class="p">],</span><span class="n">p</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span>
135        <span class="k">except</span><span class="p">:</span>
136            <span class="bp">self</span><span class="o">.</span><span class="n">convergence</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">best</span><span class="p">,</span> <span class="n">best</span><span class="p">,</span><span class="n">best</span><span class="p">,</span><span class="n">best</span><span class="p">,</span><span class="n">best</span><span class="p">,</span><span class="n">best</span><span class="p">))</span>
137
138
139<span class="c"># Note: currently using bumps parameters for each parameter object so that</span>
140<span class="c"># a SasFitness can be used directly in bumps with the usual semantics.</span>
141<span class="c"># The disadvantage of this technique is that we need to copy every parameter</span>
142<span class="c"># back into the model each time the function is evaluated.  We could instead</span>
143<span class="c"># define reference parameters for each sas parameter, but then we would not</span>
144<span class="c"># be able to express constraints using python expressions in the usual way</span>
145<span class="c"># from bumps, and would instead need to use string expressions.</span></div>
146<div class="viewcode-block" id="SasFitness"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.SasFitness">[docs]</a><span class="k">class</span> <span class="nc">SasFitness</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
147    <span class="sd">&quot;&quot;&quot;</span>
148<span class="sd">    Wrap SAS model as a bumps fitness object</span>
149<span class="sd">    &quot;&quot;&quot;</span>
150    <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">data</span><span class="p">,</span> <span class="n">fitted</span><span class="o">=</span><span class="p">[],</span> <span class="n">constraints</span><span class="o">=</span><span class="p">{},</span>
151                 <span class="n">initial_values</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="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">name</span>
153        <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">model</span>
154        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">data</span>
155        <span class="bp">self</span><span class="o">.</span><span class="n">_define_pars</span><span class="p">()</span>
156        <span class="bp">self</span><span class="o">.</span><span class="n">_init_pars</span><span class="p">(</span><span class="n">kw</span><span class="p">)</span>
157        <span class="k">if</span> <span class="n">initial_values</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
158            <span class="bp">self</span><span class="o">.</span><span class="n">_reset_pars</span><span class="p">(</span><span class="n">fitted</span><span class="p">,</span> <span class="n">initial_values</span><span class="p">)</span>
159        <span class="bp">self</span><span class="o">.</span><span class="n">constraints</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">constraints</span><span class="p">)</span>
160        <span class="bp">self</span><span class="o">.</span><span class="n">set_fitted</span><span class="p">(</span><span class="n">fitted</span><span class="p">)</span>
161        <span class="bp">self</span><span class="o">.</span><span class="n">update</span><span class="p">()</span>
162
163    <span class="k">def</span> <span class="nf">_reset_pars</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">names</span><span class="p">,</span> <span class="n">values</span><span class="p">):</span>
164        <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">names</span><span class="p">,</span> <span class="n">values</span><span class="p">):</span>
165            <span class="bp">self</span><span class="o">.</span><span class="n">_pars</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">=</span> <span class="n">v</span>
166
167    <span class="k">def</span> <span class="nf">_define_pars</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
168        <span class="bp">self</span><span class="o">.</span><span class="n">_pars</span> <span class="o">=</span> <span class="p">{}</span>
169        <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">getParamList</span><span class="p">():</span>
170            <span class="n">name</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="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span><span class="n">k</span><span class="p">))</span>
171            <span class="n">value</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">getParam</span><span class="p">(</span><span class="n">k</span><span class="p">)</span>
172            <span class="n">bounds</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="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">k</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><span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">]</span>
173            <span class="bp">self</span><span class="o">.</span><span class="n">_pars</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">parameter</span><span class="o">.</span><span class="n">Parameter</span><span class="p">(</span><span class="n">value</span><span class="o">=</span><span class="n">value</span><span class="p">,</span> <span class="n">bounds</span><span class="o">=</span><span class="n">bounds</span><span class="p">,</span>
174                                                <span class="n">fixed</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="n">name</span><span class="p">)</span>
175        <span class="c">#print parameter.summarize(self._pars.values())</span>
176
177    <span class="k">def</span> <span class="nf">_init_pars</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">kw</span><span class="p">):</span>
178        <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="n">kw</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
179            <span class="c"># dispersion parameters initialized with _field instead of .field</span>
180            <span class="k">if</span> <span class="n">k</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s">&#39;_width&#39;</span><span class="p">):</span> <span class="n">k</span> <span class="o">=</span> <span class="n">k</span><span class="p">[:</span><span class="o">-</span><span class="mi">6</span><span class="p">]</span><span class="o">+</span><span class="s">&#39;.width&#39;</span>
181            <span class="k">elif</span> <span class="n">k</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s">&#39;_npts&#39;</span><span class="p">):</span> <span class="n">k</span> <span class="o">=</span> <span class="n">k</span><span class="p">[:</span><span class="o">-</span><span class="mi">5</span><span class="p">]</span><span class="o">+</span><span class="s">&#39;.npts&#39;</span>
182            <span class="k">elif</span> <span class="n">k</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s">&#39;_nsigmas&#39;</span><span class="p">):</span> <span class="n">k</span> <span class="o">=</span> <span class="n">k</span><span class="p">[:</span><span class="o">-</span><span class="mi">7</span><span class="p">]</span><span class="o">+</span><span class="s">&#39;.nsigmas&#39;</span>
183            <span class="k">elif</span> <span class="n">k</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s">&#39;_type&#39;</span><span class="p">):</span> <span class="n">k</span> <span class="o">=</span> <span class="n">k</span><span class="p">[:</span><span class="o">-</span><span class="mi">5</span><span class="p">]</span><span class="o">+</span><span class="s">&#39;.type&#39;</span>
184            <span class="k">if</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pars</span><span class="p">:</span>
185                <span class="n">formatted_pars</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="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_pars</span><span class="o">.</span><span class="n">keys</span><span class="p">()))</span>
186                <span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="s">&quot;invalid parameter </span><span class="si">%r</span><span class="s"> for </span><span class="si">%s</span><span class="s">--use one of: </span><span class="si">%s</span><span class="s">&quot;</span>
187                               <span class="o">%</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">formatted_pars</span><span class="p">))</span>
188            <span class="k">if</span> <span class="s">&#39;.&#39;</span> <span class="ow">in</span> <span class="n">k</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">k</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s">&#39;.width&#39;</span><span class="p">):</span>
189                <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="n">k</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span>
190            <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="n">parameter</span><span class="o">.</span><span class="n">BaseParameter</span><span class="p">):</span>
191                <span class="bp">self</span><span class="o">.</span><span class="n">_pars</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">v</span>
192            <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="p">(</span><span class="nb">tuple</span><span class="p">,</span><span class="nb">list</span><span class="p">)):</span>
193                <span class="n">low</span><span class="p">,</span> <span class="n">high</span> <span class="o">=</span> <span class="n">v</span>
194                <span class="bp">self</span><span class="o">.</span><span class="n">_pars</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">=</span> <span class="p">(</span><span class="n">low</span><span class="o">+</span><span class="n">high</span><span class="p">)</span><span class="o">/</span><span class="mi">2</span>
195                <span class="bp">self</span><span class="o">.</span><span class="n">_pars</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">range</span><span class="p">(</span><span class="n">low</span><span class="p">,</span><span class="n">high</span><span class="p">)</span>
196            <span class="k">else</span><span class="p">:</span>
197                <span class="bp">self</span><span class="o">.</span><span class="n">_pars</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">value</span> <span class="o">=</span> <span class="n">v</span>
198
199<div class="viewcode-block" id="SasFitness.set_fitted"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.SasFitness.set_fitted">[docs]</a>    <span class="k">def</span> <span class="nf">set_fitted</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">param_list</span><span class="p">):</span>
200        <span class="sd">&quot;&quot;&quot;</span>
201<span class="sd">        Flag a set of parameters as fitted parameters.</span>
202<span class="sd">        &quot;&quot;&quot;</span>
203        <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pars</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
204            <span class="n">p</span><span class="o">.</span><span class="n">fixed</span> <span class="o">=</span> <span class="p">(</span><span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">param_list</span> <span class="ow">or</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">constraints</span><span class="p">)</span>
205        <span class="bp">self</span><span class="o">.</span><span class="n">fitted_par_names</span> <span class="o">=</span> <span class="p">[</span><span class="n">k</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">param_list</span> <span class="k">if</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">constraints</span><span class="p">]</span>
206        <span class="bp">self</span><span class="o">.</span><span class="n">computed_par_names</span> <span class="o">=</span> <span class="p">[</span><span class="n">k</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">param_list</span> <span class="k">if</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">constraints</span><span class="p">]</span>
207        <span class="bp">self</span><span class="o">.</span><span class="n">fitted_pars</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_pars</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">fitted_par_names</span><span class="p">]</span>
208        <span class="bp">self</span><span class="o">.</span><span class="n">computed_pars</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_pars</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">computed_par_names</span><span class="p">]</span>
209
210    <span class="c"># ===== Fitness interface ====</span></div>
211<div class="viewcode-block" id="SasFitness.parameters"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.SasFitness.parameters">[docs]</a>    <span class="k">def</span> <span class="nf">parameters</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
212        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pars</span>
213</div>
214<div class="viewcode-block" id="SasFitness.update"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.SasFitness.update">[docs]</a>    <span class="k">def</span> <span class="nf">update</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
215        <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pars</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
216            <span class="c">#print &quot;updating&quot;,k,v,v.value</span>
217            <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="n">k</span><span class="p">,</span><span class="n">v</span><span class="o">.</span><span class="n">value</span><span class="p">)</span>
218        <span class="bp">self</span><span class="o">.</span><span class="n">_dirty</span> <span class="o">=</span> <span class="bp">True</span>
219</div>
220    <span class="k">def</span> <span class="nf">_recalculate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
221        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dirty</span><span class="p">:</span>
222            <span class="bp">self</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="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">residuals</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">evalDistribution</span><span class="p">)</span>
223            <span class="bp">self</span><span class="o">.</span><span class="n">_dirty</span> <span class="o">=</span> <span class="bp">False</span>
224
225<div class="viewcode-block" id="SasFitness.numpoints"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.SasFitness.numpoints">[docs]</a>    <span class="k">def</span> <span class="nf">numpoints</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
226        <span class="k">return</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">data</span><span class="o">.</span><span class="n">idx</span><span class="p">)</span> <span class="c"># number of fitted points</span>
227</div>
228<div class="viewcode-block" id="SasFitness.nllf"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.SasFitness.nllf">[docs]</a>    <span class="k">def</span> <span class="nf">nllf</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
229        <span class="k">return</span> <span class="mf">0.5</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="p">()</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span>
230</div>
231<div class="viewcode-block" id="SasFitness.theory"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.SasFitness.theory">[docs]</a>    <span class="k">def</span> <span class="nf">theory</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
232        <span class="bp">self</span><span class="o">.</span><span class="n">_recalculate</span><span class="p">()</span>
233        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_theory</span>
234</div>
235<div class="viewcode-block" id="SasFitness.residuals"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.SasFitness.residuals">[docs]</a>    <span class="k">def</span> <span class="nf">residuals</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
236        <span class="bp">self</span><span class="o">.</span><span class="n">_recalculate</span><span class="p">()</span>
237        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_residuals</span>
238
239    <span class="c"># Not implementing the data methods for now:</span>
240    <span class="c">#</span>
241    <span class="c">#     resynth_data/restore_data/save/plot</span>
242</div></div>
243<div class="viewcode-block" id="ParameterExpressions"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.ParameterExpressions">[docs]</a><span class="k">class</span> <span class="nc">ParameterExpressions</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
244    <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>
245        <span class="bp">self</span><span class="o">.</span><span class="n">models</span> <span class="o">=</span> <span class="n">models</span>
246        <span class="bp">self</span><span class="o">.</span><span class="n">_setup</span><span class="p">()</span>
247
248    <span class="k">def</span> <span class="nf">_setup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
249        <span class="n">exprs</span> <span class="o">=</span> <span class="p">{}</span>
250        <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">models</span><span class="p">:</span>
251            <span class="n">exprs</span><span class="o">.</span><span class="n">update</span><span class="p">((</span><span class="s">&quot;.&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">((</span><span class="n">M</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">k</span><span class="p">)),</span> <span class="n">v</span><span class="p">)</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">M</span><span class="o">.</span><span class="n">constraints</span><span class="o">.</span><span class="n">items</span><span class="p">())</span>
252        <span class="k">if</span> <span class="n">exprs</span><span class="p">:</span>
253            <span class="n">symtab</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="s">&quot;.&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">((</span><span class="n">M</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">k</span><span class="p">)),</span> <span class="n">p</span><span class="p">)</span>
254                          <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">models</span>
255                          <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">p</span> <span class="ow">in</span> <span class="n">M</span><span class="o">.</span><span class="n">parameters</span><span class="p">()</span><span class="o">.</span><span class="n">items</span><span class="p">())</span>
256            <span class="bp">self</span><span class="o">.</span><span class="n">update</span> <span class="o">=</span> <span class="n">compile_constraints</span><span class="p">(</span><span class="n">symtab</span><span class="p">,</span> <span class="n">exprs</span><span class="p">)</span>
257        <span class="k">else</span><span class="p">:</span>
258            <span class="bp">self</span><span class="o">.</span><span class="n">update</span> <span class="o">=</span> <span class="k">lambda</span><span class="p">:</span> <span class="mi">0</span>
259
260    <span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
261        <span class="bp">self</span><span class="o">.</span><span class="n">update</span><span class="p">()</span>
262
263    <span class="k">def</span> <span class="nf">__getstate__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
264        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">models</span>
265
266    <span class="k">def</span> <span class="nf">__setstate__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">state</span><span class="p">):</span>
267        <span class="bp">self</span><span class="o">.</span><span class="n">models</span> <span class="o">=</span> <span class="n">state</span>
268        <span class="bp">self</span><span class="o">.</span><span class="n">_setup</span><span class="p">()</span>
269</div>
270<div class="viewcode-block" id="BumpsFit"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.BumpsFit">[docs]</a><span class="k">class</span> <span class="nc">BumpsFit</span><span class="p">(</span><span class="n">FitEngine</span><span class="p">):</span>
271    <span class="sd">&quot;&quot;&quot;</span>
272<span class="sd">    Fit a model using bumps.</span>
273<span class="sd">    &quot;&quot;&quot;</span>
274    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
275        <span class="sd">&quot;&quot;&quot;</span>
276<span class="sd">        Creates a dictionary (self.fit_arrange_dict={})of FitArrange elements</span>
277<span class="sd">        with Uid as keys</span>
278<span class="sd">        &quot;&quot;&quot;</span>
279        <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>
280        <span class="bp">self</span><span class="o">.</span><span class="n">curr_thread</span> <span class="o">=</span> <span class="bp">None</span>
281
282<div class="viewcode-block" id="BumpsFit.fit"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.BumpsFit.fit">[docs]</a>    <span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">msg_q</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
283            <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>
284            <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>
285        <span class="c"># Build collection of bumps fitness calculators</span>
286        <span class="n">models</span> <span class="o">=</span> <span class="p">[</span><span class="n">SasFitness</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">get_model</span><span class="p">(),</span>
287                             <span class="n">data</span><span class="o">=</span><span class="n">M</span><span class="o">.</span><span class="n">get_data</span><span class="p">(),</span>
288                             <span class="n">constraints</span><span class="o">=</span><span class="n">M</span><span class="o">.</span><span class="n">constraints</span><span class="p">,</span>
289                             <span class="n">fitted</span><span class="o">=</span><span class="n">M</span><span class="o">.</span><span class="n">pars</span><span class="p">,</span>
290                             <span class="n">initial_values</span><span class="o">=</span><span class="n">M</span><span class="o">.</span><span class="n">vals</span> <span class="k">if</span> <span class="n">reset_flag</span> <span class="k">else</span> <span class="bp">None</span><span class="p">)</span>
291                  <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">fit_arrange_dict</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
292                  <span class="k">if</span> <span class="n">M</span><span class="o">.</span><span class="n">get_to_fit</span><span class="p">()]</span>
293        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">models</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
294            <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">&quot;Nothing to fit&quot;</span><span class="p">)</span>
295        <span class="n">problem</span> <span class="o">=</span> <span class="n">FitProblem</span><span class="p">(</span><span class="n">models</span><span class="p">)</span>
296
297        <span class="c"># TODO: need better handling of parameter expressions and bounds constraints</span>
298        <span class="c"># so that they are applied during polydispersity calculations.  This</span>
299        <span class="c"># will remove the immediate need for the setp_hook in bumps, though</span>
300        <span class="c"># bumps may still need something similar, such as a sane class structure</span>
301        <span class="c"># which allows a subclass to override setp.</span>
302        <span class="n">problem</span><span class="o">.</span><span class="n">setp_hook</span> <span class="o">=</span> <span class="n">ParameterExpressions</span><span class="p">(</span><span class="n">models</span><span class="p">)</span>
303
304        <span class="c"># Run the fit</span>
305        <span class="n">result</span> <span class="o">=</span> <span class="n">run_bumps</span><span class="p">(</span><span class="n">problem</span><span class="p">,</span> <span class="n">handler</span><span class="p">,</span> <span class="n">curr_thread</span><span class="p">)</span>
306        <span class="k">if</span> <span class="n">handler</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
307            <span class="n">handler</span><span class="o">.</span><span class="n">update_fit</span><span class="p">(</span><span class="n">last</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
308
309        <span class="c"># TODO: shouldn&#39;t reference internal parameters of fit problem</span>
310        <span class="n">varying</span> <span class="o">=</span> <span class="n">problem</span><span class="o">.</span><span class="n">_parameters</span>
311        <span class="c"># collect the results</span>
312        <span class="n">all_results</span> <span class="o">=</span> <span class="p">[]</span>
313        <span class="k">for</span> <span class="n">M</span> <span class="ow">in</span> <span class="n">problem</span><span class="o">.</span><span class="n">models</span><span class="p">:</span>
314            <span class="n">fitness</span> <span class="o">=</span> <span class="n">M</span><span class="o">.</span><span class="n">fitness</span>
315            <span class="n">fitted_index</span> <span class="o">=</span> <span class="p">[</span><span class="n">varying</span><span class="o">.</span><span class="n">index</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">fitness</span><span class="o">.</span><span class="n">fitted_pars</span><span class="p">]</span>
316            <span class="n">R</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">fitness</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">fitness</span><span class="o">.</span><span class="n">data</span><span class="p">,</span>
317                        <span class="n">param_list</span><span class="o">=</span><span class="n">fitness</span><span class="o">.</span><span class="n">fitted_par_names</span><span class="o">+</span><span class="n">fitness</span><span class="o">.</span><span class="n">computed_par_names</span><span class="p">)</span>
318            <span class="n">R</span><span class="o">.</span><span class="n">theory</span> <span class="o">=</span> <span class="n">fitness</span><span class="o">.</span><span class="n">theory</span><span class="p">()</span>
319            <span class="n">R</span><span class="o">.</span><span class="n">residuals</span> <span class="o">=</span> <span class="n">fitness</span><span class="o">.</span><span class="n">residuals</span><span class="p">()</span>
320            <span class="n">R</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">fitness</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">idx</span>
321            <span class="n">R</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>
322            <span class="c"># TODO: should scale stderr by sqrt(chisq/DOF) if dy is unknown</span>
323            <span class="n">R</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">hstack</span><span class="p">((</span><span class="n">result</span><span class="p">[</span><span class="s">&#39;stderr&#39;</span><span class="p">][</span><span class="n">fitted_index</span><span class="p">],</span>
324                                     <span class="n">numpy</span><span class="o">.</span><span class="n">NaN</span><span class="o">*</span><span class="n">numpy</span><span class="o">.</span><span class="n">ones</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fitness</span><span class="o">.</span><span class="n">computed_pars</span><span class="p">))))</span>
325            <span class="n">R</span><span class="o">.</span><span class="n">pvec</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">hstack</span><span class="p">((</span><span class="n">result</span><span class="p">[</span><span class="s">&#39;value&#39;</span><span class="p">][</span><span class="n">fitted_index</span><span class="p">],</span>
326                                  <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">fitness</span><span class="o">.</span><span class="n">computed_pars</span><span class="p">]))</span>
327            <span class="n">R</span><span class="o">.</span><span class="n">success</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="s">&#39;success&#39;</span><span class="p">]</span>
328            <span class="n">R</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">R</span><span class="o">.</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="p">(</span><span class="n">fitness</span><span class="o">.</span><span class="n">numpoints</span><span class="p">()</span> <span class="o">-</span> <span class="nb">len</span><span class="p">(</span><span class="n">fitted_index</span><span class="p">))</span>
329            <span class="n">R</span><span class="o">.</span><span class="n">convergence</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="s">&#39;convergence&#39;</span><span class="p">]</span>
330            <span class="k">if</span> <span class="n">result</span><span class="p">[</span><span class="s">&#39;uncertainty&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
331                <span class="n">R</span><span class="o">.</span><span class="n">uncertainty_state</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="s">&#39;uncertainty&#39;</span><span class="p">]</span>
332            <span class="n">all_results</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">R</span><span class="p">)</span>
333
334        <span class="k">if</span> <span class="n">q</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
335            <span class="n">q</span><span class="o">.</span><span class="n">put</span><span class="p">(</span><span class="n">all_results</span><span class="p">)</span>
336            <span class="k">return</span> <span class="n">q</span>
337        <span class="k">else</span><span class="p">:</span>
338            <span class="k">return</span> <span class="n">all_results</span>
339</div></div>
340<div class="viewcode-block" id="run_bumps"><a class="viewcode-back" href="../../../dev/api/sas.fit.html#sas.fit.BumpsFitting.run_bumps">[docs]</a><span class="k">def</span> <span class="nf">run_bumps</span><span class="p">(</span><span class="n">problem</span><span class="p">,</span> <span class="n">handler</span><span class="p">,</span> <span class="n">curr_thread</span><span class="p">):</span>
341    <span class="k">def</span> <span class="nf">abort_test</span><span class="p">():</span>
342        <span class="k">if</span> <span class="n">curr_thread</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> <span class="k">return</span> <span class="bp">False</span>
343        <span class="k">try</span><span class="p">:</span> <span class="n">curr_thread</span><span class="o">.</span><span class="n">isquit</span><span class="p">()</span>
344        <span class="k">except</span> <span class="ne">KeyboardInterrupt</span><span class="p">:</span>
345            <span class="k">if</span> <span class="n">handler</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
346                <span class="n">handler</span><span class="o">.</span><span class="n">stop</span><span class="p">(</span><span class="s">&quot;Fitting: Terminated!!!&quot;</span><span class="p">)</span>
347            <span class="k">return</span> <span class="bp">True</span>
348        <span class="k">return</span> <span class="bp">False</span>
349
350    <span class="n">fitopts</span> <span class="o">=</span> <span class="n">fitters</span><span class="o">.</span><span class="n">FIT_OPTIONS</span><span class="p">[</span><span class="n">fitters</span><span class="o">.</span><span class="n">FIT_DEFAULT</span><span class="p">]</span>
351    <span class="n">fitclass</span> <span class="o">=</span> <span class="n">fitopts</span><span class="o">.</span><span class="n">fitclass</span>
352    <span class="n">options</span> <span class="o">=</span> <span class="n">fitopts</span><span class="o">.</span><span class="n">options</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
353    <span class="n">max_step</span> <span class="o">=</span> <span class="n">fitopts</span><span class="o">.</span><span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&#39;steps&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> <span class="o">+</span> <span class="n">fitopts</span><span class="o">.</span><span class="n">options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&#39;burn&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
354    <span class="n">pars</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">problem</span><span class="o">.</span><span class="n">_parameters</span><span class="p">]</span>
355    <span class="n">options</span><span class="p">[</span><span class="s">&#39;monitors&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
356        <span class="n">BumpsMonitor</span><span class="p">(</span><span class="n">handler</span><span class="p">,</span> <span class="n">max_step</span><span class="p">,</span> <span class="n">pars</span><span class="p">,</span> <span class="n">problem</span><span class="o">.</span><span class="n">dof</span><span class="p">),</span>
357        <span class="n">ConvergenceMonitor</span><span class="p">(),</span>
358        <span class="p">]</span>
359    <span class="n">fitdriver</span> <span class="o">=</span> <span class="n">fitters</span><span class="o">.</span><span class="n">FitDriver</span><span class="p">(</span><span class="n">fitclass</span><span class="p">,</span> <span class="n">problem</span><span class="o">=</span><span class="n">problem</span><span class="p">,</span>
360                                  <span class="n">abort_test</span><span class="o">=</span><span class="n">abort_test</span><span class="p">,</span> <span class="o">**</span><span class="n">options</span><span class="p">)</span>
361    <span class="n">omp_threads</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&#39;OMP_NUM_THREADS&#39;</span><span class="p">,</span><span class="s">&#39;0&#39;</span><span class="p">))</span>
362    <span class="n">mapper</span> <span class="o">=</span> <span class="n">MPMapper</span> <span class="k">if</span> <span class="n">omp_threads</span> <span class="o">==</span> <span class="mi">1</span> <span class="k">else</span> <span class="n">SerialMapper</span>       
363    <span class="n">fitdriver</span><span class="o">.</span><span class="n">mapper</span> <span class="o">=</span> <span class="n">mapper</span><span class="o">.</span><span class="n">start_mapper</span><span class="p">(</span><span class="n">problem</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
364    <span class="c">#import time; T0 = time.time()</span>
365    <span class="k">try</span><span class="p">:</span>
366        <span class="n">best</span><span class="p">,</span> <span class="n">fbest</span> <span class="o">=</span> <span class="n">fitdriver</span><span class="o">.</span><span class="n">fit</span><span class="p">()</span>
367    <span class="k">except</span><span class="p">:</span>
368        <span class="kn">import</span> <span class="nn">traceback</span><span class="p">;</span> <span class="n">traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">()</span>
369        <span class="k">raise</span>
370    <span class="k">finally</span><span class="p">:</span>
371        <span class="n">mapper</span><span class="o">.</span><span class="n">stop_mapper</span><span class="p">(</span><span class="n">fitdriver</span><span class="o">.</span><span class="n">mapper</span><span class="p">)</span>
372
373
374    <span class="n">convergence_list</span> <span class="o">=</span> <span class="n">options</span><span class="p">[</span><span class="s">&#39;monitors&#39;</span><span class="p">][</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">convergence</span>
375    <span class="n">convergence</span> <span class="o">=</span> <span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">numpy</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">convergence_list</span><span class="p">)</span><span class="o">/</span><span class="n">problem</span><span class="o">.</span><span class="n">dof</span>
376                   <span class="k">if</span> <span class="n">convergence_list</span> <span class="k">else</span> <span class="n">numpy</span><span class="o">.</span><span class="n">empty</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">),</span><span class="s">&#39;d&#39;</span><span class="p">))</span>
377    <span class="k">return</span> <span class="p">{</span>
378        <span class="s">&#39;value&#39;</span><span class="p">:</span> <span class="n">best</span><span class="p">,</span>
379        <span class="s">&#39;stderr&#39;</span><span class="p">:</span> <span class="n">fitdriver</span><span class="o">.</span><span class="n">stderr</span><span class="p">(),</span>
380        <span class="s">&#39;success&#39;</span><span class="p">:</span> <span class="bp">True</span><span class="p">,</span> <span class="c"># better success reporting in bumps</span>
381        <span class="s">&#39;convergence&#39;</span><span class="p">:</span> <span class="n">convergence</span><span class="p">,</span>
382        <span class="s">&#39;uncertainty&#39;</span><span class="p">:</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">fitdriver</span><span class="o">.</span><span class="n">fitter</span><span class="p">,</span> <span class="s">&#39;state&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">),</span>
383        <span class="p">}</span>
384</pre></div></div>
385
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