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| 50 | <h1>Source code for park.fitmc</h1><div class="highlight"><pre> |
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| 51 | <span class="c"># The job queue needs to be in a transaction/rollback protected database.</span> |
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| 52 | <span class="c"># If the server is rebooted, long running jobs should continue to work.</span> |
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| 53 | <span class="c">#</span> |
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| 54 | <span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">division</span> |
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| 55 | <span class="kn">import</span> <span class="nn">numpy</span> |
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| 56 | |
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| 57 | <span class="kn">import</span> <span class="nn">simplex</span> |
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| 58 | |
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| 59 | <span class="kn">import</span> <span class="nn">fitresult</span><span class="o">,</span> <span class="nn">pmap</span><span class="o">,</span> <span class="nn">fit</span> |
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| 60 | |
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| 61 | <span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s">'fitmc'</span><span class="p">,</span> <span class="s">'FitMCJob'</span><span class="p">]</span> |
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| 62 | |
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| 63 | <span class="k">class</span> <span class="nc">LocalFit</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
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| 64 | <span class="sd">"""</span> |
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| 65 | <span class="sd"> Abstract interface for a local minimizer</span> |
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| 66 | |
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| 67 | <span class="sd"> See `park.fitmc.FitSimplex` for a concrete implementation.</span> |
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| 68 | <span class="sd"> """</span> |
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| 69 | <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> |
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| 70 | <span class="sd">"""</span> |
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| 71 | <span class="sd"> Minimize the value of a fitness function.</span> |
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| 72 | |
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| 73 | <span class="sd"> See `park.fitmc.Fitness` for the definition of the goodness of fit</span> |
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| 74 | <span class="sd"> object. x0 is a vector containing the initial value for the fit.</span> |
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| 75 | <span class="sd"> """</span> |
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| 76 | <span class="k">def</span> <span class="nf">abort</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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| 77 | <span class="sd">"""</span> |
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| 78 | <span class="sd"> Cancel the fit. This will be called from a separate execution</span> |
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| 79 | <span class="sd"> thread. The fit should terminate as soon as possible after this</span> |
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| 80 | <span class="sd"> function has been called. Ideally this would interrupt the</span> |
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| 81 | <span class="sd"> cur</span> |
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| 82 | <span class="sd"> """</span> |
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| 83 | |
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| 84 | <span class="k">class</span> <span class="nc">FitSimplex</span><span class="p">(</span><span class="n">LocalFit</span><span class="p">):</span> |
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| 85 | <span class="sd">"""</span> |
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| 86 | <span class="sd"> Local minimizer using Nelder-Mead simplex algorithm.</span> |
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| 87 | |
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| 88 | <span class="sd"> Simplex is robust and derivative free, though not very efficient.</span> |
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| 89 | |
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| 90 | <span class="sd"> This class wraps the bounds contrained Nelder-Mead simplex</span> |
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| 91 | <span class="sd"> implementation for `park.simplex.simplex`.</span> |
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| 92 | <span class="sd"> """</span> |
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| 93 | <span class="n">radius</span> <span class="o">=</span> <span class="mf">0.05</span> |
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| 94 | <span class="sd">"""Size of the initial simplex; this is a portion between 0 and 1"""</span> |
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| 95 | <span class="n">xtol</span> <span class="o">=</span> <span class="mi">1</span> |
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| 96 | <span class="c">#xtol = 1e-4</span> |
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| 97 | <span class="sd">"""Stop when simplex vertices are within xtol of each other"""</span> |
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| 98 | <span class="n">ftol</span> <span class="o">=</span> <span class="mf">1e-4</span> |
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| 99 | <span class="sd">"""Stop when vertex values are within ftol of each other"""</span> |
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| 100 | <span class="n">maxiter</span> <span class="o">=</span> <span class="bp">None</span> |
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| 101 | <span class="sd">"""Maximum number of iterations before fit terminates"""</span> |
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| 102 | <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> |
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| 103 | <span class="sd">"""Run the fit"""</span> |
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| 104 | <span class="bp">self</span><span class="o">.</span><span class="n">cancel</span> <span class="o">=</span> <span class="bp">False</span> |
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| 105 | <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> |
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| 106 | <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> |
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| 107 | <span class="n">result</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> |
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| 108 | <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> |
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| 109 | <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> |
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| 110 | <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> |
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| 111 | <span class="c">#print "calls:",result.calls</span> |
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| 112 | <span class="c">#print "simplex returned",result.x,result.fx</span> |
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| 113 | <span class="c"># Need to make our own copy of the fit results so that the</span> |
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| 114 | <span class="c"># values don't get stomped on by the next fit iteration.</span> |
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| 115 | <span class="n">fitpars</span> <span class="o">=</span> <span class="p">[</span><span class="n">fitresult</span><span class="o">.</span><span class="n">FitParameter</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> |
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| 116 | <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> |
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| 117 | <span class="n">res</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="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> |
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| 118 | <span class="c"># Compute the parameter uncertainties from the jacobian</span> |
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| 119 | <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> |
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| 120 | <span class="k">return</span> <span class="n">res</span> |
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| 121 | |
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| 122 | <span class="k">def</span> <span class="nf">abort</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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| 123 | <span class="sd">"""Cancel the fit in progress from another thread of execution"""</span> |
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| 124 | <span class="c"># Effectively an atomic operation; rely on GIL to protect it.</span> |
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| 125 | <span class="bp">self</span><span class="o">.</span><span class="n">cancel</span> <span class="o">=</span> <span class="bp">True</span> |
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| 126 | <span class="c"># Abort the current function evaluation if possible.</span> |
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| 127 | <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">fitness</span><span class="p">,</span><span class="s">'abort'</span><span class="p">):</span> <span class="bp">self</span><span class="o">.</span><span class="n">fitness</span><span class="o">.</span><span class="n">abort</span><span class="p">()</span> |
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| 128 | |
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| 129 | <span class="k">def</span> <span class="nf">_iscancelled</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">cancel</span> |
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| 130 | |
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| 131 | <span class="k">class</span> <span class="nc">MapMC</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
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| 132 | <span class="sd">"""</span> |
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| 133 | <span class="sd"> Evaluate a local fit at a particular start point.</span> |
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| 134 | |
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| 135 | <span class="sd"> This is the function to be mapped across a set of start points for the</span> |
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| 136 | <span class="sd"> monte carlo map-reduce implementation.</span> |
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| 137 | |
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| 138 | <span class="sd"> See `park.pmap.Mapper` for required interface.</span> |
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| 139 | <span class="sd"> """</span> |
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| 140 | <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">minimizer</span><span class="p">,</span> <span class="n">fitness</span><span class="p">):</span> |
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| 141 | <span class="bp">self</span><span class="o">.</span><span class="n">minimizer</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">fitness</span> <span class="o">=</span> <span class="n">minimizer</span><span class="p">,</span> <span class="n">fitness</span> |
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| 142 | <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">x0</span><span class="p">):</span> |
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| 143 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">minimizer</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">fitness</span><span class="p">,</span><span class="n">x0</span><span class="p">)</span> |
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| 144 | <span class="k">def</span> <span class="nf">abort</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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| 145 | <span class="bp">self</span><span class="o">.</span><span class="n">minimizer</span><span class="o">.</span><span class="n">abort</span><span class="p">()</span> |
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| 146 | |
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| 147 | <span class="k">class</span> <span class="nc">CollectMC</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
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| 148 | <span class="sd">"""</span> |
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| 149 | <span class="sd"> Collect the results from multiple start points in a Monte Carlo fit engine.</span> |
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| 150 | |
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| 151 | <span class="sd"> See `park.pmap.Collector` for required interface.</span> |
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| 152 | <span class="sd"> """</span> |
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| 153 | <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">number_expected</span><span class="p">,</span> <span class="n">handler</span><span class="p">):</span> |
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| 154 | <span class="bp">self</span><span class="o">.</span><span class="n">number_expected</span> <span class="o">=</span> <span class="n">number_expected</span> |
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| 155 | <span class="sd">"""Number of starting points to check with local optimizer"""</span> |
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| 156 | <span class="bp">self</span><span class="o">.</span><span class="n">iterations</span> <span class="o">=</span> <span class="mi">0</span> |
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| 157 | <span class="bp">self</span><span class="o">.</span><span class="n">best</span> <span class="o">=</span> <span class="bp">None</span> |
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| 158 | <span class="bp">self</span><span class="o">.</span><span class="n">calls</span> <span class="o">=</span> <span class="mi">0</span> |
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| 159 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span> <span class="o">=</span> <span class="n">handler</span> |
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| 160 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">done</span> <span class="o">=</span> <span class="bp">False</span> |
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| 161 | <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">result</span><span class="p">):</span> |
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| 162 | <span class="c"># Keep track of the amount of work done</span> |
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| 163 | <span class="bp">self</span><span class="o">.</span><span class="n">iterations</span> <span class="o">+=</span> <span class="mi">1</span> |
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| 164 | <span class="bp">self</span><span class="o">.</span><span class="n">calls</span> <span class="o">+=</span> <span class="n">result</span><span class="o">.</span><span class="n">calls</span> |
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| 165 | <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">best</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> <span class="n">result</span><span class="o">.</span><span class="n">fitness</span> <span class="o"><</span> <span class="bp">self</span><span class="o">.</span><span class="n">best</span><span class="o">.</span><span class="n">fitness</span><span class="p">:</span> |
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| 166 | <span class="bp">self</span><span class="o">.</span><span class="n">best</span> <span class="o">=</span> <span class="n">result</span> |
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| 167 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">result</span> <span class="o">=</span> <span class="n">result</span> |
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| 168 | <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> |
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| 169 | <span class="c"># Progress should go after improvement in case the fit handler</span> |
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| 170 | <span class="c"># wants to suppress intermediate improvements</span> |
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| 171 | <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="bp">self</span><span class="o">.</span><span class="n">iterations</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">number_expected</span><span class="p">)</span> |
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| 172 | <span class="k">def</span> <span class="nf">abort</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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| 173 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">done</span> <span class="o">=</span> <span class="bp">True</span> |
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| 174 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">abort</span><span class="p">()</span> |
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| 175 | <span class="k">def</span> <span class="nf">finalize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
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| 176 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">calls</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">calls</span> |
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| 177 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">done</span> <span class="o">=</span> <span class="bp">True</span> |
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| 178 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">finalize</span><span class="p">()</span> |
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| 179 | <span class="k">def</span> <span class="nf">error</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">msg</span><span class="p">):</span> |
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| 180 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">done</span> <span class="o">=</span> <span class="bp">True</span> |
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| 181 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span> |
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| 182 | |
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| 183 | <span class="k">def</span> <span class="nf">fitmc</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> <span class="n">localfit</span><span class="p">,</span> <span class="n">n</span><span class="p">,</span> <span class="n">handler</span><span class="p">):</span> |
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| 184 | <div class="viewcode-block" id="fitmc"><a class="viewcode-back" href="../../dev/api/park.html#park.fitmc.fitmc">[docs]</a> <span class="sd">"""</span> |
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| 185 | <span class="sd"> Run a monte carlo fit.</span> |
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| 186 | |
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| 187 | <span class="sd"> This procedure maps a local optimizer across a set of n initial points.</span> |
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| 188 | <span class="sd"> The initial parameter value defined by the fitness parameters defines</span> |
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| 189 | <span class="sd"> one initial point. The remainder are randomly generated within the</span> |
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| 190 | <span class="sd"> bounds of the problem.</span> |
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| 191 | |
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| 192 | <span class="sd"> localfit is the local optimizer to use. It should be a bounded</span> |
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| 193 | <span class="sd"> optimizer following the `park.fitmc.LocalFit` interface.</span> |
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| 194 | |
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| 195 | <span class="sd"> handler accepts updates to the current best set of fit parameters.</span> |
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| 196 | <span class="sd"> See `park.fitresult.FitHandler` for details.</span> |
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| 197 | <span class="sd"> """</span> |
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| 198 | <span class="c"># Generate random number within bounds. If bounds are indefinite, use [0,1]</span> |
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| 199 | <span class="c"># If bounds are semi-definite, use [low,low+1] or [high-1,high], depending</span> |
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| 200 | <span class="c"># on which limit is unbounded.</span> |
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| 201 | <span class="n">lo</span><span class="p">,</span><span class="n">hi</span> <span class="o">=</span> <span class="n">bounds</span> |
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| 202 | <span class="n">inf_lo</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">isinf</span><span class="p">(</span><span class="n">lo</span><span class="p">)</span> |
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| 203 | <span class="n">inf_hi</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">isinf</span><span class="p">(</span><span class="n">hi</span><span class="p">)</span> |
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| 204 | <span class="n">delta</span> <span class="o">=</span> <span class="n">hi</span><span class="o">-</span><span class="n">lo</span> |
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| 205 | <span class="n">delta</span><span class="p">[</span><span class="n">inf_lo</span><span class="o">|</span><span class="n">inf_hi</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.0</span> |
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| 206 | <span class="n">lo</span><span class="p">[</span><span class="n">inf_lo</span><span class="p">]</span> <span class="o">=</span> <span class="n">hi</span><span class="p">[</span><span class="n">inf_lo</span><span class="p">]</span> <span class="o">-</span> <span class="mf">1.0</span> |
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| 207 | <span class="n">lo</span><span class="p">[</span><span class="n">inf_lo</span><span class="o">&</span><span class="n">inf_hi</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.0</span> |
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| 208 | <span class="n">P</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">rand</span><span class="p">(</span><span class="n">n</span><span class="p">,</span><span class="nb">len</span><span class="p">(</span><span class="n">x0</span><span class="p">))</span><span class="o">*</span><span class="n">delta</span><span class="o">+</span><span class="n">lo</span> |
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| 209 | <span class="c">#print "Population",P</span> |
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| 210 | <span class="n">P</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">x0</span> |
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| 211 | |
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| 212 | <span class="n">pmap</span><span class="o">.</span><span class="n">pmapreduce</span><span class="p">(</span><span class="n">MapMC</span><span class="p">(</span><span class="n">localfit</span><span class="p">,</span><span class="n">fitness</span><span class="p">),</span> |
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| 213 | <span class="n">CollectMC</span><span class="p">(</span><span class="n">n</span><span class="p">,</span><span class="n">handler</span><span class="p">),</span> |
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| 214 | <span class="n">P</span><span class="p">)</span> |
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| 215 | |
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| 216 | <span class="k">class</span> <span class="nc">FitMC</span><span class="p">(</span><span class="n">fit</span><span class="o">.</span><span class="n">Fitter</span><span class="p">):</span></div> |
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| 217 | <span class="sd">"""</span> |
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| 218 | <span class="sd"> Monte Carlo optimizer.</span> |
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| 219 | |
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| 220 | <span class="sd"> This implements `park.fit.Fitter`.</span> |
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| 221 | <span class="sd"> """</span> |
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| 222 | <span class="n">localfit</span> <span class="o">=</span> <span class="n">FitSimplex</span><span class="p">()</span> |
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| 223 | <span class="n">start_points</span> <span class="o">=</span> <span class="mi">10</span> |
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| 224 | |
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| 225 | <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> |
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| 226 | <span class="sd">"""</span> |
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| 227 | <span class="sd"> Run a monte carlo fit.</span> |
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| 228 | |
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| 229 | <span class="sd"> This procedure maps a local optimizer across a set of initial points.</span> |
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| 230 | <span class="sd"> """</span> |
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| 231 | <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> |
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| 232 | <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> |
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| 233 | |
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| 234 | <span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">"__main__"</span><span class="p">:</span> |
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| 235 | <span class="n">fit</span><span class="o">.</span><span class="n">demo2</span><span class="p">(</span><span class="n">FitMC</span><span class="p">(</span><span class="n">localfit</span><span class="o">=</span><span class="n">FitSimplex</span><span class="p">(),</span><span class="n">start_points</span><span class="o">=</span><span class="mi">10</span><span class="p">))</span> |
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| 236 | </pre></div> |
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| 237 | |
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