[a462c6a] | 1 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" |
---|
| 2 | "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> |
---|
| 3 | |
---|
| 4 | |
---|
| 5 | <html xmlns="http://www.w3.org/1999/xhtml"> |
---|
| 6 | <head> |
---|
| 7 | <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> |
---|
| 8 | |
---|
| 9 | <title>park.fit — SasView 3.0.0 documentation</title> |
---|
| 10 | |
---|
| 11 | <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> |
---|
| 12 | <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> |
---|
| 13 | |
---|
| 14 | <script type="text/javascript"> |
---|
| 15 | var DOCUMENTATION_OPTIONS = { |
---|
| 16 | URL_ROOT: '../../', |
---|
| 17 | VERSION: '3.0.0', |
---|
| 18 | COLLAPSE_INDEX: false, |
---|
| 19 | FILE_SUFFIX: '.html', |
---|
| 20 | HAS_SOURCE: true |
---|
| 21 | }; |
---|
| 22 | </script> |
---|
| 23 | <script type="text/javascript" src="../../_static/jquery.js"></script> |
---|
| 24 | <script type="text/javascript" src="../../_static/underscore.js"></script> |
---|
| 25 | <script type="text/javascript" src="../../_static/doctools.js"></script> |
---|
| 26 | <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> |
---|
| 27 | <link rel="top" title="SasView 3.0.0 documentation" href="../../index.html" /> |
---|
| 28 | <link rel="up" title="Module code" href="../index.html" /> |
---|
| 29 | </head> |
---|
| 30 | <body> |
---|
| 31 | <div class="related"> |
---|
| 32 | <h3>Navigation</h3> |
---|
| 33 | <ul> |
---|
| 34 | <li class="right" style="margin-right: 10px"> |
---|
| 35 | <a href="../../genindex.html" title="General Index" |
---|
| 36 | accesskey="I">index</a></li> |
---|
| 37 | <li class="right" > |
---|
| 38 | <a href="../../py-modindex.html" title="Python Module Index" |
---|
| 39 | >modules</a> |</li> |
---|
| 40 | <li><a href="../../index.html">SasView 3.0.0 documentation</a> »</li> |
---|
| 41 | <li><a href="../index.html" accesskey="U">Module code</a> »</li> |
---|
| 42 | </ul> |
---|
| 43 | </div> |
---|
| 44 | |
---|
| 45 | <div class="document"> |
---|
| 46 | <div class="documentwrapper"> |
---|
| 47 | <div class="bodywrapper"> |
---|
| 48 | <div class="body"> |
---|
| 49 | |
---|
| 50 | <h1>Source code for park.fit</h1><div class="highlight"><pre> |
---|
| 51 | <span class="c"># This program is public domain</span> |
---|
| 52 | <span class="sd">"""</span> |
---|
| 53 | <span class="sd">Fitting service interface.</span> |
---|
| 54 | |
---|
| 55 | <span class="sd">A fit consists of a set of models and a fitting engine. The models are</span> |
---|
| 56 | <span class="sd">collected in an assembly, which manages the parameter set and the</span> |
---|
| 57 | <span class="sd">constraints between them. The models themselves are tightly coupled</span> |
---|
| 58 | <span class="sd">to the data that they are modeling and the data is invisible to the fit.</span> |
---|
| 59 | |
---|
| 60 | <span class="sd">The fitting engine can use a variety of methods depending on model.</span> |
---|
| 61 | |
---|
| 62 | |
---|
| 63 | <span class="sd">Usage</span> |
---|
| 64 | <span class="sd">=====</span> |
---|
| 65 | |
---|
| 66 | <span class="sd">The fitter can be run directly on the local machine::</span> |
---|
| 67 | |
---|
| 68 | <span class="sd"> import park</span> |
---|
| 69 | <span class="sd"> M1 = park.models.Peaks(datafile=park.sampledata('peak.dat'))</span> |
---|
| 70 | <span class="sd"> M1.add_peak('P1', 'gaussian', A=[4,6], mu=[0.2, 0.5], sigma=0.1)</span> |
---|
| 71 | <span class="sd"> result = park.fit(models=[M1])</span> |
---|
| 72 | <span class="sd"> print result</span> |
---|
| 73 | |
---|
| 74 | <span class="sd">The default settings print results every time the fit improves, and</span> |
---|
| 75 | <span class="sd">print a global result when the fit is complete. This is a suitable</span> |
---|
| 76 | <span class="sd">interface for a fitting script.</span> |
---|
| 77 | |
---|
| 78 | <span class="sd">For larger fit jobs you will want to run the fit on a remote server.</span> |
---|
| 79 | <span class="sd">The model setup is identical, but the fit call is different::</span> |
---|
| 80 | |
---|
| 81 | <span class="sd"> service = park.FitService('server:port')</span> |
---|
| 82 | <span class="sd"> result = park.fit(models=[M1], service=service)</span> |
---|
| 83 | <span class="sd"> print result</span> |
---|
| 84 | |
---|
| 85 | <span class="sd">Again, the default settings print results every time the fit improves,</span> |
---|
| 86 | <span class="sd">and print a global result when the fit is complete.</span> |
---|
| 87 | |
---|
| 88 | <span class="sd">For long running fit jobs, you want to be able to disconnect from</span> |
---|
| 89 | <span class="sd">the server after submitting the job, and later reconnect to fetch</span> |
---|
| 90 | <span class="sd">the results. An additional email field will send notification by</span> |
---|
| 91 | <span class="sd">email when the fit starts and ends, and daily updates on the status</span> |
---|
| 92 | <span class="sd">of all fits::</span> |
---|
| 93 | |
---|
| 94 | <span class="sd"> service = park.FitService('server:port')</span> |
---|
| 95 | <span class="sd"> service.notify(email='me@my.email.address',update='daily')</span> |
---|
| 96 | <span class="sd"> fit = park.Fit(models=[M1])</span> |
---|
| 97 | <span class="sd"> id = service.submit_job(fit, jobname='peaks')</span> |
---|
| 98 | <span class="sd"> print id</span> |
---|
| 99 | |
---|
| 100 | <span class="sd">The results can be retrieved either by id returned from the server,</span> |
---|
| 101 | <span class="sd">or by the given jobname::</span> |
---|
| 102 | |
---|
| 103 | <span class="sd"> import park</span> |
---|
| 104 | <span class="sd"> service = park.FitService('server:port',user='userid')</span> |
---|
| 105 | <span class="sd"> fitlist = service.retrieve('peaks')</span> |
---|
| 106 | <span class="sd"> for fit in fitlist:</span> |
---|
| 107 | <span class="sd"> print fit.summary()</span> |
---|
| 108 | |
---|
| 109 | <span class="sd">The fit itself is a complicated object, including the model, the</span> |
---|
| 110 | <span class="sd">optimizer, and the type of uncertainty analysis to perform.</span> |
---|
| 111 | |
---|
| 112 | <span class="sd">GUI Usage</span> |
---|
| 113 | <span class="sd">=========</span> |
---|
| 114 | |
---|
| 115 | <span class="sd">When used from a graphical user interface, a different programming</span> |
---|
| 116 | <span class="sd">interface is needed. In this case, the user may want to watch</span> |
---|
| 117 | <span class="sd">the progress of the fit and perhaps stop it. Also, as fits can</span> |
---|
| 118 | <span class="sd">take some time to complete, the user would like to be able to</span> |
---|
| 119 | <span class="sd">set up additional fits and run them at the same time, switching</span> |
---|
| 120 | <span class="sd">between them as necessary to monitor progress.</span> |
---|
| 121 | |
---|
| 122 | <span class="sd">"""</span> |
---|
| 123 | <span class="kn">import</span> <span class="nn">time</span><span class="o">,</span> <span class="nn">thread</span> |
---|
| 124 | |
---|
| 125 | <span class="kn">import</span> <span class="nn">numpy</span> |
---|
| 126 | |
---|
| 127 | <span class="kn">import</span> <span class="nn">assembly</span><span class="o">,</span> <span class="nn">fitresult</span> |
---|
| 128 | |
---|
| 129 | <div class="viewcode-block" id="Objective"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.Objective">[docs]</a><span class="k">class</span> <span class="nc">Objective</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
---|
| 130 | <span class="sd">"""</span> |
---|
| 131 | <span class="sd"> Abstract interface to the fitness function for the park minimizer</span> |
---|
| 132 | <span class="sd"> classes.</span> |
---|
| 133 | |
---|
| 134 | <span class="sd"> Park provides a specific implementation `park.assembly.Assembly`.</span> |
---|
| 135 | |
---|
| 136 | <span class="sd"> TODO: add a results() method to return model specific info to the</span> |
---|
| 137 | <span class="sd"> TODO: fit handler.</span> |
---|
| 138 | <span class="sd"> """</span> |
---|
| 139 | <div class="viewcode-block" id="Objective.residuals"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.Objective.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> <span class="n">p</span><span class="p">):</span> |
---|
| 140 | <span class="sd">"""</span> |
---|
| 141 | <span class="sd"> Some fitters, notably Levenberg-Marquardt, operate directly on the</span> |
---|
| 142 | <span class="sd"> residuals vector. If the individual residuals are not available,</span> |
---|
| 143 | <span class="sd"> then LM cannot be used.</span> |
---|
| 144 | |
---|
| 145 | <span class="sd"> This method is optional.</span> |
---|
| 146 | <span class="sd"> """</span> |
---|
| 147 | <span class="k">raise</span> <span class="ne">NotImplementedError</span> |
---|
| 148 | </div> |
---|
| 149 | <div class="viewcode-block" id="Objective.residuals_deriv"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.Objective.residuals_deriv">[docs]</a> <span class="k">def</span> <span class="nf">residuals_deriv</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">p</span><span class="p">):</span> |
---|
| 150 | <span class="sd">"""</span> |
---|
| 151 | <span class="sd"> Returns residuals and derivatives with respect to the given</span> |
---|
| 152 | <span class="sd"> parameters.</span> |
---|
| 153 | |
---|
| 154 | <span class="sd"> If these are unavailable in the model, then they can be approximated</span> |
---|
| 155 | <span class="sd"> by numerical derivatives, though it is generally better to use a</span> |
---|
| 156 | <span class="sd"> derivative free optimizer such as coliny or cobyla which can use the</span> |
---|
| 157 | <span class="sd"> function evaluations more efficiently. In any case, your objective</span> |
---|
| 158 | <span class="sd"> function is responsible for calculating these.</span> |
---|
| 159 | |
---|
| 160 | <span class="sd"> This method is optional.</span> |
---|
| 161 | <span class="sd"> """</span> |
---|
| 162 | <span class="k">raise</span> <span class="ne">NotImplementedError</span> |
---|
| 163 | </div> |
---|
| 164 | <div class="viewcode-block" id="Objective.fit_parameters"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.Objective.fit_parameters">[docs]</a> <span class="k">def</span> <span class="nf">fit_parameters</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
| 165 | <span class="sd">"""</span> |
---|
| 166 | <span class="sd"> Returns a list of fit parameters. Each parameter has a name,</span> |
---|
| 167 | <span class="sd"> an initial value and a range.</span> |
---|
| 168 | |
---|
| 169 | <span class="sd"> See `park.fitresult.FitParameter` for an example.</span> |
---|
| 170 | |
---|
| 171 | <span class="sd"> On each function evaluation a new parameter set will be passed</span> |
---|
| 172 | <span class="sd"> to the fitter, with values in the same order as the list of</span> |
---|
| 173 | <span class="sd"> parameters.</span> |
---|
| 174 | <span class="sd"> """</span> |
---|
| 175 | <span class="k">raise</span> <span class="ne">NotImplementedError</span> |
---|
| 176 | </div> |
---|
| 177 | <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">p</span><span class="p">):</span> |
---|
| 178 | <span class="sd">"""</span> |
---|
| 179 | <span class="sd"> Returns the objective value for parameter set p .</span> |
---|
| 180 | <span class="sd"> """</span> |
---|
| 181 | <span class="k">raise</span> <span class="ne">NotImplementedError</span> |
---|
| 182 | |
---|
| 183 | <div class="viewcode-block" id="Objective.abort"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.Objective.abort">[docs]</a> <span class="k">def</span> <span class="nf">abort</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
| 184 | <span class="sd">"""</span> |
---|
| 185 | <span class="sd"> Halts the current function evaluation, and has it return inf.</span> |
---|
| 186 | <span class="sd"> This will be called from a separate thread. If the function</span> |
---|
| 187 | <span class="sd"> contains an expensive calculation, it should reset an abort</span> |
---|
| 188 | <span class="sd"> flag before each evaluation and test it periodically.</span> |
---|
| 189 | |
---|
| 190 | <span class="sd"> This method is optional.</span> |
---|
| 191 | <span class="sd"> """</span> |
---|
| 192 | </div></div> |
---|
| 193 | <div class="viewcode-block" id="Fitter"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.Fitter">[docs]</a><span class="k">class</span> <span class="nc">Fitter</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
---|
| 194 | <span class="sd">"""Abstract interface for a fitness optimizer.</span> |
---|
| 195 | |
---|
| 196 | <span class="sd"> A fitter has a single method, fit, which takes an objective</span> |
---|
| 197 | <span class="sd"> function (`park.fit.Objective`) and a handler.</span> |
---|
| 198 | |
---|
| 199 | <span class="sd"> For a concrete instance see `park.fitmc.FitMC`.</span> |
---|
| 200 | <span class="sd"> """</span> |
---|
| 201 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span> |
---|
| 202 | <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> |
---|
| 203 | <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">k</span><span class="p">):</span> |
---|
| 204 | <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="n">v</span><span class="p">)</span> |
---|
| 205 | <span class="k">else</span><span class="p">:</span> |
---|
| 206 | <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span><span class="n">k</span><span class="o">+</span><span class="s">" is not an attribute of "</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span><span class="p">)</span> |
---|
| 207 | |
---|
| 208 | <span class="k">def</span> <span class="nf">_threaded</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fn</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span> |
---|
| 209 | <span class="n">thread</span><span class="o">.</span><span class="n">start_new_thread</span><span class="p">(</span><span class="n">fn</span><span class="p">,</span><span class="n">args</span><span class="p">,</span><span class="n">kw</span><span class="p">)</span> |
---|
| 210 | |
---|
| 211 | |
---|
| 212 | <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> |
---|
| 213 | <span class="sd">"""</span> |
---|
| 214 | <span class="sd"> Run the actual fit in a separate thread</span> |
---|
| 215 | |
---|
| 216 | <span class="sd"> Each cycle k of n:</span> |
---|
| 217 | <span class="sd"> self.handler.progress(k,n)</span> |
---|
| 218 | <span class="sd"> Each improvement:</span> |
---|
| 219 | <span class="sd"> self.handler.result.update(x,fx,ncalls)</span> |
---|
| 220 | <span class="sd"> self.handler.improvement()</span> |
---|
| 221 | <span class="sd"> On completion (if not already performed):</span> |
---|
| 222 | <span class="sd"> self.hander.result.update(x,fx,ncalls)</span> |
---|
| 223 | <span class="sd"> self.handler.done</span> |
---|
| 224 | <span class="sd"> self.handler.finalize()</span> |
---|
| 225 | <span class="sd"> """</span> |
---|
| 226 | <span class="k">raise</span> <span class="ne">NotImplementedError</span> |
---|
| 227 | |
---|
| 228 | <div class="viewcode-block" id="Fitter.fit"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.Fitter.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">fitness</span><span class="p">,</span> <span class="n">handler</span><span class="p">):</span> |
---|
| 229 | <span class="sd">"""</span> |
---|
| 230 | <span class="sd"> Global optimizer.</span> |
---|
| 231 | |
---|
| 232 | <span class="sd"> This function should return immediately</span> |
---|
| 233 | <span class="sd"> """</span> |
---|
| 234 | <span class="c"># Determine initial value and bounds</span> |
---|
| 235 | <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> |
---|
| 236 | <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> |
---|
| 237 | <span class="n">x0</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span><span class="o">.</span><span class="n">value</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pars</span><span class="p">]</span> |
---|
| 238 | |
---|
| 239 | <span class="c"># Initialize the monitor and results.</span> |
---|
| 240 | <span class="c"># Need to make our own copy of the fit results so that the</span> |
---|
| 241 | <span class="c"># values don't get stomped on by the next fit iteration.</span> |
---|
| 242 | <span class="n">handler</span><span class="o">.</span><span class="n">done</span> <span class="o">=</span> <span class="bp">False</span> |
---|
| 243 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span> <span class="o">=</span> <span class="n">handler</span> |
---|
| 244 | <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> |
---|
| 245 | <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">x0</span><span class="p">)]</span> |
---|
| 246 | <span class="n">handler</span><span class="o">.</span><span class="n">result</span> <span class="o">=</span> <span class="n">fitresult</span><span class="o">.</span><span class="n">FitResult</span><span class="p">(</span><span class="n">fitpars</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">numpy</span><span class="o">.</span><span class="n">NaN</span><span class="p">)</span> |
---|
| 247 | |
---|
| 248 | <span class="c"># Run the fit (fit should perform _progress and _improvement updates)</span> |
---|
| 249 | <span class="c"># This function may return before the fit is complete.</span> |
---|
| 250 | <span class="bp">self</span><span class="o">.</span><span class="n">_fit</span><span class="p">(</span><span class="n">fitness</span><span class="p">,</span> <span class="n">x0</span><span class="p">,</span> <span class="n">bounds</span><span class="p">)</span> |
---|
| 251 | </div></div> |
---|
| 252 | <div class="viewcode-block" id="FitJob"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.FitJob">[docs]</a><span class="k">class</span> <span class="nc">FitJob</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
---|
| 253 | <span class="sd">"""</span> |
---|
| 254 | <span class="sd"> Fit job.</span> |
---|
| 255 | |
---|
| 256 | <span class="sd"> This implements `park.job.Job`.</span> |
---|
| 257 | <span class="sd"> """</span> |
---|
| 258 | <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">objective</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">fitter</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> |
---|
| 259 | <span class="bp">self</span><span class="o">.</span><span class="n">fitter</span> <span class="o">=</span> <span class="n">fitter</span> |
---|
| 260 | <span class="bp">self</span><span class="o">.</span><span class="n">objective</span> <span class="o">=</span> <span class="n">objective</span> |
---|
| 261 | <span class="bp">self</span><span class="o">.</span><span class="n">handler</span> <span class="o">=</span> <span class="n">handler</span> |
---|
| 262 | <div class="viewcode-block" id="FitJob.run"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.FitJob.run">[docs]</a> <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
| 263 | <span class="bp">self</span><span class="o">.</span><span class="n">fitter</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">objective</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">handler</span><span class="p">)</span> |
---|
| 264 | </div></div> |
---|
| 265 | <div class="viewcode-block" id="LocalQueue"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.LocalQueue">[docs]</a><span class="k">class</span> <span class="nc">LocalQueue</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
---|
| 266 | <span class="sd">"""</span> |
---|
| 267 | <span class="sd"> Simple interface to the local job queue. Currently supports start and</span> |
---|
| 268 | <span class="sd"> wait. Needs to support stop and status. Also, needs to be a proper queue,</span> |
---|
| 269 | <span class="sd"> and needs to allow jobs to run in separate processes according to priority,</span> |
---|
| 270 | <span class="sd"> etc. All the essentials of the remote queuing system without the remote</span> |
---|
| 271 | <span class="sd"> calls.</span> |
---|
| 272 | |
---|
| 273 | <span class="sd"> Unlike the remote queue, the local queue need not maintain persistence.</span> |
---|
| 274 | <span class="sd"> """</span> |
---|
| 275 | <span class="n">running</span> <span class="o">=</span> <span class="bp">False</span> |
---|
| 276 | <div class="viewcode-block" id="LocalQueue.start"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.LocalQueue.start">[docs]</a> <span class="k">def</span> <span class="nf">start</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">job</span><span class="p">):</span> |
---|
| 277 | <span class="bp">self</span><span class="o">.</span><span class="n">job</span> <span class="o">=</span> <span class="n">job</span> |
---|
| 278 | <span class="n">job</span><span class="o">.</span><span class="n">run</span><span class="p">()</span> |
---|
| 279 | <span class="k">return</span> <span class="nb">id</span><span class="p">(</span><span class="n">job</span><span class="p">)</span> |
---|
| 280 | </div> |
---|
| 281 | <div class="viewcode-block" id="LocalQueue.wait"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.LocalQueue.wait">[docs]</a> <span class="k">def</span> <span class="nf">wait</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">interval</span><span class="o">=.</span><span class="mi">1</span><span class="p">):</span> |
---|
| 282 | <span class="sd">"""</span> |
---|
| 283 | <span class="sd"> Wait for the job to complete. This is used in scripts to impose</span> |
---|
| 284 | <span class="sd"> a synchronous interface to the fitting service.</span> |
---|
| 285 | <span class="sd"> """</span> |
---|
| 286 | <span class="k">while</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">job</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">done</span><span class="p">:</span> |
---|
| 287 | <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="n">interval</span><span class="p">)</span> |
---|
| 288 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">job</span><span class="o">.</span><span class="n">handler</span><span class="o">.</span><span class="n">result</span> |
---|
| 289 | </div></div> |
---|
| 290 | <div class="viewcode-block" id="fit"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.fit">[docs]</a><span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="n">models</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">fitter</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">service</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> |
---|
| 291 | <span class="sd">"""</span> |
---|
| 292 | <span class="sd"> Start a fit with a set of models. The model set must be</span> |
---|
| 293 | <span class="sd"> in a form accepted by `park.assembly.Assembly`.</span> |
---|
| 294 | |
---|
| 295 | <span class="sd"> This is a convenience function which sets up the default</span> |
---|
| 296 | <span class="sd"> optimizer and uses the local fitting engine to do the work.</span> |
---|
| 297 | <span class="sd"> Progress reports are printed as they are received.</span> |
---|
| 298 | |
---|
| 299 | <span class="sd"> The choice of fitter, service and handler can be specified</span> |
---|
| 300 | <span class="sd"> by the caller.</span> |
---|
| 301 | |
---|
| 302 | <span class="sd"> The default fitter is FitMC, which is a monte carlo Nelder-Mead</span> |
---|
| 303 | <span class="sd"> simplex local optimizer with 100 random start points.</span> |
---|
| 304 | |
---|
| 305 | <span class="sd"> The default handler does nothing. Instead, ConsoleUpdate could</span> |
---|
| 306 | <span class="sd"> be used to report progress during the fit.</span> |
---|
| 307 | |
---|
| 308 | <span class="sd"> The default service is to run in a separate thread with FitThread.</span> |
---|
| 309 | <span class="sd"> Note that this will change soon to run in a separate process on</span> |
---|
| 310 | <span class="sd"> the local machine so that python's global interpreter lock does</span> |
---|
| 311 | <span class="sd"> not interfere with parallelism.</span> |
---|
| 312 | <span class="sd"> """</span> |
---|
| 313 | <span class="k">if</span> <span class="n">models</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">'fit expected a list of models'</span><span class="p">)</span> |
---|
| 314 | <span class="k">if</span> <span class="n">service</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> <span class="n">service</span> <span class="o">=</span> <span class="n">LocalQueue</span><span class="p">()</span> |
---|
| 315 | <span class="k">if</span> <span class="n">fitter</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> |
---|
| 316 | <span class="kn">import</span> <span class="nn">fitmc</span> |
---|
| 317 | <span class="n">fitter</span> <span class="o">=</span> <span class="n">fitmc</span><span class="o">.</span><span class="n">FitMC</span><span class="p">()</span> |
---|
| 318 | <span class="k">if</span> <span class="n">handler</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span> <span class="n">handler</span> <span class="o">=</span> <span class="n">fitresult</span><span class="o">.</span><span class="n">FitHandler</span><span class="p">()</span> |
---|
| 319 | |
---|
| 320 | <span class="n">objective</span> <span class="o">=</span> <span class="n">assembly</span><span class="o">.</span><span class="n">Assembly</span><span class="p">(</span><span class="n">models</span><span class="p">)</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">models</span><span class="p">,</span><span class="nb">list</span><span class="p">)</span> <span class="k">else</span> <span class="n">models</span> |
---|
| 321 | <span class="n">job</span> <span class="o">=</span> <span class="n">FitJob</span><span class="p">(</span><span class="n">objective</span><span class="p">,</span><span class="n">fitter</span><span class="p">,</span><span class="n">handler</span><span class="p">)</span> |
---|
| 322 | <span class="n">service</span><span class="o">.</span><span class="n">start</span><span class="p">(</span><span class="n">job</span><span class="p">)</span> |
---|
| 323 | <span class="k">return</span> <span class="n">service</span><span class="o">.</span><span class="n">wait</span><span class="p">()</span> |
---|
| 324 | |
---|
| 325 | </div> |
---|
| 326 | <div class="viewcode-block" id="assembly_example"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.assembly_example">[docs]</a><span class="k">def</span> <span class="nf">assembly_example</span><span class="p">():</span> |
---|
| 327 | <span class="kn">import</span> <span class="nn">park</span><span class="o">,</span> <span class="nn">time</span> |
---|
| 328 | <span class="n">problem</span> <span class="o">=</span> <span class="n">park</span><span class="o">.</span><span class="n">assembly</span><span class="o">.</span><span class="n">example</span><span class="p">()</span> |
---|
| 329 | <span class="c">#result = fit(problem)</span> |
---|
| 330 | <span class="c">#result.print_summary()</span> |
---|
| 331 | <span class="n">handler</span><span class="o">=</span><span class="n">fitresult</span><span class="o">.</span><span class="n">ConsoleUpdate</span><span class="p">(</span><span class="n">improvement_delta</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span><span class="n">progress_delta</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> |
---|
| 332 | <span class="c">#result = fit(problem, handler=handler)</span> |
---|
| 333 | <span class="n">result</span> <span class="o">=</span> <span class="n">fit</span><span class="p">(</span><span class="n">problem</span><span class="p">)</span> |
---|
| 334 | <span class="k">print</span> <span class="s">"=== Fit complete ==="</span> |
---|
| 335 | <span class="n">result</span><span class="o">.</span><span class="n">print_summary</span><span class="p">()</span> |
---|
| 336 | <span class="k">print</span> <span class="s">"=== Target values ==="</span> |
---|
| 337 | <span class="k">print</span> <span class="s">"M1: a=1, c=1.5"</span> |
---|
| 338 | <span class="k">print</span> <span class="s">"M2: a=2.5, c=3"</span> |
---|
| 339 | |
---|
| 340 | <span class="k">if</span> <span class="bp">False</span><span class="p">:</span> <span class="c"># Detailed results</span> |
---|
| 341 | <span class="k">print</span> <span class="s">"parameter vector"</span><span class="p">,</span><span class="n">result</span><span class="o">.</span><span class="n">pvec</span> |
---|
| 342 | <span class="n">problem</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">pvec</span><span class="p">)</span> |
---|
| 343 | <span class="k">print</span> <span class="s">"residuals"</span><span class="p">,</span><span class="n">problem</span><span class="o">.</span><span class="n">residuals</span> |
---|
| 344 | <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">m</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">problem</span><span class="o">.</span><span class="n">parts</span><span class="p">):</span> |
---|
| 345 | <span class="k">print</span> <span class="s">"Model"</span><span class="p">,</span><span class="n">k</span><span class="p">,</span><span class="s">"chisq"</span><span class="p">,</span><span class="n">m</span><span class="o">.</span><span class="n">chisq</span><span class="p">,</span><span class="s">"weight"</span><span class="p">,</span><span class="n">m</span><span class="o">.</span><span class="n">weight</span> |
---|
| 346 | <span class="k">print</span> <span class="s">"pars"</span><span class="p">,</span><span class="n">m</span><span class="o">.</span><span class="n">fitness</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">a</span><span class="p">,</span><span class="n">m</span><span class="o">.</span><span class="n">fitness</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">c</span> |
---|
| 347 | <span class="k">print</span> <span class="s">"x"</span><span class="p">,</span><span class="n">m</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">fit_x</span> |
---|
| 348 | <span class="k">print</span> <span class="s">"y"</span><span class="p">,</span><span class="n">m</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">fit_y</span> |
---|
| 349 | <span class="k">print</span> <span class="s">"f(x)"</span><span class="p">,</span><span class="n">m</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">fx</span> |
---|
| 350 | <span class="k">print</span> <span class="s">"(y-f(x))/dy"</span><span class="p">,</span><span class="n">m</span><span class="o">.</span><span class="n">residuals</span> |
---|
| 351 | |
---|
| 352 | </div> |
---|
| 353 | <div class="viewcode-block" id="demo"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.demo">[docs]</a><span class="k">def</span> <span class="nf">demo</span><span class="p">(</span><span class="n">fitter</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
---|
| 354 | <span class="sd">"""Multiple minima example"""</span> |
---|
| 355 | <span class="kn">import</span> <span class="nn">time</span><span class="o">,</span> <span class="nn">math</span> |
---|
| 356 | <span class="k">class</span> <span class="nc">MultiMin</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
---|
| 357 | <span class="k">def</span> <span class="nf">fit_parameters</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
| 358 | <span class="k">return</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="s">'x1'</span><span class="p">,[</span><span class="o">-</span><span class="mi">5</span><span class="p">,</span><span class="mi">5</span><span class="p">],</span><span class="mi">1</span><span class="p">)]</span> |
---|
| 359 | <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">p</span><span class="p">):</span> |
---|
| 360 | <span class="n">x</span><span class="o">=</span><span class="n">p</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> |
---|
| 361 | <span class="n">fx</span> <span class="o">=</span> <span class="n">x</span><span class="o">**</span><span class="mi">2</span> <span class="o">+</span> <span class="n">math</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">math</span><span class="o">.</span><span class="n">pi</span><span class="o">*</span><span class="n">x</span><span class="o">+</span><span class="mi">3</span><span class="o">*</span><span class="n">math</span><span class="o">.</span><span class="n">pi</span><span class="o">/</span><span class="mi">2</span><span class="p">)</span> |
---|
| 362 | <span class="k">return</span> <span class="n">fx</span> |
---|
| 363 | <span class="n">handler</span> <span class="o">=</span> <span class="n">fitresult</span><span class="o">.</span><span class="n">ConsoleUpdate</span><span class="p">()</span> <span class="c"># Show updates on the console</span> |
---|
| 364 | <span class="n">handler</span><span class="o">.</span><span class="n">progress_delta</span> <span class="o">=</span> <span class="mi">1</span> <span class="c"># Update user every second</span> |
---|
| 365 | <span class="n">handler</span><span class="o">.</span><span class="n">improvement_delta</span> <span class="o">=</span> <span class="mf">0.1</span> <span class="c"># Show improvements almost immediately</span> |
---|
| 366 | <span class="n">fitter</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">MultiMin</span><span class="p">(),</span> <span class="n">handler</span><span class="p">)</span> |
---|
| 367 | <span class="k">while</span> <span class="ow">not</span> <span class="n">handler</span><span class="o">.</span><span class="n">done</span><span class="p">:</span> <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span> |
---|
| 368 | </div> |
---|
| 369 | <div class="viewcode-block" id="demo2"><a class="viewcode-back" href="../../dev/api/park.html#park.fit.demo2">[docs]</a><span class="k">def</span> <span class="nf">demo2</span><span class="p">(</span><span class="n">fitter</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> |
---|
| 370 | <span class="kn">import</span> <span class="nn">park</span><span class="o">,</span> <span class="nn">time</span> |
---|
| 371 | <span class="n">problem</span> <span class="o">=</span> <span class="n">park</span><span class="o">.</span><span class="n">assembly</span><span class="o">.</span><span class="n">example</span><span class="p">()</span> |
---|
| 372 | <span class="n">handler</span> <span class="o">=</span> <span class="n">fitresult</span><span class="o">.</span><span class="n">ConsoleUpdate</span><span class="p">()</span> <span class="c"># Show updates on the console</span> |
---|
| 373 | <span class="n">handler</span><span class="o">.</span><span class="n">progress_delta</span> <span class="o">=</span> <span class="mi">1</span> <span class="c"># Update user every second</span> |
---|
| 374 | <span class="n">handler</span><span class="o">.</span><span class="n">improvement_delta</span> <span class="o">=</span> <span class="mi">1</span> <span class="c"># Show improvements at the same rate</span> |
---|
| 375 | <span class="n">fitter</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">problem</span><span class="p">,</span> <span class="n">handler</span><span class="p">)</span> |
---|
| 376 | <span class="k">while</span> <span class="ow">not</span> <span class="n">handler</span><span class="o">.</span><span class="n">done</span><span class="p">:</span> <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span> |
---|
| 377 | |
---|
| 378 | |
---|
| 379 | </div> |
---|
| 380 | <span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">"__main__"</span><span class="p">:</span> |
---|
| 381 | <span class="c">#main()</span> |
---|
| 382 | <span class="n">assembly_example</span><span class="p">()</span> |
---|
| 383 | </pre></div> |
---|
| 384 | |
---|
| 385 | </div> |
---|
| 386 | </div> |
---|
| 387 | </div> |
---|
| 388 | <div class="sphinxsidebar"> |
---|
| 389 | <div class="sphinxsidebarwrapper"> |
---|
| 390 | <div id="searchbox" style="display: none"> |
---|
| 391 | <h3>Quick search</h3> |
---|
| 392 | <form class="search" action="../../search.html" method="get"> |
---|
| 393 | <input type="text" name="q" /> |
---|
| 394 | <input type="submit" value="Go" /> |
---|
| 395 | <input type="hidden" name="check_keywords" value="yes" /> |
---|
| 396 | <input type="hidden" name="area" value="default" /> |
---|
| 397 | </form> |
---|
| 398 | <p class="searchtip" style="font-size: 90%"> |
---|
| 399 | Enter search terms or a module, class or function name. |
---|
| 400 | </p> |
---|
| 401 | </div> |
---|
| 402 | <script type="text/javascript">$('#searchbox').show(0);</script> |
---|
| 403 | </div> |
---|
| 404 | </div> |
---|
| 405 | <div class="clearer"></div> |
---|
| 406 | </div> |
---|
| 407 | <div class="related"> |
---|
| 408 | <h3>Navigation</h3> |
---|
| 409 | <ul> |
---|
| 410 | <li class="right" style="margin-right: 10px"> |
---|
| 411 | <a href="../../genindex.html" title="General Index" |
---|
| 412 | >index</a></li> |
---|
| 413 | <li class="right" > |
---|
| 414 | <a href="../../py-modindex.html" title="Python Module Index" |
---|
| 415 | >modules</a> |</li> |
---|
| 416 | <li><a href="../../index.html">SasView 3.0.0 documentation</a> »</li> |
---|
| 417 | <li><a href="../index.html" >Module code</a> »</li> |
---|
| 418 | </ul> |
---|
| 419 | </div> |
---|
| 420 | <div class="footer"> |
---|
| 421 | © Copyright 2013, The SasView Project. |
---|
| 422 | Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. |
---|
| 423 | </div> |
---|
| 424 | </body> |
---|
| 425 | </html> |
---|