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50 | <h1>Source code for park.fit</h1><div class="highlight"><pre> |
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51 | <span class="c"># This program is public domain</span> |
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52 | <span class="sd">"""</span> |
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53 | <span class="sd">Fitting service interface.</span> |
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54 | |
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55 | <span class="sd">A fit consists of a set of models and a fitting engine. The models are</span> |
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56 | <span class="sd">collected in an assembly, which manages the parameter set and the</span> |
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57 | <span class="sd">constraints between them. The models themselves are tightly coupled</span> |
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58 | <span class="sd">to the data that they are modeling and the data is invisible to the fit.</span> |
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59 | |
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60 | <span class="sd">The fitting engine can use a variety of methods depending on model.</span> |
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61 | |
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62 | |
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63 | <span class="sd">Usage</span> |
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64 | <span class="sd">=====</span> |
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65 | |
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66 | <span class="sd">The fitter can be run directly on the local machine::</span> |
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67 | |
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68 | <span class="sd"> import park</span> |
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69 | <span class="sd"> M1 = park.models.Peaks(datafile=park.sampledata('peak.dat'))</span> |
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70 | <span class="sd"> M1.add_peak('P1', 'gaussian', A=[4,6], mu=[0.2, 0.5], sigma=0.1)</span> |
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71 | <span class="sd"> result = park.fit(models=[M1])</span> |
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72 | <span class="sd"> print result</span> |
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73 | |
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74 | <span class="sd">The default settings print results every time the fit improves, and</span> |
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75 | <span class="sd">print a global result when the fit is complete. This is a suitable</span> |
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76 | <span class="sd">interface for a fitting script.</span> |
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77 | |
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78 | <span class="sd">For larger fit jobs you will want to run the fit on a remote server.</span> |
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79 | <span class="sd">The model setup is identical, but the fit call is different::</span> |
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80 | |
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81 | <span class="sd"> service = park.FitService('server:port')</span> |
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82 | <span class="sd"> result = park.fit(models=[M1], service=service)</span> |
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83 | <span class="sd"> print result</span> |
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84 | |
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85 | <span class="sd">Again, the default settings print results every time the fit improves,</span> |
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86 | <span class="sd">and print a global result when the fit is complete.</span> |
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87 | |
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88 | <span class="sd">For long running fit jobs, you want to be able to disconnect from</span> |
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89 | <span class="sd">the server after submitting the job, and later reconnect to fetch</span> |
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90 | <span class="sd">the results. An additional email field will send notification by</span> |
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91 | <span class="sd">email when the fit starts and ends, and daily updates on the status</span> |
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92 | <span class="sd">of all fits::</span> |
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93 | |
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94 | <span class="sd"> service = park.FitService('server:port')</span> |
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95 | <span class="sd"> service.notify(email='me@my.email.address',update='daily')</span> |
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96 | <span class="sd"> fit = park.Fit(models=[M1])</span> |
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97 | <span class="sd"> id = service.submit_job(fit, jobname='peaks')</span> |
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98 | <span class="sd"> print id</span> |
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99 | |
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100 | <span class="sd">The results can be retrieved either by id returned from the server,</span> |
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101 | <span class="sd">or by the given jobname::</span> |
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102 | |
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103 | <span class="sd"> import park</span> |
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104 | <span class="sd"> service = park.FitService('server:port',user='userid')</span> |
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105 | <span class="sd"> fitlist = service.retrieve('peaks')</span> |
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106 | <span class="sd"> for fit in fitlist:</span> |
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107 | <span class="sd"> print fit.summary()</span> |
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108 | |
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109 | <span class="sd">The fit itself is a complicated object, including the model, the</span> |
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110 | <span class="sd">optimizer, and the type of uncertainty analysis to perform.</span> |
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111 | |
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112 | <span class="sd">GUI Usage</span> |
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113 | <span class="sd">=========</span> |
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114 | |
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115 | <span class="sd">When used from a graphical user interface, a different programming</span> |
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116 | <span class="sd">interface is needed. In this case, the user may want to watch</span> |
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117 | <span class="sd">the progress of the fit and perhaps stop it. Also, as fits can</span> |
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118 | <span class="sd">take some time to complete, the user would like to be able to</span> |
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119 | <span class="sd">set up additional fits and run them at the same time, switching</span> |
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120 | <span class="sd">between them as necessary to monitor progress.</span> |
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121 | |
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122 | <span class="sd">"""</span> |
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123 | <span class="kn">import</span> <span class="nn">time</span><span class="o">,</span> <span class="nn">thread</span> |
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124 | |
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125 | <span class="kn">import</span> <span class="nn">numpy</span> |
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126 | |
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127 | <span class="kn">import</span> <span class="nn">assembly</span><span class="o">,</span> <span class="nn">fitresult</span> |
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128 | |
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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> |
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130 | <span class="sd">"""</span> |
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131 | <span class="sd"> Abstract interface to the fitness function for the park minimizer</span> |
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132 | <span class="sd"> classes.</span> |
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133 | |
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134 | <span class="sd"> Park provides a specific implementation `park.assembly.Assembly`.</span> |
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135 | |
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136 | <span class="sd"> TODO: add a results() method to return model specific info to the</span> |
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137 | <span class="sd"> TODO: fit handler.</span> |
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138 | <span class="sd"> """</span> |
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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> |
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140 | <span class="sd">"""</span> |
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141 | <span class="sd"> Some fitters, notably Levenberg-Marquardt, operate directly on the</span> |
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142 | <span class="sd"> residuals vector. If the individual residuals are not available,</span> |
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143 | <span class="sd"> then LM cannot be used.</span> |
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144 | |
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145 | <span class="sd"> This method is optional.</span> |
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146 | <span class="sd"> """</span> |
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147 | <span class="k">raise</span> <span class="ne">NotImplementedError</span> |
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148 | </div> |
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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> |
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150 | <span class="sd">"""</span> |
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151 | <span class="sd"> Returns residuals and derivatives with respect to the given</span> |
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152 | <span class="sd"> parameters.</span> |
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153 | |
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154 | <span class="sd"> If these are unavailable in the model, then they can be approximated</span> |
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155 | <span class="sd"> by numerical derivatives, though it is generally better to use a</span> |
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156 | <span class="sd"> derivative free optimizer such as coliny or cobyla which can use the</span> |
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157 | <span class="sd"> function evaluations more efficiently. In any case, your objective</span> |
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158 | <span class="sd"> function is responsible for calculating these.</span> |
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159 | |
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160 | <span class="sd"> This method is optional.</span> |
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161 | <span class="sd"> """</span> |
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162 | <span class="k">raise</span> <span class="ne">NotImplementedError</span> |
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163 | </div> |
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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> |
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165 | <span class="sd">"""</span> |
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166 | <span class="sd"> Returns a list of fit parameters. Each parameter has a name,</span> |
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167 | <span class="sd"> an initial value and a range.</span> |
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168 | |
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169 | <span class="sd"> See `park.fitresult.FitParameter` for an example.</span> |
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170 | |
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171 | <span class="sd"> On each function evaluation a new parameter set will be passed</span> |
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172 | <span class="sd"> to the fitter, with values in the same order as the list of</span> |
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173 | <span class="sd"> parameters.</span> |
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174 | <span class="sd"> """</span> |
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175 | <span class="k">raise</span> <span class="ne">NotImplementedError</span> |
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176 | </div> |
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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> |
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178 | <span class="sd">"""</span> |
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179 | <span class="sd"> Returns the objective value for parameter set p .</span> |
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180 | <span class="sd"> """</span> |
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181 | <span class="k">raise</span> <span class="ne">NotImplementedError</span> |
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182 | |
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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> |
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184 | <span class="sd">"""</span> |
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185 | <span class="sd"> Halts the current function evaluation, and has it return inf.</span> |
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186 | <span class="sd"> This will be called from a separate thread. If the function</span> |
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187 | <span class="sd"> contains an expensive calculation, it should reset an abort</span> |
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188 | <span class="sd"> flag before each evaluation and test it periodically.</span> |
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189 | |
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190 | <span class="sd"> This method is optional.</span> |
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191 | <span class="sd"> """</span> |
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192 | </div></div> |
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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> |
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194 | <span class="sd">"""Abstract interface for a fitness optimizer.</span> |
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195 | |
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196 | <span class="sd"> A fitter has a single method, fit, which takes an objective</span> |
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197 | <span class="sd"> function (`park.fit.Objective`) and a handler.</span> |
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198 | |
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199 | <span class="sd"> For a concrete instance see `park.fitmc.FitMC`.</span> |
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200 | <span class="sd"> """</span> |
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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> |
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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> |
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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> |
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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> |
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205 | <span class="k">else</span><span class="p">:</span> |
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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> |
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207 | |
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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> |
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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> |
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210 | |
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211 | |
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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> |
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213 | <span class="sd">"""</span> |
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214 | <span class="sd"> Run the actual fit in a separate thread</span> |
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215 | |
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216 | <span class="sd"> Each cycle k of n:</span> |
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217 | <span class="sd"> self.handler.progress(k,n)</span> |
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218 | <span class="sd"> Each improvement:</span> |
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219 | <span class="sd"> self.handler.result.update(x,fx,ncalls)</span> |
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220 | <span class="sd"> self.handler.improvement()</span> |
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221 | <span class="sd"> On completion (if not already performed):</span> |
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222 | <span class="sd"> self.hander.result.update(x,fx,ncalls)</span> |
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223 | <span class="sd"> self.handler.done</span> |
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224 | <span class="sd"> self.handler.finalize()</span> |
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225 | <span class="sd"> """</span> |
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226 | <span class="k">raise</span> <span class="ne">NotImplementedError</span> |
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227 | |
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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> |
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229 | <span class="sd">"""</span> |
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230 | <span class="sd"> Global optimizer.</span> |
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231 | |
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232 | <span class="sd"> This function should return immediately</span> |
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233 | <span class="sd"> """</span> |
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234 | <span class="c"># Determine initial value and bounds</span> |
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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> |
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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> |
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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> |
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238 | |
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239 | <span class="c"># Initialize the monitor and results.</span> |
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240 | <span class="c"># Need to make our own copy of the fit results so that the</span> |
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241 | <span class="c"># values don't get stomped on by the next fit iteration.</span> |
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242 | <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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243 | <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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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> |
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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> |
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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> |
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247 | |
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248 | <span class="c"># Run the fit (fit should perform _progress and _improvement updates)</span> |
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249 | <span class="c"># This function may return before the fit is complete.</span> |
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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> |
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251 | </div></div> |
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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> |
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253 | <span class="sd">"""</span> |
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254 | <span class="sd"> Fit job.</span> |
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255 | |
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256 | <span class="sd"> This implements `park.job.Job`.</span> |
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257 | <span class="sd"> """</span> |
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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> |
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259 | <span class="bp">self</span><span class="o">.</span><span class="n">fitter</span> <span class="o">=</span> <span class="n">fitter</span> |
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260 | <span class="bp">self</span><span class="o">.</span><span class="n">objective</span> <span class="o">=</span> <span class="n">objective</span> |
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261 | <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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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> |
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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> |
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264 | </div></div> |
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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> |
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266 | <span class="sd">"""</span> |
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267 | <span class="sd"> Simple interface to the local job queue. Currently supports start and</span> |
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268 | <span class="sd"> wait. Needs to support stop and status. Also, needs to be a proper queue,</span> |
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269 | <span class="sd"> and needs to allow jobs to run in separate processes according to priority,</span> |
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270 | <span class="sd"> etc. All the essentials of the remote queuing system without the remote</span> |
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271 | <span class="sd"> calls.</span> |
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272 | |
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273 | <span class="sd"> Unlike the remote queue, the local queue need not maintain persistence.</span> |
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274 | <span class="sd"> """</span> |
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275 | <span class="n">running</span> <span class="o">=</span> <span class="bp">False</span> |
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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> |
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277 | <span class="bp">self</span><span class="o">.</span><span class="n">job</span> <span class="o">=</span> <span class="n">job</span> |
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278 | <span class="n">job</span><span class="o">.</span><span class="n">run</span><span class="p">()</span> |
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279 | <span class="k">return</span> <span class="nb">id</span><span class="p">(</span><span class="n">job</span><span class="p">)</span> |
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280 | </div> |
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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> |
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282 | <span class="sd">"""</span> |
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283 | <span class="sd"> Wait for the job to complete. This is used in scripts to impose</span> |
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284 | <span class="sd"> a synchronous interface to the fitting service.</span> |
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285 | <span class="sd"> """</span> |
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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> |
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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> |
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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> |
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289 | </div></div> |
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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> |
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291 | <span class="sd">"""</span> |
---|
292 | <span class="sd"> Start a fit with a set of models. The model set must be</span> |
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293 | <span class="sd"> in a form accepted by `park.assembly.Assembly`.</span> |
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294 | |
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295 | <span class="sd"> This is a convenience function which sets up the default</span> |
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296 | <span class="sd"> optimizer and uses the local fitting engine to do the work.</span> |
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297 | <span class="sd"> Progress reports are printed as they are received.</span> |
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298 | |
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299 | <span class="sd"> The choice of fitter, service and handler can be specified</span> |
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300 | <span class="sd"> by the caller.</span> |
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301 | |
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302 | <span class="sd"> The default fitter is FitMC, which is a monte carlo Nelder-Mead</span> |
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303 | <span class="sd"> simplex local optimizer with 100 random start points.</span> |
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304 | |
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305 | <span class="sd"> The default handler does nothing. Instead, ConsoleUpdate could</span> |
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306 | <span class="sd"> be used to report progress during the fit.</span> |
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307 | |
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308 | <span class="sd"> The default service is to run in a separate thread with FitThread.</span> |
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309 | <span class="sd"> Note that this will change soon to run in a separate process on</span> |
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310 | <span class="sd"> the local machine so that python's global interpreter lock does</span> |
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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> |
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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> |
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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> |
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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> |
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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 | |
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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> |
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384 | |
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385 | </div> |
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388 | <div class="sphinxsidebar"> |
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399 | Enter search terms or a module, class or function name. |
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400 | </p> |
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