[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.model — 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.model</h1><div class="highlight"><pre> |
---|
| 51 | <span class="c"># This program is public domain</span> |
---|
| 52 | <span class="sd">"""</span> |
---|
| 53 | <span class="sd">Define a park fitting model.</span> |
---|
| 54 | |
---|
| 55 | <span class="sd">Usage</span> |
---|
| 56 | <span class="sd">-----</span> |
---|
| 57 | |
---|
| 58 | <span class="sd">The simplest sort of fitting model is something like the following::</span> |
---|
| 59 | |
---|
| 60 | <span class="sd"> import numpy</span> |
---|
| 61 | <span class="sd"> import park</span> |
---|
| 62 | <span class="sd"> def G(x,mu,sigma):</span> |
---|
| 63 | <span class="sd"> return numpy.exp(-0.5*(x-mu)**2/sigma**2)</span> |
---|
| 64 | |
---|
| 65 | <span class="sd"> class Gauss(park.Model):</span> |
---|
| 66 | <span class="sd"> parameters = ['center','width','scale']</span> |
---|
| 67 | <span class="sd"> def eval(self,x):</span> |
---|
| 68 | <span class="sd"> return self.scale * G(x,self.center,self.width)</span> |
---|
| 69 | |
---|
| 70 | <span class="sd">It has a function which is evaluated at a series of x values and</span> |
---|
| 71 | <span class="sd">a set of adjustable parameters controlling the shape of f(x).</span> |
---|
| 72 | |
---|
| 73 | <span class="sd">You can check your module with something like the following::</span> |
---|
| 74 | |
---|
| 75 | <span class="sd"> $ ipython -pylab</span> |
---|
| 76 | |
---|
| 77 | <span class="sd"> from gauss import Gauss</span> |
---|
| 78 | |
---|
| 79 | <span class="sd"> g = Gauss(center=5,width=1,scale=10)</span> |
---|
| 80 | <span class="sd"> x = asarray([1,2,3,4,5])</span> |
---|
| 81 | <span class="sd"> y = g(x)</span> |
---|
| 82 | <span class="sd"> plot(x,y)</span> |
---|
| 83 | |
---|
| 84 | <span class="sd">This should produce a plot of the Gaussian peak.</span> |
---|
| 85 | |
---|
| 86 | <span class="sd">You will then want to try your model with some data. Create a file</span> |
---|
| 87 | <span class="sd">with some dummy data, such as gauss.dat::</span> |
---|
| 88 | |
---|
| 89 | <span class="sd"> # x y</span> |
---|
| 90 | <span class="sd"> 4 2</span> |
---|
| 91 | <span class="sd"> 5 6</span> |
---|
| 92 | <span class="sd"> 6 7</span> |
---|
| 93 | <span class="sd"> 7 3</span> |
---|
| 94 | |
---|
| 95 | <span class="sd">In order to match the model to data, you need to define a fitness</span> |
---|
| 96 | <span class="sd">object. This shows the difference between the model and the data,</span> |
---|
| 97 | <span class="sd">which you can then plot or sum to create a weighted chisq value::</span> |
---|
| 98 | |
---|
| 99 | <span class="sd"> f = park.Fitness(g, 'gauss.dat')</span> |
---|
| 100 | <span class="sd"> plot(f.data.fit_x, f.residuals())</span> |
---|
| 101 | |
---|
| 102 | <span class="sd">The data file can have up to four columns, either x,y or x,y,dy</span> |
---|
| 103 | <span class="sd">or x,dx,y,dy where x,y are the measurement points and values,</span> |
---|
| 104 | <span class="sd">dx is the instrument resolution in x and dy is the uncertainty</span> |
---|
| 105 | <span class="sd">in the measurement value y. You can pass any keyword arguments</span> |
---|
| 106 | <span class="sd">to data.load that are accepted by numpy.loadtxt. For example,</span> |
---|
| 107 | <span class="sd">you can reorder columns or skip rows. Additionally, you can modify</span> |
---|
| 108 | <span class="sd">data attributes directly x,y,dx,dy and calc_x. See help on park.Data1D</span> |
---|
| 109 | <span class="sd">for details.</span> |
---|
| 110 | |
---|
| 111 | <span class="sd">Once you have your model debugged you can use it in a fit::</span> |
---|
| 112 | |
---|
| 113 | <span class="sd"> g = Gauss(center=[3,5],scale=7.2,width=[1,3])</span> |
---|
| 114 | <span class="sd"> result = park.fit((g, 'gauss.dat'))</span> |
---|
| 115 | <span class="sd"> result.plot()</span> |
---|
| 116 | |
---|
| 117 | <span class="sd">In this example, center and width are allowed to vary but scale is fixed.</span> |
---|
| 118 | |
---|
| 119 | <span class="sd">Existing models can be readily adapted to Park::</span> |
---|
| 120 | |
---|
| 121 | <span class="sd"> class Gauss(object):</span> |
---|
| 122 | <span class="sd"> "Existing model"</span> |
---|
| 123 | <span class="sd"> center,width,scale = 0,1,1</span> |
---|
| 124 | <span class="sd"> def __init__(self,**kw):</span> |
---|
| 125 | <span class="sd"> for k,v in kw.items(): setattr(self,k,v)</span> |
---|
| 126 | <span class="sd"> def eval(self,x):</span> |
---|
| 127 | <span class="sd"> return self.scale *G(x,self.center,self.width)</span> |
---|
| 128 | |
---|
| 129 | <span class="sd"> class GaussAdaptor(Gauss,Model):</span> |
---|
| 130 | <span class="sd"> "PARK adaptor"</span> |
---|
| 131 | <span class="sd"> parameters = ['center','width','scale']</span> |
---|
| 132 | <span class="sd"> def __init__(self,*args,**kw):</span> |
---|
| 133 | <span class="sd"> Model.__init__(self,*args)</span> |
---|
| 134 | <span class="sd"> Gauss.__init__(self,**kw)</span> |
---|
| 135 | |
---|
| 136 | <span class="sd"> g = GaussAdaptor(center=[3,5],scale=7.2,width=[1,3])</span> |
---|
| 137 | <span class="sd"> result = park.fit((g, 'gauss.dat'))</span> |
---|
| 138 | <span class="sd"> result.plot()</span> |
---|
| 139 | |
---|
| 140 | <span class="sd">Models can become much more complex than the ones described above,</span> |
---|
| 141 | <span class="sd">including multilevel models where fitting parameters can be added</span> |
---|
| 142 | <span class="sd">and removed dynamically.</span> |
---|
| 143 | |
---|
| 144 | <span class="sd">In many cases the park optimizer will need an adaptor for pre-existing</span> |
---|
| 145 | <span class="sd">models. The adaptor above relies on python properties to translate</span> |
---|
| 146 | <span class="sd">model.par access into model._par.get() and model._par.set() where _par</span> |
---|
| 147 | <span class="sd">is the internal name for par. This technique works for simple static</span> |
---|
| 148 | <span class="sd">models, but will not work well for sophisticated models which have,</span> |
---|
| 149 | <span class="sd">for example, a dynamic parameter set where the model parameters cannot</span> |
---|
| 150 | <span class="sd">be set as properties. A solution to this problem is to subclass the</span> |
---|
| 151 | <span class="sd">park.Parameter and override the value attribute as a property.</span> |
---|
| 152 | |
---|
| 153 | <span class="sd">Once models are defined they can be used in a variety of contexts, such</span> |
---|
| 154 | <span class="sd">as simultaneous fitting with constraints between the parameters. With</span> |
---|
| 155 | <span class="sd">some care in defining the model, computationally intensive fits can</span> |
---|
| 156 | <span class="sd">be distributed across multiple processors. We provide a simple user</span> |
---|
| 157 | <span class="sd">interface for interacting with the model parameters and managing fits.</span> |
---|
| 158 | <span class="sd">This can be extended with model specialized model editors which format</span> |
---|
| 159 | <span class="sd">the parameters in a sensible way for the model, or allow direct manipulation</span> |
---|
| 160 | <span class="sd">of the model structure. The underlying fitting engine can also be</span> |
---|
| 161 | <span class="sd">used directly from your own user interface.</span> |
---|
| 162 | |
---|
| 163 | <span class="sd">"""</span> |
---|
| 164 | |
---|
| 165 | <span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s">'Model'</span><span class="p">]</span> |
---|
| 166 | |
---|
| 167 | <span class="kn">import</span> <span class="nn">park</span> |
---|
| 168 | <span class="kn">from</span> <span class="nn">park.parameter</span> <span class="kn">import</span> <span class="n">Parameter</span><span class="p">,</span> <span class="n">ParameterSet</span> |
---|
| 169 | <span class="kn">from</span> <span class="nn">copy</span> <span class="kn">import</span> <span class="n">copy</span><span class="p">,</span> <span class="n">deepcopy</span> |
---|
| 170 | |
---|
| 171 | |
---|
| 172 | <span class="k">class</span> <span class="nc">ParameterProperty</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
---|
| 173 | <span class="sd">"""</span> |
---|
| 174 | <span class="sd"> Attribute accessor for a named parameter.</span> |
---|
| 175 | |
---|
| 176 | <span class="sd"> Objects of class ParameterProperty act similarly to normal property</span> |
---|
| 177 | <span class="sd"> objects in that assignment to object.attr triggers the __set__</span> |
---|
| 178 | <span class="sd"> method of ParameterProperty and queries of the value object.attr</span> |
---|
| 179 | <span class="sd"> triggers the __get__ method. These methods look up the actual</span> |
---|
| 180 | <span class="sd"> parameter in the dictionary model.parameterset, delegating the</span> |
---|
| 181 | <span class="sd"> the set/get methods of the underlying parameter object.</span> |
---|
| 182 | |
---|
| 183 | <span class="sd"> For example::</span> |
---|
| 184 | |
---|
| 185 | <span class="sd"> model.P1 = 5</span> |
---|
| 186 | <span class="sd"> print model.P1</span> |
---|
| 187 | |
---|
| 188 | <span class="sd"> is equivalent to::</span> |
---|
| 189 | |
---|
| 190 | <span class="sd"> model.parameterset['P1'].set(5)</span> |
---|
| 191 | <span class="sd"> print model.parameterset['P1'].get()</span> |
---|
| 192 | |
---|
| 193 | <span class="sd"> To enable this behaviour, the model developer must assign a</span> |
---|
| 194 | <span class="sd"> ParameterProperty object to a class attribute of the model. It</span> |
---|
| 195 | <span class="sd"> must be a class attribute. Properties assigned as an instance</span> |
---|
| 196 | <span class="sd"> attribute in the __init__ of the class will not be recognized</span> |
---|
| 197 | <span class="sd"> as properties.</span> |
---|
| 198 | |
---|
| 199 | <span class="sd"> An example model will look something like the following::</span> |
---|
| 200 | |
---|
| 201 | <span class="sd"> class MyModel:</span> |
---|
| 202 | <span class="sd"> # A property must be assigned as a class attribute!</span> |
---|
| 203 | <span class="sd"> P1 = ParameterProperty('P1')</span> |
---|
| 204 | <span class="sd"> P2 = ParameterProperty('P2')</span> |
---|
| 205 | <span class="sd"> def __init__(self, P1=None, P2=None):</span> |
---|
| 206 | <span class="sd"> parP1 = Parameter('P1')</span> |
---|
| 207 | <span class="sd"> if P1 is not None: parP1.set(P1)</span> |
---|
| 208 | <span class="sd"> parP2 = Parameter('P2')</span> |
---|
| 209 | <span class="sd"> if P2 is not None: parP2.set(P2)</span> |
---|
| 210 | <span class="sd"> self.parameterset = { 'P1': parP1, 'P2': parP2 }</span> |
---|
| 211 | |
---|
| 212 | <span class="sd"> This work is done implicitly by MetaModel, and by subclassing</span> |
---|
| 213 | <span class="sd"> the class Model, the model developer does not ever need to</span> |
---|
| 214 | <span class="sd"> use ParameterProperty.</span> |
---|
| 215 | <span class="sd"> """</span> |
---|
| 216 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">name</span><span class="p">,</span><span class="o">**</span><span class="n">kw</span><span class="p">):</span> |
---|
| 217 | <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span> |
---|
| 218 | <span class="k">def</span> <span class="nf">__get__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">instance</span><span class="p">,</span><span class="n">cls</span><span class="p">):</span> |
---|
| 219 | <span class="k">return</span> <span class="n">instance</span><span class="o">.</span><span class="n">parameterset</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">()</span> |
---|
| 220 | <span class="k">def</span> <span class="nf">__set__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">instance</span><span class="p">,</span><span class="n">value</span><span class="p">):</span> |
---|
| 221 | <span class="n">instance</span><span class="o">.</span><span class="n">parameterset</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">]</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">value</span><span class="p">)</span> |
---|
| 222 | |
---|
| 223 | |
---|
| 224 | <span class="k">class</span> <span class="nc">MetaModel</span><span class="p">(</span><span class="nb">type</span><span class="p">):</span> |
---|
| 225 | <span class="sd">"""</span> |
---|
| 226 | <span class="sd"> Interpret parameters.</span> |
---|
| 227 | |
---|
| 228 | <span class="sd"> This is a meta class, and the usual meta class rules apply. That is,</span> |
---|
| 229 | <span class="sd"> the Model base class should be defined like::</span> |
---|
| 230 | |
---|
| 231 | <span class="sd"> class Model(object):</span> |
---|
| 232 | <span class="sd"> __metaclass__ = MetaModel</span> |
---|
| 233 | <span class="sd"> ...</span> |
---|
| 234 | |
---|
| 235 | <span class="sd"> The MetaModel.__new__ method is called whenever a new Model</span> |
---|
| 236 | <span class="sd"> class is created. The name of the model, its superclasses and</span> |
---|
| 237 | <span class="sd"> its attributes are passed to MetaModel.__new__ which creates the</span> |
---|
| 238 | <span class="sd"> actual class. It is not called for new instances of the model.</span> |
---|
| 239 | |
---|
| 240 | <span class="sd"> MetaModel is designed to simplify the definition of parameters for</span> |
---|
| 241 | <span class="sd"> the model. When processing the class, MetaModel defines</span> |
---|
| 242 | <span class="sd"> parameters which is a list of names of all the parameters in the</span> |
---|
| 243 | <span class="sd"> model, and parameterset, which is a dictionary of the actual</span> |
---|
| 244 | <span class="sd"> parameters and any parameter sets in the model.</span> |
---|
| 245 | |
---|
| 246 | <span class="sd"> Parameters can be defined using a list of names in the parameter</span> |
---|
| 247 | <span class="sd"> attribute, or by defining the individual parameters as separate</span> |
---|
| 248 | <span class="sd"> attributes of class Parameter.</span> |
---|
| 249 | |
---|
| 250 | <span class="sd"> For example, the following defines parameters P1, P2, and P3::</span> |
---|
| 251 | |
---|
| 252 | <span class="sd"> class MyModel(Model):</span> |
---|
| 253 | <span class="sd"> parameters = ['P1','P2']</span> |
---|
| 254 | <span class="sd"> P2 = Parameter(range=[0,inf])</span> |
---|
| 255 | <span class="sd"> P3 = Parameter()</span> |
---|
| 256 | |
---|
| 257 | <span class="sd"> For each parameter, MetaModel will define a parameter accessor,</span> |
---|
| 258 | <span class="sd"> and add the parameter definition to the parameter set. The accessor</span> |
---|
| 259 | <span class="sd"> delegates query and assignment to the Parameter get/set methods. The</span> |
---|
| 260 | <span class="sd"> attributes of the particular parameter instance can be</span> |
---|
| 261 | <span class="sd"> adjusted using model.parameterset['name'].attribute = value.</span> |
---|
| 262 | <span class="sd"> """</span> |
---|
| 263 | <span class="k">def</span> <span class="nf">__new__</span><span class="p">(</span><span class="n">cls</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">bases</span><span class="p">,</span> <span class="nb">vars</span><span class="p">):</span> |
---|
| 264 | <span class="c">#print 'calling model meta',vars</span> |
---|
| 265 | |
---|
| 266 | <span class="c"># Find all the parameters for the model. The listed parameters</span> |
---|
| 267 | <span class="c"># are defined using::</span> |
---|
| 268 | <span class="c"># parameters = ['P1', 'P2', ...]</span> |
---|
| 269 | <span class="c"># The remaining parameters are defined individually::</span> |
---|
| 270 | <span class="c"># P3 = Parameter()</span> |
---|
| 271 | <span class="c"># P4 = Parameter()</span> |
---|
| 272 | <span class="c"># The undefined parameters are those that are listed but not defined.</span> |
---|
| 273 | <span class="n">listed</span> <span class="o">=</span> <span class="nb">vars</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">'parameters'</span><span class="p">,[])</span> |
---|
| 274 | <span class="n">defined</span> <span class="o">=</span> <span class="p">[</span><span class="n">k</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">vars</span><span class="o">.</span><span class="n">items</span><span class="p">()</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">v</span><span class="p">,</span><span class="n">Parameter</span><span class="p">)]</span> |
---|
| 275 | <span class="n">undefined</span> <span class="o">=</span> <span class="p">[</span><span class="n">k</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">listed</span> <span class="k">if</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">defined</span><span class="p">]</span> |
---|
| 276 | <span class="c">#print listed,defined,undefined</span> |
---|
| 277 | |
---|
| 278 | <span class="c"># Define a getter/setter for every parameter so that the user</span> |
---|
| 279 | <span class="c"># can say model.name to access parameter name.</span> |
---|
| 280 | <span class="c">#</span> |
---|
| 281 | <span class="c"># Create a parameter object for every undefined parameter.</span> |
---|
| 282 | <span class="c"># Check if the base class defines a default value, and use</span> |
---|
| 283 | <span class="c"># that for the initial value. We don't want to do this for</span> |
---|
| 284 | <span class="c"># parameters explicitly defined since the user may have</span> |
---|
| 285 | <span class="c"># given them a default value already.</span> |
---|
| 286 | <span class="c">#</span> |
---|
| 287 | <span class="c"># For predefined parameters we must set the name explicitly.</span> |
---|
| 288 | <span class="c"># This saves the user from having to use, e.g.::</span> |
---|
| 289 | <span class="c"># P1 = Parameter('P1')</span> |
---|
| 290 | <span class="n">pars</span> <span class="o">=</span> <span class="p">[]</span> |
---|
| 291 | <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">undefined</span><span class="p">:</span> |
---|
| 292 | <span class="c"># Check if the attribute value is initialized in a base class</span> |
---|
| 293 | <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">bases</span><span class="p">:</span> |
---|
| 294 | <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">b</span><span class="p">,</span><span class="n">p</span><span class="p">):</span> |
---|
| 295 | <span class="n">value</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">b</span><span class="p">,</span><span class="n">p</span><span class="p">)</span> |
---|
| 296 | <span class="k">break</span> |
---|
| 297 | <span class="k">else</span><span class="p">:</span> |
---|
| 298 | <span class="n">value</span> <span class="o">=</span> <span class="mf">0.</span> |
---|
| 299 | <span class="c">#print "looking up value in base as",value</span> |
---|
| 300 | <span class="n">pars</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Parameter</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">p</span><span class="p">,</span><span class="n">value</span><span class="o">=</span><span class="n">value</span><span class="p">))</span> |
---|
| 301 | <span class="nb">vars</span><span class="p">[</span><span class="n">p</span><span class="p">]</span> <span class="o">=</span> <span class="n">ParameterProperty</span><span class="p">(</span><span class="n">p</span><span class="p">)</span> |
---|
| 302 | <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">defined</span><span class="p">:</span> |
---|
| 303 | <span class="c"># Make sure parameter name is correct. Note that we are using</span> |
---|
| 304 | <span class="c"># _name rather than .name to access the name attribute since</span> |
---|
| 305 | <span class="c"># name is a read-only parameter.</span> |
---|
| 306 | <span class="nb">vars</span><span class="p">[</span><span class="n">p</span><span class="p">]</span><span class="o">.</span><span class="n">_name</span> <span class="o">=</span> <span class="n">p</span> |
---|
| 307 | <span class="n">pars</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">vars</span><span class="p">[</span><span class="n">p</span><span class="p">])</span> |
---|
| 308 | <span class="nb">vars</span><span class="p">[</span><span class="n">p</span><span class="p">]</span> <span class="o">=</span> <span class="n">ParameterProperty</span><span class="p">(</span><span class="n">p</span><span class="p">)</span> |
---|
| 309 | |
---|
| 310 | <span class="c"># Construct the class attributes 'parameters' and 'parameterset'.</span> |
---|
| 311 | <span class="c"># Listed parameters are given first, with unlisted parameters</span> |
---|
| 312 | <span class="c"># following alphabetically. For hierarchical parameter sets,</span> |
---|
| 313 | <span class="c"># we also need to include the defined sets.</span> |
---|
| 314 | <span class="n">unlisted</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">defined</span><span class="o">+</span><span class="n">undefined</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">(</span><span class="n">listed</span><span class="p">))</span> |
---|
| 315 | <span class="n">unlisted</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span> |
---|
| 316 | <span class="n">parameters</span> <span class="o">=</span> <span class="n">listed</span> <span class="o">+</span> <span class="n">unlisted</span> |
---|
| 317 | <span class="n">parsets</span> <span class="o">=</span> <span class="p">[</span><span class="n">k</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">vars</span><span class="o">.</span><span class="n">items</span><span class="p">()</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">v</span><span class="p">,</span><span class="n">ParameterSet</span><span class="p">)]</span> |
---|
| 318 | <span class="nb">vars</span><span class="p">[</span><span class="s">'parameters'</span><span class="p">]</span> <span class="o">=</span> <span class="n">parameters</span> |
---|
| 319 | <span class="nb">vars</span><span class="p">[</span><span class="s">'parameterset'</span><span class="p">]</span> <span class="o">=</span> <span class="n">ParameterSet</span><span class="p">(</span><span class="n">pars</span><span class="o">=</span><span class="n">pars</span><span class="o">+</span><span class="n">parsets</span><span class="p">)</span> |
---|
| 320 | <span class="c">#print 'pars',vars['parameters']</span> |
---|
| 321 | <span class="c">#print 'parset',vars['parameterset']</span> |
---|
| 322 | |
---|
| 323 | <span class="c"># Return a new specialized instance of the class with parameters</span> |
---|
| 324 | <span class="c"># and parameterset made explicit.</span> |
---|
| 325 | <span class="k">return</span> <span class="nb">type</span><span class="o">.</span><span class="n">__new__</span><span class="p">(</span><span class="n">cls</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">bases</span><span class="p">,</span> <span class="nb">vars</span><span class="p">)</span> |
---|
| 326 | |
---|
| 327 | <div class="viewcode-block" id="Model"><a class="viewcode-back" href="../../dev/api/park.html#park.model.Model">[docs]</a><span class="k">class</span> <span class="nc">Model</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
---|
| 328 | <span class="sd">"""</span> |
---|
| 329 | <span class="sd"> Model definition.</span> |
---|
| 330 | |
---|
| 331 | <span class="sd"> The model manages attribute access to the fitting parameters and</span> |
---|
| 332 | <span class="sd"> also manages the dataset.</span> |
---|
| 333 | |
---|
| 334 | <span class="sd"> derivatives ['p1','p2',...]</span> |
---|
| 335 | <span class="sd"> List of parameters for which the model can calculate</span> |
---|
| 336 | <span class="sd"> derivatives. The derivs</span> |
---|
| 337 | <span class="sd"> The model function can compute the derivative with respect</span> |
---|
| 338 | <span class="sd"> to this parameter. The function model.derivs(x,[p1,p2,...])</span> |
---|
| 339 | <span class="sd"> will return (f(x),df/dp1(x), ...). The parameters and their</span> |
---|
| 340 | <span class="sd"> order are determined by the fitting engine.</span> |
---|
| 341 | |
---|
| 342 | <span class="sd"> Note: This is a property of the model, not the fit.</span> |
---|
| 343 | <span class="sd"> Numerical derivatives will be used if the parameter is</span> |
---|
| 344 | <span class="sd"> used in an expression or if no analytic derivative is</span> |
---|
| 345 | <span class="sd"> available for the parameter. Automatic differentiation</span> |
---|
| 346 | <span class="sd"> on parameter expressions is possible, but beyond the scope</span> |
---|
| 347 | <span class="sd"> of this project.</span> |
---|
| 348 | |
---|
| 349 | <span class="sd"> eval(x)</span> |
---|
| 350 | <span class="sd"> Evaluate the model at x. This must be defined by the subclass.</span> |
---|
| 351 | |
---|
| 352 | <span class="sd"> eval_deriv(x,pars=[])</span> |
---|
| 353 | <span class="sd"> Evaluate the model and the derivatives at x. This must be</span> |
---|
| 354 | <span class="sd"> defined by the subclass.</span> |
---|
| 355 | |
---|
| 356 | <span class="sd"> parameters</span> |
---|
| 357 | <span class="sd"> The names of the model parameters. If this is not provided, then</span> |
---|
| 358 | <span class="sd"> the model will search the subclass for park.Parameter attributes</span> |
---|
| 359 | <span class="sd"> and construct the list of names from that. Any parameters in the</span> |
---|
| 360 | <span class="sd"> list not already defined as park.Parameter attributes will be</span> |
---|
| 361 | <span class="sd"> defined as parameters with a default of 0.</span> |
---|
| 362 | |
---|
| 363 | <span class="sd"> parameterset</span> |
---|
| 364 | <span class="sd"> The set of parameters defined by the model. These are the</span> |
---|
| 365 | <span class="sd"> parameters themselves, gathered into a park.ParameterSet.</span> |
---|
| 366 | |
---|
| 367 | <span class="sd"> The minimum fittng model if you choose not to subclass park.Model</span> |
---|
| 368 | <span class="sd"> requires parameterset and a residuals() method.</span> |
---|
| 369 | <span class="sd"> """</span> |
---|
| 370 | <span class="n">__metaclass__</span> <span class="o">=</span> <span class="n">MetaModel</span> |
---|
| 371 | <span class="n">derivatives</span> <span class="o">=</span> <span class="p">[]</span> |
---|
| 372 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="o">*</span><span class="n">args</span><span class="p">,</span><span class="o">**</span><span class="n">kw</span><span class="p">):</span> |
---|
| 373 | <span class="sd">"""</span> |
---|
| 374 | <span class="sd"> Initialize the model.</span> |
---|
| 375 | |
---|
| 376 | <span class="sd"> Model('name',P1=value, P2=Value, ...)</span> |
---|
| 377 | |
---|
| 378 | <span class="sd"> When overriding __init__ in the subclass be sure to call</span> |
---|
| 379 | <span class="sd"> Model.__init__(self, *args, **kw). This makes a private</span> |
---|
| 380 | <span class="sd"> copy of the parameterset for the model and initializes</span> |
---|
| 381 | <span class="sd"> any parameters set using keyword arguments.</span> |
---|
| 382 | <span class="sd"> """</span> |
---|
| 383 | <span class="c">#print 'calling model init on',id(self)</span> |
---|
| 384 | <span class="c"># To avoid trashing the Model.parname = Parameter() template</span> |
---|
| 385 | <span class="c"># when we create an instance and accessor for the parameter</span> |
---|
| 386 | <span class="c"># we need to make sure that we are using our own copy of the</span> |
---|
| 387 | <span class="c"># model dictionary stored in vars</span> |
---|
| 388 | <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span><span class="o">></span><span class="mi">1</span><span class="p">:</span> <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">"expect name as model parameter"</span><span class="p">)</span> |
---|
| 389 | <span class="n">name</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span><span class="o">>=</span><span class="mi">1</span> <span class="k">else</span> <span class="s">'unknown'</span> |
---|
| 390 | <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="p">)</span> |
---|
| 391 | <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> |
---|
| 392 | <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> |
---|
| 393 | <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">_name</span> <span class="o">=</span> <span class="n">name</span> |
---|
| 394 | <span class="c">#print 'done',id(self)</span> |
---|
| 395 | |
---|
| 396 | <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">x</span><span class="p">,</span> <span class="n">pars</span><span class="o">=</span><span class="p">[]):</span> |
---|
| 397 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">eval</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> |
---|
| 398 | |
---|
| 399 | <div class="viewcode-block" id="Model.eval"><a class="viewcode-back" href="../../dev/api/park.html#park.model.Model.eval">[docs]</a> <span class="k">def</span> <span class="nf">eval</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span> |
---|
| 400 | <span class="sd">"""</span> |
---|
| 401 | <span class="sd"> Evaluate the model at x.</span> |
---|
| 402 | |
---|
| 403 | <span class="sd"> This method needs to be specialized in the model to evaluate the</span> |
---|
| 404 | <span class="sd"> model function. Alternatively, the model can implement is own</span> |
---|
| 405 | <span class="sd"> version of residuals which calculates the residuals directly</span> |
---|
| 406 | <span class="sd"> instead of calling eval.</span> |
---|
| 407 | <span class="sd"> """</span> |
---|
| 408 | <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s">'Model needs to implement eval'</span><span class="p">)</span> |
---|
| 409 | </div> |
---|
| 410 | <div class="viewcode-block" id="Model.eval_derivs"><a class="viewcode-back" href="../../dev/api/park.html#park.model.Model.eval_derivs">[docs]</a> <span class="k">def</span> <span class="nf">eval_derivs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">pars</span><span class="o">=</span><span class="p">[]):</span> |
---|
| 411 | <span class="sd">"""</span> |
---|
| 412 | <span class="sd"> Evaluate the model and derivatives wrt pars at x.</span> |
---|
| 413 | |
---|
| 414 | <span class="sd"> pars is a list of the names of the parameters for which derivatives</span> |
---|
| 415 | <span class="sd"> are desired.</span> |
---|
| 416 | |
---|
| 417 | <span class="sd"> This method needs to be specialized in the model to evaluate the</span> |
---|
| 418 | <span class="sd"> model function. Alternatively, the model can implement is own</span> |
---|
| 419 | <span class="sd"> version of residuals which calculates the residuals directly</span> |
---|
| 420 | <span class="sd"> instead of calling eval.</span> |
---|
| 421 | <span class="sd"> """</span> |
---|
| 422 | <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s">'Model needs to implement eval_derivs'</span><span class="p">)</span> |
---|
| 423 | </div> |
---|
| 424 | <div class="viewcode-block" id="Model.set"><a class="viewcode-back" href="../../dev/api/park.html#park.model.Model.set">[docs]</a> <span class="k">def</span> <span class="nf">set</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> |
---|
| 425 | <span class="sd">"""</span> |
---|
| 426 | <span class="sd"> Set the initial value for a set of parameters.</span> |
---|
| 427 | |
---|
| 428 | <span class="sd"> E.g., model.set(width=3,center=5)</span> |
---|
| 429 | <span class="sd"> """</span> |
---|
| 430 | <span class="c"># This is a convenience funciton for the user.</span> |
---|
| 431 | <span class="c">#</span> |
---|
| 432 | <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> |
---|
| 433 | <span class="bp">self</span><span class="o">.</span><span class="n">parameterset</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> |
---|
| 434 | |
---|
| 435 | </div></div> |
---|
| 436 | <span class="k">def</span> <span class="nf">add_parameter</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span> |
---|
| 437 | <span class="sd">"""</span> |
---|
| 438 | <span class="sd"> Add a parameter to an existing park model.</span> |
---|
| 439 | |
---|
| 440 | <span class="sd"> Note: this may not work if it is operating on a BaseModel.</span> |
---|
| 441 | <span class="sd"> """</span> |
---|
| 442 | <span class="nb">setattr</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">__class__</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">park</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">ParameterProperty</span><span class="p">(</span><span class="n">name</span><span class="p">))</span> |
---|
| 443 | <span class="n">model</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">park</span><span class="o">.</span><span class="n">Parameter</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">name</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">))</span> |
---|
| 444 | |
---|
| 445 | |
---|
| 446 | <span class="k">def</span> <span class="nf">test</span><span class="p">():</span> |
---|
| 447 | <span class="c"># Gauss theory function</span> |
---|
| 448 | <span class="kn">import</span> <span class="nn">numpy</span> |
---|
| 449 | <span class="n">eps</span><span class="p">,</span><span class="n">inf</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">finfo</span><span class="p">(</span><span class="s">'d'</span><span class="p">)</span><span class="o">.</span><span class="n">eps</span><span class="p">,</span><span class="n">numpy</span><span class="o">.</span><span class="n">inf</span> |
---|
| 450 | <span class="k">def</span> <span class="nf">G</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">mu</span><span class="p">,</span><span class="n">sigma</span><span class="p">):</span> |
---|
| 451 | <span class="n">mu</span><span class="p">,</span><span class="n">sigma</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">mu</span><span class="p">),</span><span class="n">numpy</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">sigma</span><span class="p">)</span> |
---|
| 452 | <span class="k">return</span> <span class="n">numpy</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="mf">0.5</span><span class="o">*</span><span class="p">(</span><span class="n">x</span><span class="o">-</span><span class="n">mu</span><span class="p">)</span><span class="o">**</span><span class="mi">2</span><span class="o">/</span><span class="n">sigma</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span> |
---|
| 453 | |
---|
| 454 | <span class="c"># === Minimal model ===</span> |
---|
| 455 | <span class="c"># just list the fitting parameters and define the function.</span> |
---|
| 456 | <span class="k">class</span> <span class="nc">Gauss</span><span class="p">(</span><span class="n">Model</span><span class="p">):</span> |
---|
| 457 | <span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span><span class="s">'center'</span><span class="p">,</span><span class="s">'width'</span><span class="p">,</span><span class="s">'scale'</span><span class="p">]</span> |
---|
| 458 | <span class="k">def</span> <span class="nf">eval</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">x</span><span class="p">):</span> |
---|
| 459 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">scale</span> <span class="o">*</span> <span class="n">G</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">center</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">width</span><span class="p">)</span> |
---|
| 460 | |
---|
| 461 | <span class="c"># Create a couple of models and make sure they don't conflict</span> |
---|
| 462 | <span class="n">g1</span> <span class="o">=</span> <span class="n">Gauss</span><span class="p">(</span><span class="n">center</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span><span class="n">width</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span><span class="n">scale</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span> |
---|
| 463 | <span class="k">assert</span> <span class="n">g1</span><span class="o">.</span><span class="n">center</span> <span class="o">==</span> <span class="mi">5</span> |
---|
| 464 | <span class="n">g2</span> <span class="o">=</span> <span class="n">Gauss</span><span class="p">(</span><span class="n">center</span><span class="o">=</span><span class="mi">6</span><span class="p">,</span><span class="n">width</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> |
---|
| 465 | <span class="k">assert</span> <span class="n">g1</span><span class="o">.</span><span class="n">center</span> <span class="o">==</span> <span class="mi">5</span> |
---|
| 466 | <span class="k">assert</span> <span class="n">g2</span><span class="o">.</span><span class="n">center</span> <span class="o">==</span> <span class="mi">6</span> |
---|
| 467 | <span class="k">assert</span> <span class="n">g1</span><span class="p">(</span><span class="mi">5</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span> |
---|
| 468 | <span class="k">assert</span> <span class="n">g2</span><span class="p">(</span><span class="mi">6</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> |
---|
| 469 | |
---|
| 470 | <span class="c"># === explore parameters ===</span> |
---|
| 471 | <span class="c"># dedicated model using park parameters directly, and defining derivatives</span> |
---|
| 472 | <span class="k">class</span> <span class="nc">Gauss</span><span class="p">(</span><span class="n">Model</span><span class="p">):</span> |
---|
| 473 | <span class="n">center</span> <span class="o">=</span> <span class="n">Parameter</span><span class="p">(</span><span class="n">value</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> |
---|
| 474 | <span class="n">tip</span><span class="o">=</span><span class="s">'Peak center'</span><span class="p">)</span> |
---|
| 475 | <span class="n">width</span> <span class="o">=</span> <span class="n">Parameter</span><span class="p">(</span><span class="n">value</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> |
---|
| 476 | <span class="n">limits</span><span class="o">=</span><span class="p">(</span><span class="n">eps</span><span class="p">,</span><span class="n">inf</span><span class="p">),</span> |
---|
| 477 | <span class="n">tip</span><span class="o">=</span><span class="s">'Peak width (1-sigma)'</span><span class="p">)</span> |
---|
| 478 | <span class="n">scale</span> <span class="o">=</span> <span class="n">Parameter</span><span class="p">(</span><span class="n">value</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> |
---|
| 479 | <span class="n">limits</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">inf</span><span class="p">),</span> |
---|
| 480 | <span class="n">tip</span><span class="o">=</span><span class="s">'Peak scale (>0)'</span><span class="p">)</span> |
---|
| 481 | <span class="k">def</span> <span class="nf">eval</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">x</span><span class="p">):</span> |
---|
| 482 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">scale</span> <span class="o">*</span> <span class="n">G</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">center</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">width</span><span class="p">)</span> |
---|
| 483 | |
---|
| 484 | <span class="c"># Derivatives</span> |
---|
| 485 | <span class="n">derivatives</span> <span class="o">=</span> <span class="p">[</span><span class="s">'center'</span><span class="p">,</span><span class="s">'width'</span><span class="p">,</span><span class="s">'scale'</span><span class="p">]</span> |
---|
| 486 | <span class="k">def</span> <span class="nf">dscale</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">g</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span> |
---|
| 487 | <span class="k">return</span> <span class="n">g</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">scale</span> |
---|
| 488 | <span class="k">def</span> <span class="nf">dcenter</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">g</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span> |
---|
| 489 | <span class="k">return</span> <span class="mi">2</span><span class="o">*</span><span class="p">(</span><span class="n">x</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">center</span><span class="p">)</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">width</span><span class="o">*</span><span class="n">g</span> |
---|
| 490 | <span class="k">def</span> <span class="nf">dwidth</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">g</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span> |
---|
| 491 | <span class="k">return</span> <span class="mi">2</span><span class="o">*</span><span class="p">(</span><span class="n">x</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">center</span><span class="p">)</span><span class="o">/</span><span class="bp">self</span><span class="o">.</span><span class="n">width</span><span class="o">**</span><span class="mi">3</span><span class="o">*</span><span class="n">g</span> |
---|
| 492 | <span class="n">dmap</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">scale</span><span class="o">=</span><span class="n">dscale</span><span class="p">,</span><span class="n">center</span><span class="o">=</span><span class="n">dcenter</span><span class="p">,</span><span class="n">width</span><span class="o">=</span><span class="n">dwidth</span><span class="p">)</span> |
---|
| 493 | <span class="k">def</span> <span class="nf">eval_derivs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">x</span><span class="p">,</span><span class="n">pars</span><span class="o">=</span><span class="p">[]):</span> |
---|
| 494 | <span class="sd">"""</span> |
---|
| 495 | <span class="sd"> Calculate function value and derivatives wrt to the parameters.</span> |
---|
| 496 | |
---|
| 497 | <span class="sd"> pars is a list of parameter names, possibly consisting of any</span> |
---|
| 498 | <span class="sd"> parameter with deriv=True.</span> |
---|
| 499 | <span class="sd"> """</span> |
---|
| 500 | <span class="n">g</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">eval</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> |
---|
| 501 | <span class="n">dg</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">dmap</span><span class="p">[</span><span class="n">p</span><span class="p">](</span><span class="bp">self</span><span class="p">,</span><span class="n">g</span><span class="p">,</span><span class="n">x</span><span class="p">)</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> |
---|
| 502 | <span class="k">return</span> <span class="p">[</span><span class="n">g</span><span class="p">]</span><span class="o">+</span><span class="n">dg</span> |
---|
| 503 | |
---|
| 504 | <span class="n">g1</span> <span class="o">=</span> <span class="n">Gauss</span><span class="p">(</span><span class="n">center</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span> |
---|
| 505 | <span class="n">g1</span><span class="o">.</span><span class="n">parameterset</span><span class="p">[</span><span class="s">'center'</span><span class="p">]</span><span class="o">.</span><span class="n">tip</span> <span class="o">=</span> <span class="s">'This is the center'</span> |
---|
| 506 | <span class="k">assert</span> <span class="n">g1</span><span class="o">.</span><span class="n">center</span> <span class="o">==</span> <span class="mi">5</span> |
---|
| 507 | <span class="n">g2</span> <span class="o">=</span> <span class="n">Gauss</span><span class="p">(</span><span class="n">center</span><span class="o">=</span><span class="mi">6</span><span class="p">)</span> |
---|
| 508 | <span class="k">assert</span> <span class="n">g1</span><span class="o">.</span><span class="n">center</span> <span class="o">==</span> <span class="mi">5</span> |
---|
| 509 | <span class="k">assert</span> <span class="n">g2</span><span class="o">.</span><span class="n">center</span> <span class="o">==</span> <span class="mi">6</span> |
---|
| 510 | <span class="k">assert</span> <span class="n">g1</span><span class="p">(</span><span class="mi">5</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> |
---|
| 511 | <span class="k">assert</span> <span class="n">g2</span><span class="p">(</span><span class="mi">6</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> |
---|
| 512 | |
---|
| 513 | <span class="c"># ====== Test wrapper =======</span> |
---|
| 514 | <span class="c"># delegate to existing model via inheritence</span> |
---|
| 515 | <span class="k">class</span> <span class="nc">Gauss</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
---|
| 516 | <span class="sd">"""Pre-existing model"""</span> |
---|
| 517 | <span class="n">center</span><span class="p">,</span><span class="n">width</span><span class="p">,</span><span class="n">scale</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">1</span> |
---|
| 518 | <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> |
---|
| 519 | <span class="c">#print "calling BaseGauss init on",id(self)</span> |
---|
| 520 | <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> <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> |
---|
| 521 | <span class="c">#print "done",id(self)</span> |
---|
| 522 | <span class="k">def</span> <span class="nf">eval</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">x</span><span class="p">):</span> |
---|
| 523 | <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">scale</span> <span class="o">*</span><span class="n">G</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">center</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">width</span><span class="p">)</span> |
---|
| 524 | |
---|
| 525 | <span class="k">class</span> <span class="nc">GaussAdaptor</span><span class="p">(</span><span class="n">Gauss</span><span class="p">,</span><span class="n">Model</span><span class="p">):</span> |
---|
| 526 | <span class="sd">"""PARK wrapper"""</span> |
---|
| 527 | <span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span><span class="s">'center'</span><span class="p">,</span><span class="s">'width'</span><span class="p">,</span><span class="s">'scale'</span><span class="p">]</span> |
---|
| 528 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="o">*</span><span class="n">args</span><span class="p">,</span><span class="o">**</span><span class="n">kw</span><span class="p">):</span> |
---|
| 529 | <span class="c">#print "calling Gauss init on",id(self)</span> |
---|
| 530 | <span class="n">Model</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="o">*</span><span class="n">args</span><span class="p">)</span> |
---|
| 531 | <span class="n">Gauss</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="o">**</span><span class="n">kw</span><span class="p">)</span> |
---|
| 532 | <span class="c">#print "done",id(self)</span> |
---|
| 533 | |
---|
| 534 | <span class="n">g1</span> <span class="o">=</span> <span class="n">GaussAdaptor</span><span class="p">(</span><span class="n">center</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span> |
---|
| 535 | <span class="n">g2</span> <span class="o">=</span> <span class="n">GaussAdaptor</span><span class="p">(</span><span class="n">center</span><span class="o">=</span><span class="mi">6</span><span class="p">)</span> |
---|
| 536 | <span class="n">g3</span> <span class="o">=</span> <span class="n">GaussAdaptor</span><span class="p">()</span> |
---|
| 537 | <span class="k">assert</span> <span class="n">g1</span><span class="o">.</span><span class="n">center</span> <span class="o">==</span> <span class="mi">5</span> |
---|
| 538 | <span class="k">assert</span> <span class="n">g2</span><span class="o">.</span><span class="n">center</span> <span class="o">==</span> <span class="mi">6</span> |
---|
| 539 | <span class="k">assert</span> <span class="n">g3</span><span class="o">.</span><span class="n">scale</span> <span class="o">==</span> <span class="mi">1</span> |
---|
| 540 | <span class="k">assert</span> <span class="n">g1</span><span class="p">(</span><span class="mi">5</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> |
---|
| 541 | <span class="k">assert</span> <span class="n">g2</span><span class="p">(</span><span class="mi">6</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> |
---|
| 542 | |
---|
| 543 | <span class="n">g4</span> <span class="o">=</span> <span class="n">GaussAdaptor</span><span class="p">(</span><span class="s">'M3'</span><span class="p">,</span><span class="n">center</span><span class="o">=</span><span class="mi">6</span><span class="p">)</span> |
---|
| 544 | <span class="k">assert</span> <span class="n">g4</span><span class="o">.</span><span class="n">parameterset</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s">'M3'</span> |
---|
| 545 | |
---|
| 546 | <span class="c"># dedicated multilevel model using park parameters directly</span> |
---|
| 547 | <span class="k">class</span> <span class="nc">MultiGauss</span><span class="p">(</span><span class="n">Model</span><span class="p">):</span> |
---|
| 548 | <span class="k">def</span> <span class="nf">add</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">name</span><span class="p">,</span><span class="n">model</span><span class="p">):</span> |
---|
| 549 | <span class="k">pass</span> |
---|
| 550 | |
---|
| 551 | <span class="c"># wrapped model using park parameters indirectly</span> |
---|
| 552 | <span class="k">class</span> <span class="nc">BaseMultiGauss</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> |
---|
| 553 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
| 554 | <span class="bp">self</span><span class="o">.</span><span class="n">models</span> <span class="o">=</span> <span class="p">[]</span> |
---|
| 555 | <span class="k">def</span> <span class="nf">add</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> |
---|
| 556 | <span class="bp">self</span><span class="o">.</span><span class="n">models</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">BaseGauss</span><span class="p">(</span><span class="o">**</span><span class="n">kw</span><span class="p">))</span> |
---|
| 557 | <span class="k">class</span> <span class="nc">WrapMultiGauss</span><span class="p">(</span><span class="n">BaseMultiGauss</span><span class="p">,</span><span class="n">Model</span><span class="p">):</span> |
---|
| 558 | <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> |
---|
| 559 | <span class="k">pass</span> |
---|
| 560 | |
---|
| 561 | <span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">"__main__"</span><span class="p">:</span> <span class="n">test</span><span class="p">()</span> |
---|
| 562 | </pre></div> |
---|
| 563 | |
---|
| 564 | </div> |
---|
| 565 | </div> |
---|
| 566 | </div> |
---|
| 567 | <div class="sphinxsidebar"> |
---|
| 568 | <div class="sphinxsidebarwrapper"> |
---|
| 569 | <div id="searchbox" style="display: none"> |
---|
| 570 | <h3>Quick search</h3> |
---|
| 571 | <form class="search" action="../../search.html" method="get"> |
---|
| 572 | <input type="text" name="q" /> |
---|
| 573 | <input type="submit" value="Go" /> |
---|
| 574 | <input type="hidden" name="check_keywords" value="yes" /> |
---|
| 575 | <input type="hidden" name="area" value="default" /> |
---|
| 576 | </form> |
---|
| 577 | <p class="searchtip" style="font-size: 90%"> |
---|
| 578 | Enter search terms or a module, class or function name. |
---|
| 579 | </p> |
---|
| 580 | </div> |
---|
| 581 | <script type="text/javascript">$('#searchbox').show(0);</script> |
---|
| 582 | </div> |
---|
| 583 | </div> |
---|
| 584 | <div class="clearer"></div> |
---|
| 585 | </div> |
---|
| 586 | <div class="related"> |
---|
| 587 | <h3>Navigation</h3> |
---|
| 588 | <ul> |
---|
| 589 | <li class="right" style="margin-right: 10px"> |
---|
| 590 | <a href="../../genindex.html" title="General Index" |
---|
| 591 | >index</a></li> |
---|
| 592 | <li class="right" > |
---|
| 593 | <a href="../../py-modindex.html" title="Python Module Index" |
---|
| 594 | >modules</a> |</li> |
---|
| 595 | <li><a href="../../index.html">SasView 3.0.0 documentation</a> »</li> |
---|
| 596 | <li><a href="../index.html" >Module code</a> »</li> |
---|
| 597 | </ul> |
---|
| 598 | </div> |
---|
| 599 | <div class="footer"> |
---|
| 600 | © Copyright 2013, The SasView Project. |
---|
| 601 | Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. |
---|
| 602 | </div> |
---|
| 603 | </body> |
---|
| 604 | </html> |
---|