source: sasview/_modules/park/fitresult.html @ a462c6a

gh-pages
Last change on this file since a462c6a was a462c6a, checked in by ajj, 9 years ago

Rebuild to fix index and modules docs

  • Property mode set to 100644
File size: 38.2 KB
Line 
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.fitresult &mdash; 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> &raquo;</li>
41          <li><a href="../index.html" accesskey="U">Module code</a> &raquo;</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.fitresult</h1><div class="highlight"><pre>
51<span class="kn">import</span> <span class="nn">sys</span><span class="o">,</span> <span class="nn">math</span><span class="o">,</span> <span class="nn">time</span>
52<span class="kn">import</span> <span class="nn">numpy</span>
53
54<span class="kn">from</span> <span class="nn">formatnum</span> <span class="kn">import</span> <span class="n">format_uncertainty</span>
55
56<div class="viewcode-block" id="FitHandler"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitHandler">[docs]</a><span class="k">class</span> <span class="nc">FitHandler</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
57    <span class="sd">&quot;&quot;&quot;</span>
58<span class="sd">    Abstract interface for fit thread handler.</span>
59
60<span class="sd">    The methods in this class are called by the optimizer as the fit</span>
61<span class="sd">    progresses.</span>
62
63<span class="sd">    Note that it is up to the optimizer to call the fit handler correctly,</span>
64<span class="sd">    reporting all status changes and maintaining the &#39;done&#39; flag.</span>
65<span class="sd">    &quot;&quot;&quot;</span>
66    <span class="n">done</span> <span class="o">=</span> <span class="bp">False</span>
67    <span class="sd">&quot;&quot;&quot;True when the fit job is complete&quot;&quot;&quot;</span>
68    <span class="n">result</span> <span class="o">=</span> <span class="bp">None</span>
69    <span class="sd">&quot;&quot;&quot;The current best result of the fit&quot;&quot;&quot;</span>
70
71<div class="viewcode-block" id="FitHandler.improvement"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitHandler.improvement">[docs]</a>    <span class="k">def</span> <span class="nf">improvement</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
72        <span class="sd">&quot;&quot;&quot;</span>
73<span class="sd">        Called when a result is observed which is better than previous</span>
74<span class="sd">        results from the fit.</span>
75
76<span class="sd">        result is a FitResult object, with parameters, #calls and fitness.</span>
77<span class="sd">        &quot;&quot;&quot;</span></div>
78<div class="viewcode-block" id="FitHandler.error"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitHandler.error">[docs]</a>    <span class="k">def</span> <span class="nf">error</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">msg</span><span class="p">):</span>
79        <span class="sd">&quot;&quot;&quot;</span>
80<span class="sd">        Model had an error; print traceback</span>
81<span class="sd">        &quot;&quot;&quot;</span></div>
82<div class="viewcode-block" id="FitHandler.progress"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitHandler.progress">[docs]</a>    <span class="k">def</span> <span class="nf">progress</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">current</span><span class="p">,</span> <span class="n">expected</span><span class="p">):</span>
83        <span class="sd">&quot;&quot;&quot;</span>
84<span class="sd">        Called each cycle of the fit, reporting the current and the</span>
85<span class="sd">        expected amount of work.   The meaning of these values is</span>
86<span class="sd">        optimizer dependent, but they can be converted into a percent</span>
87<span class="sd">        complete using (100*current)//expected.</span>
88
89<span class="sd">        Progress is updated each iteration of the fit, whatever that</span>
90<span class="sd">        means for the particular optimization algorithm.  It is called</span>
91<span class="sd">        after any calls to improvement for the iteration so that the</span>
92<span class="sd">        update handler can control I/O bandwidth by suppressing</span>
93<span class="sd">        intermediate improvements until the fit is complete.</span>
94<span class="sd">        &quot;&quot;&quot;</span></div>
95<div class="viewcode-block" id="FitHandler.finalize"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitHandler.finalize">[docs]</a>    <span class="k">def</span> <span class="nf">finalize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
96        <span class="sd">&quot;&quot;&quot;</span>
97<span class="sd">        Fit is complete; best results are reported</span>
98<span class="sd">        &quot;&quot;&quot;</span></div>
99<div class="viewcode-block" id="FitHandler.abort"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitHandler.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>
100        <span class="sd">&quot;&quot;&quot;</span>
101<span class="sd">        Fit was aborted.</span>
102<span class="sd">        &quot;&quot;&quot;</span>
103</div></div>
104<div class="viewcode-block" id="ConsoleUpdate"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.ConsoleUpdate">[docs]</a><span class="k">class</span> <span class="nc">ConsoleUpdate</span><span class="p">(</span><span class="n">FitHandler</span><span class="p">):</span>
105    <span class="sd">&quot;&quot;&quot;</span>
106<span class="sd">    Print progress to the console.</span>
107<span class="sd">    &quot;&quot;&quot;</span>
108    <span class="n">isbetter</span> <span class="o">=</span> <span class="bp">False</span>
109    <span class="sd">&quot;&quot;&quot;Record whether results improved since last update&quot;&quot;&quot;</span>
110    <span class="n">progress_delta</span> <span class="o">=</span>  <span class="mi">60</span>
111    <span class="sd">&quot;&quot;&quot;Number of seconds between progress updates&quot;&quot;&quot;</span>
112    <span class="n">improvement_delta</span> <span class="o">=</span> <span class="mi">5</span>
113    <span class="sd">&quot;&quot;&quot;Number of seconds between improvement updates&quot;&quot;&quot;</span>
114    <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">quiet</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span><span class="n">progress_delta</span><span class="o">=</span><span class="mi">60</span><span class="p">,</span><span class="n">improvement_delta</span><span class="o">=</span><span class="mi">5</span><span class="p">):</span>
115        <span class="sd">&quot;&quot;&quot;</span>
116<span class="sd">        If quiet is true, only print out final summary, not progress and</span>
117<span class="sd">        improvements.</span>
118<span class="sd">        &quot;&quot;&quot;</span>
119        <span class="c">#import traceback; traceback.print_stack()</span>
120        <span class="bp">self</span><span class="o">.</span><span class="n">progress_time</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
121        <span class="bp">self</span><span class="o">.</span><span class="n">progress_percent</span> <span class="o">=</span> <span class="mi">0</span>
122        <span class="bp">self</span><span class="o">.</span><span class="n">improvement_time</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">progress_time</span>
123        <span class="bp">self</span><span class="o">.</span><span class="n">isbetter</span> <span class="o">=</span> <span class="bp">False</span>
124        <span class="bp">self</span><span class="o">.</span><span class="n">quiet</span> <span class="o">=</span> <span class="n">quiet</span>
125        <span class="bp">self</span><span class="o">.</span><span class="n">progress_delta</span> <span class="o">=</span> <span class="n">progress_delta</span>
126        <span class="bp">self</span><span class="o">.</span><span class="n">improvement_delta</span> <span class="o">=</span> <span class="n">improvement_delta</span>
127
128<div class="viewcode-block" id="ConsoleUpdate.progress"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.ConsoleUpdate.progress">[docs]</a>    <span class="k">def</span> <span class="nf">progress</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">n</span><span class="p">):</span>
129        <span class="sd">&quot;&quot;&quot;</span>
130<span class="sd">        Report on progress.</span>
131<span class="sd">        &quot;&quot;&quot;</span>
132        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">quiet</span><span class="p">:</span> <span class="k">return</span>
133        <span class="n">t</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
134        <span class="n">p</span> <span class="o">=</span> <span class="nb">int</span><span class="p">((</span><span class="mi">100</span><span class="o">*</span><span class="n">k</span><span class="p">)</span><span class="o">//</span><span class="n">n</span><span class="p">)</span>
135
136        <span class="c"># Show improvements if there are any</span>
137        <span class="n">dt</span> <span class="o">=</span> <span class="n">t</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">improvement_time</span>
138        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">isbetter</span> <span class="ow">and</span> <span class="n">dt</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">improvement_delta</span><span class="p">:</span>
139            <span class="bp">self</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">print_summary</span><span class="p">()</span>
140            <span class="bp">self</span><span class="o">.</span><span class="n">isbetter</span> <span class="o">=</span> <span class="bp">False</span>
141            <span class="bp">self</span><span class="o">.</span><span class="n">improvement_time</span> <span class="o">=</span> <span class="n">t</span>
142
143        <span class="c"># Update percent complete</span>
144        <span class="n">dp</span> <span class="o">=</span> <span class="n">p</span><span class="o">-</span><span class="bp">self</span><span class="o">.</span><span class="n">progress_percent</span>
145        <span class="k">if</span> <span class="n">dp</span> <span class="o">&lt;</span> <span class="mi">1</span><span class="p">:</span> <span class="k">return</span>
146        <span class="n">dt</span> <span class="o">=</span> <span class="n">t</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">progress_time</span>
147        <span class="k">if</span> <span class="n">dt</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">progress_delta</span><span class="p">:</span>
148            <span class="k">if</span> <span class="mi">1</span> <span class="o">&lt;=</span> <span class="n">dp</span> <span class="o">&lt;=</span> <span class="mi">2</span><span class="p">:</span>
149                <span class="k">print</span> <span class="s">&quot;</span><span class="si">%d%%</span><span class="s"> complete&quot;</span><span class="o">%</span><span class="n">p</span>
150                <span class="bp">self</span><span class="o">.</span><span class="n">progress_percent</span> <span class="o">=</span> <span class="n">p</span>
151                <span class="bp">self</span><span class="o">.</span><span class="n">progress_time</span> <span class="o">=</span> <span class="n">t</span>
152            <span class="k">elif</span> <span class="mi">2</span> <span class="o">&lt;</span> <span class="n">dp</span> <span class="o">&lt;=</span> <span class="mi">5</span><span class="p">:</span>
153                <span class="k">if</span> <span class="n">p</span><span class="o">//</span><span class="mi">5</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">progress_percent</span><span class="o">//</span><span class="mi">5</span><span class="p">:</span>
154                    <span class="k">print</span> <span class="s">&quot;</span><span class="si">%d%%</span><span class="s"> complete&quot;</span><span class="o">%</span><span class="p">(</span><span class="mi">5</span><span class="o">*</span><span class="p">(</span><span class="n">p</span><span class="o">//</span><span class="mi">5</span><span class="p">))</span>
155                    <span class="bp">self</span><span class="o">.</span><span class="n">progress_percent</span> <span class="o">=</span> <span class="n">p</span>
156                    <span class="bp">self</span><span class="o">.</span><span class="n">progress_time</span> <span class="o">=</span> <span class="n">t</span>
157            <span class="k">else</span><span class="p">:</span>
158                <span class="k">if</span> <span class="n">p</span><span class="o">//</span><span class="mi">10</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">progress_percent</span><span class="o">//</span><span class="mi">10</span><span class="p">:</span>
159                    <span class="k">print</span> <span class="s">&quot;</span><span class="si">%d%%</span><span class="s"> complete&quot;</span><span class="o">%</span><span class="p">(</span><span class="mi">10</span><span class="o">*</span><span class="p">(</span><span class="n">p</span><span class="o">//</span><span class="mi">10</span><span class="p">))</span>
160                    <span class="bp">self</span><span class="o">.</span><span class="n">progress_percent</span> <span class="o">=</span> <span class="n">p</span>
161                    <span class="bp">self</span><span class="o">.</span><span class="n">progress_time</span> <span class="o">=</span> <span class="n">t</span>
162</div>
163<div class="viewcode-block" id="ConsoleUpdate.improvement"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.ConsoleUpdate.improvement">[docs]</a>    <span class="k">def</span> <span class="nf">improvement</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
164        <span class="sd">&quot;&quot;&quot;</span>
165<span class="sd">        Called when a result is observed which is better than previous</span>
166<span class="sd">        results from the fit.</span>
167<span class="sd">        &quot;&quot;&quot;</span>
168        <span class="bp">self</span><span class="o">.</span><span class="n">isbetter</span> <span class="o">=</span> <span class="bp">True</span>
169</div>
170<div class="viewcode-block" id="ConsoleUpdate.error"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.ConsoleUpdate.error">[docs]</a>    <span class="k">def</span> <span class="nf">error</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">msg</span><span class="p">):</span>
171        <span class="sd">&quot;&quot;&quot;</span>
172<span class="sd">        Model had an error; print traceback</span>
173<span class="sd">        &quot;&quot;&quot;</span>
174        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">isbetter</span><span class="p">:</span>
175            <span class="bp">self</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">print_summary</span><span class="p">()</span>
176        <span class="k">print</span> <span class="n">msg</span>
177</div>
178<div class="viewcode-block" id="ConsoleUpdate.finalize"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.ConsoleUpdate.finalize">[docs]</a>    <span class="k">def</span> <span class="nf">finalize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
179        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">isbetter</span><span class="p">:</span>
180            <span class="bp">self</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">print_summary</span><span class="p">()</span>
181        <span class="k">print</span> <span class="s">&quot;Total function calls:&quot;</span><span class="p">,</span><span class="bp">self</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">calls</span>
182</div>
183<div class="viewcode-block" id="ConsoleUpdate.abort"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.ConsoleUpdate.abort">[docs]</a>    <span class="k">def</span> <span class="nf">abort</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
184        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">isbetter</span><span class="p">:</span>
185            <span class="bp">self</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">print_summary</span><span class="p">()</span>
186
187</div></div>
188<div class="viewcode-block" id="FitParameter"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitParameter">[docs]</a><span class="k">class</span> <span class="nc">FitParameter</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
189    <span class="sd">&quot;&quot;&quot;</span>
190<span class="sd">    Fit result for an individual parameter.</span>
191<span class="sd">    &quot;&quot;&quot;</span>
192    <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="nb">range</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
193        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
194        <span class="bp">self</span><span class="o">.</span><span class="n">range</span> <span class="o">=</span> <span class="nb">range</span>
195        <span class="bp">self</span><span class="o">.</span><span class="n">value</span> <span class="o">=</span> <span class="n">value</span>
196        <span class="bp">self</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="bp">None</span>
197<div class="viewcode-block" id="FitParameter.summarize"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitParameter.summarize">[docs]</a>    <span class="k">def</span> <span class="nf">summarize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
198        <span class="sd">&quot;&quot;&quot;</span>
199<span class="sd">        Return parameter range string.</span>
200
201<span class="sd">        E.g.,  &quot;       Gold .....|.... 5.2043 in [2,7]&quot;</span>
202<span class="sd">        &quot;&quot;&quot;</span>
203        <span class="n">bar</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;.&#39;</span><span class="p">]</span><span class="o">*</span><span class="mi">10</span>
204        <span class="n">lo</span><span class="p">,</span><span class="n">hi</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">range</span>
205        <span class="k">if</span> <span class="n">numpy</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">lo</span><span class="p">)</span><span class="ow">and</span> <span class="n">numpy</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">hi</span><span class="p">):</span>
206            <span class="n">portion</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">value</span><span class="o">-</span><span class="n">lo</span><span class="p">)</span><span class="o">/</span><span class="p">(</span><span class="n">hi</span><span class="o">-</span><span class="n">lo</span><span class="p">)</span>
207            <span class="k">if</span> <span class="n">portion</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">:</span> <span class="n">portion</span> <span class="o">=</span> <span class="mf">0.</span>
208            <span class="k">elif</span> <span class="n">portion</span> <span class="o">&gt;=</span> <span class="mi">1</span><span class="p">:</span> <span class="n">portion</span> <span class="o">=</span> <span class="mf">0.99999999</span>
209            <span class="n">barpos</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">math</span><span class="o">.</span><span class="n">floor</span><span class="p">(</span><span class="n">portion</span><span class="o">*</span><span class="nb">len</span><span class="p">(</span><span class="n">bar</span><span class="p">)))</span>
210            <span class="n">bar</span><span class="p">[</span><span class="n">barpos</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;|&#39;</span>
211        <span class="n">bar</span> <span class="o">=</span> <span class="s">&quot;&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">bar</span><span class="p">)</span>
212        <span class="n">lostr</span> <span class="o">=</span> <span class="s">&quot;[</span><span class="si">%g</span><span class="s">&quot;</span><span class="o">%</span><span class="n">lo</span> <span class="k">if</span> <span class="n">numpy</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">lo</span><span class="p">)</span> <span class="k">else</span> <span class="s">&quot;(-inf&quot;</span>
213        <span class="n">histr</span> <span class="o">=</span> <span class="s">&quot;</span><span class="si">%g</span><span class="s">]&quot;</span><span class="o">%</span><span class="n">hi</span> <span class="k">if</span> <span class="n">numpy</span><span class="o">.</span><span class="n">isfinite</span><span class="p">(</span><span class="n">hi</span><span class="p">)</span> <span class="k">else</span> <span class="s">&quot;inf)&quot;</span>
214        <span class="n">valstr</span> <span class="o">=</span> <span class="n">format_uncertainty</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">value</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">stderr</span><span class="p">)</span>
215        <span class="k">return</span> <span class="s">&quot;</span><span class="si">%25s</span><span class="s"> </span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s"> in </span><span class="si">%s</span><span class="s">,</span><span class="si">%s</span><span class="s">&quot;</span>  <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span><span class="n">bar</span><span class="p">,</span><span class="n">valstr</span><span class="p">,</span><span class="n">lostr</span><span class="p">,</span><span class="n">histr</span><span class="p">)</span></div>
216    <span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
217        <span class="k">return</span> <span class="s">&quot;FitParameter(&#39;</span><span class="si">%s</span><span class="s">&#39;)&quot;</span><span class="o">%</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span>
218</div>
219<div class="viewcode-block" id="FitResult"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitResult">[docs]</a><span class="k">class</span> <span class="nc">FitResult</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
220    <span class="sd">&quot;&quot;&quot;</span>
221<span class="sd">    Container for reporting fit results.</span>
222<span class="sd">    &quot;&quot;&quot;</span>
223    <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">parameters</span><span class="p">,</span> <span class="n">calls</span><span class="p">,</span> <span class="n">fitness</span><span class="p">):</span>
224        <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span> <span class="o">=</span> <span class="n">parameters</span>
225        <span class="sd">&quot;&quot;&quot;Fit parameter list, each with name, range and value attributes.&quot;&quot;&quot;</span>
226        <span class="bp">self</span><span class="o">.</span><span class="n">calls</span> <span class="o">=</span> <span class="n">calls</span>
227        <span class="sd">&quot;&quot;&quot;Number of function calls&quot;&quot;&quot;</span>
228        <span class="bp">self</span><span class="o">.</span><span class="n">fitness</span> <span class="o">=</span> <span class="n">fitness</span>
229        <span class="sd">&quot;&quot;&quot;Value of the goodness of fit metric&quot;&quot;&quot;</span>
230        <span class="bp">self</span><span class="o">.</span><span class="n">pvec</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</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="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">])</span>
231        <span class="sd">&quot;&quot;&quot;Parameter vector&quot;&quot;&quot;</span>
232        <span class="bp">self</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="bp">None</span>
233        <span class="sd">&quot;&quot;&quot;Parameter uncertainties&quot;&quot;&quot;</span>
234        <span class="bp">self</span><span class="o">.</span><span class="n">cov</span> <span class="o">=</span> <span class="bp">None</span>
235        <span class="sd">&quot;&quot;&quot;Covariance matrix&quot;&quot;&quot;</span>
236
237<div class="viewcode-block" id="FitResult.update"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitResult.update">[docs]</a>    <span class="k">def</span> <span class="nf">update</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pvec</span><span class="p">,</span> <span class="n">fitness</span><span class="p">,</span> <span class="n">calls</span><span class="p">):</span>
238        <span class="bp">self</span><span class="o">.</span><span class="n">calls</span> <span class="o">=</span> <span class="n">calls</span>
239        <span class="bp">self</span><span class="o">.</span><span class="n">fitness</span> <span class="o">=</span> <span class="n">fitness</span>
240        <span class="bp">self</span><span class="o">.</span><span class="n">pvec</span> <span class="o">=</span> <span class="n">pvec</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
241        <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">p</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">):</span>
242            <span class="n">p</span><span class="o">.</span><span class="n">value</span> <span class="o">=</span> <span class="n">pvec</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
243</div>
244<div class="viewcode-block" id="FitResult.calc_cov"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitResult.calc_cov">[docs]</a>    <span class="k">def</span> <span class="nf">calc_cov</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fn</span><span class="p">):</span>
245        <span class="sd">&quot;&quot;&quot;</span>
246<span class="sd">        Return the covariance matrix inv(J&#39;J) at point p.</span>
247<span class="sd">        &quot;&quot;&quot;</span>
248        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">fn</span><span class="p">,</span> <span class="s">&#39;jacobian&#39;</span><span class="p">):</span>
249            <span class="c"># Find cov of f at p</span>
250            <span class="c">#     cov(f,p) = inv(J&#39;J)</span>
251            <span class="c"># Use SVD</span>
252            <span class="c">#     J = U S V&#39;</span>
253            <span class="c">#     J&#39;J = (U S V&#39;)&#39; (U S V&#39;)</span>
254            <span class="c">#         = V S&#39; U&#39; U S V&#39;</span>
255            <span class="c">#         = V S S V&#39;</span>
256            <span class="c">#     inv(J&#39;J) = inv(V S S V&#39;)</span>
257            <span class="c">#              = inv(V&#39;) inv(S S) inv(V)</span>
258            <span class="c">#              = V inv (S S) V&#39;</span>
259            <span class="n">J</span> <span class="o">=</span> <span class="n">fn</span><span class="o">.</span><span class="n">jacobian</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pvec</span><span class="p">)</span>
260            <span class="n">u</span><span class="p">,</span><span class="n">s</span><span class="p">,</span><span class="n">vh</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">svd</span><span class="p">(</span><span class="n">J</span><span class="p">,</span><span class="mi">0</span><span class="p">)</span>
261            <span class="n">JTJinv</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">vh</span><span class="o">.</span><span class="n">T</span><span class="o">.</span><span class="n">conj</span><span class="p">()</span><span class="o">/</span><span class="n">s</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span><span class="n">vh</span><span class="p">)</span>
262            <span class="bp">self</span><span class="o">.</span><span class="n">set_cov</span><span class="p">(</span><span class="n">JTJinv</span><span class="p">)</span>
263</div>
264<div class="viewcode-block" id="FitResult.set_cov"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitResult.set_cov">[docs]</a>    <span class="k">def</span> <span class="nf">set_cov</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cov</span><span class="p">):</span>
265        <span class="sd">&quot;&quot;&quot;</span>
266<span class="sd">        Return the covariance matrix inv(J&#39;J) at point p.</span>
267<span class="sd">        &quot;&quot;&quot;</span>
268        <span class="bp">self</span><span class="o">.</span><span class="n">cov</span> <span class="o">=</span> <span class="n">cov</span>
269        <span class="k">if</span> <span class="n">cov</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
270            <span class="bp">self</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">cov</span><span class="p">))</span>
271            <span class="c"># Set the uncertainties on the individual parameters</span>
272            <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">p</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">):</span>
273                <span class="n">p</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">stderr</span><span class="p">[</span><span class="n">k</span><span class="p">]</span>
274        <span class="k">else</span><span class="p">:</span>
275            <span class="bp">self</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="bp">None</span>
276            <span class="c"># Reset the uncertainties on the individual parameters</span>
277            <span class="k">for</span> <span class="n">k</span><span class="p">,</span><span class="n">p</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">):</span>
278                <span class="n">p</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="bp">None</span>
279</div>
280    <span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
281        <span class="c">#import traceback; traceback.print_stack()</span>
282        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> <span class="k">return</span> <span class="s">&quot;No results&quot;</span>
283        <span class="n">L</span> <span class="o">=</span> <span class="p">[</span><span class="s">&quot;P</span><span class="si">%-3d</span><span class="s"> </span><span class="si">%s</span><span class="s">&quot;</span><span class="o">%</span><span class="p">(</span><span class="n">n</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="n">p</span><span class="o">.</span><span class="n">summarize</span><span class="p">())</span> <span class="k">for</span> <span class="n">n</span><span class="p">,</span><span class="n">p</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="p">)]</span>
284        <span class="n">L</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">&quot;=== goodness of fit: </span><span class="si">%g</span><span class="s">&quot;</span><span class="o">%</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">fitness</span><span class="p">))</span>
285        <span class="k">return</span> <span class="s">&quot;</span><span class="se">\n</span><span class="s">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">L</span><span class="p">)</span>
286
287<div class="viewcode-block" id="FitResult.print_summary"><a class="viewcode-back" href="../../dev/api/park.html#park.fitresult.FitResult.print_summary">[docs]</a>    <span class="k">def</span> <span class="nf">print_summary</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fid</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">):</span>
288        <span class="k">print</span> <span class="o">&gt;&gt;</span><span class="n">fid</span><span class="p">,</span> <span class="bp">self</span>
289</pre></div></div></div>
290
291          </div>
292        </div>
293      </div>
294      <div class="sphinxsidebar">
295        <div class="sphinxsidebarwrapper">
296<div id="searchbox" style="display: none">
297  <h3>Quick search</h3>
298    <form class="search" action="../../search.html" method="get">
299      <input type="text" name="q" />
300      <input type="submit" value="Go" />
301      <input type="hidden" name="check_keywords" value="yes" />
302      <input type="hidden" name="area" value="default" />
303    </form>
304    <p class="searchtip" style="font-size: 90%">
305    Enter search terms or a module, class or function name.
306    </p>
307</div>
308<script type="text/javascript">$('#searchbox').show(0);</script>
309        </div>
310      </div>
311      <div class="clearer"></div>
312    </div>
313    <div class="related">
314      <h3>Navigation</h3>
315      <ul>
316        <li class="right" style="margin-right: 10px">
317          <a href="../../genindex.html" title="General Index"
318             >index</a></li>
319        <li class="right" >
320          <a href="../../py-modindex.html" title="Python Module Index"
321             >modules</a> |</li>
322        <li><a href="../../index.html">SasView 3.0.0 documentation</a> &raquo;</li>
323          <li><a href="../index.html" >Module code</a> &raquo;</li> 
324      </ul>
325    </div>
326    <div class="footer">
327        &copy; Copyright 2013, The SasView Project.
328      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
329    </div>
330  </body>
331</html>
Note: See TracBrowser for help on using the repository browser.