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35        <h2 class="heading"><span>3.1. Bumps interface</span></h2>
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50       
51  <div class="section" id="bumps-interface">
52<h1>3.1. Bumps interface<a class="headerlink" href="#bumps-interface" title="Permalink to this headline">¶</a></h1>
53<div class="section" id="module-sasmodels.bumps_model">
54<span id="sasmodels-bumps-model"></span><h2>3.1.1. <a class="reference internal" href="#module-sasmodels.bumps_model" title="sasmodels.bumps_model"><tt class="xref py py-mod docutils literal"><span class="pre">sasmodels.bumps_model</span></tt></a><a class="headerlink" href="#module-sasmodels.bumps_model" title="Permalink to this headline">¶</a></h2>
55<p>Wrap sasmodels for direct use by bumps.</p>
56<p><a class="reference internal" href="#sasmodels.bumps_model.Model" title="sasmodels.bumps_model.Model"><tt class="xref py py-class docutils literal"><span class="pre">Model</span></tt></a> is a wrapper for the sasmodels kernel which defines a
57bumps <em>Parameter</em> box for each kernel parameter.  <em>Model</em> accepts keyword
58arguments to set the initial value for each parameter.</p>
59<p><a class="reference internal" href="#sasmodels.bumps_model.Experiment" title="sasmodels.bumps_model.Experiment"><tt class="xref py py-class docutils literal"><span class="pre">Experiment</span></tt></a> combines the <em>Model</em> function with a data file loaded by the
60sasview data loader.  <em>Experiment</em> takes a <em>cutoff</em> parameter controlling
61how far the polydispersity integral extends.</p>
62<p>A variety of helper functions are provided:</p>
63<blockquote>
64<div><p><a class="reference internal" href="#sasmodels.bumps_model.load_data" title="sasmodels.bumps_model.load_data"><tt class="xref py py-func docutils literal"><span class="pre">load_data()</span></tt></a> loads a sasview data file.</p>
65<p><a class="reference internal" href="#sasmodels.bumps_model.empty_data1D" title="sasmodels.bumps_model.empty_data1D"><tt class="xref py py-func docutils literal"><span class="pre">empty_data1D()</span></tt></a> creates an empty dataset, which is useful for plotting
66a theory function before the data is measured.</p>
67<p><a class="reference internal" href="#sasmodels.bumps_model.empty_data2D" title="sasmodels.bumps_model.empty_data2D"><tt class="xref py py-func docutils literal"><span class="pre">empty_data2D()</span></tt></a> creates an empty 2D dataset.</p>
68<p><a class="reference internal" href="#sasmodels.bumps_model.set_beam_stop" title="sasmodels.bumps_model.set_beam_stop"><tt class="xref py py-func docutils literal"><span class="pre">set_beam_stop()</span></tt></a> masks the beam stop from the data.</p>
69<p><a class="reference internal" href="#sasmodels.bumps_model.set_half" title="sasmodels.bumps_model.set_half"><tt class="xref py py-func docutils literal"><span class="pre">set_half()</span></tt></a> selects the right or left half of the data, which can
70be useful for shear measurements which have not been properly corrected
71for path length and reflections.</p>
72<p><a class="reference internal" href="#sasmodels.bumps_model.set_top" title="sasmodels.bumps_model.set_top"><tt class="xref py py-func docutils literal"><span class="pre">set_top()</span></tt></a> cuts the top part off the data.</p>
73<p><a class="reference internal" href="#sasmodels.bumps_model.plot_data" title="sasmodels.bumps_model.plot_data"><tt class="xref py py-func docutils literal"><span class="pre">plot_data()</span></tt></a> plots the data file.</p>
74<p><a class="reference internal" href="#sasmodels.bumps_model.plot_theory" title="sasmodels.bumps_model.plot_theory"><tt class="xref py py-func docutils literal"><span class="pre">plot_theory()</span></tt></a> plots a calculated result from the model.</p>
75</div></blockquote>
76<dl class="class">
77<dt id="sasmodels.bumps_model.Experiment">
78<em class="property">class </em><tt class="descclassname">sasmodels.bumps_model.</tt><tt class="descname">Experiment</tt><big>(</big><em>data</em>, <em>model</em>, <em>cutoff=1e-05</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.Experiment" title="Permalink to this definition">¶</a></dt>
79<dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">object</span></tt></p>
80<p>Return a bumps wrapper for a SAS model.</p>
81<p><em>data</em> is the data to be fitted.</p>
82<p><em>model</em> is the SAS model from <tt class="xref py py-func docutils literal"><span class="pre">core.load_model()</span></tt>.</p>
83<p><em>cutoff</em> is the integration cutoff, which avoids computing the
84the SAS model where the polydispersity weight is low.</p>
85<p>Model parameters can be initialized with additional keyword
86arguments, or by assigning to model.parameter_name.value.</p>
87<p>The resulting bumps model can be used directly in a FitProblem call.</p>
88<dl class="method">
89<dt id="sasmodels.bumps_model.Experiment.nllf">
90<tt class="descname">nllf</tt><big>(</big><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.Experiment.nllf" title="Permalink to this definition">¶</a></dt>
91<dd></dd></dl>
92
93<dl class="method">
94<dt id="sasmodels.bumps_model.Experiment.numpoints">
95<tt class="descname">numpoints</tt><big>(</big><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.Experiment.numpoints" title="Permalink to this definition">¶</a></dt>
96<dd><p>Return the number of points</p>
97</dd></dl>
98
99<dl class="method">
100<dt id="sasmodels.bumps_model.Experiment.parameters">
101<tt class="descname">parameters</tt><big>(</big><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.Experiment.parameters" title="Permalink to this definition">¶</a></dt>
102<dd><p>Return a dictionary of parameters</p>
103</dd></dl>
104
105<dl class="method">
106<dt id="sasmodels.bumps_model.Experiment.plot">
107<tt class="descname">plot</tt><big>(</big><em>view='log'</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.Experiment.plot" title="Permalink to this definition">¶</a></dt>
108<dd><p>Plot the data and residuals.</p>
109</dd></dl>
110
111<dl class="method">
112<dt id="sasmodels.bumps_model.Experiment.residuals">
113<tt class="descname">residuals</tt><big>(</big><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.Experiment.residuals" title="Permalink to this definition">¶</a></dt>
114<dd></dd></dl>
115
116<dl class="method">
117<dt id="sasmodels.bumps_model.Experiment.save">
118<tt class="descname">save</tt><big>(</big><em>basename</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.Experiment.save" title="Permalink to this definition">¶</a></dt>
119<dd></dd></dl>
120
121<dl class="method">
122<dt id="sasmodels.bumps_model.Experiment.simulate_data">
123<tt class="descname">simulate_data</tt><big>(</big><em>noise=None</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.Experiment.simulate_data" title="Permalink to this definition">¶</a></dt>
124<dd></dd></dl>
125
126<dl class="method">
127<dt id="sasmodels.bumps_model.Experiment.theory">
128<tt class="descname">theory</tt><big>(</big><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.Experiment.theory" title="Permalink to this definition">¶</a></dt>
129<dd></dd></dl>
130
131<dl class="method">
132<dt id="sasmodels.bumps_model.Experiment.update">
133<tt class="descname">update</tt><big>(</big><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.Experiment.update" title="Permalink to this definition">¶</a></dt>
134<dd></dd></dl>
135
136</dd></dl>
137
138<dl class="class">
139<dt id="sasmodels.bumps_model.Model">
140<em class="property">class </em><tt class="descclassname">sasmodels.bumps_model.</tt><tt class="descname">Model</tt><big>(</big><em>kernel</em>, <em>**kw</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.Model" title="Permalink to this definition">¶</a></dt>
141<dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">object</span></tt></p>
142<dl class="method">
143<dt id="sasmodels.bumps_model.Model.parameters">
144<tt class="descname">parameters</tt><big>(</big><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.Model.parameters" title="Permalink to this definition">¶</a></dt>
145<dd><p>Return a dictionary of parameters</p>
146</dd></dl>
147
148</dd></dl>
149
150<dl class="function">
151<dt id="sasmodels.bumps_model.BumpsModel">
152<tt class="descclassname">sasmodels.bumps_model.</tt><tt class="descname">BumpsModel</tt><big>(</big><em>data</em>, <em>model</em>, <em>cutoff=1e-05</em>, <em>**kw</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.BumpsModel" title="Permalink to this definition">¶</a></dt>
153<dd></dd></dl>
154
155<dl class="function">
156<dt id="sasmodels.bumps_model.delay">
157<tt class="descclassname">sasmodels.bumps_model.</tt><tt class="descname">delay</tt><big>(</big><em>dt</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.delay" title="Permalink to this definition">¶</a></dt>
158<dd><p>Return number date-time delta as number seconds</p>
159</dd></dl>
160
161<dl class="function">
162<dt id="sasmodels.bumps_model.demo">
163<tt class="descclassname">sasmodels.bumps_model.</tt><tt class="descname">demo</tt><big>(</big><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.demo" title="Permalink to this definition">¶</a></dt>
164<dd></dd></dl>
165
166<dl class="function">
167<dt id="sasmodels.bumps_model.empty_data1D">
168<tt class="descclassname">sasmodels.bumps_model.</tt><tt class="descname">empty_data1D</tt><big>(</big><em>q</em>, <em>resolution=0.05</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.empty_data1D" title="Permalink to this definition">¶</a></dt>
169<dd><p>Create empty 1D data using the given <em>q</em> as the x value.</p>
170<p><em>resolution</em> dq/q defaults to 5%.</p>
171</dd></dl>
172
173<dl class="function">
174<dt id="sasmodels.bumps_model.empty_data2D">
175<tt class="descclassname">sasmodels.bumps_model.</tt><tt class="descname">empty_data2D</tt><big>(</big><em>qx</em>, <em>qy=None</em>, <em>resolution=0.05</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.empty_data2D" title="Permalink to this definition">¶</a></dt>
176<dd><p>Create empty 2D data using the given mesh.</p>
177<p>If <em>qy</em> is missing, create a square mesh with <em>qy=qx</em>.</p>
178<p><em>resolution</em> dq/q defaults to 5%.</p>
179</dd></dl>
180
181<dl class="function">
182<dt id="sasmodels.bumps_model.load_data">
183<tt class="descclassname">sasmodels.bumps_model.</tt><tt class="descname">load_data</tt><big>(</big><em>filename</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.load_data" title="Permalink to this definition">¶</a></dt>
184<dd><p>Load data using a sasview loader.</p>
185</dd></dl>
186
187<dl class="function">
188<dt id="sasmodels.bumps_model.plot_data">
189<tt class="descclassname">sasmodels.bumps_model.</tt><tt class="descname">plot_data</tt><big>(</big><em>data</em>, <em>view='log'</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.plot_data" title="Permalink to this definition">¶</a></dt>
190<dd><p>Plot data loaded by the sasview loader.</p>
191</dd></dl>
192
193<dl class="function">
194<dt id="sasmodels.bumps_model.plot_theory">
195<tt class="descclassname">sasmodels.bumps_model.</tt><tt class="descname">plot_theory</tt><big>(</big><em>data</em>, <em>theory</em>, <em>view='log'</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.plot_theory" title="Permalink to this definition">¶</a></dt>
196<dd></dd></dl>
197
198<dl class="function">
199<dt id="sasmodels.bumps_model.set_beam_stop">
200<tt class="descclassname">sasmodels.bumps_model.</tt><tt class="descname">set_beam_stop</tt><big>(</big><em>data</em>, <em>radius</em>, <em>outer=None</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.set_beam_stop" title="Permalink to this definition">¶</a></dt>
201<dd><p>Add a beam stop of the given <em>radius</em>.  If <em>outer</em>, make an annulus.</p>
202</dd></dl>
203
204<dl class="function">
205<dt id="sasmodels.bumps_model.set_half">
206<tt class="descclassname">sasmodels.bumps_model.</tt><tt class="descname">set_half</tt><big>(</big><em>data</em>, <em>half</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.set_half" title="Permalink to this definition">¶</a></dt>
207<dd><p>Select half of the data, either &#8220;right&#8221; or &#8220;left&#8221;.</p>
208</dd></dl>
209
210<dl class="function">
211<dt id="sasmodels.bumps_model.set_top">
212<tt class="descclassname">sasmodels.bumps_model.</tt><tt class="descname">set_top</tt><big>(</big><em>data</em>, <em>cutoff</em><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.set_top" title="Permalink to this definition">¶</a></dt>
213<dd><p>Chop the top off the data, above <em>cutoff</em>.</p>
214</dd></dl>
215
216<dl class="function">
217<dt id="sasmodels.bumps_model.tic">
218<tt class="descclassname">sasmodels.bumps_model.</tt><tt class="descname">tic</tt><big>(</big><big>)</big><a class="headerlink" href="#sasmodels.bumps_model.tic" title="Permalink to this definition">¶</a></dt>
219<dd><p>Timer function.</p>
220<p>Use &#8220;toc=tic()&#8221; to start the clock and &#8220;toc()&#8221; to measure
221a time interval.</p>
222</dd></dl>
223
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