Index: Invariant/docs/sphinx/_build/html/api/index.html
===================================================================
--- Invariant/docs/sphinx/_build/html/api/index.html	(revision a45622ac8115822394e753d4fd89c8c08a2b11b3)
+++ Invariant/docs/sphinx/_build/html/api/index.html	(revision a45622ac8115822394e753d4fd89c8c08a2b11b3)
@@ -0,0 +1,133 @@
+
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Reference &mdash; invariant v0.1.0 documentation</title>
+    <link rel="stylesheet" href="../_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '../',
+        VERSION:     '0.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="../_static/jquery.js"></script>
+    <script type="text/javascript" src="../_static/underscore.js"></script>
+    <script type="text/javascript" src="../_static/doctools.js"></script>
+    <link rel="top" title="invariant v0.1.0 documentation" href="../index.html" />
+    <link rel="next" title="invariant" href="invariant.html" />
+    <link rel="prev" title="Welcome to invariantâs documentation!" href="../index.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="right" >
+          <a href="invariant.html" title="invariant"
+             accesskey="N">next</a> |</li>
+        <li class="right" >
+          <a href="../index.html" title="Welcome to invariantâs documentation!"
+             accesskey="P">previous</a> |</li>
+        <li><a href="../index.html">invariant v0.1.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="reference">
+<span id="api-index"></span><h1>Reference<a class="headerlink" href="#reference" title="Permalink to this headline">Â¶</a></h1>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Release:</th><td class="field-body">0.1.0</td>
+</tr>
+<tr class="field"><th class="field-name">Date:</th><td class="field-body">June 01, 2010</td>
+</tr>
+</tbody>
+</table>
+<div class="toctree-wrapper compound">
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="invariant.html">invariant</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="invariant.html#module-sans.invariant.invariant"><tt class="docutils literal"><span class="pre">sans.invariant.invariant</span></tt></a></li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+  <h4>Previous topic</h4>
+  <p class="topless"><a href="../index.html"
+                        title="previous chapter">Welcome to invariant&#8217;s documentation!</a></p>
+  <h4>Next topic</h4>
+  <p class="topless"><a href="invariant.html"
+                        title="next chapter">invariant</a></p>
+  <h3>This Page</h3>
+  <ul class="this-page-menu">
+    <li><a href="../_sources/api/index.txt"
+           rel="nofollow">Show Source</a></li>
+  </ul>
+<div id="searchbox" style="display: none">
+  <h3>Quick search</h3>
+    <form class="search" action="../search.html" method="get">
+      <input type="text" name="q" size="18" />
+      <input type="submit" value="Go" />
+      <input type="hidden" name="check_keywords" value="yes" />
+      <input type="hidden" name="area" value="default" />
+    </form>
+    <p class="searchtip" style="font-size: 90%">
+    Enter search terms or a module, class or function name.
+    </p>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="right" >
+          <a href="invariant.html" title="invariant"
+             >next</a> |</li>
+        <li class="right" >
+          <a href="../index.html" title="Welcome to invariantâs documentation!"
+             >previous</a> |</li>
+        <li><a href="../index.html">invariant v0.1.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+        &copy; Copyright 2010, sans group.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.0b1.
+    </div>
+  </body>
+</html>
Index: Invariant/docs/sphinx/_build/html/api/invariant.html
===================================================================
--- Invariant/docs/sphinx/_build/html/api/invariant.html	(revision a45622ac8115822394e753d4fd89c8c08a2b11b3)
+++ Invariant/docs/sphinx/_build/html/api/invariant.html	(revision a45622ac8115822394e753d4fd89c8c08a2b11b3)
@@ -0,0 +1,721 @@
+
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>invariant &mdash; invariant v0.1.0 documentation</title>
+    <link rel="stylesheet" href="../_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '../',
+        VERSION:     '0.1.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="../_static/jquery.js"></script>
+    <script type="text/javascript" src="../_static/underscore.js"></script>
+    <script type="text/javascript" src="../_static/doctools.js"></script>
+    <link rel="top" title="invariant v0.1.0 documentation" href="../index.html" />
+    <link rel="up" title="Reference" href="index.html" />
+    <link rel="prev" title="Reference" href="index.html" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="right" >
+          <a href="index.html" title="Reference"
+             accesskey="P">previous</a> |</li>
+        <li><a href="../index.html">invariant v0.1.0 documentation</a> &raquo;</li>
+          <li><a href="index.html" accesskey="U">Reference</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="invariant">
+<h1>invariant<a class="headerlink" href="#invariant" title="Permalink to this headline">Â¶</a></h1>
+<div class="section" id="module-sans.invariant.invariant">
+<span id="sans-invariant-invariant"></span><h2><a class="reference internal" href="#module-sans.invariant.invariant"><tt class="xref py py-mod docutils literal"><span class="pre">sans.invariant.invariant</span></tt></a><a class="headerlink" href="#module-sans.invariant.invariant" title="Permalink to this headline">Â¶</a></h2>
+<p>This module implements invariant and its related computations.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">author:</th><td class="field-body">Gervaise B. Alina/UTK</td>
+</tr>
+<tr class="field"><th class="field-name">author:</th><td class="field-body">Mathieu Doucet/UTK</td>
+</tr>
+<tr class="field"><th class="field-name">author:</th><td class="field-body">Jae Cho/UTK</td>
+</tr>
+</tbody>
+</table>
+<dl class="class">
+<dt id="sans.invariant.invariant.Extrapolator">
+<em class="property">class </em><tt class="descclassname">sans.invariant.invariant.</tt><tt class="descname">Extrapolator</tt><big>(</big><em>data</em>, <em>model=None</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Extrapolator" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Extrapolate I(q) distribution using a given model</p>
+<dl class="method">
+<dt id="sans.invariant.invariant.Extrapolator.fit">
+<tt class="descname">fit</tt><big>(</big><em>power=None</em>, <em>qmin=None</em>, <em>qmax=None</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Extrapolator.fit" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Fit data for y = ax + b  return a and b</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>power</strong> &#8211; a fixed, otherwise None</li>
+<li><strong>qmin</strong> &#8211; Minimum Q-value</li>
+<li><strong>qmax</strong> &#8211; Maximum Q-value</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="sans.invariant.invariant.Guinier">
+<em class="property">class </em><tt class="descclassname">sans.invariant.invariant.</tt><tt class="descname">Guinier</tt><big>(</big><em>scale=1</em>, <em>radius=60</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Guinier" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#sans.invariant.invariant.Transform" title="sans.invariant.invariant.Transform"><tt class="xref py py-class docutils literal"><span class="pre">sans.invariant.invariant.Transform</span></tt></a></p>
+<p>class of type Transform that performs operations related to guinier 
+function</p>
+<dl class="method">
+<dt id="sans.invariant.invariant.Guinier.evaluate_model">
+<tt class="descname">evaluate_model</tt><big>(</big><em>x</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Guinier.evaluate_model" title="Permalink to this definition">Â¶</a></dt>
+<dd>return F(x)= scale* e-((radius*x)**2/3)</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.Guinier.evaluate_model_errors">
+<tt class="descname">evaluate_model_errors</tt><big>(</big><em>x</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Guinier.evaluate_model_errors" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Returns the error on I(q) for the given array of q-values</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>x</strong> &#8211; array of q-values</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.Guinier.extract_model_parameters">
+<tt class="descname">extract_model_parameters</tt><big>(</big><em>constant</em>, <em>slope</em>, <em>dconstant=0</em>, <em>dslope=0</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Guinier.extract_model_parameters" title="Permalink to this definition">Â¶</a></dt>
+<dd>assign new value to the scale and the radius</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.Guinier.get_allowed_bins">
+<tt class="descname">get_allowed_bins</tt><big>(</big><em>data</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Guinier.get_allowed_bins" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Goes through the data points and returns a list of boolean values
+to indicate whether each points is allowed by the model or not.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>data</strong> &#8211; Data1D object</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.Guinier.linearize_data">
+<tt class="descname">linearize_data</tt><big>(</big><em>data</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Guinier.linearize_data" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Linearize data so that a linear fit can be performed. 
+Filter out the data that can&#8217;t be transformed.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>data</strong> &#8211; LoadData1D instance</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.Guinier.linearize_q_value">
+<tt class="descname">linearize_q_value</tt><big>(</big><em>value</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Guinier.linearize_q_value" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Transform the input q-value for linearization</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>value</strong> &#8211; q-value</li>
+</ul>
+</td>
+</tr>
+<tr class="field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">q*q</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="sans.invariant.invariant.InvariantCalculator">
+<em class="property">class </em><tt class="descclassname">sans.invariant.invariant.</tt><tt class="descname">InvariantCalculator</tt><big>(</big><em>data</em>, <em>background=0</em>, <em>scale=1</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.InvariantCalculator" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">object</span></tt></p>
+<p>Compute invariant if data is given.
+Can provide volume fraction and surface area if the user provides
+Porod constant  and contrast values.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Precondition :</th><td class="field-body">the user must send a data of type DataLoader.Data1D
+the user provide background and scale values.</td>
+</tr>
+<tr class="field"><th class="field-name">Note :</th><td class="field-body">Some computations depends on each others.</td>
+</tr>
+</tbody>
+</table>
+<dl class="method">
+<dt id="sans.invariant.invariant.InvariantCalculator.get_data">
+<tt class="descname">get_data</tt><big>(</big><big>)</big><a class="headerlink" href="#sans.invariant.invariant.InvariantCalculator.get_data" title="Permalink to this definition">Â¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Returns:</th><td class="field-body">self._data</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.InvariantCalculator.get_extra_data_high">
+<tt class="descname">get_extra_data_high</tt><big>(</big><em>npts_in=None</em>, <em>q_end=10</em>, <em>npts=20</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.InvariantCalculator.get_extra_data_high" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Returns the extrapolated data used for the high-Q invariant calculation.
+By default, the distribution will cover the data points used for the 
+extrapolation. The number of overlap points is a parameter (npts_in).
+By default, the maximum q-value of the distribution will be Q_MAXIMUM, 
+the maximum q-value used when extrapolating for the purpose of the 
+invariant calculation.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>npts_in</strong> &#8211; number of data points for which the extrapolated data overlap</li>
+<li><strong>q_end</strong> &#8211; is the maximum value to uses for extrapolated data</li>
+<li><strong>npts</strong> &#8211; the number of points in the extrapolated distribution</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.InvariantCalculator.get_extra_data_low">
+<tt class="descname">get_extra_data_low</tt><big>(</big><em>npts_in=None</em>, <em>q_start=None</em>, <em>npts=20</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.InvariantCalculator.get_extra_data_low" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Returns the extrapolated data used for the loew-Q invariant calculation.
+By default, the distribution will cover the data points used for the 
+extrapolation. The number of overlap points is a parameter (npts_in).
+By default, the maximum q-value of the distribution will be  
+the minimum q-value used when extrapolating for the purpose of the 
+invariant calculation.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>npts_in</strong> &#8211; number of data points for which the extrapolated data overlap</li>
+<li><strong>q_start</strong> &#8211; is the minimum value to uses for extrapolated data</li>
+<li><strong>npts</strong> &#8211; the number of points in the extrapolated distribution</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.InvariantCalculator.get_extrapolation_power">
+<tt class="descname">get_extrapolation_power</tt><big>(</big><em>range='high'</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.InvariantCalculator.get_extrapolation_power" title="Permalink to this definition">Â¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Returns:</th><td class="field-body">the fitted power for power law function for a given extrapolation range</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.InvariantCalculator.get_qstar">
+<tt class="descname">get_qstar</tt><big>(</big><em>extrapolation=None</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.InvariantCalculator.get_qstar" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Compute the invariant of the local copy of data.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>extrapolation</strong> &#8211; string to apply optional extrapolation</li>
+</ul>
+</td>
+</tr>
+<tr class="field"><th class="field-name">Return q_star:</th><td class="field-body"><p class="first">invariant of the data within data&#8217;s q range</p>
+</td>
+</tr>
+<tr class="field"><th class="field-name">Warning :</th><td class="field-body"><p class="first last">When using setting data to Data1D , the user is responsible of
+checking that the scale and the background are properly apply to the data</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.InvariantCalculator.get_qstar_high">
+<tt class="descname">get_qstar_high</tt><big>(</big><big>)</big><a class="headerlink" href="#sans.invariant.invariant.InvariantCalculator.get_qstar_high" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Compute the invariant for extrapolated data at high q range.</p>
+<dl class="docutils">
+<dt>Implementation:</dt>
+<dd>data = self._get_extra_data_high()
+return self._get_qstar()</dd>
+</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Return q_star:</th><td class="field-body">the invariant for data extrapolated at high q.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.InvariantCalculator.get_qstar_low">
+<tt class="descname">get_qstar_low</tt><big>(</big><big>)</big><a class="headerlink" href="#sans.invariant.invariant.InvariantCalculator.get_qstar_low" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Compute the invariant for extrapolated data at low q range.</p>
+<dl class="docutils">
+<dt>Implementation:</dt>
+<dd>data = self._get_extra_data_low()
+return self._get_qstar()</dd>
+</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Return q_star:</th><td class="field-body">the invariant for data extrapolated at low q.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.InvariantCalculator.get_qstar_with_error">
+<tt class="descname">get_qstar_with_error</tt><big>(</big><em>extrapolation=None</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.InvariantCalculator.get_qstar_with_error" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Compute the invariant uncertainty.
+This uncertainty computation depends on whether or not the data is
+smeared.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>extrapolation</strong> &#8211; string to apply optional extrapolation</li>
+</ul>
+</td>
+</tr>
+<tr class="field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">invariant, the invariant uncertainty</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.InvariantCalculator.get_surface">
+<tt class="descname">get_surface</tt><big>(</big><em>contrast</em>, <em>porod_const</em>, <em>extrapolation=None</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.InvariantCalculator.get_surface" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Compute the specific surface from the data.</p>
+<p>Implementation:</p>
+<div class="highlight-python"><pre>V =  self.get_volume_fraction(contrast, extrapolation)
+
+Compute the surface given by:
+  surface = (2*pi *V(1- V)*porod_const)/ q_star</pre>
+</div>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>contrast</strong> &#8211; contrast value to compute the volume</li>
+<li><strong>porod_const</strong> &#8211; Porod constant to compute the surface</li>
+<li><strong>extrapolation</strong> &#8211; string to apply optional extrapolation</li>
+</ul>
+</td>
+</tr>
+<tr class="field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">specific surface</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.InvariantCalculator.get_surface_with_error">
+<tt class="descname">get_surface_with_error</tt><big>(</big><em>contrast</em>, <em>porod_const</em>, <em>extrapolation=None</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.InvariantCalculator.get_surface_with_error" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Compute uncertainty of the surface value as well as the surface value.
+The uncertainty is given as follow:</p>
+<div class="highlight-python"><pre>dS = porod_const *2*pi[( dV -2*V*dV)/q_star
+     + dq_star(v-v**2)
+     
+q_star: the invariant value
+dq_star: the invariant uncertainty
+V: the volume fraction value
+dV: the volume uncertainty</pre>
+</div>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>contrast</strong> &#8211; contrast value</li>
+<li><strong>porod_const</strong> &#8211; porod constant value</li>
+<li><strong>extrapolation</strong> &#8211; string to apply optional extrapolation</li>
+</ul>
+</td>
+</tr>
+<tr class="field"><th class="field-name">Return S, dS:</th><td class="field-body"><p class="first last">the surface, with its uncertainty</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.InvariantCalculator.get_volume_fraction">
+<tt class="descname">get_volume_fraction</tt><big>(</big><em>contrast</em>, <em>extrapolation=None</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.InvariantCalculator.get_volume_fraction" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Compute volume fraction is deduced as follow:</p>
+<div class="highlight-python"><pre>q_star = 2*(pi*contrast)**2* volume( 1- volume)
+for k = 10^(-8)*q_star/(2*(pi*|contrast|)**2)
+we get 2 values of volume:
+     with   1 - 4 * k &gt;= 0
+     volume1 = (1- sqrt(1- 4*k))/2
+     volume2 = (1+ sqrt(1- 4*k))/2
+
+q_star: the invariant value included extrapolation is applied
+             unit  1/A^(3)*1/cm
+        q_star = self.get_qstar()
+        
+the result returned will be 0 &lt;= volume &lt;= 1</pre>
+</div>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>contrast</strong> &#8211; contrast value provides by the user of type float.
+contrast unit is 1/A^(2)= 10^(16)cm^(2)</li>
+<li><strong>extrapolation</strong> &#8211; string to apply optional extrapolation</li>
+</ul>
+</td>
+</tr>
+<tr class="field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">volume fraction</p>
+</td>
+</tr>
+<tr class="field"><th class="field-name">Note :</th><td class="field-body"><p class="first last">volume fraction must have no unit</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.InvariantCalculator.get_volume_fraction_with_error">
+<tt class="descname">get_volume_fraction_with_error</tt><big>(</big><em>contrast</em>, <em>extrapolation=None</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.InvariantCalculator.get_volume_fraction_with_error" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Compute uncertainty on volume value as well as the volume fraction
+This uncertainty is given by the following equation:</p>
+<div class="highlight-python"><pre>dV = 0.5 * (4*k* dq_star) /(2* math.sqrt(1-k* q_star))
+                     
+for k = 10^(-8)*q_star/(2*(pi*|contrast|)**2)
+
+q_star: the invariant value including extrapolated value if existing
+dq_star: the invariant uncertainty
+dV: the volume uncertainty</pre>
+</div>
+<p>The uncertainty will be set to -1 if it can&#8217;t be computed.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>contrast</strong> &#8211; contrast value</li>
+<li><strong>extrapolation</strong> &#8211; string to apply optional extrapolation</li>
+</ul>
+</td>
+</tr>
+<tr class="field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">V, dV = volume fraction, error on volume fraction</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.InvariantCalculator.set_extrapolation">
+<tt class="descname">set_extrapolation</tt><big>(</big><em>range</em>, <em>npts=4</em>, <em>function=None</em>, <em>power=None</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.InvariantCalculator.set_extrapolation" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Set the extrapolation parameters for the high or low Q-range.
+Note that this does not turn extrapolation on or off.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>range</strong> &#8211; a keyword set the type of extrapolation . type string</li>
+<li><strong>npts</strong> &#8211; the numbers of q points of data to consider for extrapolation</li>
+<li><strong>function</strong> &#8211; a keyword to select the function to use for extrapolation.
+of type string.</li>
+<li><strong>power</strong> &#8211; an power to apply power_low function</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="sans.invariant.invariant.PowerLaw">
+<em class="property">class </em><tt class="descclassname">sans.invariant.invariant.</tt><tt class="descname">PowerLaw</tt><big>(</big><em>scale=1</em>, <em>power=4</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.PowerLaw" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#sans.invariant.invariant.Transform" title="sans.invariant.invariant.Transform"><tt class="xref py py-class docutils literal"><span class="pre">sans.invariant.invariant.Transform</span></tt></a></p>
+<p>class of type transform that perform operation related to power_law 
+function</p>
+<dl class="method">
+<dt id="sans.invariant.invariant.PowerLaw.evaluate_model">
+<tt class="descname">evaluate_model</tt><big>(</big><em>x</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.PowerLaw.evaluate_model" title="Permalink to this definition">Â¶</a></dt>
+<dd>given a scale and a radius transform x, y using a power_law
+function</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.PowerLaw.evaluate_model_errors">
+<tt class="descname">evaluate_model_errors</tt><big>(</big><em>x</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.PowerLaw.evaluate_model_errors" title="Permalink to this definition">Â¶</a></dt>
+<dd>Returns the error on I(q) for the given array of q-values
+:param x: array of q-values</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.PowerLaw.extract_model_parameters">
+<tt class="descname">extract_model_parameters</tt><big>(</big><em>constant</em>, <em>slope</em>, <em>dconstant=0</em>, <em>dslope=0</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.PowerLaw.extract_model_parameters" title="Permalink to this definition">Â¶</a></dt>
+<dd>Assign new value to the scale and the power</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.PowerLaw.get_allowed_bins">
+<tt class="descname">get_allowed_bins</tt><big>(</big><em>data</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.PowerLaw.get_allowed_bins" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Goes through the data points and returns a list of boolean values
+to indicate whether each points is allowed by the model or not.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>data</strong> &#8211; Data1D object</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.PowerLaw.linearize_data">
+<tt class="descname">linearize_data</tt><big>(</big><em>data</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.PowerLaw.linearize_data" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Linearize data so that a linear fit can be performed. 
+Filter out the data that can&#8217;t be transformed.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>data</strong> &#8211; LoadData1D instance</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.PowerLaw.linearize_q_value">
+<tt class="descname">linearize_q_value</tt><big>(</big><em>value</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.PowerLaw.linearize_q_value" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Transform the input q-value for linearization</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>value</strong> &#8211; q-value</li>
+</ul>
+</td>
+</tr>
+<tr class="field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">log(q)</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="sans.invariant.invariant.Transform">
+<em class="property">class </em><tt class="descclassname">sans.invariant.invariant.</tt><tt class="descname">Transform</tt><a class="headerlink" href="#sans.invariant.invariant.Transform" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">object</span></tt></p>
+<p>Define interface that need to compute a function or an inverse
+function given some x, y</p>
+<dl class="method">
+<dt id="sans.invariant.invariant.Transform.evaluate_model">
+<tt class="descname">evaluate_model</tt><big>(</big><em>x</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Transform.evaluate_model" title="Permalink to this definition">Â¶</a></dt>
+<dd>Returns an array f(x) values where f is the Transform function.</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.Transform.evaluate_model_errors">
+<tt class="descname">evaluate_model_errors</tt><big>(</big><em>x</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Transform.evaluate_model_errors" title="Permalink to this definition">Â¶</a></dt>
+<dd>Returns an array of I(q) errors</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.Transform.extract_model_parameters">
+<tt class="descname">extract_model_parameters</tt><big>(</big><em>constant</em>, <em>slope</em>, <em>dconstant=0</em>, <em>dslope=0</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Transform.extract_model_parameters" title="Permalink to this definition">Â¶</a></dt>
+<dd>set private member</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.Transform.get_allowed_bins">
+<tt class="descname">get_allowed_bins</tt><big>(</big><em>data</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Transform.get_allowed_bins" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Goes through the data points and returns a list of boolean values
+to indicate whether each points is allowed by the model or not.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>data</strong> &#8211; Data1D object</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.Transform.linearize_data">
+<tt class="descname">linearize_data</tt><big>(</big><em>data</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Transform.linearize_data" title="Permalink to this definition">Â¶</a></dt>
+<dd><p>Linearize data so that a linear fit can be performed. 
+Filter out the data that can&#8217;t be transformed.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>data</strong> &#8211; LoadData1D instance</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sans.invariant.invariant.Transform.linearize_q_value">
+<tt class="descname">linearize_q_value</tt><big>(</big><em>value</em><big>)</big><a class="headerlink" href="#sans.invariant.invariant.Transform.linearize_q_value" title="Permalink to this definition">Â¶</a></dt>
+<dd>Transform the input q-value for linearization</dd></dl>
+
+</dd></dl>
+
+</div>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+  <h3><a href="../index.html">Table Of Contents</a></h3>
+  <ul>
+<li><a class="reference internal" href="#">invariant</a><ul>
+<li><a class="reference internal" href="#module-sans.invariant.invariant"><tt class="docutils literal"><span class="pre">sans.invariant.invariant</span></tt></a></li>
+</ul>
+</li>
+</ul>
+
+  <h4>Previous topic</h4>
+  <p class="topless"><a href="index.html"
+                        title="previous chapter">Reference</a></p>
+  <h3>This Page</h3>
+  <ul class="this-page-menu">
+    <li><a href="../_sources/api/invariant.txt"
+           rel="nofollow">Show Source</a></li>
+  </ul>
+<div id="searchbox" style="display: none">
+  <h3>Quick search</h3>
+    <form class="search" action="../search.html" method="get">
+      <input type="text" name="q" size="18" />
+      <input type="submit" value="Go" />
+      <input type="hidden" name="check_keywords" value="yes" />
+      <input type="hidden" name="area" value="default" />
+    </form>
+    <p class="searchtip" style="font-size: 90%">
+    Enter search terms or a module, class or function name.
+    </p>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="right" >
+          <a href="index.html" title="Reference"
+             >previous</a> |</li>
+        <li><a href="../index.html">invariant v0.1.0 documentation</a> &raquo;</li>
+          <li><a href="index.html" >Reference</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+        &copy; Copyright 2010, sans group.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.0b1.
+    </div>
+  </body>
+</html>
