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<a href="#pub-types">Public Types</a> &#124;
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<div class="title">CICAAnalysis Class Reference<div class="ingroups"><a class="el" href="group__perf.html">Perfusion Analysis</a></div></div>  </div>
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<p>class for ICA analysis and use of such data. This class implements basic operations for of ICA. It makes use of the ITPP implementation of FastICA.  
 <a href="classCICAAnalysis.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="core_2ica_8hh_source.html">mia/core/ica.hh</a>&gt;</code></p>
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Public Types</h2></td></tr>
<tr class="memitem:a318235a6e1e0652a184ebcf96e8cf2fa"><td class="memItemLeft" align="right" valign="top">typedef std::set&lt; size_t &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCICAAnalysis.html#a318235a6e1e0652a184ebcf96e8cf2fa">IndexSet</a></td></tr>
<tr class="memdesc:a318235a6e1e0652a184ebcf96e8cf2fa"><td class="mdescLeft">&#160;</td><td class="mdescRight">defines a set of indices used for mixing  <a href="#a318235a6e1e0652a184ebcf96e8cf2fa">More...</a><br/></td></tr>
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<tr class="memitem:aba765112467475dd6caf0331769b1759"><td class="memItemLeft" align="right" valign="top">typedef itpp::Vec<br class="typebreak"/>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
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<tr class="memitem:a93756fc82ac1d4f22a1cdd40f11d0f76"><td class="memItemLeft" align="right" valign="top">std::vector&lt; float &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCICAAnalysis.html#a93756fc82ac1d4f22a1cdd40f11d0f76">get_delta_feature</a> (const <a class="el" href="classCICAAnalysis.html#a318235a6e1e0652a184ebcf96e8cf2fa">IndexSet</a> &amp;plus, const <a class="el" href="classCICAAnalysis.html#a318235a6e1e0652a184ebcf96e8cf2fa">IndexSet</a> &amp;minus) const </td></tr>
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<tr class="memitem:a43211793dbfac602b8a32bbaf418a15c"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCICAAnalysis.html#a43211793dbfac602b8a32bbaf418a15c">run</a> (size_t nica, std::vector&lt; std::vector&lt; float &gt; &gt; guess)</td></tr>
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<tr class="memitem:aa860041295c388f3a29471fe845dadd2"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classCICAAnalysis.html#aa860041295c388f3a29471fe845dadd2">run_auto</a> (int max_ica, int min_ica, float corr_thresh=0.9)</td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>class for ICA analysis and use of such data. This class implements basic operations for of ICA. It makes use of the ITPP implementation of FastICA. </p>

<p>Definition at line <a class="el" href="core_2ica_8hh_source.html#l00041">41</a> of file <a class="el" href="core_2ica_8hh_source.html">core/ica.hh</a>.</p>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
<a class="anchor" id="a318235a6e1e0652a184ebcf96e8cf2fa"></a>
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          <td class="memname">typedef std::set&lt;size_t&gt; <a class="el" href="classCICAAnalysis.html#a318235a6e1e0652a184ebcf96e8cf2fa">CICAAnalysis::IndexSet</a></td>
        </tr>
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<p>defines a set of indices used for mixing </p>

<p>Definition at line <a class="el" href="core_2ica_8hh_source.html#l00063">63</a> of file <a class="el" href="core_2ica_8hh_source.html">core/ica.hh</a>.</p>

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          <td class="memname">typedef itpp::Vec&lt;itpp::mat::value_type&gt; <a class="el" href="classCICAAnalysis.html#aba765112467475dd6caf0331769b1759">CICAAnalysis::itppvector</a></td>
        </tr>
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<p>The type of a vector as used by IT++. </p>

<p>Definition at line <a class="el" href="core_2ica_8hh_source.html#l00045">45</a> of file <a class="el" href="core_2ica_8hh_source.html">core/ica.hh</a>.</p>

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<h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
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          <td class="memname">CICAAnalysis::CICAAnalysis </td>
          <td>(</td>
          <td class="paramtype">const itpp::mat &amp;&#160;</td>
          <td class="paramname"><em>ic</em>, </td>
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        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const itpp::mat &amp;&#160;</td>
          <td class="paramname"><em>mix</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const std::vector&lt; float &gt; &amp;&#160;</td>
          <td class="paramname"><em>mean</em>&#160;</td>
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        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
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<p>Initialize an ICA based of predefined data - this is unly used for test cases. </p>

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          <td class="memname">CICAAnalysis::CICAAnalysis </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>series_length</em>, </td>
        </tr>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>slice_size</em>&#160;</td>
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          <td></td>
          <td>)</td>
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<p>Main constructor of the ICA, i.e. you want to use this. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">series_length</td><td>number of data sets that will be provided </td></tr>
    <tr><td class="paramname">slice_size</td><td>number of elements each set containes </td></tr>
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  </dd>
</dl>

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          <td class="memname">CICAAnalysis::~CICAAnalysis </td>
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<h2 class="groupheader">Member Function Documentation</h2>
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          <td class="memname">std::vector&lt;float&gt; CICAAnalysis::get_delta_feature </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classCICAAnalysis.html#a318235a6e1e0652a184ebcf96e8cf2fa">IndexSet</a> &amp;&#160;</td>
          <td class="paramname"><em>plus</em>, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="classCICAAnalysis.html#a318235a6e1e0652a184ebcf96e8cf2fa">IndexSet</a> &amp;&#160;</td>
          <td class="paramname"><em>minus</em>&#160;</td>
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          <td></td>
          <td>)</td>
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<p>Evaluate a mix of the feature signals by adding and subtractig individual features. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">plus</td><td>features o be added </td></tr>
    <tr><td class="paramname">minus</td><td>features to be subtracted </td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>the feature mix </dd></dl>

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          <td class="memname">std::vector&lt;float&gt; CICAAnalysis::get_feature_row </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>row</em></td><td>)</td>
          <td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the feature vector of <em>row</em> </dd></dl>

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          <td class="memname">std::vector&lt;float&gt; CICAAnalysis::get_incomplete_mix </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>idx</em>, </td>
        </tr>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="classCICAAnalysis.html#a318235a6e1e0652a184ebcf96e8cf2fa">IndexSet</a> &amp;&#160;</td>
          <td class="paramname"><em>skip</em>&#160;</td>
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          <td>)</td>
          <td></td><td> const</td>
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<p>Evaluate an incomplete mixed signal. Here the features are given that are <em>not</em> to be used. </p>
<dl class="section see"><dt>See Also</dt><dd><a class="el" href="classCICAAnalysis.html#a9079c41b471615baf5aa0dbe5d872e9d">get_partial_mix</a> </dd></dl>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">idx</td><td>series index </td></tr>
    <tr><td class="paramname">skip</td><td>a set of feature indices that will be skipped when evaluating the mix </td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>the mixed signal </dd></dl>

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          <td class="memname">std::vector&lt;float&gt; CICAAnalysis::get_mix </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>idx</em></td><td>)</td>
          <td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the complete mixed signal at series index <em>idx</em> </dd></dl>

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          <td class="memname">std::vector&lt;float&gt; CICAAnalysis::get_mix_series </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>row</em></td><td>)</td>
          <td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the mixing signal curve of the feature <em>row</em> </dd></dl>

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          <td class="memname"><a class="el" href="group__perf.html#ga1eb3f50ef92b476cc8628d73e0361b0e">CSlopeColumns</a> CICAAnalysis::get_mixing_curves </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>a vector containing all mixing curves </dd></dl>

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          <td class="memname">size_t CICAAnalysis::get_ncomponents </td>
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          <td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the number of actual ICs </dd></dl>

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          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>idx</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="classCICAAnalysis.html#a318235a6e1e0652a184ebcf96e8cf2fa">IndexSet</a> &amp;&#160;</td>
          <td class="paramname"><em>use</em>&#160;</td>
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          <td></td>
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<p>Evaluate an incomplete mixed signal. Here the features are given that are <em>used</em> to create the mix. </p>
<dl class="section see"><dt>See Also</dt><dd><a class="el" href="classCICAAnalysis.html#a7243d01092ef6028cb68a8f2d325af1f">get_incomplete_mix</a> </dd></dl>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">idx</td><td>series index </td></tr>
    <tr><td class="paramname">use</td><td>the set of feature indices that will be used to evaluate the mix </td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>an incolmplete mixed signal. </dd></dl>

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          <td class="memname">void CICAAnalysis::normalize_ICs </td>
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<p>Normalize the ICs in the following manner: Scale and shift the range of the ICs to [-1, 1] Scale the mixing curved to compensate for the required scaling move the means of the time points to compensate for the shifting. </p>

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<p>Normalize the mixing curves to have a zero mean. As a result a mean image is created that containes the sum of the ICs weighted by the required mean shift. </p>

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          <td class="memname">bool CICAAnalysis::run </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>nica</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">std::vector&lt; std::vector&lt; float &gt; &gt;&#160;</td>
          <td class="paramname"><em>guess</em>&#160;</td>
        </tr>
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          <td></td>
          <td>)</td>
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<p>Run the independed component analysis using the given numbers of components </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">nica</td><td>number of indentepended components </td></tr>
    <tr><td class="paramname">guess</td><td>initial guess for the ICA, pass an empty vector of you don't want to use this feature </td></tr>
  </table>
  </dd>
</dl>

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          <td class="memname">void CICAAnalysis::run_auto </td>
          <td>(</td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>max_ica</em>, </td>
        </tr>
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          <td></td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>min_ica</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">float&#160;</td>
          <td class="paramname"><em>corr_thresh</em> = <code>0.9</code>&#160;</td>
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          <td></td>
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<p>Run the independed component analysis with an estimation of the optimal number of components. (experimental) </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">max_ica</td><td>maximum number of independend components </td></tr>
    <tr><td class="paramname">min_ica</td><td>minimum number of independend components </td></tr>
    <tr><td class="paramname">corr_thresh</td><td>minimum absolute correation of the mixing signals to joins two components </td></tr>
  </table>
  </dd>
</dl>

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          <td class="memname">void CICAAnalysis::set_approach </td>
          <td>(</td>
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          <td class="paramname"><em>approach</em></td><td>)</td>
          <td></td>
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<p>Set the ICA approach to either FICA_APPROACH_DEFL(default) or FICA_APPROACH_SYMM. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">approach</td><td></td></tr>
  </table>
  </dd>
</dl>

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          <td class="memname">void CICAAnalysis::set_max_iterations </td>
          <td>(</td>
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          <td class="paramname"><em>n</em></td><td>)</td>
          <td></td>
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<p>sets the number of iterations in the ICA </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">n</td><td></td></tr>
  </table>
  </dd>
</dl>

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          <td class="memname">void CICAAnalysis::set_mixing_series </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>index</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const std::vector&lt; float &gt; &amp;&#160;</td>
          <td class="paramname"><em>series</em>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
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<p>Replace a mixing signal curve </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">index</td><td>of the curve to be replaced </td></tr>
    <tr><td class="paramname">series</td><td>new data for mixing curve </td></tr>
  </table>
  </dd>
</dl>

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          <td class="memname">void CICAAnalysis::set_row </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>row</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">Iterator&#160;</td>
          <td class="paramname"><em>begin</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">Iterator&#160;</td>
          <td class="paramname"><em>end</em>&#160;</td>
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        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
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<p>Set on row of input data </p>
<dl class="tparams"><dt>Template Parameters</dt><dd>
  <table class="tparams">
    <tr><td class="paramname">Iterator</td><td>input data iterator, must follow the model of a forward iterator </td></tr>
  </table>
  </dd>
</dl>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">row</td><td>index of the input slice </td></tr>
    <tr><td class="paramname">begin</td><td>start iterator of input data </td></tr>
    <tr><td class="paramname">end</td><td>end iterator of input data </td></tr>
  </table>
  </dd>
</dl>

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<hr/>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="core_2ica_8hh_source.html">core/ica.hh</a></li>
</ul>
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