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<a href="#pub-types">Public Types</a> |
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<div class="title">TDataSeriesICA< Data > Class Template Reference<div class="ingroups"><a class="el" href="group__perf.html">Perfusion Analysis</a></div></div> </div>
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<p>Templated representation of a ICA series analyis.
<a href="classTDataSeriesICA.html#details">More...</a></p>
<p><code>#include <<a class="el" href="ica__template_8hh_source.html">mia/core/ica_template.hh</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:abf047c36d9a604352a386acda29eadaa"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classCICAAnalysis.html#a318235a6e1e0652a184ebcf96e8cf2fa">CICAAnalysis::IndexSet</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#abf047c36d9a604352a386acda29eadaa">IndexSet</a></td></tr>
<tr class="separator:abf047c36d9a604352a386acda29eadaa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad38dd876b00397346dd6722fc31beed2"><td class="memItemLeft" align="right" valign="top">typedef Data::Pointer </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#ad38dd876b00397346dd6722fc31beed2">PData</a></td></tr>
<tr class="separator:ad38dd876b00397346dd6722fc31beed2"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:aa4e02c7eff568d668776342354aa6cca"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classTDataSeriesICA.html#ad38dd876b00397346dd6722fc31beed2">PData</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#aa4e02c7eff568d668776342354aa6cca">get_delta_feature</a> (const <a class="el" href="classTDataSeriesICA.html#abf047c36d9a604352a386acda29eadaa">IndexSet</a> &plus, const <a class="el" href="classTDataSeriesICA.html#abf047c36d9a604352a386acda29eadaa">IndexSet</a> &minus) const </td></tr>
<tr class="separator:aa4e02c7eff568d668776342354aa6cca"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a114e6c5a966769026345197fad0fed74"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classTDataSeriesICA.html#ad38dd876b00397346dd6722fc31beed2">PData</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#a114e6c5a966769026345197fad0fed74">get_feature_image</a> (size_t idx) const </td></tr>
<tr class="separator:a114e6c5a966769026345197fad0fed74"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3ff185845df92a08e8776d63c2f420a9"><td class="memItemLeft" align="right" valign="top">Data </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#a3ff185845df92a08e8776d63c2f420a9">get_incomplete_mix</a> (size_t idx, const <a class="el" href="classTDataSeriesICA.html#abf047c36d9a604352a386acda29eadaa">IndexSet</a> &skip) const </td></tr>
<tr class="separator:a3ff185845df92a08e8776d63c2f420a9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaf09a88b4099f8fd065f1a33c057035e"><td class="memItemLeft" align="right" valign="top">const Data & </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#aaf09a88b4099f8fd065f1a33c057035e">get_mean_image</a> () const </td></tr>
<tr class="separator:aaf09a88b4099f8fd065f1a33c057035e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad08c69b4026b2c992f679ca206b26ed7"><td class="memItemLeft" align="right" valign="top">Data </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#ad08c69b4026b2c992f679ca206b26ed7">get_mix</a> (size_t idx) const </td></tr>
<tr class="separator:ad08c69b4026b2c992f679ca206b26ed7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac4e33b7c0f9e1d0275dee8aaac08d27c"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__perf.html#ga1eb3f50ef92b476cc8628d73e0361b0e">CSlopeColumns</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#ac4e33b7c0f9e1d0275dee8aaac08d27c">get_mixing_curves</a> () const </td></tr>
<tr class="separator:ac4e33b7c0f9e1d0275dee8aaac08d27c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4902019f8efc816cd09dd15ab6623288"><td class="memItemLeft" align="right" valign="top">Data </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#a4902019f8efc816cd09dd15ab6623288">get_partial_mix</a> (size_t idx, const <a class="el" href="classTDataSeriesICA.html#abf047c36d9a604352a386acda29eadaa">IndexSet</a> &comps) const </td></tr>
<tr class="separator:a4902019f8efc816cd09dd15ab6623288"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9ec1f4e38aa2d6ef24c39b786c242576"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#a9ec1f4e38aa2d6ef24c39b786c242576">normalize</a> ()</td></tr>
<tr class="separator:a9ec1f4e38aa2d6ef24c39b786c242576"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af0c800a93dffa1edc33e2235a3d0952a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#af0c800a93dffa1edc33e2235a3d0952a">normalize_Mix</a> ()</td></tr>
<tr class="memdesc:af0c800a93dffa1edc33e2235a3d0952a"><td class="mdescLeft"> </td><td class="mdescRight">Normalizes the Mixing Matrix columns to have zero mean. <a href="#af0c800a93dffa1edc33e2235a3d0952a">More...</a><br/></td></tr>
<tr class="separator:af0c800a93dffa1edc33e2235a3d0952a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af9ca5fd0caa0d54fd6b8b40e2758dd99"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#af9ca5fd0caa0d54fd6b8b40e2758dd99">run</a> (size_t ncomponents, bool strip_mean, bool ica_normalize, std::vector< std::vector< float > > guess=std::vector< std::vector< float > >())</td></tr>
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<tr class="memitem:a5e50c5d803cab939210e8569d2abdaab"><td class="memItemLeft" align="right" valign="top">size_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#a5e50c5d803cab939210e8569d2abdaab">run_auto</a> (int max_ica, int min_ica, float corr_thresh)</td></tr>
<tr class="separator:a5e50c5d803cab939210e8569d2abdaab"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac9146cbdf0bb7c1ec3ceaf075ddf8c47"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#ac9146cbdf0bb7c1ec3ceaf075ddf8c47">set_approach</a> (int approach)</td></tr>
<tr class="separator:ac9146cbdf0bb7c1ec3ceaf075ddf8c47"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a96613cbc5559ebd0693474e15e8b8a27"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#a96613cbc5559ebd0693474e15e8b8a27">set_max_iterations</a> (int n)</td></tr>
<tr class="separator:a96613cbc5559ebd0693474e15e8b8a27"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a74574d86ebc69adbc2c17c74d31e7c45"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#a74574d86ebc69adbc2c17c74d31e7c45">set_mixing_series</a> (size_t index, const std::vector< float > &series)</td></tr>
<tr class="separator:a74574d86ebc69adbc2c17c74d31e7c45"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9be0094ef3ffb3146d373a98ebfead15"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#a9be0094ef3ffb3146d373a98ebfead15">TDataSeriesICA</a> (const std::vector< Data > &initializer, bool strip_mean)</td></tr>
<tr class="memdesc:a9be0094ef3ffb3146d373a98ebfead15"><td class="mdescLeft"> </td><td class="mdescRight">ICA initialization. <a href="#a9be0094ef3ffb3146d373a98ebfead15">More...</a><br/></td></tr>
<tr class="separator:a9be0094ef3ffb3146d373a98ebfead15"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9ea8c775a3c7c02ab3dcd1e8ef30fda0"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classTDataSeriesICA.html#a9ea8c775a3c7c02ab3dcd1e8ef30fda0">~TDataSeriesICA</a> ()</td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><h3>template<class Data><br/>
class TDataSeriesICA< Data ></h3>
<p>Templated representation of a ICA series analyis. </p>
<p>This class provides a generic implementation for the ICA analysis of data series. </p>
<dl class="tparams"><dt>Template Parameters</dt><dd>
<table class="tparams">
<tr><td class="paramname">Data</td><td>some kind of data set ofwhich series are analyzed The class <em>Data</em> must somehow provide:<ul>
<li>a typedef <em>Pointer</em> for a pointer like representation of itself or on of its base classes (preferable based on boost::shared_ptr)</li>
<li>a typedef <em>dimsize_type</em> for its the size seperated into dimensions</li>
<li>a method <em>get_size()</em> that returns <em>dimsize_type</em> </li>
<li>a method <em>size()</em> that returns the number of elements hold by itself</li>
<li>STL comaptible const and non-const iterators returned by functions named <em>begin()</em> and <em>end()</em> </li>
</ul>
</td></tr>
</table>
</dd>
</dl>
<p>Definition at line <a class="el" href="ica__template_8hh_source.html#l00060">60</a> of file <a class="el" href="ica__template_8hh_source.html">ica_template.hh</a>.</p>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
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template<class Data > </div>
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<td class="memname">typedef <a class="el" href="classCICAAnalysis.html#a318235a6e1e0652a184ebcf96e8cf2fa">CICAAnalysis::IndexSet</a> <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::<a class="el" href="classTDataSeriesICA.html#abf047c36d9a604352a386acda29eadaa">IndexSet</a></td>
</tr>
</table>
</div><div class="memdoc">
<p>a set of indices used for addressing a subset of the independend componsts </p>
<p>Definition at line <a class="el" href="ica__template_8hh_source.html#l00064">64</a> of file <a class="el" href="ica__template_8hh_source.html">ica_template.hh</a>.</p>
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template<class Data > </div>
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<td class="memname">typedef Data::Pointer <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::<a class="el" href="classTDataSeriesICA.html#ad38dd876b00397346dd6722fc31beed2">PData</a></td>
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<p>a (shared) pointer to itself </p>
<p>Definition at line <a class="el" href="ica__template_8hh_source.html#l00067">67</a> of file <a class="el" href="ica__template_8hh_source.html">ica_template.hh</a>.</p>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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template<class Data > </div>
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<td class="memname"><a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::<a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a> </td>
<td>(</td>
<td class="paramtype">const std::vector< Data > & </td>
<td class="paramname"><em>initializer</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"><em>strip_mean</em> </td>
</tr>
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<td></td>
<td>)</td>
<td></td><td></td>
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<p>ICA initialization. </p>
<p>The contructor for an ICA </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">initializer</td><td>data set containing all the time steps of input data </td></tr>
<tr><td class="paramname">strip_mean</td><td>strip the mean from the series before processing </td></tr>
</table>
</dd>
</dl>
</div>
</div>
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template<class Data > </div>
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<td class="memname"><a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::~<a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
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<h2 class="groupheader">Member Function Documentation</h2>
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template<class Data > </div>
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<td class="memname"><a class="el" href="classTDataSeriesICA.html#ad38dd876b00397346dd6722fc31beed2">PData</a> <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::get_delta_feature </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classTDataSeriesICA.html#abf047c36d9a604352a386acda29eadaa">IndexSet</a> & </td>
<td class="paramname"><em>plus</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="classTDataSeriesICA.html#abf047c36d9a604352a386acda29eadaa">IndexSet</a> & </td>
<td class="paramname"><em>minus</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td> const</td>
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<p>Evaluate a mix as sum and difference of ICs </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">plus</td><td>add these ICs </td></tr>
<tr><td class="paramname">minus</td><td>subtract these ICs </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>the combined signal </dd></dl>
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<td class="memname"><a class="el" href="classTDataSeriesICA.html#ad38dd876b00397346dd6722fc31beed2">PData</a> <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::get_feature_image </td>
<td>(</td>
<td class="paramtype">size_t </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 feature data relating to component <em>idx</em> </dd></dl>
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<td class="memname">Data <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::get_incomplete_mix </td>
<td>(</td>
<td class="paramtype">size_t </td>
<td class="paramname"><em>idx</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="classTDataSeriesICA.html#abf047c36d9a604352a386acda29eadaa">IndexSet</a> & </td>
<td class="paramname"><em>skip</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td> const</td>
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<p>Evaluate a partial mix of the ICs </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">idx</td><td>time indes </td></tr>
<tr><td class="paramname">skip</td><td>set of components to skip when mixing </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>the mixed data </dd></dl>
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<td class="memname">const Data& <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::get_mean_image </td>
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<td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the mean of the input data </dd></dl>
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<td class="memname">Data <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::get_mix </td>
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<td class="paramtype">size_t </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 mixed signal at index <em>idx</em> </dd></dl>
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<td class="memname"><a class="el" href="group__perf.html#ga1eb3f50ef92b476cc8628d73e0361b0e">CSlopeColumns</a> <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::get_mixing_curves </td>
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<dl class="section return"><dt>Returns</dt><dd>the mixing curves as vector of vectors </dd></dl>
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<td class="memname">Data <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::get_partial_mix </td>
<td>(</td>
<td class="paramtype">size_t </td>
<td class="paramname"><em>idx</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">const <a class="el" href="classTDataSeriesICA.html#abf047c36d9a604352a386acda29eadaa">IndexSet</a> & </td>
<td class="paramname"><em>comps</em> </td>
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<p>Evaluate a partial mix of the ICs by using the given indes set </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">idx</td><td>time indes </td></tr>
<tr><td class="paramname">comps</td><td>set of components to use when mixing </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>the mixed data </dd></dl>
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<td class="memname">void <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::normalize </td>
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<p>Normalizes the ICs to the range of [-1,1] and correct the mixing matrix accordingly. This operation does not change the output of a mix. </p>
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<td class="memname">void <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::normalize_Mix </td>
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<p>Normalizes the Mixing Matrix columns to have zero mean. </p>
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<td class="memname">bool <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::run </td>
<td>(</td>
<td class="paramtype">size_t </td>
<td class="paramname"><em>ncomponents</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">bool </td>
<td class="paramname"><em>strip_mean</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">bool </td>
<td class="paramname"><em>ica_normalize</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">std::vector< std::vector< float > > </td>
<td class="paramname"><em>guess</em> = <code>std::vector< std::vector< float > >()</code> </td>
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<p>Runs the ICA </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">ncomponents</td><td>retained components </td></tr>
<tr><td class="paramname">strip_mean</td><td>strip the mean from the input </td></tr>
<tr><td class="paramname">ica_normalize</td><td>normalize the ICA after processing </td></tr>
<tr><td class="paramname">guess</td><td>provide an initial guess (leave empty, if not wanted) </td></tr>
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</dd>
</dl>
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<td class="memname">size_t <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::run_auto </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>max_ica</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">int </td>
<td class="paramname"><em>min_ica</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">float </td>
<td class="paramname"><em>corr_thresh</em> </td>
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<p>Run the independed component analysis with an estimation of the optimal number of components based on mixing curve correlation (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>
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<dl class="section return"><dt>Returns</dt><dd>number of obtained independend components </dd></dl>
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<td class="memname">void <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::set_approach </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>approach</em></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>
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<tr><td class="paramname">approach</td><td></td></tr>
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</dd>
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<td class="memname">void <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::set_max_iterations </td>
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<td class="paramtype">int </td>
<td class="paramname"><em>n</em></td><td>)</td>
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<p>sets the number of iterations in the ICA </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">n</td><td></td></tr>
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</dd>
</dl>
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<td class="memname">void <a class="el" href="classTDataSeriesICA.html">TDataSeriesICA</a>< Data >::set_mixing_series </td>
<td>(</td>
<td class="paramtype">size_t </td>
<td class="paramname"><em>index</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::vector< float > & </td>
<td class="paramname"><em>series</em> </td>
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<td></td>
<td>)</td>
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<p>replace a mixing series by a new set </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">index</td><td>component number of the mixing curve to be replaced </td></tr>
<tr><td class="paramname">series</td><td>new mixing data </td></tr>
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</dd>
</dl>
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<hr/>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="ica__template_8hh_source.html">ica_template.hh</a></li>
</ul>
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