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<div class="title">C2DPerfusionAnalysis Class Reference<div class="ingroups"><a class="el" href="group__perf.html">Perfusion Analysis</a></div></div>  </div>
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<p>A class to run an ICA on a heart perfusion series.  
 <a href="classC2DPerfusionAnalysis.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="perfusion_8hh_source.html">mia/2d/perfusion.hh</a>&gt;</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:a25755f7b99b77fc08245c3bb2c42f974"><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classC2DPerfusionAnalysis.html#a25755f7b99b77fc08245c3bb2c42f974">EBoxSegmentation</a> { <a class="el" href="classC2DPerfusionAnalysis.html#a25755f7b99b77fc08245c3bb2c42f974acdc9d1d17c995c0be2ae280dfea6f06d">bs_delta_feature</a>, 
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<tr class="memdesc:a25755f7b99b77fc08245c3bb2c42f974"><td class="mdescLeft">&#160;</td><td class="mdescRight">Possible bases for LV-RV heart segmentation.  <a href="classC2DPerfusionAnalysis.html#a25755f7b99b77fc08245c3bb2c42f974">More...</a><br/></td></tr>
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Public Member Functions</h2></td></tr>
<tr class="memitem:ae9bf19da8e7b9dcfafb2df4f5ff7fecf"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classC2DPerfusionAnalysis.html#ae9bf19da8e7b9dcfafb2df4f5ff7fecf">C2DPerfusionAnalysis</a> (size_t components, bool <a class="el" href="normalize_8hh.html#aec17f6da6d9b6395599a4ad5bc29c969">normalize</a>, bool meanstrip)</td></tr>
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<tr class="memitem:a67990ed93e4c072fe1fa123780e0b57c"><td class="memItemLeft" align="right" valign="top">std::vector&lt; <a class="el" href="2d_2image_8hh.html#a6ed03a22f44b5f4926f823612784edcc">C2DFImage</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classC2DPerfusionAnalysis.html#a67990ed93e4c072fe1fa123780e0b57c">get_references</a> () const </td></tr>
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</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-attribs"></a>
Static Public Attributes</h2></td></tr>
<tr class="memitem:a4491fc0525acd71df13e72c02dab7ff7"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classTDictMap.html">TDictMap</a>&lt; <a class="el" href="classC2DPerfusionAnalysis.html#a25755f7b99b77fc08245c3bb2c42f974">EBoxSegmentation</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classC2DPerfusionAnalysis.html#a4491fc0525acd71df13e72c02dab7ff7">segmethod_dict</a></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>A class to run an ICA on a heart perfusion series. </p>
<p>This class provides the tools for ICA based 2D perfusion image series. This class is specifically designed for the analysis of free breathingly aquired myocardial perfusion images. </p>

<p>Definition at line <a class="el" href="perfusion_8hh_source.html#l00041">41</a> of file <a class="el" href="perfusion_8hh_source.html">perfusion.hh</a>.</p>
</div><h2 class="groupheader">Member Enumeration Documentation</h2>
<a class="anchor" id="a25755f7b99b77fc08245c3bb2c42f974"></a>
<div class="memitem">
<div class="memproto">
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          <td class="memname">enum <a class="el" href="classC2DPerfusionAnalysis.html#a25755f7b99b77fc08245c3bb2c42f974">C2DPerfusionAnalysis::EBoxSegmentation</a></td>
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<p>Possible bases for LV-RV heart segmentation. </p>
<table class="fieldtable">
<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><em><a class="anchor" id="a25755f7b99b77fc08245c3bb2c42f974acdc9d1d17c995c0be2ae280dfea6f06d"></a>bs_delta_feature</em>&#160;</td><td class="fielddoc">
<p>Segmentation based on the difference of the LV and RV feature images </p>
</td></tr>
<tr><td class="fieldname"><em><a class="anchor" id="a25755f7b99b77fc08245c3bb2c42f974a493318d0a787b9ee897d44ccf06c2c03"></a>bs_delta_peak</em>&#160;</td><td class="fielddoc">
<p>Segmentation based on the difference of the LV and RV peak enhancenemt images </p>
</td></tr>
<tr><td class="fieldname"><em><a class="anchor" id="a25755f7b99b77fc08245c3bb2c42f974a551bcaa46346cbfbf39a84c12a38c33d"></a>bs_features</em>&#160;</td><td class="fielddoc">
<p>Segmentation based on the LV and RV feature images </p>
</td></tr>
<tr><td class="fieldname"><em><a class="anchor" id="a25755f7b99b77fc08245c3bb2c42f974ada023a6025c89d2e890316f0bd78acbf"></a>bs_unknown</em>&#160;</td><td class="fielddoc">
<p>place holder </p>
</td></tr>
</table>

<p>Definition at line <a class="el" href="perfusion_8hh_source.html#l00044">44</a> of file <a class="el" href="perfusion_8hh_source.html">perfusion.hh</a>.</p>

</div>
</div>
<h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
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          <td class="memname">C2DPerfusionAnalysis::C2DPerfusionAnalysis </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>components</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">bool&#160;</td>
          <td class="paramname"><em>normalize</em>, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">bool&#160;</td>
          <td class="paramname"><em>meanstrip</em>&#160;</td>
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          <td></td>
          <td>)</td>
          <td></td><td></td>
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<p>Constructor </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">components</td><td>number of independend components, 0 = auto estimate from [3,4,5,6,7] </td></tr>
    <tr><td class="paramname">normalize</td><td>normalize feature images </td></tr>
    <tr><td class="paramname">meanstrip</td><td>strip mean from mixing time curves </td></tr>
  </table>
  </dd>
</dl>

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<h2 class="groupheader">Member Function Documentation</h2>
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          <td class="memname"><a class="el" href="group__filtering.html#ga501624d72546095b1d82ccf41a496fc4">P2DFilter</a> C2DPerfusionAnalysis::get_crop_filter </td>
          <td>(</td>
          <td class="paramtype">float&#160;</td>
          <td class="paramname"><em>scale</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="2d_2vector_8hh.html#a11b5d262e935234ba1d72bc6423bd2e4">C2DBounds</a> &amp;&#160;</td>
          <td class="paramname"><em>crop_start</em>, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="classC2DPerfusionAnalysis.html#a25755f7b99b77fc08245c3bb2c42f974">EBoxSegmentation</a>&#160;</td>
          <td class="paramname"><em>approach</em>, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const std::string &amp;&#160;</td>
          <td class="paramname"><em>save_features</em> = <code>&quot;&quot;</code>&#160;</td>
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          <td></td>
          <td>)</td>
          <td></td><td> const</td>
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<p>Evaluate an image cropping filter. This code is specifically designed to deal with the segmentantion of the left heart ventricle in short axis heart MRI The algorithm evaluates the centers of the LV and the RV and uses the distance between both to estimata a bounding box. Some heuristics are used to check whether the segmentation makes sense</p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramdir"></td><td class="paramname">scale</td><td>enlargement scale of the bounding box to create the cropping region </td></tr>
    <tr><td class="paramdir">[out]</td><td class="paramname">crop_start</td><td>returns the left upper corner of the cropping region that can be used to adjust segmentations </td></tr>
    <tr><td class="paramdir"></td><td class="paramname">approach</td><td>on what input data to base thesegmentation on </td></tr>
    <tr><td class="paramdir"></td><td class="paramname">save_features</td><td>if not empty store feature images in files with this prefix </td></tr>
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  </dd>
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<dl class="section return"><dt>Returns</dt><dd>the cropping filter or C2DFilterPlugin::ProductPtr() if the segmentation fails. </dd></dl>

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          <td class="memname"><a class="el" href="2d_2image_8hh.html#a3b497bfcf91fc4390de06b5a8fdf2c73">P2DImage</a> C2DPerfusionAnalysis::get_feature_image </td>
          <td>(</td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>index</em></td><td>)</td>
          <td> const</td>
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<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">index</td><td>of the feature image requested, set negative to request the mean image. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>the requested feature image </dd></dl>

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          <td class="memname">int C2DPerfusionAnalysis::get_LV_idx </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the LV enhancement IC index of -1 if it could not be identified </dd></dl>

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          <td class="memname">int C2DPerfusionAnalysis::get_LV_peak_idx </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the LV peak enhancement IC index of -1 if it could not be identified </dd></dl>

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          <td class="memname">int C2DPerfusionAnalysis::get_LV_peak_time </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the LV maximum peak enhancement time index, or -1 if not identified </dd></dl>

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          <td class="memname">int C2DPerfusionAnalysis::get_perfusion_idx </td>
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          <td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the perfusion enhancement IC index of -1 if it could not be identified </dd></dl>

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          <td class="memname">std::vector&lt;<a class="el" href="2d_2image_8hh.html#a6ed03a22f44b5f4926f823612784edcc">C2DFImage</a>&gt; C2DPerfusionAnalysis::get_references </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
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<p>Create uncropped reference images that try to omit the movement component in the image series. </p>

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          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the RV enhancement IC index of -1 if it could not be identified </dd></dl>

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          <td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the RV peak enhancement IC index of -1 if it could not be identified </dd></dl>

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          <td class="paramname"></td><td>)</td>
          <td> const</td>
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<dl class="section return"><dt>Returns</dt><dd>the RV maximum peak enhancement time index, or -1 if not identified </dd></dl>

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          <td class="paramname"></td><td>)</td>
          <td> const</td>
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<dl class="section return"><dt>Returns</dt><dd><em>true</em> if a periodic component could be identified in the given series </dd></dl>

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          <td class="memname">bool C2DPerfusionAnalysis::run </td>
          <td>(</td>
          <td class="paramtype">const std::vector&lt; <a class="el" href="2d_2image_8hh.html#a6ed03a22f44b5f4926f823612784edcc">C2DFImage</a> &gt; &amp;&#160;</td>
          <td class="paramname"><em>series</em></td><td>)</td>
          <td></td>
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<p>Run the ICA analysis - keeps a copy of the image series </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">series</td><td>image series should contain more images thennumber of requested components </td></tr>
  </table>
  </dd>
</dl>

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          <td class="memname">void C2DPerfusionAnalysis::save_coefs </td>
          <td>(</td>
          <td class="paramtype">const std::string &amp;&#160;</td>
          <td class="paramname"><em>coefs_name</em></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
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<p>Save the mixin matrix to a file. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">coefs_name</td><td>output file name </td></tr>
  </table>
  </dd>
</dl>

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          <td class="memname">void C2DPerfusionAnalysis::save_feature_images </td>
          <td>(</td>
          <td class="paramtype">const std::string &amp;&#160;</td>
          <td class="paramname"><em>base_name</em></td><td>)</td>
          <td> const</td>
        </tr>
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<p>Save the feature image to some PNG files. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">base_name</td><td>output file name base </td></tr>
  </table>
  </dd>
</dl>

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          <td class="memname">void C2DPerfusionAnalysis::set_approach </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>approach</em></td><td>)</td>
          <td></td>
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<p>Set the ICA seperation approach </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">approach</td><td>FICA_APPROACH_SYMM or FICA_APPROACH_DEFL </td></tr>
  </table>
  </dd>
</dl>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000014">Todo:</a></b></dt><dd>the parameter should be an enum </dd></dl>

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          <td class="memname">void C2DPerfusionAnalysis::set_max_ica_iterations </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>maxiter</em></td><td>)</td>
          <td></td>
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<p>Set the number of ICA iterations </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">maxiter</td><td></td></tr>
  </table>
  </dd>
</dl>

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          <td class="memname">void C2DPerfusionAnalysis::set_use_guess_model </td>
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<p>Use an experimental model to create a initial guess. </p>

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<h2 class="groupheader">Field Documentation</h2>
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          <td class="memname"><a class="el" href="classTDictMap.html">TDictMap</a>&lt;<a class="el" href="classC2DPerfusionAnalysis.html#a25755f7b99b77fc08245c3bb2c42f974">EBoxSegmentation</a>&gt; C2DPerfusionAnalysis::segmethod_dict</td>
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<span class="mlabels"><span class="mlabel">static</span></span>  </td>
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<p>Dictionary for segmentation method flags </p>

<p>Definition at line <a class="el" href="perfusion_8hh_source.html#l00141">141</a> of file <a class="el" href="perfusion_8hh_source.html">perfusion.hh</a>.</p>

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<hr/>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="perfusion_8hh_source.html">perfusion.hh</a></li>
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