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<div id="projectname">Computer Assited Medical Intervention Tool Kit
 <span id="projectnumber">version 4.0</span>
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<div class="title">Reference Class Reference<div class="ingroups"><a class="el" href="group__group__cepmodeling.html">CEP Modeling</a> » <a class="el" href="group__group__cepmodeling__libraries.html">Libraries</a> » <a class="el" href="group__group__cepmodeling__libraries__mml.html">MML</a></div></div> </div>
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<p>A reference is used to compare to simulated data.
<a href="classReference.html#details">More...</a></p>
<p><code>#include <<a class="el" href="Reference_8h_source.html">Reference.h</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structReference_1_1timeStep.html">timeStep</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">private structure with monitors for a time step <a href="structReference_1_1timeStep.html#details">More...</a><br /></td></tr>
<tr class="separator:"><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:aa617c2c9b8f0a034fd8bdd944fe0b24e"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#aa617c2c9b8f0a034fd8bdd944fe0b24e">getDistanceToTriangularMesh</a> (double pos[3], double &dist)</td></tr>
<tr class="memdesc:aa617c2c9b8f0a034fd8bdd944fe0b24e"><td class="mdescLeft"> </td><td class="mdescRight">get distance to a triangular mesh, the target of the reference must contain triangles. <a href="#aa617c2c9b8f0a034fd8bdd944fe0b24e">More...</a><br /></td></tr>
<tr class="separator:aa617c2c9b8f0a034fd8bdd944fe0b24e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a64ef08c4cace3ec39a105b669828c8da"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#a64ef08c4cace3ec39a105b669828c8da">getMonitoredData</a> (std::string type, double ref[])</td></tr>
<tr class="memdesc:a64ef08c4cace3ec39a105b669828c8da"><td class="mdescLeft"> </td><td class="mdescRight">get the the values of a given monitor which do not depend of time or an atom (e.g. <a href="#a64ef08c4cace3ec39a105b669828c8da">More...</a><br /></td></tr>
<tr class="separator:a64ef08c4cace3ec39a105b669828c8da"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a46477a6bda1564c1e9b708a86c07bfc3"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#a46477a6bda1564c1e9b708a86c07bfc3">getMonitoredData</a> (std::string type, double time, double &realTime, double ref[])</td></tr>
<tr class="memdesc:a46477a6bda1564c1e9b708a86c07bfc3"><td class="mdescLeft"> </td><td class="mdescRight">get the the values of a given monitor at a given time which do not depend an atom (e.g. <a href="#a46477a6bda1564c1e9b708a86c07bfc3">More...</a><br /></td></tr>
<tr class="separator:a46477a6bda1564c1e9b708a86c07bfc3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9d1f6d150a211a713949c8bf6eae71de"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#a9d1f6d150a211a713949c8bf6eae71de">getMonitoredData</a> (std::string type, double time, int index, double &realTime, double ref[])</td></tr>
<tr class="memdesc:a9d1f6d150a211a713949c8bf6eae71de"><td class="mdescLeft"> </td><td class="mdescRight">get the the values of a given monitor at a given time and a given atom's index (e.g. <a href="#a9d1f6d150a211a713949c8bf6eae71de">More...</a><br /></td></tr>
<tr class="separator:a9d1f6d150a211a713949c8bf6eae71de"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a90bfd9f49b91ea555848cb7ff1683468"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#a90bfd9f49b91ea555848cb7ff1683468">getNearest</a> (double pos[3], double time, double ref[3])</td></tr>
<tr class="memdesc:a90bfd9f49b91ea555848cb7ff1683468"><td class="mdescLeft"> </td><td class="mdescRight">get the nearest reference point in the "target" using "Position" monitor at given time <a href="#a90bfd9f49b91ea555848cb7ff1683468">More...</a><br /></td></tr>
<tr class="separator:a90bfd9f49b91ea555848cb7ff1683468"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa15b22233ce91120d625c4b0fd5a5665"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#aa15b22233ce91120d625c4b0fd5a5665">getNearest</a> (double pos[3], double ref[3])</td></tr>
<tr class="memdesc:aa15b22233ce91120d625c4b0fd5a5665"><td class="mdescLeft"> </td><td class="mdescRight">get the nearest reference point in the "target" using "Position" monitor of the PML <a class="el" href="classReference.html" title="A reference is used to compare to simulated data. ">Reference</a>. <a href="#aa15b22233ce91120d625c4b0fd5a5665">More...</a><br /></td></tr>
<tr class="separator:aa15b22233ce91120d625c4b0fd5a5665"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac386a753d9e9c1c3aaab13ae8e3ae874"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#ac386a753d9e9c1c3aaab13ae8e3ae874">Reference</a> (mml::Reference reference, <a class="el" href="classMonitoringManager.html">MonitoringManager</a> *<a class="el" href="classReference.html#ac54faba56902bd0c90207baec5a6f94c">monitoringManager</a>)</td></tr>
<tr class="memdesc:ac386a753d9e9c1c3aaab13ae8e3ae874"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="#ac386a753d9e9c1c3aaab13ae8e3ae874">More...</a><br /></td></tr>
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<tr class="memitem:aa1b72463417e38d965585a5ff88740d0"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#aa1b72463417e38d965585a5ff88740d0">toString</a> ()</td></tr>
<tr class="memdesc:aa1b72463417e38d965585a5ff88740d0"><td class="mdescLeft"> </td><td class="mdescRight">return a string relative to <a class="el" href="classReference.html" title="A reference is used to compare to simulated data. ">Reference</a> type <a href="#aa1b72463417e38d965585a5ff88740d0">More...</a><br /></td></tr>
<tr class="separator:aa1b72463417e38d965585a5ff88740d0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a40d21c5f6f98084f8badfcd481773e93"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#a40d21c5f6f98084f8badfcd481773e93">~Reference</a> ()</td></tr>
<tr class="memdesc:a40d21c5f6f98084f8badfcd481773e93"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a40d21c5f6f98084f8badfcd481773e93">More...</a><br /></td></tr>
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</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-attribs"></a>
Private Attributes</h2></td></tr>
<tr class="memitem:ab9a9a045b5f255a853ee0fc4272b4e89"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#ab9a9a045b5f255a853ee0fc4272b4e89">CurrentIndex</a></td></tr>
<tr class="memdesc:ab9a9a045b5f255a853ee0fc4272b4e89"><td class="mdescLeft"> </td><td class="mdescRight">current data index, stored to avoid search from beginning in the data vector <a href="#ab9a9a045b5f255a853ee0fc4272b4e89">More...</a><br /></td></tr>
<tr class="separator:ab9a9a045b5f255a853ee0fc4272b4e89"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a48c84f06284d5756f5dfb7185226600b"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="structReference_1_1timeStep.html">timeStep</a> * > </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#a48c84f06284d5756f5dfb7185226600b">data</a></td></tr>
<tr class="memdesc:a48c84f06284d5756f5dfb7185226600b"><td class="mdescLeft"> </td><td class="mdescRight">vector which contain alls monitors for each time step <a href="#a48c84f06284d5756f5dfb7185226600b">More...</a><br /></td></tr>
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<tr class="memitem:a38682939216dd2d4cb60a420e843647d"><td class="memItemLeft" align="right" valign="top">std::auto_ptr< mml::MonitoringOut > </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#a38682939216dd2d4cb60a420e843647d">mmlOut</a></td></tr>
<tr class="memdesc:a38682939216dd2d4cb60a420e843647d"><td class="mdescLeft"> </td><td class="mdescRight">Object in the file generated by xsdcxx. <a href="#a38682939216dd2d4cb60a420e843647d">More...</a><br /></td></tr>
<tr class="separator:a38682939216dd2d4cb60a420e843647d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab79a82695717a6ac840737094c376dc7"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#ab79a82695717a6ac840737094c376dc7">mmlOutFile</a></td></tr>
<tr class="memdesc:ab79a82695717a6ac840737094c376dc7"><td class="mdescLeft"> </td><td class="mdescRight">the mmlOut document <a href="#ab79a82695717a6ac840737094c376dc7">More...</a><br /></td></tr>
<tr class="separator:ab79a82695717a6ac840737094c376dc7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac54faba56902bd0c90207baec5a6f94c"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classMonitoringManager.html">MonitoringManager</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#ac54faba56902bd0c90207baec5a6f94c">monitoringManager</a></td></tr>
<tr class="memdesc:ac54faba56902bd0c90207baec5a6f94c"><td class="mdescLeft"> </td><td class="mdescRight">monitoring manager <a href="#ac54faba56902bd0c90207baec5a6f94c">More...</a><br /></td></tr>
<tr class="separator:ac54faba56902bd0c90207baec5a6f94c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adc1deb573a400a28021df476911e3435"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classPhysicalModel.html">PhysicalModel</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#adc1deb573a400a28021df476911e3435">pml</a></td></tr>
<tr class="memdesc:adc1deb573a400a28021df476911e3435"><td class="mdescLeft"> </td><td class="mdescRight">pml of the reference <a href="#adc1deb573a400a28021df476911e3435">More...</a><br /></td></tr>
<tr class="separator:adc1deb573a400a28021df476911e3435"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac959e6a1f93f408464b7fa7da3b7420a"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classReference.html#ac959e6a1f93f408464b7fa7da3b7420a">target</a></td></tr>
<tr class="memdesc:ac959e6a1f93f408464b7fa7da3b7420a"><td class="mdescLeft"> </td><td class="mdescRight">target <a href="#ac959e6a1f93f408464b7fa7da3b7420a">More...</a><br /></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>A reference is used to compare to simulated data. </p>
<p>An instance of this class corresponds to the data-binding for type <a class="el" href="classReference.html" title="A reference is used to compare to simulated data. ">Reference</a> of MonitoringModel.xsd.</p>
<p>A reference therefore contains:</p><ul>
<li>a MMLout (xml type MonitoringOut)</li>
<li>a target to consider inside the MMLout</li>
</ul>
<p>All MonitoringOut data is also managed by this class. A MonitoringOut contains:</p><ul>
<li>the path to a PML document, this is managed by the pml private attribute.</li>
<li>vector of timestep that contains (time, vector values), this is managed by inner struct <a class="el" href="structReference_1_1timeStep.html" title="private structure with monitors for a time step ">timeStep</a>.</li>
</ul>
<p>The PML document given in the MMLout is called the PML <a class="el" href="classReference.html" title="A reference is used to compare to simulated data. ">Reference</a>.</p>
<p>The PML <a class="el" href="classReference.html" title="A reference is used to compare to simulated data. ">Reference</a> can either be at any state (beginning, rest shape, final step...etc...) It is mainly used to get the list of Structure/Component to be used in correlation with the target field of the reference.</p>
<dl class="section note"><dt>Note</dt><dd>Some monitors are directly using the position of the atoms given in the PML <a class="el" href="classReference.html" title="A reference is used to compare to simulated data. ">Reference</a> to compute their values. Therefore it is STONGLY advised to give a PML <a class="el" href="classReference.html" title="A reference is used to compare to simulated data. ">Reference</a> that corresponds to the FINAL step of the simulation (position at the end of the simulation/experiments). </dd></dl>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
<a id="ac386a753d9e9c1c3aaab13ae8e3ae874"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ac386a753d9e9c1c3aaab13ae8e3ae874">◆ </a></span>Reference()</h2>
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<td class="memname">Reference::Reference </td>
<td>(</td>
<td class="paramtype">mml::Reference </td>
<td class="paramname"><em>reference</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classMonitoringManager.html">MonitoringManager</a> * </td>
<td class="paramname"><em>monitoringManager</em> </td>
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<p>constructor </p>
<p class="reference">References <a class="el" href="classMonitorFactory.html#a4a8cd39c6ce95486071d389bd39188d3">MonitorFactory::createMonitor()</a>, <a class="el" href="classReference.html#ab9a9a045b5f255a853ee0fc4272b4e89">CurrentIndex</a>, <a class="el" href="classReference.html#a48c84f06284d5756f5dfb7185226600b">data</a>, <a class="el" href="classMonitoringManager.html#a917be6ed96d5324338471f49cb9fe72d">MonitoringManager::getmmlFileFolder()</a>, <a class="el" href="classMonitor.html#acf8459ec6444dbbddfda769518d9c267">Monitor::getTypeName()</a>, <a class="el" href="classReference.html#a38682939216dd2d4cb60a420e843647d">mmlOut</a>, <a class="el" href="classReference.html#ab79a82695717a6ac840737094c376dc7">mmlOutFile</a>, <a class="el" href="classReference.html#ac54faba56902bd0c90207baec5a6f94c">monitoringManager</a>, <a class="el" href="structReference_1_1timeStep.html#a354f18a2fd070dbe16ac7f7b24cefc28">Reference::timeStep::monitorsMap</a>, <a class="el" href="classReference.html#adc1deb573a400a28021df476911e3435">pml</a>, <a class="el" href="classReference.html#ac959e6a1f93f408464b7fa7da3b7420a">target</a>, and <a class="el" href="structReference_1_1timeStep.html#a66198416ce76d24b5b1127ac2a03c33e">Reference::timeStep::time</a>.</p>
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</div>
<a id="a40d21c5f6f98084f8badfcd481773e93"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a40d21c5f6f98084f8badfcd481773e93">◆ </a></span>~Reference()</h2>
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<td class="memname">Reference::~Reference </td>
<td>(</td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<p>destructor </p>
<p class="reference">References <a class="el" href="classReference.html#a48c84f06284d5756f5dfb7185226600b">data</a>, <a class="el" href="structReference_1_1timeStep.html#a354f18a2fd070dbe16ac7f7b24cefc28">Reference::timeStep::monitorsMap</a>, and <a class="el" href="classReference.html#adc1deb573a400a28021df476911e3435">pml</a>.</p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#aa617c2c9b8f0a034fd8bdd944fe0b24e">◆ </a></span>getDistanceToTriangularMesh()</h2>
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<td class="memname">bool Reference::getDistanceToTriangularMesh </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"><em>pos</em>[3], </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double & </td>
<td class="paramname"><em>dist</em> </td>
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<p>get distance to a triangular mesh, the target of the reference must contain triangles. </p>
<p>This is a fast method that gives the distance relatively to the triangles in the PML <a class="el" href="classReference.html" title="A reference is used to compare to simulated data. ">Reference</a>.</p>
<dl class="section note"><dt>Note</dt><dd>This is a heuristic version, which means, it does not test all triangles to find the lowest. It first look for the nearest atom in the PML <a class="el" href="classReference.html" title="A reference is used to compare to simulated data. ">Reference</a> and then only check the triangles around this nearest atom.</dd>
<dd>
This is not the exact distance to the nearest triangle, but an approximation given by the function <a class="el" href="Tools_8cpp.html#ad7f4b3c0bce68001e9a799dc1081d71d" title="compute the distance of a point to the plane defined by a 3D triangle. ">distanceToTrianglePlane()</a>.</dd></dl>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">pos</td><td>atom's position (with eventual offset) </td></tr>
<tr><td class="paramname">dist</td><td>the distance </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>true if method succeded (a triangular mesh was found) </dd></dl>
<p class="reference">References <a class="el" href="classAtomIterator.html#a96ddda733a21b0d0f244236336da057a">AtomIterator::begin()</a>, <a class="el" href="classAtomIterator.html#a3c2c4a98880a3e24fc4613fe4486059d">AtomIterator::currentAtom()</a>, <a class="el" href="Tools_8h.html#a7a7682b10827c2f1b183750695ed84d0">distance()</a>, <a class="el" href="Tools_8cpp.html#ad7f4b3c0bce68001e9a799dc1081d71d">distanceToTrianglePlane()</a>, <a class="el" href="classAtomIterator.html#afd84594f5dad470161ba462c2af860bb">AtomIterator::end()</a>, <a class="el" href="classStructure.html#a9a21135d09e8292affb68647dee9d1a7">Structure::getAllStructuralComponents()</a>, <a class="el" href="classAtom.html#a4ac7762cfcdfff37fe8cd4370a24d79b">Atom::getPosition()</a>, <a class="el" href="classCell.html#aa15ae2bf870c36166041d8d840d34957">Cell::getProperties()</a>, <a class="el" href="classStructuralComponent.html#a2bfab6723909acea409f6a09b25a6676">StructuralComponent::getStructure()</a>, <a class="el" href="classStructureProperties.html#a424fa864b33071bff1e23a9dc8166ebd">StructureProperties::getType()</a>, <a class="el" href="classAtomIterator.html#ad718bec73413837fcc5951b909404d5c">AtomIterator::next()</a>, <a class="el" href="classReference.html#adc1deb573a400a28021df476911e3435">pml</a>, <a class="el" href="classReference.html#ac959e6a1f93f408464b7fa7da3b7420a">target</a>, and <a class="el" href="classStructureProperties.html#a9180a07ccc47844f526e879201d75731aafad539f241ab0931a414284f3658974">StructureProperties::TRIANGLE</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a64ef08c4cace3ec39a105b669828c8da">◆ </a></span>getMonitoredData() <span class="overload">[1/3]</span></h2>
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<td class="memname">bool Reference::getMonitoredData </td>
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<td class="paramtype">std::string </td>
<td class="paramname"><em>type</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>ref</em>[] </td>
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<p>get the the values of a given monitor which do not depend of time or an atom (e.g. </p>
<p>geometrical data) </p><dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">type</td><td>name of the monitor, must be a existing monitor in the mmlOut document </td></tr>
<tr><td class="paramname">ref</td><td>a table where data will be stored </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>true if method succeded (an existing monitor named "type" was found) </dd></dl>
<p class="reference">Referenced by <a class="el" href="classReference.html#a90bfd9f49b91ea555848cb7ff1683468">getNearest()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a46477a6bda1564c1e9b708a86c07bfc3">◆ </a></span>getMonitoredData() <span class="overload">[2/3]</span></h2>
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<td class="memname">bool Reference::getMonitoredData </td>
<td>(</td>
<td class="paramtype">std::string </td>
<td class="paramname"><em>type</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>time</em>, </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double & </td>
<td class="paramname"><em>realTime</em>, </td>
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<td class="paramtype">double </td>
<td class="paramname"><em>ref</em>[] </td>
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<p>get the the values of a given monitor at a given time which do not depend an atom (e.g. </p>
<p>volume) if there is no corresponding time in reference, it return data for the first higher time. </p><dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">type</td><td>name of the monitor, must be a existing monitor in the mmlOut document </td></tr>
<tr><td class="paramname">time</td><td>time to get the values </td></tr>
<tr><td class="paramname">realTime</td><td>the nearest time found if realTime=infinity, the nearest is the final state </td></tr>
<tr><td class="paramname">ref</td><td>a table where data will be stored </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>true if method succeded </dd></dl>
<p class="reference">References <a class="el" href="classReference.html#ab9a9a045b5f255a853ee0fc4272b4e89">CurrentIndex</a>, <a class="el" href="classReference.html#a48c84f06284d5756f5dfb7185226600b">data</a>, and <a class="el" href="classMonitor.html#a5c25532b62fb6bbcef096210b937894ea5969071342f9e59a0a19cdca9f7b4599">Monitor::SCALAR</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a9d1f6d150a211a713949c8bf6eae71de">◆ </a></span>getMonitoredData() <span class="overload">[3/3]</span></h2>
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<td class="memname">bool Reference::getMonitoredData </td>
<td>(</td>
<td class="paramtype">std::string </td>
<td class="paramname"><em>type</em>, </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>time</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>index</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double & </td>
<td class="paramname"><em>realTime</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>ref</em>[] </td>
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<p>get the the values of a given monitor at a given time and a given atom's index (e.g. </p>
<p>position) </p><dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">type</td><td>name of the monitor, must be a existing monitor in the mmlOut document </td></tr>
<tr><td class="paramname">time</td><td>time to get the values </td></tr>
<tr><td class="paramname">index</td><td>atom's index </td></tr>
<tr><td class="paramname">realTime</td><td>the nearest time found if realTime=infinity, the nearest is the final state </td></tr>
<tr><td class="paramname">ref</td><td>a table where data will be stored </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>true if method succeded </dd></dl>
<p class="reference">References <a class="el" href="classReference.html#ab9a9a045b5f255a853ee0fc4272b4e89">CurrentIndex</a>, and <a class="el" href="classReference.html#a48c84f06284d5756f5dfb7185226600b">data</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a90bfd9f49b91ea555848cb7ff1683468">◆ </a></span>getNearest() <span class="overload">[1/2]</span></h2>
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<td class="memname">bool Reference::getNearest </td>
<td>(</td>
<td class="paramtype">double </td>
<td class="paramname"><em>pos</em>[3], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>time</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>ref</em>[3] </td>
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<p>get the nearest reference point in the "target" using "Position" monitor at given time </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">pos</td><td>atom's position (with eventual offset) </td></tr>
<tr><td class="paramname">time</td><td>time to get the <a class="el" href="classPosition.html" title="A simple criterion based on position calculation. ">Position</a> </td></tr>
<tr><td class="paramname">ref</td><td>a table where positon of the nearest atom in reference will be stored </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>true if method succeded (a nearest atom was found in reference) </dd></dl>
<p class="reference">References <a class="el" href="classAtomIterator.html#a96ddda733a21b0d0f244236336da057a">AtomIterator::begin()</a>, <a class="el" href="classAtomIterator.html#a3c2c4a98880a3e24fc4613fe4486059d">AtomIterator::currentAtom()</a>, <a class="el" href="Tools_8h.html#a7a7682b10827c2f1b183750695ed84d0">distance()</a>, <a class="el" href="classAtomIterator.html#afd84594f5dad470161ba462c2af860bb">AtomIterator::end()</a>, <a class="el" href="classStructure.html#a04b2fc52d7cc2af4356620f1d7e09c18">Structure::getIndex()</a>, <a class="el" href="classReference.html#a64ef08c4cace3ec39a105b669828c8da">getMonitoredData()</a>, <a class="el" href="classAtomIterator.html#ad718bec73413837fcc5951b909404d5c">AtomIterator::next()</a>, <a class="el" href="classReference.html#adc1deb573a400a28021df476911e3435">pml</a>, and <a class="el" href="classReference.html#ac959e6a1f93f408464b7fa7da3b7420a">target</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aa15b22233ce91120d625c4b0fd5a5665">◆ </a></span>getNearest() <span class="overload">[2/2]</span></h2>
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<td class="memname">bool Reference::getNearest </td>
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<td class="paramtype">double </td>
<td class="paramname"><em>pos</em>[3], </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"><em>ref</em>[3] </td>
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<p>get the nearest reference point in the "target" using "Position" monitor of the PML <a class="el" href="classReference.html" title="A reference is used to compare to simulated data. ">Reference</a>. </p>
<p>This is a fast method that gives the nearest position relatively to the PML <a class="el" href="classReference.html" title="A reference is used to compare to simulated data. ">Reference</a>.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">pos</td><td>atom's position (with eventual offset) </td></tr>
<tr><td class="paramname">ref</td><td>a table where positon of the nearest atom in reference will be stored </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>true if method succeded (a nearest atom was found in reference) </dd></dl>
<p class="reference">References <a class="el" href="classAtomIterator.html#a96ddda733a21b0d0f244236336da057a">AtomIterator::begin()</a>, <a class="el" href="classAtomIterator.html#a3c2c4a98880a3e24fc4613fe4486059d">AtomIterator::currentAtom()</a>, <a class="el" href="Tools_8h.html#a7a7682b10827c2f1b183750695ed84d0">distance()</a>, <a class="el" href="classAtomIterator.html#afd84594f5dad470161ba462c2af860bb">AtomIterator::end()</a>, <a class="el" href="classAtom.html#a4ac7762cfcdfff37fe8cd4370a24d79b">Atom::getPosition()</a>, <a class="el" href="classAtomIterator.html#ad718bec73413837fcc5951b909404d5c">AtomIterator::next()</a>, <a class="el" href="classReference.html#adc1deb573a400a28021df476911e3435">pml</a>, and <a class="el" href="classReference.html#ac959e6a1f93f408464b7fa7da3b7420a">target</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aa1b72463417e38d965585a5ff88740d0">◆ </a></span>toString()</h2>
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<p>return a string relative to <a class="el" href="classReference.html" title="A reference is used to compare to simulated data. ">Reference</a> type </p>
<p class="reference">References <a class="el" href="classReference.html#ab79a82695717a6ac840737094c376dc7">mmlOutFile</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#ab9a9a045b5f255a853ee0fc4272b4e89">◆ </a></span>CurrentIndex</h2>
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<td class="memname">int Reference::CurrentIndex</td>
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<p>current data index, stored to avoid search from beginning in the data vector </p>
<p class="reference">Referenced by <a class="el" href="classReference.html#a46477a6bda1564c1e9b708a86c07bfc3">getMonitoredData()</a>, and <a class="el" href="classReference.html#ac386a753d9e9c1c3aaab13ae8e3ae874">Reference()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a48c84f06284d5756f5dfb7185226600b">◆ </a></span>data</h2>
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<td class="memname">std::vector<<a class="el" href="structReference_1_1timeStep.html">timeStep</a>*> Reference::data</td>
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<p>vector which contain alls monitors for each time step </p>
<p class="reference">Referenced by <a class="el" href="classReference.html#a46477a6bda1564c1e9b708a86c07bfc3">getMonitoredData()</a>, <a class="el" href="classReference.html#ac386a753d9e9c1c3aaab13ae8e3ae874">Reference()</a>, and <a class="el" href="classReference.html#a40d21c5f6f98084f8badfcd481773e93">~Reference()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a38682939216dd2d4cb60a420e843647d">◆ </a></span>mmlOut</h2>
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<td class="memname">std::auto_ptr<mml::MonitoringOut> Reference::mmlOut</td>
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<p>Object in the file generated by xsdcxx. </p>
<p class="reference">Referenced by <a class="el" href="classReference.html#ac386a753d9e9c1c3aaab13ae8e3ae874">Reference()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ab79a82695717a6ac840737094c376dc7">◆ </a></span>mmlOutFile</h2>
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<td class="memname">std::string Reference::mmlOutFile</td>
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<p>the mmlOut document </p>
<p class="reference">Referenced by <a class="el" href="classReference.html#ac386a753d9e9c1c3aaab13ae8e3ae874">Reference()</a>, and <a class="el" href="classReference.html#aa1b72463417e38d965585a5ff88740d0">toString()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ac54faba56902bd0c90207baec5a6f94c">◆ </a></span>monitoringManager</h2>
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<td class="memname"><a class="el" href="classMonitoringManager.html">MonitoringManager</a>* Reference::monitoringManager</td>
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<p>monitoring manager </p>
<p class="reference">Referenced by <a class="el" href="classReference.html#ac386a753d9e9c1c3aaab13ae8e3ae874">Reference()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#adc1deb573a400a28021df476911e3435">◆ </a></span>pml</h2>
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<td class="memname"><a class="el" href="classPhysicalModel.html">PhysicalModel</a>* Reference::pml</td>
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<p>pml of the reference </p>
<p class="reference">Referenced by <a class="el" href="classReference.html#aa617c2c9b8f0a034fd8bdd944fe0b24e">getDistanceToTriangularMesh()</a>, <a class="el" href="classReference.html#a90bfd9f49b91ea555848cb7ff1683468">getNearest()</a>, <a class="el" href="classReference.html#ac386a753d9e9c1c3aaab13ae8e3ae874">Reference()</a>, and <a class="el" href="classReference.html#a40d21c5f6f98084f8badfcd481773e93">~Reference()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ac959e6a1f93f408464b7fa7da3b7420a">◆ </a></span>target</h2>
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<td class="memname">std::string Reference::target</td>
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<p>target </p>
<p class="reference">Referenced by <a class="el" href="classReference.html#aa617c2c9b8f0a034fd8bdd944fe0b24e">getDistanceToTriangularMesh()</a>, <a class="el" href="classReference.html#a90bfd9f49b91ea555848cb7ff1683468">getNearest()</a>, and <a class="el" href="classReference.html#ac386a753d9e9c1c3aaab13ae8e3ae874">Reference()</a>.</p>
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<hr/>The documentation for this class was generated from the following files:<ul>
<li><a class="el" href="Reference_8h_source.html">Reference.h</a></li>
<li><a class="el" href="Reference_8cpp.html">Reference.cpp</a></li>
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