swh:1:snp:e6d42e6731ce66e3c09de07ac49964c03139e990
Tip revision: 26b818c8be2be41dd673d938b403c5c7562635de authored by Travis CI on 28 November 2019, 13:55:12 UTC
Deploy code docs to GitHub Pages Travis build: 305
Deploy code docs to GitHub Pages Travis build: 305
Tip revision: 26b818c
_ox_model_t2_two_param_8hxx_source.html
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.6"/>
<title>Tomato: lib/OxModelT2TwoParam.hxx Source File</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="navtree.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="resize.js"></script>
<script type="text/javascript" src="navtree.js"></script>
<script type="text/javascript">
$(document).ready(initResizable);
$(window).load(resizeHeight);
</script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/search.js"></script>
<script type="text/javascript">
$(document).ready(function() { searchBox.OnSelectItem(0); });
</script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">Tomato
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.6 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
<div id="navrow1" class="tabs">
<ul class="tablist">
<li><a href="index.html"><span>Main Page</span></a></li>
<li><a href="pages.html"><span>Related Pages</span></a></li>
<li><a href="annotated.html"><span>Classes</span></a></li>
<li class="current"><a href="files.html"><span>Files</span></a></li>
<li>
<div id="MSearchBox" class="MSearchBoxInactive">
<span class="left">
<img id="MSearchSelect" src="search/mag_sel.png"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
alt=""/>
<input type="text" id="MSearchField" value="Search" accesskey="S"
onfocus="searchBox.OnSearchFieldFocus(true)"
onblur="searchBox.OnSearchFieldFocus(false)"
onkeyup="searchBox.OnSearchFieldChange(event)"/>
</span><span class="right">
<a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
</span>
</div>
</li>
</ul>
</div>
<div id="navrow2" class="tabs2">
<ul class="tablist">
<li><a href="files.html"><span>File List</span></a></li>
<li><a href="globals.html"><span>File Members</span></a></li>
</ul>
</div>
</div><!-- top -->
<div id="side-nav" class="ui-resizable side-nav-resizable">
<div id="nav-tree">
<div id="nav-tree-contents">
<div id="nav-sync" class="sync"></div>
</div>
</div>
<div id="splitbar" style="-moz-user-select:none;"
class="ui-resizable-handle">
</div>
</div>
<script type="text/javascript">
$(document).ready(function(){initNavTree('_ox_model_t2_two_param_8hxx_source.html','');});
</script>
<div id="doc-content">
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
<div class="header">
<div class="headertitle">
<div class="title">OxModelT2TwoParam.hxx</div> </div>
</div><!--header-->
<div class="contents">
<a href="_ox_model_t2_two_param_8hxx.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> </div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor">#ifndef Tomato_OXModelT2TwoParam_HXX</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor"></span><span class="preprocessor">#define Tomato_OXModelT2TwoParam_HXX</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="keyword">namespace </span>Ox {</div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> </div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> </div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span>  <span class="keyword">template</span>< <span class="keyword">typename</span> MeasureType ></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span>  MeasureType</div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  <a class="code" href="class_ox_1_1_model_t2_two_param.html#a1401dbd94a7a23903f22013af44c4648">ModelT2TwoParam<MeasureType></a></div>
<div class="line"><a name="l00016"></a><span class="lineno"><a class="line" href="class_ox_1_1_model_t2_two_param.html#a1401dbd94a7a23903f22013af44c4648"> 16</a></span> <a class="code" href="class_ox_1_1_model_t2_two_param.html#a1401dbd94a7a23903f22013af44c4648"> ::calcModelValue</a>(<span class="keyword">const</span> MeasureType* parameters, MeasureType time){</div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  MeasureType A = parameters[0];</div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  MeasureType T2 = parameters[1];</div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> </div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span>  <span class="keywordflow">if</span> (fabs(T2) < std::numeric_limits<MeasureType>::min())</div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  <span class="keywordflow">return</span> A;</div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> </div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  <span class="keywordflow">return</span> A * exp( -time / T2 );</div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  }</div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> </div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  <span class="keyword">template</span>< <span class="keyword">typename</span> MeasureType ></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  <span class="keywordtype">void</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  <a class="code" href="class_ox_1_1_model_t2_two_param.html#a7f4e4edc966189fb95f6fcbbd6417c5f">ModelT2TwoParam<MeasureType></a></div>
<div class="line"><a name="l00029"></a><span class="lineno"><a class="line" href="class_ox_1_1_model_t2_two_param.html#a7f4e4edc966189fb95f6fcbbd6417c5f"> 29</a></span> <a class="code" href="class_ox_1_1_model_t2_two_param.html#a7f4e4edc966189fb95f6fcbbd6417c5f"> ::calcLSResiduals</a>(<span class="keyword">const</span> MeasureType* parameters, MeasureType* residuals){</div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> </div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> nSamples = this->_nSamples;</div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> </div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i = 0; i < nSamples; i++) {</div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  MeasureType invTime = this->_EchoTimes[i];</div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  MeasureType measured = this->_Signal[i];</div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  MeasureType calculated = 0;</div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> </div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  calculated = calcModelValue(parameters, invTime);</div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  residuals[i] = calculated - measured;</div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  }</div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  }</div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keyword">template</span>< <span class="keyword">typename</span> MeasureType ></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keywordtype">void</span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <a class="code" href="class_ox_1_1_model_t2_two_param.html#af056e278a340918eb57f23f63ba2f23c">ModelT2TwoParam<MeasureType></a></div>
<div class="line"><a name="l00047"></a><span class="lineno"><a class="line" href="class_ox_1_1_model_t2_two_param.html#af056e278a340918eb57f23f63ba2f23c"> 47</a></span> <a class="code" href="class_ox_1_1_model_t2_two_param.html#af056e278a340918eb57f23f63ba2f23c"> ::calcLSJacobian</a>(<span class="keyword">const</span> MeasureType* parameters, MeasureType* jacobian){</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keywordtype">int</span> nSamples = this->_nSamples;</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  MeasureType A = parameters[0];</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  MeasureType T2 = parameters[1];</div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  MeasureType echoTime, myexp;</div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < nSamples; i++) {</div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  echoTime = this->_EchoTimes[i];</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  myexp = exp(-echoTime / T2);</div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span> </div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="comment">// calculated in matlab</span></div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="comment">// syms A T2 t</span></div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="comment">// f=A*exp(-t./T2); diff(f,A), diff(f,T2)</span></div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  jacobian[i*2+0] = myexp;</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  jacobian[i*2+1] = A * echoTime * myexp / T2 / T2;</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  }</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  }</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keyword">template</span>< <span class="keyword">typename</span> MeasureType ></div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  MeasureType</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <a class="code" href="class_ox_1_1_model_t2_two_param.html#abd88af16b5860a18632453ca1ce858b4">ModelT2TwoParam<MeasureType></a></div>
<div class="line"><a name="l00070"></a><span class="lineno"><a class="line" href="class_ox_1_1_model_t2_two_param.html#abd88af16b5860a18632453ca1ce858b4"> 70</a></span> <a class="code" href="class_ox_1_1_model_t2_two_param.html#abd88af16b5860a18632453ca1ce858b4"> ::calcCostValue</a>(<span class="keyword">const</span> MeasureType* parameters){</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keywordtype">int</span> nSamples = this->_nSamples;</div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span> </div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  calcLSResiduals(parameters, this->_Residuals);</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  MeasureType result = 0;</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < nSamples; ++i) {</div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  result = result + this->_Residuals[i] * this->_Residuals[i];</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  }</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordflow">return</span> result;</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  }</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keyword">template</span>< <span class="keyword">typename</span> MeasureType ></div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordtype">void</span></div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <a class="code" href="class_ox_1_1_model_t2_two_param.html#a4957d8cf05666364c6c21483fd0f9fa9">ModelT2TwoParam<MeasureType></a></div>
<div class="line"><a name="l00087"></a><span class="lineno"><a class="line" href="class_ox_1_1_model_t2_two_param.html#a4957d8cf05666364c6c21483fd0f9fa9"> 87</a></span> <a class="code" href="class_ox_1_1_model_t2_two_param.html#a4957d8cf05666364c6c21483fd0f9fa9"> ::calcCostDerivative</a>(<span class="keyword">const</span> MeasureType* parameters, MeasureType* derivative){</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> </div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="keywordtype">int</span> nSamples = this->_nSamples;</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span> </div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  derivative[0] = 0;</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  derivative[1] = 0;</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> </div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  MeasureType measured, echoTime, myexp;</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> </div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  MeasureType A = parameters[0];</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  MeasureType T2 = parameters[1];</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span> </div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="comment">// calculated in matlab</span></div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="comment">// syms A T2 t y</span></div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="comment">// f=(A+exp(-t./T2)-y).^2; diff(f,A), diff(f,T2)</span></div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < nSamples; ++i){</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  measured = this->getSignal()[i];</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  echoTime = this->getEchoTimes()[i];</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  myexp = exp(-echoTime / T2);</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> </div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  derivative[0] = derivative[0] + A*2 - measured*2 + myexp*2;;</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  derivative[1] = derivative[1] + 2 * echoTime * myexp * (A - measured + myexp) / T2 / T2;</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  }</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  }</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span> } <span class="comment">//namespace Ox</span></div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span> </div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span> <span class="preprocessor">#endif //Tomato_OXModelT2TwoParam_HXX</span></div>
<div class="ttc" id="class_ox_1_1_model_t2_two_param_html_a7f4e4edc966189fb95f6fcbbd6417c5f"><div class="ttname"><a href="class_ox_1_1_model_t2_two_param.html#a7f4e4edc966189fb95f6fcbbd6417c5f">Ox::ModelT2TwoParam::calcLSResiduals</a></div><div class="ttdeci">virtual void calcLSResiduals(const MeasureType *parameters, MeasureType *residuals)</div><div class="ttdef"><b>Definition:</b> OxModelT2TwoParam.hxx:29</div></div>
<div class="ttc" id="class_ox_1_1_model_t2_two_param_html_abd88af16b5860a18632453ca1ce858b4"><div class="ttname"><a href="class_ox_1_1_model_t2_two_param.html#abd88af16b5860a18632453ca1ce858b4">Ox::ModelT2TwoParam::calcCostValue</a></div><div class="ttdeci">virtual MeasureType calcCostValue(const MeasureType *parameters)</div><div class="ttdef"><b>Definition:</b> OxModelT2TwoParam.hxx:70</div></div>
<div class="ttc" id="class_ox_1_1_model_t2_two_param_html_a4957d8cf05666364c6c21483fd0f9fa9"><div class="ttname"><a href="class_ox_1_1_model_t2_two_param.html#a4957d8cf05666364c6c21483fd0f9fa9">Ox::ModelT2TwoParam::calcCostDerivative</a></div><div class="ttdeci">virtual void calcCostDerivative(const MeasureType *parameters, MeasureType *derivative)</div><div class="ttdef"><b>Definition:</b> OxModelT2TwoParam.hxx:87</div></div>
<div class="ttc" id="class_ox_1_1_model_t2_two_param_html_af056e278a340918eb57f23f63ba2f23c"><div class="ttname"><a href="class_ox_1_1_model_t2_two_param.html#af056e278a340918eb57f23f63ba2f23c">Ox::ModelT2TwoParam::calcLSJacobian</a></div><div class="ttdeci">virtual void calcLSJacobian(const MeasureType *parameters, MeasureType *jacobian)</div><div class="ttdef"><b>Definition:</b> OxModelT2TwoParam.hxx:47</div></div>
<div class="ttc" id="class_ox_1_1_model_t2_two_param_html_a1401dbd94a7a23903f22013af44c4648"><div class="ttname"><a href="class_ox_1_1_model_t2_two_param.html#a1401dbd94a7a23903f22013af44c4648">Ox::ModelT2TwoParam::calcModelValue</a></div><div class="ttdeci">virtual MeasureType calcModelValue(const MeasureType *parameters, MeasureType time)</div><div class="ttdef"><b>Definition:</b> OxModelT2TwoParam.hxx:16</div></div>
</div><!-- fragment --></div><!-- contents -->
</div><!-- doc-content -->
<!-- start footer part -->
<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
<ul>
<li class="navelem"><a class="el" href="dir_97aefd0d527b934f1d99a682da8fe6a9.html">lib</a></li><li class="navelem"><a class="el" href="_ox_model_t2_two_param_8hxx.html">OxModelT2TwoParam.hxx</a></li>
<li class="footer">Generated by
<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
</ul>
</div>
</body>
</html>