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
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<div class="title">OxCalculatorT1Shmolli.hxx</div> </div>
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<a href="_ox_calculator_t1_shmolli_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_OXCALCULATORT1SHMOLLI_HXX</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor"></span><span class="preprocessor">#define TOMATO_OXCALCULATORT1SHMOLLI_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>  <span class="keyword">template</span>< <span class="keyword">typename</span> MeasureType ></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span>  <span class="keywordtype">int</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span>  <a class="code" href="class_ox_1_1_calculator_t1_shmolli.html#a6464c63f20ecd9de842d722e5d9d2866">CalculatorT1Shmolli<MeasureType></a></div>
<div class="line"><a name="l00015"></a><span class="lineno"><a class="line" href="class_ox_1_1_calculator_t1_shmolli.html#a6464c63f20ecd9de842d722e5d9d2866"> 15</a></span> <a class="code" href="class_ox_1_1_calculator_t1_shmolli.html#a6464c63f20ecd9de842d722e5d9d2866"> ::prepareToCalculate</a>(){</div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  <span class="comment">// Shmolli 51111 needs exactly 7 samples</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  <span class="keywordflow">if</span> (this->getNSamples() != 7){</div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"T1_SHMOLLI reconstruction available only for 7 samples."</span>);</div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span>  }</div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> </div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// // base class prepareToCalculate()</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// if(Calculator<MeasureType>::prepareToCalculate() == 1) {</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// return 1; // EXIT_FAILURE</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// }</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> </div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  <span class="comment">// if fitter does not have to iterate, do not calculate</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  <span class="keywordflow">if</span> (this->getFitter()->getMaxFunctionEvals() == 0){</div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="keywordflow">return</span> 1; <span class="comment">// EXIT_FAILURE</span></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> </div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  <span class="comment">// verify invTimes are sorted</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < this->getNSamples()-1; i++){</div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keywordflow">if</span> (this->getInvTimes()[i] > this->getInvTimes()[i+1]){</div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"InvTimes have to be sorted!"</span>);</div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  }</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> </div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="comment">// calculate sign</span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  this->getSignCalculator()->setNSamples(this->getNSamples());</div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  this->getSignCalculator()->setInvTimes(this->getInvTimes());</div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  this->getSignCalculator()->setSigMag(this->getSigMag());</div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  this->getSignCalculator()->setSigPha(this->getSigPha());</div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  this->getSignCalculator()->setSignal(this->_Signal);</div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  this->getSignCalculator()->setSigns(this->_Signs);</div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> </div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  this->getSignCalculator()->calculateSign();</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="comment">// calculate start point</span></div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  this->getStartPointCalculator()->setNDims(this->_nDims);</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keywordflow">if</span> (!this->getStartPointCalculator()->getInputStartPoint()){</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keywordflow">if</span> (this->_nDims == 3){</div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  MeasureType <span class="keyword">const</span> temp[] = {100, 200, 1000};</div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  this->getStartPointCalculator()->setInputStartPoint(temp);</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  } <span class="keywordflow">else</span> {</div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Calculator: Set InputStartPoint in StartPointCalculator"</span>);</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  }</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>  this->getStartPointCalculator()->setNSamples(this->getNSamples());</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  this->getStartPointCalculator()->setInvTimes(this->getInvTimes());</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  this->getStartPointCalculator()->setSigMag(this->getSigMag());</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  this->getStartPointCalculator()->setSigns(this->getSigns());</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  this->getStartPointCalculator()->setCalculatedStartPoint(this->_StartPoint);</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>  this->getStartPointCalculator()->calculateStartPoint();</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="comment">// calculate TRR</span></div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  calculateTRRaverageHB();</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keywordflow">return</span> 0; <span class="comment">// EXIT_SUCCESS</span></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> </div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keyword">template</span>< <span class="keyword">typename</span> MeasureType ></div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordtype">int</span></div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <a class="code" href="class_ox_1_1_calculator_t1_shmolli.html">CalculatorT1Shmolli<MeasureType></a></div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> <a class="code" href="class_ox_1_1_calculator_t1_shmolli.html"> ::getStartPointSKPShmolli</a>(<span class="keyword">const</span> MeasureType * invTimes5, <span class="keyword">const</span> MeasureType * invTimes6, <span class="keyword">const</span> MeasureType * invTimes7,</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keyword">const</span> MeasureType * sigMag5, <span class="keyword">const</span> MeasureType * sigMag6, <span class="keyword">const</span> MeasureType * sigMag7,</div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keyword">const</span> MeasureType * signs5, <span class="keyword">const</span> MeasureType * signs6, <span class="keyword">const</span> MeasureType * signs7){</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>  <span class="keywordtype">int</span> nStartFitPoints = 0;</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <a class="code" href="class_ox_1_1_start_point_calculator.html">StartPointCalculator<MeasureType></a> *startPointCalculator = this->getStartPointCalculator();</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  startPointCalculator->setCalculatedStartPoint(this->_StartPoint);</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordflow">if</span> (this->getSigPha()){</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  startPointCalculator->setNSamples(5);</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  startPointCalculator->setInvTimes(invTimes5);</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  startPointCalculator->setSigMag(sigMag5);</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  startPointCalculator->setSigns(signs5);</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  nStartFitPoints = startPointCalculator-><a class="code" href="class_ox_1_1_start_point_calculator.html#a9d1132410d68eb16f3f71ec4015c0b2f">calculateStartPoint</a>();</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span> </div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordflow">if</span>( nStartFitPoints < 3 ) {</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  startPointCalculator->setNSamples(6);</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  startPointCalculator->setInvTimes(invTimes6);</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  startPointCalculator->setSigMag(sigMag6);</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  startPointCalculator->setSigns(signs6);</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  nStartFitPoints = startPointCalculator-><a class="code" href="class_ox_1_1_start_point_calculator.html#a9d1132410d68eb16f3f71ec4015c0b2f">calculateStartPoint</a>();</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="keywordflow">if</span>( nStartFitPoints < 3 ) {</div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  startPointCalculator->setNSamples(7);</div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  startPointCalculator->setInvTimes(invTimes7);</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  startPointCalculator->setSigMag(sigMag7);</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  startPointCalculator->setSigns(signs7);</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  startPointCalculator-><a class="code" href="class_ox_1_1_start_point_calculator.html#a9d1132410d68eb16f3f71ec4015c0b2f">calculateStartPoint</a>();</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  }</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  } <span class="keywordflow">else</span> {</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keywordflow">if</span>( nStartFitPoints < 3 ) {</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  startPointCalculator->setNSamples(7);</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  startPointCalculator->setInvTimes(invTimes7);</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  startPointCalculator->setSigMag(sigMag7);</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  startPointCalculator->setSigns(signs7);</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  startPointCalculator-><a class="code" href="class_ox_1_1_start_point_calculator.html#a9d1132410d68eb16f3f71ec4015c0b2f">calculateStartPoint</a>();</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> </div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="keywordflow">return</span> 0; <span class="comment">// EXIT_SUCCESS</span></div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  }</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span> </div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="keyword">template</span>< <span class="keyword">typename</span> MeasureType ></div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="keywordtype">int</span></div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <a class="code" href="class_ox_1_1_calculator_t1_shmolli.html#a2c4444b1aa40e3f01b7cf0b8e7f7672b">CalculatorT1Shmolli<MeasureType></a></div>
<div class="line"><a name="l00122"></a><span class="lineno"><a class="line" href="class_ox_1_1_calculator_t1_shmolli.html#a2c4444b1aa40e3f01b7cf0b8e7f7672b"> 122</a></span> <a class="code" href="class_ox_1_1_calculator_t1_shmolli.html#a2c4444b1aa40e3f01b7cf0b8e7f7672b"> ::calculateTRRaverageHB</a>(){</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span> </div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="comment">// if shmolli (7 samples)</span></div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keyword">const</span> MeasureType *invTimes = this->getInvTimes();</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  MeasureType invTimesDifferences[4];</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keywordflow">if</span> (this->_nSamples == 7) {</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  invTimesDifferences[0] = invTimes[3] - invTimes[0];</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  invTimesDifferences[1] = invTimes[4] - invTimes[3];</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  invTimesDifferences[2] = invTimes[5] - invTimes[4];</div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  invTimesDifferences[3] = invTimes[6] - invTimes[5];</div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  }</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> </div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  _TRRaverageHB = KWUtil::calcMeanArray(4, invTimesDifferences);</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="comment">// m_TRRaverageHB = KWUtil::calcMedianArray(4, invTimesDifferences);</span></div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="keywordflow">return</span> 0; <span class="comment">// EXIT_SUCCESS</span></div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  }</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span> </div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="keyword">template</span>< <span class="keyword">typename</span> MeasureType ></div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="keywordtype">int</span></div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <a class="code" href="class_ox_1_1_calculator_t1_shmolli.html#ac689ebbf27f95f6fa2559cc13a824db0">CalculatorT1Shmolli<MeasureType></a></div>
<div class="line"><a name="l00143"></a><span class="lineno"><a class="line" href="class_ox_1_1_calculator_t1_shmolli.html#ac689ebbf27f95f6fa2559cc13a824db0"> 143</a></span> <a class="code" href="class_ox_1_1_calculator_t1_shmolli.html#ac689ebbf27f95f6fa2559cc13a824db0"> ::calculate</a>(){</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  this->_Results = std::map <std::string, MeasureType>();</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> </div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="comment">// calculate if higher than the cutoff</span></div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="keywordflow">if</span> (KWUtil::calcMeanArray(this->getNSamples(), this->getSigMag()) < this->getMeanCutOff()) {</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="keywordflow">return</span> 0; <span class="comment">// EXIT_SUCCESS</span></div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  }</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> </div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="comment">// continue only if prepareToCalculate was successful</span></div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="keywordflow">if</span>(this->prepareToCalculate() == 1){ <span class="comment">//EXIT_FAILURE</span></div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <span class="keywordflow">return</span> 1; <span class="comment">// EXIT_FAILURE</span></div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  }</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> </div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <span class="comment">// some initialisation</span></div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keyword">const</span> <span class="keywordtype">double</span> MaxTIForSignInvert = (this->MAX_T1_TRESHOLD * 0.67);</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  MeasureType lastValue = 1e32;</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  MeasureType lastValueTemp = lastValue;</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> </div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="comment">// nShmolliSamplesUsed = 5 // =(T1s567[0] < TRRaverageHB) && (T1s567[0] > 1);</span></div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <span class="comment">// nShmolliSamplesUsed = 6 // =(chi567[1]*T1s567[1] < (chi567[0]*TRRaverageHB )) && (T1s567[1] > 1);</span></div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  <span class="comment">// nShmolliSamplesUsed = 7 // =((chi567[2]*T1s567[2]) < (chi567[1]* TRRaverageHB*0.4 )) && (T1s567[2] > 1);</span></div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span> </div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="comment">// temporary defs here</span></div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="keywordtype">double</span> T1temp = 0;</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <span class="keywordtype">double</span> chiTemp = 1e32; <span class="comment">// legacy reasons</span></div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> nShmolliSamplesUsed = 0;</div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  MeasureType TRRaverageHB = this->_TRRaverageHB;</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span> </div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  std::map <std::string, MeasureType> results0, results5, results6, results7;</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  MeasureType signal5[5], signal6[6], signal7[7];</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  MeasureType invTimes5[5], invTimes6[6], invTimes7[7];</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  MeasureType signs5[5], signs6[6], signs7[7];</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span> </div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  getShmolliSamples(this->_InvTimes, invTimes5, invTimes6, invTimes7);</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  getShmolliSamples(this->_Signal, signal5, signal6, signal7);</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  getShmolliSamples(this->_Signs, signs5, signs6, signs7);</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span> </div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  this->getStartPointSKPShmolli(</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  invTimes5, invTimes6, invTimes7,</div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  signal5, signal6, signal7,</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  signs5, signs6, signs7);</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span> </div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  signs5[0] = -1; <span class="comment">// KW: Why only in the 5 samples case and not in the 6 or 7 samples case? small amount of pixels (94) influenced by it</span></div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  signal5[0] = -fabs(signal5[0]);</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span> </div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="comment">// 5els fitting</span></div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  results5 = this->calculateMolli(5, invTimes5, signal5, signs5);</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span> </div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  <span class="keywordflow">if</span> (results5[<span class="stringliteral">"A"</span>] > 1){ <span class="comment">// converged</span></div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  nShmolliSamplesUsed = 5;</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  T1temp = results5[<span class="stringliteral">"T1"</span>];</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  chiTemp = results5[<span class="stringliteral">"ChiSqrt"</span>]; <span class="comment">// legacy</span></div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  } <span class="keywordflow">else</span> {</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  chiTemp = results5[<span class="stringliteral">"LastValue"</span>]; <span class="comment">// legacy, very small amount of pixels (3) influenced by it</span></div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  }</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span> </div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <span class="comment">// 6els fitting</span></div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  results6 = this->calculateMolli(6, invTimes6, signal6, signs6);</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span> </div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  <span class="keywordflow">if</span> ((T1temp <= TRRaverageHB) <span class="comment">// KW: has to be T1temp in these cases that do not converge</span></div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  || (results6[<span class="stringliteral">"A"</span>] <= 1) <span class="comment">// not converged</span></div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  || (results6[<span class="stringliteral">"T1"</span>] <= 0.4 * TRRaverageHB) <span class="comment">// prevent from errors in v.short range. KW: very small amount of pixels (14) influenced by it</span></div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  )</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  {</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span> </div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  <span class="keywordflow">if</span> ((results6[<span class="stringliteral">"A"</span>] > 1) <span class="comment">// converged</span></div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  && (results6[<span class="stringliteral">"ChiSqrt"</span>] * results6[<span class="stringliteral">"T1"</span>] < chiTemp * TRRaverageHB))</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  {</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  nShmolliSamplesUsed = 6;</div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  T1temp = results6[<span class="stringliteral">"T1"</span>];</div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  }</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> </div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  <span class="comment">// 7els fitting</span></div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  results7 = this->calculateMolli(7, invTimes7, signal7, signs7);</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span> </div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="keywordflow">if</span> ((results7[<span class="stringliteral">"A"</span>] > 1) <span class="comment">// converged</span></div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  && (results7[<span class="stringliteral">"ChiSqrt"</span>] * results7[<span class="stringliteral">"T1"</span>] < results6[<span class="stringliteral">"ChiSqrt"</span>] * TRRaverageHB * 0.4) <span class="comment">// KW: in the article results5 instead of 6. 1422 pixels influenced by change</span></div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  && (T1temp < TRRaverageHB) <span class="comment">// KW: not a single pixel influenced by it</span></div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  )</div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  {</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  nShmolliSamplesUsed = 7; <span class="comment">// use all 3 IR only if SD improvement compensates for a limit of 5*MAxT1<2*T_HB</span></div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  }</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  }</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span> </div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="comment">// assign output values</span></div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  <span class="keywordflow">if</span> (nShmolliSamplesUsed == 5) {</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  this->_Results = results5;</div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  }</div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (nShmolliSamplesUsed == 6) {</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  this->_Results = results6;</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  }</div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (nShmolliSamplesUsed == 7) {</div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  this->_Results = results7;</div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  } <span class="keywordflow">else</span> {</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  this->_Results = results0;</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="comment">//std::cout << "ShMOLLI calculation error" << std::endl;</span></div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <span class="comment">//throw itk::ExceptionObject(__FILE__, __LINE__, "ShMOLLI calculation error");</span></div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  }</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  this->_Results[<span class="stringliteral">"NShmolliSamplesUsed"</span>] = nShmolliSamplesUsed;</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  this->_Results[<span class="stringliteral">"hasBeenCalculated"</span>] = 1;</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span> </div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  <span class="keywordflow">return</span> 0; <span class="comment">// EXIT_SUCCESS</span></div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  }</div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span> </div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  <span class="keyword">template</span>< <span class="keyword">typename</span> MeasureType ></div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <span class="keywordtype">int</span></div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <a class="code" href="class_ox_1_1_calculator_t1_shmolli.html">CalculatorT1Shmolli<MeasureType></a></div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span> <a class="code" href="class_ox_1_1_calculator_t1_shmolli.html"> ::getShmolliSamples</a>(<span class="keyword">const</span> MeasureType* inArray, MeasureType* outArray5, MeasureType* outArray6, MeasureType* outArray7){</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <span class="keywordtype">int</span> indexes7[] = {0,1,2,3,4,5,6};</div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keywordtype">int</span> indexes6[] = {0,1,3,4,5,6};</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  <span class="keywordtype">int</span> indexes5[] = {0,3,4,5,6};</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < 7; i++) outArray7[i] = inArray[indexes7[i]];</div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < 6; i++) outArray6[i] = inArray[indexes6[i]];</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < 5; i++) outArray5[i] = inArray[indexes5[i]];</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  <span class="keywordflow">return</span> 0; <span class="comment">// EXIT_SUCCESS</span></div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  }</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span> </div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span> } <span class="comment">//namespace Ox</span></div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span> </div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span> <span class="preprocessor">#endif //TOMATO_OXCALCULATORT1SHMOLLI_HXX</span></div>
<div class="ttc" id="class_ox_1_1_calculator_t1_shmolli_html_a2c4444b1aa40e3f01b7cf0b8e7f7672b"><div class="ttname"><a href="class_ox_1_1_calculator_t1_shmolli.html#a2c4444b1aa40e3f01b7cf0b8e7f7672b">Ox::CalculatorT1Shmolli::calculateTRRaverageHB</a></div><div class="ttdeci">int calculateTRRaverageHB()</div><div class="ttdef"><b>Definition:</b> OxCalculatorT1Shmolli.hxx:122</div></div>
<div class="ttc" id="class_ox_1_1_calculator_t1_shmolli_html_ac689ebbf27f95f6fa2559cc13a824db0"><div class="ttname"><a href="class_ox_1_1_calculator_t1_shmolli.html#ac689ebbf27f95f6fa2559cc13a824db0">Ox::CalculatorT1Shmolli::calculate</a></div><div class="ttdeci">virtual int calculate()</div><div class="ttdef"><b>Definition:</b> OxCalculatorT1Shmolli.hxx:143</div></div>
<div class="ttc" id="class_ox_1_1_calculator_t1_shmolli_html_a6464c63f20ecd9de842d722e5d9d2866"><div class="ttname"><a href="class_ox_1_1_calculator_t1_shmolli.html#a6464c63f20ecd9de842d722e5d9d2866">Ox::CalculatorT1Shmolli::prepareToCalculate</a></div><div class="ttdeci">virtual int prepareToCalculate()</div><div class="ttdef"><b>Definition:</b> OxCalculatorT1Shmolli.hxx:15</div></div>
<div class="ttc" id="class_ox_1_1_calculator_t1_shmolli_html"><div class="ttname"><a href="class_ox_1_1_calculator_t1_shmolli.html">Ox::CalculatorT1Shmolli</a></div><div class="ttdef"><b>Definition:</b> OxCalculatorT1Shmolli.h:22</div></div>
<div class="ttc" id="class_ox_1_1_start_point_calculator_html"><div class="ttname"><a href="class_ox_1_1_start_point_calculator.html">Ox::StartPointCalculator</a></div><div class="ttdef"><b>Definition:</b> OxStartPointCalculator.h:21</div></div>
<div class="ttc" id="class_ox_1_1_start_point_calculator_html_a9d1132410d68eb16f3f71ec4015c0b2f"><div class="ttname"><a href="class_ox_1_1_start_point_calculator.html#a9d1132410d68eb16f3f71ec4015c0b2f">Ox::StartPointCalculator::calculateStartPoint</a></div><div class="ttdeci">virtual int calculateStartPoint()=0</div></div>
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