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">OxOriginalShmolliDicomReader.hxx</div> </div>
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<a href="_ox_original_shmolli_dicom_reader_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_OxOriginalShmolliDicomReader_HXX</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor"></span><span class="preprocessor">#define Tomato_OxOriginalShmolliDicomReader_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="preprocessor">#include <itkImageFileReaderKW.h></span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#include "<a class="code" href="_ox_original_shmolli_dicom_reader_8h.html">OxOriginalShmolliDicomReader.h</a>"</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">namespace </span>Ox {</div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> </div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  <span class="keyword">template</span>< <span class="keyword">typename</span> MeasureType ></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  <span class="keywordtype">int</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  OriginalShmolliDicomReader<MeasureType></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  ::readAndSort() {</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="comment">// Mag</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  <span class="keyword">typename</span> ReadFileListFilterType::Pointer readerMag = ReadFileListFilterType::New();</div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span>  readerMag->SetFileList(_filesMag);</div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  readerMag->Update();</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>  <span class="keyword">typename</span> SortInvTimesImageFilterType::Pointer sorterMag = SortInvTimesImageFilterType::New();</div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  sorterMag->SetInvTimesNonSorted(readerMag->GetInvTimes());</div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  sorterMag->SetInput(readerMag->GetOutput());</div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  sorterMag->Update();</div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> </div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="comment">// pha</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  <span class="keyword">typename</span> ReadFileListFilterType::Pointer readerPha = ReadFileListFilterType::New();</div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  readerPha->SetFileList(_filesPha);</div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  readerPha->Update();</div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keyword">typename</span> SortInvTimesImageFilterType::Pointer sorterPha = SortInvTimesImageFilterType::New();</div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  sorterPha->SetInvTimesNonSorted(readerPha->GetInvTimes());</div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  sorterPha->SetInput(readerPha->GetOutput());</div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  sorterPha->Update();</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>  <span class="keywordflow">if</span> (sorterMag->GetInvTimesSorted() == sorterPha->GetInvTimesSorted()){</div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  vnl_vector<InputPixelType > temp = sorterMag->GetInvTimesSorted();</div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  _nSamples = temp.size();</div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="keyword">delete</span> [] _invTimes;</div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  _invTimes = <span class="keyword">new</span> InputPixelType[_nSamples];</div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  KWUtil::copyArrayToArray(_nSamples, _invTimes, temp.data_block());</div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  } <span class="keywordflow">else</span> {</div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keywordflow">throw</span> std::runtime_error(<span class="stringliteral">"Mag and Pha inv times are not equal"</span>);</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> </div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  _imageMag = sorterMag->GetOutput();</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  _imagePha = sorterPha->GetOutput();</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keywordflow">if</span> (_filesT1.size() > 0) {</div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="keyword">typename</span> itk::ImageFileReader<Image2dType>::Pointer reader = itk::ImageFileReader<Image2dType>::New();</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  reader->SetFileName(_filesT1.at(0));</div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  reader->Update();</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  _imageT1color = reader->GetOutput();</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> </div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keywordflow">if</span> (_filesT1.size() > 1) {</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keyword">typename</span> itk::ImageFileReader<Image2dType>::Pointer reader = itk::ImageFileReader<Image2dType>::New();</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  reader->SetFileName(_filesT1.at(1));</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  reader->Update();</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  _imageT1grey = reader->GetOutput();</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="keywordflow">if</span> (_filesFitparams.size() > 0) {</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keyword">typename</span> itk::ImageFileReader<Image2dType>::Pointer reader = itk::ImageFileReader<Image2dType>::New();</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  reader->SetFileName(_filesFitparams.at(0));</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  reader->Update();</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  _imageR2 = reader->GetOutput();</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> </div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordflow">if</span> (_filesFitparams.size() > 1) {</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keyword">typename</span> itk::ImageFileReader<Image2dType>::Pointer reader = itk::ImageFileReader<Image2dType>::New();</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  reader->SetFileName(_filesFitparams.at(1));</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  reader->Update();</div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  _imageA = reader->GetOutput();</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">if</span> (_filesFitparams.size() > 2) {</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keyword">typename</span> itk::ImageFileReader<Image2dType>::Pointer reader = itk::ImageFileReader<Image2dType>::New();</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  reader->SetFileName(_filesFitparams.at(2));</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  reader->Update();</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  _imageB = reader->GetOutput();</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  }</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keywordflow">if</span> (_filesFitparams.size() > 3) {</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="keyword">typename</span> itk::ImageFileReader<Image2dType>::Pointer reader = itk::ImageFileReader<Image2dType>::New();</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  reader->SetFileName(_filesFitparams.at(3));</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  reader->Update();</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  _imageT1star = reader->GetOutput();</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> </div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="keywordflow">if</span> (_filesFitparams.size() > 4) {</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keyword">typename</span> itk::ImageFileReader<Image2dType>::Pointer reader = itk::ImageFileReader<Image2dType>::New();</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  reader->SetFileName(_filesFitparams.at(4));</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  reader->Update();</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  _imageNShmolliSamplesUsed = reader->GetOutput();</div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  }</div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keywordflow">if</span> (_filesFitparams.size() > 5) {</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="keyword">typename</span> itk::ImageFileReader<Image2dType>::Pointer reader = itk::ImageFileReader<Image2dType>::New();</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  reader->SetFileName(_filesFitparams.at(5));</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  reader->Update();</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  _imageChiSqrt = reader->GetOutput();</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  }</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordflow">if</span> (_filesFitparams.size() > 6) {</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keyword">typename</span> itk::ImageFileReader<Image2dType>::Pointer reader = itk::ImageFileReader<Image2dType>::New();</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  reader->SetFileName(_filesFitparams.at(6));</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  reader->Update();</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  _imageSnr = reader->GetOutput();</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>  OriginalShmolliDicomReader<MeasureType></div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  ::copyFromImage(MeasureType* array, <span class="keyword">const</span> <span class="keyword">typename</span> Image3dType::Pointer image, <span class="keyword">const</span> <span class="keyword">typename</span> Image3dType::IndexType index){</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="keyword">typename</span> Image3dType::SizeType size = image->GetLargestPossibleRegion().GetSize();</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keyword">typename</span> Image3dType::IndexType tempIndex = index;</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span> </div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < size[2]; ++i){</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  tempIndex[2] = i;</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  array[i] = image->GetPixel(tempIndex);</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  }</div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> </div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordflow">return</span> 0; <span class="comment">//EXIT_SUCCESS</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> </div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span> } <span class="comment">// namespace Ox</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> </div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span> <span class="preprocessor">#endif //Tomato_OxOriginalShmolliDicomReader_H</span></div>
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