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<a href="cc__helper_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno"> 1</span><span class="comment">/* Copyright (c) 2008-2022 the MRtrix3 contributors.</span></div>
<div class="line"><a id="l00002" name="l00002"></a><span class="lineno"> 2</span><span class="comment"> *</span></div>
<div class="line"><a id="l00003" name="l00003"></a><span class="lineno"> 3</span><span class="comment"> * This Source Code Form is subject to the terms of the Mozilla Public</span></div>
<div class="line"><a id="l00004" name="l00004"></a><span class="lineno"> 4</span><span class="comment"> * License, v. 2.0. If a copy of the MPL was not distributed with this</span></div>
<div class="line"><a id="l00005" name="l00005"></a><span class="lineno"> 5</span><span class="comment"> * file, You can obtain one at http://mozilla.org/MPL/2.0/.</span></div>
<div class="line"><a id="l00006" name="l00006"></a><span class="lineno"> 6</span><span class="comment"> *</span></div>
<div class="line"><a id="l00007" name="l00007"></a><span class="lineno"> 7</span><span class="comment"> * Covered Software is provided under this License on an "as is"</span></div>
<div class="line"><a id="l00008" name="l00008"></a><span class="lineno"> 8</span><span class="comment"> * basis, without warranty of any kind, either expressed, implied, or</span></div>
<div class="line"><a id="l00009" name="l00009"></a><span class="lineno"> 9</span><span class="comment"> * statutory, including, without limitation, warranties that the</span></div>
<div class="line"><a id="l00010" name="l00010"></a><span class="lineno"> 10</span><span class="comment"> * Covered Software is free of defects, merchantable, fit for a</span></div>
<div class="line"><a id="l00011" name="l00011"></a><span class="lineno"> 11</span><span class="comment"> * particular purpose or non-infringing.</span></div>
<div class="line"><a id="l00012" name="l00012"></a><span class="lineno"> 12</span><span class="comment"> * See the Mozilla Public License v. 2.0 for more details.</span></div>
<div class="line"><a id="l00013" name="l00013"></a><span class="lineno"> 13</span><span class="comment"> *</span></div>
<div class="line"><a id="l00014" name="l00014"></a><span class="lineno"> 14</span><span class="comment"> * For more details, see http://www.mrtrix.org/.</span></div>
<div class="line"><a id="l00015" name="l00015"></a><span class="lineno"> 15</span><span class="comment"> */</span></div>
<div class="line"><a id="l00016" name="l00016"></a><span class="lineno"> 16</span> </div>
<div class="line"><a id="l00017" name="l00017"></a><span class="lineno"> 17</span> </div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="preprocessor">#ifndef __registration_metric_cc_helper_h__</span></div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span><span class="preprocessor">#define __registration_metric_cc_helper_h__</span></div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span> </div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span><span class="preprocessor">#include "<a class="code" href="debug_8h.html">debug.h</a>"</span></div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span><span class="preprocessor">#include "<a class="code" href="math_8h.html">math/math.h</a>"</span></div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span><span class="preprocessor">#include "<a class="code" href="image__helpers_8h.html">image_helpers.h</a>"</span></div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span><span class="preprocessor">#include "<a class="code" href="neighbourhooditerator_8h.html">algo/neighbourhooditerator.h</a>"</span></div>
<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span> </div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespace_m_r.html">MR</a></div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span>{</div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span> <span class="keyword">namespace </span>Registration</div>
<div class="line"><a id="l00029" name="l00029"></a><span class="lineno"> 29</span> {</div>
<div class="line"><a id="l00030" name="l00030"></a><span class="lineno"><a class="line" href="namespace_m_r_1_1_registration_1_1_metric.html"> 30</a></span> <span class="keyword">namespace </span>Metric</div>
<div class="line"><a id="l00031" name="l00031"></a><span class="lineno"> 31</span> {</div>
<div class="line"><a id="l00032" name="l00032"></a><span class="lineno"> 32</span> </div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span> <span class="keyword">template</span> <<span class="keyword">class</span> Im1ImageType, <span class="keyword">class</span> Im2ImageType, <span class="keyword">class</span> Im1MaskType, <span class="keyword">class</span> Im2MaskType, <span class="keyword">class</span> DerivedImageType></div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"><a class="line" href="namespace_m_r_1_1_registration_1_1_metric.html#ad9304a7702146c3c98cd3570e5bcf0a0"> 34</a></span> <span class="keywordtype">void</span> <a class="code hl_function" href="namespace_m_r_1_1_registration_1_1_metric.html#ad9304a7702146c3c98cd3570e5bcf0a0">cc_precompute</a> (Im1ImageType& im1_image,</div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> Im2ImageType& im2_image,</div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> Im1MaskType& im1_mask,</div>
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span> Im2MaskType& im2_mask,</div>
<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> DerivedImageType& A,</div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> DerivedImageType& B,</div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> DerivedImageType& C,</div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> DerivedImageType& im1_meansubtr,</div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"> 42</span> DerivedImageType& im2_meansubtr,</div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> <span class="keyword">const</span> <a class="code hl_class" href="class_m_r_1_1vector.html">vector<size_t></a>& extent) {</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> <span class="comment">// TODO check extent</span></div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> <span class="keywordtype">int</span> nmax = extent[0] * extent[1] * extent[2];</div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> Eigen::VectorXd n1 = Eigen::VectorXd(nmax);</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> Eigen::VectorXd n2 = Eigen::VectorXd(nmax);</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> Eigen::Vector3d pos;</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> <span class="keywordflow">for</span> (<span class="keyword">auto</span> l = <a class="code hl_function" href="group__loop.html#ga2210102d90cf5ddfe7089fc025e7a3d8">Loop</a>(<span class="stringliteral">"precomputing cross correlation values"</span>) (im1_image); l; ++l) {</div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> pos[0] = im1_image.index(0);</div>
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> pos[1] = im1_image.index(1);</div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> pos[2] = im1_image.index(2);</div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> assign_pos_of(im1_image, 0, 3).to(A, B, C, im1_meansubtr, im2_meansubtr);</div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> <a class="code hl_typedef" href="namespace_m_r.html#a43bad69d4b870a61e1d93cd69b7b1270">default_type</a> m1(0.0);</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> <a class="code hl_typedef" href="namespace_m_r.html#a43bad69d4b870a61e1d93cd69b7b1270">default_type</a> m2(0.0);</div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> </div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> n1.setZero();</div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> n2.setZero();</div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> </div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> <span class="keywordtype">int</span> nvox(0);</div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> <span class="keyword">auto</span> niter = <a class="code hl_class" href="class_m_r_1_1_neighbourhood_iterator.html">NeighbourhoodIterator</a>(im1_image, extent);</div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> <span class="keywordflow">while</span> (niter.loop()) {</div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> <span class="keywordflow">if</span> (im1_mask.valid()) {</div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> assign_pos_of(niter, 0, 3).to(im1_mask);</div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"> 65</span> <span class="keywordflow">if</span> (!im1_mask.value())</div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> <span class="keywordflow">continue</span>;</div>
<div class="line"><a id="l00067" name="l00067"></a><span class="lineno"> 67</span> }</div>
<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span> <span class="keywordflow">if</span> (im2_mask.valid()) {</div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> assign_pos_of(niter, 0, 3).to(im2_mask);</div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> <span class="keywordflow">if</span> (!im2_mask.value())</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> <span class="keywordflow">continue</span>;</div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> }</div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> assign_pos_of(niter, 0, 3).to(im1_image);</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> assign_pos_of(niter, 0, 3).to(im2_image);</div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> </div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> n1[nvox] = im1_image.value();</div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> n2[nvox] = im2_image.value();</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> </div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> m1 += n1[nvox];</div>
<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> m2 += n2[nvox];</div>
<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> nvox++;</div>
<div class="line"><a id="l00082" name="l00082"></a><span class="lineno"> 82</span> }</div>
<div class="line"><a id="l00083" name="l00083"></a><span class="lineno"> 83</span> </div>
<div class="line"><a id="l00084" name="l00084"></a><span class="lineno"> 84</span> <span class="keywordflow">if</span> (nvox == 0) {</div>
<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> A.value() = <a class="code hl_variable" href="namespace_m_r.html#ac8c755bf9a6bd0ee7dfe784c1aff7fcb">NaN</a>;</div>
<div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</span> C.value() = <a class="code hl_variable" href="namespace_m_r.html#ac8c755bf9a6bd0ee7dfe784c1aff7fcb">NaN</a>;</div>
<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span> B.value() = <a class="code hl_variable" href="namespace_m_r.html#ac8c755bf9a6bd0ee7dfe784c1aff7fcb">NaN</a>;</div>
<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span> im1_meansubtr.value() = <a class="code hl_variable" href="namespace_m_r.html#ac8c755bf9a6bd0ee7dfe784c1aff7fcb">NaN</a>;</div>
<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> im2_meansubtr.value() = <a class="code hl_variable" href="namespace_m_r.html#ac8c755bf9a6bd0ee7dfe784c1aff7fcb">NaN</a>;</div>
<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> <span class="keywordflow">continue</span>;</div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> }</div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> </div>
<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> <span class="comment">// local mean subtracted</span></div>
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> n1.array() -= n1.sum() / nvox;</div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> n2.array() -= n2.sum() / nvox;</div>
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> A.value() = n1.adjoint() * n2;</div>
<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span> B.value() = n1.adjoint() * n1;</div>
<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> C.value() = n2.adjoint() * n2;</div>
<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> </div>
<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span> <span class="comment">// reset image positions</span></div>
<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span> im1_image.index(0) = pos[0];</div>
<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span> im1_image.index(1) = pos[1];</div>
<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> im1_image.index(2) = pos[2];</div>
<div class="line"><a id="l00104" name="l00104"></a><span class="lineno"> 104</span> </div>
<div class="line"><a id="l00105" name="l00105"></a><span class="lineno"> 105</span> im2_image.index(0) = pos[0];</div>
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</span> im2_image.index(1) = pos[1];</div>
<div class="line"><a id="l00107" name="l00107"></a><span class="lineno"> 107</span> im2_image.index(2) = pos[2];</div>
<div class="line"><a id="l00108" name="l00108"></a><span class="lineno"> 108</span> </div>
<div class="line"><a id="l00109" name="l00109"></a><span class="lineno"> 109</span> im1_meansubtr.value() = im1_image.value() - m1 / nvox;</div>
<div class="line"><a id="l00110" name="l00110"></a><span class="lineno"> 110</span> im2_meansubtr.value() = im2_image.value() - m2 / nvox;</div>
<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"> 111</span> }</div>
<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</span> </div>
<div class="line"><a id="l00113" name="l00113"></a><span class="lineno"> 113</span> }</div>
<div class="line"><a id="l00114" name="l00114"></a><span class="lineno"> 114</span> </div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> }</div>
<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> }</div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span>}</div>
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span><span class="preprocessor">#endif</span></div>
<div class="ttc" id="aclass_m_r_1_1_neighbourhood_iterator_html"><div class="ttname"><a href="class_m_r_1_1_neighbourhood_iterator.html">MR::NeighbourhoodIterator</a></div><div class="ttdoc">a dummy image to iterate over a certain neighbourhood, useful for multi-threaded looping.</div><div class="ttdef"><b>Definition:</b> <a href="neighbourhooditerator_8h_source.html#l00039">neighbourhooditerator.h:40</a></div></div>
<div class="ttc" id="aclass_m_r_1_1vector_html"><div class="ttname"><a href="class_m_r_1_1vector.html">MR::vector< size_t ></a></div></div>
<div class="ttc" id="adebug_8h_html"><div class="ttname"><a href="debug_8h.html">debug.h</a></div></div>
<div class="ttc" id="agroup__loop_html_ga2210102d90cf5ddfe7089fc025e7a3d8"><div class="ttname"><a href="group__loop.html#ga2210102d90cf5ddfe7089fc025e7a3d8">MR::Loop</a></div><div class="ttdeci">FORCE_INLINE LoopAlongAxes Loop()</div><div class="ttdef"><b>Definition:</b> <a href="algo_2loop_8h_source.html#l00419">loop.h:419</a></div></div>
<div class="ttc" id="aimage__helpers_8h_html"><div class="ttname"><a href="image__helpers_8h.html">image_helpers.h</a></div></div>
<div class="ttc" id="amath_8h_html"><div class="ttname"><a href="math_8h.html">math.h</a></div></div>
<div class="ttc" id="anamespace_m_r_1_1_registration_1_1_metric_html_ad9304a7702146c3c98cd3570e5bcf0a0"><div class="ttname"><a href="namespace_m_r_1_1_registration_1_1_metric.html#ad9304a7702146c3c98cd3570e5bcf0a0">MR::Registration::Metric::cc_precompute</a></div><div class="ttdeci">void cc_precompute(Im1ImageType &im1_image, Im2ImageType &im2_image, Im1MaskType &im1_mask, Im2MaskType &im2_mask, DerivedImageType &A, DerivedImageType &B, DerivedImageType &C, DerivedImageType &im1_meansubtr, DerivedImageType &im2_meansubtr, const vector< size_t > &extent)</div><div class="ttdef"><b>Definition:</b> <a href="cc__helper_8h_source.html#l00034">cc_helper.h:34</a></div></div>
<div class="ttc" id="anamespace_m_r_html"><div class="ttname"><a href="namespace_m_r.html">MR</a></div><div class="ttdef"><b>Definition:</b> <a href="core_2adapter_2base_8h_source.html#l00023">base.h:24</a></div></div>
<div class="ttc" id="anamespace_m_r_html_a43bad69d4b870a61e1d93cd69b7b1270"><div class="ttname"><a href="namespace_m_r.html#a43bad69d4b870a61e1d93cd69b7b1270">MR::default_type</a></div><div class="ttdeci">double default_type</div><div class="ttdoc">the default type used throughout MRtrix</div><div class="ttdef"><b>Definition:</b> <a href="src_2surface_2types_8h_source.html#l00228">types.h:228</a></div></div>
<div class="ttc" id="anamespace_m_r_html_ac8c755bf9a6bd0ee7dfe784c1aff7fcb"><div class="ttname"><a href="namespace_m_r.html#ac8c755bf9a6bd0ee7dfe784c1aff7fcb">MR::NaN</a></div><div class="ttdeci">constexpr default_type NaN</div><div class="ttdef"><b>Definition:</b> <a href="src_2surface_2types_8h_source.html#l00230">types.h:230</a></div></div>
<div class="ttc" id="aneighbourhooditerator_8h_html"><div class="ttname"><a href="neighbourhooditerator_8h.html">neighbourhooditerator.h</a></div></div>
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