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<a href="basic_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><span class="preprocessor">#ifndef __dwi_tractography_seeding_basic_h__</span></div>
<div class="line"><a id="l00018" name="l00018"></a><span class="lineno"> 18</span><span class="preprocessor">#define __dwi_tractography_seeding_basic_h__</span></div>
<div class="line"><a id="l00019" name="l00019"></a><span class="lineno"> 19</span> </div>
<div class="line"><a id="l00020" name="l00020"></a><span class="lineno"> 20</span><span class="preprocessor">#include "<a class="code" href="dwi_2tractography_2roi_8h.html">dwi/tractography/roi.h</a>"</span></div>
<div class="line"><a id="l00021" name="l00021"></a><span class="lineno"> 21</span><span class="preprocessor">#include "<a class="code" href="src_2dwi_2tractography_2seeding_2base_8h.html">dwi/tractography/seeding/base.h</a>"</span></div>
<div class="line"><a id="l00022" name="l00022"></a><span class="lineno"> 22</span> </div>
<div class="line"><a id="l00023" name="l00023"></a><span class="lineno"> 23</span> </div>
<div class="line"><a id="l00024" name="l00024"></a><span class="lineno"> 24</span><span class="comment">// By default, the rejection sampler will perform its sampling based on image intensity values,</span></div>
<div class="line"><a id="l00025" name="l00025"></a><span class="lineno"> 25</span><span class="comment">// and then randomly select a position within that voxel</span></div>
<div class="line"><a id="l00026" name="l00026"></a><span class="lineno"> 26</span><span class="comment">// Use this flag to instead perform rejection sampling on the trilinear-interpolated value</span></div>
<div class="line"><a id="l00027" name="l00027"></a><span class="lineno"> 27</span><span class="comment">// at each trial seed point</span></div>
<div class="line"><a id="l00028" name="l00028"></a><span class="lineno"> 28</span><span class="comment">//#define REJECTION_SAMPLING_USE_INTERPOLATION</span></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"> 30</span> </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><span class="keyword">namespace </span><a class="code hl_namespace" href="namespace_m_r.html">MR</a></div>
<div class="line"><a id="l00033" name="l00033"></a><span class="lineno"> 33</span>{</div>
<div class="line"><a id="l00034" name="l00034"></a><span class="lineno"> 34</span> <span class="keyword">namespace </span>DWI</div>
<div class="line"><a id="l00035" name="l00035"></a><span class="lineno"> 35</span> {</div>
<div class="line"><a id="l00036" name="l00036"></a><span class="lineno"> 36</span> <span class="keyword">namespace </span>Tractography</div>
<div class="line"><a id="l00037" name="l00037"></a><span class="lineno"> 37</span> {</div>
<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"> 38</span> <span class="keyword">namespace </span>Seeding</div>
<div class="line"><a id="l00039" name="l00039"></a><span class="lineno"> 39</span> {</div>
<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"> 40</span> </div>
<div class="line"><a id="l00041" name="l00041"></a><span class="lineno"> 41</span> </div>
<div class="line"><a id="l00042" name="l00042"></a><span class="lineno"><a class="line" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_sphere.html"> 42</a></span> <span class="keyword">class </span><a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_sphere.html">Sphere</a> : <span class="keyword">public</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html">Base</a></div>
<div class="line"><a id="l00043" name="l00043"></a><span class="lineno"> 43</span> { MEMALIGN(<a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_sphere.html">Sphere</a>)</div>
<div class="line"><a id="l00044" name="l00044"></a><span class="lineno"> 44</span> </div>
<div class="line"><a id="l00045" name="l00045"></a><span class="lineno"> 45</span> <span class="keyword">public</span>:</div>
<div class="line"><a id="l00046" name="l00046"></a><span class="lineno"> 46</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_sphere.html">Sphere</a> (<span class="keyword">const</span> std::string& in) :</div>
<div class="line"><a id="l00047" name="l00047"></a><span class="lineno"> 47</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html">Base</a> (in, <span class="stringliteral">"sphere"</span>, <a class="code hl_define" href="src_2dwi_2tractography_2seeding_2base_8h.html#aa5fd5f27448bc33809bf3e8cc5230f6f">MAX_TRACKING_SEED_ATTEMPTS_RANDOM</a>) {</div>
<div class="line"><a id="l00048" name="l00048"></a><span class="lineno"> 48</span> <span class="keyword">auto</span> F = <a class="code hl_function" href="namespace_m_r.html#a439319adcbcb16a7b275a81bc77980b3">parse_floats</a> (in);</div>
<div class="line"><a id="l00049" name="l00049"></a><span class="lineno"> 49</span> <span class="keywordflow">if</span> (F.size() != 4)</div>
<div class="line"><a id="l00050" name="l00050"></a><span class="lineno"> 50</span> <span class="keywordflow">throw</span> <a class="code hl_class" href="class_m_r_1_1_exception.html">Exception</a> (<span class="stringliteral">"Could not parse seed \""</span> + in + <span class="stringliteral">"\" as a spherical seed point; needs to be 4 comma-separated values (XYZ position, then radius)"</span>);</div>
<div class="line"><a id="l00051" name="l00051"></a><span class="lineno"> 51</span> pos = { float(F[0]), float(F[1]), float(F[2]) };</div>
<div class="line"><a id="l00052" name="l00052"></a><span class="lineno"> 52</span> rad = F[3];</div>
<div class="line"><a id="l00053" name="l00053"></a><span class="lineno"> 53</span> <a class="code hl_variable" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html#aab9182ae96f52427f6aefa4666d5d030">volume</a> = 4.0*<a class="code hl_variable" href="group__mathconstants.html#gafe1ee4d398733ae71a15130062a9c2a4">Math::pi</a>*<a class="code hl_function" href="group__elfun.html#gaa5be6dfa9c446af78ea87902e6214d8b">Math::pow3</a>(rad)/3.0;</div>
<div class="line"><a id="l00054" name="l00054"></a><span class="lineno"> 54</span> }</div>
<div class="line"><a id="l00055" name="l00055"></a><span class="lineno"> 55</span> </div>
<div class="line"><a id="l00056" name="l00056"></a><span class="lineno"> 56</span> <span class="keyword">virtual</span> <span class="keywordtype">bool</span> get_seed (Eigen::Vector3f& p) <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00057" name="l00057"></a><span class="lineno"> 57</span> </div>
<div class="line"><a id="l00058" name="l00058"></a><span class="lineno"> 58</span> <span class="keyword">private</span>:</div>
<div class="line"><a id="l00059" name="l00059"></a><span class="lineno"> 59</span> Eigen::Vector3f pos;</div>
<div class="line"><a id="l00060" name="l00060"></a><span class="lineno"> 60</span> <span class="keywordtype">float</span> rad;</div>
<div class="line"><a id="l00061" name="l00061"></a><span class="lineno"> 61</span> </div>
<div class="line"><a id="l00062" name="l00062"></a><span class="lineno"> 62</span> };</div>
<div class="line"><a id="l00063" name="l00063"></a><span class="lineno"> 63</span> </div>
<div class="line"><a id="l00064" name="l00064"></a><span class="lineno"> 64</span> </div>
<div class="line"><a id="l00065" name="l00065"></a><span class="lineno"><a class="line" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_seed_mask.html"> 65</a></span> <span class="keyword">class </span><a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_seed_mask.html">SeedMask</a> : <span class="keyword">public</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html">Base</a></div>
<div class="line"><a id="l00066" name="l00066"></a><span class="lineno"> 66</span> { MEMALIGN(<a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_seed_mask.html">SeedMask</a>)</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="keyword">public</span>:</div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_seed_mask.html">SeedMask</a> (<span class="keyword">const</span> std::string& in) :</div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html">Base</a> (in, <span class="stringliteral">"random seeding mask"</span>, <a class="code hl_define" href="src_2dwi_2tractography_2seeding_2base_8h.html#aa5fd5f27448bc33809bf3e8cc5230f6f">MAX_TRACKING_SEED_ATTEMPTS_RANDOM</a>),</div>
<div class="line"><a id="l00071" name="l00071"></a><span class="lineno"> 71</span> mask (in) {</div>
<div class="line"><a id="l00072" name="l00072"></a><span class="lineno"> 72</span> <a class="code hl_variable" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html#aab9182ae96f52427f6aefa4666d5d030">volume</a> = <a class="code hl_function" href="namespace_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding.html#a1ffdf9bf69e45b06562948cb7c51a16f">get_count</a> (mask) * mask.<a class="code hl_function" href="class_m_r_1_1_image.html#a97f1c7cd03d65aa74372b58d8a1f366e">spacing</a>(0) * mask.<a class="code hl_function" href="class_m_r_1_1_image.html#a97f1c7cd03d65aa74372b58d8a1f366e">spacing</a>(1) * mask.<a class="code hl_function" href="class_m_r_1_1_image.html#a97f1c7cd03d65aa74372b58d8a1f366e">spacing</a>(2);</div>
<div class="line"><a id="l00073" name="l00073"></a><span class="lineno"> 73</span> }</div>
<div class="line"><a id="l00074" name="l00074"></a><span class="lineno"> 74</span> </div>
<div class="line"><a id="l00075" name="l00075"></a><span class="lineno"> 75</span> <span class="keyword">virtual</span> <span class="keywordtype">bool</span> get_seed (Eigen::Vector3f& p) <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00076" name="l00076"></a><span class="lineno"> 76</span> </div>
<div class="line"><a id="l00077" name="l00077"></a><span class="lineno"> 77</span> <span class="keyword">private</span>:</div>
<div class="line"><a id="l00078" name="l00078"></a><span class="lineno"> 78</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_mask.html">Mask</a> mask;</div>
<div class="line"><a id="l00079" name="l00079"></a><span class="lineno"> 79</span> </div>
<div class="line"><a id="l00080" name="l00080"></a><span class="lineno"> 80</span> };</div>
<div class="line"><a id="l00081" name="l00081"></a><span class="lineno"> 81</span> </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"><a class="line" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_random__per__voxel.html"> 84</a></span> <span class="keyword">class </span><a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_random__per__voxel.html">Random_per_voxel</a> : <span class="keyword">public</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html">Base</a></div>
<div class="line"><a id="l00085" name="l00085"></a><span class="lineno"> 85</span> { MEMALIGN(<a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_random__per__voxel.html">Random_per_voxel</a>)</div>
<div class="line"><a id="l00086" name="l00086"></a><span class="lineno"> 86</span> </div>
<div class="line"><a id="l00087" name="l00087"></a><span class="lineno"> 87</span> <span class="keyword">public</span>:</div>
<div class="line"><a id="l00088" name="l00088"></a><span class="lineno"> 88</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_random__per__voxel.html">Random_per_voxel</a> (<span class="keyword">const</span> std::string& in, <span class="keyword">const</span> <span class="keywordtype">size_t</span> num_per_voxel) :</div>
<div class="line"><a id="l00089" name="l00089"></a><span class="lineno"> 89</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html">Base</a> (in, <span class="stringliteral">"random per voxel"</span>, <a class="code hl_define" href="src_2dwi_2tractography_2seeding_2base_8h.html#aa3cf37d9ed697f9c8843155e84d8513d">MAX_TRACKING_SEED_ATTEMPTS_FIXED</a>),</div>
<div class="line"><a id="l00090" name="l00090"></a><span class="lineno"> 90</span> mask (in),</div>
<div class="line"><a id="l00091" name="l00091"></a><span class="lineno"> 91</span> num (num_per_voxel),</div>
<div class="line"><a id="l00092" name="l00092"></a><span class="lineno"> 92</span> inc (0),</div>
<div class="line"><a id="l00093" name="l00093"></a><span class="lineno"> 93</span> expired (<span class="keyword">false</span>) {</div>
<div class="line"><a id="l00094" name="l00094"></a><span class="lineno"> 94</span> <a class="code hl_variable" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html#a782cd5352d32c27ff388e1190d50320d">count</a> = <a class="code hl_function" href="namespace_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding.html#a1ffdf9bf69e45b06562948cb7c51a16f">get_count</a> (mask) * num_per_voxel;</div>
<div class="line"><a id="l00095" name="l00095"></a><span class="lineno"> 95</span> mask.index(0) = 0; mask.index(1) = 0; mask.index(2) = -1;</div>
<div class="line"><a id="l00096" name="l00096"></a><span class="lineno"> 96</span> }</div>
<div class="line"><a id="l00097" name="l00097"></a><span class="lineno"> 97</span> </div>
<div class="line"><a id="l00098" name="l00098"></a><span class="lineno"> 98</span> <span class="keyword">virtual</span> <span class="keywordtype">bool</span> get_seed (Eigen::Vector3f& p) <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00099" name="l00099"></a><span class="lineno"> 99</span> <span class="keyword">virtual</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_random__per__voxel.html">~Random_per_voxel</a>() { }</div>
<div class="line"><a id="l00100" name="l00100"></a><span class="lineno"> 100</span> </div>
<div class="line"><a id="l00101" name="l00101"></a><span class="lineno"> 101</span> <span class="keyword">private</span>:</div>
<div class="line"><a id="l00102" name="l00102"></a><span class="lineno"> 102</span> <span class="keyword">mutable</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_mask.html">Mask</a> mask;</div>
<div class="line"><a id="l00103" name="l00103"></a><span class="lineno"> 103</span> <span class="keyword">const</span> <span class="keywordtype">size_t</span> num;</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> <span class="keyword">mutable</span> uint32_t inc;</div>
<div class="line"><a id="l00106" name="l00106"></a><span class="lineno"> 106</span> <span class="keyword">mutable</span> <span class="keywordtype">bool</span> expired;</div>
<div class="line"><a id="l00107" name="l00107"></a><span class="lineno"> 107</span> };</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> </div>
<div class="line"><a id="l00110" name="l00110"></a><span class="lineno"> 110</span> </div>
<div class="line"><a id="l00111" name="l00111"></a><span class="lineno"><a class="line" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_grid__per__voxel.html"> 111</a></span> <span class="keyword">class </span><a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_grid__per__voxel.html">Grid_per_voxel</a> : <span class="keyword">public</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html">Base</a></div>
<div class="line"><a id="l00112" name="l00112"></a><span class="lineno"> 112</span> { MEMALIGN(<a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_grid__per__voxel.html">Grid_per_voxel</a>)</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> <span class="keyword">public</span>:</div>
<div class="line"><a id="l00115" name="l00115"></a><span class="lineno"> 115</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_grid__per__voxel.html">Grid_per_voxel</a> (<span class="keyword">const</span> std::string& in, <span class="keyword">const</span> <span class="keywordtype">size_t</span> os_factor) :</div>
<div class="line"><a id="l00116" name="l00116"></a><span class="lineno"> 116</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html">Base</a> (in, <span class="stringliteral">"grid per voxel"</span>, <a class="code hl_define" href="src_2dwi_2tractography_2seeding_2base_8h.html#aa3cf37d9ed697f9c8843155e84d8513d">MAX_TRACKING_SEED_ATTEMPTS_FIXED</a>),</div>
<div class="line"><a id="l00117" name="l00117"></a><span class="lineno"> 117</span> mask (in),</div>
<div class="line"><a id="l00118" name="l00118"></a><span class="lineno"> 118</span> os (os_factor),</div>
<div class="line"><a id="l00119" name="l00119"></a><span class="lineno"> 119</span> pos (os, os, os),</div>
<div class="line"><a id="l00120" name="l00120"></a><span class="lineno"> 120</span> offset (-0.5 + (1.0 / (2*os))),</div>
<div class="line"><a id="l00121" name="l00121"></a><span class="lineno"> 121</span> step (1.0 / os),</div>
<div class="line"><a id="l00122" name="l00122"></a><span class="lineno"> 122</span> expired (<span class="keyword">false</span>) {</div>
<div class="line"><a id="l00123" name="l00123"></a><span class="lineno"> 123</span> <a class="code hl_variable" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html#a782cd5352d32c27ff388e1190d50320d">count</a> = <a class="code hl_function" href="namespace_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding.html#a1ffdf9bf69e45b06562948cb7c51a16f">get_count</a> (mask) * <a class="code hl_function" href="group__elfun.html#gaa5be6dfa9c446af78ea87902e6214d8b">Math::pow3</a> (os_factor);</div>
<div class="line"><a id="l00124" name="l00124"></a><span class="lineno"> 124</span> }</div>
<div class="line"><a id="l00125" name="l00125"></a><span class="lineno"> 125</span> </div>
<div class="line"><a id="l00126" name="l00126"></a><span class="lineno"> 126</span> <span class="keyword">virtual</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_grid__per__voxel.html">~Grid_per_voxel</a>() { }</div>
<div class="line"><a id="l00127" name="l00127"></a><span class="lineno"> 127</span> <span class="keyword">virtual</span> <span class="keywordtype">bool</span> get_seed (Eigen::Vector3f& p) <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00128" name="l00128"></a><span class="lineno"> 128</span> </div>
<div class="line"><a id="l00129" name="l00129"></a><span class="lineno"> 129</span> </div>
<div class="line"><a id="l00130" name="l00130"></a><span class="lineno"> 130</span> <span class="keyword">private</span>:</div>
<div class="line"><a id="l00131" name="l00131"></a><span class="lineno"> 131</span> <span class="keyword">mutable</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_mask.html">Mask</a> mask;</div>
<div class="line"><a id="l00132" name="l00132"></a><span class="lineno"> 132</span> <span class="keyword">const</span> <span class="keywordtype">int</span> os;</div>
<div class="line"><a id="l00133" name="l00133"></a><span class="lineno"> 133</span> <span class="keyword">mutable</span> Eigen::Vector3i pos;</div>
<div class="line"><a id="l00134" name="l00134"></a><span class="lineno"> 134</span> <span class="keyword">const</span> <span class="keywordtype">float</span> offset, step;</div>
<div class="line"><a id="l00135" name="l00135"></a><span class="lineno"> 135</span> <span class="keyword">mutable</span> <span class="keywordtype">bool</span> expired;</div>
<div class="line"><a id="l00136" name="l00136"></a><span class="lineno"> 136</span> </div>
<div class="line"><a id="l00137" name="l00137"></a><span class="lineno"> 137</span> };</div>
<div class="line"><a id="l00138" name="l00138"></a><span class="lineno"> 138</span> </div>
<div class="line"><a id="l00139" name="l00139"></a><span class="lineno"> 139</span> </div>
<div class="line"><a id="l00140" name="l00140"></a><span class="lineno"> 140</span> </div>
<div class="line"><a id="l00141" name="l00141"></a><span class="lineno"><a class="line" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_rejection.html"> 141</a></span> <span class="keyword">class </span><a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_rejection.html">Rejection</a> : <span class="keyword">public</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html">Base</a></div>
<div class="line"><a id="l00142" name="l00142"></a><span class="lineno"> 142</span> { <a class="code hl_define" href="src_2surface_2types_8h.html#a11d7eae3ab5178ebcf0e62cae9c26cd4">MEMALIGN</a>(<a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_rejection.html">Rejection</a>)</div>
<div class="line"><a id="l00143" name="l00143"></a><span class="lineno"> 143</span> <span class="keyword">public</span>:</div>
<div class="line"><a id="l00144" name="l00144"></a><span class="lineno"> 144</span> <span class="keyword">using</span> <a class="code hl_typedef" href="namespace_m_r.html#a8445ea7a4001a6e8532def9abb86d59e">transform_type</a> = Eigen::Transform<float, 3, Eigen::AffineCompact>;</div>
<div class="line"><a id="l00145" name="l00145"></a><span class="lineno"> 145</span> <a class="code hl_class" href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_rejection.html">Rejection</a> (<span class="keyword">const</span> std::string&);</div>
<div class="line"><a id="l00146" name="l00146"></a><span class="lineno"> 146</span> </div>
<div class="line"><a id="l00147" name="l00147"></a><span class="lineno"> 147</span> </div>
<div class="line"><a id="l00148" name="l00148"></a><span class="lineno"> 148</span> <span class="keyword">virtual</span> <span class="keywordtype">bool</span> get_seed (Eigen::Vector3f& p) <span class="keyword">const override</span>;</div>
<div class="line"><a id="l00149" name="l00149"></a><span class="lineno"> 149</span> </div>
<div class="line"><a id="l00150" name="l00150"></a><span class="lineno"> 150</span> <span class="keyword">private</span>:</div>
<div class="line"><a id="l00151" name="l00151"></a><span class="lineno"> 151</span><span class="preprocessor">#ifdef REJECTION_SAMPLING_USE_INTERPOLATION</span></div>
<div class="line"><a id="l00152" name="l00152"></a><span class="lineno"> 152</span> <a class="code hl_class" href="class_m_r_1_1_interp_1_1_linear_interp_3_01_image_type_00_01_linear_interp_processing_type_1_1_value_01_4.html">Interp::Linear<Image<float></a>> interp;</div>
<div class="line"><a id="l00153" name="l00153"></a><span class="lineno"> 153</span><span class="preprocessor">#else</span></div>
<div class="line"><a id="l00154" name="l00154"></a><span class="lineno"> 154</span> <a class="code hl_class" href="class_m_r_1_1_image.html">Image<float></a> image;</div>
<div class="line"><a id="l00155" name="l00155"></a><span class="lineno"> 155</span> <a class="code hl_typedef" href="namespace_m_r.html#a8445ea7a4001a6e8532def9abb86d59e">transform_type</a> voxel2scanner;</div>
<div class="line"><a id="l00156" name="l00156"></a><span class="lineno"> 156</span><span class="preprocessor">#endif</span></div>
<div class="line"><a id="l00157" name="l00157"></a><span class="lineno"> 157</span> <span class="keywordtype">float</span> max;</div>
<div class="line"><a id="l00158" name="l00158"></a><span class="lineno"> 158</span> </div>
<div class="line"><a id="l00159" name="l00159"></a><span class="lineno"> 159</span> };</div>
<div class="line"><a id="l00160" name="l00160"></a><span class="lineno"> 160</span> </div>
<div class="line"><a id="l00161" name="l00161"></a><span class="lineno"> 161</span> </div>
<div class="line"><a id="l00162" name="l00162"></a><span class="lineno"> 162</span> </div>
<div class="line"><a id="l00163" name="l00163"></a><span class="lineno"> 163</span> </div>
<div class="line"><a id="l00164" name="l00164"></a><span class="lineno"> 164</span> </div>
<div class="line"><a id="l00165" name="l00165"></a><span class="lineno"> 165</span> </div>
<div class="line"><a id="l00166" name="l00166"></a><span class="lineno"> 166</span> }</div>
<div class="line"><a id="l00167" name="l00167"></a><span class="lineno"> 167</span> }</div>
<div class="line"><a id="l00168" name="l00168"></a><span class="lineno"> 168</span> }</div>
<div class="line"><a id="l00169" name="l00169"></a><span class="lineno"> 169</span>}</div>
<div class="line"><a id="l00170" name="l00170"></a><span class="lineno"> 170</span> </div>
<div class="line"><a id="l00171" name="l00171"></a><span class="lineno"> 171</span><span class="preprocessor">#endif</span></div>
<div class="line"><a id="l00172" name="l00172"></a><span class="lineno"> 172</span> </div>
<div class="ttc" id="aclass_m_r_1_1_d_w_i_1_1_tractography_1_1_mask_html"><div class="ttname"><a href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_mask.html">MR::DWI::Tractography::Mask</a></div><div class="ttdef"><b>Definition:</b> <a href="dwi_2tractography_2roi_8h_source.html#l00041">roi.h:41</a></div></div>
<div class="ttc" id="aclass_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base_html"><div class="ttname"><a href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html">MR::DWI::Tractography::Seeding::Base</a></div><div class="ttdef"><b>Definition:</b> <a href="src_2dwi_2tractography_2seeding_2base_8h_source.html#l00097">base.h:97</a></div></div>
<div class="ttc" id="aclass_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base_html_a782cd5352d32c27ff388e1190d50320d"><div class="ttname"><a href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html#a782cd5352d32c27ff388e1190d50320d">MR::DWI::Tractography::Seeding::Base::count</a></div><div class="ttdeci">uint32_t count</div><div class="ttdef"><b>Definition:</b> <a href="src_2dwi_2tractography_2seeding_2base_8h_source.html#l00128">base.h:128</a></div></div>
<div class="ttc" id="aclass_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base_html_aab9182ae96f52427f6aefa4666d5d030"><div class="ttname"><a href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_base.html#aab9182ae96f52427f6aefa4666d5d030">MR::DWI::Tractography::Seeding::Base::volume</a></div><div class="ttdeci">float volume</div><div class="ttdef"><b>Definition:</b> <a href="src_2dwi_2tractography_2seeding_2base_8h_source.html#l00127">base.h:127</a></div></div>
<div class="ttc" id="aclass_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_grid__per__voxel_html"><div class="ttname"><a href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_grid__per__voxel.html">MR::DWI::Tractography::Seeding::Grid_per_voxel</a></div><div class="ttdef"><b>Definition:</b> <a href="basic_8h_source.html#l00111">basic.h:112</a></div></div>
<div class="ttc" id="aclass_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_random__per__voxel_html"><div class="ttname"><a href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_random__per__voxel.html">MR::DWI::Tractography::Seeding::Random_per_voxel</a></div><div class="ttdef"><b>Definition:</b> <a href="basic_8h_source.html#l00084">basic.h:85</a></div></div>
<div class="ttc" id="aclass_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_rejection_html"><div class="ttname"><a href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_rejection.html">MR::DWI::Tractography::Seeding::Rejection</a></div><div class="ttdef"><b>Definition:</b> <a href="basic_8h_source.html#l00141">basic.h:142</a></div></div>
<div class="ttc" id="aclass_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_seed_mask_html"><div class="ttname"><a href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_seed_mask.html">MR::DWI::Tractography::Seeding::SeedMask</a></div><div class="ttdef"><b>Definition:</b> <a href="basic_8h_source.html#l00065">basic.h:66</a></div></div>
<div class="ttc" id="aclass_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_sphere_html"><div class="ttname"><a href="class_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_1_1_sphere.html">MR::DWI::Tractography::Seeding::Sphere</a></div><div class="ttdef"><b>Definition:</b> <a href="basic_8h_source.html#l00042">basic.h:43</a></div></div>
<div class="ttc" id="aclass_m_r_1_1_exception_html"><div class="ttname"><a href="class_m_r_1_1_exception.html">MR::Exception</a></div><div class="ttdef"><b>Definition:</b> <a href="exception_8h_source.html#l00080">exception.h:80</a></div></div>
<div class="ttc" id="aclass_m_r_1_1_image_html"><div class="ttname"><a href="class_m_r_1_1_image.html">MR::Image< float ></a></div></div>
<div class="ttc" id="aclass_m_r_1_1_image_html_a97f1c7cd03d65aa74372b58d8a1f366e"><div class="ttname"><a href="class_m_r_1_1_image.html#a97f1c7cd03d65aa74372b58d8a1f366e">MR::Image::spacing</a></div><div class="ttdeci">default_type spacing(size_t axis) const</div><div class="ttdef"><b>Definition:</b> <a href="image_8h_source.html#l00067">image.h:67</a></div></div>
<div class="ttc" id="aclass_m_r_1_1_interp_1_1_linear_interp_3_01_image_type_00_01_linear_interp_processing_type_1_1_value_01_4_html"><div class="ttname"><a href="class_m_r_1_1_interp_1_1_linear_interp_3_01_image_type_00_01_linear_interp_processing_type_1_1_value_01_4.html">MR::Interp::LinearInterp< ImageType, LinearInterpProcessingType::Value ></a></div><div class="ttdef"><b>Definition:</b> <a href="core_2interp_2linear_8h_source.html#l00130">linear.h:132</a></div></div>
<div class="ttc" id="adwi_2tractography_2roi_8h_html"><div class="ttname"><a href="dwi_2tractography_2roi_8h.html">roi.h</a></div></div>
<div class="ttc" id="agroup__elfun_html_gaa5be6dfa9c446af78ea87902e6214d8b"><div class="ttname"><a href="group__elfun.html#gaa5be6dfa9c446af78ea87902e6214d8b">MR::Math::pow3</a></div><div class="ttdeci">constexpr T pow3(const T &v)</div><div class="ttdef"><b>Definition:</b> <a href="math_8h_source.html#l00054">math.h:54</a></div></div>
<div class="ttc" id="agroup__mathconstants_html_gafe1ee4d398733ae71a15130062a9c2a4"><div class="ttname"><a href="group__mathconstants.html#gafe1ee4d398733ae71a15130062a9c2a4">MR::Math::pi</a></div><div class="ttdeci">constexpr double pi</div><div class="ttdef"><b>Definition:</b> <a href="math_8h_source.html#l00040">math.h:40</a></div></div>
<div class="ttc" id="anamespace_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding_html_a1ffdf9bf69e45b06562948cb7c51a16f"><div class="ttname"><a href="namespace_m_r_1_1_d_w_i_1_1_tractography_1_1_seeding.html#a1ffdf9bf69e45b06562948cb7c51a16f">MR::DWI::Tractography::Seeding::get_count</a></div><div class="ttdeci">uint32_t get_count(ImageType &data)</div><div class="ttdef"><b>Definition:</b> <a href="src_2dwi_2tractography_2seeding_2base_8h_source.html#l00067">base.h:67</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_a439319adcbcb16a7b275a81bc77980b3"><div class="ttname"><a href="namespace_m_r.html#a439319adcbcb16a7b275a81bc77980b3">MR::parse_floats</a></div><div class="ttdeci">vector< default_type > parse_floats(const std::string &spec)</div></div>
<div class="ttc" id="anamespace_m_r_html_a8445ea7a4001a6e8532def9abb86d59e"><div class="ttname"><a href="namespace_m_r.html#a8445ea7a4001a6e8532def9abb86d59e">MR::transform_type</a></div><div class="ttdeci">Eigen::Transform< default_type, 3, Eigen::AffineCompact > transform_type</div><div class="ttdoc">the type for the affine transform of an image:</div><div class="ttdef"><b>Definition:</b> <a href="src_2surface_2types_8h_source.html#l00234">types.h:234</a></div></div>
<div class="ttc" id="asrc_2dwi_2tractography_2seeding_2base_8h_html"><div class="ttname"><a href="src_2dwi_2tractography_2seeding_2base_8h.html">base.h</a></div></div>
<div class="ttc" id="asrc_2dwi_2tractography_2seeding_2base_8h_html_aa3cf37d9ed697f9c8843155e84d8513d"><div class="ttname"><a href="src_2dwi_2tractography_2seeding_2base_8h.html#aa3cf37d9ed697f9c8843155e84d8513d">MAX_TRACKING_SEED_ATTEMPTS_FIXED</a></div><div class="ttdeci">#define MAX_TRACKING_SEED_ATTEMPTS_FIXED</div><div class="ttdef"><b>Definition:</b> <a href="src_2dwi_2tractography_2seeding_2base_8h_source.html#l00049">base.h:49</a></div></div>
<div class="ttc" id="asrc_2dwi_2tractography_2seeding_2base_8h_html_aa5fd5f27448bc33809bf3e8cc5230f6f"><div class="ttname"><a href="src_2dwi_2tractography_2seeding_2base_8h.html#aa5fd5f27448bc33809bf3e8cc5230f6f">MAX_TRACKING_SEED_ATTEMPTS_RANDOM</a></div><div class="ttdeci">#define MAX_TRACKING_SEED_ATTEMPTS_RANDOM</div><div class="ttdef"><b>Definition:</b> <a href="src_2dwi_2tractography_2seeding_2base_8h_source.html#l00035">base.h:35</a></div></div>
<div class="ttc" id="asrc_2surface_2types_8h_html_a11d7eae3ab5178ebcf0e62cae9c26cd4"><div class="ttname"><a href="src_2surface_2types_8h.html#a11d7eae3ab5178ebcf0e62cae9c26cd4">MEMALIGN</a></div><div class="ttdeci">#define MEMALIGN(...)</div><div class="ttdef"><b>Definition:</b> <a href="src_2surface_2types_8h_source.html#l00185">types.h:185</a></div></div>
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