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annotate OrthancStone/Sources/Toolbox/DicomStructure2.cpp @ 1688:c14dd6e11ddd

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author Benjamin Golinvaux <bgo@osimis.io>
date Wed, 25 Nov 2020 17:03:08 +0100
parents 52b8b96cb55f
children 9ac2a65d4172
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1 /**
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2 * Stone of Orthanc
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2020 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU Lesser General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * Lesser General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU Lesser General Public
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18 * License along with this program. If not, see
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19 * <http://www.gnu.org/licenses/>.
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20 **/
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22 #ifdef BGO_ENABLE_DICOMSTRUCTURESETLOADER2
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23
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24 #include "DicomStructure2.h"
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25
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26 #include "../Toolbox/GeometryToolbox.h"
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27 #include "../Toolbox/DisjointDataSet.h"
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28
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29 namespace OrthancStone
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30 {
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31 // see header
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32 //void DicomStructure2::ComputeNormal()
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33 //{
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34 // try
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35 // {
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36 // if (polygons_.size() > 0)
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37 // {
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38
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39 // // TODO: check all polygons are OK
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40 // const DicomStructurePolygon2 polygon = polygons_[0];
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41 // $$$$$$$$$$$$$$$$$
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42 // state_ = NormalComputed;
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43 // }
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44 // else
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45 // {
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46 // // bogus! no polygons. Let's assign a "nothing here" value
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47 // LinearAlgebra::AssignVector(normal_, 0, 0, 0);
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48 // state_ = Invalid;
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49 // }
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50 // }
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51 // catch (const Orthanc::OrthancException& e)
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52 // {
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53 // state_ = Invalid;
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54 // if (e.HasDetails())
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55 // {
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56 // LOG(ERROR) << "OrthancException in ComputeNormal: " << e.What() << " Details: " << e.GetDetails();
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57 // }
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58 // else
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59 // {
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60 // LOG(ERROR) << "OrthancException in ComputeNormal: " << e.What();
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61 // }
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62 // throw;
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63 // }
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64 // catch (const std::exception& e)
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65 // {
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66 // state_ = Invalid;
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67 // LOG(ERROR) << "std::exception in ComputeNormal: " << e.what();
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68 // throw;
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69 // }
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70 // catch (...)
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71 // {
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72 // state_ = Invalid;
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73 // LOG(ERROR) << "Unknown exception in ComputeNormal";
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74 // throw;
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75 // }
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76 //}
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77
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78 void DicomStructure2::ComputeSliceThickness()
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79 {
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80 if (state_ != NormalComputed)
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81 {
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82 LOG(ERROR) << "DicomStructure2::ComputeSliceThickness - state must be NormalComputed";
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83 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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84 }
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85 if (polygons_.size() < 2)
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86 {
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87 // cannot compute thickness if there are not at least 2 slabs (structures)
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88 sliceThickness_ = 1.0;
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89 state_ = Invalid;
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90 }
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91 else
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92 {
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93 // normal can be (1,0,0), (0,1,0) or (0,0,1), nothing else.
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94 // these can be compared with == (exact double representation)
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95 if (normal_[0] == 1)
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96 {
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97 // in a single polygon, all the points have the same X
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98 sliceThickness_ = fabs(polygons_[0].GetPoint(0)[0] - polygons_[1].GetPoint(0)[0]);
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99 }
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100 else if (normal_[1] == 1)
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101 {
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102 // in a single polygon, all the points have the same X
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103 sliceThickness_ = fabs(polygons_[0].GetPoint(0)[1] - polygons_[1].GetPoint(0)[1]);
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104 }
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105 else if (normal_[2] == 1)
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106 {
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107 // in a single polygon, all the points have the same X
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108 sliceThickness_ = fabs(polygons_[0].GetPoint(0)[2] - polygons_[1].GetPoint(0)[2]);
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109 }
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110 else
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111 {
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112 ORTHANC_ASSERT(false);
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113 state_ = Invalid;
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114 }
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115 }
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116 state_ = Valid;
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117 }
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118
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119 void DicomStructure2::AddPolygon(const DicomStructurePolygon2& polygon)
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120 {
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121 if (state_ != Building)
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122 {
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123 LOG(ERROR) << "DicomStructure2::AddPolygon - can only add polygon while building";
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124 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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125 }
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126 polygons_.push_back(polygon);
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127 }
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128
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129 void DicomStructure2::ComputeDependentProperties()
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130 {
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131 if (state_ != Building)
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132 {
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133 LOG(ERROR) << "DicomStructure2::ComputeDependentProperties - can only be called once";
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134 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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135 }
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136 for (size_t i = 0; i < polygons_.size(); ++i)
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137 {
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138 // "compute" the polygon normal
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139 polygons_[i].ComputeDependentProperties();
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140 }
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141 if (polygons_.size() > 0)
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142 {
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143 normal_ = polygons_[0].GetNormal();
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144 state_ = NormalComputed;
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145 }
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146 else
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147 {
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148 LinearAlgebra::AssignVector(normal_, 0, 0, 0);
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149 state_ = Invalid; // THIS MAY HAPPEN !!! (for instance for instance 72c773ac-5059f2c4-2e6a9120-4fd4bca1-45701661 :) )
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150 }
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151 if (polygons_.size() >= 2)
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152 ComputeSliceThickness(); // this will change state_ from NormalComputed to Valid
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153 }
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154
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155 Vector DicomStructure2::GetNormal() const
998
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156 {
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157 if (state_ != Valid && state_ != Invalid)
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158 {
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159 LOG(ERROR) << "DicomStructure2::GetNormal() -- please call ComputeDependentProperties first.";
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160 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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161 }
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162 if (state_ == Invalid)
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163 {
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164 LOG(ERROR) << "DicomStructure2::GetNormal() -- The Dicom structure is invalid. The normal is set to 0,0,0";
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165 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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166 }
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167 return normal_;
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168 }
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169
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170 const DicomStructurePolygon2* DicomStructure2::GetPolygonClosestToSlice(
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171 const CoordinateSystem3D& plane) const
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172 {
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173 ORTHANC_ASSERT(state_ == Valid);
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174
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175 // we assume 0,0,1 for now
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176 ORTHANC_ASSERT(LinearAlgebra::IsNear(plane.GetNormal()[0], 0.0));
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177 ORTHANC_ASSERT(LinearAlgebra::IsNear(plane.GetNormal()[1], 0.0));
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178
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179 for (size_t i = 0; i < polygons_.size(); ++i)
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180 {
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181 const DicomStructurePolygon2& polygon = polygons_[i];
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182
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183 // "height" of cutting plane
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184 double cutZ = plane.GetOrigin()[2];
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185
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186 if (LinearAlgebra::IsNear(
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187 cutZ, polygon.GetZ(),
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188 sliceThickness_ / 2.0 /* in mm */))
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189 return &polygon;
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190 }
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191 return NULL;
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192 }
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193
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194
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195 bool DicomStructure2::Project(std::vector< std::pair<Point2D, Point2D> > & segments, const CoordinateSystem3D & plane) const
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196 {
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197 segments.clear();
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198
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199 Vector normal = GetNormal();
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200
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201 size_t totalRectCount = 0;
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202
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203 // dummy var
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204 bool isOpposite = false;
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205
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206 // This is an axial projection
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207 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, plane.GetNormal()))
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208 {
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209 const DicomStructurePolygon2* polygon = GetPolygonClosestToSlice(plane);
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210 if (polygon)
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211 {
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212 polygon->ProjectOnParallelPlane(segments, plane);
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213 }
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214 }
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215 else
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216 {
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217 // let's compute the dot product of the plane normal and the polygons
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218 // normal.
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219 double dot = LinearAlgebra::DotProduct(plane.GetNormal(), normal);
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220
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221 if (LinearAlgebra::IsNear(dot, 0))
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222 {
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223 // Coronal or sagittal projection
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224
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225 // vector of vector of rectangles that will be merged in a single big contour:
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226
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227 // each polygon slab cut by a perpendicular plane yields 0..* rectangles
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228 std::vector< RtStructRectanglesInSlab > rectanglesForEachSlab;
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229
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230 for (size_t i = 0; i < polygons_.size(); ++i)
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231 {
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232 // book an entry for this slab
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233 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab());
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234
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235 // let's compute the intersection between the polygon and the plane
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236 // intersections are in plane coords
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237 std::vector<Point2D> intersections;
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238
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239 polygons_[i].ProjectOnConstantPlane(intersections, plane);
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240
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241 // for each pair of intersections, we add a rectangle.
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242 if ((intersections.size() % 2) != 0)
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243 {
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244 LOG(WARNING) << "Odd number of intersections between structure "
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245 << name_ << ", polygon # " << i
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246 << " and plane where X axis is parallel to polygon normal vector";
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247 }
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248
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249 size_t numRects = intersections.size() / 2;
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250
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251 // we keep count of the total number of rects for vector pre-allocations
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252 totalRectCount += numRects;
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253
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254 for (size_t iRect = 0; iRect < numRects; ++iRect)
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255 {
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256 RtStructRectangleInSlab rectangle;
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257 ORTHANC_ASSERT(LinearAlgebra::IsNear(intersections[2 * iRect].y, intersections[2 * iRect + 1].y));
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258 ORTHANC_ASSERT((2 * iRect + 1) < intersections.size());
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259 double x1 = intersections[2 * iRect].x;
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260 double x2 = intersections[2 * iRect + 1].x;
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261 double y1 = intersections[2 * iRect].y - sliceThickness_ * 0.5;
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262 double y2 = intersections[2 * iRect].y + sliceThickness_ * 0.5;
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263
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264 rectangle.xmin = std::min(x1, x2);
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265 rectangle.xmax = std::max(x1, x2);
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266 rectangle.ymin = std::min(y1, y2);
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267 rectangle.ymax = std::max(y1, y2);
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268
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269 // TODO: keep them sorted!!!!
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270
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271 rectanglesForEachSlab.back().push_back(rectangle);
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272 }
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273 }
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274 // now we need to merge all the slabs into a set of polygons (1 or more)
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275 ConvertListOfSlabsToSegments(segments, rectanglesForEachSlab, totalRectCount);
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276 }
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277 else
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278 {
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279 // plane is not perpendicular to the polygons
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280 // 180.0 / [Math]::Pi = 57.2957795130823
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281 double acDot = 57.2957795130823 * acos(dot);
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282 LOG(ERROR) << "DicomStructure2::Project -- cutting plane must be "
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283 << "perpendicular to the structures, but dot product is: "
998
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284 << dot << " and (180/pi)*acos(dot) = " << acDot;
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285 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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286 }
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287 }
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288 return segments.size() != 0;
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289 }
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290 }
1019
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291
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292 #endif
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293 // BGO_ENABLE_DICOMSTRUCTURESETLOADER2
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294