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annotate OrthancStone/Sources/Toolbox/CoordinateSystem3D.cpp @ 1717:391c798e4dae

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fix for KNIX sample dataset
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 01 Dec 2020 10:08:26 +0100
parents af312e145980
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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28956ed68280 agpl 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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23 #include "CoordinateSystem3D.h"
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25 #include "LinearAlgebra.h"
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26 #include "GeometryToolbox.h"
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27
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28 #include <Logging.h>
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29 #include <Toolbox.h>
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30 #include <OrthancException.h>
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32 namespace OrthancStone
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33 {
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34 void CoordinateSystem3D::CheckAndComputeNormal()
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35 {
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36 /**
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37 * DICOM expects normal vectors to define the axes: "The row and
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38 * column direction cosine vectors shall be normal, i.e., the dot
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39 * product of each direction cosine vector with itself shall be
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40 * unity."
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41 * http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.6.2.html
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42 **/
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43 if (!LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(axisX_), 1.0) ||
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44 !LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(axisY_), 1.0))
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45 {
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46 LOG(WARNING) << "Invalid 3D geometry: Axes are not normal vectors";
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47 SetupCanonical();
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48 }
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49
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50 /**
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51 * The vectors within "Image Orientation Patient" must be
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52 * orthogonal, according to the DICOM specification: "The row and
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53 * column direction cosine vectors shall be orthogonal, i.e.,
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54 * their dot product shall be zero."
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55 * http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.6.2.html
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56 *
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57 * The "0.00001" threshold is needed for KNIX (on this sample
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58 * image, the inner product equals "0.000003", which is rejected
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59 * by "LinearAlgebra::IsCloseToZero()").
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60 **/
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61 else if (!LinearAlgebra::IsNear(0, boost::numeric::ublas::inner_prod(axisX_, axisY_), 0.00001))
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62 {
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63 LOG(WARNING) << "Invalid 3D geometry: Image orientation patient is not orthogonal";
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64 SetupCanonical();
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65 }
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66 else
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67 {
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68 LinearAlgebra::CrossProduct(normal_, axisX_, axisY_);
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69
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70 d_ = -(normal_[0] * origin_[0] + normal_[1] * origin_[1] + normal_[2] * origin_[2]);
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71
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72 // Just a sanity check, it should be useless by construction (*)
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73 assert(LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(normal_), 1.0));
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74 }
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75 }
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78 void CoordinateSystem3D::SetupCanonical()
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79 {
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80 valid_ = false;
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81
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82 LinearAlgebra::AssignVector(origin_, 0, 0, 0);
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83 LinearAlgebra::AssignVector(axisX_, 1, 0, 0);
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84 LinearAlgebra::AssignVector(axisY_, 0, 1, 0);
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85 LinearAlgebra::AssignVector(normal_, 0, 0, 1);
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86 d_ = 0;
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87 }
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90 CoordinateSystem3D::CoordinateSystem3D(const Vector& origin,
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91 const Vector& axisX,
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92 const Vector& axisY) :
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93 valid_(true),
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94 origin_(origin),
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95 axisX_(axisX),
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96 axisY_(axisY)
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97 {
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98 CheckAndComputeNormal();
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99 }
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100
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101
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102 void CoordinateSystem3D::Setup(const std::string& imagePositionPatient,
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103 const std::string& imageOrientationPatient)
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104 {
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105 valid_ = true;
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106
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107 std::string tmpPosition = Orthanc::Toolbox::StripSpaces(imagePositionPatient);
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108 std::string tmpOrientation = Orthanc::Toolbox::StripSpaces(imageOrientationPatient);
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109
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110 Vector orientation;
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111 if (!LinearAlgebra::ParseVector(origin_, tmpPosition) ||
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112 !LinearAlgebra::ParseVector(orientation, tmpOrientation) ||
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113 origin_.size() != 3 ||
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114 orientation.size() != 6)
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115 {
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116 LOG(WARNING) << "Bad 3D geometry: image position/orientation patient: \""
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117 << tmpPosition << "\" / \"" << tmpOrientation << "\"";
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118 SetupCanonical();
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119 }
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120 else
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121 {
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122 axisX_.resize(3);
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123 axisX_[0] = orientation[0];
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124 axisX_[1] = orientation[1];
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125 axisX_[2] = orientation[2];
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126
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127 axisY_.resize(3);
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128 axisY_[0] = orientation[3];
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129 axisY_[1] = orientation[4];
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130 axisY_[2] = orientation[5];
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131
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132 CheckAndComputeNormal();
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133 }
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134 }
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135
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136
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137 CoordinateSystem3D::CoordinateSystem3D(const IDicomDataset& dicom)
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138 {
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139 std::string a, b;
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140
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141 if (dicom.GetStringValue(a, DicomPath(Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT)) &&
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142 dicom.GetStringValue(b, DicomPath(Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT)))
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143 {
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144 Setup(a, b);
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145 }
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146 else
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147 {
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148 SetupCanonical();
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149 }
122
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150 }
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151
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152
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153 CoordinateSystem3D::CoordinateSystem3D(const Orthanc::DicomMap& dicom)
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154 {
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155 std::string a, b;
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156
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157 if (dicom.LookupStringValue(a, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
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158 dicom.LookupStringValue(b, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
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159 {
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160 Setup(a, b);
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161 }
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162 else
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163 {
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164 SetupCanonical();
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165 }
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166 }
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168
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169 void CoordinateSystem3D::SetOrigin(const Vector& origin)
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170 {
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171 if (origin.size() != 3)
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172 {
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173 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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174 }
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175 else
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176 {
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177 origin_ = origin;
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178 }
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179 }
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180
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181
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182 Vector CoordinateSystem3D::MapSliceToWorldCoordinates(double x,
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183 double y) const
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184 {
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185 return origin_ + x * axisX_ + y * axisY_;
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186 }
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187
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188
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189 double CoordinateSystem3D::ProjectAlongNormal(const Vector& point) const
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190 {
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191 return boost::numeric::ublas::inner_prod(point, normal_);
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192 }
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193
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194 void CoordinateSystem3D::ProjectPoint2(double& offsetX, double& offsetY, const Vector& point) const
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195 {
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196 // Project the point onto the slice
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197 double projectionX,projectionY,projectionZ;
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198 GeometryToolbox::ProjectPointOntoPlane2(projectionX, projectionY, projectionZ, point, normal_, origin_);
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199
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200 // As the axes are orthonormal vectors thanks to
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201 // CheckAndComputeNormal(), the following dot products give the
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202 // offset of the origin of the slice wrt. the origin of the
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203 // reference plane https://en.wikipedia.org/wiki/Vector_projection
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204 offsetX = axisX_[0] * (projectionX - origin_[0]) + axisX_[1] * (projectionY - origin_[1]) + axisX_[2] * (projectionZ - origin_[2]);
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205 offsetY = axisY_[0] * (projectionX - origin_[0]) + axisY_[1] * (projectionY - origin_[1]) + axisY_[2] * (projectionZ - origin_[2]);
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206 }
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207
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208 void CoordinateSystem3D::ProjectPoint(double& offsetX,
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209 double& offsetY,
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210 const Vector& point) const
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211 {
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212 // Project the point onto the slice
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213 Vector projection;
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214 GeometryToolbox::ProjectPointOntoPlane(projection, point, normal_, origin_);
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215
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216 // As the axes are orthonormal vectors thanks to
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217 // CheckAndComputeNormal(), the following dot products give the
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218 // offset of the origin of the slice wrt. the origin of the
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219 // reference plane https://en.wikipedia.org/wiki/Vector_projection
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220 offsetX = boost::numeric::ublas::inner_prod(axisX_, projection - origin_);
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221 offsetY = boost::numeric::ublas::inner_prod(axisY_, projection - origin_);
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222 }
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223
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224 bool CoordinateSystem3D::IntersectSegment(Vector& p,
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225 const Vector& edgeFrom,
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226 const Vector& edgeTo) const
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227 {
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228 return GeometryToolbox::IntersectPlaneAndSegment(p, normal_, d_, edgeFrom, edgeTo);
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229 }
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230
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231
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232 bool CoordinateSystem3D::IntersectLine(Vector& p,
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233 const Vector& origin,
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234 const Vector& direction) const
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235 {
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236 return GeometryToolbox::IntersectPlaneAndLine(p, normal_, d_, origin, direction);
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237 }
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238
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239
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240 double CoordinateSystem3D::ComputeDistance(const Vector& p) const
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241 {
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242 /**
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243 * "normal_" is an unit vector (*) => sqrt(a_1^2+a_2^2+a_3^2) = 1,
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244 * and the denominator equals 1 by construction.
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245 * https://en.wikipedia.org/wiki/Distance_from_a_point_to_a_plane#Closest_point_and_distance_for_a_hyperplane_and_arbitrary_point
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246 **/
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247
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248 return std::abs(boost::numeric::ublas::inner_prod(p, normal_) + d_);
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249 }
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250
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251
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252 bool CoordinateSystem3D::ComputeDistance(double& distance,
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253 const CoordinateSystem3D& a,
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254 const CoordinateSystem3D& b)
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255 {
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256 bool opposite = false; // Ignored
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257
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258 if (GeometryToolbox::IsParallelOrOpposite(opposite, a.GetNormal(), b.GetNormal()))
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259 {
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260 distance = std::abs(a.ProjectAlongNormal(a.GetOrigin()) -
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261 a.ProjectAlongNormal(b.GetOrigin()));
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262 return true;
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263 }
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264 else
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265 {
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266 return false;
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267 }
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268 }
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32eaf4929b08 OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
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269
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270 std::ostream& operator<< (std::ostream& s, const CoordinateSystem3D& that)
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271 {
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272 s << "origin: " << that.origin_ << " normal: " << that.normal_
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273 << " axisX: " << that.axisX_ << " axisY: " << that.axisY_
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274 << " D: " << that.d_;
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275 return s;
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276 }
32eaf4929b08 OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
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277
1161
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278
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279 CoordinateSystem3D CoordinateSystem3D::NormalizeCuttingPlane(const CoordinateSystem3D& plane)
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280 {
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281 double ox, oy;
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282 plane.ProjectPoint(ox, oy, LinearAlgebra::CreateVector(0, 0, 0));
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283
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284 CoordinateSystem3D normalized(plane);
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285 normalized.SetOrigin(plane.MapSliceToWorldCoordinates(ox, oy));
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286 return normalized;
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287 }
1648
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288
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289
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290 CoordinateSystem3D CoordinateSystem3D::CreateFromPlaneGeneralForm(double a,
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291 double b,
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292 double c,
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293 double d)
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294 {
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295 /**
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296 * "a*x + b*y + c*z + d = 0" => The un-normalized normal is vector
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297 * (a,b,c).
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298 **/
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299
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300 Vector normal;
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301 LinearAlgebra::AssignVector(normal, a, b, c);
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302
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303
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304 /**
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305 * Choose the origin of plane, as the point that is closest to the
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306 * origin of the axes (0,0,0).
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307 * https://en.wikipedia.org/wiki/Distance_from_a_point_to_a_plane#Restatement_using_linear_algebra
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308 **/
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309
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310 double squaredNorm = a * a + b * b + c * c;
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311 if (LinearAlgebra::IsCloseToZero(squaredNorm))
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312 {
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313 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadGeometry, "Singular matrix");
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314 }
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315
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316 Vector origin = -d * normal / squaredNorm;
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317
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318
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319 /**
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320 * Select the X axis by computing a vector that is perpendicular
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321 * to the normal.
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322 *
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323 * "Exactly 1 and only 1 of the bools get set; b0/b1/b2 gets set
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324 * if dimension "i" has magnitude strictly less than all
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325 * subsequent dimensions and not greater than all previous
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326 * dimensions. We then have a unit vector with a single non-zero
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327 * dimension that corresponds to a dimension of minimum magnitude
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328 * in "normal". The cross product of this with "normal" is
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329 * orthogonal to "normal" by definition of cross product. Consider
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330 * now that the cross product is numerically unstable only when
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331 * the two vectors are very closely aligned. Consider that our
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332 * unit vector is large in only a single dimension and that that
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333 * dimension corresponds to the dimension where "normal" was
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334 * small. It's thus guaranteed to be loosely orthogonal to
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335 * "normal" before taking the cross product, with least
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336 * orthogonality in the case where all dimensions of "normal" are
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337 * equal. In this least-orthogonal case, we're still quite
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338 * orthogonal given that our unit vector has all but one dimension
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339 * 0 whereas "normal" has all equal. We thus avoid the unstable
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340 * case of taking the cross product of two nearly-aligned
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341 * vectors." https://stackoverflow.com/a/43454629/881731
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342 **/
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343
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344 bool b0 = (normal[0] < normal[1]) && (normal[0] < normal[2]);
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345 bool b1 = (normal[1] <= normal[0]) && (normal[1] < normal[2]);
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346 bool b2 = (normal[2] <= normal[0]) && (normal[2] <= normal[1]);
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347 Vector swap = LinearAlgebra::CreateVector(b0 ? 1 : 0, b1 ? 1 : 0, b2 ? 1 : 0);
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348
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349 Vector axisX;
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350 LinearAlgebra::CrossProduct(axisX, normal, swap);
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351 LinearAlgebra::NormalizeVector(axisX);
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352
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353
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354 /**
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355 * The Y axis follows as the cross-product of the normal and the X
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356 * axis.
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357 **/
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358
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359 Vector axisY;
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360 LinearAlgebra::CrossProduct(axisY, axisX, normal);
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361 LinearAlgebra::NormalizeVector(axisY);
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362
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363 return CoordinateSystem3D(origin, axisX, axisY);
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364 }
1650
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365
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366
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367 CoordinateSystem3D CoordinateSystem3D::CreateFromThreePoints(const Vector& a,
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368 const Vector& b,
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369 const Vector& c)
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370 {
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371 Vector axisX = b - a;
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372 LinearAlgebra::NormalizeVector(axisX);
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373
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374 Vector normal;
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375 LinearAlgebra::CrossProduct(normal, axisX, c - a);
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376
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377 Vector axisY;
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378 LinearAlgebra::CrossProduct(axisY, axisX, normal);
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379 LinearAlgebra::NormalizeVector(axisY);
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380
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381 return CoordinateSystem3D(a, axisX, axisY);
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382 }
0
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383 }