Mercurial > hg > orthanc-stone

annotate Framework/Toolbox/CoordinateSystem3D.cpp @ 1326:55166e57a77c broker

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author Benjamin Golinvaux <bgo@osimis.io>
date Tue, 24 Mar 2020 21:32:35 +0100
parents 7ec8fea061b9
children 30deba7bc8e2
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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 Affero 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 * Affero 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 Affero General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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21
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22 #include "CoordinateSystem3D.h"
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24 #include "LinearAlgebra.h"
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25 #include "GeometryToolbox.h"
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26
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27 #include <Core/Logging.h>
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28 #include <Core/Toolbox.h>
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29 #include <Core/OrthancException.h>
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31 namespace OrthancStone
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32 {
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33 void CoordinateSystem3D::CheckAndComputeNormal()
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34 {
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35 // DICOM expects normal vectors to define the axes: "The row and
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36 // column direction cosine vectors shall be normal, i.e., the dot
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37 // product of each direction cosine vector with itself shall be
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38 // unity."
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39 // http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.6.2.html
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40 if (!LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(axisX_), 1.0) ||
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41 !LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(axisY_), 1.0))
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42 {
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43 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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44 }
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46 // The vectors within "Image Orientation Patient" must be
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47 // orthogonal, according to the DICOM specification: "The row and
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48 // column direction cosine vectors shall be orthogonal, i.e.,
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49 // their dot product shall be zero."
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50 // http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.6.2.html
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51 if (!LinearAlgebra::IsCloseToZero(boost::numeric::ublas::inner_prod(axisX_, axisY_)))
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52 {
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53 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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54 }
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55
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56 LinearAlgebra::CrossProduct(normal_, axisX_, axisY_);
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57
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58 d_ = -(normal_[0] * origin_[0] + normal_[1] * origin_[1] + normal_[2] * origin_[2]);
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59
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60 // Just a sanity check, it should be useless by construction
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61 assert(LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(normal_), 1.0));
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62 }
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64
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65 void CoordinateSystem3D::SetupCanonical()
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66 {
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67 LinearAlgebra::AssignVector(origin_, 0, 0, 0);
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68 LinearAlgebra::AssignVector(axisX_, 1, 0, 0);
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69 LinearAlgebra::AssignVector(axisY_, 0, 1, 0);
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70 CheckAndComputeNormal();
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71 }
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74 CoordinateSystem3D::CoordinateSystem3D(const Vector& origin,
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75 const Vector& axisX,
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76 const Vector& axisY) :
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77 origin_(origin),
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78 axisX_(axisX),
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79 axisY_(axisY)
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80 {
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81 CheckAndComputeNormal();
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82 }
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85 void CoordinateSystem3D::Setup(const std::string& imagePositionPatient,
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86 const std::string& imageOrientationPatient)
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87 {
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88 std::string tmpPosition = Orthanc::Toolbox::StripSpaces(imagePositionPatient);
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89 std::string tmpOrientation = Orthanc::Toolbox::StripSpaces(imageOrientationPatient);
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90
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91 Vector orientation;
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92 if (!LinearAlgebra::ParseVector(origin_, tmpPosition) ||
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93 !LinearAlgebra::ParseVector(orientation, tmpOrientation) ||
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94 origin_.size() != 3 ||
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95 orientation.size() != 6)
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96 {
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97 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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98 }
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99
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100 axisX_.resize(3);
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101 axisX_[0] = orientation[0];
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102 axisX_[1] = orientation[1];
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103 axisX_[2] = orientation[2];
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104
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105 axisY_.resize(3);
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106 axisY_[0] = orientation[3];
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107 axisY_[1] = orientation[4];
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108 axisY_[2] = orientation[5];
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109
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110 CheckAndComputeNormal();
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111 }
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114 CoordinateSystem3D::CoordinateSystem3D(const OrthancPlugins::IDicomDataset& dicom)
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115 {
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116 std::string a, b;
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117
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118 if (dicom.GetStringValue(a, OrthancPlugins::DICOM_TAG_IMAGE_POSITION_PATIENT) &&
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119 dicom.GetStringValue(b, OrthancPlugins::DICOM_TAG_IMAGE_ORIENTATION_PATIENT))
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120 {
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121 Setup(a, b);
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122 }
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123 else
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124 {
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125 SetupCanonical();
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126 }
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127 }
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128
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129
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130 CoordinateSystem3D::CoordinateSystem3D(const Orthanc::DicomMap& dicom)
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131 {
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132 std::string a, b;
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133
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134 if (dicom.LookupStringValue(a, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
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135 dicom.LookupStringValue(b, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
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136 {
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137 Setup(a, b);
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138 }
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139 else
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140 {
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141 SetupCanonical();
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142 }
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143 }
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145
760
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146 void CoordinateSystem3D::SetOrigin(const Vector& origin)
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147 {
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148 if (origin.size() != 3)
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149 {
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150 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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151 }
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152 else
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153 {
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154 origin_ = origin;
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155 }
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156 }
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157
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158
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159 Vector CoordinateSystem3D::MapSliceToWorldCoordinates(double x,
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160 double y) const
0
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161 {
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162 return origin_ + x * axisX_ + y * axisY_;
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163 }
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164
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165
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166 double CoordinateSystem3D::ProjectAlongNormal(const Vector& point) const
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167 {
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168 return boost::numeric::ublas::inner_prod(point, normal_);
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169 }
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170
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171 void CoordinateSystem3D::ProjectPoint2(double& offsetX, double& offsetY, const Vector& point) const
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172 {
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173 // Project the point onto the slice
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174 double projectionX,projectionY,projectionZ;
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175 GeometryToolbox::ProjectPointOntoPlane2(projectionX, projectionY, projectionZ, point, normal_, origin_);
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176
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177 // As the axes are orthonormal vectors thanks to
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178 // CheckAndComputeNormal(), the following dot products give the
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179 // offset of the origin of the slice wrt. the origin of the
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180 // reference plane https://en.wikipedia.org/wiki/Vector_projection
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181 offsetX = axisX_[0] * (projectionX - origin_[0]) + axisX_[1] * (projectionY - origin_[1]) + axisX_[2] * (projectionZ - origin_[2]);
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182 offsetY = axisY_[0] * (projectionX - origin_[0]) + axisY_[1] * (projectionY - origin_[1]) + axisY_[2] * (projectionZ - origin_[2]);
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183 }
0
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184
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185 void CoordinateSystem3D::ProjectPoint(double& offsetX,
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186 double& offsetY,
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187 const Vector& point) const
0
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188 {
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189 // Project the point onto the slice
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190 Vector projection;
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191 GeometryToolbox::ProjectPointOntoPlane(projection, point, normal_, origin_);
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192
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193 // As the axes are orthonormal vectors thanks to
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194 // CheckAndComputeNormal(), the following dot products give the
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195 // offset of the origin of the slice wrt. the origin of the
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196 // reference plane https://en.wikipedia.org/wiki/Vector_projection
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197 offsetX = boost::numeric::ublas::inner_prod(axisX_, projection - origin_);
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198 offsetY = boost::numeric::ublas::inner_prod(axisY_, projection - origin_);
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199 }
151
c5044bbfc303 CoordinateSystem3D::IntersectSegment()
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200
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201 bool CoordinateSystem3D::IntersectSegment(Vector& p,
151
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202 const Vector& edgeFrom,
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203 const Vector& edgeTo) const
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204 {
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2309e8d86efe IntersectPlaneAndLine
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205 return GeometryToolbox::IntersectPlaneAndSegment(p, normal_, d_, edgeFrom, edgeTo);
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206 }
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207
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208
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209 bool CoordinateSystem3D::IntersectLine(Vector& p,
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210 const Vector& origin,
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211 const Vector& direction) const
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212 {
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213 return GeometryToolbox::IntersectPlaneAndLine(p, normal_, d_, origin, direction);
151
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214 }
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215
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216
757
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217 bool CoordinateSystem3D::ComputeDistance(double& distance,
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218 const CoordinateSystem3D& a,
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219 const CoordinateSystem3D& b)
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220 {
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221 bool opposite = false; // Ignored
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222
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223 if (OrthancStone::GeometryToolbox::IsParallelOrOpposite(
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224 opposite, a.GetNormal(), b.GetNormal()))
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225 {
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226 distance = std::abs(a.ProjectAlongNormal(a.GetOrigin()) -
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227 a.ProjectAlongNormal(b.GetOrigin()));
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228 return true;
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229 }
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230 else
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231 {
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232 return false;
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233 }
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234 }
949
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235
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236 std::ostream& operator<< (std::ostream& s, const CoordinateSystem3D& that)
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237 {
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238 s << "origin: " << that.origin_ << " normal: " << that.normal_
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239 << " axisX: " << that.axisX_ << " axisY: " << that.axisY_
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240 << " D: " << that.d_;
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241 return s;
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242 }
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243
1161
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244
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245 CoordinateSystem3D CoordinateSystem3D::NormalizeCuttingPlane(const CoordinateSystem3D& plane)
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246 {
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247 double ox, oy;
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248 plane.ProjectPoint(ox, oy, LinearAlgebra::CreateVector(0, 0, 0));
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249
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250 CoordinateSystem3D normalized(plane);
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251 normalized.SetOrigin(plane.MapSliceToWorldCoordinates(ox, oy));
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252 return normalized;
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253 }
0
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254 }