Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/CoordinateSystem3D.cpp @ 1834:126522623e20
replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 10 Jun 2021 12:07:04 +0200 |
| parents | 9ac2a65d4172 |
| children | 3889ae96d2e9 |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 2 * Stone of Orthanc | |
| 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
| 4 * Department, University Hospital of Liege, Belgium | |
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5 * Copyright (C) 2017-2021 Osimis S.A., Belgium |
| 0 | 6 * |
| 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 |
| 47 | 9 * as published by the Free Software Foundation, either version 3 of |
| 10 * the License, or (at your option) any later version. | |
| 0 | 11 * |
| 12 * This program is distributed in the hope that it will be useful, but | |
| 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/>. |
| 0 | 20 **/ |
| 21 | |
| 22 | |
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23 #include "CoordinateSystem3D.h" |
| 0 | 24 |
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25 #include "LinearAlgebra.h" |
| 0 | 26 #include "GeometryToolbox.h" |
| 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> |
| 0 | 31 |
| 32 namespace OrthancStone | |
| 33 { | |
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34 void CoordinateSystem3D::CheckAndComputeNormal() |
| 0 | 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)) |
| 0 | 45 { |
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46 LOG(WARNING) << "Invalid 3D geometry: Axes are not normal vectors"; |
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47 SetupCanonical(); |
| 0 | 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)) |
| 0 | 62 { |
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63 LOG(WARNING) << "Invalid 3D geometry: Image orientation patient is not orthogonal"; |
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64 SetupCanonical(); |
| 0 | 65 } |
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66 else |
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67 { |
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68 LinearAlgebra::CrossProduct(normal_, axisX_, axisY_); |
| 0 | 69 |
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70 d_ = -(normal_[0] * origin_[0] + normal_[1] * origin_[1] + normal_[2] * origin_[2]); |
| 0 | 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 } |
| 0 | 75 } |
| 76 | |
| 77 | |
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78 void CoordinateSystem3D::SetupCanonical() |
| 0 | 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; |
| 0 | 87 } |
| 88 | |
| 89 | |
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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), |
| 0 | 94 origin_(origin), |
| 95 axisX_(axisX), | |
| 96 axisY_(axisY) | |
| 97 { | |
| 98 CheckAndComputeNormal(); | |
| 99 } | |
| 100 | |
| 101 | |
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102 void CoordinateSystem3D::Setup(const std::string& imagePositionPatient, |
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103 const std::string& imageOrientationPatient) |
| 0 | 104 { |
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105 valid_ = true; |
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106 |
| 0 | 107 std::string tmpPosition = Orthanc::Toolbox::StripSpaces(imagePositionPatient); |
| 108 std::string tmpOrientation = Orthanc::Toolbox::StripSpaces(imageOrientationPatient); | |
| 109 | |
| 110 Vector orientation; | |
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111 if (!LinearAlgebra::ParseVector(origin_, tmpPosition) || |
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112 !LinearAlgebra::ParseVector(orientation, tmpOrientation) || |
| 0 | 113 origin_.size() != 3 || |
| 114 orientation.size() != 6) | |
| 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(); |
| 0 | 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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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]; |
| 0 | 131 |
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132 CheckAndComputeNormal(); |
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133 } |
| 0 | 134 } |
| 135 | |
| 136 | |
| 1504 | 137 CoordinateSystem3D::CoordinateSystem3D(const IDicomDataset& dicom) |
| 0 | 138 { |
| 32 | 139 std::string a, b; |
| 140 | |
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141 if (dicom.GetStringValue(a, Orthanc::DicomPath(Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT)) && |
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142 dicom.GetStringValue(b, Orthanc::DicomPath(Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT))) |
| 0 | 143 { |
| 32 | 144 Setup(a, b); |
| 0 | 145 } |
| 146 else | |
| 147 { | |
| 148 SetupCanonical(); | |
| 149 } | |
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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 } |
| 0 | 167 |
| 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 |
| 0 | 184 { |
| 185 return origin_ + x * axisX_ + y * axisY_; | |
| 186 } | |
| 187 | |
| 188 | |
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189 double CoordinateSystem3D::ProjectAlongNormal(const Vector& point) const |
| 0 | 190 { |
| 191 return boost::numeric::ublas::inner_prod(point, normal_); | |
| 192 } | |
| 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 } |
| 0 | 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 |
| 0 | 211 { |
| 212 // Project the point onto the slice | |
| 213 Vector projection; | |
| 214 GeometryToolbox::ProjectPointOntoPlane(projection, point, normal_, origin_); | |
| 215 | |
| 216 // As the axes are orthonormal vectors thanks to | |
| 217 // CheckAndComputeNormal(), the following dot products give the | |
| 218 // offset of the origin of the slice wrt. the origin of the | |
| 219 // reference plane https://en.wikipedia.org/wiki/Vector_projection | |
| 220 offsetX = boost::numeric::ublas::inner_prod(axisX_, projection - origin_); | |
| 221 offsetY = boost::numeric::ublas::inner_prod(axisY_, projection - origin_); | |
| 222 } | |
|
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223 |
| 152 | 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 { |
|
157
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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 |
| 757 | 252 bool CoordinateSystem3D::ComputeDistance(double& distance, |
| 253 const CoordinateSystem3D& a, | |
| 254 const CoordinateSystem3D& b) | |
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255 { |
| 986 | 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 } |
|
949
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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 } |
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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 |
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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 } |
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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 } |
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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 | 383 } |