Mercurial > hg > orthanc-stone

annotate Framework/Toolbox/CoordinateSystem3D.cpp @ 1327:4f8db2d202c8 broker

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OrthancSeriesProgressiveLoader now has two modes that can be selected at object creation : - progressive (will first load jpeg50, then jpeg90 then PAM) - non-progressive (will directly load PAM (uncompressed)) Please note that the slice loading order remains dynamic and depending upon the slice that the client code wishes to extract from the volume.
author Benjamin Golinvaux <bgo@osimis.io>
date Wed, 25 Mar 2020 14:34:27 +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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144
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145
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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
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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 }
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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
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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
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200
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201 bool CoordinateSystem3D::IntersectSegment(Vector& p,
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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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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);
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214 }
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215
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216
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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
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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 }