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annotate Framework/Toolbox/DicomStructureSet.h @ 1180:9c8f557ea799 broker

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ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 20 Nov 2019 17:34:17 +0100
parents 3c7cdbf32e2a
children 0ca50d275b9a
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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) 2017-2019 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 #pragma once
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24 #if !defined(ORTHANC_ENABLE_DCMTK)
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25 # error The macro ORTHANC_ENABLE_DCMTK must be defined
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26 #endif
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27
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28 #include "DicomStructureSetUtils.h"
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29 #include "CoordinateSystem3D.h"
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30 #include "Extent2D.h"
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31 #include "../Scene2D/Color.h"
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32 #include "../Scene2D/PolylineSceneLayer.h"
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34 #if ORTHANC_ENABLE_DCMTK == 1
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35 # include <Core/DicomParsing/ParsedDicomFile.h>
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36 #endif
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37
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38 //#define USE_BOOST_UNION_FOR_POLYGONS 1
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39
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40 #include <Plugins/Samples/Common/FullOrthancDataset.h>
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41
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42 #include <list>
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43
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44 namespace OrthancStone
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45 {
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46 class DicomStructureSet : public boost::noncopyable
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47 {
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48 private:
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49 struct ReferencedSlice
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50 {
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51 std::string seriesInstanceUid_;
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52 CoordinateSystem3D geometry_;
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53 double thickness_;
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54
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55 ReferencedSlice()
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56 {
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57 }
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58
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59 ReferencedSlice(const std::string& seriesInstanceUid,
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60 const CoordinateSystem3D& geometry,
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61 double thickness) :
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62 seriesInstanceUid_(seriesInstanceUid),
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63 geometry_(geometry),
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64 thickness_(thickness)
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65 {
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66 }
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67 };
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68
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69 typedef std::map<std::string, ReferencedSlice> ReferencedSlices;
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71 typedef std::vector<Vector> Points;
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73 class Polygon
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74 {
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75 private:
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76 std::string sopInstanceUid_;
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77 bool hasSlice_;
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78 CoordinateSystem3D geometry_;
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79 double projectionAlongNormal_;
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80 double sliceThickness_; // In millimeters
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81 Points points_;
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82 Extent2D extent_;
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83
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84 void CheckPointIsOnSlice(const Vector& v) const;
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85 bool IsPointOnSliceIfAny(const Vector& v) const;
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86
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87 public:
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88 Polygon(const std::string& sopInstanceUid) :
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89 sopInstanceUid_(sopInstanceUid),
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90 hasSlice_(false)
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91 {
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92 }
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93
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94 void Reserve(size_t n)
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95 {
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96 points_.reserve(n);
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97 }
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98
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99 void AddPoint(const Vector& v);
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100
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101 bool UpdateReferencedSlice(const ReferencedSlices& slices);
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102
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103 bool IsOnSlice(const CoordinateSystem3D& geometry) const;
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104
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105 const Vector& GetGeometryOrigin() const
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106 {
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107 return geometry_.GetOrigin();
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108 }
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110 const std::string& GetSopInstanceUid() const
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111 {
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112 return sopInstanceUid_;
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113 }
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114
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115 const Points& GetPoints() const
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116 {
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117 return points_;
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118 }
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119
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120 double GetSliceThickness() const
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121 {
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122 return sliceThickness_;
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123 }
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124
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125 bool Project(double& x1,
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126 double& y1,
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127 double& x2,
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128 double& y2,
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129 const CoordinateSystem3D& slice) const;
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130 };
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131
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132 typedef std::list<Polygon> Polygons;
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133
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134 struct Structure
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135 {
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136 std::string name_;
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137 std::string interpretation_;
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138 Polygons polygons_;
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139 uint8_t red_;
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140 uint8_t green_;
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141 uint8_t blue_;
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142 };
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143
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144 typedef std::vector<Structure> Structures;
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145
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146 Structures structures_;
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147 ReferencedSlices referencedSlices_;
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148
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149 void Setup(const OrthancPlugins::IDicomDataset& dataset);
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150
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151 const Structure& GetStructure(size_t index) const;
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152
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153 Structure& GetStructure(size_t index);
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154
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155 bool ProjectStructure(
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156 #if USE_BOOST_UNION_FOR_POLYGONS == 1
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157 std::vector< std::vector<Point2D> >& polygons,
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158 #else
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159 std::vector< std::pair<Point2D, Point2D> >& segments,
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160 #endif
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161 const Structure& structure,
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162 const CoordinateSystem3D& slice) const;
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163
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164 public:
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165 DicomStructureSet(const OrthancPlugins::FullOrthancDataset& instance)
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166 {
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167 Setup(instance);
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168 }
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169
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170 #if ORTHANC_ENABLE_DCMTK == 1
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171 DicomStructureSet(Orthanc::ParsedDicomFile& instance);
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172 #endif
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173
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174 size_t GetStructuresCount() const
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175 {
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176 return structures_.size();
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177 }
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178
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179 Vector GetStructureCenter(size_t index) const;
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180
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181 const std::string& GetStructureName(size_t index) const;
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182
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183 const std::string& GetStructureInterpretation(size_t index) const;
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184
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185 Color GetStructureColor(size_t index) const;
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186
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187 // TODO - remove
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188 void GetStructureColor(uint8_t& red,
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189 uint8_t& green,
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190 uint8_t& blue,
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191 size_t index) const;
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192
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193 void GetReferencedInstances(std::set<std::string>& instances);
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194
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195 void AddReferencedSlice(const std::string& sopInstanceUid,
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196 const std::string& seriesInstanceUid,
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197 const CoordinateSystem3D& geometry,
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198 double thickness);
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199
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200 void AddReferencedSlice(const Orthanc::DicomMap& dataset);
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201
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202 void CheckReferencedSlices();
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203
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204 Vector GetNormal() const;
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205
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206 #if USE_BOOST_UNION_FOR_POLYGONS == 1
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207 bool ProjectStructure(std::vector< std::vector<Point2D> >& polygons,
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208 size_t index,
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209 const CoordinateSystem3D& slice) const
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210 {
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211 return ProjectStructure(polygons, GetStructure(index), slice);
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212 }
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213 #else
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214 bool ProjectStructure(std::vector< std::pair<Point2D, Point2D> >& segments,
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215 size_t index,
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216 const CoordinateSystem3D& slice) const
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217 {
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218 return ProjectStructure(segments, GetStructure(index), slice);
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219 }
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220 #endif
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221
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222 void ProjectOntoLayer(PolylineSceneLayer& layer,
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223 const CoordinateSystem3D& plane,
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224 size_t structureIndex,
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225 const Color& color) const;
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226
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227 void ProjectOntoLayer(PolylineSceneLayer& layer,
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228 const CoordinateSystem3D& plane,
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229 size_t structureIndex) const
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230 {
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231 ProjectOntoLayer(layer, plane, structureIndex, GetStructureColor(structureIndex));
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232 }
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233 };
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234 }