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annotate OrthancStone/Sources/Toolbox/DicomStructureSet.h @ 1584:bd180f97c734

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parsing osirix annotations
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 21 Oct 2020 17:33:17 +0200
parents 85e117739eca
children 4fb8fdf03314
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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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22 #pragma once
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23
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24 #include "../OrthancStone.h"
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25
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26 #if !defined(ORTHANC_ENABLE_DCMTK)
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27 # error The macro ORTHANC_ENABLE_DCMTK must be defined
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28 #endif
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29
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30 #include "DicomStructureSetUtils.h"
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31 #include "CoordinateSystem3D.h"
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32 #include "Extent2D.h"
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33 #include "OrthancDatasets/FullOrthancDataset.h"
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34 #include "../Scene2D/Color.h"
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35 #include "../Scene2D/PolylineSceneLayer.h"
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37 #if ORTHANC_ENABLE_DCMTK == 1
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38 # include <DicomParsing/ParsedDicomFile.h>
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39 #endif
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41 //#define USE_BOOST_UNION_FOR_POLYGONS 1
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44 #include <list>
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45
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46 namespace OrthancStone
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47 {
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48 class DicomStructureSet : public boost::noncopyable
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49 {
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50 private:
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51 struct ReferencedSlice
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52 {
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53 std::string seriesInstanceUid_;
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54 CoordinateSystem3D geometry_;
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55 double thickness_;
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56
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57 ReferencedSlice()
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58 {
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59 }
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60
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61 ReferencedSlice(const std::string& seriesInstanceUid,
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62 const CoordinateSystem3D& geometry,
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63 double thickness) :
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64 seriesInstanceUid_(seriesInstanceUid),
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65 geometry_(geometry),
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66 thickness_(thickness)
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67 {
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68 }
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69 };
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70
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71 typedef std::map<std::string, ReferencedSlice> ReferencedSlices;
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72
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73 typedef std::vector<Vector> Points;
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75 class Polygon
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76 {
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77 private:
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78 std::string sopInstanceUid_;
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79 bool hasSlice_;
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80 CoordinateSystem3D geometry_;
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81 double projectionAlongNormal_;
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82 double sliceThickness_; // In millimeters
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83 Points points_;
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84 Extent2D extent_;
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85
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86 void CheckPointIsOnSlice(const Vector& v) const;
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87 bool IsPointOnSliceIfAny(const Vector& v) const;
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88
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89 public:
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90 explicit Polygon(const std::string& sopInstanceUid) :
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91 sopInstanceUid_(sopInstanceUid),
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92 hasSlice_(false),
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93 projectionAlongNormal_(0),
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94 sliceThickness_(0)
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95 {
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96 }
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97
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98 void Reserve(size_t n)
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99 {
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100 points_.reserve(n);
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101 }
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102
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103 void AddPoint(const Vector& v);
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104
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105 bool UpdateReferencedSlice(const ReferencedSlices& slices);
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106
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107 bool IsOnSlice(const CoordinateSystem3D& geometry) const;
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108
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109 const Vector& GetGeometryOrigin() const
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110 {
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111 return geometry_.GetOrigin();
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112 }
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114 const std::string& GetSopInstanceUid() const
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115 {
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116 return sopInstanceUid_;
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117 }
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118
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119 const Points& GetPoints() const
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120 {
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121 return points_;
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122 }
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124 double GetSliceThickness() const
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125 {
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126 return sliceThickness_;
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127 }
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128
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129 bool Project(double& x1,
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130 double& y1,
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131 double& x2,
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132 double& y2,
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133 const CoordinateSystem3D& slice) const;
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134 };
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135
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136 typedef std::list<Polygon> Polygons;
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137
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138 struct Structure
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139 {
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140 std::string name_;
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141 std::string interpretation_;
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142 Polygons polygons_;
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143 uint8_t red_;
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144 uint8_t green_;
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145 uint8_t blue_;
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146 };
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147
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148 typedef std::vector<Structure> Structures;
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149
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150 Structures structures_;
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151 ReferencedSlices referencedSlices_;
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152
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153 void Setup(const IDicomDataset& dataset);
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154
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155 const Structure& GetStructure(size_t index) const;
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156
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157 Structure& GetStructure(size_t index);
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158
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159 bool ProjectStructure(
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160 #if USE_BOOST_UNION_FOR_POLYGONS == 1
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161 std::vector< std::vector<Point2D> >& polygons,
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162 #else
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163 std::vector< std::pair<Point2D, Point2D> >& segments,
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164 #endif
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165 const Structure& structure,
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166 const CoordinateSystem3D& slice) const;
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167
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168 public:
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169 explicit DicomStructureSet(const FullOrthancDataset& instance)
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170 {
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171 Setup(instance);
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172 }
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173
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174 #if ORTHANC_ENABLE_DCMTK == 1
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175 explicit DicomStructureSet(Orthanc::ParsedDicomFile& instance);
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176 #endif
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177
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178 size_t GetStructuresCount() const
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179 {
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180 return structures_.size();
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181 }
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182
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183 Vector GetStructureCenter(size_t index) const;
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184
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185 const std::string& GetStructureName(size_t index) const;
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186
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187 const std::string& GetStructureInterpretation(size_t index) const;
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188
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189 Color GetStructureColor(size_t index) const;
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190
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191 // TODO - remove
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192 void GetStructureColor(uint8_t& red,
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193 uint8_t& green,
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194 uint8_t& blue,
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195 size_t index) const;
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196
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197 void GetReferencedInstances(std::set<std::string>& instances);
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198
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199 void AddReferencedSlice(const std::string& sopInstanceUid,
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200 const std::string& seriesInstanceUid,
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201 const CoordinateSystem3D& geometry,
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202 double thickness);
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203
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204 void AddReferencedSlice(const Orthanc::DicomMap& dataset);
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205
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206 void CheckReferencedSlices();
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207
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208 Vector GetNormal() const;
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209
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210 #if USE_BOOST_UNION_FOR_POLYGONS == 1
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211 bool ProjectStructure(std::vector< std::vector<Point2D> >& polygons,
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212 size_t index,
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213 const CoordinateSystem3D& slice) const
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214 {
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215 return ProjectStructure(polygons, GetStructure(index), slice);
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216 }
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217 #else
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218 bool ProjectStructure(std::vector< std::pair<Point2D, Point2D> >& segments,
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219 size_t index,
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220 const CoordinateSystem3D& slice) const
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221 {
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222 return ProjectStructure(segments, GetStructure(index), slice);
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223 }
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224 #endif
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225
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226 void ProjectOntoLayer(PolylineSceneLayer& layer,
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227 const CoordinateSystem3D& plane,
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228 size_t structureIndex,
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229 const Color& color) const;
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230
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231 void ProjectOntoLayer(PolylineSceneLayer& layer,
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232 const CoordinateSystem3D& plane,
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233 size_t structureIndex) const
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234 {
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235 ProjectOntoLayer(layer, plane, structureIndex, GetStructureColor(structureIndex));
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236 }
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237 };
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238 }