Mercurial > hg > orthanc-stone

annotate OrthancStone/Sources/Toolbox/DicomStructureSet.h @ 2123:538c7b7c6e46 deep-learning

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integration mainline->deep-learning
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 22 Mar 2024 16:11:42 +0100
parents c23eef785569
children 16c01cc201e7
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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) 2017-2024 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU Lesser General Public License
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28956ed68280 agpl license
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10 * as published by the Free Software Foundation, either version 3 of
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11 * the License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * Lesser General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU Lesser General Public
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19 * License along with this program. If not, see
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20 * <http://www.gnu.org/licenses/>.
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21 **/
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24 #pragma once
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25
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26 #include "../OrthancStone.h"
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27
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28 #if !defined(ORTHANC_ENABLE_DCMTK)
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29 # error The macro ORTHANC_ENABLE_DCMTK must be defined
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30 #endif
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31
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32 #include "CoordinateSystem3D.h"
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33 #include "Extent2D.h"
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34 #include "OrthancDatasets/FullOrthancDataset.h"
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35 #include "../Scene2D/Color.h"
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36 #include "../Scene2D/PolylineSceneLayer.h"
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37 #include "../Scene2D/ScenePoint2D.h"
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39 #if ORTHANC_ENABLE_DCMTK == 1
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40 # include <DicomParsing/ParsedDicomFile.h>
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41 #endif
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42
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43
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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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74
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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 bool IsPointOnSliceIfAny(const Vector& v) const;
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87
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88 public:
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89 explicit Polygon(const std::string& sopInstanceUid) :
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90 sopInstanceUid_(sopInstanceUid),
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91 hasSlice_(false),
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92 projectionAlongNormal_(0),
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93 sliceThickness_(0)
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94 {
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95 }
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96
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97 void Reserve(size_t n)
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98 {
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99 points_.reserve(n);
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100 }
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101
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102 void AddPoint(const Vector& v);
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103
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104 bool UpdateReferencedSlice(const ReferencedSlices& slices);
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105
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106 bool IsOnSlice(const CoordinateSystem3D& cuttingPlane,
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107 const Vector& estimatedNormal,
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108 double estimatedSliceThickness) const;
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109
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110 const Vector& GetGeometryOrigin() const
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111 {
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112 return geometry_.GetOrigin();
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113 }
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114
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115 const std::string& GetSopInstanceUid() const
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116 {
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117 return sopInstanceUid_;
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118 }
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119
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120 const Points& GetPoints() const
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121 {
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122 return points_;
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123 }
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124
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125 double GetSliceThickness() const
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126 {
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127 return sliceThickness_;
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128 }
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129
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130 bool Project(double& x1,
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131 double& y1,
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132 double& x2,
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133 double& y2,
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134 const CoordinateSystem3D& cuttingPlane,
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135 const Vector& estimatedNormal,
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136 double estimatedSliceThickness) const;
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137 };
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138
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139 typedef std::list<Polygon> Polygons;
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140
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141 struct Structure
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142 {
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143 std::string name_;
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144 std::string interpretation_;
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145 Polygons polygons_;
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146 uint8_t red_;
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147 uint8_t green_;
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148 uint8_t blue_;
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149 };
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150
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151 typedef std::vector<Structure> Structures;
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152 typedef std::map<std::string, size_t> StructureNamesIndex;
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153
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154 Structures structures_;
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155 ReferencedSlices referencedSlices_;
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156 Vector estimatedNormal_;
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157 double estimatedSliceThickness_;
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158 StructureNamesIndex structureNamesIndex_;
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159
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160
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161 void Setup(const IDicomDataset& dataset);
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162
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163 const Structure& GetStructure(size_t index) const;
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164
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165 Structure& GetStructure(size_t index);
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166
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167 bool ProjectStructure(std::vector< std::vector<ScenePoint2D> >& chains,
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168 const Structure& structure,
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169 const CoordinateSystem3D& cuttingPlane) const;
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170
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171 void EstimateGeometry();
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172
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173 public:
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174 explicit DicomStructureSet(const FullOrthancDataset& instance)
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175 {
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176 Setup(instance);
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177 }
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178
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179 #if ORTHANC_ENABLE_DCMTK == 1
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180 explicit DicomStructureSet(Orthanc::ParsedDicomFile& instance);
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181 #endif
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182
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183 size_t GetStructuresCount() const
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184 {
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185 return structures_.size();
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186 }
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187
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188 Vector GetStructureCenter(size_t index) const;
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189
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190 const std::string& GetStructureName(size_t index) const;
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191
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192 const std::string& GetStructureInterpretation(size_t index) const;
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193
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194 Color GetStructureColor(size_t index) const;
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195
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196 void GetReferencedInstances(std::set<std::string>& instances) const;
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197
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198 void AddReferencedSlice(const std::string& sopInstanceUid,
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199 const std::string& seriesInstanceUid,
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200 const CoordinateSystem3D& geometry,
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201 double thickness);
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202
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203 void AddReferencedSlice(const Orthanc::DicomMap& dataset);
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204
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205 void CheckReferencedSlices();
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206
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207 Vector GetNormal() const;
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208
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209 bool ProjectStructure(std::vector< std::vector<ScenePoint2D> >& chains,
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210 size_t index,
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211 const CoordinateSystem3D& cuttingPlane) const
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212 {
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213 return ProjectStructure(chains, GetStructure(index), cuttingPlane);
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214 }
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215
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216 void ProjectOntoLayer(PolylineSceneLayer& layer,
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217 const CoordinateSystem3D& cuttingPlane,
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218 size_t structureIndex,
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219 const Color& color) const;
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220
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221 void ProjectOntoLayer(PolylineSceneLayer& layer,
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222 const CoordinateSystem3D& cuttingPlane,
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223 size_t structureIndex) const
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224 {
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225 ProjectOntoLayer(layer, cuttingPlane, structureIndex, GetStructureColor(structureIndex));
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226 }
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227
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228 void GetStructurePoints(std::list< std::vector<Vector> >& target,
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229 size_t structureIndex,
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230 const std::string& sopInstanceUid) const;
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231
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232 const Vector& GetEstimatedNormal() const
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233 {
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234 return estimatedNormal_;
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235 }
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236
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237 const double GetEstimatedSliceThickness() const
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238 {
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239 return estimatedSliceThickness_;
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240 }
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241
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242 bool LookupStructureName(size_t& structureIndex /* out */,
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243 const std::string& name) const;
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244 };
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245 }