Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet.cpp @ 629:8d66efecd91c am-dev
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| author | Alain Mazy <alain@mazy.be> |
|---|---|
| date | Wed, 08 May 2019 16:38:25 +0200 |
| parents | 11fa6f00e33c |
| children | 8e31b174ab26 |
| 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 | |
| 439 | 5 * Copyright (C) 2017-2019 Osimis S.A., Belgium |
| 0 | 6 * |
| 7 * This program is free software: you can redistribute it and/or | |
| 47 | 8 * modify it under the terms of the GNU Affero General Public License |
| 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 | |
| 47 | 14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
| 15 * Affero General Public License for more details. | |
| 16 * | |
| 17 * You should have received a copy of the GNU Affero General Public License | |
| 0 | 18 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
| 19 **/ | |
| 20 | |
| 21 | |
| 22 #include "DicomStructureSet.h" | |
| 23 | |
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24 #include "../Toolbox/GeometryToolbox.h" |
| 35 | 25 #include "../Toolbox/MessagingToolbox.h" |
| 0 | 26 |
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27 #include <Core/Logging.h> |
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28 #include <Core/OrthancException.h> |
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29 #include <Plugins/Samples/Common/FullOrthancDataset.h> |
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30 #include <Plugins/Samples/Common/DicomDatasetReader.h> |
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31 |
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32 #include <limits> |
| 0 | 33 #include <stdio.h> |
| 34 #include <boost/lexical_cast.hpp> | |
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35 #include <boost/geometry.hpp> |
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36 #include <boost/geometry/geometries/point_xy.hpp> |
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37 #include <boost/geometry/geometries/polygon.hpp> |
| 137 | 38 #include <boost/geometry/multi/geometries/multi_polygon.hpp> |
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39 |
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40 typedef boost::geometry::model::d2::point_xy<double> BoostPoint; |
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41 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon; |
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42 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon; |
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43 |
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44 |
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45 static void Union(BoostMultiPolygon& output, |
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46 std::vector<BoostPolygon>& input) |
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47 { |
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48 for (size_t i = 0; i < input.size(); i++) |
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49 { |
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50 boost::geometry::correct(input[i]); |
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51 } |
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52 |
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53 if (input.size() == 0) |
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54 { |
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55 output.clear(); |
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56 } |
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57 else if (input.size() == 1) |
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58 { |
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59 output.resize(1); |
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60 output[0] = input[0]; |
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61 } |
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62 else |
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63 { |
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64 boost::geometry::union_(input[0], input[1], output); |
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65 |
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66 for (size_t i = 0; i < input.size(); i++) |
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67 { |
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68 BoostMultiPolygon tmp; |
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69 boost::geometry::union_(output, input[i], tmp); |
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70 output = tmp; |
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71 } |
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72 } |
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73 } |
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74 |
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75 |
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76 static BoostPolygon CreateRectangle(float x1, float y1, |
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77 float x2, float y2) |
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78 { |
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79 BoostPolygon r; |
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80 boost::geometry::append(r, BoostPoint(x1, y1)); |
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81 boost::geometry::append(r, BoostPoint(x1, y2)); |
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82 boost::geometry::append(r, BoostPoint(x2, y2)); |
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83 boost::geometry::append(r, BoostPoint(x2, y1)); |
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84 return r; |
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85 } |
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86 |
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87 |
| 0 | 88 |
| 89 namespace OrthancStone | |
| 90 { | |
| 32 | 91 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
| 92 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
| 93 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
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94 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050); |
| 32 | 95 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); |
| 96 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
| 97 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
| 98 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
| 99 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
| 100 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
| 101 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
| 102 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
| 0 | 103 |
| 104 | |
| 105 static uint8_t ConvertColor(double v) | |
| 106 { | |
| 107 if (v < 0) | |
| 108 { | |
| 109 return 0; | |
| 110 } | |
| 111 else if (v >= 255) | |
| 112 { | |
| 113 return 255; | |
| 114 } | |
| 115 else | |
| 116 { | |
| 117 return static_cast<uint8_t>(v); | |
| 118 } | |
| 119 } | |
| 120 | |
| 121 | |
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122 static bool ParseVector(Vector& target, |
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123 const OrthancPlugins::IDicomDataset& dataset, |
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124 const OrthancPlugins::DicomPath& tag) |
| 0 | 125 { |
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126 std::string value; |
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127 return (dataset.GetStringValue(value, tag) && |
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128 LinearAlgebra::ParseVector(target, value)); |
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129 } |
| 0 | 130 |
| 131 | |
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132 void DicomStructureSet::Polygon::CheckPoint(const Vector& v) |
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133 { |
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134 if (hasSlice_) |
| 0 | 135 { |
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136 if (!LinearAlgebra::IsNear(GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()), |
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137 projectionAlongNormal_, |
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138 sliceThickness_ / 2.0 /* in mm */)) |
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139 { |
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140 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance"; |
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141 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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142 } |
| 0 | 143 } |
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144 } |
| 0 | 145 |
| 146 | |
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147 void DicomStructureSet::Polygon::AddPoint(const Vector& v) |
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148 { |
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149 CheckPoint(v); |
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150 points_.push_back(v); |
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151 } |
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152 |
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153 |
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154 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices) |
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155 { |
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156 if (hasSlice_) |
| 0 | 157 { |
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158 return true; |
| 32 | 159 } |
| 160 else | |
| 161 { | |
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162 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_); |
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163 |
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164 if (it == slices.end()) |
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165 { |
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166 return false; |
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167 } |
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168 else |
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169 { |
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170 const CoordinateSystem3D& geometry = it->second.geometry_; |
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171 |
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172 hasSlice_ = true; |
| 131 | 173 geometry_ = geometry; |
| 174 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal()); | |
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175 sliceThickness_ = it->second.thickness_; |
| 0 | 176 |
| 131 | 177 extent_.Reset(); |
| 178 | |
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179 for (Points::const_iterator it = points_.begin(); it != points_.end(); ++it) |
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180 { |
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181 CheckPoint(*it); |
| 131 | 182 |
| 183 double x, y; | |
| 184 geometry.ProjectPoint(x, y, *it); | |
| 185 extent_.AddPoint(x, y); | |
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186 } |
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187 |
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188 return true; |
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189 } |
| 0 | 190 } |
| 191 } | |
| 192 | |
| 193 | |
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194 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const |
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195 { |
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196 bool isOpposite; |
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197 |
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198 if (points_.empty() || |
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199 !hasSlice_ || |
| 131 | 200 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal())) |
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201 { |
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202 return false; |
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203 } |
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204 |
| 131 | 205 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal()); |
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206 |
|
158
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207 return (LinearAlgebra::IsNear(d, projectionAlongNormal_, |
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208 sliceThickness_ / 2.0)); |
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209 } |
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210 |
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211 |
| 131 | 212 bool DicomStructureSet::Polygon::Project(double& x1, |
| 213 double& y1, | |
| 214 double& x2, | |
| 215 double& y2, | |
| 216 const CoordinateSystem3D& slice) const | |
| 217 { | |
|
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218 // TODO Optimize this method using a sweep-line algorithm for polygons |
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219 |
| 131 | 220 if (!hasSlice_ || |
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221 points_.size() <= 1) |
| 131 | 222 { |
| 223 return false; | |
| 224 } | |
| 225 | |
| 226 double x, y; | |
| 227 geometry_.ProjectPoint(x, y, slice.GetOrigin()); | |
| 228 | |
| 229 bool isOpposite; | |
| 230 if (GeometryToolbox::IsParallelOrOpposite | |
| 231 (isOpposite, slice.GetNormal(), geometry_.GetAxisY())) | |
| 232 { | |
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233 if (y < extent_.GetY1() || |
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234 y > extent_.GetY2()) |
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235 { |
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236 // The polygon does not intersect the input slice |
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237 return false; |
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238 } |
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239 |
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240 bool isFirst = true; |
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241 double xmin = std::numeric_limits<double>::infinity(); |
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242 double xmax = -std::numeric_limits<double>::infinity(); |
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243 |
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244 double prevX, prevY; |
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245 geometry_.ProjectPoint(prevX, prevY, points_[points_.size() - 1]); |
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246 |
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247 for (size_t i = 0; i < points_.size(); i++) |
| 131 | 248 { |
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249 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py |
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250 double curX, curY; |
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251 geometry_.ProjectPoint(curX, curY, points_[i]); |
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252 |
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253 if ((prevY < y && curY > y) || |
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254 (prevY > y && curY < y)) |
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255 { |
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256 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY); |
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257 xmin = std::min(xmin, p); |
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258 xmax = std::max(xmax, p); |
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259 isFirst = false; |
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260 } |
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261 |
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262 prevX = curX; |
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263 prevY = curY; |
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264 } |
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265 |
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266 if (isFirst) |
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267 { |
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268 return false; |
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269 } |
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270 else |
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271 { |
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272 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) + |
| 131 | 273 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
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274 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) - |
| 131 | 275 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
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276 |
| 131 | 277 slice.ProjectPoint(x1, y1, p1); |
| 278 slice.ProjectPoint(x2, y2, p2); | |
| 279 return true; | |
| 280 } | |
| 281 } | |
| 282 else if (GeometryToolbox::IsParallelOrOpposite | |
| 283 (isOpposite, slice.GetNormal(), geometry_.GetAxisX())) | |
| 284 { | |
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285 if (x < extent_.GetX1() || |
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286 x > extent_.GetX2()) |
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287 { |
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288 return false; |
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289 } |
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290 |
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291 bool isFirst = true; |
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292 double ymin = std::numeric_limits<double>::infinity(); |
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293 double ymax = -std::numeric_limits<double>::infinity(); |
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294 |
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295 double prevX, prevY; |
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296 geometry_.ProjectPoint(prevX, prevY, points_[points_.size() - 1]); |
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297 |
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298 for (size_t i = 0; i < points_.size(); i++) |
| 131 | 299 { |
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300 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py |
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301 double curX, curY; |
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302 geometry_.ProjectPoint(curX, curY, points_[i]); |
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303 |
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304 if ((prevX < x && curX > x) || |
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305 (prevX > x && curX < x)) |
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306 { |
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307 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX); |
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308 ymin = std::min(ymin, p); |
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309 ymax = std::max(ymax, p); |
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310 isFirst = false; |
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311 } |
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312 |
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313 prevX = curX; |
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314 prevY = curY; |
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315 } |
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316 |
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317 if (isFirst) |
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318 { |
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319 return false; |
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320 } |
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321 else |
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322 { |
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323 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) + |
| 131 | 324 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
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325 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) - |
| 131 | 326 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
| 327 | |
| 328 slice.ProjectPoint(x1, y1, p1); | |
| 329 slice.ProjectPoint(x2, y2, p2); | |
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330 |
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331 // TODO WHY THIS??? |
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332 y1 = -y1; |
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333 y2 = -y2; |
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334 |
| 131 | 335 return true; |
| 336 } | |
| 337 } | |
| 338 else | |
| 339 { | |
| 340 // Should not happen | |
| 341 return false; | |
| 342 } | |
| 343 } | |
| 344 | |
| 345 | |
| 0 | 346 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
| 347 { | |
| 348 if (index >= structures_.size()) | |
| 349 { | |
| 125 | 350 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
| 0 | 351 } |
| 352 | |
| 353 return structures_[index]; | |
| 354 } | |
| 355 | |
| 356 | |
| 125 | 357 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) |
| 0 | 358 { |
| 125 | 359 if (index >= structures_.size()) |
| 360 { | |
| 361 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 0 | 362 } |
| 363 | |
| 364 return structures_[index]; | |
| 365 } | |
| 366 | |
| 367 | |
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368 DicomStructureSet::DicomStructureSet(const OrthancPlugins::FullOrthancDataset& tags) |
| 0 | 369 { |
| 32 | 370 using namespace OrthancPlugins; |
| 0 | 371 |
| 32 | 372 DicomDatasetReader reader(tags); |
| 373 | |
| 374 size_t count, tmp; | |
| 375 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || | |
| 376 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || | |
| 377 tmp != count || | |
| 378 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || | |
| 379 tmp != count) | |
| 0 | 380 { |
| 381 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 382 } | |
| 383 | |
| 32 | 384 structures_.resize(count); |
| 385 for (size_t i = 0; i < count; i++) | |
| 386 { | |
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387 structures_[i].interpretation_ = reader.GetStringValue |
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388 (DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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389 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
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390 "No interpretation"); |
| 0 | 391 |
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392 structures_[i].name_ = reader.GetStringValue |
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393 (DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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394 DICOM_TAG_ROI_NAME), |
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395 "No interpretation"); |
| 0 | 396 |
| 397 Vector color; | |
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398 if (ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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399 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
| 32 | 400 color.size() == 3) |
| 0 | 401 { |
| 32 | 402 structures_[i].red_ = ConvertColor(color[0]); |
| 403 structures_[i].green_ = ConvertColor(color[1]); | |
| 404 structures_[i].blue_ = ConvertColor(color[2]); | |
| 405 } | |
| 406 else | |
| 407 { | |
| 408 structures_[i].red_ = 255; | |
| 409 structures_[i].green_ = 0; | |
| 410 structures_[i].blue_ = 0; | |
| 0 | 411 } |
| 412 | |
| 32 | 413 size_t countSlices; |
| 414 if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, | |
| 415 DICOM_TAG_CONTOUR_SEQUENCE))) | |
| 416 { | |
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417 countSlices = 0; |
| 32 | 418 } |
| 0 | 419 |
| 420 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_ | |
| 421 << "\" with interpretation \"" << structures_[i].interpretation_ | |
| 32 | 422 << "\" containing " << countSlices << " slices (color: " |
| 0 | 423 << static_cast<int>(structures_[i].red_) << "," |
| 424 << static_cast<int>(structures_[i].green_) << "," | |
| 425 << static_cast<int>(structures_[i].blue_) << ")"; | |
| 426 | |
| 32 | 427 for (size_t j = 0; j < countSlices; j++) |
| 0 | 428 { |
| 32 | 429 unsigned int countPoints; |
| 0 | 430 |
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431 if (!reader.GetUnsignedIntegerValue |
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432 (countPoints, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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433 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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434 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS))) |
| 32 | 435 { |
| 436 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 437 } | |
| 438 | |
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439 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
| 0 | 440 |
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441 std::string type = reader.GetMandatoryStringValue |
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442 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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443 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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444 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE)); |
| 32 | 445 if (type != "CLOSED_PLANAR") |
| 0 | 446 { |
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447 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
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448 continue; |
| 0 | 449 } |
| 450 | |
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451 size_t size; |
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452 if (!tags.GetSequenceSize(size, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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453 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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454 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE)) || |
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455 size != 1) |
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456 { |
| 0 | 457 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
| 458 } | |
| 459 | |
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460 std::string sopInstanceUid = reader.GetMandatoryStringValue |
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461 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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462 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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463 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
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464 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID)); |
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465 |
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466 std::string slicesData = reader.GetMandatoryStringValue |
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467 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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468 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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469 DICOM_TAG_CONTOUR_DATA)); |
| 0 | 470 |
| 471 Vector points; | |
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472 if (!LinearAlgebra::ParseVector(points, slicesData) || |
| 32 | 473 points.size() != 3 * countPoints) |
| 0 | 474 { |
| 475 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 476 } | |
| 477 | |
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478 Polygon polygon(sopInstanceUid); |
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479 polygon.Reserve(countPoints); |
| 0 | 480 |
| 32 | 481 for (size_t k = 0; k < countPoints; k++) |
| 0 | 482 { |
| 483 Vector v(3); | |
| 484 v[0] = points[3 * k]; | |
| 485 v[1] = points[3 * k + 1]; | |
| 486 v[2] = points[3 * k + 2]; | |
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487 polygon.AddPoint(v); |
| 0 | 488 } |
| 489 | |
| 490 structures_[i].polygons_.push_back(polygon); | |
| 491 } | |
| 492 } | |
| 493 } | |
| 494 | |
| 495 | |
| 496 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
| 497 { | |
| 498 const Structure& structure = GetStructure(index); | |
| 499 | |
| 500 Vector center; | |
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501 LinearAlgebra::AssignVector(center, 0, 0, 0); |
| 0 | 502 if (structure.polygons_.empty()) |
| 503 { | |
| 504 return center; | |
| 505 } | |
| 506 | |
| 507 double n = static_cast<double>(structure.polygons_.size()); | |
| 508 | |
| 509 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
| 510 polygon != structure.polygons_.end(); ++polygon) | |
| 511 { | |
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512 if (!polygon->GetPoints().empty()) |
| 0 | 513 { |
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514 center += polygon->GetPoints().front() / n; |
| 0 | 515 } |
| 516 } | |
| 517 | |
| 518 return center; | |
| 519 } | |
| 520 | |
| 521 | |
| 522 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
| 523 { | |
| 524 return GetStructure(index).name_; | |
| 525 } | |
| 526 | |
| 527 | |
| 528 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
| 529 { | |
| 530 return GetStructure(index).interpretation_; | |
| 531 } | |
| 532 | |
| 533 | |
| 534 void DicomStructureSet::GetStructureColor(uint8_t& red, | |
| 535 uint8_t& green, | |
| 536 uint8_t& blue, | |
| 537 size_t index) const | |
| 538 { | |
| 539 const Structure& s = GetStructure(index); | |
| 540 red = s.red_; | |
| 541 green = s.green_; | |
| 542 blue = s.blue_; | |
| 543 } | |
| 544 | |
| 545 | |
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546 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) |
| 0 | 547 { |
| 548 for (Structures::const_iterator structure = structures_.begin(); | |
| 549 structure != structures_.end(); ++structure) | |
| 550 { | |
| 551 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
| 552 polygon != structure->polygons_.end(); ++polygon) | |
| 553 { | |
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554 instances.insert(polygon->GetSopInstanceUid()); |
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555 } |
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556 } |
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557 } |
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558 |
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559 |
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560 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
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561 const std::string& seriesInstanceUid, |
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562 const CoordinateSystem3D& geometry, |
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563 double thickness) |
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564 { |
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565 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
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566 { |
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567 // This geometry is already known |
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568 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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569 } |
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570 else |
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571 { |
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572 if (thickness < 0) |
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573 { |
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574 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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575 } |
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576 |
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577 if (!referencedSlices_.empty()) |
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578 { |
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579 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
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580 |
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581 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
| 0 | 582 { |
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583 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
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584 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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585 } |
| 0 | 586 |
|
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587 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
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588 { |
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589 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
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590 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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591 } |
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592 } |
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593 |
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594 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
| 0 | 595 |
| 131 | 596 for (Structures::iterator structure = structures_.begin(); |
| 597 structure != structures_.end(); ++structure) | |
| 598 { | |
| 599 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
| 600 polygon != structure->polygons_.end(); ++polygon) | |
| 601 { | |
| 602 polygon->UpdateReferencedSlice(referencedSlices_); | |
| 603 } | |
| 604 } | |
|
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605 } |
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606 } |
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607 |
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608 |
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609 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
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610 { |
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611 CoordinateSystem3D slice(dataset); |
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612 |
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613 double thickness = 1; // 1 mm by default |
| 0 | 614 |
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615 std::string s; |
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616 Vector v; |
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617 if (dataset.CopyToString(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
|
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618 LinearAlgebra::ParseVector(v, s) && |
|
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619 v.size() > 0) |
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620 { |
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621 thickness = v[0]; |
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622 } |
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623 |
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624 std::string instance, series; |
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625 if (dataset.CopyToString(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) && |
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626 dataset.CopyToString(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
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627 { |
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628 AddReferencedSlice(instance, series, slice, thickness); |
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629 } |
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630 else |
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631 { |
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632 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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633 } |
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634 } |
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635 |
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636 |
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637 void DicomStructureSet::CheckReferencedSlices() |
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638 { |
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639 for (Structures::iterator structure = structures_.begin(); |
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640 structure != structures_.end(); ++structure) |
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641 { |
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642 for (Polygons::iterator polygon = structure->polygons_.begin(); |
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643 polygon != structure->polygons_.end(); ++polygon) |
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644 { |
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645 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
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646 { |
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647 LOG(ERROR) << "Missing information about referenced instance: " |
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648 << polygon->GetSopInstanceUid(); |
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649 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 0 | 650 } |
| 651 } | |
| 652 } | |
|
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653 } |
| 0 | 654 |
|
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655 |
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656 Vector DicomStructureSet::GetNormal() const |
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657 { |
|
126
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658 if (referencedSlices_.empty()) |
|
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659 { |
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660 Vector v; |
|
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661 LinearAlgebra::AssignVector(v, 0, 0, 1); |
|
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662 return v; |
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663 } |
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664 else |
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665 { |
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666 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
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667 } |
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668 } |
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669 |
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670 |
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671 DicomStructureSet* DicomStructureSet::SynchronousLoad(OrthancPlugins::IOrthancConnection& orthanc, |
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672 const std::string& instanceId) |
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673 { |
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674 const std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050"; |
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675 OrthancPlugins::FullOrthancDataset dataset(orthanc, uri); |
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676 |
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677 std::auto_ptr<DicomStructureSet> result(new DicomStructureSet(dataset)); |
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678 |
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679 std::set<std::string> instances; |
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680 result->GetReferencedInstances(instances); |
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681 |
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682 for (std::set<std::string>::const_iterator it = instances.begin(); |
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683 it != instances.end(); ++it) |
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684 { |
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685 Json::Value lookup; |
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686 MessagingToolbox::RestApiPost(lookup, orthanc, "/tools/lookup", *it); |
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687 |
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688 if (lookup.type() != Json::arrayValue || |
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689 lookup.size() != 1 || |
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690 !lookup[0].isMember("Type") || |
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691 !lookup[0].isMember("Path") || |
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692 lookup[0]["Type"].type() != Json::stringValue || |
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693 lookup[0]["ID"].type() != Json::stringValue || |
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694 lookup[0]["Type"].asString() != "Instance") |
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695 { |
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696 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
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697 } |
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698 |
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699 OrthancPlugins::FullOrthancDataset slice |
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700 (orthanc, "/instances/" + lookup[0]["ID"].asString() + "/tags"); |
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701 Orthanc::DicomMap m; |
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702 MessagingToolbox::ConvertDataset(m, slice); |
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703 result->AddReferencedSlice(m); |
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704 } |
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705 |
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706 result->CheckReferencedSlices(); |
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707 |
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708 return result.release(); |
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709 } |
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710 |
| 125 | 711 |
| 712 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<PolygonPoint> >& polygons, | |
| 713 Structure& structure, | |
| 714 const CoordinateSystem3D& slice) | |
| 715 { | |
| 716 polygons.clear(); | |
| 717 | |
| 718 Vector normal = GetNormal(); | |
| 719 | |
| 720 bool isOpposite; | |
| 721 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal())) | |
| 722 { | |
| 723 // This is an axial projection | |
| 724 | |
| 725 for (Polygons::iterator polygon = structure.polygons_.begin(); | |
| 726 polygon != structure.polygons_.end(); ++polygon) | |
| 727 { | |
| 728 if (polygon->IsOnSlice(slice)) | |
| 729 { | |
| 730 polygons.push_back(std::vector<PolygonPoint>()); | |
| 731 | |
| 732 for (Points::const_iterator p = polygon->GetPoints().begin(); | |
| 733 p != polygon->GetPoints().end(); ++p) | |
| 734 { | |
| 735 double x, y; | |
| 736 slice.ProjectPoint(x, y, *p); | |
| 737 polygons.back().push_back(std::make_pair(x, y)); | |
| 738 } | |
| 739 } | |
| 740 } | |
| 741 | |
| 742 return true; | |
| 743 } | |
| 744 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) || | |
| 745 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY())) | |
| 746 { | |
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747 #if 1 |
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748 // Sagittal or coronal projection |
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749 std::vector<BoostPolygon> projected; |
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750 |
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751 for (Polygons::iterator polygon = structure.polygons_.begin(); |
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752 polygon != structure.polygons_.end(); ++polygon) |
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753 { |
| 131 | 754 double x1, y1, x2, y2; |
| 755 if (polygon->Project(x1, y1, x2, y2, slice)) | |
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756 { |
|
516
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757 projected.push_back(CreateRectangle( |
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758 static_cast<float>(x1), |
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759 static_cast<float>(y1), |
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760 static_cast<float>(x2), |
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761 static_cast<float>(y2))); |
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762 } |
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763 } |
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764 |
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765 BoostMultiPolygon merged; |
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766 Union(merged, projected); |
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767 |
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768 polygons.resize(merged.size()); |
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769 for (size_t i = 0; i < merged.size(); i++) |
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770 { |
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771 const std::vector<BoostPoint>& outer = merged[i].outer(); |
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772 |
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773 polygons[i].resize(outer.size()); |
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774 for (size_t j = 0; j < outer.size(); j++) |
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775 { |
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776 polygons[i][j] = std::make_pair(outer[j].x(), outer[j].y()); |
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777 } |
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778 } |
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779 #else |
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780 for (Polygons::iterator polygon = structure.polygons_.begin(); |
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781 polygon != structure.polygons_.end(); ++polygon) |
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782 { |
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783 double x1, y1, x2, y2; |
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784 if (polygon->Project(x1, y1, x2, y2, slice)) |
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785 { |
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786 std::vector<PolygonPoint> p(4); |
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787 p[0] = std::make_pair(x1, y1); |
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788 p[1] = std::make_pair(x2, y1); |
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789 p[2] = std::make_pair(x2, y2); |
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790 p[3] = std::make_pair(x1, y2); |
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791 polygons.push_back(p); |
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792 } |
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793 } |
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794 #endif |
| 125 | 795 |
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796 return true; |
| 125 | 797 } |
| 798 else | |
| 799 { | |
| 800 return false; | |
| 801 } | |
| 0 | 802 } |
| 803 } |