Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet.cpp @ 135:e2fe9352f240 wasm
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 02 Jan 2018 09:56:08 +0100 |
parents | 35c2b85836ce |
children | a30ff4866a1e |
rev | line source |
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0 | 1 /** |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
135
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5 * Copyright (C) 2017-2018 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 | |
35 | 24 #include "../Toolbox/MessagingToolbox.h" |
0 | 25 |
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26 #include <Core/Logging.h> |
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27 #include <Core/OrthancException.h> |
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28 #include <Plugins/Samples/Common/FullOrthancDataset.h> |
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29 #include <Plugins/Samples/Common/DicomDatasetReader.h> |
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30 |
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31 #include <limits> |
0 | 32 #include <stdio.h> |
33 #include <boost/lexical_cast.hpp> | |
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34 #include <boost/geometry.hpp> |
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35 #include <boost/geometry/geometries/point_xy.hpp> |
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36 #include <boost/geometry/geometries/polygon.hpp> |
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37 |
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38 typedef boost::geometry::model::d2::point_xy<double> BoostPoint; |
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39 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon; |
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40 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon; |
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41 |
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42 |
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43 static void Union(BoostMultiPolygon& output, |
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44 std::vector<BoostPolygon>& input) |
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45 { |
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46 for (size_t i = 0; i < input.size(); i++) |
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47 { |
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48 boost::geometry::correct(input[i]); |
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49 } |
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50 |
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51 if (input.size() == 0) |
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52 { |
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53 output.clear(); |
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54 } |
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55 else if (input.size() == 1) |
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56 { |
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57 output.resize(1); |
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58 output[0] = input[0]; |
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59 } |
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60 else |
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61 { |
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62 boost::geometry::union_(input[0], input[1], output); |
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63 |
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64 for (size_t i = 0; i < input.size(); i++) |
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65 { |
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66 BoostMultiPolygon tmp; |
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67 boost::geometry::union_(output, input[i], tmp); |
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68 output = tmp; |
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69 } |
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70 } |
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71 } |
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72 |
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73 |
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74 static BoostPolygon CreateRectangle(float x1, float y1, |
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75 float x2, float y2) |
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76 { |
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77 BoostPolygon r; |
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78 boost::geometry::append(r, BoostPoint(x1, y1)); |
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79 boost::geometry::append(r, BoostPoint(x1, y2)); |
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80 boost::geometry::append(r, BoostPoint(x2, y2)); |
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81 boost::geometry::append(r, BoostPoint(x2, y1)); |
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82 return r; |
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83 } |
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84 |
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85 |
0 | 86 |
87 namespace OrthancStone | |
88 { | |
32 | 89 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
90 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
91 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
122
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92 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050); |
32 | 93 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); |
94 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
95 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
96 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
97 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
98 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
99 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
100 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
0 | 101 |
102 | |
103 static uint8_t ConvertColor(double v) | |
104 { | |
105 if (v < 0) | |
106 { | |
107 return 0; | |
108 } | |
109 else if (v >= 255) | |
110 { | |
111 return 255; | |
112 } | |
113 else | |
114 { | |
115 return static_cast<uint8_t>(v); | |
116 } | |
117 } | |
118 | |
119 | |
118
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120 static bool ParseVector(Vector& target, |
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121 const OrthancPlugins::IDicomDataset& dataset, |
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122 const OrthancPlugins::DicomPath& tag) |
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123 { |
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124 std::string value; |
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125 return (dataset.GetStringValue(value, tag) && |
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126 GeometryToolbox::ParseVector(target, value)); |
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127 } |
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128 |
0 | 129 |
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130 void DicomStructureSet::Polygon::CheckPoint(const Vector& v) |
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131 { |
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132 if (hasSlice_) |
0 | 133 { |
131 | 134 if (!GeometryToolbox::IsNear(GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()), |
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135 projectionAlongNormal_, |
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136 sliceThickness_ / 2.0 /* in mm */)) |
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137 { |
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138 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance"; |
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139 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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140 } |
0 | 141 } |
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142 } |
0 | 143 |
144 | |
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145 void DicomStructureSet::Polygon::AddPoint(const Vector& v) |
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146 { |
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147 CheckPoint(v); |
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148 points_.push_back(v); |
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149 } |
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150 |
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151 |
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152 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices) |
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153 { |
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154 if (hasSlice_) |
0 | 155 { |
122
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156 return true; |
32 | 157 } |
158 else | |
159 { | |
122
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160 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_); |
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161 |
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162 if (it == slices.end()) |
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163 { |
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164 return false; |
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165 } |
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166 else |
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167 { |
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168 const CoordinateSystem3D& geometry = it->second.geometry_; |
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169 |
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170 hasSlice_ = true; |
131 | 171 geometry_ = geometry; |
172 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal()); | |
122
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173 sliceThickness_ = it->second.thickness_; |
0 | 174 |
131 | 175 extent_.Reset(); |
176 | |
122
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177 for (Points::const_iterator it = points_.begin(); it != points_.end(); ++it) |
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178 { |
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179 CheckPoint(*it); |
131 | 180 |
181 double x, y; | |
182 geometry.ProjectPoint(x, y, *it); | |
183 extent_.AddPoint(x, y); | |
122
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184 } |
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185 |
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186 return true; |
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187 } |
0 | 188 } |
189 } | |
190 | |
191 | |
122
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192 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const |
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193 { |
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194 bool isOpposite; |
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195 |
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196 if (points_.empty() || |
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197 !hasSlice_ || |
131 | 198 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal())) |
122
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199 { |
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200 return false; |
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201 } |
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202 |
131 | 203 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal()); |
122
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204 |
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205 return (GeometryToolbox::IsNear(d, projectionAlongNormal_, |
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206 sliceThickness_ / 2.0)); |
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207 } |
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208 |
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209 |
131 | 210 bool DicomStructureSet::Polygon::Project(double& x1, |
211 double& y1, | |
212 double& x2, | |
213 double& y2, | |
214 const CoordinateSystem3D& slice) const | |
215 { | |
132
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216 // TODO Optimize this method using a sweep-line algorithm for polygons |
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217 |
131 | 218 if (!hasSlice_ || |
132
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219 points_.size() <= 1) |
131 | 220 { |
221 return false; | |
222 } | |
223 | |
224 double x, y; | |
225 geometry_.ProjectPoint(x, y, slice.GetOrigin()); | |
226 | |
227 bool isOpposite; | |
228 if (GeometryToolbox::IsParallelOrOpposite | |
229 (isOpposite, slice.GetNormal(), geometry_.GetAxisY())) | |
230 { | |
132
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231 if (y < extent_.GetY1() || |
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232 y > extent_.GetY2()) |
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233 { |
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234 // The polygon does not intersect the input slice |
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235 return false; |
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236 } |
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237 |
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238 bool isFirst = true; |
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239 double xmin = std::numeric_limits<double>::infinity(); |
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240 double xmax = -std::numeric_limits<double>::infinity(); |
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241 |
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242 double prevX, prevY; |
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243 geometry_.ProjectPoint(prevX, prevY, points_[points_.size() - 1]); |
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244 |
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245 for (size_t i = 0; i < points_.size(); i++) |
131 | 246 { |
132
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247 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py |
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248 double curX, curY; |
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249 geometry_.ProjectPoint(curX, curY, points_[i]); |
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250 |
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251 if ((prevY < y && curY > y) || |
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252 (prevY > y && curY < y)) |
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253 { |
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254 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY); |
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255 xmin = std::min(xmin, p); |
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256 xmax = std::max(xmax, p); |
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257 isFirst = false; |
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258 } |
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259 |
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260 prevX = curX; |
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261 prevY = curY; |
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262 } |
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263 |
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264 if (isFirst) |
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265 { |
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266 return false; |
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267 } |
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268 else |
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269 { |
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270 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) + |
131 | 271 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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272 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) - |
131 | 273 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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274 |
131 | 275 slice.ProjectPoint(x1, y1, p1); |
276 slice.ProjectPoint(x2, y2, p2); | |
277 return true; | |
278 } | |
279 } | |
280 else if (GeometryToolbox::IsParallelOrOpposite | |
281 (isOpposite, slice.GetNormal(), geometry_.GetAxisX())) | |
282 { | |
132
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283 if (x < extent_.GetX1() || |
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284 x > extent_.GetX2()) |
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285 { |
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286 return false; |
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287 } |
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288 |
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289 bool isFirst = true; |
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290 double ymin = std::numeric_limits<double>::infinity(); |
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291 double ymax = -std::numeric_limits<double>::infinity(); |
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292 |
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293 double prevX, prevY; |
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294 geometry_.ProjectPoint(prevX, prevY, points_[points_.size() - 1]); |
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295 |
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296 for (size_t i = 0; i < points_.size(); i++) |
131 | 297 { |
132
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298 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py |
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299 double curX, curY; |
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300 geometry_.ProjectPoint(curX, curY, points_[i]); |
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301 |
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302 if ((prevX < x && curX > x) || |
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303 (prevX > x && curX < x)) |
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304 { |
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305 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX); |
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306 ymin = std::min(ymin, p); |
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307 ymax = std::max(ymax, p); |
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308 isFirst = false; |
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309 } |
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310 |
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311 prevX = curX; |
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312 prevY = curY; |
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313 } |
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314 |
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315 if (isFirst) |
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316 { |
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317 return false; |
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318 } |
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319 else |
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320 { |
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321 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) + |
131 | 322 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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323 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) - |
131 | 324 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
325 | |
326 slice.ProjectPoint(x1, y1, p1); | |
327 slice.ProjectPoint(x2, y2, p2); | |
132
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328 |
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329 // TODO WHY THIS??? |
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330 y1 = -y1; |
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331 y2 = -y2; |
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332 |
131 | 333 return true; |
334 } | |
335 } | |
336 else | |
337 { | |
338 // Should not happen | |
339 return false; | |
340 } | |
341 } | |
342 | |
343 | |
0 | 344 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
345 { | |
346 if (index >= structures_.size()) | |
347 { | |
125 | 348 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
349 } | |
350 | |
351 return structures_[index]; | |
352 } | |
353 | |
354 | |
355 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) | |
356 { | |
357 if (index >= structures_.size()) | |
358 { | |
359 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
0 | 360 } |
361 | |
362 return structures_[index]; | |
363 } | |
364 | |
365 | |
122
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366 DicomStructureSet::DicomStructureSet(const OrthancPlugins::FullOrthancDataset& tags) |
0 | 367 { |
32 | 368 using namespace OrthancPlugins; |
0 | 369 |
32 | 370 DicomDatasetReader reader(tags); |
371 | |
372 size_t count, tmp; | |
373 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || | |
374 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || | |
375 tmp != count || | |
376 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || | |
377 tmp != count) | |
0 | 378 { |
379 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
380 } | |
381 | |
32 | 382 structures_.resize(count); |
383 for (size_t i = 0; i < count; i++) | |
384 { | |
122
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385 structures_[i].interpretation_ = reader.GetStringValue |
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386 (DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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387 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
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388 "No interpretation"); |
0 | 389 |
122
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390 structures_[i].name_ = reader.GetStringValue |
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391 (DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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392 DICOM_TAG_ROI_NAME), |
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393 "No interpretation"); |
0 | 394 |
395 Vector color; | |
118
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396 if (ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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397 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
32 | 398 color.size() == 3) |
0 | 399 { |
32 | 400 structures_[i].red_ = ConvertColor(color[0]); |
401 structures_[i].green_ = ConvertColor(color[1]); | |
402 structures_[i].blue_ = ConvertColor(color[2]); | |
403 } | |
404 else | |
405 { | |
406 structures_[i].red_ = 255; | |
407 structures_[i].green_ = 0; | |
408 structures_[i].blue_ = 0; | |
0 | 409 } |
410 | |
32 | 411 size_t countSlices; |
412 if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, | |
413 DICOM_TAG_CONTOUR_SEQUENCE))) | |
414 { | |
121
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415 countSlices = 0; |
32 | 416 } |
0 | 417 |
418 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_ | |
419 << "\" with interpretation \"" << structures_[i].interpretation_ | |
32 | 420 << "\" containing " << countSlices << " slices (color: " |
0 | 421 << static_cast<int>(structures_[i].red_) << "," |
422 << static_cast<int>(structures_[i].green_) << "," | |
423 << static_cast<int>(structures_[i].blue_) << ")"; | |
424 | |
32 | 425 for (size_t j = 0; j < countSlices; j++) |
0 | 426 { |
32 | 427 unsigned int countPoints; |
0 | 428 |
122
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429 if (!reader.GetUnsignedIntegerValue |
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430 (countPoints, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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431 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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432 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS))) |
32 | 433 { |
434 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
435 } | |
436 | |
121
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437 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
0 | 438 |
122
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439 std::string type = reader.GetMandatoryStringValue |
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440 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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441 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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442 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE)); |
32 | 443 if (type != "CLOSED_PLANAR") |
0 | 444 { |
32 | 445 LOG(ERROR) << "Cannot handle contour with geometry type: " << type; |
0 | 446 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
447 } | |
448 | |
122
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449 size_t size; |
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450 if (!tags.GetSequenceSize(size, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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451 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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452 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE)) || |
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453 size != 1) |
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454 { |
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455 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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456 } |
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457 |
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458 std::string sopInstanceUid = reader.GetMandatoryStringValue |
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459 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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460 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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461 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
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462 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID)); |
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463 |
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464 std::string slicesData = reader.GetMandatoryStringValue |
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465 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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466 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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467 DICOM_TAG_CONTOUR_DATA)); |
0 | 468 |
469 Vector points; | |
470 if (!GeometryToolbox::ParseVector(points, slicesData) || | |
32 | 471 points.size() != 3 * countPoints) |
0 | 472 { |
473 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
474 } | |
475 | |
122
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476 Polygon polygon(sopInstanceUid); |
132
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477 polygon.Reserve(countPoints); |
0 | 478 |
32 | 479 for (size_t k = 0; k < countPoints; k++) |
0 | 480 { |
481 Vector v(3); | |
482 v[0] = points[3 * k]; | |
483 v[1] = points[3 * k + 1]; | |
484 v[2] = points[3 * k + 2]; | |
122
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485 polygon.AddPoint(v); |
0 | 486 } |
487 | |
488 structures_[i].polygons_.push_back(polygon); | |
489 } | |
490 } | |
491 } | |
492 | |
493 | |
494 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
495 { | |
496 const Structure& structure = GetStructure(index); | |
497 | |
498 Vector center; | |
499 GeometryToolbox::AssignVector(center, 0, 0, 0); | |
500 if (structure.polygons_.empty()) | |
501 { | |
502 return center; | |
503 } | |
504 | |
505 double n = static_cast<double>(structure.polygons_.size()); | |
506 | |
507 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
508 polygon != structure.polygons_.end(); ++polygon) | |
509 { | |
122
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510 if (!polygon->GetPoints().empty()) |
0 | 511 { |
122
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512 center += polygon->GetPoints().front() / n; |
0 | 513 } |
514 } | |
515 | |
516 return center; | |
517 } | |
518 | |
519 | |
520 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
521 { | |
522 return GetStructure(index).name_; | |
523 } | |
524 | |
525 | |
526 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
527 { | |
528 return GetStructure(index).interpretation_; | |
529 } | |
530 | |
531 | |
532 void DicomStructureSet::GetStructureColor(uint8_t& red, | |
533 uint8_t& green, | |
534 uint8_t& blue, | |
535 size_t index) const | |
536 { | |
537 const Structure& s = GetStructure(index); | |
538 red = s.red_; | |
539 green = s.green_; | |
540 blue = s.blue_; | |
541 } | |
542 | |
543 | |
122
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544 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) |
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545 { |
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546 for (Structures::const_iterator structure = structures_.begin(); |
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547 structure != structures_.end(); ++structure) |
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548 { |
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549 for (Polygons::const_iterator polygon = structure->polygons_.begin(); |
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550 polygon != structure->polygons_.end(); ++polygon) |
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551 { |
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552 instances.insert(polygon->GetSopInstanceUid()); |
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553 } |
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554 } |
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555 } |
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556 |
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557 |
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558 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
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559 const std::string& seriesInstanceUid, |
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560 const CoordinateSystem3D& geometry, |
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561 double thickness) |
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562 { |
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563 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
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564 { |
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565 // This geometry is already known |
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566 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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567 } |
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568 else |
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569 { |
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570 if (thickness < 0) |
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571 { |
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572 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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573 } |
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574 |
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575 if (!referencedSlices_.empty()) |
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576 { |
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577 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
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578 |
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579 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
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580 { |
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581 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
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582 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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583 } |
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584 |
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585 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
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586 { |
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587 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
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588 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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589 } |
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590 } |
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591 |
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592 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
131 | 593 |
594 for (Structures::iterator structure = structures_.begin(); | |
595 structure != structures_.end(); ++structure) | |
596 { | |
597 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
598 polygon != structure->polygons_.end(); ++polygon) | |
599 { | |
600 polygon->UpdateReferencedSlice(referencedSlices_); | |
601 } | |
602 } | |
122
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603 } |
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604 } |
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605 |
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606 |
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607 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
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608 { |
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609 CoordinateSystem3D slice(dataset); |
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610 |
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611 double thickness = 1; // 1 mm by default |
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612 |
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613 std::string s; |
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614 Vector v; |
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615 if (dataset.CopyToString(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
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616 GeometryToolbox::ParseVector(v, s) && |
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617 v.size() > 0) |
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618 { |
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619 thickness = v[0]; |
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620 } |
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621 |
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622 std::string instance, series; |
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623 if (dataset.CopyToString(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) && |
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624 dataset.CopyToString(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
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625 { |
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626 AddReferencedSlice(instance, series, slice, thickness); |
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627 } |
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628 else |
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629 { |
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630 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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631 } |
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632 } |
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633 |
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634 |
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635 void DicomStructureSet::CheckReferencedSlices() |
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636 { |
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637 for (Structures::iterator structure = structures_.begin(); |
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638 structure != structures_.end(); ++structure) |
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639 { |
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640 for (Polygons::iterator polygon = structure->polygons_.begin(); |
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641 polygon != structure->polygons_.end(); ++polygon) |
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642 { |
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643 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
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644 { |
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645 LOG(ERROR) << "Missing information about referenced instance: " |
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646 << polygon->GetSopInstanceUid(); |
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647 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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648 } |
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649 } |
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650 } |
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651 } |
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652 |
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653 |
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654 Vector DicomStructureSet::GetNormal() const |
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655 { |
126
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656 if (referencedSlices_.empty()) |
122
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657 { |
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658 Vector v; |
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659 GeometryToolbox::AssignVector(v, 0, 0, 1); |
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660 return v; |
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661 } |
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662 else |
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663 { |
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664 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
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665 } |
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666 } |
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667 |
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668 |
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669 DicomStructureSet* DicomStructureSet::SynchronousLoad(OrthancPlugins::IOrthancConnection& orthanc, |
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670 const std::string& instanceId) |
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671 { |
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672 const std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050"; |
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673 OrthancPlugins::FullOrthancDataset dataset(orthanc, uri); |
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674 |
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675 std::auto_ptr<DicomStructureSet> result(new DicomStructureSet(dataset)); |
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676 |
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677 std::set<std::string> instances; |
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678 result->GetReferencedInstances(instances); |
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679 |
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680 for (std::set<std::string>::const_iterator it = instances.begin(); |
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681 it != instances.end(); ++it) |
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682 { |
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683 Json::Value lookup; |
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684 MessagingToolbox::RestApiPost(lookup, orthanc, "/tools/lookup", *it); |
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685 |
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686 if (lookup.type() != Json::arrayValue || |
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687 lookup.size() != 1 || |
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688 !lookup[0].isMember("Type") || |
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689 !lookup[0].isMember("Path") || |
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690 lookup[0]["Type"].type() != Json::stringValue || |
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691 lookup[0]["ID"].type() != Json::stringValue || |
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692 lookup[0]["Type"].asString() != "Instance") |
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693 { |
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694 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
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695 } |
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696 |
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697 OrthancPlugins::FullOrthancDataset slice |
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698 (orthanc, "/instances/" + lookup[0]["ID"].asString() + "/tags"); |
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699 Orthanc::DicomMap m; |
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700 MessagingToolbox::ConvertDataset(m, slice); |
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701 result->AddReferencedSlice(m); |
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702 } |
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703 |
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704 result->CheckReferencedSlices(); |
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705 |
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706 return result.release(); |
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707 } |
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708 |
125 | 709 |
710 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<PolygonPoint> >& polygons, | |
711 Structure& structure, | |
712 const CoordinateSystem3D& slice) | |
713 { | |
714 polygons.clear(); | |
715 | |
716 Vector normal = GetNormal(); | |
717 | |
718 bool isOpposite; | |
719 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal())) | |
720 { | |
721 // This is an axial projection | |
722 | |
723 for (Polygons::iterator polygon = structure.polygons_.begin(); | |
724 polygon != structure.polygons_.end(); ++polygon) | |
725 { | |
726 if (polygon->IsOnSlice(slice)) | |
727 { | |
728 polygons.push_back(std::vector<PolygonPoint>()); | |
729 | |
730 for (Points::const_iterator p = polygon->GetPoints().begin(); | |
731 p != polygon->GetPoints().end(); ++p) | |
732 { | |
733 double x, y; | |
734 slice.ProjectPoint(x, y, *p); | |
735 polygons.back().push_back(std::make_pair(x, y)); | |
736 } | |
737 } | |
738 } | |
739 | |
740 return true; | |
741 } | |
742 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) || | |
743 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY())) | |
744 { | |
132
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745 #if 1 |
126
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746 // Sagittal or coronal projection |
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747 std::vector<BoostPolygon> projected; |
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748 |
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749 for (Polygons::iterator polygon = structure.polygons_.begin(); |
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750 polygon != structure.polygons_.end(); ++polygon) |
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751 { |
131 | 752 double x1, y1, x2, y2; |
753 if (polygon->Project(x1, y1, x2, y2, slice)) | |
126
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754 { |
131 | 755 projected.push_back(CreateRectangle(x1, y1, x2, y2)); |
126
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756 } |
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757 } |
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758 |
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759 BoostMultiPolygon merged; |
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760 Union(merged, projected); |
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761 |
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762 polygons.resize(merged.size()); |
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763 for (size_t i = 0; i < merged.size(); i++) |
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764 { |
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765 const std::vector<BoostPoint>& outer = merged[i].outer(); |
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766 |
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767 polygons[i].resize(outer.size()); |
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768 for (size_t j = 0; j < outer.size(); j++) |
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769 { |
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770 polygons[i][j] = std::make_pair(outer[j].x(), outer[j].y()); |
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771 } |
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772 } |
132
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773 #else |
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774 for (Polygons::iterator polygon = structure.polygons_.begin(); |
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775 polygon != structure.polygons_.end(); ++polygon) |
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776 { |
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777 double x1, y1, x2, y2; |
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778 if (polygon->Project(x1, y1, x2, y2, slice)) |
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779 { |
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780 std::vector<PolygonPoint> p(4); |
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781 p[0] = std::make_pair(x1, y1); |
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782 p[1] = std::make_pair(x2, y1); |
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783 p[2] = std::make_pair(x2, y2); |
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784 p[3] = std::make_pair(x1, y2); |
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785 polygons.push_back(p); |
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786 } |
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787 } |
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788 #endif |
125 | 789 |
126
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790 return true; |
125 | 791 } |
792 else | |
793 { | |
794 return false; | |
795 } | |
796 } | |
0 | 797 } |