Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet.cpp @ 841:266e2b0b9abc
better error reporting in DicomStructureSetLoader + fixed POST request logic
in WebAssemblyOracle + support for LookupTableTextureSceneLayer in OpenGL (NOT
using shaders!) (2 new files) + a few small non-functional changes
| author | Benjamin Golinvaux <bgo@osimis.io> |
|---|---|
| date | Tue, 11 Jun 2019 15:41:21 +0200 |
| parents | 61ba4b504e9a |
| children | 32eaf4929b08 |
| 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" |
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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> |
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33 #include <boost/geometry.hpp> |
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34 #include <boost/geometry/geometries/point_xy.hpp> |
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35 #include <boost/geometry/geometries/polygon.hpp> |
| 137 | 36 #include <boost/geometry/multi/geometries/multi_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); | |
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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 | |
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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) |
| 0 | 123 { |
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124 std::string value; |
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125 return (dataset.GetStringValue(value, tag) && |
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126 LinearAlgebra::ParseVector(target, value)); |
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127 } |
| 0 | 128 |
| 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 { |
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134 if (!LinearAlgebra::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 { |
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156 return true; |
| 32 | 157 } |
| 158 else | |
| 159 { | |
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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()); | |
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173 sliceThickness_ = it->second.thickness_; |
| 0 | 174 |
| 131 | 175 extent_.Reset(); |
| 176 | |
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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); | |
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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 | |
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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())) |
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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()); |
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204 |
|
158
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205 return (LinearAlgebra::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 { | |
|
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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_ || |
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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 { | |
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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 { |
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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()); |
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272 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) - |
| 131 | 273 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
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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 { | |
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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 { |
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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()); |
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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); | |
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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); |
| 0 | 349 } |
| 350 | |
| 351 return structures_[index]; | |
| 352 } | |
| 353 | |
| 354 | |
| 125 | 355 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) |
| 0 | 356 { |
| 125 | 357 if (index >= structures_.size()) |
| 358 { | |
| 359 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 0 | 360 } |
| 361 | |
| 362 return structures_[index]; | |
| 363 } | |
| 364 | |
| 365 | |
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366 DicomStructureSet::DicomStructureSet(const OrthancPlugins::FullOrthancDataset& tags) |
| 0 | 367 { |
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368 OrthancPlugins::DicomDatasetReader reader(tags); |
| 32 | 369 |
| 370 size_t count, tmp; | |
| 371 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || | |
| 372 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || | |
| 373 tmp != count || | |
| 374 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || | |
| 375 tmp != count) | |
| 0 | 376 { |
| 377 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 378 } | |
| 379 | |
| 32 | 380 structures_.resize(count); |
| 381 for (size_t i = 0; i < count; i++) | |
| 382 { | |
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383 structures_[i].interpretation_ = reader.GetStringValue |
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384 (OrthancPlugins::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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385 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
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386 "No interpretation"); |
| 0 | 387 |
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388 structures_[i].name_ = reader.GetStringValue |
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389 (OrthancPlugins::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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390 DICOM_TAG_ROI_NAME), |
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391 "No interpretation"); |
| 0 | 392 |
| 393 Vector color; | |
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394 if (ParseVector(color, tags, OrthancPlugins::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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395 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
| 32 | 396 color.size() == 3) |
| 0 | 397 { |
| 32 | 398 structures_[i].red_ = ConvertColor(color[0]); |
| 399 structures_[i].green_ = ConvertColor(color[1]); | |
| 400 structures_[i].blue_ = ConvertColor(color[2]); | |
| 401 } | |
| 402 else | |
| 403 { | |
| 404 structures_[i].red_ = 255; | |
| 405 structures_[i].green_ = 0; | |
| 406 structures_[i].blue_ = 0; | |
| 0 | 407 } |
| 408 | |
| 32 | 409 size_t countSlices; |
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410 if (!tags.GetSequenceSize(countSlices, OrthancPlugins::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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411 DICOM_TAG_CONTOUR_SEQUENCE))) |
| 32 | 412 { |
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413 countSlices = 0; |
| 32 | 414 } |
| 0 | 415 |
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416 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ |
| 0 | 417 << "\" with interpretation \"" << structures_[i].interpretation_ |
| 32 | 418 << "\" containing " << countSlices << " slices (color: " |
| 0 | 419 << static_cast<int>(structures_[i].red_) << "," |
| 420 << static_cast<int>(structures_[i].green_) << "," | |
| 421 << static_cast<int>(structures_[i].blue_) << ")"; | |
| 422 | |
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423 // These temporary variables avoid allocating many vectors in the loop below |
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424 OrthancPlugins::DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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425 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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426 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS); |
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427 |
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428 OrthancPlugins::DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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429 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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430 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE); |
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431 |
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432 OrthancPlugins::DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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433 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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434 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); |
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435 |
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436 OrthancPlugins::DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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437 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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438 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
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439 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); |
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440 |
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441 OrthancPlugins::DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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442 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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443 DICOM_TAG_CONTOUR_DATA); |
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444 |
| 32 | 445 for (size_t j = 0; j < countSlices; j++) |
| 0 | 446 { |
| 32 | 447 unsigned int countPoints; |
| 0 | 448 |
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449 countPointsPath.SetPrefixIndex(1, j); |
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450 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) |
| 32 | 451 { |
| 452 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 453 } | |
| 454 | |
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455 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
| 0 | 456 |
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457 geometricTypePath.SetPrefixIndex(1, j); |
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458 std::string type = reader.GetMandatoryStringValue(geometricTypePath); |
| 32 | 459 if (type != "CLOSED_PLANAR") |
| 0 | 460 { |
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461 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
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462 continue; |
| 0 | 463 } |
| 464 | |
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465 size_t size; |
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466 |
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467 imageSequencePath.SetPrefixIndex(1, j); |
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468 if (!tags.GetSequenceSize(size, imageSequencePath) || |
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469 size != 1) |
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470 { |
| 0 | 471 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
| 472 } | |
| 473 | |
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474 referencedInstancePath.SetPrefixIndex(1, j); |
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475 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); |
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476 |
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477 contourDataPath.SetPrefixIndex(1, j); |
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478 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); |
| 0 | 479 |
| 480 Vector points; | |
|
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481 if (!LinearAlgebra::ParseVector(points, slicesData) || |
| 32 | 482 points.size() != 3 * countPoints) |
| 0 | 483 { |
| 484 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 485 } | |
| 486 | |
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487 Polygon polygon(sopInstanceUid); |
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488 polygon.Reserve(countPoints); |
| 0 | 489 |
| 32 | 490 for (size_t k = 0; k < countPoints; k++) |
| 0 | 491 { |
| 492 Vector v(3); | |
| 493 v[0] = points[3 * k]; | |
| 494 v[1] = points[3 * k + 1]; | |
| 495 v[2] = points[3 * k + 2]; | |
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496 polygon.AddPoint(v); |
| 0 | 497 } |
| 498 | |
| 499 structures_[i].polygons_.push_back(polygon); | |
| 500 } | |
| 501 } | |
| 502 } | |
| 503 | |
| 504 | |
| 505 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
| 506 { | |
| 507 const Structure& structure = GetStructure(index); | |
| 508 | |
| 509 Vector center; | |
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510 LinearAlgebra::AssignVector(center, 0, 0, 0); |
| 0 | 511 if (structure.polygons_.empty()) |
| 512 { | |
| 513 return center; | |
| 514 } | |
| 515 | |
| 516 double n = static_cast<double>(structure.polygons_.size()); | |
| 517 | |
| 518 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
| 519 polygon != structure.polygons_.end(); ++polygon) | |
| 520 { | |
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521 if (!polygon->GetPoints().empty()) |
| 0 | 522 { |
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523 center += polygon->GetPoints().front() / n; |
| 0 | 524 } |
| 525 } | |
| 526 | |
| 527 return center; | |
| 528 } | |
| 529 | |
| 530 | |
| 531 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
| 532 { | |
| 533 return GetStructure(index).name_; | |
| 534 } | |
| 535 | |
| 536 | |
| 537 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
| 538 { | |
| 539 return GetStructure(index).interpretation_; | |
| 540 } | |
| 541 | |
| 542 | |
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543 Color DicomStructureSet::GetStructureColor(size_t index) const |
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544 { |
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545 const Structure& s = GetStructure(index); |
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546 return Color(s.red_, s.green_, s.blue_); |
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547 } |
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548 |
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549 |
| 0 | 550 void DicomStructureSet::GetStructureColor(uint8_t& red, |
| 551 uint8_t& green, | |
| 552 uint8_t& blue, | |
| 553 size_t index) const | |
| 554 { | |
| 555 const Structure& s = GetStructure(index); | |
| 556 red = s.red_; | |
| 557 green = s.green_; | |
| 558 blue = s.blue_; | |
| 559 } | |
| 560 | |
| 561 | |
|
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562 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) |
| 0 | 563 { |
| 564 for (Structures::const_iterator structure = structures_.begin(); | |
| 565 structure != structures_.end(); ++structure) | |
| 566 { | |
| 567 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
| 568 polygon != structure->polygons_.end(); ++polygon) | |
| 569 { | |
|
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570 instances.insert(polygon->GetSopInstanceUid()); |
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571 } |
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572 } |
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573 } |
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574 |
|
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575 |
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576 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
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577 const std::string& seriesInstanceUid, |
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578 const CoordinateSystem3D& geometry, |
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579 double thickness) |
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580 { |
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581 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
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582 { |
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583 // This geometry is already known |
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584 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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585 } |
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586 else |
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587 { |
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588 if (thickness < 0) |
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589 { |
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590 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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591 } |
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592 |
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593 if (!referencedSlices_.empty()) |
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594 { |
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595 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
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596 |
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597 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
| 0 | 598 { |
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599 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
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600 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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601 } |
| 0 | 602 |
|
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603 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
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604 { |
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605 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
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606 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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607 } |
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608 } |
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609 |
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610 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
| 0 | 611 |
| 131 | 612 for (Structures::iterator structure = structures_.begin(); |
| 613 structure != structures_.end(); ++structure) | |
| 614 { | |
| 615 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
| 616 polygon != structure->polygons_.end(); ++polygon) | |
| 617 { | |
| 618 polygon->UpdateReferencedSlice(referencedSlices_); | |
| 619 } | |
| 620 } | |
|
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621 } |
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622 } |
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623 |
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624 |
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625 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
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626 { |
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627 CoordinateSystem3D slice(dataset); |
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628 |
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629 double thickness = 1; // 1 mm by default |
| 0 | 630 |
|
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631 std::string s; |
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632 Vector v; |
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633 if (dataset.CopyToString(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
|
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634 LinearAlgebra::ParseVector(v, s) && |
|
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635 v.size() > 0) |
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636 { |
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637 thickness = v[0]; |
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638 } |
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639 |
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640 std::string instance, series; |
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641 if (dataset.CopyToString(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) && |
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642 dataset.CopyToString(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
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643 { |
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644 AddReferencedSlice(instance, series, slice, thickness); |
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645 } |
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646 else |
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647 { |
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648 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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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 void DicomStructureSet::CheckReferencedSlices() |
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654 { |
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655 for (Structures::iterator structure = structures_.begin(); |
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656 structure != structures_.end(); ++structure) |
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657 { |
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658 for (Polygons::iterator polygon = structure->polygons_.begin(); |
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659 polygon != structure->polygons_.end(); ++polygon) |
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660 { |
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661 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
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662 { |
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663 LOG(ERROR) << "Missing information about referenced instance: " |
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664 << polygon->GetSopInstanceUid(); |
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665 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 0 | 666 } |
| 667 } | |
| 668 } | |
|
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669 } |
| 0 | 670 |
|
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671 |
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672 Vector DicomStructureSet::GetNormal() const |
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673 { |
|
126
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674 if (referencedSlices_.empty()) |
|
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675 { |
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676 Vector v; |
|
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677 LinearAlgebra::AssignVector(v, 0, 0, 1); |
|
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678 return v; |
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679 } |
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680 else |
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681 { |
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682 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
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683 } |
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684 } |
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685 |
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686 |
| 125 | 687 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<PolygonPoint> >& polygons, |
| 794 | 688 const Structure& structure, |
| 689 const CoordinateSystem3D& slice) const | |
| 125 | 690 { |
| 691 polygons.clear(); | |
| 692 | |
| 693 Vector normal = GetNormal(); | |
| 694 | |
| 695 bool isOpposite; | |
| 696 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal())) | |
| 697 { | |
| 698 // This is an axial projection | |
| 699 | |
| 794 | 700 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
| 125 | 701 polygon != structure.polygons_.end(); ++polygon) |
| 702 { | |
| 703 if (polygon->IsOnSlice(slice)) | |
| 704 { | |
| 705 polygons.push_back(std::vector<PolygonPoint>()); | |
| 706 | |
| 707 for (Points::const_iterator p = polygon->GetPoints().begin(); | |
| 708 p != polygon->GetPoints().end(); ++p) | |
| 709 { | |
| 710 double x, y; | |
| 711 slice.ProjectPoint(x, y, *p); | |
| 712 polygons.back().push_back(std::make_pair(x, y)); | |
| 713 } | |
| 714 } | |
| 715 } | |
| 716 | |
| 717 return true; | |
| 718 } | |
| 719 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) || | |
| 720 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY())) | |
| 721 { | |
|
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722 #if 1 |
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723 // Sagittal or coronal projection |
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724 std::vector<BoostPolygon> projected; |
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725 |
| 794 | 726 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
|
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727 polygon != structure.polygons_.end(); ++polygon) |
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728 { |
| 131 | 729 double x1, y1, x2, y2; |
| 730 if (polygon->Project(x1, y1, x2, y2, slice)) | |
|
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731 { |
|
516
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732 projected.push_back(CreateRectangle( |
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733 static_cast<float>(x1), |
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734 static_cast<float>(y1), |
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735 static_cast<float>(x2), |
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736 static_cast<float>(y2))); |
|
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737 } |
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738 } |
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739 |
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740 BoostMultiPolygon merged; |
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741 Union(merged, projected); |
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742 |
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743 polygons.resize(merged.size()); |
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744 for (size_t i = 0; i < merged.size(); i++) |
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745 { |
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746 const std::vector<BoostPoint>& outer = merged[i].outer(); |
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747 |
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748 polygons[i].resize(outer.size()); |
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749 for (size_t j = 0; j < outer.size(); j++) |
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750 { |
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751 polygons[i][j] = std::make_pair(outer[j].x(), outer[j].y()); |
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752 } |
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753 } |
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754 #else |
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755 for (Polygons::iterator polygon = structure.polygons_.begin(); |
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756 polygon != structure.polygons_.end(); ++polygon) |
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757 { |
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758 double x1, y1, x2, y2; |
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759 if (polygon->Project(x1, y1, x2, y2, slice)) |
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760 { |
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761 std::vector<PolygonPoint> p(4); |
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762 p[0] = std::make_pair(x1, y1); |
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763 p[1] = std::make_pair(x2, y1); |
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764 p[2] = std::make_pair(x2, y2); |
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765 p[3] = std::make_pair(x1, y2); |
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766 polygons.push_back(p); |
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767 } |
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768 } |
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769 #endif |
| 125 | 770 |
|
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771 return true; |
| 125 | 772 } |
| 773 else | |
| 774 { | |
| 775 return false; | |
| 776 } | |
| 0 | 777 } |
| 778 } |