Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet.cpp @ 959:13e078adfb94 toa2019082301
Better error log in fetch failure callback +
timeout 600sec in OrthancRestApiCommand +
guard against dead controller access in PanSceneTracker +
relaxed DicomStructureSet AddReferenceSlice method to accept extraneous adds
of the same slice (while trying to understand how it happens in the first place)
| author | Benjamin Golinvaux <bgo@osimis.io> |
|---|---|
| date | Fri, 23 Aug 2019 14:16:45 +0200 |
| parents | a7351ad54960 |
| children | c20dbaab360c |
| 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 | |
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365 DicomStructureSet::DicomStructureSet(const OrthancPlugins::FullOrthancDataset& tags) |
| 0 | 366 { |
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367 OrthancPlugins::DicomDatasetReader reader(tags); |
| 32 | 368 |
| 369 size_t count, tmp; | |
| 370 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || | |
| 371 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || | |
| 372 tmp != count || | |
| 373 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || | |
| 374 tmp != count) | |
| 0 | 375 { |
| 376 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 377 } | |
| 378 | |
| 32 | 379 structures_.resize(count); |
| 380 for (size_t i = 0; i < count; i++) | |
| 381 { | |
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382 structures_[i].interpretation_ = reader.GetStringValue |
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383 (OrthancPlugins::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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384 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
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385 "No interpretation"); |
| 0 | 386 |
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387 structures_[i].name_ = reader.GetStringValue |
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388 (OrthancPlugins::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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389 DICOM_TAG_ROI_NAME), |
|
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OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
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390 "No name"); |
| 0 | 391 |
| 392 Vector color; | |
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393 if (ParseVector(color, tags, OrthancPlugins::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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394 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
| 32 | 395 color.size() == 3) |
| 0 | 396 { |
| 32 | 397 structures_[i].red_ = ConvertColor(color[0]); |
| 398 structures_[i].green_ = ConvertColor(color[1]); | |
| 399 structures_[i].blue_ = ConvertColor(color[2]); | |
| 400 } | |
| 401 else | |
| 402 { | |
| 403 structures_[i].red_ = 255; | |
| 404 structures_[i].green_ = 0; | |
| 405 structures_[i].blue_ = 0; | |
| 0 | 406 } |
| 407 | |
| 32 | 408 size_t countSlices; |
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409 if (!tags.GetSequenceSize(countSlices, OrthancPlugins::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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410 DICOM_TAG_CONTOUR_SEQUENCE))) |
| 32 | 411 { |
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412 countSlices = 0; |
| 32 | 413 } |
| 0 | 414 |
|
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415 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ |
| 0 | 416 << "\" with interpretation \"" << structures_[i].interpretation_ |
| 32 | 417 << "\" containing " << countSlices << " slices (color: " |
| 0 | 418 << static_cast<int>(structures_[i].red_) << "," |
| 419 << static_cast<int>(structures_[i].green_) << "," | |
| 420 << static_cast<int>(structures_[i].blue_) << ")"; | |
| 421 | |
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422 // These temporary variables avoid allocating many vectors in the loop below |
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423 OrthancPlugins::DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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424 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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425 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS); |
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426 |
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427 OrthancPlugins::DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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428 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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429 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE); |
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430 |
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431 OrthancPlugins::DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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432 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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433 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); |
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434 |
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435 OrthancPlugins::DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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436 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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437 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
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438 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); |
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439 |
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440 OrthancPlugins::DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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441 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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442 DICOM_TAG_CONTOUR_DATA); |
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443 |
| 32 | 444 for (size_t j = 0; j < countSlices; j++) |
| 0 | 445 { |
| 32 | 446 unsigned int countPoints; |
| 0 | 447 |
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448 countPointsPath.SetPrefixIndex(1, j); |
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449 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) |
| 32 | 450 { |
| 451 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 452 } | |
| 453 | |
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454 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
| 0 | 455 |
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456 geometricTypePath.SetPrefixIndex(1, j); |
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457 std::string type = reader.GetMandatoryStringValue(geometricTypePath); |
| 32 | 458 if (type != "CLOSED_PLANAR") |
| 0 | 459 { |
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460 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
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461 continue; |
| 0 | 462 } |
| 463 | |
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464 size_t size; |
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465 |
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466 imageSequencePath.SetPrefixIndex(1, j); |
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467 if (!tags.GetSequenceSize(size, imageSequencePath) || |
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468 size != 1) |
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469 { |
| 0 | 470 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
| 471 } | |
| 472 | |
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473 referencedInstancePath.SetPrefixIndex(1, j); |
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474 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); |
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475 |
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476 contourDataPath.SetPrefixIndex(1, j); |
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477 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); |
| 0 | 478 |
| 479 Vector points; | |
|
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480 if (!LinearAlgebra::ParseVector(points, slicesData) || |
| 32 | 481 points.size() != 3 * countPoints) |
| 0 | 482 { |
| 483 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 484 } | |
| 485 | |
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486 Polygon polygon(sopInstanceUid); |
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487 polygon.Reserve(countPoints); |
| 0 | 488 |
| 32 | 489 for (size_t k = 0; k < countPoints; k++) |
| 0 | 490 { |
| 491 Vector v(3); | |
| 492 v[0] = points[3 * k]; | |
| 493 v[1] = points[3 * k + 1]; | |
| 494 v[2] = points[3 * k + 2]; | |
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495 polygon.AddPoint(v); |
| 0 | 496 } |
| 497 | |
| 498 structures_[i].polygons_.push_back(polygon); | |
| 499 } | |
| 500 } | |
| 501 } | |
| 502 | |
| 503 | |
| 504 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
| 505 { | |
| 506 const Structure& structure = GetStructure(index); | |
| 507 | |
| 508 Vector center; | |
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509 LinearAlgebra::AssignVector(center, 0, 0, 0); |
| 0 | 510 if (structure.polygons_.empty()) |
| 511 { | |
| 512 return center; | |
| 513 } | |
| 514 | |
| 515 double n = static_cast<double>(structure.polygons_.size()); | |
| 516 | |
| 517 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
| 518 polygon != structure.polygons_.end(); ++polygon) | |
| 519 { | |
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520 if (!polygon->GetPoints().empty()) |
| 0 | 521 { |
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522 center += polygon->GetPoints().front() / n; |
| 0 | 523 } |
| 524 } | |
| 525 | |
| 526 return center; | |
| 527 } | |
| 528 | |
| 529 | |
| 530 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
| 531 { | |
| 532 return GetStructure(index).name_; | |
| 533 } | |
| 534 | |
| 535 | |
| 536 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
| 537 { | |
| 538 return GetStructure(index).interpretation_; | |
| 539 } | |
| 540 | |
| 541 | |
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542 Color DicomStructureSet::GetStructureColor(size_t index) const |
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543 { |
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544 const Structure& s = GetStructure(index); |
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545 return Color(s.red_, s.green_, s.blue_); |
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546 } |
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547 |
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548 |
| 0 | 549 void DicomStructureSet::GetStructureColor(uint8_t& red, |
| 550 uint8_t& green, | |
| 551 uint8_t& blue, | |
| 552 size_t index) const | |
| 553 { | |
| 554 const Structure& s = GetStructure(index); | |
| 555 red = s.red_; | |
| 556 green = s.green_; | |
| 557 blue = s.blue_; | |
| 558 } | |
| 559 | |
| 560 | |
|
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561 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) |
| 0 | 562 { |
| 563 for (Structures::const_iterator structure = structures_.begin(); | |
| 564 structure != structures_.end(); ++structure) | |
| 565 { | |
| 566 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
| 567 polygon != structure->polygons_.end(); ++polygon) | |
| 568 { | |
|
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569 instances.insert(polygon->GetSopInstanceUid()); |
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570 } |
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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 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
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576 const std::string& seriesInstanceUid, |
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577 const CoordinateSystem3D& geometry, |
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578 double thickness) |
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579 { |
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580 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
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581 { |
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582 // This geometry is already known |
|
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583 LOG(ERROR) << "DicomStructureSet::AddReferencedSlice(): (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()). sopInstanceUid = " << sopInstanceUid; |
|
959
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584 |
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585 // TODO: the following assertion has been disabled on 20190822 by BGO |
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586 // because it occurred from time to time. Since it wrecked havoc on the |
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587 |
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588 //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
|
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589 } |
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590 else |
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591 { |
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592 if (thickness < 0) |
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593 { |
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594 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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595 } |
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596 |
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597 if (!referencedSlices_.empty()) |
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598 { |
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599 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
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600 |
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601 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
| 0 | 602 { |
|
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603 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
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604 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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605 } |
| 0 | 606 |
|
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607 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
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608 { |
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609 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
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610 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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611 } |
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612 } |
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613 |
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614 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
| 0 | 615 |
| 131 | 616 for (Structures::iterator structure = structures_.begin(); |
| 617 structure != structures_.end(); ++structure) | |
| 618 { | |
| 619 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
| 620 polygon != structure->polygons_.end(); ++polygon) | |
| 621 { | |
| 622 polygon->UpdateReferencedSlice(referencedSlices_); | |
| 623 } | |
| 624 } | |
|
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625 } |
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626 } |
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627 |
|
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628 |
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629 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
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630 { |
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631 CoordinateSystem3D slice(dataset); |
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632 |
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633 double thickness = 1; // 1 mm by default |
| 0 | 634 |
|
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635 std::string s; |
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636 Vector v; |
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637 if (dataset.CopyToString(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
|
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638 LinearAlgebra::ParseVector(v, s) && |
|
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639 v.size() > 0) |
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640 { |
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641 thickness = v[0]; |
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642 } |
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643 |
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644 std::string instance, series; |
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645 if (dataset.CopyToString(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) && |
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646 dataset.CopyToString(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
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647 { |
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648 AddReferencedSlice(instance, series, slice, thickness); |
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649 } |
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650 else |
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651 { |
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652 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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653 } |
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654 } |
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655 |
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656 |
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657 void DicomStructureSet::CheckReferencedSlices() |
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658 { |
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659 for (Structures::iterator structure = structures_.begin(); |
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660 structure != structures_.end(); ++structure) |
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661 { |
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662 for (Polygons::iterator polygon = structure->polygons_.begin(); |
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663 polygon != structure->polygons_.end(); ++polygon) |
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664 { |
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665 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
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666 { |
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667 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): missing information about referenced instance: " |
|
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668 << polygon->GetSopInstanceUid(); |
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669 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 0 | 670 } |
| 671 } | |
| 672 } | |
|
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673 } |
| 0 | 674 |
|
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675 |
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676 Vector DicomStructureSet::GetNormal() const |
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677 { |
|
126
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678 if (referencedSlices_.empty()) |
|
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679 { |
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680 Vector v; |
|
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681 LinearAlgebra::AssignVector(v, 0, 0, 1); |
|
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682 return v; |
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683 } |
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684 else |
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685 { |
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686 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
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687 } |
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688 } |
|
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689 |
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690 |
| 125 | 691 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<PolygonPoint> >& polygons, |
| 794 | 692 const Structure& structure, |
| 693 const CoordinateSystem3D& slice) const | |
| 125 | 694 { |
| 695 polygons.clear(); | |
| 696 | |
| 697 Vector normal = GetNormal(); | |
| 698 | |
| 699 bool isOpposite; | |
| 700 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal())) | |
| 701 { | |
| 702 // This is an axial projection | |
| 703 | |
| 794 | 704 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
| 125 | 705 polygon != structure.polygons_.end(); ++polygon) |
| 706 { | |
| 707 if (polygon->IsOnSlice(slice)) | |
| 708 { | |
| 709 polygons.push_back(std::vector<PolygonPoint>()); | |
| 710 | |
| 711 for (Points::const_iterator p = polygon->GetPoints().begin(); | |
| 712 p != polygon->GetPoints().end(); ++p) | |
| 713 { | |
| 714 double x, y; | |
| 715 slice.ProjectPoint(x, y, *p); | |
| 716 polygons.back().push_back(std::make_pair(x, y)); | |
| 717 } | |
| 718 } | |
| 719 } | |
| 720 | |
| 721 return true; | |
| 722 } | |
| 723 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) || | |
| 724 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY())) | |
| 725 { | |
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726 #if 1 |
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727 // Sagittal or coronal projection |
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728 std::vector<BoostPolygon> projected; |
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729 |
| 794 | 730 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
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731 polygon != structure.polygons_.end(); ++polygon) |
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732 { |
| 131 | 733 double x1, y1, x2, y2; |
| 734 if (polygon->Project(x1, y1, x2, y2, slice)) | |
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735 { |
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516
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736 projected.push_back(CreateRectangle( |
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737 static_cast<float>(x1), |
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738 static_cast<float>(y1), |
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739 static_cast<float>(x2), |
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740 static_cast<float>(y2))); |
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741 } |
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742 } |
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743 |
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744 BoostMultiPolygon merged; |
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745 Union(merged, projected); |
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746 |
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747 polygons.resize(merged.size()); |
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748 for (size_t i = 0; i < merged.size(); i++) |
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749 { |
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750 const std::vector<BoostPoint>& outer = merged[i].outer(); |
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751 |
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752 polygons[i].resize(outer.size()); |
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753 for (size_t j = 0; j < outer.size(); j++) |
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754 { |
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755 polygons[i][j] = std::make_pair(outer[j].x(), outer[j].y()); |
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756 } |
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757 } |
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758 #else |
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759 for (Polygons::iterator polygon = structure.polygons_.begin(); |
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760 polygon != structure.polygons_.end(); ++polygon) |
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761 { |
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762 double x1, y1, x2, y2; |
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763 if (polygon->Project(x1, y1, x2, y2, slice)) |
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764 { |
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765 std::vector<PolygonPoint> p(4); |
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766 p[0] = std::make_pair(x1, y1); |
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767 p[1] = std::make_pair(x2, y1); |
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768 p[2] = std::make_pair(x2, y2); |
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769 p[3] = std::make_pair(x1, y2); |
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770 polygons.push_back(p); |
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771 } |
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772 } |
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773 #endif |
| 125 | 774 |
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775 return true; |
| 125 | 776 } |
| 777 else | |
| 778 { | |
| 779 return false; | |
| 780 } | |
| 0 | 781 } |
| 782 } |