Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet.cpp @ 981:c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
| author | Benjamin Golinvaux <bgo@osimis.io> |
|---|---|
| date | Fri, 06 Sep 2019 09:38:18 +0200 |
| parents | 13e078adfb94 |
| children | 4c9b4c4de814 |
| 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 <Core/Toolbox.h> |
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29 #include <Plugins/Samples/Common/FullOrthancDataset.h> |
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30 #include <Plugins/Samples/Common/DicomDatasetReader.h> |
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31 |
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32 #include <limits> |
| 0 | 33 #include <stdio.h> |
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34 #include <boost/geometry.hpp> |
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35 #include <boost/geometry/geometries/point_xy.hpp> |
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36 #include <boost/geometry/geometries/polygon.hpp> |
| 137 | 37 #include <boost/geometry/multi/geometries/multi_polygon.hpp> |
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38 |
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39 typedef boost::geometry::model::d2::point_xy<double> BoostPoint; |
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40 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon; |
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41 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon; |
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42 |
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43 |
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44 static void Union(BoostMultiPolygon& output, |
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45 std::vector<BoostPolygon>& input) |
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46 { |
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47 for (size_t i = 0; i < input.size(); i++) |
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48 { |
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49 boost::geometry::correct(input[i]); |
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50 } |
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51 |
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52 if (input.size() == 0) |
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53 { |
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54 output.clear(); |
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55 } |
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56 else if (input.size() == 1) |
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57 { |
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58 output.resize(1); |
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59 output[0] = input[0]; |
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60 } |
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61 else |
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62 { |
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63 boost::geometry::union_(input[0], input[1], output); |
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64 |
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65 for (size_t i = 0; i < input.size(); i++) |
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66 { |
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67 BoostMultiPolygon tmp; |
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68 boost::geometry::union_(output, input[i], tmp); |
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69 output = tmp; |
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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 |
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75 static BoostPolygon CreateRectangle(float x1, float y1, |
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76 float x2, float y2) |
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77 { |
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78 BoostPolygon r; |
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79 boost::geometry::append(r, BoostPoint(x1, y1)); |
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80 boost::geometry::append(r, BoostPoint(x1, y2)); |
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81 boost::geometry::append(r, BoostPoint(x2, y2)); |
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82 boost::geometry::append(r, BoostPoint(x2, y1)); |
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83 return r; |
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84 } |
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85 |
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86 |
| 0 | 87 |
| 88 namespace OrthancStone | |
| 89 { | |
| 32 | 90 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
| 91 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
| 92 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
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93 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050); |
| 32 | 94 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); |
| 95 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
| 96 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
| 97 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
| 98 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
| 99 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
| 100 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
| 101 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
| 0 | 102 |
| 103 | |
| 104 static uint8_t ConvertColor(double v) | |
| 105 { | |
| 106 if (v < 0) | |
| 107 { | |
| 108 return 0; | |
| 109 } | |
| 110 else if (v >= 255) | |
| 111 { | |
| 112 return 255; | |
| 113 } | |
| 114 else | |
| 115 { | |
| 116 return static_cast<uint8_t>(v); | |
| 117 } | |
| 118 } | |
| 119 | |
| 120 | |
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121 static bool ParseVector(Vector& target, |
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122 const OrthancPlugins::IDicomDataset& dataset, |
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123 const OrthancPlugins::DicomPath& tag) |
| 0 | 124 { |
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125 std::string value; |
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126 return (dataset.GetStringValue(value, tag) && |
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127 LinearAlgebra::ParseVector(target, value)); |
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128 } |
| 0 | 129 |
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130 void DicomStructureSet::Polygon::CheckPointIsOnSlice(const Vector& v) const |
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131 { |
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132 if (hasSlice_) |
| 0 | 133 { |
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134 double magnitude = |
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135 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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136 if(!LinearAlgebra::IsNear( |
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137 magnitude, |
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138 projectionAlongNormal_, |
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139 sliceThickness_ / 2.0 /* in mm */ )) |
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140 { |
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141 LOG(ERROR) << "This RT-STRUCT contains a point that is off the " |
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142 << "slice of its instance | " |
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143 << "magnitude = " << magnitude << " | " |
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144 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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145 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
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146 |
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147 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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148 } |
| 0 | 149 } |
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150 } |
| 0 | 151 |
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152 bool DicomStructureSet::Polygon::IsPointOnSlice(const Vector& v) const |
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153 { |
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154 if (hasSlice_) |
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155 { |
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156 double magnitude = |
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157 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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158 bool onSlice = LinearAlgebra::IsNear( |
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159 magnitude, |
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160 projectionAlongNormal_, |
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161 sliceThickness_ / 2.0 /* in mm */); |
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162 if (!onSlice) |
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163 { |
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164 LOG(WARNING) << "This RT-STRUCT contains a point that is off the " |
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165 << "slice of its instance | " |
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166 << "magnitude = " << magnitude << " | " |
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167 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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168 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
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169 } |
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170 return onSlice; |
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171 } |
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172 else |
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173 { |
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174 return false; |
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175 } |
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176 } |
| 0 | 177 |
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178 void DicomStructureSet::Polygon::AddPoint(const Vector& v) |
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179 { |
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180 #if 1 |
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181 // BGO 2019-09-03 |
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182 if (IsPointOnSlice(v)) |
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183 { |
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184 points_.push_back(v); |
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185 } |
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186 #else |
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187 CheckPoint(v); |
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188 points_.push_back(v); |
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189 #endif |
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190 } |
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191 |
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192 |
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193 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices) |
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194 { |
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195 if (hasSlice_) |
| 0 | 196 { |
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197 return true; |
| 32 | 198 } |
| 199 else | |
| 200 { | |
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201 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_); |
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202 |
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203 if (it == slices.end()) |
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204 { |
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205 return false; |
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206 } |
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207 else |
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208 { |
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209 const CoordinateSystem3D& geometry = it->second.geometry_; |
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210 |
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211 hasSlice_ = true; |
| 131 | 212 geometry_ = geometry; |
| 213 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal()); | |
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214 sliceThickness_ = it->second.thickness_; |
| 0 | 215 |
| 131 | 216 extent_.Reset(); |
| 217 | |
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218 for (Points::const_iterator it = points_.begin(); it != points_.end(); ++it) |
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219 { |
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220 if (IsPointOnSlice(*it)) |
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221 { |
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222 double x, y; |
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223 geometry.ProjectPoint(x, y, *it); |
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224 extent_.AddPoint(x, y); |
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225 } |
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226 } |
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227 return true; |
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228 } |
| 0 | 229 } |
| 230 } | |
| 231 | |
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232 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const |
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233 { |
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234 bool isOpposite = false; |
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235 |
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236 if (points_.empty() || |
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237 !hasSlice_ || |
| 131 | 238 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal())) |
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239 { |
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240 return false; |
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241 } |
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242 |
| 131 | 243 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal()); |
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244 |
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158
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245 return (LinearAlgebra::IsNear(d, projectionAlongNormal_, |
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246 sliceThickness_ / 2.0)); |
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247 } |
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248 |
| 131 | 249 bool DicomStructureSet::Polygon::Project(double& x1, |
| 250 double& y1, | |
| 251 double& x2, | |
| 252 double& y2, | |
| 253 const CoordinateSystem3D& slice) const | |
| 254 { | |
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255 // TODO: optimize this method using a sweep-line algorithm for polygons |
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256 |
| 131 | 257 if (!hasSlice_ || |
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258 points_.size() <= 1) |
| 131 | 259 { |
| 260 return false; | |
| 261 } | |
| 262 | |
| 263 double x, y; | |
| 264 geometry_.ProjectPoint(x, y, slice.GetOrigin()); | |
| 265 | |
| 266 bool isOpposite; | |
| 267 if (GeometryToolbox::IsParallelOrOpposite | |
| 268 (isOpposite, slice.GetNormal(), geometry_.GetAxisY())) | |
| 269 { | |
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270 if (y < extent_.GetY1() || |
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271 y > extent_.GetY2()) |
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272 { |
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273 // The polygon does not intersect the input slice |
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274 return false; |
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275 } |
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276 |
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277 bool isFirst = true; |
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278 double xmin = std::numeric_limits<double>::infinity(); |
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279 double xmax = -std::numeric_limits<double>::infinity(); |
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280 |
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281 double prevX, prevY; |
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282 geometry_.ProjectPoint(prevX, prevY, points_[points_.size() - 1]); |
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283 |
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284 for (size_t i = 0; i < points_.size(); i++) |
| 131 | 285 { |
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286 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py |
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287 double curX, curY; |
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288 geometry_.ProjectPoint(curX, curY, points_[i]); |
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289 |
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290 if ((prevY < y && curY > y) || |
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291 (prevY > y && curY < y)) |
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292 { |
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293 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY); |
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294 xmin = std::min(xmin, p); |
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295 xmax = std::max(xmax, p); |
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296 isFirst = false; |
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297 } |
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298 |
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299 prevX = curX; |
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300 prevY = curY; |
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301 } |
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302 |
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303 if (isFirst) |
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304 { |
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305 return false; |
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306 } |
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307 else |
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308 { |
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309 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) + |
| 131 | 310 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
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311 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) - |
| 131 | 312 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
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313 |
| 131 | 314 slice.ProjectPoint(x1, y1, p1); |
| 315 slice.ProjectPoint(x2, y2, p2); | |
| 316 return true; | |
| 317 } | |
| 318 } | |
| 319 else if (GeometryToolbox::IsParallelOrOpposite | |
| 320 (isOpposite, slice.GetNormal(), geometry_.GetAxisX())) | |
| 321 { | |
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322 if (x < extent_.GetX1() || |
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323 x > extent_.GetX2()) |
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324 { |
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325 return false; |
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326 } |
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327 |
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328 bool isFirst = true; |
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329 double ymin = std::numeric_limits<double>::infinity(); |
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330 double ymax = -std::numeric_limits<double>::infinity(); |
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331 |
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332 double prevX, prevY; |
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333 geometry_.ProjectPoint(prevX, prevY, points_[points_.size() - 1]); |
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334 |
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335 for (size_t i = 0; i < points_.size(); i++) |
| 131 | 336 { |
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337 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py |
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338 double curX, curY; |
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339 geometry_.ProjectPoint(curX, curY, points_[i]); |
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340 |
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341 if ((prevX < x && curX > x) || |
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342 (prevX > x && curX < x)) |
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343 { |
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344 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX); |
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345 ymin = std::min(ymin, p); |
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346 ymax = std::max(ymax, p); |
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347 isFirst = false; |
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348 } |
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349 |
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350 prevX = curX; |
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351 prevY = curY; |
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352 } |
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353 |
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354 if (isFirst) |
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355 { |
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356 return false; |
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357 } |
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358 else |
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359 { |
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360 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) + |
| 131 | 361 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
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362 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) - |
| 131 | 363 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
| 364 | |
| 365 slice.ProjectPoint(x1, y1, p1); | |
| 366 slice.ProjectPoint(x2, y2, p2); | |
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367 |
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368 // TODO WHY THIS??? |
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369 y1 = -y1; |
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370 y2 = -y2; |
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371 |
| 131 | 372 return true; |
| 373 } | |
| 374 } | |
| 375 else | |
| 376 { | |
| 377 // Should not happen | |
| 378 return false; | |
| 379 } | |
| 380 } | |
| 381 | |
| 382 | |
| 0 | 383 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
| 384 { | |
| 385 if (index >= structures_.size()) | |
| 386 { | |
| 125 | 387 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
| 0 | 388 } |
| 389 | |
| 390 return structures_[index]; | |
| 391 } | |
| 392 | |
| 393 | |
| 125 | 394 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) |
| 0 | 395 { |
| 125 | 396 if (index >= structures_.size()) |
| 397 { | |
| 398 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 0 | 399 } |
| 400 | |
| 401 return structures_[index]; | |
| 402 } | |
| 403 | |
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404 DicomStructureSet::DicomStructureSet(const OrthancPlugins::FullOrthancDataset& tags) |
| 0 | 405 { |
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406 OrthancPlugins::DicomDatasetReader reader(tags); |
| 32 | 407 |
| 408 size_t count, tmp; | |
| 409 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || | |
| 410 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || | |
| 411 tmp != count || | |
| 412 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || | |
| 413 tmp != count) | |
| 0 | 414 { |
| 415 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 416 } | |
| 417 | |
| 32 | 418 structures_.resize(count); |
| 419 for (size_t i = 0; i < count; i++) | |
| 420 { | |
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421 structures_[i].interpretation_ = reader.GetStringValue |
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422 (OrthancPlugins::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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423 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
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424 "No interpretation"); |
| 0 | 425 |
|
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426 structures_[i].name_ = reader.GetStringValue |
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427 (OrthancPlugins::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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428 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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429 "No name"); |
| 0 | 430 |
| 431 Vector color; | |
|
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432 if (ParseVector(color, tags, OrthancPlugins::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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433 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
| 32 | 434 color.size() == 3) |
| 0 | 435 { |
| 32 | 436 structures_[i].red_ = ConvertColor(color[0]); |
| 437 structures_[i].green_ = ConvertColor(color[1]); | |
| 438 structures_[i].blue_ = ConvertColor(color[2]); | |
| 439 } | |
| 440 else | |
| 441 { | |
| 442 structures_[i].red_ = 255; | |
| 443 structures_[i].green_ = 0; | |
| 444 structures_[i].blue_ = 0; | |
| 0 | 445 } |
| 446 | |
| 32 | 447 size_t countSlices; |
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448 if (!tags.GetSequenceSize(countSlices, OrthancPlugins::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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449 DICOM_TAG_CONTOUR_SEQUENCE))) |
| 32 | 450 { |
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451 countSlices = 0; |
| 32 | 452 } |
| 0 | 453 |
|
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better error reporting in DicomStructureSetLoader + fixed POST request logic
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parents:
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|
454 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ |
| 0 | 455 << "\" with interpretation \"" << structures_[i].interpretation_ |
| 32 | 456 << "\" containing " << countSlices << " slices (color: " |
| 0 | 457 << static_cast<int>(structures_[i].red_) << "," |
| 458 << static_cast<int>(structures_[i].green_) << "," | |
| 459 << static_cast<int>(structures_[i].blue_) << ")"; | |
| 460 | |
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461 // These temporary variables avoid allocating many vectors in the loop below |
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462 OrthancPlugins::DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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463 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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464 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS); |
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465 |
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466 OrthancPlugins::DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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467 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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468 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE); |
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469 |
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470 OrthancPlugins::DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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471 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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472 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); |
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473 |
|
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474 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155) |
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475 OrthancPlugins::DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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476 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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477 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
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478 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); |
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479 |
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480 OrthancPlugins::DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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481 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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482 DICOM_TAG_CONTOUR_DATA); |
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483 |
| 32 | 484 for (size_t j = 0; j < countSlices; j++) |
| 0 | 485 { |
| 32 | 486 unsigned int countPoints; |
| 0 | 487 |
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488 countPointsPath.SetPrefixIndex(1, j); |
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489 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) |
| 32 | 490 { |
| 491 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 492 } | |
| 493 | |
|
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494 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
| 0 | 495 |
|
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496 geometricTypePath.SetPrefixIndex(1, j); |
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497 std::string type = reader.GetMandatoryStringValue(geometricTypePath); |
| 32 | 498 if (type != "CLOSED_PLANAR") |
| 0 | 499 { |
|
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500 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
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501 continue; |
| 0 | 502 } |
| 503 | |
|
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504 size_t size; |
|
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505 |
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506 imageSequencePath.SetPrefixIndex(1, j); |
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parents:
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|
507 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1) |
|
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508 { |
|
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509 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry."; |
| 0 | 510 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
| 511 } | |
| 512 | |
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513 referencedInstancePath.SetPrefixIndex(1, j); |
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514 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); |
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|
515 |
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516 contourDataPath.SetPrefixIndex(1, j); |
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517 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); |
| 0 | 518 |
| 519 Vector points; | |
|
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|
520 if (!LinearAlgebra::ParseVector(points, slicesData) || |
| 32 | 521 points.size() != 3 * countPoints) |
| 0 | 522 { |
| 523 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 524 } | |
| 525 | |
|
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changeset
|
526 // seen in real world |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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changeset
|
527 if(Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "") |
|
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528 { |
|
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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diff
changeset
|
529 LOG(ERROR) << "WARNING. The following Dicom tag (Referenced SOP Instance UID) contains an empty value : // (3006,0039)[" << i << "] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)"; |
|
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diff
changeset
|
530 } |
|
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|
531 |
|
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532 Polygon polygon(sopInstanceUid); |
|
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533 polygon.Reserve(countPoints); |
| 0 | 534 |
| 32 | 535 for (size_t k = 0; k < countPoints; k++) |
| 0 | 536 { |
| 537 Vector v(3); | |
| 538 v[0] = points[3 * k]; | |
| 539 v[1] = points[3 * k + 1]; | |
| 540 v[2] = points[3 * k + 2]; | |
|
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541 polygon.AddPoint(v); |
| 0 | 542 } |
| 543 | |
| 544 structures_[i].polygons_.push_back(polygon); | |
| 545 } | |
| 546 } | |
| 547 } | |
| 548 | |
| 549 | |
| 550 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
| 551 { | |
| 552 const Structure& structure = GetStructure(index); | |
| 553 | |
| 554 Vector center; | |
|
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|
555 LinearAlgebra::AssignVector(center, 0, 0, 0); |
| 0 | 556 if (structure.polygons_.empty()) |
| 557 { | |
| 558 return center; | |
| 559 } | |
| 560 | |
| 561 double n = static_cast<double>(structure.polygons_.size()); | |
| 562 | |
| 563 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
| 564 polygon != structure.polygons_.end(); ++polygon) | |
| 565 { | |
|
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566 if (!polygon->GetPoints().empty()) |
| 0 | 567 { |
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568 center += polygon->GetPoints().front() / n; |
| 0 | 569 } |
| 570 } | |
| 571 | |
| 572 return center; | |
| 573 } | |
| 574 | |
| 575 | |
| 576 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
| 577 { | |
| 578 return GetStructure(index).name_; | |
| 579 } | |
| 580 | |
| 581 | |
| 582 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
| 583 { | |
| 584 return GetStructure(index).interpretation_; | |
| 585 } | |
| 586 | |
| 587 | |
|
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588 Color DicomStructureSet::GetStructureColor(size_t index) const |
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589 { |
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changeset
|
590 const Structure& s = GetStructure(index); |
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591 return Color(s.red_, s.green_, s.blue_); |
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592 } |
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593 |
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changeset
|
594 |
| 0 | 595 void DicomStructureSet::GetStructureColor(uint8_t& red, |
| 596 uint8_t& green, | |
| 597 uint8_t& blue, | |
| 598 size_t index) const | |
| 599 { | |
| 600 const Structure& s = GetStructure(index); | |
| 601 red = s.red_; | |
| 602 green = s.green_; | |
| 603 blue = s.blue_; | |
| 604 } | |
| 605 | |
| 606 | |
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607 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) |
| 0 | 608 { |
| 609 for (Structures::const_iterator structure = structures_.begin(); | |
| 610 structure != structures_.end(); ++structure) | |
| 611 { | |
| 612 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
| 613 polygon != structure->polygons_.end(); ++polygon) | |
| 614 { | |
|
122
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615 instances.insert(polygon->GetSopInstanceUid()); |
|
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616 } |
|
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617 } |
|
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618 } |
|
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619 |
|
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620 |
|
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621 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
|
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622 const std::string& seriesInstanceUid, |
|
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623 const CoordinateSystem3D& geometry, |
|
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624 double thickness) |
|
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625 { |
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626 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
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627 { |
|
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628 // This geometry is already known |
|
956
a7351ad54960
Made IsContextLost automatically set the flag by checking with the emscripten
Benjamin Golinvaux <bgo@osimis.io>
parents:
949
diff
changeset
|
629 LOG(ERROR) << "DicomStructureSet::AddReferencedSlice(): (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()). sopInstanceUid = " << sopInstanceUid; |
|
981
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
630 |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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|
631 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
|
122
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632 } |
|
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633 else |
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634 { |
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635 if (thickness < 0) |
|
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636 { |
|
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637 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
|
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638 } |
|
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639 |
|
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640 if (!referencedSlices_.empty()) |
|
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|
641 { |
|
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642 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
|
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|
643 |
|
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refactoring DicomStructureSet
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644 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
| 0 | 645 { |
|
122
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refactoring DicomStructureSet
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646 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
|
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647 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
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refactoring DicomStructureSet
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|
648 } |
| 0 | 649 |
|
122
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650 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
|
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|
651 { |
|
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|
652 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
|
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653 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
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|
654 } |
|
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|
655 } |
|
e3433dabfb8d
refactoring DicomStructureSet
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changeset
|
656 |
|
e3433dabfb8d
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|
657 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
| 0 | 658 |
| 131 | 659 for (Structures::iterator structure = structures_.begin(); |
| 660 structure != structures_.end(); ++structure) | |
| 661 { | |
| 662 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
| 663 polygon != structure->polygons_.end(); ++polygon) | |
| 664 { | |
| 665 polygon->UpdateReferencedSlice(referencedSlices_); | |
| 666 } | |
| 667 } | |
|
122
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|
668 } |
|
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|
669 } |
|
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|
670 |
|
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refactoring DicomStructureSet
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changeset
|
671 |
|
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|
672 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
|
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|
673 { |
|
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|
674 CoordinateSystem3D slice(dataset); |
|
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changeset
|
675 |
|
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refactoring DicomStructureSet
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|
676 double thickness = 1; // 1 mm by default |
| 0 | 677 |
|
122
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|
678 std::string s; |
|
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|
679 Vector v; |
|
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parents:
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diff
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|
680 if (dataset.CopyToString(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
|
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
137
diff
changeset
|
681 LinearAlgebra::ParseVector(v, s) && |
|
122
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parents:
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|
682 v.size() > 0) |
|
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|
683 { |
|
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changeset
|
684 thickness = v[0]; |
|
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changeset
|
685 } |
|
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parents:
121
diff
changeset
|
686 |
|
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refactoring DicomStructureSet
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parents:
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diff
changeset
|
687 std::string instance, series; |
|
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|
688 if (dataset.CopyToString(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) && |
|
e3433dabfb8d
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diff
changeset
|
689 dataset.CopyToString(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
|
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|
690 { |
|
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|
691 AddReferencedSlice(instance, series, slice, thickness); |
|
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changeset
|
692 } |
|
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diff
changeset
|
693 else |
|
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refactoring DicomStructureSet
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parents:
121
diff
changeset
|
694 { |
|
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refactoring DicomStructureSet
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parents:
121
diff
changeset
|
695 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
696 } |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
697 } |
|
e3433dabfb8d
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parents:
121
diff
changeset
|
698 |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
changeset
|
699 |
|
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refactoring DicomStructureSet
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parents:
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diff
changeset
|
700 void DicomStructureSet::CheckReferencedSlices() |
|
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parents:
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changeset
|
701 { |
|
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refactoring DicomStructureSet
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changeset
|
702 for (Structures::iterator structure = structures_.begin(); |
|
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|
703 structure != structures_.end(); ++structure) |
|
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changeset
|
704 { |
|
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|
705 for (Polygons::iterator polygon = structure->polygons_.begin(); |
|
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|
706 polygon != structure->polygons_.end(); ++polygon) |
|
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parents:
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changeset
|
707 { |
|
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|
708 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
|
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changeset
|
709 { |
|
981
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
710 std::string sopInstanceUid = polygon->GetSopInstanceUid(); |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
711 if (Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "") |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
712 { |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
713 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
714 << " missing information about referenced instance " |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
715 << "(sopInstanceUid is empty!)"; |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
716 } |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
717 else |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
718 { |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
719 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
720 << " missing information about referenced instance " |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
721 << "(sopInstanceUid = " << sopInstanceUid << ")"; |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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722 } |
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723 //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 0 | 724 } |
| 725 } | |
| 726 } | |
|
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727 } |
| 0 | 728 |
|
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729 |
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730 Vector DicomStructureSet::GetNormal() const |
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731 { |
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732 if (referencedSlices_.empty()) |
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733 { |
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734 Vector v; |
|
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735 LinearAlgebra::AssignVector(v, 0, 0, 1); |
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736 return v; |
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737 } |
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738 else |
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739 { |
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740 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
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741 } |
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742 } |
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743 |
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744 |
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981
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745 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<PolygonPoint2D> >& polygons, |
| 794 | 746 const Structure& structure, |
| 747 const CoordinateSystem3D& slice) const | |
| 125 | 748 { |
| 749 polygons.clear(); | |
| 750 | |
| 751 Vector normal = GetNormal(); | |
| 752 | |
| 753 bool isOpposite; | |
| 754 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal())) | |
| 755 { | |
| 756 // This is an axial projection | |
| 757 | |
| 794 | 758 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
| 125 | 759 polygon != structure.polygons_.end(); ++polygon) |
| 760 { | |
| 761 if (polygon->IsOnSlice(slice)) | |
| 762 { | |
|
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763 polygons.push_back(std::vector<PolygonPoint2D>()); |
| 125 | 764 |
| 765 for (Points::const_iterator p = polygon->GetPoints().begin(); | |
| 766 p != polygon->GetPoints().end(); ++p) | |
| 767 { | |
| 768 double x, y; | |
| 769 slice.ProjectPoint(x, y, *p); | |
| 770 polygons.back().push_back(std::make_pair(x, y)); | |
| 771 } | |
| 772 } | |
| 773 } | |
| 774 | |
| 775 return true; | |
| 776 } | |
| 777 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) || | |
| 778 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY())) | |
| 779 { | |
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780 #if 1 |
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781 // Sagittal or coronal projection |
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782 std::vector<BoostPolygon> projected; |
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783 |
| 794 | 784 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
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785 polygon != structure.polygons_.end(); ++polygon) |
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786 { |
| 131 | 787 double x1, y1, x2, y2; |
| 788 if (polygon->Project(x1, y1, x2, y2, slice)) | |
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789 { |
|
516
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790 projected.push_back(CreateRectangle( |
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791 static_cast<float>(x1), |
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792 static_cast<float>(y1), |
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793 static_cast<float>(x2), |
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794 static_cast<float>(y2))); |
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795 } |
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796 } |
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797 |
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798 BoostMultiPolygon merged; |
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799 Union(merged, projected); |
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800 |
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801 polygons.resize(merged.size()); |
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802 for (size_t i = 0; i < merged.size(); i++) |
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803 { |
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804 const std::vector<BoostPoint>& outer = merged[i].outer(); |
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805 |
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806 polygons[i].resize(outer.size()); |
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807 for (size_t j = 0; j < outer.size(); j++) |
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808 { |
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809 polygons[i][j] = std::make_pair(outer[j].x(), outer[j].y()); |
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810 } |
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811 } |
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812 #else |
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813 for (Polygons::iterator polygon = structure.polygons_.begin(); |
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814 polygon != structure.polygons_.end(); ++polygon) |
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815 { |
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816 double x1, y1, x2, y2; |
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817 if (polygon->Project(x1, y1, x2, y2, slice)) |
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818 { |
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819 std::vector<PolygonPoint2D> p(4); |
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820 p[0] = std::make_pair(x1, y1); |
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821 p[1] = std::make_pair(x2, y1); |
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822 p[2] = std::make_pair(x2, y2); |
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823 p[3] = std::make_pair(x1, y2); |
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824 polygons.push_back(p); |
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825 } |
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826 } |
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827 #endif |
| 125 | 828 |
|
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829 return true; |
| 125 | 830 } |
| 831 else | |
| 832 { | |
| 833 return false; | |
| 834 } | |
| 0 | 835 } |
| 836 } |