Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomStructureSet.cpp @ 1908:affde38b84de
moved tentative bgo reimplementation of rt-struct into graveyard
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 01 Feb 2022 08:38:32 +0100 |
parents | e318b524ad3f |
children | 782ba9eb6f22 |
rev | line source |
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0 | 1 /** |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
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5 * Copyright (C) 2017-2022 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
0 | 7 * |
8 * This program is free software: you can redistribute it and/or | |
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9 * modify it under the terms of the GNU Lesser General Public License |
47 | 10 * as published by the Free Software Foundation, either version 3 of |
11 * the License, or (at your option) any later version. | |
0 | 12 * |
13 * This program is distributed in the hope that it will be useful, but | |
14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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16 * Lesser General Public License for more details. |
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17 * |
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18 * You should have received a copy of the GNU Lesser General Public |
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19 * License along with this program. If not, see |
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20 * <http://www.gnu.org/licenses/>. |
0 | 21 **/ |
22 | |
23 | |
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24 #define USE_BOOST_UNION_FOR_POLYGONS 0 |
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25 |
0 | 26 #include "DicomStructureSet.h" |
27 | |
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28 #include "BucketAccumulator2D.h" |
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29 #include "GenericToolbox.h" |
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30 #include "GeometryToolbox.h" |
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31 #include "OrthancDatasets/DicomDatasetReader.h" |
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32 |
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33 #include <Logging.h> |
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34 #include <OrthancException.h> |
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35 #include <Toolbox.h> |
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36 |
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37 #if defined(_MSC_VER) |
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38 # pragma warning(push) |
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39 # pragma warning(disable:4244) |
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40 #endif |
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41 |
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42 #if STONE_TIME_BLOCKING_OPS |
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43 # include <boost/date_time/posix_time/posix_time.hpp> |
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44 #endif |
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45 |
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46 #if !defined(USE_BOOST_UNION_FOR_POLYGONS) |
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47 # error Macro USE_BOOST_UNION_FOR_POLYGONS must be defined |
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48 #endif |
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49 |
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50 #include <limits> |
0 | 51 #include <stdio.h> |
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52 #include <boost/math/constants/constants.hpp> |
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53 |
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54 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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55 # include <boost/geometry.hpp> |
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56 # include <boost/geometry/geometries/point_xy.hpp> |
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57 # include <boost/geometry/geometries/polygon.hpp> |
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58 # include <boost/geometry/multi/geometries/multi_polygon.hpp> |
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59 #else |
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60 # include "UnionOfRectangles.h" |
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61 #endif |
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62 |
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63 #if defined(_MSC_VER) |
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64 # pragma warning(pop) |
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65 #endif |
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66 |
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67 #if ORTHANC_ENABLE_DCMTK == 1 |
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68 # include "ParsedDicomDataset.h" |
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69 #endif |
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70 |
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71 |
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72 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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73 |
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74 typedef boost::geometry::model::d2::point_xy<double> BoostPoint; |
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75 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon; |
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76 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon; |
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77 |
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78 static void Union(BoostMultiPolygon& output, |
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79 std::vector<BoostPolygon>& input) |
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80 { |
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81 for (size_t i = 0; i < input.size(); i++) |
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82 { |
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83 boost::geometry::correct(input[i]); |
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84 } |
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85 |
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86 if (input.size() == 0) |
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87 { |
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88 output.clear(); |
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89 } |
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90 else if (input.size() == 1) |
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91 { |
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92 output.resize(1); |
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93 output[0] = input[0]; |
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94 } |
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95 else |
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96 { |
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97 boost::geometry::union_(input[0], input[1], output); |
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98 |
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99 for (size_t i = 0; i < input.size(); i++) |
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100 { |
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101 BoostMultiPolygon tmp; |
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102 boost::geometry::union_(output, input[i], tmp); |
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103 output = tmp; |
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104 } |
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105 } |
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106 } |
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107 |
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108 static BoostPolygon CreateRectangle(float x1, float y1, |
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109 float x2, float y2) |
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110 { |
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111 BoostPolygon r; |
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112 boost::geometry::append(r, BoostPoint(x1, y1)); |
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113 boost::geometry::append(r, BoostPoint(x1, y2)); |
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114 boost::geometry::append(r, BoostPoint(x2, y2)); |
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115 boost::geometry::append(r, BoostPoint(x2, y1)); |
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116 return r; |
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117 } |
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118 |
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119 #endif |
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120 |
0 | 121 |
122 namespace OrthancStone | |
123 { | |
1504 | 124 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
125 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
126 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
127 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050); | |
128 static const Orthanc::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); | |
129 static const Orthanc::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
130 static const Orthanc::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
131 static const Orthanc::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
132 static const Orthanc::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
133 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
134 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
135 static const Orthanc::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
0 | 136 |
137 | |
138 static uint8_t ConvertColor(double v) | |
139 { | |
140 if (v < 0) | |
141 { | |
142 return 0; | |
143 } | |
144 else if (v >= 255) | |
145 { | |
146 return 255; | |
147 } | |
148 else | |
149 { | |
150 return static_cast<uint8_t>(v); | |
151 } | |
152 } | |
153 | |
154 | |
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155 static bool FastParseVector(Vector& target, |
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156 const IDicomDataset& dataset, |
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157 const Orthanc::DicomPath& tag) |
0 | 158 { |
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159 std::string value; |
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160 return (dataset.GetStringValue(value, tag) && |
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161 GenericToolbox::FastParseVector(target, value)); |
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162 } |
0 | 163 |
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164 bool DicomStructureSet::Polygon::IsPointOnSliceIfAny(const Vector& v) const |
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165 { |
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166 if (hasSlice_) |
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167 { |
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168 double magnitude = |
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169 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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170 bool onSlice = LinearAlgebra::IsNear( |
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171 magnitude, |
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172 projectionAlongNormal_, |
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173 sliceThickness_ / 2.0 /* in mm */); |
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174 if (!onSlice) |
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175 { |
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176 LOG(WARNING) << "This RT-STRUCT contains a point that is off the " |
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177 << "slice of its instance | " |
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178 << "magnitude = " << magnitude << " | " |
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179 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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180 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
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181 } |
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182 return onSlice; |
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183 } |
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184 else |
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185 { |
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186 return true; |
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187 } |
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188 } |
0 | 189 |
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190 void DicomStructureSet::Polygon::AddPoint(const Vector& v) |
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191 { |
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192 #if 1 |
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193 // BGO 2019-09-03 |
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194 if (IsPointOnSliceIfAny(v)) |
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195 { |
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196 points_.push_back(v); |
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197 } |
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198 #else |
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199 CheckPoint(v); |
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200 points_.push_back(v); |
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201 #endif |
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202 } |
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203 |
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204 |
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205 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices) |
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206 { |
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207 if (hasSlice_) |
0 | 208 { |
122
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209 return true; |
32 | 210 } |
211 else | |
212 { | |
122
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213 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_); |
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214 |
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215 if (it == slices.end()) |
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216 { |
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217 return false; |
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218 } |
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219 else |
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220 { |
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221 // return true; // TODO - TEST |
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222 |
122
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223 const CoordinateSystem3D& geometry = it->second.geometry_; |
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224 |
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225 hasSlice_ = true; |
131 | 226 geometry_ = geometry; |
227 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal()); | |
122
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228 sliceThickness_ = it->second.thickness_; |
0 | 229 |
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230 extent_.Clear(); |
131 | 231 |
1571 | 232 for (Points::const_iterator it2 = points_.begin(); it2 != points_.end(); ++it2) |
122
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233 { |
1571 | 234 if (IsPointOnSliceIfAny(*it2)) |
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235 { |
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236 double x, y; |
1571 | 237 geometry.ProjectPoint2(x, y, *it2); |
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238 extent_.AddPoint(x, y); |
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239 } |
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240 } |
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241 return true; |
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242 } |
0 | 243 } |
244 } | |
245 | |
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246 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice, |
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247 const Vector& estimatedNormal, |
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248 double estimatedSliceThickness) const |
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249 { |
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250 bool isOpposite = false; |
122
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251 |
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252 if (points_.empty()) |
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253 { |
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254 return false; |
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255 } |
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256 else if (hasSlice_) |
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257 { |
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258 // Use the actual geometry of this specific slice |
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259 if (!GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal())) |
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260 { |
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261 return false; |
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262 } |
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263 else |
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264 { |
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265 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal()); |
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266 return (LinearAlgebra::IsNear(d, projectionAlongNormal_, sliceThickness_ / 2.0)); |
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267 } |
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268 } |
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269 else |
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270 { |
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271 // Use the estimated geometry for the global RT-STRUCT volume |
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272 if (!GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), estimatedNormal)) |
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273 { |
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274 return false; |
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275 } |
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276 else |
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277 { |
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278 double d1 = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), estimatedNormal); |
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279 double d2 = GeometryToolbox::ProjectAlongNormal(points_.front(), estimatedNormal); |
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280 return (LinearAlgebra::IsNear(d1, d2, estimatedSliceThickness / 2.0)); |
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281 } |
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282 } |
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283 } |
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284 |
131 | 285 bool DicomStructureSet::Polygon::Project(double& x1, |
286 double& y1, | |
287 double& x2, | |
288 double& y2, | |
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289 const CoordinateSystem3D& slice, |
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290 const Vector& estimatedNormal, |
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291 double estimatedSliceThickness) const |
131 | 292 { |
293 if (!hasSlice_ || | |
132
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294 points_.size() <= 1) |
131 | 295 { |
296 return false; | |
297 } | |
298 | |
299 double x, y; | |
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300 geometry_.ProjectPoint2(x, y, slice.GetOrigin()); |
131 | 301 |
302 bool isOpposite; | |
303 if (GeometryToolbox::IsParallelOrOpposite | |
304 (isOpposite, slice.GetNormal(), geometry_.GetAxisY())) | |
305 { | |
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306 // plane is constant Y |
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307 |
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308 if (y < extent_.GetY1() || |
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309 y > extent_.GetY2()) |
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310 { |
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311 // The polygon does not intersect the input slice |
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312 return false; |
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313 } |
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314 |
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315 bool isFirst = true; |
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316 double xmin = std::numeric_limits<double>::infinity(); |
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317 double xmax = -std::numeric_limits<double>::infinity(); |
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318 |
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319 double prevX, prevY; |
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320 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
132
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321 |
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322 for (size_t i = 0; i < points_.size(); i++) |
131 | 323 { |
132
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324 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py |
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325 double curX, curY; |
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326 geometry_.ProjectPoint2(curX, curY, points_[i]); |
132
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327 |
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328 // if prev* and cur* are on opposite sides of y, this means that the |
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329 // segment intersects the plane. |
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330 if ((prevY <= y && curY >= y) || |
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331 (prevY >= y && curY <= y)) |
132
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332 { |
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333 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY); |
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334 xmin = std::min(xmin, p); |
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335 xmax = std::max(xmax, p); |
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336 isFirst = false; |
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337 |
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338 // xmin and xmax represent the extent of the rectangle along the |
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339 // intersection between the plane and the polygon geometry |
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340 |
132
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341 } |
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342 |
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343 prevX = curX; |
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344 prevY = curY; |
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345 } |
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346 |
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347 // if NO segment intersects the plane |
132
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348 if (isFirst) |
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349 { |
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350 return false; |
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351 } |
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352 else |
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353 { |
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354 // y is the plane y coord in the polygon geometry |
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355 // xmin and xmax are ALSO expressed in the polygon geometry |
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356 |
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357 // let's convert them to 3D world geometry... |
132
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358 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) + |
131 | 359 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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360 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) - |
131 | 361 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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362 |
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363 // then to the cutting plane geometry... |
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364 slice.ProjectPoint2(x1, y1, p1); |
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365 slice.ProjectPoint2(x2, y2, p2); |
131 | 366 return true; |
367 } | |
368 } | |
369 else if (GeometryToolbox::IsParallelOrOpposite | |
370 (isOpposite, slice.GetNormal(), geometry_.GetAxisX())) | |
371 { | |
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372 // plane is constant X => Sagittal view (remember that in the |
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373 // sagittal projection, the normal must be swapped) |
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374 |
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375 |
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376 /* |
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377 Please read the comments in the section above, by taking into account |
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378 the fact that, in this case, the plane has a constant X, not Y (in |
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379 polygon geometry_ coordinates) |
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380 */ |
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381 |
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382 if (x < extent_.GetX1() || |
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383 x > extent_.GetX2()) |
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384 { |
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385 return false; |
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386 } |
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387 |
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388 bool isFirst = true; |
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389 double ymin = std::numeric_limits<double>::infinity(); |
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390 double ymax = -std::numeric_limits<double>::infinity(); |
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391 |
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392 double prevX, prevY; |
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393 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
132
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394 |
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395 for (size_t i = 0; i < points_.size(); i++) |
131 | 396 { |
132
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397 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py |
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398 double curX, curY; |
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399 geometry_.ProjectPoint2(curX, curY, points_[i]); |
132
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400 |
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401 if ((prevX <= x && curX >= x) || |
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402 (prevX >= x && curX <= x)) |
132
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403 { |
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404 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX); |
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405 ymin = std::min(ymin, p); |
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406 ymax = std::max(ymax, p); |
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407 isFirst = false; |
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408 } |
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409 |
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410 prevX = curX; |
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411 prevY = curY; |
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412 } |
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413 |
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414 if (isFirst) |
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415 { |
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416 return false; |
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417 } |
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418 else |
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419 { |
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420 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) + |
131 | 421 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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422 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) - |
131 | 423 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
424 | |
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425 slice.ProjectPoint2(x1, y1, p1); |
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426 slice.ProjectPoint2(x2, y2, p2); |
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427 |
131 | 428 return true; |
429 } | |
430 } | |
431 else | |
432 { | |
433 // Should not happen | |
434 return false; | |
435 } | |
436 } | |
437 | |
438 | |
0 | 439 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
440 { | |
441 if (index >= structures_.size()) | |
442 { | |
125 | 443 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
0 | 444 } |
445 | |
446 return structures_[index]; | |
447 } | |
448 | |
449 | |
125 | 450 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) |
0 | 451 { |
125 | 452 if (index >= structures_.size()) |
453 { | |
454 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
0 | 455 } |
456 | |
457 return structures_[index]; | |
458 } | |
459 | |
1504 | 460 void DicomStructureSet::Setup(const IDicomDataset& tags) |
0 | 461 { |
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462 #if STONE_TIME_BLOCKING_OPS |
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463 boost::posix_time::ptime timerStart = boost::posix_time::microsec_clock::universal_time(); |
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464 #endif |
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465 |
1504 | 466 DicomDatasetReader reader(tags); |
32 | 467 |
468 size_t count, tmp; | |
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469 if (!tags.GetSequenceSize(count, Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE)) || |
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470 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE)) || |
32 | 471 tmp != count || |
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472 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE)) || |
32 | 473 tmp != count) |
0 | 474 { |
475 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
476 } | |
477 | |
32 | 478 structures_.resize(count); |
479 for (size_t i = 0; i < count; i++) | |
480 { | |
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481 structures_[i].interpretation_ = reader.GetStringValue |
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482 (Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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483 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
122
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484 "No interpretation"); |
0 | 485 |
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486 structures_[i].name_ = reader.GetStringValue |
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487 (Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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488 DICOM_TAG_ROI_NAME), |
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489 "No name"); |
0 | 490 |
491 Vector color; | |
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492 if (FastParseVector(color, tags, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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493 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
32 | 494 color.size() == 3) |
0 | 495 { |
32 | 496 structures_[i].red_ = ConvertColor(color[0]); |
497 structures_[i].green_ = ConvertColor(color[1]); | |
498 structures_[i].blue_ = ConvertColor(color[2]); | |
499 } | |
500 else | |
501 { | |
502 structures_[i].red_ = 255; | |
503 structures_[i].green_ = 0; | |
504 structures_[i].blue_ = 0; | |
0 | 505 } |
506 | |
32 | 507 size_t countSlices; |
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508 if (!tags.GetSequenceSize(countSlices, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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509 DICOM_TAG_CONTOUR_SEQUENCE))) |
32 | 510 { |
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511 countSlices = 0; |
32 | 512 } |
0 | 513 |
841
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514 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ |
1178
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515 << "\" with interpretation \"" << structures_[i].interpretation_ |
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516 << "\" containing " << countSlices << " slices (color: " |
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517 << static_cast<int>(structures_[i].red_) << "," |
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518 << static_cast<int>(structures_[i].green_) << "," |
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519 << static_cast<int>(structures_[i].blue_) << ")"; |
0 | 520 |
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521 /** |
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522 * These temporary variables avoid allocating many vectors in |
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523 * the loop below (indeed, "Orthanc::DicomPath" handles a |
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524 * "std::vector<PrefixItem>") |
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525 **/ |
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526 Orthanc::DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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527 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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528 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS); |
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529 |
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530 Orthanc::DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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531 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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532 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE); |
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533 |
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534 Orthanc::DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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535 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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536 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); |
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537 |
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
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538 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155) |
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539 Orthanc::DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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540 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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541 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
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542 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); |
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543 |
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544 Orthanc::DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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545 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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546 DICOM_TAG_CONTOUR_DATA); |
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547 |
32 | 548 for (size_t j = 0; j < countSlices; j++) |
0 | 549 { |
32 | 550 unsigned int countPoints; |
0 | 551 |
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552 countPointsPath.SetPrefixIndex(1, j); |
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553 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) |
32 | 554 { |
555 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
556 } | |
557 | |
121
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558 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
0 | 559 |
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560 geometricTypePath.SetPrefixIndex(1, j); |
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optimizing constructor of DicomStructureSet
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561 std::string type = reader.GetMandatoryStringValue(geometricTypePath); |
32 | 562 if (type != "CLOSED_PLANAR") |
0 | 563 { |
173
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564 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
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565 continue; |
0 | 566 } |
567 | |
122
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568 size_t size; |
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569 |
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|
570 imageSequencePath.SetPrefixIndex(1, j); |
981
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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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571 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1) |
122
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572 { |
981
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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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573 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry."; |
0 | 574 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
575 } | |
576 | |
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577 referencedInstancePath.SetPrefixIndex(1, j); |
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578 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); |
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579 |
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580 contourDataPath.SetPrefixIndex(1, j); |
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581 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); |
0 | 582 |
583 Vector points; | |
1751
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584 |
946eb7200b82
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585 if (!GenericToolbox::FastParseVector(points, slicesData) || |
32 | 586 points.size() != 3 * countPoints) |
0 | 587 { |
588 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
589 } | |
590 | |
981
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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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591 // 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
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592 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:
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593 { |
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diff
changeset
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594 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)"; |
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
|
595 } |
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:
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diff
changeset
|
596 |
122
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|
597 Polygon polygon(sopInstanceUid); |
132
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|
598 polygon.Reserve(countPoints); |
0 | 599 |
32 | 600 for (size_t k = 0; k < countPoints; k++) |
0 | 601 { |
602 Vector v(3); | |
603 v[0] = points[3 * k]; | |
604 v[1] = points[3 * k + 1]; | |
605 v[2] = points[3 * k + 2]; | |
122
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|
606 polygon.AddPoint(v); |
0 | 607 } |
608 | |
609 structures_[i].polygons_.push_back(polygon); | |
610 } | |
611 } | |
1892
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1890
diff
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|
612 |
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changeset
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613 EstimateGeometry(); |
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estimated geometry of rt-struct
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614 |
1751
946eb7200b82
FastParseVector usage + timing instrumentation guarded by STONE_TIME_BLOCKING_OPS
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changeset
|
615 #if STONE_TIME_BLOCKING_OPS |
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diff
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|
616 boost::posix_time::ptime timerEnd = boost::posix_time::microsec_clock::universal_time(); |
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diff
changeset
|
617 boost::posix_time::time_duration duration = timerEnd - timerStart; |
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diff
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|
618 int64_t durationMs = duration.total_milliseconds(); |
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diff
changeset
|
619 LOG(WARNING) << "DicomStructureSet::Setup took " << durationMs << " ms"; |
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FastParseVector usage + timing instrumentation guarded by STONE_TIME_BLOCKING_OPS
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diff
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|
620 #endif |
0 | 621 } |
622 | |
623 | |
1180
9c8f557ea799
ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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parents:
1178
diff
changeset
|
624 #if ORTHANC_ENABLE_DCMTK == 1 |
9c8f557ea799
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1178
diff
changeset
|
625 DicomStructureSet::DicomStructureSet(Orthanc::ParsedDicomFile& instance) |
9c8f557ea799
ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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diff
changeset
|
626 { |
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ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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parents:
1178
diff
changeset
|
627 ParsedDicomDataset dataset(instance); |
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ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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1178
diff
changeset
|
628 Setup(dataset); |
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diff
changeset
|
629 } |
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ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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diff
changeset
|
630 #endif |
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changeset
|
631 |
9c8f557ea799
ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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1178
diff
changeset
|
632 |
0 | 633 Vector DicomStructureSet::GetStructureCenter(size_t index) const |
634 { | |
635 const Structure& structure = GetStructure(index); | |
636 | |
637 Vector center; | |
158
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LinearAlgebra toolbox
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parents:
137
diff
changeset
|
638 LinearAlgebra::AssignVector(center, 0, 0, 0); |
0 | 639 if (structure.polygons_.empty()) |
640 { | |
641 return center; | |
642 } | |
643 | |
644 double n = static_cast<double>(structure.polygons_.size()); | |
645 | |
646 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
647 polygon != structure.polygons_.end(); ++polygon) | |
648 { | |
122
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refactoring DicomStructureSet
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649 if (!polygon->GetPoints().empty()) |
0 | 650 { |
122
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refactoring DicomStructureSet
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|
651 center += polygon->GetPoints().front() / n; |
0 | 652 } |
653 } | |
654 | |
655 return center; | |
656 } | |
657 | |
658 | |
659 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
660 { | |
661 return GetStructure(index).name_; | |
662 } | |
663 | |
664 | |
665 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
666 { | |
667 return GetStructure(index).interpretation_; | |
668 } | |
669 | |
670 | |
804
61ba4b504e9a
PolylineSceneLayer now has one color per chain
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parents:
794
diff
changeset
|
671 Color DicomStructureSet::GetStructureColor(size_t index) const |
61ba4b504e9a
PolylineSceneLayer now has one color per chain
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parents:
794
diff
changeset
|
672 { |
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PolylineSceneLayer now has one color per chain
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parents:
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diff
changeset
|
673 const Structure& s = GetStructure(index); |
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PolylineSceneLayer now has one color per chain
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diff
changeset
|
674 return Color(s.red_, s.green_, s.blue_); |
61ba4b504e9a
PolylineSceneLayer now has one color per chain
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parents:
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diff
changeset
|
675 } |
61ba4b504e9a
PolylineSceneLayer now has one color per chain
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parents:
794
diff
changeset
|
676 |
61ba4b504e9a
PolylineSceneLayer now has one color per chain
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parents:
794
diff
changeset
|
677 |
1885
ddaee6b96501
retrieving rt-struct info
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diff
changeset
|
678 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) const |
0 | 679 { |
680 for (Structures::const_iterator structure = structures_.begin(); | |
681 structure != structures_.end(); ++structure) | |
682 { | |
683 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
684 polygon != structure->polygons_.end(); ++polygon) | |
685 { | |
122
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refactoring DicomStructureSet
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686 instances.insert(polygon->GetSopInstanceUid()); |
e3433dabfb8d
refactoring DicomStructureSet
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687 } |
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diff
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|
688 } |
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diff
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|
689 } |
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|
690 |
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refactoring DicomStructureSet
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|
691 |
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changeset
|
692 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
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diff
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693 const std::string& seriesInstanceUid, |
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diff
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694 const CoordinateSystem3D& geometry, |
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refactoring DicomStructureSet
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695 double thickness) |
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696 { |
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697 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
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698 { |
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|
699 // This geometry is already known |
956
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Made IsContextLost automatically set the flag by checking with the emscripten
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diff
changeset
|
700 LOG(ERROR) << "DicomStructureSet::AddReferencedSlice(): (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()). sopInstanceUid = " << sopInstanceUid; |
981
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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
|
701 |
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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parents:
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diff
changeset
|
702 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
122
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refactoring DicomStructureSet
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703 } |
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704 else |
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705 { |
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706 if (thickness < 0) |
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refactoring DicomStructureSet
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diff
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707 { |
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refactoring DicomStructureSet
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changeset
|
708 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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709 } |
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refactoring DicomStructureSet
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diff
changeset
|
710 |
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refactoring DicomStructureSet
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|
711 if (!referencedSlices_.empty()) |
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refactoring DicomStructureSet
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121
diff
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712 { |
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refactoring DicomStructureSet
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changeset
|
713 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
714 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
715 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
0 | 716 { |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
717 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
718 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
719 } |
0 | 720 |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
721 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
722 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
723 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
724 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
725 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
726 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
727 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
728 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
0 | 729 |
131 | 730 for (Structures::iterator structure = structures_.begin(); |
731 structure != structures_.end(); ++structure) | |
732 { | |
733 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
734 polygon != structure->polygons_.end(); ++polygon) | |
735 { | |
736 polygon->UpdateReferencedSlice(referencedSlices_); | |
737 } | |
738 } | |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
739 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
740 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
741 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
742 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
743 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
744 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
745 CoordinateSystem3D slice(dataset); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
746 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
747 double thickness = 1; // 1 mm by default |
0 | 748 |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
749 std::string s; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
750 Vector v; |
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
751 if (dataset.LookupStringValue(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
137
diff
changeset
|
752 LinearAlgebra::ParseVector(v, s) && |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
753 v.size() > 0) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
754 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
755 thickness = v[0]; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
756 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
757 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
758 std::string instance, series; |
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
759 if (dataset.LookupStringValue(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) && |
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
760 dataset.LookupStringValue(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
761 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
762 AddReferencedSlice(instance, series, slice, thickness); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
763 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
764 else |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
765 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
766 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
767 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
768 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
769 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
770 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
771 void DicomStructureSet::CheckReferencedSlices() |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
772 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
773 for (Structures::iterator structure = structures_.begin(); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
774 structure != structures_.end(); ++structure) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
775 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
776 for (Polygons::iterator polygon = structure->polygons_.begin(); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
777 polygon != structure->polygons_.end(); ++polygon) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
778 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
779 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
780 { |
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
|
781 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
|
782 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
|
783 { |
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
|
784 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
785 << " missing information about referenced instance " |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
786 << "(sopInstanceUid is empty!)"; |
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
|
787 } |
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
|
788 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
|
789 { |
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
|
790 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
791 << " missing information about referenced instance " |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
792 << "(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
|
793 } |
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
|
794 //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
0 | 795 } |
796 } | |
797 } | |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
798 } |
0 | 799 |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
800 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
801 Vector DicomStructureSet::GetNormal() const |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
802 { |
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
803 if (referencedSlices_.empty()) |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
804 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
805 Vector v; |
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
137
diff
changeset
|
806 LinearAlgebra::AssignVector(v, 0, 0, 1); |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
807 return v; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
808 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
809 else |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
810 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
811 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
812 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
813 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
814 |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
815 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<ScenePoint2D> >& chains, |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
816 const Structure& structure, |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
817 const CoordinateSystem3D& sourceSlice) const |
125 | 818 { |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
819 const CoordinateSystem3D slice = CoordinateSystem3D::NormalizeCuttingPlane(sourceSlice); |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
820 |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
821 chains.clear(); |
125 | 822 |
823 Vector normal = GetNormal(); | |
824 | |
825 bool isOpposite; | |
826 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal())) | |
827 { | |
828 // This is an axial projection | |
829 | |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
830 chains.reserve(structure.polygons_.size()); |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
831 |
794 | 832 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
125 | 833 polygon != structure.polygons_.end(); ++polygon) |
834 { | |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
835 const Points& points = polygon->GetPoints(); |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
836 |
1904
738814c24574
speed up rendering of axial slices of RT-STRUCT
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1898
diff
changeset
|
837 if (polygon->IsOnSlice(slice, GetEstimatedNormal(), GetEstimatedSliceThickness()) && |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
838 !points.empty()) |
125 | 839 { |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
840 chains.push_back(std::vector<ScenePoint2D>()); |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
841 chains.back().reserve(points.size() + 1); |
125 | 842 |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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843 for (Points::const_iterator p = points.begin(); |
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844 p != points.end(); ++p) |
125 | 845 { |
846 double x, y; | |
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Benjamin Golinvaux <bgo@osimis.io>
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|
847 slice.ProjectPoint2(x, y, *p); |
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848 chains.back().push_back(ScenePoint2D(x, y)); |
125 | 849 } |
1000
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850 |
1896
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851 double x0, y0; |
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852 slice.ProjectPoint2(x0, y0, points.front()); |
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853 chains.back().push_back(ScenePoint2D(x0, y0)); |
125 | 854 } |
855 } | |
856 | |
857 return true; | |
858 } | |
859 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) || | |
860 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY())) | |
861 { | |
126
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862 // Sagittal or coronal projection |
1000
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863 |
1178
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864 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
126
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865 std::vector<BoostPolygon> projected; |
1162
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866 |
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867 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
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868 polygon != structure.polygons_.end(); ++polygon) |
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869 { |
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870 double x1, y1, x2, y2; |
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871 |
1905
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872 if (polygon->Project(x1, y1, x2, y2, slice, GetEstimatedNormal(), GetEstimatedSliceThickness())) |
1162
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873 { |
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874 projected.push_back(CreateRectangle(x1, y1, x2, y2)); |
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875 } |
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876 } |
1897
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877 |
144f8f82c15a
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|
878 BoostMultiPolygon merged; |
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879 Union(merged, projected); |
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880 |
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|
881 chains.resize(merged.size()); |
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882 for (size_t i = 0; i < merged.size(); i++) |
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883 { |
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884 const std::vector<BoostPoint>& outer = merged[i].outer(); |
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|
885 |
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886 chains[i].resize(outer.size()); |
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887 for (size_t j = 0; j < outer.size(); j++) |
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|
888 { |
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889 chains[i][j] = ScenePoint2D(outer[j].x(), outer[j].y()); |
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|
890 } |
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891 } |
1898
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892 |
1908
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moved tentative bgo reimplementation of rt-struct into graveyard
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|
893 #else |
1898
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changeset
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894 |
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895 std::list<Extent2D> rectangles; |
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896 |
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897 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
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898 polygon != structure.polygons_.end(); ++polygon) |
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899 { |
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900 double x1, y1, x2, y2; |
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901 |
1905
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diff
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|
902 if (polygon->Project(x1, y1, x2, y2, slice, GetEstimatedNormal(), GetEstimatedSliceThickness())) |
1898
a5e54bd87b25
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changeset
|
903 { |
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|
904 rectangles.push_back(Extent2D(x1, y1, x2, y2)); |
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|
905 } |
a5e54bd87b25
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|
906 } |
a5e54bd87b25
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changeset
|
907 |
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|
908 typedef std::list< std::vector<ScenePoint2D> > Contours; |
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changeset
|
909 |
a5e54bd87b25
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|
910 Contours contours; |
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|
911 UnionOfRectangles::Apply(contours, rectangles); |
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changeset
|
912 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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diff
changeset
|
913 chains.reserve(contours.size()); |
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changeset
|
914 |
a5e54bd87b25
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|
915 for (Contours::const_iterator it = contours.begin(); it != contours.end(); ++it) |
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|
916 { |
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|
917 chains.push_back(*it); |
a5e54bd87b25
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|
918 } |
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|
919 |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
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|
920 #endif |
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|
921 |
126
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diff
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|
922 return true; |
125 | 923 } |
924 else | |
925 { | |
926 return false; | |
927 } | |
0 | 928 } |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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diff
changeset
|
929 |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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changeset
|
930 |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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changeset
|
931 void DicomStructureSet::ProjectOntoLayer(PolylineSceneLayer& layer, |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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|
932 const CoordinateSystem3D& plane, |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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|
933 size_t structureIndex, |
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DicomStructureSet::ProjectOntoLayer()
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|
934 const Color& color) const |
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DicomStructureSet::ProjectOntoLayer()
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935 { |
1896
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simplified signature of DicomStructureSet::ProjectStructure()
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|
936 std::vector< std::vector<ScenePoint2D> > chains; |
b3c08e607d9f
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|
937 |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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|
938 if (ProjectStructure(chains, structureIndex, plane)) |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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|
939 { |
1896
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940 for (size_t j = 0; j < chains.size(); j++) |
1178
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DicomStructureSet::ProjectOntoLayer()
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|
941 { |
1896
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simplified signature of DicomStructureSet::ProjectStructure()
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|
942 layer.AddChain(chains[j], false, color.GetRed(), color.GetGreen(), color.GetBlue()); |
1178
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DicomStructureSet::ProjectOntoLayer()
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|
943 } |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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|
944 } |
3c7cdbf32e2a
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|
945 } |
1885
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|
946 |
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|
947 |
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|
948 void DicomStructureSet::GetStructurePoints(std::list< std::vector<Vector> >& target, |
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949 size_t structureIndex, |
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950 const std::string& sopInstanceUid) const |
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951 { |
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|
952 target.clear(); |
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953 |
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954 const Structure& structure = GetStructure(structureIndex); |
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955 |
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|
956 // TODO - Could be optimized by adding a multimap on "Structure", mapping |
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957 // from SOP Instance UID to polygons |
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958 |
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959 for (Polygons::const_iterator it = structure.polygons_.begin(); |
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960 it != structure.polygons_.end(); ++it) |
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961 { |
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962 if (it->GetSopInstanceUid() == sopInstanceUid) |
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963 { |
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changeset
|
964 target.push_back(it->GetPoints()); |
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|
965 } |
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966 } |
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|
967 } |
1890
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968 |
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969 |
1892
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970 void DicomStructureSet::EstimateGeometry() |
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971 { |
1892
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972 static const double PI = boost::math::constants::pi<double>(); |
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973 |
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974 BucketAccumulator2D accumulator(0, PI, 9, /* for acos() */ |
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975 -PI, PI, 9, /* for atan() */ |
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976 true /* store values */); |
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977 |
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978 unsigned int countPolygons = 0; |
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979 for (size_t i = 0; i < structures_.size(); i++) |
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980 { |
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981 const Polygons& polygons = structures_[i].polygons_; |
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982 |
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983 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
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984 { |
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985 countPolygons++; |
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|
986 |
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987 const Points& points = it->GetPoints(); |
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988 |
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989 if (points.size() >= 3) |
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990 { |
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|
991 // Compute the normal of the polygon using 3 successive points |
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992 Vector normal; |
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993 bool valid = false; |
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|
994 |
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995 for (size_t i = 0; i + 2 < points.size(); i++) |
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996 { |
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997 const Vector& a = points[i]; |
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998 const Vector& b = points[i + 1]; |
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999 const Vector& c = points[i + 2]; |
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1000 LinearAlgebra::CrossProduct(normal, b - a, c - a); // (*) |
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1001 LinearAlgebra::NormalizeVector(normal); |
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|
1002 |
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1003 if (LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(normal), 1.0)) // (**) |
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1004 { |
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1005 valid = true; |
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1006 break; |
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|
1007 } |
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|
1008 } |
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1009 |
1892
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1010 if (valid) |
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1011 { |
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1012 // Check that all the points of the polygon lie in the plane defined by the normal |
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1013 double d1 = GeometryToolbox::ProjectAlongNormal(points[0], normal); |
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|
1014 |
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1015 for (size_t i = 1; i < points.size(); i++) |
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|
1016 { |
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1017 double d2 = GeometryToolbox::ProjectAlongNormal(points[i], normal); |
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1018 |
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1019 if (!LinearAlgebra::IsNear(d1, d2)) |
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|
1020 { |
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1021 valid = false; |
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1022 break; |
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|
1023 } |
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|
1024 } |
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|
1025 } |
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|
1026 |
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|
1027 if (valid) |
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|
1028 { |
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|
1029 if (normal[2] < 0) |
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|
1030 { |
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diff
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|
1031 normal = -normal; |
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|
1032 } |
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diff
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|
1033 |
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diff
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|
1034 // The normal is a non-zero unit vector because of (*) and (**), so "r == 1" |
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diff
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|
1035 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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|
1036 |
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diff
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|
1037 const double theta = acos(normal[2]); |
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1038 const double phi = atan(normal[1]); |
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|
1039 accumulator.AddValue(theta, phi); |
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diff
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|
1040 } |
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diff
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|
1041 } |
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|
1042 } |
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|
1043 } |
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|
1044 |
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diff
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|
1045 size_t bestX, bestY; |
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|
1046 accumulator.FindBestBucket(bestX, bestY); |
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diff
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|
1047 |
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diff
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|
1048 if (accumulator.GetBucketContentSize(bestX, bestY) > 0) |
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diff
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|
1049 { |
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diff
changeset
|
1050 double normalTheta, normalPhi; |
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|
1051 accumulator.ComputeBestMedian(normalTheta, normalPhi); |
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diff
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|
1052 |
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diff
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|
1053 // Back to (x,y,z) normal, taking "r == 1" |
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|
1054 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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1055 double sinTheta = sin(normalTheta); |
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1056 estimatedNormal_ = LinearAlgebra::CreateVector(sinTheta * cos(normalPhi), sinTheta * sin(normalPhi), cos(normalTheta)); |
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|
1057 } |
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|
1058 |
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|
1059 std::vector<double> polygonsProjection; |
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|
1060 polygonsProjection.reserve(countPolygons); |
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|
1061 |
1890
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|
1062 for (size_t i = 0; i < structures_.size(); i++) |
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|
1063 { |
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1064 const Polygons& polygons = structures_[i].polygons_; |
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|
1065 |
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|
1066 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
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|
1067 { |
6ce81914f7e4
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|
1068 const Points& points = it->GetPoints(); |
1892
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1069 polygonsProjection.push_back(GeometryToolbox::ProjectAlongNormal(points[0], estimatedNormal_)); |
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|
1070 } |
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|
1071 } |
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|
1072 |
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diff
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|
1073 std::sort(polygonsProjection.begin(), polygonsProjection.end()); |
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|
1074 |
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|
1075 std::vector<double> deltas; |
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1076 deltas.reserve(polygonsProjection.size()); |
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diff
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|
1077 |
1892
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|
1078 for (size_t i = 0; i + 1 < polygonsProjection.size(); i++) |
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|
1079 { |
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
1080 if (!LinearAlgebra::IsNear(polygonsProjection[i], polygonsProjection[i + 1])) |
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
1081 { |
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
1082 assert(polygonsProjection[i + 1] > polygonsProjection[i]); |
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
1083 deltas.push_back(polygonsProjection[i + 1] - polygonsProjection[i]); |
1890
6ce81914f7e4
added classes BucketAccumulator1D/2D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1885
diff
changeset
|
1084 } |
6ce81914f7e4
added classes BucketAccumulator1D/2D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1885
diff
changeset
|
1085 } |
1892
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
1086 |
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
1087 if (deltas.empty()) |
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
1088 { |
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
1089 estimatedSliceThickness_ = 1; |
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
1090 } |
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
1091 else |
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
1092 { |
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
1093 estimatedSliceThickness_ = LinearAlgebra::ComputeMedian(deltas); |
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
1094 } |
1890
6ce81914f7e4
added classes BucketAccumulator1D/2D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1885
diff
changeset
|
1095 } |
0 | 1096 } |