Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomStructureSet.cpp @ 1909:782ba9eb6f22
improved variable names
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 01 Feb 2022 08:56:36 +0100 |
parents | affde38b84de |
children | f81cdf283859 |
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 |
122
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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& cuttingPlane, |
1904
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247 const Vector& estimatedNormal, |
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248 double estimatedSliceThickness) const |
122
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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, cuttingPlane.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(cuttingPlane.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, cuttingPlane.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(cuttingPlane.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& cuttingPlane, |
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290 const Vector& estimatedNormal, |
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291 double estimatedSliceThickness) const |
131 | 292 { |
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293 #if 0 |
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294 if (points_.size() <= 1) |
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295 { |
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296 return false; |
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297 } |
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298 |
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299 Vector normal = estimatedNormal; |
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300 double thickness = estimatedSliceThickness; |
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301 if (hasSlice_) |
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302 { |
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303 normal = geometry_.GetNormal(); |
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304 thickness = sliceThickness_; |
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305 } |
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306 |
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307 bool isOpposite; |
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308 if (!GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cuttingPlane.GetAxisX()) && |
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309 !GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cuttingPlane.GetAxisY())) |
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310 { |
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311 printf("UUUU\n"); |
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312 return false; |
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313 } |
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314 |
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315 return false; |
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316 |
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317 #else |
131 | 318 if (!hasSlice_ || |
132
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319 points_.size() <= 1) |
131 | 320 { |
321 return false; | |
322 } | |
323 | |
324 double x, y; | |
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325 geometry_.ProjectPoint2(x, y, cuttingPlane.GetOrigin()); |
131 | 326 |
327 bool isOpposite; | |
328 if (GeometryToolbox::IsParallelOrOpposite | |
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329 (isOpposite, cuttingPlane.GetNormal(), geometry_.GetAxisY())) |
131 | 330 { |
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331 // plane is constant Y |
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332 |
132
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333 if (y < extent_.GetY1() || |
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334 y > extent_.GetY2()) |
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335 { |
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336 // The polygon does not intersect the input slice |
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337 return false; |
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338 } |
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339 |
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340 bool isFirst = true; |
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341 double xmin = std::numeric_limits<double>::infinity(); |
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342 double xmax = -std::numeric_limits<double>::infinity(); |
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343 |
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344 double prevX, prevY; |
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345 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
132
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346 |
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347 for (size_t i = 0; i < points_.size(); i++) |
131 | 348 { |
132
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349 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py |
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350 double curX, curY; |
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351 geometry_.ProjectPoint2(curX, curY, points_[i]); |
132
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352 |
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353 // if prev* and cur* are on opposite sides of y, this means that the |
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354 // segment intersects the plane. |
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355 if ((prevY <= y && curY >= y) || |
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356 (prevY >= y && curY <= y)) |
132
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357 { |
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358 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY); |
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359 xmin = std::min(xmin, p); |
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360 xmax = std::max(xmax, p); |
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361 isFirst = false; |
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362 |
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363 // xmin and xmax represent the extent of the rectangle along the |
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364 // intersection between the plane and the polygon geometry |
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365 |
132
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366 } |
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367 |
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368 prevX = curX; |
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369 prevY = curY; |
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370 } |
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371 |
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372 // if NO segment intersects the plane |
132
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373 if (isFirst) |
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374 { |
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375 return false; |
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376 } |
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377 else |
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378 { |
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379 // y is the plane y coord in the polygon geometry |
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380 // xmin and xmax are ALSO expressed in the polygon geometry |
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381 |
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382 // let's convert them to 3D world geometry... |
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383 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) + |
131 | 384 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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385 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) - |
131 | 386 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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387 |
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388 // then to the cutting plane geometry... |
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389 cuttingPlane.ProjectPoint2(x1, y1, p1); |
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390 cuttingPlane.ProjectPoint2(x2, y2, p2); |
131 | 391 return true; |
392 } | |
393 } | |
394 else if (GeometryToolbox::IsParallelOrOpposite | |
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395 (isOpposite, cuttingPlane.GetNormal(), geometry_.GetAxisX())) |
131 | 396 { |
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397 // plane is constant X => Sagittal view (remember that in the |
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398 // sagittal projection, the normal must be swapped) |
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399 |
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400 |
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401 /* |
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402 Please read the comments in the section above, by taking into account |
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403 the fact that, in this case, the plane has a constant X, not Y (in |
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404 polygon geometry_ coordinates) |
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405 */ |
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406 |
132
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407 if (x < extent_.GetX1() || |
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408 x > extent_.GetX2()) |
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409 { |
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410 return false; |
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411 } |
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412 |
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413 bool isFirst = true; |
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414 double ymin = std::numeric_limits<double>::infinity(); |
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415 double ymax = -std::numeric_limits<double>::infinity(); |
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416 |
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417 double prevX, prevY; |
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418 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
132
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419 |
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420 for (size_t i = 0; i < points_.size(); i++) |
131 | 421 { |
132
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422 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py |
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423 double curX, curY; |
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424 geometry_.ProjectPoint2(curX, curY, points_[i]); |
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425 |
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426 if ((prevX <= x && curX >= x) || |
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427 (prevX >= x && curX <= x)) |
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428 { |
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429 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX); |
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430 ymin = std::min(ymin, p); |
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431 ymax = std::max(ymax, p); |
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432 isFirst = false; |
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433 } |
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434 |
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435 prevX = curX; |
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436 prevY = curY; |
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437 } |
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438 |
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439 if (isFirst) |
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440 { |
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441 return false; |
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442 } |
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443 else |
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444 { |
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445 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) + |
131 | 446 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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447 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) - |
131 | 448 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
449 | |
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450 cuttingPlane.ProjectPoint2(x1, y1, p1); |
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451 cuttingPlane.ProjectPoint2(x2, y2, p2); |
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452 |
131 | 453 return true; |
454 } | |
455 } | |
456 else | |
457 { | |
458 // Should not happen | |
459 return false; | |
460 } | |
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461 #endif |
131 | 462 } |
463 | |
464 | |
0 | 465 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
466 { | |
467 if (index >= structures_.size()) | |
468 { | |
125 | 469 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
0 | 470 } |
471 | |
472 return structures_[index]; | |
473 } | |
474 | |
475 | |
125 | 476 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) |
0 | 477 { |
125 | 478 if (index >= structures_.size()) |
479 { | |
480 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
0 | 481 } |
482 | |
483 return structures_[index]; | |
484 } | |
485 | |
1504 | 486 void DicomStructureSet::Setup(const IDicomDataset& tags) |
0 | 487 { |
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488 #if STONE_TIME_BLOCKING_OPS |
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489 boost::posix_time::ptime timerStart = boost::posix_time::microsec_clock::universal_time(); |
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490 #endif |
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491 |
1504 | 492 DicomDatasetReader reader(tags); |
32 | 493 |
494 size_t count, tmp; | |
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495 if (!tags.GetSequenceSize(count, Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE)) || |
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496 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE)) || |
32 | 497 tmp != count || |
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498 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE)) || |
32 | 499 tmp != count) |
0 | 500 { |
501 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
502 } | |
503 | |
32 | 504 structures_.resize(count); |
505 for (size_t i = 0; i < count; i++) | |
506 { | |
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507 structures_[i].interpretation_ = reader.GetStringValue |
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508 (Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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509 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
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510 "No interpretation"); |
0 | 511 |
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512 structures_[i].name_ = reader.GetStringValue |
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513 (Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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514 DICOM_TAG_ROI_NAME), |
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515 "No name"); |
0 | 516 |
517 Vector color; | |
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518 if (FastParseVector(color, tags, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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519 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
32 | 520 color.size() == 3) |
0 | 521 { |
32 | 522 structures_[i].red_ = ConvertColor(color[0]); |
523 structures_[i].green_ = ConvertColor(color[1]); | |
524 structures_[i].blue_ = ConvertColor(color[2]); | |
525 } | |
526 else | |
527 { | |
528 structures_[i].red_ = 255; | |
529 structures_[i].green_ = 0; | |
530 structures_[i].blue_ = 0; | |
0 | 531 } |
532 | |
32 | 533 size_t countSlices; |
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534 if (!tags.GetSequenceSize(countSlices, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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535 DICOM_TAG_CONTOUR_SEQUENCE))) |
32 | 536 { |
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537 countSlices = 0; |
32 | 538 } |
0 | 539 |
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540 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ |
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541 << "\" with interpretation \"" << structures_[i].interpretation_ |
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542 << "\" containing " << countSlices << " slices (color: " |
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543 << static_cast<int>(structures_[i].red_) << "," |
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544 << static_cast<int>(structures_[i].green_) << "," |
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545 << static_cast<int>(structures_[i].blue_) << ")"; |
0 | 546 |
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547 /** |
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548 * These temporary variables avoid allocating many vectors in |
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549 * the loop below (indeed, "Orthanc::DicomPath" handles a |
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550 * "std::vector<PrefixItem>") |
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551 **/ |
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552 Orthanc::DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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553 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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554 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS); |
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555 |
1834
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556 Orthanc::DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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557 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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558 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE); |
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559 |
1834
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560 Orthanc::DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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561 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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562 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); |
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563 |
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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564 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155) |
1834
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565 Orthanc::DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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566 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
126522623e20
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567 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
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568 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); |
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569 |
1834
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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570 Orthanc::DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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571 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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572 DICOM_TAG_CONTOUR_DATA); |
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573 |
32 | 574 for (size_t j = 0; j < countSlices; j++) |
0 | 575 { |
32 | 576 unsigned int countPoints; |
0 | 577 |
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578 countPointsPath.SetPrefixIndex(1, j); |
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579 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) |
32 | 580 { |
581 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
582 } | |
583 | |
121
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584 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
0 | 585 |
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586 geometricTypePath.SetPrefixIndex(1, j); |
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587 std::string type = reader.GetMandatoryStringValue(geometricTypePath); |
32 | 588 if (type != "CLOSED_PLANAR") |
0 | 589 { |
173
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590 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
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591 continue; |
0 | 592 } |
593 | |
122
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594 size_t size; |
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595 |
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596 imageSequencePath.SetPrefixIndex(1, j); |
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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597 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1) |
122
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598 { |
981
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599 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry."; |
0 | 600 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
601 } | |
602 | |
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603 referencedInstancePath.SetPrefixIndex(1, j); |
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604 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); |
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605 |
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606 contourDataPath.SetPrefixIndex(1, j); |
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607 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); |
0 | 608 |
609 Vector points; | |
1751
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|
610 |
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611 if (!GenericToolbox::FastParseVector(points, slicesData) || |
32 | 612 points.size() != 3 * countPoints) |
0 | 613 { |
614 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
615 } | |
616 | |
981
c20dbaab360c
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changeset
|
617 // seen in real world |
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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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changeset
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618 if(Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "") |
c20dbaab360c
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parents:
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changeset
|
619 { |
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changeset
|
620 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
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parents:
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diff
changeset
|
621 } |
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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
|
622 |
122
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refactoring DicomStructureSet
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|
623 Polygon polygon(sopInstanceUid); |
132
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|
624 polygon.Reserve(countPoints); |
0 | 625 |
32 | 626 for (size_t k = 0; k < countPoints; k++) |
0 | 627 { |
628 Vector v(3); | |
629 v[0] = points[3 * k]; | |
630 v[1] = points[3 * k + 1]; | |
631 v[2] = points[3 * k + 2]; | |
122
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632 polygon.AddPoint(v); |
0 | 633 } |
634 | |
635 structures_[i].polygons_.push_back(polygon); | |
636 } | |
637 } | |
1892
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|
638 |
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estimated geometry of rt-struct
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|
639 EstimateGeometry(); |
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changeset
|
640 |
1751
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641 #if STONE_TIME_BLOCKING_OPS |
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changeset
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642 boost::posix_time::ptime timerEnd = boost::posix_time::microsec_clock::universal_time(); |
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643 boost::posix_time::time_duration duration = timerEnd - timerStart; |
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|
644 int64_t durationMs = duration.total_milliseconds(); |
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|
645 LOG(WARNING) << "DicomStructureSet::Setup took " << durationMs << " ms"; |
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|
646 #endif |
0 | 647 } |
648 | |
649 | |
1180
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650 #if ORTHANC_ENABLE_DCMTK == 1 |
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|
651 DicomStructureSet::DicomStructureSet(Orthanc::ParsedDicomFile& instance) |
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652 { |
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|
653 ParsedDicomDataset dataset(instance); |
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|
654 Setup(dataset); |
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|
655 } |
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|
656 #endif |
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|
657 |
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changeset
|
658 |
0 | 659 Vector DicomStructureSet::GetStructureCenter(size_t index) const |
660 { | |
661 const Structure& structure = GetStructure(index); | |
662 | |
663 Vector center; | |
158
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LinearAlgebra toolbox
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|
664 LinearAlgebra::AssignVector(center, 0, 0, 0); |
0 | 665 if (structure.polygons_.empty()) |
666 { | |
667 return center; | |
668 } | |
669 | |
670 double n = static_cast<double>(structure.polygons_.size()); | |
671 | |
672 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
673 polygon != structure.polygons_.end(); ++polygon) | |
674 { | |
122
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675 if (!polygon->GetPoints().empty()) |
0 | 676 { |
122
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677 center += polygon->GetPoints().front() / n; |
0 | 678 } |
679 } | |
680 | |
681 return center; | |
682 } | |
683 | |
684 | |
685 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
686 { | |
687 return GetStructure(index).name_; | |
688 } | |
689 | |
690 | |
691 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
692 { | |
693 return GetStructure(index).interpretation_; | |
694 } | |
695 | |
696 | |
804
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|
697 Color DicomStructureSet::GetStructureColor(size_t index) const |
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|
698 { |
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changeset
|
699 const Structure& s = GetStructure(index); |
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|
700 return Color(s.red_, s.green_, s.blue_); |
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changeset
|
701 } |
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diff
changeset
|
702 |
61ba4b504e9a
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diff
changeset
|
703 |
1885
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retrieving rt-struct info
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changeset
|
704 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) const |
0 | 705 { |
706 for (Structures::const_iterator structure = structures_.begin(); | |
707 structure != structures_.end(); ++structure) | |
708 { | |
709 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
710 polygon != structure->polygons_.end(); ++polygon) | |
711 { | |
122
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712 instances.insert(polygon->GetSopInstanceUid()); |
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713 } |
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|
714 } |
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|
715 } |
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changeset
|
716 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
717 |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
718 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
719 const std::string& seriesInstanceUid, |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
720 const CoordinateSystem3D& geometry, |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
721 double thickness) |
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 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
724 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
725 // This geometry is already known |
956
a7351ad54960
Made IsContextLost automatically set the flag by checking with the emscripten
Benjamin Golinvaux <bgo@osimis.io>
parents:
949
diff
changeset
|
726 LOG(ERROR) << "DicomStructureSet::AddReferencedSlice(): (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()). sopInstanceUid = " << sopInstanceUid; |
981
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
727 |
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
|
728 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
729 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
730 else |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
731 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
732 if (thickness < 0) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
733 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
734 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
735 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
736 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
737 if (!referencedSlices_.empty()) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
738 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
739 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
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 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
0 | 742 { |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
743 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
744 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
745 } |
0 | 746 |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
747 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
748 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
749 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
750 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
751 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
752 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
753 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
754 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
0 | 755 |
131 | 756 for (Structures::iterator structure = structures_.begin(); |
757 structure != structures_.end(); ++structure) | |
758 { | |
759 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
760 polygon != structure->polygons_.end(); ++polygon) | |
761 { | |
762 polygon->UpdateReferencedSlice(referencedSlices_); | |
763 } | |
764 } | |
122
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 } |
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 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
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 CoordinateSystem3D slice(dataset); |
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 double thickness = 1; // 1 mm by default |
0 | 774 |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
775 std::string s; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
776 Vector v; |
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
777 if (dataset.LookupStringValue(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
137
diff
changeset
|
778 LinearAlgebra::ParseVector(v, s) && |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
779 v.size() > 0) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
780 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
781 thickness = v[0]; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
782 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
783 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
784 std::string instance, series; |
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
785 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
|
786 dataset.LookupStringValue(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
787 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
788 AddReferencedSlice(instance, series, slice, thickness); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
789 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
790 else |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
791 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
792 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
793 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
794 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
795 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
796 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
797 void DicomStructureSet::CheckReferencedSlices() |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
798 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
799 for (Structures::iterator structure = structures_.begin(); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
800 structure != structures_.end(); ++structure) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
801 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
802 for (Polygons::iterator polygon = structure->polygons_.begin(); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
803 polygon != structure->polygons_.end(); ++polygon) |
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 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
806 { |
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
|
807 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
|
808 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
|
809 { |
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
|
810 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
811 << " missing information about referenced instance " |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
812 << "(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
|
813 } |
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
|
814 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
|
815 { |
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
|
816 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
817 << " missing information about referenced instance " |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
818 << "(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
|
819 } |
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
|
820 //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
0 | 821 } |
822 } | |
823 } | |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
824 } |
0 | 825 |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
826 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
827 Vector DicomStructureSet::GetNormal() const |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
828 { |
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
829 if (referencedSlices_.empty()) |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
830 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
831 Vector v; |
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
137
diff
changeset
|
832 LinearAlgebra::AssignVector(v, 0, 0, 1); |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
833 return v; |
e3433dabfb8d
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834 } |
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|
835 else |
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836 { |
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837 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
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|
838 } |
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|
839 } |
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refactoring DicomStructureSet
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diff
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|
840 |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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parents:
1895
diff
changeset
|
841 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<ScenePoint2D> >& chains, |
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simplified signature of DicomStructureSet::ProjectStructure()
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|
842 const Structure& structure, |
1909
782ba9eb6f22
improved variable names
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diff
changeset
|
843 const CoordinateSystem3D& cuttingPlane) const |
125 | 844 { |
1909
782ba9eb6f22
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parents:
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diff
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|
845 const CoordinateSystem3D cutting = CoordinateSystem3D::NormalizeCuttingPlane(cuttingPlane); |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
846 |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
847 chains.clear(); |
125 | 848 |
849 Vector normal = GetNormal(); | |
850 | |
851 bool isOpposite; | |
1909
782ba9eb6f22
improved variable names
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parents:
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diff
changeset
|
852 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cutting.GetNormal())) |
125 | 853 { |
854 // This is an axial projection | |
855 | |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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diff
changeset
|
856 chains.reserve(structure.polygons_.size()); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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857 |
794 | 858 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
125 | 859 polygon != structure.polygons_.end(); ++polygon) |
860 { | |
1896
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861 const Points& points = polygon->GetPoints(); |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
862 |
1909
782ba9eb6f22
improved variable names
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changeset
|
863 if (polygon->IsOnSlice(cutting, GetEstimatedNormal(), GetEstimatedSliceThickness()) && |
1896
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simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
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|
864 !points.empty()) |
125 | 865 { |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
866 chains.push_back(std::vector<ScenePoint2D>()); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
867 chains.back().reserve(points.size() + 1); |
125 | 868 |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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diff
changeset
|
869 for (Points::const_iterator p = points.begin(); |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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parents:
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|
870 p != points.end(); ++p) |
125 | 871 { |
872 double x, y; | |
1909
782ba9eb6f22
improved variable names
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diff
changeset
|
873 cutting.ProjectPoint2(x, y, *p); |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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|
874 chains.back().push_back(ScenePoint2D(x, y)); |
125 | 875 } |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
876 |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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parents:
1895
diff
changeset
|
877 double x0, y0; |
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
878 cutting.ProjectPoint2(x0, y0, points.front()); |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
879 chains.back().push_back(ScenePoint2D(x0, y0)); |
125 | 880 } |
881 } | |
882 | |
883 return true; | |
884 } | |
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
885 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cutting.GetAxisX()) || |
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
886 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cutting.GetAxisY())) |
125 | 887 { |
126
c9e88e7935a4
rt-struct projection
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diff
changeset
|
888 // Sagittal or coronal projection |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
889 |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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diff
changeset
|
890 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
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125
diff
changeset
|
891 std::vector<BoostPolygon> projected; |
1162
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
892 |
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
893 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
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1013
diff
changeset
|
894 polygon != structure.polygons_.end(); ++polygon) |
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
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parents:
1013
diff
changeset
|
895 { |
709aa65aca17
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1013
diff
changeset
|
896 double x1, y1, x2, y2; |
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
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1013
diff
changeset
|
897 |
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
898 if (polygon->Project(x1, y1, x2, y2, cutting, GetEstimatedNormal(), GetEstimatedSliceThickness())) |
1162
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
899 { |
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
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1013
diff
changeset
|
900 projected.push_back(CreateRectangle(x1, y1, x2, y2)); |
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
901 } |
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
902 } |
1897
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
903 |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
904 BoostMultiPolygon merged; |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
905 Union(merged, projected); |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
906 |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
907 chains.resize(merged.size()); |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
908 for (size_t i = 0; i < merged.size(); i++) |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
909 { |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
910 const std::vector<BoostPoint>& outer = merged[i].outer(); |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
911 |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
912 chains[i].resize(outer.size()); |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
913 for (size_t j = 0; j < outer.size(); j++) |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
914 { |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
915 chains[i][j] = ScenePoint2D(outer[j].x(), outer[j].y()); |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
916 } |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
917 } |
1898
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
918 |
1908
affde38b84de
moved tentative bgo reimplementation of rt-struct into graveyard
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1905
diff
changeset
|
919 #else |
1898
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
920 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
921 std::list<Extent2D> rectangles; |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
922 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
923 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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parents:
1897
diff
changeset
|
924 polygon != structure.polygons_.end(); ++polygon) |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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1897
diff
changeset
|
925 { |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
926 double x1, y1, x2, y2; |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
927 |
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
928 if (polygon->Project(x1, y1, x2, y2, cutting, GetEstimatedNormal(), GetEstimatedSliceThickness())) |
1898
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
929 { |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
930 rectangles.push_back(Extent2D(x1, y1, x2, y2)); |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
931 } |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
932 } |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
933 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
934 typedef std::list< std::vector<ScenePoint2D> > Contours; |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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parents:
1897
diff
changeset
|
935 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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parents:
1897
diff
changeset
|
936 Contours contours; |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
937 UnionOfRectangles::Apply(contours, rectangles); |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
938 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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parents:
1897
diff
changeset
|
939 chains.reserve(contours.size()); |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
940 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
941 for (Contours::const_iterator it = contours.begin(); it != contours.end(); ++it) |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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parents:
1897
diff
changeset
|
942 { |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
943 chains.push_back(*it); |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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parents:
1897
diff
changeset
|
944 } |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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1897
diff
changeset
|
945 |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
946 #endif |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
947 |
126
c9e88e7935a4
rt-struct projection
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parents:
125
diff
changeset
|
948 return true; |
125 | 949 } |
950 else | |
951 { | |
952 return false; | |
953 } | |
0 | 954 } |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
955 |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
956 |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
957 void DicomStructureSet::ProjectOntoLayer(PolylineSceneLayer& layer, |
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
958 const CoordinateSystem3D& cuttingPlane, |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
959 size_t structureIndex, |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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parents:
1170
diff
changeset
|
960 const Color& color) const |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
961 { |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
962 std::vector< std::vector<ScenePoint2D> > chains; |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
963 |
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
964 if (ProjectStructure(chains, structureIndex, cuttingPlane)) |
1178
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965 { |
1896
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966 for (size_t j = 0; j < chains.size(); j++) |
1178
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967 { |
1896
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968 layer.AddChain(chains[j], false, color.GetRed(), color.GetGreen(), color.GetBlue()); |
1178
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969 } |
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970 } |
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971 } |
1885
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972 |
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973 |
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974 void DicomStructureSet::GetStructurePoints(std::list< std::vector<Vector> >& target, |
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975 size_t structureIndex, |
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976 const std::string& sopInstanceUid) const |
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977 { |
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978 target.clear(); |
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979 |
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980 const Structure& structure = GetStructure(structureIndex); |
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981 |
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982 // TODO - Could be optimized by adding a multimap on "Structure", mapping |
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983 // from SOP Instance UID to polygons |
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984 |
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985 for (Polygons::const_iterator it = structure.polygons_.begin(); |
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986 it != structure.polygons_.end(); ++it) |
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987 { |
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988 if (it->GetSopInstanceUid() == sopInstanceUid) |
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989 { |
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990 target.push_back(it->GetPoints()); |
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991 } |
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992 } |
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993 } |
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994 |
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995 |
1892
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996 void DicomStructureSet::EstimateGeometry() |
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997 { |
1892
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998 static const double PI = boost::math::constants::pi<double>(); |
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999 |
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1000 BucketAccumulator2D accumulator(0, PI, 9, /* for acos() */ |
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1001 -PI, PI, 9, /* for atan() */ |
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1002 true /* store values */); |
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1003 |
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1004 unsigned int countPolygons = 0; |
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1005 for (size_t i = 0; i < structures_.size(); i++) |
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1006 { |
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1007 const Polygons& polygons = structures_[i].polygons_; |
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1008 |
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1009 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
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1010 { |
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1011 countPolygons++; |
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1012 |
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1013 const Points& points = it->GetPoints(); |
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1014 |
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1015 if (points.size() >= 3) |
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1016 { |
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1017 // Compute the normal of the polygon using 3 successive points |
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1018 Vector normal; |
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1019 bool valid = false; |
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1020 |
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1021 for (size_t i = 0; i + 2 < points.size(); i++) |
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1022 { |
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1023 const Vector& a = points[i]; |
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1024 const Vector& b = points[i + 1]; |
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1025 const Vector& c = points[i + 2]; |
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1026 LinearAlgebra::CrossProduct(normal, b - a, c - a); // (*) |
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1027 LinearAlgebra::NormalizeVector(normal); |
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1028 |
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1029 if (LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(normal), 1.0)) // (**) |
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|
1030 { |
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1031 valid = true; |
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1032 break; |
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1033 } |
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1034 } |
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1035 |
1892
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1036 if (valid) |
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|
1037 { |
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1038 // Check that all the points of the polygon lie in the plane defined by the normal |
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1039 double d1 = GeometryToolbox::ProjectAlongNormal(points[0], normal); |
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1040 |
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1041 for (size_t i = 1; i < points.size(); i++) |
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|
1042 { |
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1043 double d2 = GeometryToolbox::ProjectAlongNormal(points[i], normal); |
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1044 |
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1045 if (!LinearAlgebra::IsNear(d1, d2)) |
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|
1046 { |
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1047 valid = false; |
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1048 break; |
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1049 } |
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|
1050 } |
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1051 } |
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|
1052 |
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1053 if (valid) |
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1054 { |
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1055 if (normal[2] < 0) |
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1056 { |
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1057 normal = -normal; |
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1058 } |
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|
1059 |
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1060 // The normal is a non-zero unit vector because of (*) and (**), so "r == 1" |
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1061 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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1062 |
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1063 const double theta = acos(normal[2]); |
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1064 const double phi = atan(normal[1]); |
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1065 accumulator.AddValue(theta, phi); |
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|
1066 } |
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|
1067 } |
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|
1068 } |
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|
1069 } |
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|
1070 |
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1071 size_t bestX, bestY; |
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1072 accumulator.FindBestBucket(bestX, bestY); |
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1073 |
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1074 if (accumulator.GetBucketContentSize(bestX, bestY) > 0) |
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1075 { |
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1076 double normalTheta, normalPhi; |
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1077 accumulator.ComputeBestMedian(normalTheta, normalPhi); |
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1078 |
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1079 // Back to (x,y,z) normal, taking "r == 1" |
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1080 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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1081 double sinTheta = sin(normalTheta); |
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1082 estimatedNormal_ = LinearAlgebra::CreateVector(sinTheta * cos(normalPhi), sinTheta * sin(normalPhi), cos(normalTheta)); |
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1083 } |
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1084 |
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1085 std::vector<double> polygonsProjection; |
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1086 polygonsProjection.reserve(countPolygons); |
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1087 |
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1088 for (size_t i = 0; i < structures_.size(); i++) |
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1089 { |
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1090 const Polygons& polygons = structures_[i].polygons_; |
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1091 |
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1092 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
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1093 { |
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1094 const Points& points = it->GetPoints(); |
1892
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1095 polygonsProjection.push_back(GeometryToolbox::ProjectAlongNormal(points[0], estimatedNormal_)); |
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1096 } |
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1097 } |
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1098 |
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1099 std::sort(polygonsProjection.begin(), polygonsProjection.end()); |
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1100 |
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1101 std::vector<double> deltas; |
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1102 deltas.reserve(polygonsProjection.size()); |
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1103 |
1892
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1104 for (size_t i = 0; i + 1 < polygonsProjection.size(); i++) |
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1105 { |
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1106 if (!LinearAlgebra::IsNear(polygonsProjection[i], polygonsProjection[i + 1])) |
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1107 { |
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1108 assert(polygonsProjection[i + 1] > polygonsProjection[i]); |
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1109 deltas.push_back(polygonsProjection[i + 1] - polygonsProjection[i]); |
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1110 } |
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1111 } |
1892
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1112 |
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1113 if (deltas.empty()) |
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1114 { |
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1115 estimatedSliceThickness_ = 1; |
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1116 } |
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1117 else |
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1118 { |
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1119 estimatedSliceThickness_ = LinearAlgebra::ComputeMedian(deltas); |
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1120 } |
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1121 } |
0 | 1122 } |