Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomStructureSet.cpp @ 1895:14c8f339d480
removed redundant definitions Point2D, Point3D and Vector3D from DicomStructureSetUtils.h
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 19 Jan 2022 14:51:55 +0100 |
parents | 90b5e116a5f9 |
children | b3c08e607d9f |
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 | |
24 #include "DicomStructureSet.h" | |
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25 #include "DicomStructureSetUtils.h" // TODO REMOVE |
0 | 26 |
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27 #include "BucketAccumulator2D.h" |
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28 #include "GenericToolbox.h" |
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29 #include "GeometryToolbox.h" |
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30 #include "OrthancDatasets/DicomDatasetReader.h" |
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31 |
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32 #include <Logging.h> |
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33 #include <OrthancException.h> |
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34 #include <Toolbox.h> |
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35 |
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36 #if defined(_MSC_VER) |
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37 # pragma warning(push) |
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38 # pragma warning(disable:4244) |
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39 #endif |
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40 |
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41 #if STONE_TIME_BLOCKING_OPS |
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42 # include <boost/date_time/posix_time/posix_time.hpp> |
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43 #endif |
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44 |
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45 #include <limits> |
0 | 46 #include <stdio.h> |
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47 #include <boost/math/constants/constants.hpp> |
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48 #include <boost/geometry.hpp> |
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49 #include <boost/geometry/geometries/point_xy.hpp> |
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50 #include <boost/geometry/geometries/polygon.hpp> |
137 | 51 #include <boost/geometry/multi/geometries/multi_polygon.hpp> |
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52 |
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53 #if defined(_MSC_VER) |
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54 # pragma warning(pop) |
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55 #endif |
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56 |
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57 #if ORTHANC_ENABLE_DCMTK == 1 |
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58 # include "ParsedDicomDataset.h" |
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59 #endif |
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60 |
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61 |
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62 typedef boost::geometry::model::d2::point_xy<double> BoostPoint; |
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63 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon; |
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64 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon; |
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65 |
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66 |
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67 static void Union(BoostMultiPolygon& output, |
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68 std::vector<BoostPolygon>& input) |
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69 { |
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70 for (size_t i = 0; i < input.size(); i++) |
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71 { |
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72 boost::geometry::correct(input[i]); |
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73 } |
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74 |
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75 if (input.size() == 0) |
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76 { |
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77 output.clear(); |
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78 } |
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79 else if (input.size() == 1) |
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80 { |
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81 output.resize(1); |
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82 output[0] = input[0]; |
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83 } |
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84 else |
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85 { |
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86 boost::geometry::union_(input[0], input[1], output); |
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87 |
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88 for (size_t i = 0; i < input.size(); i++) |
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89 { |
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90 BoostMultiPolygon tmp; |
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91 boost::geometry::union_(output, input[i], tmp); |
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92 output = tmp; |
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93 } |
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94 } |
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95 } |
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96 |
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97 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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98 |
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99 static BoostPolygon CreateRectangle(float x1, float y1, |
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100 float x2, float y2) |
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101 { |
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102 BoostPolygon r; |
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103 boost::geometry::append(r, BoostPoint(x1, y1)); |
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104 boost::geometry::append(r, BoostPoint(x1, y2)); |
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105 boost::geometry::append(r, BoostPoint(x2, y2)); |
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106 boost::geometry::append(r, BoostPoint(x2, y1)); |
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107 return r; |
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108 } |
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109 |
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110 #else |
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111 |
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112 namespace OrthancStone |
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113 { |
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114 static RtStructRectangleInSlab CreateRectangle(float x1, float y1, |
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115 float x2, float y2) |
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116 { |
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117 RtStructRectangleInSlab rect; |
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118 rect.xmin = std::min(x1, x2); |
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119 rect.xmax = std::max(x1, x2); |
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120 rect.ymin = std::min(y1, y2); |
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121 rect.ymax = std::max(y1, y2); |
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122 return rect; |
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123 } |
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124 |
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125 bool CompareRectanglesForProjection(const std::pair<RtStructRectangleInSlab,double>& r1, const std::pair<RtStructRectangleInSlab, double>& r2) |
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126 { |
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127 return r1.second < r2.second; |
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128 } |
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129 |
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130 bool CompareSlabsY(const RtStructRectanglesInSlab& r1, const RtStructRectanglesInSlab& r2) |
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131 { |
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132 if ((r1.size() == 0) || (r2.size() == 0)) |
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133 return false; |
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134 |
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135 return r1[0].ymax < r2[0].ymax; |
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136 } |
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137 } |
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138 |
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139 #endif |
0 | 140 |
141 namespace OrthancStone | |
142 { | |
1504 | 143 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
144 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
145 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
146 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050); | |
147 static const Orthanc::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); | |
148 static const Orthanc::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
149 static const Orthanc::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
150 static const Orthanc::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
151 static const Orthanc::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
152 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
153 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
154 static const Orthanc::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
0 | 155 |
156 | |
157 static uint8_t ConvertColor(double v) | |
158 { | |
159 if (v < 0) | |
160 { | |
161 return 0; | |
162 } | |
163 else if (v >= 255) | |
164 { | |
165 return 255; | |
166 } | |
167 else | |
168 { | |
169 return static_cast<uint8_t>(v); | |
170 } | |
171 } | |
172 | |
173 | |
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174 static bool FastParseVector(Vector& target, |
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175 const IDicomDataset& dataset, |
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176 const Orthanc::DicomPath& tag) |
0 | 177 { |
118
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178 std::string value; |
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179 return (dataset.GetStringValue(value, tag) && |
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180 GenericToolbox::FastParseVector(target, value)); |
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181 } |
0 | 182 |
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183 void DicomStructureSet::Polygon::CheckPointIsOnSlice(const Vector& v) const |
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184 { |
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185 if (hasSlice_) |
0 | 186 { |
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187 double magnitude = |
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188 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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189 if(!LinearAlgebra::IsNear( |
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190 magnitude, |
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191 projectionAlongNormal_, |
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192 sliceThickness_ / 2.0 /* in mm */ )) |
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193 { |
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194 LOG(ERROR) << "This RT-STRUCT contains a point that is off the " |
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195 << "slice of its instance | " |
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196 << "magnitude = " << magnitude << " | " |
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197 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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198 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
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199 |
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200 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
122
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201 } |
0 | 202 } |
122
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203 } |
0 | 204 |
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205 bool DicomStructureSet::Polygon::IsPointOnSliceIfAny(const Vector& v) const |
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206 { |
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207 if (hasSlice_) |
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208 { |
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209 double magnitude = |
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210 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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211 bool onSlice = LinearAlgebra::IsNear( |
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212 magnitude, |
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213 projectionAlongNormal_, |
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214 sliceThickness_ / 2.0 /* in mm */); |
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215 if (!onSlice) |
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216 { |
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217 LOG(WARNING) << "This RT-STRUCT contains a point that is off the " |
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218 << "slice of its instance | " |
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219 << "magnitude = " << magnitude << " | " |
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220 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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221 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
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222 } |
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223 return onSlice; |
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224 } |
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225 else |
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226 { |
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227 return true; |
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228 } |
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229 } |
0 | 230 |
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231 void DicomStructureSet::Polygon::AddPoint(const Vector& v) |
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232 { |
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233 #if 1 |
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234 // BGO 2019-09-03 |
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235 if (IsPointOnSliceIfAny(v)) |
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236 { |
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237 points_.push_back(v); |
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238 } |
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239 #else |
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240 CheckPoint(v); |
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241 points_.push_back(v); |
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242 #endif |
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243 } |
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244 |
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245 |
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246 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices) |
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247 { |
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248 if (hasSlice_) |
0 | 249 { |
122
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250 return true; |
32 | 251 } |
252 else | |
253 { | |
122
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254 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_); |
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255 |
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256 if (it == slices.end()) |
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257 { |
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258 return false; |
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259 } |
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260 else |
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261 { |
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262 const CoordinateSystem3D& geometry = it->second.geometry_; |
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263 |
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264 hasSlice_ = true; |
131 | 265 geometry_ = geometry; |
266 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal()); | |
122
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267 sliceThickness_ = it->second.thickness_; |
0 | 268 |
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269 extent_.Clear(); |
131 | 270 |
1571 | 271 for (Points::const_iterator it2 = points_.begin(); it2 != points_.end(); ++it2) |
122
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272 { |
1571 | 273 if (IsPointOnSliceIfAny(*it2)) |
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274 { |
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275 double x, y; |
1571 | 276 geometry.ProjectPoint2(x, y, *it2); |
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277 extent_.AddPoint(x, y); |
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278 } |
122
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279 } |
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280 return true; |
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281 } |
0 | 282 } |
283 } | |
284 | |
122
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285 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const |
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286 { |
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287 bool isOpposite = false; |
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288 |
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289 if (points_.empty() || |
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290 !hasSlice_ || |
131 | 291 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal())) |
122
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292 { |
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293 return false; |
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294 } |
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295 |
131 | 296 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal()); |
122
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297 |
158
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298 return (LinearAlgebra::IsNear(d, projectionAlongNormal_, |
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299 sliceThickness_ / 2.0)); |
122
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300 } |
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301 |
131 | 302 bool DicomStructureSet::Polygon::Project(double& x1, |
303 double& y1, | |
304 double& x2, | |
305 double& y2, | |
306 const CoordinateSystem3D& slice) const | |
307 { | |
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308 // TODO: optimize this method using a sweep-line algorithm for polygons |
132
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309 |
131 | 310 if (!hasSlice_ || |
132
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311 points_.size() <= 1) |
131 | 312 { |
313 return false; | |
314 } | |
315 | |
316 double x, y; | |
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317 geometry_.ProjectPoint2(x, y, slice.GetOrigin()); |
131 | 318 |
319 bool isOpposite; | |
320 if (GeometryToolbox::IsParallelOrOpposite | |
321 (isOpposite, slice.GetNormal(), geometry_.GetAxisY())) | |
322 { | |
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323 // plane is constant Y |
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324 |
132
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325 if (y < extent_.GetY1() || |
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326 y > extent_.GetY2()) |
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327 { |
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328 // The polygon does not intersect the input slice |
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329 return false; |
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330 } |
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331 |
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332 bool isFirst = true; |
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333 double xmin = std::numeric_limits<double>::infinity(); |
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334 double xmax = -std::numeric_limits<double>::infinity(); |
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335 |
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336 double prevX, prevY; |
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337 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
132
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338 |
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339 for (size_t i = 0; i < points_.size(); i++) |
131 | 340 { |
132
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341 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py |
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342 double curX, curY; |
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343 geometry_.ProjectPoint2(curX, curY, points_[i]); |
132
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344 |
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345 // if prev* and cur* are on opposite sides of y, this means that the |
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346 // segment intersects the plane. |
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347 if ((prevY <= y && curY >= y) || |
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348 (prevY >= y && curY <= y)) |
132
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349 { |
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350 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY); |
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351 xmin = std::min(xmin, p); |
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352 xmax = std::max(xmax, p); |
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353 isFirst = false; |
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354 |
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355 // xmin and xmax represent the extent of the rectangle along the |
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356 // intersection between the plane and the polygon geometry |
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357 |
132
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358 } |
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359 |
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360 prevX = curX; |
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361 prevY = curY; |
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362 } |
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363 |
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364 // if NO segment intersects the plane |
132
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365 if (isFirst) |
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366 { |
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367 return false; |
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368 } |
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369 else |
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370 { |
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371 // y is the plane y coord in the polygon geometry |
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372 // xmin and xmax are ALSO expressed in the polygon geometry |
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373 |
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374 // let's convert them to 3D world geometry... |
132
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375 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) + |
131 | 376 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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377 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) - |
131 | 378 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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379 |
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380 // then to the cutting plane geometry... |
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381 slice.ProjectPoint2(x1, y1, p1); |
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382 slice.ProjectPoint2(x2, y2, p2); |
131 | 383 return true; |
384 } | |
385 } | |
386 else if (GeometryToolbox::IsParallelOrOpposite | |
387 (isOpposite, slice.GetNormal(), geometry_.GetAxisX())) | |
388 { | |
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389 // plane is constant X => Sagittal view (remember that in the |
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390 // sagittal projection, the normal must be swapped) |
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391 |
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392 |
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393 /* |
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394 Please read the comments in the section above, by taking into account |
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395 the fact that, in this case, the plane has a constant X, not Y (in |
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396 polygon geometry_ coordinates) |
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397 */ |
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398 |
132
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399 if (x < extent_.GetX1() || |
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400 x > extent_.GetX2()) |
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401 { |
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402 return false; |
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403 } |
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404 |
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405 bool isFirst = true; |
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406 double ymin = std::numeric_limits<double>::infinity(); |
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407 double ymax = -std::numeric_limits<double>::infinity(); |
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408 |
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409 double prevX, prevY; |
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410 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
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411 |
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412 for (size_t i = 0; i < points_.size(); i++) |
131 | 413 { |
132
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414 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py |
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415 double curX, curY; |
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416 geometry_.ProjectPoint2(curX, curY, points_[i]); |
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417 |
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418 if ((prevX <= x && curX >= x) || |
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419 (prevX >= x && curX <= x)) |
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420 { |
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421 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX); |
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422 ymin = std::min(ymin, p); |
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423 ymax = std::max(ymax, p); |
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424 isFirst = false; |
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425 } |
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426 |
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427 prevX = curX; |
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428 prevY = curY; |
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429 } |
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430 |
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431 if (isFirst) |
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432 { |
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433 return false; |
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434 } |
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435 else |
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436 { |
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437 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) + |
131 | 438 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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439 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) - |
131 | 440 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
441 | |
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442 slice.ProjectPoint2(x1, y1, p1); |
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443 slice.ProjectPoint2(x2, y2, p2); |
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444 |
131 | 445 return true; |
446 } | |
447 } | |
448 else | |
449 { | |
450 // Should not happen | |
451 return false; | |
452 } | |
453 } | |
454 | |
455 | |
0 | 456 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
457 { | |
458 if (index >= structures_.size()) | |
459 { | |
125 | 460 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
0 | 461 } |
462 | |
463 return structures_[index]; | |
464 } | |
465 | |
466 | |
125 | 467 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) |
0 | 468 { |
125 | 469 if (index >= structures_.size()) |
470 { | |
471 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
0 | 472 } |
473 | |
474 return structures_[index]; | |
475 } | |
476 | |
1504 | 477 void DicomStructureSet::Setup(const IDicomDataset& tags) |
0 | 478 { |
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479 #if STONE_TIME_BLOCKING_OPS |
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480 boost::posix_time::ptime timerStart = boost::posix_time::microsec_clock::universal_time(); |
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481 #endif |
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482 |
1504 | 483 DicomDatasetReader reader(tags); |
32 | 484 |
485 size_t count, tmp; | |
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486 if (!tags.GetSequenceSize(count, Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE)) || |
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487 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE)) || |
32 | 488 tmp != count || |
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489 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE)) || |
32 | 490 tmp != count) |
0 | 491 { |
492 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
493 } | |
494 | |
32 | 495 structures_.resize(count); |
496 for (size_t i = 0; i < count; i++) | |
497 { | |
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498 structures_[i].interpretation_ = reader.GetStringValue |
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499 (Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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500 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
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501 "No interpretation"); |
0 | 502 |
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503 structures_[i].name_ = reader.GetStringValue |
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504 (Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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505 DICOM_TAG_ROI_NAME), |
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506 "No name"); |
0 | 507 |
508 Vector color; | |
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509 if (FastParseVector(color, tags, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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510 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
32 | 511 color.size() == 3) |
0 | 512 { |
32 | 513 structures_[i].red_ = ConvertColor(color[0]); |
514 structures_[i].green_ = ConvertColor(color[1]); | |
515 structures_[i].blue_ = ConvertColor(color[2]); | |
516 } | |
517 else | |
518 { | |
519 structures_[i].red_ = 255; | |
520 structures_[i].green_ = 0; | |
521 structures_[i].blue_ = 0; | |
0 | 522 } |
523 | |
32 | 524 size_t countSlices; |
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525 if (!tags.GetSequenceSize(countSlices, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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526 DICOM_TAG_CONTOUR_SEQUENCE))) |
32 | 527 { |
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528 countSlices = 0; |
32 | 529 } |
0 | 530 |
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531 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ |
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532 << "\" with interpretation \"" << structures_[i].interpretation_ |
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533 << "\" containing " << countSlices << " slices (color: " |
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534 << static_cast<int>(structures_[i].red_) << "," |
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535 << static_cast<int>(structures_[i].green_) << "," |
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536 << static_cast<int>(structures_[i].blue_) << ")"; |
0 | 537 |
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538 /** |
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539 * These temporary variables avoid allocating many vectors in |
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540 * the loop below (indeed, "Orthanc::DicomPath" handles a |
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541 * "std::vector<PrefixItem>") |
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542 **/ |
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543 Orthanc::DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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544 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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545 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS); |
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546 |
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547 Orthanc::DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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548 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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549 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE); |
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550 |
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551 Orthanc::DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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552 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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553 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); |
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|
554 |
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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parents:
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diff
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|
555 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155) |
1834
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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556 Orthanc::DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
126522623e20
replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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557 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
126522623e20
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558 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
126522623e20
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559 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); |
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560 |
1834
126522623e20
replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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561 Orthanc::DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
126522623e20
replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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562 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
126522623e20
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563 DICOM_TAG_CONTOUR_DATA); |
786
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564 |
32 | 565 for (size_t j = 0; j < countSlices; j++) |
0 | 566 { |
32 | 567 unsigned int countPoints; |
0 | 568 |
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569 countPointsPath.SetPrefixIndex(1, j); |
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optimizing constructor of DicomStructureSet
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570 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) |
32 | 571 { |
572 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
573 } | |
574 | |
121
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575 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
0 | 576 |
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optimizing constructor of DicomStructureSet
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|
577 geometricTypePath.SetPrefixIndex(1, j); |
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optimizing constructor of DicomStructureSet
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578 std::string type = reader.GetMandatoryStringValue(geometricTypePath); |
32 | 579 if (type != "CLOSED_PLANAR") |
0 | 580 { |
173
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581 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
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582 continue; |
0 | 583 } |
584 | |
122
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585 size_t size; |
786
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586 |
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587 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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parents:
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588 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1) |
122
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589 { |
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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diff
changeset
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590 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry."; |
0 | 591 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
592 } | |
593 | |
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594 referencedInstancePath.SetPrefixIndex(1, j); |
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595 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); |
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|
596 |
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597 contourDataPath.SetPrefixIndex(1, j); |
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598 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); |
0 | 599 |
600 Vector points; | |
1751
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601 |
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602 if (!GenericToolbox::FastParseVector(points, slicesData) || |
32 | 603 points.size() != 3 * countPoints) |
0 | 604 { |
605 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
606 } | |
607 | |
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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changeset
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608 // seen in real world |
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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changeset
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609 if(Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "") |
c20dbaab360c
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parents:
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changeset
|
610 { |
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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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611 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
|
612 } |
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
|
613 |
122
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refactoring DicomStructureSet
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|
614 Polygon polygon(sopInstanceUid); |
132
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fix rtstruct projections
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|
615 polygon.Reserve(countPoints); |
0 | 616 |
32 | 617 for (size_t k = 0; k < countPoints; k++) |
0 | 618 { |
619 Vector v(3); | |
620 v[0] = points[3 * k]; | |
621 v[1] = points[3 * k + 1]; | |
622 v[2] = points[3 * k + 2]; | |
122
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623 polygon.AddPoint(v); |
0 | 624 } |
625 | |
626 structures_[i].polygons_.push_back(polygon); | |
627 } | |
628 } | |
1892
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changeset
|
629 |
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|
630 EstimateGeometry(); |
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changeset
|
631 |
1751
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632 #if STONE_TIME_BLOCKING_OPS |
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changeset
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633 boost::posix_time::ptime timerEnd = boost::posix_time::microsec_clock::universal_time(); |
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|
634 boost::posix_time::time_duration duration = timerEnd - timerStart; |
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changeset
|
635 int64_t durationMs = duration.total_milliseconds(); |
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|
636 LOG(WARNING) << "DicomStructureSet::Setup took " << durationMs << " ms"; |
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|
637 #endif |
0 | 638 } |
639 | |
640 | |
1180
9c8f557ea799
ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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changeset
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641 #if ORTHANC_ENABLE_DCMTK == 1 |
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changeset
|
642 DicomStructureSet::DicomStructureSet(Orthanc::ParsedDicomFile& instance) |
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|
643 { |
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ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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diff
changeset
|
644 ParsedDicomDataset dataset(instance); |
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changeset
|
645 Setup(dataset); |
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|
646 } |
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647 #endif |
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changeset
|
648 |
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changeset
|
649 |
0 | 650 Vector DicomStructureSet::GetStructureCenter(size_t index) const |
651 { | |
652 const Structure& structure = GetStructure(index); | |
653 | |
654 Vector center; | |
158
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LinearAlgebra toolbox
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137
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changeset
|
655 LinearAlgebra::AssignVector(center, 0, 0, 0); |
0 | 656 if (structure.polygons_.empty()) |
657 { | |
658 return center; | |
659 } | |
660 | |
661 double n = static_cast<double>(structure.polygons_.size()); | |
662 | |
663 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
664 polygon != structure.polygons_.end(); ++polygon) | |
665 { | |
122
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666 if (!polygon->GetPoints().empty()) |
0 | 667 { |
122
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|
668 center += polygon->GetPoints().front() / n; |
0 | 669 } |
670 } | |
671 | |
672 return center; | |
673 } | |
674 | |
675 | |
676 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
677 { | |
678 return GetStructure(index).name_; | |
679 } | |
680 | |
681 | |
682 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
683 { | |
684 return GetStructure(index).interpretation_; | |
685 } | |
686 | |
687 | |
804
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PolylineSceneLayer now has one color per chain
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688 Color DicomStructureSet::GetStructureColor(size_t index) const |
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PolylineSceneLayer now has one color per chain
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|
689 { |
61ba4b504e9a
PolylineSceneLayer now has one color per chain
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changeset
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690 const Structure& s = GetStructure(index); |
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changeset
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691 return Color(s.red_, s.green_, s.blue_); |
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diff
changeset
|
692 } |
61ba4b504e9a
PolylineSceneLayer now has one color per chain
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diff
changeset
|
693 |
61ba4b504e9a
PolylineSceneLayer now has one color per chain
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diff
changeset
|
694 |
1885
ddaee6b96501
retrieving rt-struct info
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changeset
|
695 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) const |
0 | 696 { |
697 for (Structures::const_iterator structure = structures_.begin(); | |
698 structure != structures_.end(); ++structure) | |
699 { | |
700 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
701 polygon != structure->polygons_.end(); ++polygon) | |
702 { | |
122
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refactoring DicomStructureSet
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703 instances.insert(polygon->GetSopInstanceUid()); |
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704 } |
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|
705 } |
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refactoring DicomStructureSet
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changeset
|
706 } |
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refactoring DicomStructureSet
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changeset
|
707 |
e3433dabfb8d
refactoring DicomStructureSet
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changeset
|
708 |
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refactoring DicomStructureSet
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changeset
|
709 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
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|
710 const std::string& seriesInstanceUid, |
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changeset
|
711 const CoordinateSystem3D& geometry, |
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refactoring DicomStructureSet
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712 double thickness) |
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refactoring DicomStructureSet
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|
713 { |
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|
714 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
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715 { |
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refactoring DicomStructureSet
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changeset
|
716 // This geometry is already known |
956
a7351ad54960
Made IsContextLost automatically set the flag by checking with the emscripten
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949
diff
changeset
|
717 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
|
718 |
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
719 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
720 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
721 else |
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 (thickness < 0) |
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
726 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
727 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
728 if (!referencedSlices_.empty()) |
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 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
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 (reference.seriesInstanceUid_ != seriesInstanceUid) |
0 | 733 { |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
734 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
735 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
736 } |
0 | 737 |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
738 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
739 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
740 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
741 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
742 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
743 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
744 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
745 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
0 | 746 |
131 | 747 for (Structures::iterator structure = structures_.begin(); |
748 structure != structures_.end(); ++structure) | |
749 { | |
750 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
751 polygon != structure->polygons_.end(); ++polygon) | |
752 { | |
753 polygon->UpdateReferencedSlice(referencedSlices_); | |
754 } | |
755 } | |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
756 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
757 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
758 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
759 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
760 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
761 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
762 CoordinateSystem3D slice(dataset); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
763 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
764 double thickness = 1; // 1 mm by default |
0 | 765 |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
766 std::string s; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
767 Vector v; |
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
768 if (dataset.LookupStringValue(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
137
diff
changeset
|
769 LinearAlgebra::ParseVector(v, s) && |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
770 v.size() > 0) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
771 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
772 thickness = v[0]; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
773 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
774 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
775 std::string instance, series; |
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
776 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
|
777 dataset.LookupStringValue(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
778 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
779 AddReferencedSlice(instance, series, slice, thickness); |
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 else |
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
784 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
785 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
786 |
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 void DicomStructureSet::CheckReferencedSlices() |
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 for (Structures::iterator structure = structures_.begin(); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
791 structure != structures_.end(); ++structure) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
792 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
793 for (Polygons::iterator polygon = structure->polygons_.begin(); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
794 polygon != structure->polygons_.end(); ++polygon) |
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 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
797 { |
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
|
798 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
|
799 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
|
800 { |
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
|
801 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
802 << " missing information about referenced instance " |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
803 << "(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
|
804 } |
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
|
805 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
|
806 { |
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 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
808 << " missing information about referenced instance " |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
809 << "(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
|
810 } |
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
|
811 //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
0 | 812 } |
813 } | |
814 } | |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
815 } |
0 | 816 |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
817 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
818 Vector DicomStructureSet::GetNormal() const |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
819 { |
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
820 if (referencedSlices_.empty()) |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
821 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
822 Vector v; |
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
137
diff
changeset
|
823 LinearAlgebra::AssignVector(v, 0, 0, 1); |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
824 return v; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
825 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
826 else |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
827 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
828 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
829 } |
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 |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
832 bool DicomStructureSet::ProjectStructure( |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
833 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
1895
14c8f339d480
removed redundant definitions Point2D, Point3D and Vector3D from DicomStructureSetUtils.h
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1893
diff
changeset
|
834 std::vector< std::vector<ScenePoint2D> >& polygons, |
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835 #else |
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836 std::vector< std::pair<ScenePoint2D, ScenePoint2D> >& segments, |
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837 #endif |
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838 const Structure& structure, |
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839 const CoordinateSystem3D& sourceSlice) const |
125 | 840 { |
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841 const CoordinateSystem3D slice = CoordinateSystem3D::NormalizeCuttingPlane(sourceSlice); |
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842 |
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843 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
125 | 844 polygons.clear(); |
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845 #else |
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846 segments.clear(); |
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847 #endif |
125 | 848 |
849 Vector normal = GetNormal(); | |
850 | |
851 bool isOpposite; | |
852 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal())) | |
853 { | |
854 // This is an axial projection | |
855 | |
794 | 856 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
125 | 857 polygon != structure.polygons_.end(); ++polygon) |
858 { | |
859 if (polygon->IsOnSlice(slice)) | |
860 { | |
1178
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861 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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862 polygons.push_back(std::vector<ScenePoint2D>()); |
125 | 863 |
864 for (Points::const_iterator p = polygon->GetPoints().begin(); | |
865 p != polygon->GetPoints().end(); ++p) | |
866 { | |
867 double x, y; | |
1013
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868 slice.ProjectPoint2(x, y, *p); |
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869 polygons.back().push_back(ScenePoint2D(x, y)); |
125 | 870 } |
1000
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871 #else |
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872 // we need to add all the segments corresponding to this polygon |
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873 const std::vector<Vector>& points3D = polygon->GetPoints(); |
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874 if (points3D.size() >= 3) |
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875 { |
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|
876 ScenePoint2D prev2D; |
1000
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|
877 { |
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|
878 Vector prev = points3D[0]; |
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|
879 double prevX, prevY; |
1013
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diff
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880 slice.ProjectPoint2(prevX, prevY, prev); |
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|
881 prev2D = ScenePoint2D(prevX, prevY); |
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882 } |
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|
883 |
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884 size_t pointCount = points3D.size(); |
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885 for (size_t ipt = 1; ipt < pointCount; ++ipt) |
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|
886 { |
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diff
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|
887 Vector next = points3D[ipt]; |
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diff
changeset
|
888 double nextX, nextY; |
1013
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diff
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|
889 slice.ProjectPoint2(nextX, nextY, next); |
1895
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removed redundant definitions Point2D, Point3D and Vector3D from DicomStructureSetUtils.h
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diff
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|
890 ScenePoint2D next2D(nextX, nextY); |
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diff
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|
891 segments.push_back(std::pair<ScenePoint2D, ScenePoint2D>(prev2D, next2D)); |
1000
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diff
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|
892 prev2D = next2D; |
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diff
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|
893 } |
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|
894 } |
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|
895 else |
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diff
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|
896 { |
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diff
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|
897 LOG(ERROR) << "Contour with less than 3 points!"; |
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diff
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|
898 // !!! |
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|
899 } |
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diff
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|
900 #endif |
125 | 901 } |
902 } | |
903 | |
904 return true; | |
905 } | |
906 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) || | |
907 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY())) | |
908 { | |
132
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131
diff
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|
909 #if 1 |
126
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diff
changeset
|
910 // Sagittal or coronal projection |
1000
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|
911 |
1178
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DicomStructureSet::ProjectOntoLayer()
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diff
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|
912 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
126
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125
diff
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|
913 std::vector<BoostPolygon> projected; |
1162
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diff
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|
914 |
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
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diff
changeset
|
915 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
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diff
changeset
|
916 polygon != structure.polygons_.end(); ++polygon) |
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recovery of USE_BOOST_UNION_FOR_POLYGONS
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|
917 { |
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recovery of USE_BOOST_UNION_FOR_POLYGONS
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diff
changeset
|
918 double x1, y1, x2, y2; |
709aa65aca17
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changeset
|
919 |
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
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diff
changeset
|
920 if (polygon->Project(x1, y1, x2, y2, slice)) |
709aa65aca17
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|
921 { |
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diff
changeset
|
922 projected.push_back(CreateRectangle(x1, y1, x2, y2)); |
709aa65aca17
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|
923 } |
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
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|
924 } |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
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|
925 #else |
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diff
changeset
|
926 // this will contain the intersection of the polygon slab with |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
927 // the cutting plane, projected on the cutting plane coord system |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
928 // (that yields a rectangle) + the Z coordinate of the polygon |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
929 // (this is required to group polygons with the same Z later) |
50e5acf5553b
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Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
930 std::vector<std::pair<RtStructRectangleInSlab, double> > projected; |
1162
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|
931 |
794 | 932 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
126
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diff
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|
933 polygon != structure.polygons_.end(); ++polygon) |
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diff
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934 { |
131 | 935 double x1, y1, x2, y2; |
1000
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changed RTSTRUCT rendering from polygons to segments
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diff
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|
936 |
131 | 937 if (polygon->Project(x1, y1, x2, y2, slice)) |
126
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diff
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|
938 { |
1000
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|
939 double curZ = polygon->GetGeometryOrigin()[2]; |
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|
940 |
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diff
changeset
|
941 // x1,y1 and x2,y2 are in "slice" coordinates (the cutting plane |
50e5acf5553b
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diff
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|
942 // geometry) |
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diff
changeset
|
943 projected.push_back(std::make_pair(CreateRectangle( |
1178
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DicomStructureSet::ProjectOntoLayer()
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944 static_cast<float>(x1), |
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945 static_cast<float>(y1), |
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946 static_cast<float>(x2), |
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947 static_cast<float>(y2)),curZ)); |
126
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948 } |
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949 } |
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diff
changeset
|
950 #endif |
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|
951 |
1178
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DicomStructureSet::ProjectOntoLayer()
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changeset
|
952 #if USE_BOOST_UNION_FOR_POLYGONS != 1 |
1000
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changed RTSTRUCT rendering from polygons to segments
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changeset
|
953 // projected contains a set of rectangles specified by two opposite |
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changed RTSTRUCT rendering from polygons to segments
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diff
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|
954 // corners (x1,y1,x2,y2) |
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diff
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|
955 // we need to merge them |
50e5acf5553b
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|
956 // each slab yields ONE polygon! |
126
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diff
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|
957 |
1000
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changed RTSTRUCT rendering from polygons to segments
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diff
changeset
|
958 // we need to sorted all the rectangles that originate from the same Z |
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diff
changeset
|
959 // into lanes. To make sure they are grouped together in the array, we |
50e5acf5553b
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diff
changeset
|
960 // sort it. |
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changeset
|
961 std::sort(projected.begin(), projected.end(), CompareRectanglesForProjection); |
50e5acf5553b
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|
962 |
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diff
changeset
|
963 std::vector<RtStructRectanglesInSlab> rectanglesForEachSlab; |
50e5acf5553b
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changeset
|
964 rectanglesForEachSlab.reserve(projected.size()); |
50e5acf5553b
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diff
changeset
|
965 |
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changed RTSTRUCT rendering from polygons to segments
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changeset
|
966 double curZ = 0; |
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changeset
|
967 for (size_t i = 0; i < projected.size(); ++i) |
50e5acf5553b
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|
968 { |
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diff
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|
969 #if 0 |
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diff
changeset
|
970 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
50e5acf5553b
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|
971 #else |
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diff
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|
972 if (i == 0) |
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diff
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|
973 { |
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changed RTSTRUCT rendering from polygons to segments
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diff
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|
974 curZ = projected[i].second; |
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diff
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|
975 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
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diff
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|
976 } |
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diff
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|
977 else |
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diff
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|
978 { |
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diff
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|
979 // this check is needed to prevent creating a new slab if |
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diff
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|
980 // the new polygon is at the same Z coord than last one |
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changed RTSTRUCT rendering from polygons to segments
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diff
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981 if (!LinearAlgebra::IsNear(curZ, projected[i].second)) |
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diff
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|
982 { |
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Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
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|
983 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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diff
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|
984 curZ = projected[i].second; |
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diff
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|
985 } |
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diff
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|
986 } |
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diff
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|
987 #endif |
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diff
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|
988 |
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diff
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989 rectanglesForEachSlab.back().push_back(projected[i].first); |
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changed RTSTRUCT rendering from polygons to segments
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diff
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|
990 |
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parents:
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diff
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|
991 // as long as they have the same y, we should put them into the same lane |
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changed RTSTRUCT rendering from polygons to segments
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diff
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|
992 // BUT in Sebastien's code, there is only one polygon per lane. |
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diff
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|
993 |
50e5acf5553b
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994
diff
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|
994 //std::cout << "rect: xmin = " << rect.xmin << " xmax = " << rect.xmax << " ymin = " << rect.ymin << " ymax = " << rect.ymax << std::endl; |
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diff
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|
995 } |
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994
diff
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|
996 |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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994
diff
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|
997 // now we need to sort the slabs in increasing Y order (see ConvertListOfSlabsToSegments) |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
changeset
|
998 std::sort(rectanglesForEachSlab.begin(), rectanglesForEachSlab.end(), CompareSlabsY); |
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diff
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|
999 |
50e5acf5553b
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diff
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|
1000 ConvertListOfSlabsToSegments(segments, rectanglesForEachSlab, projected.size()); |
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diff
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|
1001 #else |
126
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diff
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|
1002 BoostMultiPolygon merged; |
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diff
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|
1003 Union(merged, projected); |
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diff
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|
1004 |
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diff
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|
1005 polygons.resize(merged.size()); |
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diff
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1006 for (size_t i = 0; i < merged.size(); i++) |
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diff
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1007 { |
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diff
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1008 const std::vector<BoostPoint>& outer = merged[i].outer(); |
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1009 |
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|
1010 polygons[i].resize(outer.size()); |
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1011 for (size_t j = 0; j < outer.size(); j++) |
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1012 { |
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1013 polygons[i][j] = ScenePoint2D(outer[j].x(), outer[j].y()); |
126
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1014 } |
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1015 } |
1000
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|
1016 #endif |
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1017 |
132
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1018 #else |
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1019 for (Polygons::iterator polygon = structure.polygons_.begin(); |
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1020 polygon != structure.polygons_.end(); ++polygon) |
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diff
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|
1021 { |
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1022 double x1, y1, x2, y2; |
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1023 if (polygon->Project(x1, y1, x2, y2, slice)) |
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1024 { |
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diff
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1025 std::vector<ScenePoint2D> p(4); |
132
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1026 p[0] = std::make_pair(x1, y1); |
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1027 p[1] = std::make_pair(x2, y1); |
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1028 p[2] = std::make_pair(x2, y2); |
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1029 p[3] = std::make_pair(x1, y2); |
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1030 polygons.push_back(p); |
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1031 } |
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|
1032 } |
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1033 #endif |
125 | 1034 |
126
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1035 return true; |
125 | 1036 } |
1037 else | |
1038 { | |
1039 return false; | |
1040 } | |
0 | 1041 } |
1178
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|
1042 |
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diff
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|
1043 |
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1044 void DicomStructureSet::ProjectOntoLayer(PolylineSceneLayer& layer, |
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1045 const CoordinateSystem3D& plane, |
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1046 size_t structureIndex, |
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1047 const Color& color) const |
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1048 { |
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diff
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1049 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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|
1050 std::vector< std::vector<ScenePoint2D> > polygons; |
1178
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1051 if (ProjectStructure(polygons, structureIndex, plane)) |
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|
1052 { |
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diff
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1053 for (size_t j = 0; j < polygons.size(); j++) |
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1054 { |
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DicomStructureSet::ProjectOntoLayer()
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diff
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|
1055 std::vector<ScenePoint2D> chain; |
3c7cdbf32e2a
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|
1056 chain.reserve(polygons[j].size()); |
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1057 |
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1058 for (size_t k = 0; k < polygons[j].size(); k++) |
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1059 { |
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diff
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1060 chain.push_back(ScenePoint2D(polygons[j][k].x, polygons[j][k].y)); |
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1061 } |
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1062 |
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DicomStructureSet::ProjectOntoLayer()
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1063 layer.AddChain(chain, true, color.GetRed(), color.GetGreen(), color.GetBlue()); |
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1064 } |
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1065 } |
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|
1066 |
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1067 #else |
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|
1068 std::vector< std::pair<ScenePoint2D, ScenePoint2D> > segments; |
1178
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1069 |
3c7cdbf32e2a
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|
1070 if (ProjectStructure(segments, structureIndex, plane)) |
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|
1071 { |
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|
1072 for (size_t j = 0; j < segments.size(); j++) |
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1073 { |
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|
1074 std::vector<ScenePoint2D> chain(2); |
1895
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|
1075 chain[0] = ScenePoint2D(segments[j].first.GetX(), segments[j].first.GetY()); |
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|
1076 chain[1] = ScenePoint2D(segments[j].second.GetX(), segments[j].second.GetY()); |
1178
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|
1077 layer.AddChain(chain, false, color.GetRed(), color.GetGreen(), color.GetBlue()); |
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1078 } |
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|
1079 } |
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|
1080 #endif |
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1081 } |
1885
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1082 |
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1083 |
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1084 void DicomStructureSet::GetStructurePoints(std::list< std::vector<Vector> >& target, |
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1085 size_t structureIndex, |
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1086 const std::string& sopInstanceUid) const |
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1087 { |
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1088 target.clear(); |
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1089 |
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1090 const Structure& structure = GetStructure(structureIndex); |
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1091 |
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1092 // TODO - Could be optimized by adding a multimap on "Structure", mapping |
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1093 // from SOP Instance UID to polygons |
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1094 |
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1095 for (Polygons::const_iterator it = structure.polygons_.begin(); |
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1096 it != structure.polygons_.end(); ++it) |
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1097 { |
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1098 if (it->GetSopInstanceUid() == sopInstanceUid) |
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1099 { |
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1100 target.push_back(it->GetPoints()); |
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1101 } |
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1102 } |
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1103 } |
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1104 |
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1105 |
1892
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1106 void DicomStructureSet::EstimateGeometry() |
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1107 { |
1892
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1108 static const double PI = boost::math::constants::pi<double>(); |
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1109 |
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1110 BucketAccumulator2D accumulator(0, PI, 9, /* for acos() */ |
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1111 -PI, PI, 9, /* for atan() */ |
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1112 true /* store values */); |
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1113 |
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1114 unsigned int countPolygons = 0; |
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1115 for (size_t i = 0; i < structures_.size(); i++) |
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1116 { |
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1117 const Polygons& polygons = structures_[i].polygons_; |
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1118 |
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1119 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
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1120 { |
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1121 countPolygons++; |
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1122 |
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1123 const Points& points = it->GetPoints(); |
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1124 |
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1125 if (points.size() >= 3) |
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1126 { |
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1127 // Compute the normal of the polygon using 3 successive points |
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1128 Vector normal; |
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1129 bool valid = false; |
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1130 |
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1131 for (size_t i = 0; i + 2 < points.size(); i++) |
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1132 { |
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1133 const Vector& a = points[i]; |
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1134 const Vector& b = points[i + 1]; |
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1135 const Vector& c = points[i + 2]; |
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1136 LinearAlgebra::CrossProduct(normal, b - a, c - a); // (*) |
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1137 LinearAlgebra::NormalizeVector(normal); |
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1138 |
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1139 if (LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(normal), 1.0)) // (**) |
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1140 { |
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1141 valid = true; |
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1142 break; |
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1143 } |
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1144 } |
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1145 |
1892
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1146 if (valid) |
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1147 { |
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1148 // Check that all the points of the polygon lie in the plane defined by the normal |
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1149 double d1 = GeometryToolbox::ProjectAlongNormal(points[0], normal); |
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1150 |
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1151 for (size_t i = 1; i < points.size(); i++) |
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1152 { |
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1153 double d2 = GeometryToolbox::ProjectAlongNormal(points[i], normal); |
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1154 |
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1155 if (!LinearAlgebra::IsNear(d1, d2)) |
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1156 { |
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1157 valid = false; |
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1158 break; |
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1159 } |
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|
1160 } |
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|
1161 } |
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|
1162 |
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1163 if (valid) |
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1164 { |
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1165 if (normal[2] < 0) |
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1166 { |
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1167 normal = -normal; |
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1168 } |
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|
1169 |
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1170 // The normal is a non-zero unit vector because of (*) and (**), so "r == 1" |
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1171 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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1172 |
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1173 const double theta = acos(normal[2]); |
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1174 const double phi = atan(normal[1]); |
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1175 accumulator.AddValue(theta, phi); |
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1176 } |
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|
1177 } |
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|
1178 } |
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1179 } |
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1180 |
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1181 size_t bestX, bestY; |
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1182 accumulator.FindBestBucket(bestX, bestY); |
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1183 |
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1184 if (accumulator.GetBucketContentSize(bestX, bestY) > 0) |
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1185 { |
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1186 double normalTheta, normalPhi; |
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1187 accumulator.ComputeBestMedian(normalTheta, normalPhi); |
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1188 |
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1189 // Back to (x,y,z) normal, taking "r == 1" |
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1190 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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1191 double sinTheta = sin(normalTheta); |
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1192 estimatedNormal_ = LinearAlgebra::CreateVector(sinTheta * cos(normalPhi), sinTheta * sin(normalPhi), cos(normalTheta)); |
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1193 } |
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1194 |
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1195 std::vector<double> polygonsProjection; |
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1196 polygonsProjection.reserve(countPolygons); |
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1197 |
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1198 for (size_t i = 0; i < structures_.size(); i++) |
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|
1199 { |
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1200 const Polygons& polygons = structures_[i].polygons_; |
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1201 |
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1202 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
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1203 { |
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1204 const Points& points = it->GetPoints(); |
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1205 polygonsProjection.push_back(GeometryToolbox::ProjectAlongNormal(points[0], estimatedNormal_)); |
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1206 } |
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1207 } |
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1208 |
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1209 std::sort(polygonsProjection.begin(), polygonsProjection.end()); |
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1210 |
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1211 std::vector<double> deltas; |
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1212 deltas.reserve(polygonsProjection.size()); |
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parents:
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1213 |
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1214 for (size_t i = 0; i + 1 < polygonsProjection.size(); i++) |
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1215 { |
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1216 if (!LinearAlgebra::IsNear(polygonsProjection[i], polygonsProjection[i + 1])) |
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parents:
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1217 { |
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1218 assert(polygonsProjection[i + 1] > polygonsProjection[i]); |
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1219 deltas.push_back(polygonsProjection[i + 1] - polygonsProjection[i]); |
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parents:
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1220 } |
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1221 } |
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1222 |
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1223 if (deltas.empty()) |
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1224 { |
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1225 estimatedSliceThickness_ = 1; |
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1226 } |
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1227 else |
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1228 { |
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|
1229 estimatedSliceThickness_ = LinearAlgebra::ComputeMedian(deltas); |
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1230 } |
1890
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1231 } |
0 | 1232 } |