Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomStructureSet.cpp @ 1896:b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 26 Jan 2022 17:19:37 +0100 |
parents | 14c8f339d480 |
children | 144f8f82c15a |
rev | line source |
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0 | 1 /** |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
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5 * Copyright (C) 2017-2022 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
0 | 7 * |
8 * This program is free software: you can redistribute it and/or | |
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9 * modify it under the terms of the GNU Lesser General Public License |
47 | 10 * as published by the Free Software Foundation, either version 3 of |
11 * the License, or (at your option) any later version. | |
0 | 12 * |
13 * This program is distributed in the hope that it will be useful, but | |
14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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16 * Lesser General Public License for more details. |
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17 * |
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18 * You should have received a copy of the GNU Lesser General Public |
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19 * License along with this program. If not, see |
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20 * <http://www.gnu.org/licenses/>. |
0 | 21 **/ |
22 | |
23 | |
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24 #define USE_BOOST_UNION_FOR_POLYGONS 1 |
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25 |
0 | 26 #include "DicomStructureSet.h" |
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27 #include "DicomStructureSetUtils.h" // TODO REMOVE |
0 | 28 |
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29 #include "BucketAccumulator2D.h" |
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30 #include "GenericToolbox.h" |
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31 #include "GeometryToolbox.h" |
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32 #include "OrthancDatasets/DicomDatasetReader.h" |
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33 |
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34 #include <Logging.h> |
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35 #include <OrthancException.h> |
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36 #include <Toolbox.h> |
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37 |
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38 #if defined(_MSC_VER) |
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39 # pragma warning(push) |
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40 # pragma warning(disable:4244) |
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41 #endif |
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42 |
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43 #if STONE_TIME_BLOCKING_OPS |
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44 # include <boost/date_time/posix_time/posix_time.hpp> |
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45 #endif |
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46 |
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47 #if !defined(USE_BOOST_UNION_FOR_POLYGONS) |
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48 # error Macro USE_BOOST_UNION_FOR_POLYGONS must be defined |
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49 #endif |
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50 |
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51 #include <limits> |
0 | 52 #include <stdio.h> |
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53 #include <boost/math/constants/constants.hpp> |
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54 |
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55 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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56 # include <boost/geometry.hpp> |
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57 # include <boost/geometry/geometries/point_xy.hpp> |
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58 # include <boost/geometry/geometries/polygon.hpp> |
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59 # include <boost/geometry/multi/geometries/multi_polygon.hpp> |
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60 #endif |
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61 |
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62 #if defined(_MSC_VER) |
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63 # pragma warning(pop) |
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64 #endif |
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65 |
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66 #if ORTHANC_ENABLE_DCMTK == 1 |
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67 # include "ParsedDicomDataset.h" |
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68 #endif |
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69 |
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70 |
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71 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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72 |
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73 typedef boost::geometry::model::d2::point_xy<double> BoostPoint; |
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74 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon; |
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75 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon; |
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76 |
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77 static void Union(BoostMultiPolygon& output, |
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78 std::vector<BoostPolygon>& input) |
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79 { |
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80 for (size_t i = 0; i < input.size(); i++) |
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81 { |
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82 boost::geometry::correct(input[i]); |
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83 } |
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84 |
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85 if (input.size() == 0) |
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86 { |
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87 output.clear(); |
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88 } |
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89 else if (input.size() == 1) |
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90 { |
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91 output.resize(1); |
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92 output[0] = input[0]; |
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93 } |
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94 else |
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95 { |
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96 boost::geometry::union_(input[0], input[1], output); |
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97 |
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98 for (size_t i = 0; i < input.size(); i++) |
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99 { |
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100 BoostMultiPolygon tmp; |
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101 boost::geometry::union_(output, input[i], tmp); |
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102 output = tmp; |
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103 } |
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104 } |
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105 } |
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106 |
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107 static BoostPolygon CreateRectangle(float x1, float y1, |
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108 float x2, float y2) |
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109 { |
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110 BoostPolygon r; |
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111 boost::geometry::append(r, BoostPoint(x1, y1)); |
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112 boost::geometry::append(r, BoostPoint(x1, y2)); |
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113 boost::geometry::append(r, BoostPoint(x2, y2)); |
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114 boost::geometry::append(r, BoostPoint(x2, y1)); |
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115 return r; |
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116 } |
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117 |
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118 #else |
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119 |
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120 namespace OrthancStone |
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121 { |
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122 static RtStructRectangleInSlab CreateRectangle(float x1, float y1, |
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123 float x2, float y2) |
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124 { |
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125 RtStructRectangleInSlab rect; |
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126 rect.xmin = std::min(x1, x2); |
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127 rect.xmax = std::max(x1, x2); |
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128 rect.ymin = std::min(y1, y2); |
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129 rect.ymax = std::max(y1, y2); |
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130 return rect; |
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131 } |
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132 |
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133 bool CompareRectanglesForProjection(const std::pair<RtStructRectangleInSlab,double>& r1, |
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134 const std::pair<RtStructRectangleInSlab, double>& r2) |
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135 { |
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136 return r1.second < r2.second; |
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137 } |
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138 |
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139 bool CompareSlabsY(const RtStructRectanglesInSlab& r1, |
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140 const RtStructRectanglesInSlab& r2) |
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141 { |
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142 if ((r1.size() == 0) || (r2.size() == 0)) |
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143 return false; |
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144 |
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145 return r1[0].ymax < r2[0].ymax; |
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146 } |
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147 } |
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148 |
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149 #endif |
0 | 150 |
151 namespace OrthancStone | |
152 { | |
1504 | 153 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
154 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
155 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
156 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050); | |
157 static const Orthanc::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); | |
158 static const Orthanc::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
159 static const Orthanc::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
160 static const Orthanc::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
161 static const Orthanc::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
162 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
163 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
164 static const Orthanc::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
0 | 165 |
166 | |
167 static uint8_t ConvertColor(double v) | |
168 { | |
169 if (v < 0) | |
170 { | |
171 return 0; | |
172 } | |
173 else if (v >= 255) | |
174 { | |
175 return 255; | |
176 } | |
177 else | |
178 { | |
179 return static_cast<uint8_t>(v); | |
180 } | |
181 } | |
182 | |
183 | |
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184 static bool FastParseVector(Vector& target, |
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185 const IDicomDataset& dataset, |
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186 const Orthanc::DicomPath& tag) |
0 | 187 { |
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188 std::string value; |
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189 return (dataset.GetStringValue(value, tag) && |
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190 GenericToolbox::FastParseVector(target, value)); |
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191 } |
0 | 192 |
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193 void DicomStructureSet::Polygon::CheckPointIsOnSlice(const Vector& v) const |
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194 { |
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195 if (hasSlice_) |
0 | 196 { |
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197 double magnitude = |
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198 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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199 if(!LinearAlgebra::IsNear( |
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200 magnitude, |
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201 projectionAlongNormal_, |
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202 sliceThickness_ / 2.0 /* in mm */ )) |
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203 { |
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204 LOG(ERROR) << "This RT-STRUCT contains a point that is off the " |
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205 << "slice of its instance | " |
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206 << "magnitude = " << magnitude << " | " |
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207 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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208 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
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209 |
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210 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
122
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211 } |
0 | 212 } |
122
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213 } |
0 | 214 |
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215 bool DicomStructureSet::Polygon::IsPointOnSliceIfAny(const Vector& v) const |
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216 { |
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217 if (hasSlice_) |
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218 { |
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219 double magnitude = |
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220 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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221 bool onSlice = LinearAlgebra::IsNear( |
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222 magnitude, |
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223 projectionAlongNormal_, |
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224 sliceThickness_ / 2.0 /* in mm */); |
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225 if (!onSlice) |
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226 { |
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227 LOG(WARNING) << "This RT-STRUCT contains a point that is off the " |
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228 << "slice of its instance | " |
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229 << "magnitude = " << magnitude << " | " |
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230 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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231 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
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232 } |
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233 return onSlice; |
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234 } |
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235 else |
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236 { |
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237 return true; |
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238 } |
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239 } |
0 | 240 |
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241 void DicomStructureSet::Polygon::AddPoint(const Vector& v) |
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242 { |
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243 #if 1 |
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244 // BGO 2019-09-03 |
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245 if (IsPointOnSliceIfAny(v)) |
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246 { |
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247 points_.push_back(v); |
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248 } |
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249 #else |
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250 CheckPoint(v); |
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251 points_.push_back(v); |
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252 #endif |
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253 } |
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254 |
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255 |
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256 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices) |
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257 { |
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258 if (hasSlice_) |
0 | 259 { |
122
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260 return true; |
32 | 261 } |
262 else | |
263 { | |
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264 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_); |
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265 |
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266 if (it == slices.end()) |
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267 { |
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268 return false; |
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269 } |
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270 else |
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271 { |
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272 const CoordinateSystem3D& geometry = it->second.geometry_; |
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273 |
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274 hasSlice_ = true; |
131 | 275 geometry_ = geometry; |
276 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal()); | |
122
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277 sliceThickness_ = it->second.thickness_; |
0 | 278 |
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279 extent_.Clear(); |
131 | 280 |
1571 | 281 for (Points::const_iterator it2 = points_.begin(); it2 != points_.end(); ++it2) |
122
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282 { |
1571 | 283 if (IsPointOnSliceIfAny(*it2)) |
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284 { |
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285 double x, y; |
1571 | 286 geometry.ProjectPoint2(x, y, *it2); |
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287 extent_.AddPoint(x, y); |
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288 } |
122
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289 } |
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290 return true; |
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291 } |
0 | 292 } |
293 } | |
294 | |
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295 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const |
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296 { |
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297 bool isOpposite = false; |
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298 |
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299 if (points_.empty() || |
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300 !hasSlice_ || |
131 | 301 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal())) |
122
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302 { |
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303 return false; |
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304 } |
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305 |
131 | 306 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal()); |
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307 |
158
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308 return (LinearAlgebra::IsNear(d, projectionAlongNormal_, |
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309 sliceThickness_ / 2.0)); |
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310 } |
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311 |
131 | 312 bool DicomStructureSet::Polygon::Project(double& x1, |
313 double& y1, | |
314 double& x2, | |
315 double& y2, | |
316 const CoordinateSystem3D& slice) const | |
317 { | |
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318 // TODO: optimize this method using a sweep-line algorithm for polygons |
132
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319 |
131 | 320 if (!hasSlice_ || |
132
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321 points_.size() <= 1) |
131 | 322 { |
323 return false; | |
324 } | |
325 | |
326 double x, y; | |
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327 geometry_.ProjectPoint2(x, y, slice.GetOrigin()); |
131 | 328 |
329 bool isOpposite; | |
330 if (GeometryToolbox::IsParallelOrOpposite | |
331 (isOpposite, slice.GetNormal(), geometry_.GetAxisY())) | |
332 { | |
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333 // plane is constant Y |
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334 |
132
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335 if (y < extent_.GetY1() || |
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336 y > extent_.GetY2()) |
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337 { |
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338 // The polygon does not intersect the input slice |
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339 return false; |
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340 } |
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341 |
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342 bool isFirst = true; |
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343 double xmin = std::numeric_limits<double>::infinity(); |
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344 double xmax = -std::numeric_limits<double>::infinity(); |
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345 |
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346 double prevX, prevY; |
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347 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
132
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348 |
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349 for (size_t i = 0; i < points_.size(); i++) |
131 | 350 { |
132
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351 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py |
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352 double curX, curY; |
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353 geometry_.ProjectPoint2(curX, curY, points_[i]); |
132
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354 |
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355 // if prev* and cur* are on opposite sides of y, this means that the |
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356 // segment intersects the plane. |
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357 if ((prevY <= y && curY >= y) || |
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358 (prevY >= y && curY <= y)) |
132
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359 { |
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360 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY); |
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361 xmin = std::min(xmin, p); |
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362 xmax = std::max(xmax, p); |
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363 isFirst = false; |
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364 |
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365 // xmin and xmax represent the extent of the rectangle along the |
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366 // intersection between the plane and the polygon geometry |
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367 |
132
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368 } |
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369 |
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370 prevX = curX; |
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371 prevY = curY; |
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372 } |
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373 |
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374 // if NO segment intersects the plane |
132
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375 if (isFirst) |
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376 { |
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377 return false; |
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378 } |
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379 else |
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380 { |
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381 // y is the plane y coord in the polygon geometry |
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382 // xmin and xmax are ALSO expressed in the polygon geometry |
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383 |
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384 // let's convert them to 3D world geometry... |
132
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385 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) + |
131 | 386 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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387 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) - |
131 | 388 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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389 |
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390 // then to the cutting plane geometry... |
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391 slice.ProjectPoint2(x1, y1, p1); |
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392 slice.ProjectPoint2(x2, y2, p2); |
131 | 393 return true; |
394 } | |
395 } | |
396 else if (GeometryToolbox::IsParallelOrOpposite | |
397 (isOpposite, slice.GetNormal(), geometry_.GetAxisX())) | |
398 { | |
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399 // plane is constant X => Sagittal view (remember that in the |
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400 // sagittal projection, the normal must be swapped) |
1000
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401 |
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402 |
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403 /* |
1178
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404 Please read the comments in the section above, by taking into account |
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405 the fact that, in this case, the plane has a constant X, not Y (in |
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406 polygon geometry_ coordinates) |
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407 */ |
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408 |
132
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409 if (x < extent_.GetX1() || |
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410 x > extent_.GetX2()) |
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411 { |
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412 return false; |
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413 } |
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414 |
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415 bool isFirst = true; |
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416 double ymin = std::numeric_limits<double>::infinity(); |
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417 double ymax = -std::numeric_limits<double>::infinity(); |
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418 |
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419 double prevX, prevY; |
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420 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
132
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421 |
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422 for (size_t i = 0; i < points_.size(); i++) |
131 | 423 { |
132
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424 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py |
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425 double curX, curY; |
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426 geometry_.ProjectPoint2(curX, curY, points_[i]); |
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427 |
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428 if ((prevX <= x && curX >= x) || |
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429 (prevX >= x && curX <= x)) |
132
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430 { |
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431 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX); |
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432 ymin = std::min(ymin, p); |
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433 ymax = std::max(ymax, p); |
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434 isFirst = false; |
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435 } |
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436 |
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437 prevX = curX; |
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438 prevY = curY; |
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439 } |
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440 |
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441 if (isFirst) |
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442 { |
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443 return false; |
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444 } |
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445 else |
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446 { |
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447 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) + |
131 | 448 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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449 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) - |
131 | 450 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
451 | |
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452 slice.ProjectPoint2(x1, y1, p1); |
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453 slice.ProjectPoint2(x2, y2, p2); |
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454 |
131 | 455 return true; |
456 } | |
457 } | |
458 else | |
459 { | |
460 // Should not happen | |
461 return false; | |
462 } | |
463 } | |
464 | |
465 | |
0 | 466 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
467 { | |
468 if (index >= structures_.size()) | |
469 { | |
125 | 470 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
0 | 471 } |
472 | |
473 return structures_[index]; | |
474 } | |
475 | |
476 | |
125 | 477 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) |
0 | 478 { |
125 | 479 if (index >= structures_.size()) |
480 { | |
481 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
0 | 482 } |
483 | |
484 return structures_[index]; | |
485 } | |
486 | |
1504 | 487 void DicomStructureSet::Setup(const IDicomDataset& tags) |
0 | 488 { |
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489 #if STONE_TIME_BLOCKING_OPS |
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490 boost::posix_time::ptime timerStart = boost::posix_time::microsec_clock::universal_time(); |
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491 #endif |
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492 |
1504 | 493 DicomDatasetReader reader(tags); |
32 | 494 |
495 size_t count, tmp; | |
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496 if (!tags.GetSequenceSize(count, Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE)) || |
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497 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE)) || |
32 | 498 tmp != count || |
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499 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE)) || |
32 | 500 tmp != count) |
0 | 501 { |
502 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
503 } | |
504 | |
32 | 505 structures_.resize(count); |
506 for (size_t i = 0; i < count; i++) | |
507 { | |
122
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508 structures_[i].interpretation_ = reader.GetStringValue |
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509 (Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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510 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
122
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511 "No interpretation"); |
0 | 512 |
122
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513 structures_[i].name_ = reader.GetStringValue |
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514 (Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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515 DICOM_TAG_ROI_NAME), |
949
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OrthancMultiframeVolumeLoader and OrthancSeriesVolumeProgressiveLoader now implement IGeometryProvider so that the geometry reference can be switched (CT or DOSE, for instance) + VolumeImageGeometry::SetSize renamed to VolumeImageGeometry::SetSizeInVoxels + prevent text layer update if text or properties do not change + a few stream operator<< for debug (Vector, Matrix,...) + fixed memory access aligment issues in ImageBuffer3D::ExtractSagittalSlice + fix for wrong screen Y offset of mpr slices in DicomVolumeImageMPRSlicer.
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516 "No name"); |
0 | 517 |
518 Vector color; | |
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519 if (FastParseVector(color, tags, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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520 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
32 | 521 color.size() == 3) |
0 | 522 { |
32 | 523 structures_[i].red_ = ConvertColor(color[0]); |
524 structures_[i].green_ = ConvertColor(color[1]); | |
525 structures_[i].blue_ = ConvertColor(color[2]); | |
526 } | |
527 else | |
528 { | |
529 structures_[i].red_ = 255; | |
530 structures_[i].green_ = 0; | |
531 structures_[i].blue_ = 0; | |
0 | 532 } |
533 | |
32 | 534 size_t countSlices; |
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535 if (!tags.GetSequenceSize(countSlices, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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536 DICOM_TAG_CONTOUR_SEQUENCE))) |
32 | 537 { |
121
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538 countSlices = 0; |
32 | 539 } |
0 | 540 |
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|
541 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ |
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542 << "\" with interpretation \"" << structures_[i].interpretation_ |
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543 << "\" containing " << countSlices << " slices (color: " |
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544 << static_cast<int>(structures_[i].red_) << "," |
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545 << static_cast<int>(structures_[i].green_) << "," |
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546 << static_cast<int>(structures_[i].blue_) << ")"; |
0 | 547 |
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548 /** |
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549 * These temporary variables avoid allocating many vectors in |
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550 * the loop below (indeed, "Orthanc::DicomPath" handles a |
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551 * "std::vector<PrefixItem>") |
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552 **/ |
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553 Orthanc::DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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554 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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555 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS); |
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556 |
1834
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557 Orthanc::DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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558 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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559 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE); |
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560 |
1834
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561 Orthanc::DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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562 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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563 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); |
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564 |
981
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565 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155) |
1834
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566 Orthanc::DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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567 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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568 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
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569 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); |
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570 |
1834
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571 Orthanc::DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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572 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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573 DICOM_TAG_CONTOUR_DATA); |
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574 |
32 | 575 for (size_t j = 0; j < countSlices; j++) |
0 | 576 { |
32 | 577 unsigned int countPoints; |
0 | 578 |
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579 countPointsPath.SetPrefixIndex(1, j); |
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580 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) |
32 | 581 { |
582 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
583 } | |
584 | |
121
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585 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
0 | 586 |
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587 geometricTypePath.SetPrefixIndex(1, j); |
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588 std::string type = reader.GetMandatoryStringValue(geometricTypePath); |
32 | 589 if (type != "CLOSED_PLANAR") |
0 | 590 { |
173
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591 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
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592 continue; |
0 | 593 } |
594 | |
122
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595 size_t size; |
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596 |
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597 imageSequencePath.SetPrefixIndex(1, j); |
981
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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598 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1) |
122
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599 { |
981
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600 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry."; |
0 | 601 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
602 } | |
603 | |
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604 referencedInstancePath.SetPrefixIndex(1, j); |
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605 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); |
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606 |
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607 contourDataPath.SetPrefixIndex(1, j); |
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608 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); |
0 | 609 |
610 Vector points; | |
1751
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611 |
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612 if (!GenericToolbox::FastParseVector(points, slicesData) || |
32 | 613 points.size() != 3 * countPoints) |
0 | 614 { |
615 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
616 } | |
617 | |
981
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618 // seen in real world |
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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changeset
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619 if(Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "") |
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620 { |
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changeset
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621 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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|
622 } |
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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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623 |
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624 Polygon polygon(sopInstanceUid); |
132
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625 polygon.Reserve(countPoints); |
0 | 626 |
32 | 627 for (size_t k = 0; k < countPoints; k++) |
0 | 628 { |
629 Vector v(3); | |
630 v[0] = points[3 * k]; | |
631 v[1] = points[3 * k + 1]; | |
632 v[2] = points[3 * k + 2]; | |
122
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633 polygon.AddPoint(v); |
0 | 634 } |
635 | |
636 structures_[i].polygons_.push_back(polygon); | |
637 } | |
638 } | |
1892
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639 |
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640 EstimateGeometry(); |
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641 |
1751
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642 #if STONE_TIME_BLOCKING_OPS |
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643 boost::posix_time::ptime timerEnd = boost::posix_time::microsec_clock::universal_time(); |
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644 boost::posix_time::time_duration duration = timerEnd - timerStart; |
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645 int64_t durationMs = duration.total_milliseconds(); |
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646 LOG(WARNING) << "DicomStructureSet::Setup took " << durationMs << " ms"; |
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647 #endif |
0 | 648 } |
649 | |
650 | |
1180
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651 #if ORTHANC_ENABLE_DCMTK == 1 |
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652 DicomStructureSet::DicomStructureSet(Orthanc::ParsedDicomFile& instance) |
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653 { |
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654 ParsedDicomDataset dataset(instance); |
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655 Setup(dataset); |
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656 } |
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657 #endif |
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658 |
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659 |
0 | 660 Vector DicomStructureSet::GetStructureCenter(size_t index) const |
661 { | |
662 const Structure& structure = GetStructure(index); | |
663 | |
664 Vector center; | |
158
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|
665 LinearAlgebra::AssignVector(center, 0, 0, 0); |
0 | 666 if (structure.polygons_.empty()) |
667 { | |
668 return center; | |
669 } | |
670 | |
671 double n = static_cast<double>(structure.polygons_.size()); | |
672 | |
673 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
674 polygon != structure.polygons_.end(); ++polygon) | |
675 { | |
122
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676 if (!polygon->GetPoints().empty()) |
0 | 677 { |
122
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678 center += polygon->GetPoints().front() / n; |
0 | 679 } |
680 } | |
681 | |
682 return center; | |
683 } | |
684 | |
685 | |
686 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
687 { | |
688 return GetStructure(index).name_; | |
689 } | |
690 | |
691 | |
692 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
693 { | |
694 return GetStructure(index).interpretation_; | |
695 } | |
696 | |
697 | |
804
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698 Color DicomStructureSet::GetStructureColor(size_t index) const |
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|
699 { |
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700 const Structure& s = GetStructure(index); |
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701 return Color(s.red_, s.green_, s.blue_); |
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702 } |
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703 |
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changeset
|
704 |
1885
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|
705 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) const |
0 | 706 { |
707 for (Structures::const_iterator structure = structures_.begin(); | |
708 structure != structures_.end(); ++structure) | |
709 { | |
710 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
711 polygon != structure->polygons_.end(); ++polygon) | |
712 { | |
122
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713 instances.insert(polygon->GetSopInstanceUid()); |
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refactoring DicomStructureSet
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parents:
121
diff
changeset
|
714 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
715 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
716 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
717 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
718 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
719 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
720 const std::string& seriesInstanceUid, |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
721 const CoordinateSystem3D& geometry, |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
722 double thickness) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
723 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
724 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
725 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
726 // This geometry is already known |
956
a7351ad54960
Made IsContextLost automatically set the flag by checking with the emscripten
Benjamin Golinvaux <bgo@osimis.io>
parents:
949
diff
changeset
|
727 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
|
728 |
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
|
729 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
730 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
731 else |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
732 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
733 if (thickness < 0) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
734 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
735 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
736 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
737 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
738 if (!referencedSlices_.empty()) |
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 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
741 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
742 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
0 | 743 { |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
744 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
745 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
746 } |
0 | 747 |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
748 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
749 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
750 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
751 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
752 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
753 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
754 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
755 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
0 | 756 |
131 | 757 for (Structures::iterator structure = structures_.begin(); |
758 structure != structures_.end(); ++structure) | |
759 { | |
760 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
761 polygon != structure->polygons_.end(); ++polygon) | |
762 { | |
763 polygon->UpdateReferencedSlice(referencedSlices_); | |
764 } | |
765 } | |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
766 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
767 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
768 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
769 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
770 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
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 CoordinateSystem3D slice(dataset); |
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 double thickness = 1; // 1 mm by default |
0 | 775 |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
776 std::string s; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
777 Vector v; |
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
778 if (dataset.LookupStringValue(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
137
diff
changeset
|
779 LinearAlgebra::ParseVector(v, s) && |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
780 v.size() > 0) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
781 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
782 thickness = v[0]; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
783 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
784 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
785 std::string instance, series; |
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
786 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
|
787 dataset.LookupStringValue(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
788 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
789 AddReferencedSlice(instance, series, slice, thickness); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
790 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
791 else |
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 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
794 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
795 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
796 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
797 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
798 void DicomStructureSet::CheckReferencedSlices() |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
799 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
800 for (Structures::iterator structure = structures_.begin(); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
801 structure != structures_.end(); ++structure) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
802 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
803 for (Polygons::iterator polygon = structure->polygons_.begin(); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
804 polygon != structure->polygons_.end(); ++polygon) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
805 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
806 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
807 { |
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
|
808 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
|
809 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
|
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 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
812 << " missing information about referenced instance " |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
813 << "(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
|
814 } |
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
815 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
|
816 { |
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
|
817 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
818 << " missing information about referenced instance " |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
819 << "(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
|
820 } |
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
|
821 //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
0 | 822 } |
823 } | |
824 } | |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
825 } |
0 | 826 |
122
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 Vector DicomStructureSet::GetNormal() const |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
829 { |
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
830 if (referencedSlices_.empty()) |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
831 { |
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832 Vector v; |
158
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LinearAlgebra toolbox
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833 LinearAlgebra::AssignVector(v, 0, 0, 1); |
122
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834 return v; |
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835 } |
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836 else |
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837 { |
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838 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
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839 } |
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840 } |
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841 |
1896
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842 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<ScenePoint2D> >& chains, |
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simplified signature of DicomStructureSet::ProjectStructure()
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|
843 const Structure& structure, |
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simplified signature of DicomStructureSet::ProjectStructure()
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|
844 const CoordinateSystem3D& sourceSlice) const |
125 | 845 { |
1178
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846 const CoordinateSystem3D slice = CoordinateSystem3D::NormalizeCuttingPlane(sourceSlice); |
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DicomStructureSet::ProjectOntoLayer()
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847 |
1896
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simplified signature of DicomStructureSet::ProjectStructure()
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|
848 chains.clear(); |
125 | 849 |
850 Vector normal = GetNormal(); | |
851 | |
852 bool isOpposite; | |
853 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal())) | |
854 { | |
855 // This is an axial projection | |
856 | |
1896
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simplified signature of DicomStructureSet::ProjectStructure()
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857 chains.reserve(structure.polygons_.size()); |
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858 |
794 | 859 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
125 | 860 polygon != structure.polygons_.end(); ++polygon) |
861 { | |
1896
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862 const Points& points = polygon->GetPoints(); |
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|
863 |
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simplified signature of DicomStructureSet::ProjectStructure()
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|
864 if (polygon->IsOnSlice(slice) && |
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simplified signature of DicomStructureSet::ProjectStructure()
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865 !points.empty()) |
125 | 866 { |
1896
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|
867 chains.push_back(std::vector<ScenePoint2D>()); |
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simplified signature of DicomStructureSet::ProjectStructure()
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|
868 chains.back().reserve(points.size() + 1); |
125 | 869 |
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|
870 for (Points::const_iterator p = points.begin(); |
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simplified signature of DicomStructureSet::ProjectStructure()
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|
871 p != points.end(); ++p) |
125 | 872 { |
873 double x, y; | |
1013
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Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
874 slice.ProjectPoint2(x, y, *p); |
1896
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simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
875 chains.back().push_back(ScenePoint2D(x, y)); |
125 | 876 } |
1000
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changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
877 |
1896
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simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
878 double x0, y0; |
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simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
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|
879 slice.ProjectPoint2(x0, y0, points.front()); |
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simplified signature of DicomStructureSet::ProjectStructure()
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|
880 chains.back().push_back(ScenePoint2D(x0, y0)); |
125 | 881 } |
882 } | |
883 | |
884 return true; | |
885 } | |
886 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) || | |
887 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY())) | |
888 { | |
126
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diff
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|
889 // Sagittal or coronal projection |
1000
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changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
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diff
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|
890 |
1178
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DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
891 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
126
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diff
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|
892 std::vector<BoostPolygon> projected; |
1162
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
893 |
709aa65aca17
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Sebastien Jodogne <s.jodogne@gmail.com>
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1013
diff
changeset
|
894 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
709aa65aca17
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diff
changeset
|
895 polygon != structure.polygons_.end(); ++polygon) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
896 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
897 double x1, y1, x2, y2; |
709aa65aca17
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
898 |
709aa65aca17
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
899 if (polygon->Project(x1, y1, x2, y2, slice)) |
709aa65aca17
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
900 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
901 projected.push_back(CreateRectangle(x1, y1, x2, y2)); |
709aa65aca17
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
902 } |
709aa65aca17
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
903 } |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
904 #else |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
905 // this will contain the intersection of the polygon slab with |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
906 // the cutting plane, projected on the cutting plane coord system |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
907 // (that yields a rectangle) + the Z coordinate of the polygon |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
908 // (this is required to group polygons with the same Z later) |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
909 std::vector<std::pair<RtStructRectangleInSlab, double> > projected; |
1162
709aa65aca17
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
910 |
794 | 911 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
126
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125
diff
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|
912 polygon != structure.polygons_.end(); ++polygon) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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125
diff
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|
913 { |
131 | 914 double x1, y1, x2, y2; |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
915 |
131 | 916 if (polygon->Project(x1, y1, x2, y2, slice)) |
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
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125
diff
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|
917 { |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
918 double curZ = polygon->GetGeometryOrigin()[2]; |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
919 |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
920 // x1,y1 and x2,y2 are in "slice" coordinates (the cutting plane |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
921 // geometry) |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
922 projected.push_back(std::make_pair(CreateRectangle( |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
923 static_cast<float>(x1), |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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1170
diff
changeset
|
924 static_cast<float>(y1), |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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1170
diff
changeset
|
925 static_cast<float>(x2), |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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diff
changeset
|
926 static_cast<float>(y2)),curZ)); |
126
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rt-struct projection
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125
diff
changeset
|
927 } |
c9e88e7935a4
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125
diff
changeset
|
928 } |
1162
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
929 #endif |
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
930 |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
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1170
diff
changeset
|
931 #if USE_BOOST_UNION_FOR_POLYGONS != 1 |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
932 // projected contains a set of rectangles specified by two opposite |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
933 // corners (x1,y1,x2,y2) |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
934 // we need to merge them |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
935 // each slab yields ONE polygon! |
126
c9e88e7935a4
rt-struct projection
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125
diff
changeset
|
936 |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
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parents:
994
diff
changeset
|
937 // we need to sorted all the rectangles that originate from the same Z |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
938 // into lanes. To make sure they are grouped together in the array, we |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
939 // sort it. |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
940 std::sort(projected.begin(), projected.end(), CompareRectanglesForProjection); |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
941 |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
942 std::vector<RtStructRectanglesInSlab> rectanglesForEachSlab; |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
943 rectanglesForEachSlab.reserve(projected.size()); |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
944 |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
945 double curZ = 0; |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
946 for (size_t i = 0; i < projected.size(); ++i) |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
947 { |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
948 #if 0 |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
949 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
950 #else |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
951 if (i == 0) |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
952 { |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
953 curZ = projected[i].second; |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
954 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
955 } |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
956 else |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
957 { |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
958 // this check is needed to prevent creating a new slab if |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
959 // the new polygon is at the same Z coord than last one |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
960 if (!LinearAlgebra::IsNear(curZ, projected[i].second)) |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
961 { |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
962 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
963 curZ = projected[i].second; |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
964 } |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
965 } |
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966 #endif |
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967 |
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968 rectanglesForEachSlab.back().push_back(projected[i].first); |
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969 |
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970 // as long as they have the same y, we should put them into the same lane |
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971 // BUT in Sebastien's code, there is only one polygon per lane. |
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972 |
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973 //std::cout << "rect: xmin = " << rect.xmin << " xmax = " << rect.xmax << " ymin = " << rect.ymin << " ymax = " << rect.ymax << std::endl; |
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974 } |
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975 |
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976 // now we need to sort the slabs in increasing Y order (see ConvertListOfSlabsToSegments) |
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977 std::sort(rectanglesForEachSlab.begin(), rectanglesForEachSlab.end(), CompareSlabsY); |
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978 |
1896
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979 std::vector< std::pair<ScenePoint2D, ScenePoint2D> > segments; |
1000
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980 ConvertListOfSlabsToSegments(segments, rectanglesForEachSlab, projected.size()); |
1896
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981 |
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982 chains.resize(segments.size()); |
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983 for (size_t i = 0; i < segments.size(); i++) |
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984 { |
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985 chains[i].resize(2); |
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986 chains[i][0] = segments[i].first; |
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987 chains[i][1] = segments[i].second; |
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988 } |
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989 |
1000
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990 #else |
126
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991 BoostMultiPolygon merged; |
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992 Union(merged, projected); |
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993 |
1896
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994 chains.resize(merged.size()); |
126
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995 for (size_t i = 0; i < merged.size(); i++) |
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996 { |
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997 const std::vector<BoostPoint>& outer = merged[i].outer(); |
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998 |
1896
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999 chains[i].resize(outer.size()); |
126
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1000 for (size_t j = 0; j < outer.size(); j++) |
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1001 { |
1896
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1002 chains[i][j] = ScenePoint2D(outer[j].x(), outer[j].y()); |
126
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1003 } |
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1004 } |
1000
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1005 #endif |
125 | 1006 |
126
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1007 return true; |
125 | 1008 } |
1009 else | |
1010 { | |
1011 return false; | |
1012 } | |
0 | 1013 } |
1178
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1014 |
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1015 |
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1016 void DicomStructureSet::ProjectOntoLayer(PolylineSceneLayer& layer, |
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1017 const CoordinateSystem3D& plane, |
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1018 size_t structureIndex, |
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1019 const Color& color) const |
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1020 { |
1896
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1021 std::vector< std::vector<ScenePoint2D> > chains; |
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1022 |
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1023 if (ProjectStructure(chains, structureIndex, plane)) |
1178
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1024 { |
1896
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1025 for (size_t j = 0; j < chains.size(); j++) |
1178
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1026 { |
1896
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1027 layer.AddChain(chains[j], false, color.GetRed(), color.GetGreen(), color.GetBlue()); |
1178
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1028 } |
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1029 } |
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1030 } |
1885
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1031 |
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1032 |
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1033 void DicomStructureSet::GetStructurePoints(std::list< std::vector<Vector> >& target, |
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1034 size_t structureIndex, |
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1035 const std::string& sopInstanceUid) const |
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1036 { |
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1037 target.clear(); |
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1038 |
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1039 const Structure& structure = GetStructure(structureIndex); |
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1040 |
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1041 // TODO - Could be optimized by adding a multimap on "Structure", mapping |
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1042 // from SOP Instance UID to polygons |
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1043 |
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1044 for (Polygons::const_iterator it = structure.polygons_.begin(); |
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1045 it != structure.polygons_.end(); ++it) |
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1046 { |
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1047 if (it->GetSopInstanceUid() == sopInstanceUid) |
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1048 { |
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1049 target.push_back(it->GetPoints()); |
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1050 } |
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1051 } |
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1052 } |
1890
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1053 |
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1054 |
1892
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1055 void DicomStructureSet::EstimateGeometry() |
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1056 { |
1892
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1057 static const double PI = boost::math::constants::pi<double>(); |
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1058 |
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1059 BucketAccumulator2D accumulator(0, PI, 9, /* for acos() */ |
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1060 -PI, PI, 9, /* for atan() */ |
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1061 true /* store values */); |
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1062 |
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1063 unsigned int countPolygons = 0; |
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1064 for (size_t i = 0; i < structures_.size(); i++) |
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1065 { |
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1066 const Polygons& polygons = structures_[i].polygons_; |
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1067 |
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1068 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
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1069 { |
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1070 countPolygons++; |
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1071 |
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1072 const Points& points = it->GetPoints(); |
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1073 |
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1074 if (points.size() >= 3) |
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1075 { |
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1076 // Compute the normal of the polygon using 3 successive points |
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1077 Vector normal; |
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1078 bool valid = false; |
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1079 |
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1080 for (size_t i = 0; i + 2 < points.size(); i++) |
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1081 { |
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1082 const Vector& a = points[i]; |
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1083 const Vector& b = points[i + 1]; |
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1084 const Vector& c = points[i + 2]; |
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1085 LinearAlgebra::CrossProduct(normal, b - a, c - a); // (*) |
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1086 LinearAlgebra::NormalizeVector(normal); |
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1087 |
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1088 if (LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(normal), 1.0)) // (**) |
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1089 { |
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1090 valid = true; |
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1091 break; |
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1092 } |
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1093 } |
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1094 |
1892
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1095 if (valid) |
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1096 { |
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1097 // Check that all the points of the polygon lie in the plane defined by the normal |
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1098 double d1 = GeometryToolbox::ProjectAlongNormal(points[0], normal); |
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1099 |
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1100 for (size_t i = 1; i < points.size(); i++) |
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1101 { |
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1102 double d2 = GeometryToolbox::ProjectAlongNormal(points[i], normal); |
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1103 |
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1104 if (!LinearAlgebra::IsNear(d1, d2)) |
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1105 { |
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1106 valid = false; |
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1107 break; |
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1108 } |
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1109 } |
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1110 } |
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|
1111 |
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1112 if (valid) |
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1113 { |
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1114 if (normal[2] < 0) |
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1115 { |
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1116 normal = -normal; |
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1117 } |
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|
1118 |
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1119 // The normal is a non-zero unit vector because of (*) and (**), so "r == 1" |
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1120 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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1121 |
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1122 const double theta = acos(normal[2]); |
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1123 const double phi = atan(normal[1]); |
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1124 accumulator.AddValue(theta, phi); |
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1125 } |
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|
1126 } |
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|
1127 } |
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|
1128 } |
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|
1129 |
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1130 size_t bestX, bestY; |
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1131 accumulator.FindBestBucket(bestX, bestY); |
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1132 |
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1133 if (accumulator.GetBucketContentSize(bestX, bestY) > 0) |
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|
1134 { |
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|
1135 double normalTheta, normalPhi; |
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1136 accumulator.ComputeBestMedian(normalTheta, normalPhi); |
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|
1137 |
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1138 // Back to (x,y,z) normal, taking "r == 1" |
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1139 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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1140 double sinTheta = sin(normalTheta); |
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1141 estimatedNormal_ = LinearAlgebra::CreateVector(sinTheta * cos(normalPhi), sinTheta * sin(normalPhi), cos(normalTheta)); |
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|
1142 } |
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|
1143 |
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1144 std::vector<double> polygonsProjection; |
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1145 polygonsProjection.reserve(countPolygons); |
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|
1146 |
1890
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|
1147 for (size_t i = 0; i < structures_.size(); i++) |
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|
1148 { |
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1149 const Polygons& polygons = structures_[i].polygons_; |
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|
1150 |
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|
1151 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
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1152 { |
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|
1153 const Points& points = it->GetPoints(); |
1892
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1154 polygonsProjection.push_back(GeometryToolbox::ProjectAlongNormal(points[0], estimatedNormal_)); |
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|
1155 } |
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|
1156 } |
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|
1157 |
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1158 std::sort(polygonsProjection.begin(), polygonsProjection.end()); |
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|
1159 |
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|
1160 std::vector<double> deltas; |
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1161 deltas.reserve(polygonsProjection.size()); |
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|
1162 |
1892
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1163 for (size_t i = 0; i + 1 < polygonsProjection.size(); i++) |
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1164 { |
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1165 if (!LinearAlgebra::IsNear(polygonsProjection[i], polygonsProjection[i + 1])) |
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1166 { |
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1167 assert(polygonsProjection[i + 1] > polygonsProjection[i]); |
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1168 deltas.push_back(polygonsProjection[i + 1] - polygonsProjection[i]); |
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1169 } |
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|
1170 } |
1892
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|
1171 |
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|
1172 if (deltas.empty()) |
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|
1173 { |
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|
1174 estimatedSliceThickness_ = 1; |
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|
1175 } |
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|
1176 else |
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|
1177 { |
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|
1178 estimatedSliceThickness_ = LinearAlgebra::ComputeMedian(deltas); |
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|
1179 } |
1890
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|
1180 } |
0 | 1181 } |