Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomStructureSet.cpp @ 1898:a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 26 Jan 2022 19:42:04 +0100 |
parents | 144f8f82c15a |
children | 738814c24574 |
rev | line source |
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0 | 1 /** |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
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5 * Copyright (C) 2017-2022 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
0 | 7 * |
8 * This program is free software: you can redistribute it and/or | |
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9 * modify it under the terms of the GNU Lesser General Public License |
47 | 10 * as published by the Free Software Foundation, either version 3 of |
11 * the License, or (at your option) any later version. | |
0 | 12 * |
13 * This program is distributed in the hope that it will be useful, but | |
14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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16 * Lesser General Public License for more details. |
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17 * |
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18 * You should have received a copy of the GNU Lesser General Public |
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19 * License along with this program. If not, see |
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20 * <http://www.gnu.org/licenses/>. |
0 | 21 **/ |
22 | |
23 | |
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24 #define USE_BOOST_UNION_FOR_POLYGONS 0 |
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25 |
0 | 26 #include "DicomStructureSet.h" |
27 | |
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28 #include "BucketAccumulator2D.h" |
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29 #include "GenericToolbox.h" |
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30 #include "GeometryToolbox.h" |
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31 #include "OrthancDatasets/DicomDatasetReader.h" |
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32 |
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33 #include <Logging.h> |
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34 #include <OrthancException.h> |
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35 #include <Toolbox.h> |
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36 |
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37 #if defined(_MSC_VER) |
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38 # pragma warning(push) |
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39 # pragma warning(disable:4244) |
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40 #endif |
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41 |
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42 #if STONE_TIME_BLOCKING_OPS |
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43 # include <boost/date_time/posix_time/posix_time.hpp> |
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44 #endif |
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45 |
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46 #if !defined(USE_BOOST_UNION_FOR_POLYGONS) |
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47 # error Macro USE_BOOST_UNION_FOR_POLYGONS must be defined |
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48 #endif |
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49 |
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50 #include <limits> |
0 | 51 #include <stdio.h> |
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52 #include <boost/math/constants/constants.hpp> |
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53 |
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54 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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55 # include <boost/geometry.hpp> |
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56 # include <boost/geometry/geometries/point_xy.hpp> |
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57 # include <boost/geometry/geometries/polygon.hpp> |
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58 # include <boost/geometry/multi/geometries/multi_polygon.hpp> |
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59 #else |
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60 # include "DicomStructureSetUtils.h" // TODO REMOVE |
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61 # include "UnionOfRectangles.h" |
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62 #endif |
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63 |
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64 #if defined(_MSC_VER) |
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65 # pragma warning(pop) |
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66 #endif |
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67 |
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68 #if ORTHANC_ENABLE_DCMTK == 1 |
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69 # include "ParsedDicomDataset.h" |
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70 #endif |
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71 |
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72 |
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73 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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74 |
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75 typedef boost::geometry::model::d2::point_xy<double> BoostPoint; |
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76 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon; |
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77 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon; |
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78 |
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79 static void Union(BoostMultiPolygon& output, |
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80 std::vector<BoostPolygon>& input) |
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81 { |
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82 for (size_t i = 0; i < input.size(); i++) |
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83 { |
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84 boost::geometry::correct(input[i]); |
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85 } |
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86 |
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87 if (input.size() == 0) |
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88 { |
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89 output.clear(); |
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90 } |
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91 else if (input.size() == 1) |
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92 { |
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93 output.resize(1); |
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94 output[0] = input[0]; |
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95 } |
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96 else |
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97 { |
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98 boost::geometry::union_(input[0], input[1], output); |
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99 |
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100 for (size_t i = 0; i < input.size(); i++) |
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101 { |
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102 BoostMultiPolygon tmp; |
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103 boost::geometry::union_(output, input[i], tmp); |
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104 output = tmp; |
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105 } |
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106 } |
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107 } |
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108 |
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109 static BoostPolygon CreateRectangle(float x1, float y1, |
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110 float x2, float y2) |
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111 { |
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112 BoostPolygon r; |
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113 boost::geometry::append(r, BoostPoint(x1, y1)); |
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114 boost::geometry::append(r, BoostPoint(x1, y2)); |
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115 boost::geometry::append(r, BoostPoint(x2, y2)); |
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116 boost::geometry::append(r, BoostPoint(x2, y1)); |
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117 return r; |
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118 } |
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119 |
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120 #else |
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121 |
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122 namespace OrthancStone |
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123 { |
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124 static RtStructRectangleInSlab CreateRectangle(float x1, float y1, |
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125 float x2, float y2) |
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126 { |
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127 RtStructRectangleInSlab rect; |
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128 rect.xmin = std::min(x1, x2); |
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129 rect.xmax = std::max(x1, x2); |
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130 rect.ymin = std::min(y1, y2); |
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131 rect.ymax = std::max(y1, y2); |
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132 return rect; |
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133 } |
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134 |
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135 bool CompareRectanglesForProjection(const std::pair<RtStructRectangleInSlab,double>& r1, |
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136 const std::pair<RtStructRectangleInSlab, double>& r2) |
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137 { |
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138 return r1.second < r2.second; |
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139 } |
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140 |
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141 bool CompareSlabsY(const RtStructRectanglesInSlab& r1, |
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142 const RtStructRectanglesInSlab& r2) |
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143 { |
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144 if ((r1.size() == 0) || (r2.size() == 0)) |
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145 return false; |
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146 |
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147 return r1[0].ymax < r2[0].ymax; |
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148 } |
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149 } |
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150 |
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151 #endif |
0 | 152 |
153 namespace OrthancStone | |
154 { | |
1504 | 155 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
156 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
157 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
158 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050); | |
159 static const Orthanc::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); | |
160 static const Orthanc::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
161 static const Orthanc::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
162 static const Orthanc::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
163 static const Orthanc::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
164 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
165 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
166 static const Orthanc::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
0 | 167 |
168 | |
169 static uint8_t ConvertColor(double v) | |
170 { | |
171 if (v < 0) | |
172 { | |
173 return 0; | |
174 } | |
175 else if (v >= 255) | |
176 { | |
177 return 255; | |
178 } | |
179 else | |
180 { | |
181 return static_cast<uint8_t>(v); | |
182 } | |
183 } | |
184 | |
185 | |
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186 static bool FastParseVector(Vector& target, |
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187 const IDicomDataset& dataset, |
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188 const Orthanc::DicomPath& tag) |
0 | 189 { |
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190 std::string value; |
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191 return (dataset.GetStringValue(value, tag) && |
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192 GenericToolbox::FastParseVector(target, value)); |
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193 } |
0 | 194 |
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195 bool DicomStructureSet::Polygon::IsPointOnSliceIfAny(const Vector& v) const |
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196 { |
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197 if (hasSlice_) |
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198 { |
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199 double magnitude = |
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200 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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201 bool onSlice = LinearAlgebra::IsNear( |
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202 magnitude, |
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203 projectionAlongNormal_, |
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204 sliceThickness_ / 2.0 /* in mm */); |
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205 if (!onSlice) |
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206 { |
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207 LOG(WARNING) << "This RT-STRUCT contains a point that is off the " |
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208 << "slice of its instance | " |
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209 << "magnitude = " << magnitude << " | " |
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210 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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211 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
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212 } |
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213 return onSlice; |
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214 } |
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215 else |
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216 { |
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217 return true; |
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218 } |
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219 } |
0 | 220 |
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221 void DicomStructureSet::Polygon::AddPoint(const Vector& v) |
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222 { |
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223 #if 1 |
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224 // BGO 2019-09-03 |
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225 if (IsPointOnSliceIfAny(v)) |
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226 { |
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227 points_.push_back(v); |
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228 } |
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229 #else |
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230 CheckPoint(v); |
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231 points_.push_back(v); |
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232 #endif |
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233 } |
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234 |
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235 |
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236 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices) |
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237 { |
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238 if (hasSlice_) |
0 | 239 { |
122
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240 return true; |
32 | 241 } |
242 else | |
243 { | |
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244 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_); |
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245 |
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246 if (it == slices.end()) |
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247 { |
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248 return false; |
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249 } |
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250 else |
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251 { |
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252 // return true; // TODO - TEST |
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253 |
122
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254 const CoordinateSystem3D& geometry = it->second.geometry_; |
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255 |
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256 hasSlice_ = true; |
131 | 257 geometry_ = geometry; |
258 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal()); | |
122
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259 sliceThickness_ = it->second.thickness_; |
0 | 260 |
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261 extent_.Clear(); |
131 | 262 |
1571 | 263 for (Points::const_iterator it2 = points_.begin(); it2 != points_.end(); ++it2) |
122
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264 { |
1571 | 265 if (IsPointOnSliceIfAny(*it2)) |
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266 { |
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267 double x, y; |
1571 | 268 geometry.ProjectPoint2(x, y, *it2); |
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269 extent_.AddPoint(x, y); |
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270 } |
122
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271 } |
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272 return true; |
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273 } |
0 | 274 } |
275 } | |
276 | |
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277 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const |
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278 { |
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279 bool isOpposite = false; |
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280 |
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281 if (points_.empty() || |
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282 !hasSlice_ || |
131 | 283 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal())) |
122
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284 { |
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285 return false; |
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286 } |
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287 |
131 | 288 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal()); |
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289 |
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290 return (LinearAlgebra::IsNear(d, projectionAlongNormal_, |
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291 sliceThickness_ / 2.0)); |
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292 } |
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293 |
131 | 294 bool DicomStructureSet::Polygon::Project(double& x1, |
295 double& y1, | |
296 double& x2, | |
297 double& y2, | |
298 const CoordinateSystem3D& slice) const | |
299 { | |
300 if (!hasSlice_ || | |
132
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301 points_.size() <= 1) |
131 | 302 { |
303 return false; | |
304 } | |
305 | |
306 double x, y; | |
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307 geometry_.ProjectPoint2(x, y, slice.GetOrigin()); |
131 | 308 |
309 bool isOpposite; | |
310 if (GeometryToolbox::IsParallelOrOpposite | |
311 (isOpposite, slice.GetNormal(), geometry_.GetAxisY())) | |
312 { | |
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313 // plane is constant Y |
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314 |
132
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315 if (y < extent_.GetY1() || |
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316 y > extent_.GetY2()) |
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317 { |
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318 // The polygon does not intersect the input slice |
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319 return false; |
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320 } |
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321 |
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322 bool isFirst = true; |
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323 double xmin = std::numeric_limits<double>::infinity(); |
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324 double xmax = -std::numeric_limits<double>::infinity(); |
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325 |
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326 double prevX, prevY; |
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327 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
132
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328 |
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329 for (size_t i = 0; i < points_.size(); i++) |
131 | 330 { |
132
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331 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py |
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332 double curX, curY; |
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333 geometry_.ProjectPoint2(curX, curY, points_[i]); |
132
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334 |
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335 // if prev* and cur* are on opposite sides of y, this means that the |
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336 // segment intersects the plane. |
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337 if ((prevY <= y && curY >= y) || |
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338 (prevY >= y && curY <= y)) |
132
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339 { |
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340 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY); |
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341 xmin = std::min(xmin, p); |
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342 xmax = std::max(xmax, p); |
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343 isFirst = false; |
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344 |
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345 // xmin and xmax represent the extent of the rectangle along the |
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346 // intersection between the plane and the polygon geometry |
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347 |
132
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348 } |
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349 |
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350 prevX = curX; |
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351 prevY = curY; |
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352 } |
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353 |
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354 // if NO segment intersects the plane |
132
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355 if (isFirst) |
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356 { |
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357 return false; |
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358 } |
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359 else |
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360 { |
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361 // y is the plane y coord in the polygon geometry |
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362 // xmin and xmax are ALSO expressed in the polygon geometry |
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363 |
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364 // let's convert them to 3D world geometry... |
132
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365 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) + |
131 | 366 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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367 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) - |
131 | 368 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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369 |
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370 // then to the cutting plane geometry... |
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371 slice.ProjectPoint2(x1, y1, p1); |
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372 slice.ProjectPoint2(x2, y2, p2); |
131 | 373 return true; |
374 } | |
375 } | |
376 else if (GeometryToolbox::IsParallelOrOpposite | |
377 (isOpposite, slice.GetNormal(), geometry_.GetAxisX())) | |
378 { | |
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379 // plane is constant X => Sagittal view (remember that in the |
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380 // sagittal projection, the normal must be swapped) |
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381 |
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382 |
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383 /* |
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384 Please read the comments in the section above, by taking into account |
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385 the fact that, in this case, the plane has a constant X, not Y (in |
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386 polygon geometry_ coordinates) |
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387 */ |
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388 |
132
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389 if (x < extent_.GetX1() || |
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390 x > extent_.GetX2()) |
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391 { |
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392 return false; |
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393 } |
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394 |
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395 bool isFirst = true; |
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396 double ymin = std::numeric_limits<double>::infinity(); |
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397 double ymax = -std::numeric_limits<double>::infinity(); |
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398 |
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399 double prevX, prevY; |
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400 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
132
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401 |
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402 for (size_t i = 0; i < points_.size(); i++) |
131 | 403 { |
132
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404 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py |
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405 double curX, curY; |
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406 geometry_.ProjectPoint2(curX, curY, points_[i]); |
132
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407 |
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408 if ((prevX <= x && curX >= x) || |
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409 (prevX >= x && curX <= x)) |
132
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410 { |
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411 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX); |
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412 ymin = std::min(ymin, p); |
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413 ymax = std::max(ymax, p); |
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414 isFirst = false; |
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415 } |
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416 |
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417 prevX = curX; |
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418 prevY = curY; |
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419 } |
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420 |
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421 if (isFirst) |
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422 { |
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423 return false; |
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424 } |
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425 else |
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426 { |
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427 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) + |
131 | 428 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
132
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429 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) - |
131 | 430 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
431 | |
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432 slice.ProjectPoint2(x1, y1, p1); |
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433 slice.ProjectPoint2(x2, y2, p2); |
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434 |
131 | 435 return true; |
436 } | |
437 } | |
438 else | |
439 { | |
440 // Should not happen | |
441 return false; | |
442 } | |
443 } | |
444 | |
445 | |
0 | 446 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
447 { | |
448 if (index >= structures_.size()) | |
449 { | |
125 | 450 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
0 | 451 } |
452 | |
453 return structures_[index]; | |
454 } | |
455 | |
456 | |
125 | 457 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) |
0 | 458 { |
125 | 459 if (index >= structures_.size()) |
460 { | |
461 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
0 | 462 } |
463 | |
464 return structures_[index]; | |
465 } | |
466 | |
1504 | 467 void DicomStructureSet::Setup(const IDicomDataset& tags) |
0 | 468 { |
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469 #if STONE_TIME_BLOCKING_OPS |
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470 boost::posix_time::ptime timerStart = boost::posix_time::microsec_clock::universal_time(); |
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471 #endif |
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472 |
1504 | 473 DicomDatasetReader reader(tags); |
32 | 474 |
475 size_t count, tmp; | |
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476 if (!tags.GetSequenceSize(count, Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE)) || |
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477 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE)) || |
32 | 478 tmp != count || |
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479 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE)) || |
32 | 480 tmp != count) |
0 | 481 { |
482 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
483 } | |
484 | |
32 | 485 structures_.resize(count); |
486 for (size_t i = 0; i < count; i++) | |
487 { | |
122
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488 structures_[i].interpretation_ = reader.GetStringValue |
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489 (Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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490 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
122
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491 "No interpretation"); |
0 | 492 |
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493 structures_[i].name_ = reader.GetStringValue |
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494 (Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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495 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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496 "No name"); |
0 | 497 |
498 Vector color; | |
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499 if (FastParseVector(color, tags, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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500 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
32 | 501 color.size() == 3) |
0 | 502 { |
32 | 503 structures_[i].red_ = ConvertColor(color[0]); |
504 structures_[i].green_ = ConvertColor(color[1]); | |
505 structures_[i].blue_ = ConvertColor(color[2]); | |
506 } | |
507 else | |
508 { | |
509 structures_[i].red_ = 255; | |
510 structures_[i].green_ = 0; | |
511 structures_[i].blue_ = 0; | |
0 | 512 } |
513 | |
32 | 514 size_t countSlices; |
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515 if (!tags.GetSequenceSize(countSlices, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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516 DICOM_TAG_CONTOUR_SEQUENCE))) |
32 | 517 { |
121
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518 countSlices = 0; |
32 | 519 } |
0 | 520 |
841
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parents:
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diff
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521 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ |
1178
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522 << "\" with interpretation \"" << structures_[i].interpretation_ |
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523 << "\" containing " << countSlices << " slices (color: " |
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524 << static_cast<int>(structures_[i].red_) << "," |
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525 << static_cast<int>(structures_[i].green_) << "," |
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526 << static_cast<int>(structures_[i].blue_) << ")"; |
0 | 527 |
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528 /** |
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529 * These temporary variables avoid allocating many vectors in |
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530 * the loop below (indeed, "Orthanc::DicomPath" handles a |
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531 * "std::vector<PrefixItem>") |
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532 **/ |
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533 Orthanc::DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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534 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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535 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS); |
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536 |
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537 Orthanc::DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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538 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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539 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE); |
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|
540 |
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541 Orthanc::DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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542 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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543 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); |
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|
544 |
981
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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diff
changeset
|
545 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155) |
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|
546 Orthanc::DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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547 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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548 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
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549 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); |
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changeset
|
550 |
1834
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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551 Orthanc::DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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552 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
126522623e20
replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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553 DICOM_TAG_CONTOUR_DATA); |
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optimizing constructor of DicomStructureSet
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554 |
32 | 555 for (size_t j = 0; j < countSlices; j++) |
0 | 556 { |
32 | 557 unsigned int countPoints; |
0 | 558 |
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559 countPointsPath.SetPrefixIndex(1, j); |
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560 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) |
32 | 561 { |
562 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
563 } | |
564 | |
121
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565 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
0 | 566 |
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567 geometricTypePath.SetPrefixIndex(1, j); |
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optimizing constructor of DicomStructureSet
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568 std::string type = reader.GetMandatoryStringValue(geometricTypePath); |
32 | 569 if (type != "CLOSED_PLANAR") |
0 | 570 { |
173
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571 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
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572 continue; |
0 | 573 } |
574 | |
122
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575 size_t size; |
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576 |
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changeset
|
577 imageSequencePath.SetPrefixIndex(1, j); |
981
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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578 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1) |
122
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579 { |
981
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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580 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry."; |
0 | 581 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
582 } | |
583 | |
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584 referencedInstancePath.SetPrefixIndex(1, j); |
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585 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); |
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586 |
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587 contourDataPath.SetPrefixIndex(1, j); |
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optimizing constructor of DicomStructureSet
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588 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); |
0 | 589 |
590 Vector points; | |
1751
946eb7200b82
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diff
changeset
|
591 |
946eb7200b82
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592 if (!GenericToolbox::FastParseVector(points, slicesData) || |
32 | 593 points.size() != 3 * countPoints) |
0 | 594 { |
595 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
596 } | |
597 | |
981
c20dbaab360c
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598 // 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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599 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
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changeset
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600 { |
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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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601 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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diff
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|
602 } |
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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
|
603 |
122
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refactoring DicomStructureSet
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604 Polygon polygon(sopInstanceUid); |
132
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fix rtstruct projections
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|
605 polygon.Reserve(countPoints); |
0 | 606 |
32 | 607 for (size_t k = 0; k < countPoints; k++) |
0 | 608 { |
609 Vector v(3); | |
610 v[0] = points[3 * k]; | |
611 v[1] = points[3 * k + 1]; | |
612 v[2] = points[3 * k + 2]; | |
122
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613 polygon.AddPoint(v); |
0 | 614 } |
615 | |
616 structures_[i].polygons_.push_back(polygon); | |
617 } | |
618 } | |
1892
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619 |
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620 EstimateGeometry(); |
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621 |
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946eb7200b82
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622 #if STONE_TIME_BLOCKING_OPS |
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|
623 boost::posix_time::ptime timerEnd = boost::posix_time::microsec_clock::universal_time(); |
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diff
changeset
|
624 boost::posix_time::time_duration duration = timerEnd - timerStart; |
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|
625 int64_t durationMs = duration.total_milliseconds(); |
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|
626 LOG(WARNING) << "DicomStructureSet::Setup took " << durationMs << " ms"; |
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|
627 #endif |
0 | 628 } |
629 | |
630 | |
1180
9c8f557ea799
ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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changeset
|
631 #if ORTHANC_ENABLE_DCMTK == 1 |
9c8f557ea799
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diff
changeset
|
632 DicomStructureSet::DicomStructureSet(Orthanc::ParsedDicomFile& instance) |
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ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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633 { |
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ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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diff
changeset
|
634 ParsedDicomDataset dataset(instance); |
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ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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diff
changeset
|
635 Setup(dataset); |
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ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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|
636 } |
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ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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diff
changeset
|
637 #endif |
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diff
changeset
|
638 |
9c8f557ea799
ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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diff
changeset
|
639 |
0 | 640 Vector DicomStructureSet::GetStructureCenter(size_t index) const |
641 { | |
642 const Structure& structure = GetStructure(index); | |
643 | |
644 Vector center; | |
158
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LinearAlgebra toolbox
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diff
changeset
|
645 LinearAlgebra::AssignVector(center, 0, 0, 0); |
0 | 646 if (structure.polygons_.empty()) |
647 { | |
648 return center; | |
649 } | |
650 | |
651 double n = static_cast<double>(structure.polygons_.size()); | |
652 | |
653 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
654 polygon != structure.polygons_.end(); ++polygon) | |
655 { | |
122
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refactoring DicomStructureSet
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|
656 if (!polygon->GetPoints().empty()) |
0 | 657 { |
122
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refactoring DicomStructureSet
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658 center += polygon->GetPoints().front() / n; |
0 | 659 } |
660 } | |
661 | |
662 return center; | |
663 } | |
664 | |
665 | |
666 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
667 { | |
668 return GetStructure(index).name_; | |
669 } | |
670 | |
671 | |
672 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
673 { | |
674 return GetStructure(index).interpretation_; | |
675 } | |
676 | |
677 | |
804
61ba4b504e9a
PolylineSceneLayer now has one color per chain
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diff
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|
678 Color DicomStructureSet::GetStructureColor(size_t index) const |
61ba4b504e9a
PolylineSceneLayer now has one color per chain
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diff
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|
679 { |
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PolylineSceneLayer now has one color per chain
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diff
changeset
|
680 const Structure& s = GetStructure(index); |
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PolylineSceneLayer now has one color per chain
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diff
changeset
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681 return Color(s.red_, s.green_, s.blue_); |
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PolylineSceneLayer now has one color per chain
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diff
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|
682 } |
61ba4b504e9a
PolylineSceneLayer now has one color per chain
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diff
changeset
|
683 |
61ba4b504e9a
PolylineSceneLayer now has one color per chain
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parents:
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diff
changeset
|
684 |
1885
ddaee6b96501
retrieving rt-struct info
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diff
changeset
|
685 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) const |
0 | 686 { |
687 for (Structures::const_iterator structure = structures_.begin(); | |
688 structure != structures_.end(); ++structure) | |
689 { | |
690 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
691 polygon != structure->polygons_.end(); ++polygon) | |
692 { | |
122
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refactoring DicomStructureSet
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693 instances.insert(polygon->GetSopInstanceUid()); |
e3433dabfb8d
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694 } |
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diff
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|
695 } |
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diff
changeset
|
696 } |
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|
697 |
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refactoring DicomStructureSet
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|
698 |
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refactoring DicomStructureSet
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699 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
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700 const std::string& seriesInstanceUid, |
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refactoring DicomStructureSet
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701 const CoordinateSystem3D& geometry, |
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refactoring DicomStructureSet
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702 double thickness) |
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703 { |
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704 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
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refactoring DicomStructureSet
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705 { |
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changeset
|
706 // This geometry is already known |
956
a7351ad54960
Made IsContextLost automatically set the flag by checking with the emscripten
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diff
changeset
|
707 LOG(ERROR) << "DicomStructureSet::AddReferencedSlice(): (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()). sopInstanceUid = " << sopInstanceUid; |
981
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
708 |
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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parents:
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changeset
|
709 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
122
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refactoring DicomStructureSet
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710 } |
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refactoring DicomStructureSet
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|
711 else |
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diff
changeset
|
712 { |
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refactoring DicomStructureSet
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713 if (thickness < 0) |
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refactoring DicomStructureSet
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diff
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714 { |
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refactoring DicomStructureSet
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diff
changeset
|
715 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
e3433dabfb8d
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716 } |
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refactoring DicomStructureSet
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diff
changeset
|
717 |
e3433dabfb8d
refactoring DicomStructureSet
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diff
changeset
|
718 if (!referencedSlices_.empty()) |
e3433dabfb8d
refactoring DicomStructureSet
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|
719 { |
e3433dabfb8d
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diff
changeset
|
720 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
changeset
|
721 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
722 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
0 | 723 { |
122
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
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|
724 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
e3433dabfb8d
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diff
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725 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
726 } |
0 | 727 |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
728 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
729 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
730 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
e3433dabfb8d
refactoring DicomStructureSet
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diff
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|
731 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
732 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
733 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
734 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
735 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
0 | 736 |
131 | 737 for (Structures::iterator structure = structures_.begin(); |
738 structure != structures_.end(); ++structure) | |
739 { | |
740 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
741 polygon != structure->polygons_.end(); ++polygon) | |
742 { | |
743 polygon->UpdateReferencedSlice(referencedSlices_); | |
744 } | |
745 } | |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
746 } |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
changeset
|
747 } |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
748 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
749 |
e3433dabfb8d
refactoring DicomStructureSet
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diff
changeset
|
750 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
changeset
|
751 { |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
752 CoordinateSystem3D slice(dataset); |
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 double thickness = 1; // 1 mm by default |
0 | 755 |
122
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
changeset
|
756 std::string s; |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
changeset
|
757 Vector v; |
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
758 if (dataset.LookupStringValue(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
137
diff
changeset
|
759 LinearAlgebra::ParseVector(v, s) && |
122
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
760 v.size() > 0) |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
761 { |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
762 thickness = v[0]; |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
763 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
764 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
765 std::string instance, series; |
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
766 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
|
767 dataset.LookupStringValue(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
768 { |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
769 AddReferencedSlice(instance, series, slice, thickness); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
770 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
771 else |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
772 { |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
773 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
774 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
775 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
776 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
777 |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
778 void DicomStructureSet::CheckReferencedSlices() |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
779 { |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
780 for (Structures::iterator structure = structures_.begin(); |
e3433dabfb8d
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121
diff
changeset
|
781 structure != structures_.end(); ++structure) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
782 { |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
783 for (Polygons::iterator polygon = structure->polygons_.begin(); |
e3433dabfb8d
refactoring DicomStructureSet
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121
diff
changeset
|
784 polygon != structure->polygons_.end(); ++polygon) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
785 { |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
786 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
787 { |
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
|
788 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
|
789 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
|
790 { |
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
|
791 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
792 << " missing information about referenced instance " |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
793 << "(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
|
794 } |
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
|
795 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
|
796 { |
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
|
797 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
798 << " missing information about referenced instance " |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
799 << "(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
|
800 } |
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
801 //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
0 | 802 } |
803 } | |
804 } | |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
805 } |
0 | 806 |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
807 |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
808 Vector DicomStructureSet::GetNormal() const |
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refactoring DicomStructureSet
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parents:
121
diff
changeset
|
809 { |
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
810 if (referencedSlices_.empty()) |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
811 { |
e3433dabfb8d
refactoring DicomStructureSet
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diff
changeset
|
812 Vector v; |
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
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137
diff
changeset
|
813 LinearAlgebra::AssignVector(v, 0, 0, 1); |
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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121
diff
changeset
|
814 return v; |
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refactoring DicomStructureSet
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121
diff
changeset
|
815 } |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
816 else |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
817 { |
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
818 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
e3433dabfb8d
refactoring DicomStructureSet
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diff
changeset
|
819 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
820 } |
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
821 |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
822 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<ScenePoint2D> >& chains, |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
823 const Structure& structure, |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
824 const CoordinateSystem3D& sourceSlice) const |
125 | 825 { |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
826 const CoordinateSystem3D slice = CoordinateSystem3D::NormalizeCuttingPlane(sourceSlice); |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
827 |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
828 chains.clear(); |
125 | 829 |
830 Vector normal = GetNormal(); | |
831 | |
832 bool isOpposite; | |
833 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal())) | |
834 { | |
835 // This is an axial projection | |
836 | |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
837 chains.reserve(structure.polygons_.size()); |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
838 |
794 | 839 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
125 | 840 polygon != structure.polygons_.end(); ++polygon) |
841 { | |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
842 const Points& points = polygon->GetPoints(); |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
843 |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
844 if (polygon->IsOnSlice(slice) && |
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
845 !points.empty()) |
125 | 846 { |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
847 chains.push_back(std::vector<ScenePoint2D>()); |
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simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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848 chains.back().reserve(points.size() + 1); |
125 | 849 |
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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diff
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|
850 for (Points::const_iterator p = points.begin(); |
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851 p != points.end(); ++p) |
125 | 852 { |
853 double x, y; | |
1013
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- Added an optimized ProjectPoint2 to CoordinateSystem3D. It has *not* replaced
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parents:
1006
diff
changeset
|
854 slice.ProjectPoint2(x, y, *p); |
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simplified signature of DicomStructureSet::ProjectStructure()
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855 chains.back().push_back(ScenePoint2D(x, y)); |
125 | 856 } |
1000
50e5acf5553b
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|
857 |
1896
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diff
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|
858 double x0, y0; |
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859 slice.ProjectPoint2(x0, y0, points.front()); |
b3c08e607d9f
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diff
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|
860 chains.back().push_back(ScenePoint2D(x0, y0)); |
125 | 861 } |
862 } | |
863 | |
864 return true; | |
865 } | |
866 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) || | |
867 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY())) | |
868 { | |
126
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|
869 // Sagittal or coronal projection |
1000
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Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
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|
870 |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
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|
871 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
126
c9e88e7935a4
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|
872 std::vector<BoostPolygon> projected; |
1162
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parents:
1013
diff
changeset
|
873 |
709aa65aca17
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diff
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|
874 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
709aa65aca17
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diff
changeset
|
875 polygon != structure.polygons_.end(); ++polygon) |
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parents:
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diff
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|
876 { |
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changeset
|
877 double x1, y1, x2, y2; |
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
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parents:
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diff
changeset
|
878 |
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
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parents:
1013
diff
changeset
|
879 if (polygon->Project(x1, y1, x2, y2, slice)) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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880 { |
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|
881 projected.push_back(CreateRectangle(x1, y1, x2, y2)); |
709aa65aca17
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diff
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|
882 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
883 } |
1897
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
884 |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
885 BoostMultiPolygon merged; |
144f8f82c15a
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
886 Union(merged, projected); |
144f8f82c15a
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
887 |
144f8f82c15a
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
888 chains.resize(merged.size()); |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
889 for (size_t i = 0; i < merged.size(); i++) |
144f8f82c15a
added ctrl key in RtViewerWasm
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parents:
1896
diff
changeset
|
890 { |
144f8f82c15a
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
891 const std::vector<BoostPoint>& outer = merged[i].outer(); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
892 |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
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|
893 chains[i].resize(outer.size()); |
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
894 for (size_t j = 0; j < outer.size(); j++) |
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parents:
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diff
changeset
|
895 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
896 chains[i][j] = ScenePoint2D(outer[j].x(), outer[j].y()); |
144f8f82c15a
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diff
changeset
|
897 } |
144f8f82c15a
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parents:
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diff
changeset
|
898 } |
1898
a5e54bd87b25
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
899 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
900 #elif 0 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
901 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
902 // TODO - Fix possible infinite loop in UnionOfRectangles |
a5e54bd87b25
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
903 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
904 std::list<Extent2D> rectangles; |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
905 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
906 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
a5e54bd87b25
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
907 polygon != structure.polygons_.end(); ++polygon) |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
908 { |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
909 double x1, y1, x2, y2; |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
910 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
911 if (polygon->Project(x1, y1, x2, y2, slice)) |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
912 { |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
913 rectangles.push_back(Extent2D(x1, y1, x2, y2)); |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
914 } |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
915 } |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
916 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
917 typedef std::list< std::vector<ScenePoint2D> > Contours; |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
918 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
919 Contours contours; |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
920 UnionOfRectangles::Apply(contours, rectangles); |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
921 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
922 chains.reserve(contours.size()); |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
923 |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
924 for (Contours::const_iterator it = contours.begin(); it != contours.end(); ++it) |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
925 { |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
926 chains.push_back(*it); |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
927 } |
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
928 |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
929 #else |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
930 // 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
|
931 // 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
|
932 // (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
|
933 // (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
|
934 std::vector<std::pair<RtStructRectangleInSlab, double> > projected; |
1162
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
935 |
794 | 936 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
937 polygon != structure.polygons_.end(); ++polygon) |
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
938 { |
131 | 939 double x1, y1, x2, y2; |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
940 |
131 | 941 if (polygon->Project(x1, y1, x2, y2, slice)) |
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
942 { |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
943 double curZ = polygon->GetGeometryOrigin()[2]; |
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 // 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
|
946 // geometry) |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
947 projected.push_back(std::make_pair(CreateRectangle( |
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
948 static_cast<float>(x1), |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
949 static_cast<float>(y1), |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
950 static_cast<float>(x2), |
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
951 static_cast<float>(y2)),curZ)); |
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
952 } |
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
953 } |
1162
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
954 |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
955 // 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
|
956 // corners (x1,y1,x2,y2) |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
957 // we need to merge them |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
958 // each slab yields ONE polygon! |
126
c9e88e7935a4
rt-struct projection
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125
diff
changeset
|
959 |
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
960 // 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
|
961 // 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
|
962 // sort it. |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
963 std::sort(projected.begin(), projected.end(), CompareRectanglesForProjection); |
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 std::vector<RtStructRectanglesInSlab> rectanglesForEachSlab; |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
966 rectanglesForEachSlab.reserve(projected.size()); |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
967 |
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
968 double curZ = 0; |
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969 for (size_t i = 0; i < projected.size(); ++i) |
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970 { |
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971 #if 0 |
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972 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
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973 #else |
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974 if (i == 0) |
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975 { |
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976 curZ = projected[i].second; |
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977 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
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978 } |
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|
979 else |
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980 { |
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981 // this check is needed to prevent creating a new slab if |
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982 // the new polygon is at the same Z coord than last one |
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983 if (!LinearAlgebra::IsNear(curZ, projected[i].second)) |
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984 { |
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985 rectanglesForEachSlab.push_back(RtStructRectanglesInSlab()); |
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|
986 curZ = projected[i].second; |
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987 } |
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|
988 } |
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989 #endif |
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990 |
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991 rectanglesForEachSlab.back().push_back(projected[i].first); |
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992 |
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993 // as long as they have the same y, we should put them into the same lane |
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994 // BUT in Sebastien's code, there is only one polygon per lane. |
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995 |
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996 //std::cout << "rect: xmin = " << rect.xmin << " xmax = " << rect.xmax << " ymin = " << rect.ymin << " ymax = " << rect.ymax << std::endl; |
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997 } |
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998 |
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999 // now we need to sort the slabs in increasing Y order (see ConvertListOfSlabsToSegments) |
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1000 std::sort(rectanglesForEachSlab.begin(), rectanglesForEachSlab.end(), CompareSlabsY); |
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1001 |
1896
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1002 std::vector< std::pair<ScenePoint2D, ScenePoint2D> > segments; |
1000
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1003 ConvertListOfSlabsToSegments(segments, rectanglesForEachSlab, projected.size()); |
1896
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1004 |
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1005 chains.resize(segments.size()); |
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1006 for (size_t i = 0; i < segments.size(); i++) |
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1007 { |
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diff
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1008 chains[i].resize(2); |
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1009 chains[i][0] = segments[i].first; |
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1010 chains[i][1] = segments[i].second; |
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1011 } |
1000
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1012 #endif |
125 | 1013 |
126
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1014 return true; |
125 | 1015 } |
1016 else | |
1017 { | |
1018 return false; | |
1019 } | |
0 | 1020 } |
1178
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1021 |
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1022 |
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1023 void DicomStructureSet::ProjectOntoLayer(PolylineSceneLayer& layer, |
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1024 const CoordinateSystem3D& plane, |
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1025 size_t structureIndex, |
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1026 const Color& color) const |
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1027 { |
1896
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1028 std::vector< std::vector<ScenePoint2D> > chains; |
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1029 |
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1030 if (ProjectStructure(chains, structureIndex, plane)) |
1178
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1031 { |
1896
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1032 for (size_t j = 0; j < chains.size(); j++) |
1178
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1033 { |
1896
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1034 layer.AddChain(chains[j], false, color.GetRed(), color.GetGreen(), color.GetBlue()); |
1178
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1035 } |
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1036 } |
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1037 } |
1885
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1038 |
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1039 |
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1040 void DicomStructureSet::GetStructurePoints(std::list< std::vector<Vector> >& target, |
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1041 size_t structureIndex, |
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1042 const std::string& sopInstanceUid) const |
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1043 { |
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1044 target.clear(); |
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1045 |
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1046 const Structure& structure = GetStructure(structureIndex); |
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1047 |
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1048 // TODO - Could be optimized by adding a multimap on "Structure", mapping |
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1049 // from SOP Instance UID to polygons |
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1050 |
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1051 for (Polygons::const_iterator it = structure.polygons_.begin(); |
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1052 it != structure.polygons_.end(); ++it) |
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1053 { |
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1054 if (it->GetSopInstanceUid() == sopInstanceUid) |
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1055 { |
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1056 target.push_back(it->GetPoints()); |
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1057 } |
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1058 } |
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1059 } |
1890
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1060 |
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1061 |
1892
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1062 void DicomStructureSet::EstimateGeometry() |
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1063 { |
1892
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1064 static const double PI = boost::math::constants::pi<double>(); |
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1065 |
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1066 BucketAccumulator2D accumulator(0, PI, 9, /* for acos() */ |
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1067 -PI, PI, 9, /* for atan() */ |
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1068 true /* store values */); |
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1069 |
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1070 unsigned int countPolygons = 0; |
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1071 for (size_t i = 0; i < structures_.size(); i++) |
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1072 { |
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1073 const Polygons& polygons = structures_[i].polygons_; |
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1074 |
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1075 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
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1076 { |
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1077 countPolygons++; |
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1078 |
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1079 const Points& points = it->GetPoints(); |
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1080 |
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1081 if (points.size() >= 3) |
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1082 { |
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1083 // Compute the normal of the polygon using 3 successive points |
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1084 Vector normal; |
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1085 bool valid = false; |
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1086 |
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|
1087 for (size_t i = 0; i + 2 < points.size(); i++) |
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1088 { |
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1089 const Vector& a = points[i]; |
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1090 const Vector& b = points[i + 1]; |
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1091 const Vector& c = points[i + 2]; |
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1092 LinearAlgebra::CrossProduct(normal, b - a, c - a); // (*) |
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1093 LinearAlgebra::NormalizeVector(normal); |
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1094 |
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1095 if (LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(normal), 1.0)) // (**) |
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1096 { |
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1097 valid = true; |
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1098 break; |
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1099 } |
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1100 } |
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1101 |
1892
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1102 if (valid) |
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1103 { |
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1104 // Check that all the points of the polygon lie in the plane defined by the normal |
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1105 double d1 = GeometryToolbox::ProjectAlongNormal(points[0], normal); |
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1106 |
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1107 for (size_t i = 1; i < points.size(); i++) |
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1108 { |
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1109 double d2 = GeometryToolbox::ProjectAlongNormal(points[i], normal); |
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1110 |
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1111 if (!LinearAlgebra::IsNear(d1, d2)) |
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1112 { |
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1113 valid = false; |
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1114 break; |
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|
1115 } |
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|
1116 } |
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|
1117 } |
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|
1118 |
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1119 if (valid) |
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|
1120 { |
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1121 if (normal[2] < 0) |
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|
1122 { |
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|
1123 normal = -normal; |
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|
1124 } |
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|
1125 |
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|
1126 // The normal is a non-zero unit vector because of (*) and (**), so "r == 1" |
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1127 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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|
1128 |
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1129 const double theta = acos(normal[2]); |
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1130 const double phi = atan(normal[1]); |
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|
1131 accumulator.AddValue(theta, phi); |
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|
1132 } |
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|
1133 } |
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|
1134 } |
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|
1135 } |
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|
1136 |
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1137 size_t bestX, bestY; |
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|
1138 accumulator.FindBestBucket(bestX, bestY); |
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|
1139 |
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1140 if (accumulator.GetBucketContentSize(bestX, bestY) > 0) |
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|
1141 { |
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diff
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|
1142 double normalTheta, normalPhi; |
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|
1143 accumulator.ComputeBestMedian(normalTheta, normalPhi); |
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|
1144 |
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diff
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|
1145 // Back to (x,y,z) normal, taking "r == 1" |
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|
1146 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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|
1147 double sinTheta = sin(normalTheta); |
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1148 estimatedNormal_ = LinearAlgebra::CreateVector(sinTheta * cos(normalPhi), sinTheta * sin(normalPhi), cos(normalTheta)); |
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|
1149 } |
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diff
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|
1150 |
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diff
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|
1151 std::vector<double> polygonsProjection; |
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diff
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|
1152 polygonsProjection.reserve(countPolygons); |
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|
1153 |
1890
6ce81914f7e4
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diff
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|
1154 for (size_t i = 0; i < structures_.size(); i++) |
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diff
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|
1155 { |
6ce81914f7e4
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diff
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|
1156 const Polygons& polygons = structures_[i].polygons_; |
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|
1157 |
6ce81914f7e4
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diff
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|
1158 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
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|
1159 { |
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diff
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|
1160 const Points& points = it->GetPoints(); |
1892
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1161 polygonsProjection.push_back(GeometryToolbox::ProjectAlongNormal(points[0], estimatedNormal_)); |
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|
1162 } |
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|
1163 } |
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|
1164 |
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|
1165 std::sort(polygonsProjection.begin(), polygonsProjection.end()); |
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|
1166 |
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|
1167 std::vector<double> deltas; |
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|
1168 deltas.reserve(polygonsProjection.size()); |
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|
1169 |
1892
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1170 for (size_t i = 0; i + 1 < polygonsProjection.size(); i++) |
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|
1171 { |
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|
1172 if (!LinearAlgebra::IsNear(polygonsProjection[i], polygonsProjection[i + 1])) |
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|
1173 { |
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|
1174 assert(polygonsProjection[i + 1] > polygonsProjection[i]); |
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1175 deltas.push_back(polygonsProjection[i + 1] - polygonsProjection[i]); |
1890
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|
1176 } |
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|
1177 } |
1892
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|
1178 |
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|
1179 if (deltas.empty()) |
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|
1180 { |
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diff
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|
1181 estimatedSliceThickness_ = 1; |
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|
1182 } |
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|
1183 else |
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|
1184 { |
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diff
changeset
|
1185 estimatedSliceThickness_ = LinearAlgebra::ComputeMedian(deltas); |
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diff
changeset
|
1186 } |
1890
6ce81914f7e4
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diff
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|
1187 } |
0 | 1188 } |