Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomStructureSet.cpp @ 2140:04211f6fd304 default tip
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 24 Jun 2024 21:01:33 +0200 |
| parents | 16c01cc201e7 |
| children |
| rev | line source |
|---|---|
| 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) 2017-2023 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
| 0 | 7 * |
| 8 * This program is free software: you can redistribute it and/or | |
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9 * modify it under the terms of the GNU Lesser General Public License |
| 47 | 10 * as published by the Free Software Foundation, either version 3 of |
| 11 * the License, or (at your option) any later version. | |
| 0 | 12 * |
| 13 * This program is distributed in the hope that it will be useful, but | |
| 14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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16 * Lesser General Public License for more details. |
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17 * |
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18 * You should have received a copy of the GNU Lesser General Public |
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19 * License along with this program. If not, see |
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20 * <http://www.gnu.org/licenses/>. |
| 0 | 21 **/ |
| 22 | |
| 23 | |
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24 #define USE_BOOST_UNION_FOR_POLYGONS 0 |
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25 |
| 0 | 26 #include "DicomStructureSet.h" |
| 27 | |
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28 #include "BucketAccumulator2D.h" |
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29 #include "GenericToolbox.h" |
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30 #include "GeometryToolbox.h" |
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31 #include "OrthancDatasets/DicomDatasetReader.h" |
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32 |
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33 #include <Logging.h> |
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34 #include <OrthancException.h> |
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35 #include <Toolbox.h> |
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36 |
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37 #if defined(_MSC_VER) |
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38 # pragma warning(push) |
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39 # pragma warning(disable:4244) |
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40 #endif |
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41 |
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42 #if STONE_TIME_BLOCKING_OPS |
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43 # include <boost/date_time/posix_time/posix_time.hpp> |
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44 #endif |
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45 |
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46 #if !defined(USE_BOOST_UNION_FOR_POLYGONS) |
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47 # error Macro USE_BOOST_UNION_FOR_POLYGONS must be defined |
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48 #endif |
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49 |
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50 #include <limits> |
| 0 | 51 #include <stdio.h> |
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52 #include <boost/math/constants/constants.hpp> |
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53 |
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54 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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55 # include <boost/geometry.hpp> |
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56 # include <boost/geometry/geometries/point_xy.hpp> |
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57 # include <boost/geometry/geometries/polygon.hpp> |
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58 # include <boost/geometry/multi/geometries/multi_polygon.hpp> |
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59 #else |
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60 # include "UnionOfRectangles.h" |
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61 #endif |
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62 |
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63 #if defined(_MSC_VER) |
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64 # pragma warning(pop) |
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65 #endif |
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66 |
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67 #if ORTHANC_ENABLE_DCMTK == 1 |
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68 # include "ParsedDicomDataset.h" |
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69 #endif |
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70 |
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71 |
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72 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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73 |
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74 typedef boost::geometry::model::d2::point_xy<double> BoostPoint; |
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75 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon; |
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76 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon; |
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77 |
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78 static void Union(BoostMultiPolygon& output, |
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79 std::vector<BoostPolygon>& input) |
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80 { |
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81 for (size_t i = 0; i < input.size(); i++) |
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82 { |
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83 boost::geometry::correct(input[i]); |
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84 } |
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85 |
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86 if (input.size() == 0) |
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87 { |
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88 output.clear(); |
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89 } |
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90 else if (input.size() == 1) |
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91 { |
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92 output.resize(1); |
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93 output[0] = input[0]; |
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94 } |
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95 else |
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96 { |
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97 boost::geometry::union_(input[0], input[1], output); |
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98 |
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99 for (size_t i = 0; i < input.size(); i++) |
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100 { |
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101 BoostMultiPolygon tmp; |
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102 boost::geometry::union_(output, input[i], tmp); |
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103 output = tmp; |
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104 } |
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105 } |
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106 } |
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107 |
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108 static BoostPolygon CreateRectangle(float x1, float y1, |
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109 float x2, float y2) |
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110 { |
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111 BoostPolygon r; |
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112 boost::geometry::append(r, BoostPoint(x1, y1)); |
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113 boost::geometry::append(r, BoostPoint(x1, y2)); |
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114 boost::geometry::append(r, BoostPoint(x2, y2)); |
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115 boost::geometry::append(r, BoostPoint(x2, y1)); |
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116 return r; |
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117 } |
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118 |
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1908
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119 #endif |
|
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changed RTSTRUCT rendering from polygons to segments
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120 |
| 0 | 121 |
| 122 namespace OrthancStone | |
| 123 { | |
| 1504 | 124 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
| 125 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
| 126 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
| 127 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050); | |
| 128 static const Orthanc::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); | |
| 129 static const Orthanc::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
| 130 static const Orthanc::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
| 131 static const Orthanc::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
| 132 static const Orthanc::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
| 133 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
| 134 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
| 135 static const Orthanc::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
| 0 | 136 |
| 137 | |
| 138 static uint8_t ConvertColor(double v) | |
| 139 { | |
| 140 if (v < 0) | |
| 141 { | |
| 142 return 0; | |
| 143 } | |
| 144 else if (v >= 255) | |
| 145 { | |
| 146 return 255; | |
| 147 } | |
| 148 else | |
| 149 { | |
| 150 return static_cast<uint8_t>(v); | |
| 151 } | |
| 152 } | |
| 153 | |
| 154 | |
|
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155 static bool FastParseVector(Vector& target, |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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156 const IDicomDataset& dataset, |
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157 const Orthanc::DicomPath& tag) |
| 0 | 158 { |
|
118
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159 std::string value; |
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160 return (dataset.GetStringValue(value, tag) && |
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161 GenericToolbox::FastParseVector(target, value)); |
|
118
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162 } |
| 0 | 163 |
|
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Fixed bug in DicomStructureSet that prevented points from being added to polygons
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164 bool DicomStructureSet::Polygon::IsPointOnSliceIfAny(const Vector& v) const |
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165 { |
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166 if (hasSlice_) |
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167 { |
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168 double magnitude = |
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169 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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170 bool onSlice = LinearAlgebra::IsNear( |
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171 magnitude, |
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172 projectionAlongNormal_, |
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173 sliceThickness_ / 2.0 /* in mm */); |
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174 if (!onSlice) |
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175 { |
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176 LOG(WARNING) << "This RT-STRUCT contains a point that is off the " |
|
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177 << "slice of its instance | " |
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178 << "magnitude = " << magnitude << " | " |
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179 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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180 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
|
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181 } |
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182 return onSlice; |
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183 } |
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184 else |
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185 { |
|
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4c9b4c4de814
Fixed bug in DicomStructureSet that prevented points from being added to polygons
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|
186 return true; |
|
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187 } |
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188 } |
| 0 | 189 |
|
122
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|
190 void DicomStructureSet::Polygon::AddPoint(const Vector& v) |
|
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191 { |
|
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192 #if 1 |
|
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193 // BGO 2019-09-03 |
|
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Fixed bug in DicomStructureSet that prevented points from being added to polygons
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parents:
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194 if (IsPointOnSliceIfAny(v)) |
|
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195 { |
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196 points_.push_back(v); |
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197 } |
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198 #else |
|
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199 CheckPoint(v); |
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200 points_.push_back(v); |
|
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201 #endif |
|
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202 } |
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203 |
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204 |
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205 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices) |
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206 { |
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207 if (hasSlice_) |
| 0 | 208 { |
|
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209 return true; |
| 32 | 210 } |
| 211 else | |
| 212 { | |
|
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213 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_); |
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214 |
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215 if (it == slices.end()) |
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216 { |
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217 return false; |
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218 } |
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219 else |
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220 { |
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221 const CoordinateSystem3D& geometry = it->second.geometry_; |
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222 |
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223 hasSlice_ = true; |
| 131 | 224 geometry_ = geometry; |
| 225 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal()); | |
|
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226 sliceThickness_ = it->second.thickness_; |
| 0 | 227 |
|
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228 extent_.Clear(); |
| 131 | 229 |
| 1571 | 230 for (Points::const_iterator it2 = points_.begin(); it2 != points_.end(); ++it2) |
|
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231 { |
| 1571 | 232 if (IsPointOnSliceIfAny(*it2)) |
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233 { |
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234 double x, y; |
| 1571 | 235 geometry.ProjectPoint2(x, y, *it2); |
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236 extent_.AddPoint(x, y); |
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237 } |
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238 } |
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239 return true; |
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240 } |
| 0 | 241 } |
| 242 } | |
| 243 | |
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244 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& cuttingPlane, |
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245 const Vector& estimatedNormal, |
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246 double estimatedSliceThickness) const |
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247 { |
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248 bool isOpposite = false; |
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249 |
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250 if (points_.empty()) |
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251 { |
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252 return false; |
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253 } |
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254 else if (hasSlice_) |
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255 { |
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256 // Use the actual geometry of this specific slice |
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257 if (!GeometryToolbox::IsParallelOrOpposite(isOpposite, cuttingPlane.GetNormal(), geometry_.GetNormal())) |
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258 { |
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259 return false; |
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260 } |
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261 else |
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262 { |
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263 double d = GeometryToolbox::ProjectAlongNormal(cuttingPlane.GetOrigin(), geometry_.GetNormal()); |
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264 return (LinearAlgebra::IsNear(d, projectionAlongNormal_, sliceThickness_ / 2.0)); |
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265 } |
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266 } |
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267 else |
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268 { |
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269 // Use the estimated geometry for the global RT-STRUCT volume |
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270 if (!GeometryToolbox::IsParallelOrOpposite(isOpposite, cuttingPlane.GetNormal(), estimatedNormal)) |
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271 { |
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272 return false; |
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273 } |
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274 else |
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275 { |
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276 double d1 = GeometryToolbox::ProjectAlongNormal(cuttingPlane.GetOrigin(), estimatedNormal); |
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277 double d2 = GeometryToolbox::ProjectAlongNormal(points_.front(), estimatedNormal); |
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278 return (LinearAlgebra::IsNear(d1, d2, estimatedSliceThickness / 2.0)); |
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279 } |
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280 } |
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281 } |
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282 |
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283 |
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284 static void AddSegmentIfIntersection(Extent2D& extent, |
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285 const CoordinateSystem3D& cuttingPlane, |
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286 const Vector& p1, |
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287 const Vector& p2, |
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288 double originDistance) |
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289 { |
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290 // Does this segment intersects the cutting plane? |
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291 double d1 = cuttingPlane.ProjectAlongNormal(p1); |
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292 double d2 = cuttingPlane.ProjectAlongNormal(p2); |
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293 |
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294 if ((d1 < originDistance && d2 > originDistance) || |
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295 (d1 > originDistance && d2 < originDistance)) |
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296 { |
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297 // This is an intersection: Add the segment |
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298 double x, y; |
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299 cuttingPlane.ProjectPoint2(x, y, p1); |
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300 extent.AddPoint(x, y); |
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301 cuttingPlane.ProjectPoint2(x, y, p2); |
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302 extent.AddPoint(x, y); |
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303 } |
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304 } |
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305 |
| 131 | 306 bool DicomStructureSet::Polygon::Project(double& x1, |
| 307 double& y1, | |
| 308 double& x2, | |
| 309 double& y2, | |
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310 const CoordinateSystem3D& cuttingPlane, |
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311 const Vector& estimatedNormal, |
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312 double estimatedSliceThickness) const |
| 131 | 313 { |
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314 if (points_.size() <= 1) |
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315 { |
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316 return false; |
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317 } |
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318 |
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319 Vector normal = estimatedNormal; |
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320 double thickness = estimatedSliceThickness; |
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321 if (hasSlice_) |
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322 { |
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323 normal = geometry_.GetNormal(); |
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324 thickness = sliceThickness_; |
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325 } |
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326 |
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327 bool isOpposite; |
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328 if (!GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cuttingPlane.GetAxisX()) && |
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329 !GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cuttingPlane.GetAxisY())) |
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330 { |
| 131 | 331 return false; |
| 332 } | |
| 333 | |
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334 const double d = cuttingPlane.ProjectAlongNormal(cuttingPlane.GetOrigin()); |
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335 |
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336 Extent2D extent; |
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337 AddSegmentIfIntersection(extent, cuttingPlane, points_[points_.size() - 1], points_[0], d); |
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338 for (size_t i = 1; i < points_.size(); i++) |
| 131 | 339 { |
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340 AddSegmentIfIntersection(extent, cuttingPlane, points_[i - 1], points_[i], d); |
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341 } |
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342 |
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343 if (extent.GetWidth() > 0 || |
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344 extent.GetHeight() > 0) |
| 131 | 345 { |
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346 // Let's convert them to 3D world geometry to add the slice thickness |
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347 Vector p1 = (cuttingPlane.MapSliceToWorldCoordinates(extent.GetX1(), extent.GetY1()) + |
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348 thickness / 2.0 * normal); |
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349 Vector p2 = (cuttingPlane.MapSliceToWorldCoordinates(extent.GetX2(), extent.GetY2()) - |
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350 thickness / 2.0 * normal); |
|
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351 |
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352 // Then back to the cutting plane geometry |
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353 cuttingPlane.ProjectPoint2(x1, y1, p1); |
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354 cuttingPlane.ProjectPoint2(x2, y2, p2); |
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355 return true; |
| 131 | 356 } |
| 357 else | |
| 358 { | |
| 359 return false; | |
| 360 } | |
| 361 } | |
| 362 | |
| 363 | |
| 0 | 364 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
| 365 { | |
| 366 if (index >= structures_.size()) | |
| 367 { | |
| 125 | 368 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
| 0 | 369 } |
| 370 | |
| 371 return structures_[index]; | |
| 372 } | |
| 373 | |
| 374 | |
| 125 | 375 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) |
| 0 | 376 { |
| 125 | 377 if (index >= structures_.size()) |
| 378 { | |
| 379 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 0 | 380 } |
| 381 | |
| 382 return structures_[index]; | |
| 383 } | |
| 384 | |
| 1504 | 385 void DicomStructureSet::Setup(const IDicomDataset& tags) |
| 0 | 386 { |
|
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387 #if STONE_TIME_BLOCKING_OPS |
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388 boost::posix_time::ptime timerStart = boost::posix_time::microsec_clock::universal_time(); |
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389 #endif |
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390 |
| 1504 | 391 DicomDatasetReader reader(tags); |
| 32 | 392 |
| 393 size_t count, tmp; | |
|
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394 if (!tags.GetSequenceSize(count, Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE)) || |
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395 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE)) || |
| 32 | 396 tmp != count || |
|
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397 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE)) || |
| 32 | 398 tmp != count) |
| 0 | 399 { |
| 400 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 401 } | |
| 402 | |
| 32 | 403 structures_.resize(count); |
|
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404 structureNamesIndex_.clear(); |
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405 |
| 32 | 406 for (size_t i = 0; i < count; i++) |
| 407 { | |
|
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408 structures_[i].interpretation_ = reader.GetStringValue |
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409 (Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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410 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
|
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411 "No interpretation"); |
| 0 | 412 |
|
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413 structures_[i].name_ = reader.GetStringValue |
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414 (Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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415 DICOM_TAG_ROI_NAME), |
|
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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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416 "No name"); |
| 0 | 417 |
|
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418 if (structureNamesIndex_.find(structures_[i].name_) == structureNamesIndex_.end()) |
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419 { |
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420 structureNamesIndex_[structures_[i].name_] = i; |
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421 } |
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422 else |
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423 { |
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424 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, |
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425 "RT-STRUCT with twice the same name for a structure: " + structures_[i].name_); |
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426 } |
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427 |
| 0 | 428 Vector color; |
|
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|
429 if (FastParseVector(color, tags, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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|
430 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
| 32 | 431 color.size() == 3) |
| 0 | 432 { |
| 32 | 433 structures_[i].red_ = ConvertColor(color[0]); |
| 434 structures_[i].green_ = ConvertColor(color[1]); | |
| 435 structures_[i].blue_ = ConvertColor(color[2]); | |
| 436 } | |
| 437 else | |
| 438 { | |
| 439 structures_[i].red_ = 255; | |
| 440 structures_[i].green_ = 0; | |
| 441 structures_[i].blue_ = 0; | |
| 0 | 442 } |
| 443 | |
| 32 | 444 size_t countSlices; |
|
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445 if (!tags.GetSequenceSize(countSlices, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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|
446 DICOM_TAG_CONTOUR_SEQUENCE))) |
| 32 | 447 { |
|
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|
448 countSlices = 0; |
| 32 | 449 } |
| 0 | 450 |
|
841
266e2b0b9abc
better error reporting in DicomStructureSetLoader + fixed POST request logic
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
451 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ |
|
1178
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DicomStructureSet::ProjectOntoLayer()
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452 << "\" with interpretation \"" << structures_[i].interpretation_ |
|
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DicomStructureSet::ProjectOntoLayer()
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453 << "\" containing " << countSlices << " slices (color: " |
|
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DicomStructureSet::ProjectOntoLayer()
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454 << static_cast<int>(structures_[i].red_) << "," |
|
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DicomStructureSet::ProjectOntoLayer()
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|
455 << static_cast<int>(structures_[i].green_) << "," |
|
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DicomStructureSet::ProjectOntoLayer()
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|
456 << static_cast<int>(structures_[i].blue_) << ")"; |
| 0 | 457 |
|
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|
458 /** |
|
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|
459 * These temporary variables avoid allocating many vectors in |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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|
460 * the loop below (indeed, "Orthanc::DicomPath" handles a |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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|
461 * "std::vector<PrefixItem>") |
|
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|
462 **/ |
|
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changeset
|
463 Orthanc::DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
126522623e20
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|
464 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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|
465 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS); |
|
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optimizing constructor of DicomStructureSet
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diff
changeset
|
466 |
|
1834
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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changeset
|
467 Orthanc::DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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|
468 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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|
469 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE); |
|
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|
470 |
|
1834
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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|
471 Orthanc::DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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|
472 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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|
473 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); |
|
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changeset
|
474 |
|
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
|
475 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155) |
|
1834
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diff
changeset
|
476 Orthanc::DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
126522623e20
replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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diff
changeset
|
477 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
126522623e20
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|
478 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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diff
changeset
|
479 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); |
|
786
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optimizing constructor of DicomStructureSet
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diff
changeset
|
480 |
|
1834
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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diff
changeset
|
481 Orthanc::DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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changeset
|
482 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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changeset
|
483 DICOM_TAG_CONTOUR_DATA); |
|
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diff
changeset
|
484 |
| 32 | 485 for (size_t j = 0; j < countSlices; j++) |
| 0 | 486 { |
| 32 | 487 unsigned int countPoints; |
| 0 | 488 |
|
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|
489 countPointsPath.SetPrefixIndex(1, j); |
|
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diff
changeset
|
490 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) |
| 32 | 491 { |
| 492 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 493 } | |
| 494 | |
|
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diff
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|
495 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
| 0 | 496 |
|
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changeset
|
497 geometricTypePath.SetPrefixIndex(1, j); |
|
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optimizing constructor of DicomStructureSet
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changeset
|
498 std::string type = reader.GetMandatoryStringValue(geometricTypePath); |
| 32 | 499 if (type != "CLOSED_PLANAR") |
| 0 | 500 { |
|
173
6b0411ac843a
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diff
changeset
|
501 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
|
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changeset
|
502 continue; |
| 0 | 503 } |
| 504 | |
|
122
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diff
changeset
|
505 size_t size; |
|
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diff
changeset
|
506 |
|
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optimizing constructor of DicomStructureSet
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changeset
|
507 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
Benjamin Golinvaux <bgo@osimis.io>
parents:
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diff
changeset
|
508 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1) |
|
122
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diff
changeset
|
509 { |
|
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:
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diff
changeset
|
510 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry."; |
| 0 | 511 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
| 512 } | |
| 513 | |
|
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optimizing constructor of DicomStructureSet
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diff
changeset
|
514 referencedInstancePath.SetPrefixIndex(1, j); |
|
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optimizing constructor of DicomStructureSet
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diff
changeset
|
515 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); |
|
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optimizing constructor of DicomStructureSet
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diff
changeset
|
516 |
|
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optimizing constructor of DicomStructureSet
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517 contourDataPath.SetPrefixIndex(1, j); |
|
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518 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); |
| 0 | 519 |
| 520 Vector points; | |
|
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|
521 |
|
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522 if (!GenericToolbox::FastParseVector(points, slicesData) || |
| 32 | 523 points.size() != 3 * countPoints) |
| 0 | 524 { |
| 525 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 526 } | |
| 527 | |
|
981
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528 // seen in real world |
|
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529 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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530 { |
|
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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diff
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|
531 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)"; |
|
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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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532 } |
|
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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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|
533 |
|
122
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refactoring DicomStructureSet
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|
534 Polygon polygon(sopInstanceUid); |
|
132
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535 polygon.Reserve(countPoints); |
| 0 | 536 |
| 32 | 537 for (size_t k = 0; k < countPoints; k++) |
| 0 | 538 { |
| 539 Vector v(3); | |
| 540 v[0] = points[3 * k]; | |
| 541 v[1] = points[3 * k + 1]; | |
| 542 v[2] = points[3 * k + 2]; | |
|
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543 polygon.AddPoint(v); |
| 0 | 544 } |
| 545 | |
| 546 structures_[i].polygons_.push_back(polygon); | |
| 547 } | |
| 548 } | |
|
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diff
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549 |
|
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550 EstimateGeometry(); |
|
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551 |
|
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552 #if STONE_TIME_BLOCKING_OPS |
|
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553 boost::posix_time::ptime timerEnd = boost::posix_time::microsec_clock::universal_time(); |
|
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554 boost::posix_time::time_duration duration = timerEnd - timerStart; |
|
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555 int64_t durationMs = duration.total_milliseconds(); |
|
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556 LOG(WARNING) << "DicomStructureSet::Setup took " << durationMs << " ms"; |
|
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557 #endif |
| 0 | 558 } |
| 559 | |
| 560 | |
|
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561 #if ORTHANC_ENABLE_DCMTK == 1 |
|
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562 DicomStructureSet::DicomStructureSet(Orthanc::ParsedDicomFile& instance) |
|
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563 { |
|
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564 ParsedDicomDataset dataset(instance); |
|
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|
565 Setup(dataset); |
|
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diff
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|
566 } |
|
9c8f557ea799
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diff
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|
567 #endif |
|
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|
568 |
|
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|
569 |
| 0 | 570 Vector DicomStructureSet::GetStructureCenter(size_t index) const |
| 571 { | |
| 572 const Structure& structure = GetStructure(index); | |
| 573 | |
| 574 Vector center; | |
|
158
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LinearAlgebra toolbox
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|
575 LinearAlgebra::AssignVector(center, 0, 0, 0); |
| 0 | 576 if (structure.polygons_.empty()) |
| 577 { | |
| 578 return center; | |
| 579 } | |
| 580 | |
| 581 double n = static_cast<double>(structure.polygons_.size()); | |
| 582 | |
| 583 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
| 584 polygon != structure.polygons_.end(); ++polygon) | |
| 585 { | |
|
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|
586 if (!polygon->GetPoints().empty()) |
| 0 | 587 { |
|
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588 center += polygon->GetPoints().front() / n; |
| 0 | 589 } |
| 590 } | |
| 591 | |
| 592 return center; | |
| 593 } | |
| 594 | |
| 595 | |
| 596 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
| 597 { | |
| 598 return GetStructure(index).name_; | |
| 599 } | |
| 600 | |
| 601 | |
| 602 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
| 603 { | |
| 604 return GetStructure(index).interpretation_; | |
| 605 } | |
| 606 | |
| 607 | |
|
804
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PolylineSceneLayer now has one color per chain
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diff
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|
608 Color DicomStructureSet::GetStructureColor(size_t index) const |
|
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|
609 { |
|
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PolylineSceneLayer now has one color per chain
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diff
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|
610 const Structure& s = GetStructure(index); |
|
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PolylineSceneLayer now has one color per chain
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|
611 return Color(s.red_, s.green_, s.blue_); |
|
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PolylineSceneLayer now has one color per chain
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parents:
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diff
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|
612 } |
|
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PolylineSceneLayer now has one color per chain
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diff
changeset
|
613 |
|
61ba4b504e9a
PolylineSceneLayer now has one color per chain
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parents:
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diff
changeset
|
614 |
|
1885
ddaee6b96501
retrieving rt-struct info
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diff
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|
615 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) const |
| 0 | 616 { |
| 617 for (Structures::const_iterator structure = structures_.begin(); | |
| 618 structure != structures_.end(); ++structure) | |
| 619 { | |
| 620 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
| 621 polygon != structure->polygons_.end(); ++polygon) | |
| 622 { | |
|
122
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623 instances.insert(polygon->GetSopInstanceUid()); |
|
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|
624 } |
|
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refactoring DicomStructureSet
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|
625 } |
|
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|
626 } |
|
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refactoring DicomStructureSet
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|
627 |
|
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refactoring DicomStructureSet
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diff
changeset
|
628 |
|
e3433dabfb8d
refactoring DicomStructureSet
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|
629 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
|
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|
630 const std::string& seriesInstanceUid, |
|
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|
631 const CoordinateSystem3D& geometry, |
|
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|
632 double thickness) |
|
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refactoring DicomStructureSet
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|
633 { |
|
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|
634 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
|
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|
635 { |
|
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changeset
|
636 // This geometry is already known |
|
956
a7351ad54960
Made IsContextLost automatically set the flag by checking with the emscripten
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parents:
949
diff
changeset
|
637 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
|
638 |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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parents:
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diff
changeset
|
639 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
|
122
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|
640 } |
|
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refactoring DicomStructureSet
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diff
changeset
|
641 else |
|
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refactoring DicomStructureSet
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diff
changeset
|
642 { |
|
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refactoring DicomStructureSet
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|
643 if (thickness < 0) |
|
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refactoring DicomStructureSet
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changeset
|
644 { |
|
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refactoring DicomStructureSet
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changeset
|
645 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
|
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refactoring DicomStructureSet
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|
646 } |
|
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refactoring DicomStructureSet
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diff
changeset
|
647 |
|
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refactoring DicomStructureSet
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|
648 if (!referencedSlices_.empty()) |
|
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refactoring DicomStructureSet
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|
649 { |
|
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changeset
|
650 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
|
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|
651 |
|
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refactoring DicomStructureSet
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diff
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|
652 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
| 0 | 653 { |
|
122
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|
654 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
|
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|
655 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
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refactoring DicomStructureSet
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|
656 } |
| 0 | 657 |
|
122
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|
658 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
|
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|
659 { |
|
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|
660 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
|
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|
661 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
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|
662 } |
|
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|
663 } |
|
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|
664 |
|
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|
665 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
| 0 | 666 |
| 131 | 667 for (Structures::iterator structure = structures_.begin(); |
| 668 structure != structures_.end(); ++structure) | |
| 669 { | |
| 670 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
| 671 polygon != structure->polygons_.end(); ++polygon) | |
| 672 { | |
| 673 polygon->UpdateReferencedSlice(referencedSlices_); | |
| 674 } | |
| 675 } | |
|
122
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|
676 } |
|
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|
677 } |
|
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diff
changeset
|
678 |
|
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changeset
|
679 |
|
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diff
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|
680 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
|
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681 { |
|
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|
682 CoordinateSystem3D slice(dataset); |
|
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diff
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|
683 |
|
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diff
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|
684 double thickness = 1; // 1 mm by default |
| 0 | 685 |
|
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|
686 std::string s; |
|
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diff
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|
687 Vector v; |
|
994
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fix build due to rename in Orthanc::DicomMap
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parents:
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diff
changeset
|
688 if (dataset.LookupStringValue(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
|
158
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LinearAlgebra toolbox
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diff
changeset
|
689 LinearAlgebra::ParseVector(v, s) && |
|
122
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|
690 v.size() > 0) |
|
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|
691 { |
|
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|
692 thickness = v[0]; |
|
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diff
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|
693 } |
|
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refactoring DicomStructureSet
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121
diff
changeset
|
694 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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121
diff
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|
695 std::string instance, series; |
|
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
696 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
|
697 dataset.LookupStringValue(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
|
122
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refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
698 { |
|
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refactoring DicomStructureSet
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diff
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|
699 AddReferencedSlice(instance, series, slice, thickness); |
|
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parents:
121
diff
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|
700 } |
|
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refactoring DicomStructureSet
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parents:
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diff
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|
701 else |
|
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refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
702 { |
|
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refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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|
703 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
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refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
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|
704 } |
|
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refactoring DicomStructureSet
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parents:
121
diff
changeset
|
705 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
706 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
707 |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
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diff
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|
708 void DicomStructureSet::CheckReferencedSlices() |
|
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refactoring DicomStructureSet
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diff
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|
709 { |
|
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refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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121
diff
changeset
|
710 for (Structures::iterator structure = structures_.begin(); |
|
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parents:
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diff
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|
711 structure != structures_.end(); ++structure) |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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|
712 { |
|
e3433dabfb8d
refactoring DicomStructureSet
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|
713 for (Polygons::iterator polygon = structure->polygons_.begin(); |
|
e3433dabfb8d
refactoring DicomStructureSet
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parents:
121
diff
changeset
|
714 polygon != structure->polygons_.end(); ++polygon) |
|
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refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
715 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
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|
716 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
717 { |
|
981
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
718 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
|
719 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
|
720 { |
|
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
|
721 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
722 << " missing information about referenced instance " |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
723 << "(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
|
724 } |
|
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
|
725 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
|
726 { |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
727 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
728 << " missing information about referenced instance " |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
729 << "(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
|
730 } |
|
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
|
731 //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 0 | 732 } |
| 733 } | |
| 734 } | |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
735 } |
| 0 | 736 |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
737 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
738 Vector DicomStructureSet::GetNormal() const |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
739 { |
|
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
740 if (referencedSlices_.empty()) |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
741 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
742 Vector v; |
|
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
137
diff
changeset
|
743 LinearAlgebra::AssignVector(v, 0, 0, 1); |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
744 return v; |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
745 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
746 else |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
747 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
748 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
749 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
750 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
751 |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
752 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
|
753 const Structure& structure, |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
754 const CoordinateSystem3D& cuttingPlane) const |
| 125 | 755 { |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
756 const CoordinateSystem3D cutting = CoordinateSystem3D::NormalizeCuttingPlane(cuttingPlane); |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
757 |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
758 chains.clear(); |
| 125 | 759 |
| 760 Vector normal = GetNormal(); | |
| 761 | |
| 762 bool isOpposite; | |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
763 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cutting.GetNormal())) |
| 125 | 764 { |
| 765 // This is an axial projection | |
| 766 | |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
767 chains.reserve(structure.polygons_.size()); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
768 |
| 794 | 769 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
| 125 | 770 polygon != structure.polygons_.end(); ++polygon) |
| 771 { | |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
772 const Points& points = polygon->GetPoints(); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
773 |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
774 if (polygon->IsOnSlice(cutting, GetEstimatedNormal(), GetEstimatedSliceThickness()) && |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
775 !points.empty()) |
| 125 | 776 { |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
777 chains.push_back(std::vector<ScenePoint2D>()); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
778 chains.back().reserve(points.size() + 1); |
| 125 | 779 |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
780 for (Points::const_iterator p = points.begin(); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
781 p != points.end(); ++p) |
| 125 | 782 { |
| 783 double x, y; | |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
784 cutting.ProjectPoint2(x, y, *p); |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
785 chains.back().push_back(ScenePoint2D(x, y)); |
| 125 | 786 } |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
787 |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
788 double x0, y0; |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
789 cutting.ProjectPoint2(x0, y0, points.front()); |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
790 chains.back().push_back(ScenePoint2D(x0, y0)); |
| 125 | 791 } |
| 792 } | |
| 793 | |
| 794 return true; | |
| 795 } | |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
796 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cutting.GetAxisX()) || |
|
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
797 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cutting.GetAxisY())) |
| 125 | 798 { |
|
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
799 // Sagittal or coronal projection |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
800 |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
801 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
|
126
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|
802 std::vector<BoostPolygon> projected; |
|
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changeset
|
803 |
|
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|
804 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
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|
805 polygon != structure.polygons_.end(); ++polygon) |
|
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|
806 { |
|
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changeset
|
807 double x1, y1, x2, y2; |
|
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changeset
|
808 |
|
1909
782ba9eb6f22
improved variable names
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changeset
|
809 if (polygon->Project(x1, y1, x2, y2, cutting, GetEstimatedNormal(), GetEstimatedSliceThickness())) |
|
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changeset
|
810 { |
|
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changeset
|
811 projected.push_back(CreateRectangle(x1, y1, x2, y2)); |
|
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changeset
|
812 } |
|
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changeset
|
813 } |
|
1897
144f8f82c15a
added ctrl key in RtViewerWasm
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parents:
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changeset
|
814 |
|
144f8f82c15a
added ctrl key in RtViewerWasm
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diff
changeset
|
815 BoostMultiPolygon merged; |
|
144f8f82c15a
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changeset
|
816 Union(merged, projected); |
|
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changeset
|
817 |
|
144f8f82c15a
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changeset
|
818 chains.resize(merged.size()); |
|
144f8f82c15a
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diff
changeset
|
819 for (size_t i = 0; i < merged.size(); i++) |
|
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changeset
|
820 { |
|
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changeset
|
821 const std::vector<BoostPoint>& outer = merged[i].outer(); |
|
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changeset
|
822 |
|
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changeset
|
823 chains[i].resize(outer.size()); |
|
144f8f82c15a
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changeset
|
824 for (size_t j = 0; j < outer.size(); j++) |
|
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changeset
|
825 { |
|
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changeset
|
826 chains[i][j] = ScenePoint2D(outer[j].x(), outer[j].y()); |
|
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changeset
|
827 } |
|
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changeset
|
828 } |
|
1898
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changeset
|
829 |
|
1908
affde38b84de
moved tentative bgo reimplementation of rt-struct into graveyard
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parents:
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diff
changeset
|
830 #else |
|
1898
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changeset
|
831 |
|
a5e54bd87b25
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changeset
|
832 std::list<Extent2D> rectangles; |
|
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changeset
|
833 |
|
a5e54bd87b25
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diff
changeset
|
834 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
|
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changeset
|
835 polygon != structure.polygons_.end(); ++polygon) |
|
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diff
changeset
|
836 { |
|
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diff
changeset
|
837 double x1, y1, x2, y2; |
|
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parents:
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diff
changeset
|
838 |
|
1909
782ba9eb6f22
improved variable names
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parents:
1908
diff
changeset
|
839 if (polygon->Project(x1, y1, x2, y2, cutting, GetEstimatedNormal(), GetEstimatedSliceThickness())) |
|
1898
a5e54bd87b25
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diff
changeset
|
840 { |
|
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try to use UnionOfRectangles in DicomStructureSet
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diff
changeset
|
841 rectangles.push_back(Extent2D(x1, y1, x2, y2)); |
|
a5e54bd87b25
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parents:
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diff
changeset
|
842 } |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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parents:
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diff
changeset
|
843 } |
|
a5e54bd87b25
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1897
diff
changeset
|
844 |
|
a5e54bd87b25
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parents:
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diff
changeset
|
845 typedef std::list< std::vector<ScenePoint2D> > Contours; |
|
a5e54bd87b25
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diff
changeset
|
846 |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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parents:
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diff
changeset
|
847 Contours contours; |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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parents:
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diff
changeset
|
848 UnionOfRectangles::Apply(contours, rectangles); |
|
a5e54bd87b25
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parents:
1897
diff
changeset
|
849 |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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parents:
1897
diff
changeset
|
850 chains.reserve(contours.size()); |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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parents:
1897
diff
changeset
|
851 |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
852 for (Contours::const_iterator it = contours.begin(); it != contours.end(); ++it) |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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parents:
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diff
changeset
|
853 { |
|
a5e54bd87b25
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parents:
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diff
changeset
|
854 chains.push_back(*it); |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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parents:
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diff
changeset
|
855 } |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
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parents:
1897
diff
changeset
|
856 |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
857 #endif |
|
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
858 |
|
126
c9e88e7935a4
rt-struct projection
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parents:
125
diff
changeset
|
859 return true; |
| 125 | 860 } |
| 861 else | |
| 862 { | |
| 863 return false; | |
| 864 } | |
| 0 | 865 } |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
866 |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
867 |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
868 void DicomStructureSet::ProjectOntoLayer(PolylineSceneLayer& layer, |
|
1909
782ba9eb6f22
improved variable names
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parents:
1908
diff
changeset
|
869 const CoordinateSystem3D& cuttingPlane, |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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diff
changeset
|
870 size_t structureIndex, |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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parents:
1170
diff
changeset
|
871 const Color& color) const |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
872 { |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
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parents:
1895
diff
changeset
|
873 std::vector< std::vector<ScenePoint2D> > chains; |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
874 |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
875 if (ProjectStructure(chains, structureIndex, cuttingPlane)) |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
876 { |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
877 for (size_t j = 0; j < chains.size(); j++) |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
878 { |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
879 layer.AddChain(chains[j], false, color.GetRed(), color.GetGreen(), color.GetBlue()); |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
880 } |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
881 } |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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parents:
1170
diff
changeset
|
882 } |
|
1885
ddaee6b96501
retrieving rt-struct info
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diff
changeset
|
883 |
|
ddaee6b96501
retrieving rt-struct info
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parents:
1871
diff
changeset
|
884 |
|
ddaee6b96501
retrieving rt-struct info
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parents:
1871
diff
changeset
|
885 void DicomStructureSet::GetStructurePoints(std::list< std::vector<Vector> >& target, |
|
ddaee6b96501
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changeset
|
886 size_t structureIndex, |
|
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diff
changeset
|
887 const std::string& sopInstanceUid) const |
|
ddaee6b96501
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changeset
|
888 { |
|
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diff
changeset
|
889 target.clear(); |
|
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diff
changeset
|
890 |
|
ddaee6b96501
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changeset
|
891 const Structure& structure = GetStructure(structureIndex); |
|
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diff
changeset
|
892 |
|
ddaee6b96501
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diff
changeset
|
893 // TODO - Could be optimized by adding a multimap on "Structure", mapping |
|
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changeset
|
894 // from SOP Instance UID to polygons |
|
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changeset
|
895 |
|
ddaee6b96501
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changeset
|
896 for (Polygons::const_iterator it = structure.polygons_.begin(); |
|
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changeset
|
897 it != structure.polygons_.end(); ++it) |
|
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changeset
|
898 { |
|
ddaee6b96501
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diff
changeset
|
899 if (it->GetSopInstanceUid() == sopInstanceUid) |
|
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changeset
|
900 { |
|
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changeset
|
901 target.push_back(it->GetPoints()); |
|
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changeset
|
902 } |
|
ddaee6b96501
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changeset
|
903 } |
|
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diff
changeset
|
904 } |
|
1890
6ce81914f7e4
added classes BucketAccumulator1D/2D
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diff
changeset
|
905 |
|
6ce81914f7e4
added classes BucketAccumulator1D/2D
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diff
changeset
|
906 |
|
1892
cdf91ad891a5
estimated geometry of rt-struct
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diff
changeset
|
907 void DicomStructureSet::EstimateGeometry() |
|
1890
6ce81914f7e4
added classes BucketAccumulator1D/2D
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diff
changeset
|
908 { |
|
1892
cdf91ad891a5
estimated geometry of rt-struct
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diff
changeset
|
909 static const double PI = boost::math::constants::pi<double>(); |
|
cdf91ad891a5
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changeset
|
910 |
|
cdf91ad891a5
estimated geometry of rt-struct
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1890
diff
changeset
|
911 BucketAccumulator2D accumulator(0, PI, 9, /* for acos() */ |
|
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
912 -PI, PI, 9, /* for atan() */ |
|
cdf91ad891a5
estimated geometry of rt-struct
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parents:
1890
diff
changeset
|
913 true /* store values */); |
|
cdf91ad891a5
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parents:
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diff
changeset
|
914 |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
915 unsigned int countPolygons = 0; |
|
cdf91ad891a5
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parents:
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diff
changeset
|
916 for (size_t i = 0; i < structures_.size(); i++) |
|
cdf91ad891a5
estimated geometry of rt-struct
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parents:
1890
diff
changeset
|
917 { |
|
cdf91ad891a5
estimated geometry of rt-struct
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parents:
1890
diff
changeset
|
918 const Polygons& polygons = structures_[i].polygons_; |
|
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parents:
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diff
changeset
|
919 |
|
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estimated geometry of rt-struct
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parents:
1890
diff
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|
920 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
|
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parents:
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diff
changeset
|
921 { |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
922 countPolygons++; |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
923 |
|
cdf91ad891a5
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parents:
1890
diff
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|
924 const Points& points = it->GetPoints(); |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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changeset
|
925 |
|
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
926 if (points.size() >= 3) |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
927 { |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
928 // Compute the normal of the polygon using 3 successive points |
|
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parents:
1890
diff
changeset
|
929 Vector normal; |
|
cdf91ad891a5
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parents:
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diff
changeset
|
930 bool valid = false; |
|
cdf91ad891a5
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
931 |
| 1916 | 932 for (size_t j = 0; j + 2 < points.size(); j++) |
|
1892
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
933 { |
| 1916 | 934 const Vector& a = points[j]; |
| 935 const Vector& b = points[j + 1]; | |
| 936 const Vector& c = points[j + 2]; | |
|
1892
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
937 LinearAlgebra::CrossProduct(normal, b - a, c - a); // (*) |
|
cdf91ad891a5
estimated geometry of rt-struct
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parents:
1890
diff
changeset
|
938 LinearAlgebra::NormalizeVector(normal); |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
939 |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
940 if (LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(normal), 1.0)) // (**) |
|
cdf91ad891a5
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parents:
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diff
changeset
|
941 { |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
942 valid = true; |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
943 break; |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
944 } |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
945 } |
|
1890
6ce81914f7e4
added classes BucketAccumulator1D/2D
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
946 |
|
1892
cdf91ad891a5
estimated geometry of rt-struct
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parents:
1890
diff
changeset
|
947 if (valid) |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
948 { |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
949 // Check that all the points of the polygon lie in the plane defined by the normal |
|
cdf91ad891a5
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parents:
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diff
changeset
|
950 double d1 = GeometryToolbox::ProjectAlongNormal(points[0], normal); |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
951 |
| 1916 | 952 for (size_t j = 1; j < points.size(); j++) |
|
1892
cdf91ad891a5
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parents:
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diff
changeset
|
953 { |
| 1916 | 954 double d2 = GeometryToolbox::ProjectAlongNormal(points[j], normal); |
|
1892
cdf91ad891a5
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parents:
1890
diff
changeset
|
955 |
|
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parents:
1890
diff
changeset
|
956 if (!LinearAlgebra::IsNear(d1, d2)) |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
957 { |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
958 valid = false; |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
959 break; |
|
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parents:
1890
diff
changeset
|
960 } |
|
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parents:
1890
diff
changeset
|
961 } |
|
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parents:
1890
diff
changeset
|
962 } |
|
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
963 |
|
cdf91ad891a5
estimated geometry of rt-struct
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parents:
1890
diff
changeset
|
964 if (valid) |
|
cdf91ad891a5
estimated geometry of rt-struct
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parents:
1890
diff
changeset
|
965 { |
|
cdf91ad891a5
estimated geometry of rt-struct
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parents:
1890
diff
changeset
|
966 if (normal[2] < 0) |
|
cdf91ad891a5
estimated geometry of rt-struct
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parents:
1890
diff
changeset
|
967 { |
|
cdf91ad891a5
estimated geometry of rt-struct
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parents:
1890
diff
changeset
|
968 normal = -normal; |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
969 } |
|
cdf91ad891a5
estimated geometry of rt-struct
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parents:
1890
diff
changeset
|
970 |
|
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
971 // The normal is a non-zero unit vector because of (*) and (**), so "r == 1" |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
972 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
973 |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
974 const double theta = acos(normal[2]); |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
975 const double phi = atan(normal[1]); |
|
cdf91ad891a5
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parents:
1890
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changeset
|
976 accumulator.AddValue(theta, phi); |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
977 } |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
978 } |
|
cdf91ad891a5
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1890
diff
changeset
|
979 } |
|
cdf91ad891a5
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1890
diff
changeset
|
980 } |
|
cdf91ad891a5
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parents:
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diff
changeset
|
981 |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
982 size_t bestX, bestY; |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
983 accumulator.FindBestBucket(bestX, bestY); |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
984 |
|
cdf91ad891a5
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
985 if (accumulator.GetBucketContentSize(bestX, bestY) > 0) |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
986 { |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
987 double normalTheta, normalPhi; |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
988 accumulator.ComputeBestMedian(normalTheta, normalPhi); |
|
cdf91ad891a5
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1890
diff
changeset
|
989 |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
990 // Back to (x,y,z) normal, taking "r == 1" |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
991 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
992 double sinTheta = sin(normalTheta); |
|
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parents:
1890
diff
changeset
|
993 estimatedNormal_ = LinearAlgebra::CreateVector(sinTheta * cos(normalPhi), sinTheta * sin(normalPhi), cos(normalTheta)); |
|
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parents:
1890
diff
changeset
|
994 } |
|
cdf91ad891a5
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1890
diff
changeset
|
995 |
|
cdf91ad891a5
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1890
diff
changeset
|
996 std::vector<double> polygonsProjection; |
|
cdf91ad891a5
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1890
diff
changeset
|
997 polygonsProjection.reserve(countPolygons); |
|
cdf91ad891a5
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parents:
1890
diff
changeset
|
998 |
|
1890
6ce81914f7e4
added classes BucketAccumulator1D/2D
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parents:
1885
diff
changeset
|
999 for (size_t i = 0; i < structures_.size(); i++) |
|
6ce81914f7e4
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1885
diff
changeset
|
1000 { |
|
6ce81914f7e4
added classes BucketAccumulator1D/2D
Sebastien Jodogne <s.jodogne@gmail.com>
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1885
diff
changeset
|
1001 const Polygons& polygons = structures_[i].polygons_; |
|
6ce81914f7e4
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diff
changeset
|
1002 |
|
6ce81914f7e4
added classes BucketAccumulator1D/2D
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1885
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changeset
|
1003 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
|
6ce81914f7e4
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1885
diff
changeset
|
1004 { |
|
6ce81914f7e4
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diff
changeset
|
1005 const Points& points = it->GetPoints(); |
|
1892
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|
1006 polygonsProjection.push_back(GeometryToolbox::ProjectAlongNormal(points[0], estimatedNormal_)); |
|
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changeset
|
1007 } |
|
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changeset
|
1008 } |
|
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diff
changeset
|
1009 |
|
cdf91ad891a5
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|
1010 std::sort(polygonsProjection.begin(), polygonsProjection.end()); |
|
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|
1011 |
|
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1890
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|
1012 std::vector<double> deltas; |
|
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1890
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changeset
|
1013 deltas.reserve(polygonsProjection.size()); |
|
1890
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changeset
|
1014 |
|
1892
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|
1015 for (size_t i = 0; i + 1 < polygonsProjection.size(); i++) |
|
cdf91ad891a5
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changeset
|
1016 { |
|
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diff
changeset
|
1017 if (!LinearAlgebra::IsNear(polygonsProjection[i], polygonsProjection[i + 1])) |
|
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|
1018 { |
|
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changeset
|
1019 assert(polygonsProjection[i + 1] > polygonsProjection[i]); |
|
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|
1020 deltas.push_back(polygonsProjection[i + 1] - polygonsProjection[i]); |
|
1890
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changeset
|
1021 } |
|
6ce81914f7e4
added classes BucketAccumulator1D/2D
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1885
diff
changeset
|
1022 } |
|
1892
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changeset
|
1023 |
|
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diff
changeset
|
1024 if (deltas.empty()) |
|
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diff
changeset
|
1025 { |
|
cdf91ad891a5
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1890
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1026 estimatedSliceThickness_ = 1; |
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cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
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1027 } |
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cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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1028 else |
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cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
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1029 { |
|
cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
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1030 estimatedSliceThickness_ = LinearAlgebra::ComputeMedian(deltas); |
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cdf91ad891a5
estimated geometry of rt-struct
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1890
diff
changeset
|
1031 } |
|
1890
6ce81914f7e4
added classes BucketAccumulator1D/2D
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1885
diff
changeset
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1032 } |
|
1945
98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
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1033 |
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98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
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1034 |
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98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
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1035 bool DicomStructureSet::LookupStructureName(size_t& structureIndex /* out */, |
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98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
|
1036 const std::string& name) const |
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98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
|
1037 { |
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98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
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1038 StructureNamesIndex::const_iterator found = structureNamesIndex_.find(name); |
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98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
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1039 |
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98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
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1040 if (found == structureNamesIndex_.end()) |
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98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
|
1041 { |
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98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
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1042 return false; |
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98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
|
1043 } |
|
98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
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1044 else |
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98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
|
1045 { |
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98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
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1046 structureIndex = found->second; |
|
98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
|
1047 return true; |
|
98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
|
1048 } |
|
98952be6fb97
rendering plugin: rendering of multiple structures
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1916
diff
changeset
|
1049 } |
| 0 | 1050 } |