Mercurial > hg > orthanc-stone
annotate OrthancStone/Sources/Toolbox/DicomStructureSet.cpp @ 1909:782ba9eb6f22
improved variable names
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 01 Feb 2022 08:56:36 +0100 |
| parents | affde38b84de |
| children | f81cdf283859 |
| 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) 2017-2022 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
| 0 | 7 * |
| 8 * This program is free software: you can redistribute it and/or | |
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9 * modify it under the terms of the GNU Lesser General Public License |
| 47 | 10 * as published by the Free Software Foundation, either version 3 of |
| 11 * the License, or (at your option) any later version. | |
| 0 | 12 * |
| 13 * This program is distributed in the hope that it will be useful, but | |
| 14 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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16 * Lesser General Public License for more details. |
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17 * |
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18 * You should have received a copy of the GNU Lesser General Public |
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19 * License along with this program. If not, see |
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20 * <http://www.gnu.org/licenses/>. |
| 0 | 21 **/ |
| 22 | |
| 23 | |
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24 #define USE_BOOST_UNION_FOR_POLYGONS 0 |
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25 |
| 0 | 26 #include "DicomStructureSet.h" |
| 27 | |
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28 #include "BucketAccumulator2D.h" |
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29 #include "GenericToolbox.h" |
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30 #include "GeometryToolbox.h" |
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31 #include "OrthancDatasets/DicomDatasetReader.h" |
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32 |
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33 #include <Logging.h> |
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34 #include <OrthancException.h> |
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35 #include <Toolbox.h> |
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36 |
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37 #if defined(_MSC_VER) |
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38 # pragma warning(push) |
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39 # pragma warning(disable:4244) |
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40 #endif |
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41 |
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42 #if STONE_TIME_BLOCKING_OPS |
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43 # include <boost/date_time/posix_time/posix_time.hpp> |
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44 #endif |
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45 |
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46 #if !defined(USE_BOOST_UNION_FOR_POLYGONS) |
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47 # error Macro USE_BOOST_UNION_FOR_POLYGONS must be defined |
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48 #endif |
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49 |
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50 #include <limits> |
| 0 | 51 #include <stdio.h> |
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52 #include <boost/math/constants/constants.hpp> |
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53 |
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54 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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55 # include <boost/geometry.hpp> |
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56 # include <boost/geometry/geometries/point_xy.hpp> |
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57 # include <boost/geometry/geometries/polygon.hpp> |
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58 # include <boost/geometry/multi/geometries/multi_polygon.hpp> |
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59 #else |
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60 # include "UnionOfRectangles.h" |
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61 #endif |
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62 |
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63 #if defined(_MSC_VER) |
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64 # pragma warning(pop) |
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65 #endif |
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66 |
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ParsedDicomDataset to speed up loading RT-STRUCT from parsed DICOM files
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67 #if ORTHANC_ENABLE_DCMTK == 1 |
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68 # include "ParsedDicomDataset.h" |
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69 #endif |
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70 |
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71 |
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72 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
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73 |
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74 typedef boost::geometry::model::d2::point_xy<double> BoostPoint; |
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75 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon; |
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76 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon; |
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77 |
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78 static void Union(BoostMultiPolygon& output, |
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79 std::vector<BoostPolygon>& input) |
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80 { |
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81 for (size_t i = 0; i < input.size(); i++) |
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82 { |
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83 boost::geometry::correct(input[i]); |
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84 } |
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85 |
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86 if (input.size() == 0) |
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87 { |
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88 output.clear(); |
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89 } |
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90 else if (input.size() == 1) |
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91 { |
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92 output.resize(1); |
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93 output[0] = input[0]; |
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94 } |
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95 else |
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96 { |
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97 boost::geometry::union_(input[0], input[1], output); |
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98 |
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99 for (size_t i = 0; i < input.size(); i++) |
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100 { |
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101 BoostMultiPolygon tmp; |
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102 boost::geometry::union_(output, input[i], tmp); |
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103 output = tmp; |
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104 } |
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105 } |
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106 } |
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107 |
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108 static BoostPolygon CreateRectangle(float x1, float y1, |
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109 float x2, float y2) |
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110 { |
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111 BoostPolygon r; |
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112 boost::geometry::append(r, BoostPoint(x1, y1)); |
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113 boost::geometry::append(r, BoostPoint(x1, y2)); |
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114 boost::geometry::append(r, BoostPoint(x2, y2)); |
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115 boost::geometry::append(r, BoostPoint(x2, y1)); |
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116 return r; |
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117 } |
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118 |
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119 #endif |
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120 |
| 0 | 121 |
| 122 namespace OrthancStone | |
| 123 { | |
| 1504 | 124 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
| 125 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
| 126 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040); | |
| 127 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050); | |
| 128 static const Orthanc::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); | |
| 129 static const Orthanc::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
| 130 static const Orthanc::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
| 131 static const Orthanc::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
| 132 static const Orthanc::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
| 133 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
| 134 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
| 135 static const Orthanc::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
| 0 | 136 |
| 137 | |
| 138 static uint8_t ConvertColor(double v) | |
| 139 { | |
| 140 if (v < 0) | |
| 141 { | |
| 142 return 0; | |
| 143 } | |
| 144 else if (v >= 255) | |
| 145 { | |
| 146 return 255; | |
| 147 } | |
| 148 else | |
| 149 { | |
| 150 return static_cast<uint8_t>(v); | |
| 151 } | |
| 152 } | |
| 153 | |
| 154 | |
|
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155 static bool FastParseVector(Vector& target, |
|
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156 const IDicomDataset& dataset, |
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157 const Orthanc::DicomPath& tag) |
| 0 | 158 { |
|
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)); |
|
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162 } |
| 0 | 163 |
|
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164 bool DicomStructureSet::Polygon::IsPointOnSliceIfAny(const Vector& v) const |
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165 { |
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166 if (hasSlice_) |
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167 { |
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168 double magnitude = |
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169 GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()); |
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170 bool onSlice = LinearAlgebra::IsNear( |
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171 magnitude, |
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172 projectionAlongNormal_, |
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173 sliceThickness_ / 2.0 /* in mm */); |
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174 if (!onSlice) |
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175 { |
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176 LOG(WARNING) << "This RT-STRUCT contains a point that is off the " |
|
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177 << "slice of its instance | " |
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178 << "magnitude = " << magnitude << " | " |
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179 << "projectionAlongNormal_ = " << projectionAlongNormal_ << " | " |
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180 << "tolerance (sliceThickness_ / 2.0) = " << (sliceThickness_ / 2.0); |
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181 } |
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182 return onSlice; |
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183 } |
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184 else |
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185 { |
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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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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 // return true; // TODO - TEST |
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222 |
|
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223 const CoordinateSystem3D& geometry = it->second.geometry_; |
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224 |
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225 hasSlice_ = true; |
| 131 | 226 geometry_ = geometry; |
| 227 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal()); | |
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228 sliceThickness_ = it->second.thickness_; |
| 0 | 229 |
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230 extent_.Clear(); |
| 131 | 231 |
| 1571 | 232 for (Points::const_iterator it2 = points_.begin(); it2 != points_.end(); ++it2) |
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233 { |
| 1571 | 234 if (IsPointOnSliceIfAny(*it2)) |
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235 { |
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236 double x, y; |
| 1571 | 237 geometry.ProjectPoint2(x, y, *it2); |
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238 extent_.AddPoint(x, y); |
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239 } |
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240 } |
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241 return true; |
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242 } |
| 0 | 243 } |
| 244 } | |
| 245 | |
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246 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& cuttingPlane, |
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247 const Vector& estimatedNormal, |
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248 double estimatedSliceThickness) const |
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249 { |
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250 bool isOpposite = false; |
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251 |
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252 if (points_.empty()) |
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253 { |
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254 return false; |
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255 } |
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256 else if (hasSlice_) |
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257 { |
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258 // Use the actual geometry of this specific slice |
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259 if (!GeometryToolbox::IsParallelOrOpposite(isOpposite, cuttingPlane.GetNormal(), geometry_.GetNormal())) |
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260 { |
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261 return false; |
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262 } |
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263 else |
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264 { |
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265 double d = GeometryToolbox::ProjectAlongNormal(cuttingPlane.GetOrigin(), geometry_.GetNormal()); |
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266 return (LinearAlgebra::IsNear(d, projectionAlongNormal_, sliceThickness_ / 2.0)); |
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267 } |
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268 } |
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269 else |
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270 { |
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271 // Use the estimated geometry for the global RT-STRUCT volume |
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272 if (!GeometryToolbox::IsParallelOrOpposite(isOpposite, cuttingPlane.GetNormal(), estimatedNormal)) |
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273 { |
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274 return false; |
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275 } |
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276 else |
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277 { |
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278 double d1 = GeometryToolbox::ProjectAlongNormal(cuttingPlane.GetOrigin(), estimatedNormal); |
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279 double d2 = GeometryToolbox::ProjectAlongNormal(points_.front(), estimatedNormal); |
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280 return (LinearAlgebra::IsNear(d1, d2, estimatedSliceThickness / 2.0)); |
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281 } |
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282 } |
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283 } |
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284 |
| 131 | 285 bool DicomStructureSet::Polygon::Project(double& x1, |
| 286 double& y1, | |
| 287 double& x2, | |
| 288 double& y2, | |
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289 const CoordinateSystem3D& cuttingPlane, |
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290 const Vector& estimatedNormal, |
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291 double estimatedSliceThickness) const |
| 131 | 292 { |
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293 #if 0 |
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294 if (points_.size() <= 1) |
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295 { |
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296 return false; |
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297 } |
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298 |
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299 Vector normal = estimatedNormal; |
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300 double thickness = estimatedSliceThickness; |
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301 if (hasSlice_) |
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302 { |
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303 normal = geometry_.GetNormal(); |
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304 thickness = sliceThickness_; |
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305 } |
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306 |
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307 bool isOpposite; |
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308 if (!GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cuttingPlane.GetAxisX()) && |
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309 !GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cuttingPlane.GetAxisY())) |
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310 { |
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311 printf("UUUU\n"); |
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312 return false; |
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313 } |
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314 |
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315 return false; |
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316 |
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317 #else |
| 131 | 318 if (!hasSlice_ || |
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319 points_.size() <= 1) |
| 131 | 320 { |
| 321 return false; | |
| 322 } | |
| 323 | |
| 324 double x, y; | |
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325 geometry_.ProjectPoint2(x, y, cuttingPlane.GetOrigin()); |
| 131 | 326 |
| 327 bool isOpposite; | |
| 328 if (GeometryToolbox::IsParallelOrOpposite | |
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329 (isOpposite, cuttingPlane.GetNormal(), geometry_.GetAxisY())) |
| 131 | 330 { |
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331 // plane is constant Y |
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332 |
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333 if (y < extent_.GetY1() || |
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334 y > extent_.GetY2()) |
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335 { |
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336 // The polygon does not intersect the input slice |
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337 return false; |
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338 } |
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339 |
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340 bool isFirst = true; |
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341 double xmin = std::numeric_limits<double>::infinity(); |
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342 double xmax = -std::numeric_limits<double>::infinity(); |
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343 |
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344 double prevX, prevY; |
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345 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
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346 |
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347 for (size_t i = 0; i < points_.size(); i++) |
| 131 | 348 { |
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349 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py |
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350 double curX, curY; |
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351 geometry_.ProjectPoint2(curX, curY, points_[i]); |
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352 |
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353 // if prev* and cur* are on opposite sides of y, this means that the |
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354 // segment intersects the plane. |
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355 if ((prevY <= y && curY >= y) || |
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356 (prevY >= y && curY <= y)) |
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357 { |
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358 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY); |
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359 xmin = std::min(xmin, p); |
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360 xmax = std::max(xmax, p); |
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361 isFirst = false; |
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362 |
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363 // xmin and xmax represent the extent of the rectangle along the |
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364 // intersection between the plane and the polygon geometry |
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365 |
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366 } |
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367 |
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368 prevX = curX; |
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369 prevY = curY; |
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370 } |
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371 |
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372 // if NO segment intersects the plane |
|
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373 if (isFirst) |
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374 { |
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375 return false; |
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376 } |
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377 else |
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378 { |
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379 // y is the plane y coord in the polygon geometry |
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380 // xmin and xmax are ALSO expressed in the polygon geometry |
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381 |
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382 // let's convert them to 3D world geometry... |
|
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383 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) + |
| 131 | 384 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
|
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385 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) - |
| 131 | 386 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
|
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387 |
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388 // then to the cutting plane geometry... |
|
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389 cuttingPlane.ProjectPoint2(x1, y1, p1); |
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390 cuttingPlane.ProjectPoint2(x2, y2, p2); |
| 131 | 391 return true; |
| 392 } | |
| 393 } | |
| 394 else if (GeometryToolbox::IsParallelOrOpposite | |
|
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395 (isOpposite, cuttingPlane.GetNormal(), geometry_.GetAxisX())) |
| 131 | 396 { |
|
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397 // plane is constant X => Sagittal view (remember that in the |
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398 // sagittal projection, the normal must be swapped) |
|
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399 |
|
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400 |
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401 /* |
|
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DicomStructureSet::ProjectOntoLayer()
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402 Please read the comments in the section above, by taking into account |
|
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403 the fact that, in this case, the plane has a constant X, not Y (in |
|
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404 polygon geometry_ coordinates) |
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405 */ |
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406 |
|
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407 if (x < extent_.GetX1() || |
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408 x > extent_.GetX2()) |
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409 { |
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410 return false; |
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411 } |
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412 |
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413 bool isFirst = true; |
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414 double ymin = std::numeric_limits<double>::infinity(); |
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415 double ymax = -std::numeric_limits<double>::infinity(); |
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416 |
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417 double prevX, prevY; |
|
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418 geometry_.ProjectPoint2(prevX, prevY, points_[points_.size() - 1]); |
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419 |
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420 for (size_t i = 0; i < points_.size(); i++) |
| 131 | 421 { |
|
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422 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py |
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423 double curX, curY; |
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424 geometry_.ProjectPoint2(curX, curY, points_[i]); |
|
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425 |
|
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426 if ((prevX <= x && curX >= x) || |
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427 (prevX >= x && curX <= x)) |
|
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428 { |
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429 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX); |
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430 ymin = std::min(ymin, p); |
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431 ymax = std::max(ymax, p); |
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432 isFirst = false; |
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433 } |
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434 |
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435 prevX = curX; |
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436 prevY = curY; |
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437 } |
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438 |
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439 if (isFirst) |
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440 { |
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441 return false; |
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442 } |
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443 else |
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444 { |
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445 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) + |
| 131 | 446 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
|
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447 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) - |
| 131 | 448 sliceThickness_ / 2.0 * geometry_.GetNormal()); |
| 449 | |
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|
450 cuttingPlane.ProjectPoint2(x1, y1, p1); |
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451 cuttingPlane.ProjectPoint2(x2, y2, p2); |
|
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452 |
| 131 | 453 return true; |
| 454 } | |
| 455 } | |
| 456 else | |
| 457 { | |
| 458 // Should not happen | |
| 459 return false; | |
| 460 } | |
|
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461 #endif |
| 131 | 462 } |
| 463 | |
| 464 | |
| 0 | 465 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
| 466 { | |
| 467 if (index >= structures_.size()) | |
| 468 { | |
| 125 | 469 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
| 0 | 470 } |
| 471 | |
| 472 return structures_[index]; | |
| 473 } | |
| 474 | |
| 475 | |
| 125 | 476 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) |
| 0 | 477 { |
| 125 | 478 if (index >= structures_.size()) |
| 479 { | |
| 480 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
| 0 | 481 } |
| 482 | |
| 483 return structures_[index]; | |
| 484 } | |
| 485 | |
| 1504 | 486 void DicomStructureSet::Setup(const IDicomDataset& tags) |
| 0 | 487 { |
|
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|
488 #if STONE_TIME_BLOCKING_OPS |
|
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|
489 boost::posix_time::ptime timerStart = boost::posix_time::microsec_clock::universal_time(); |
|
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|
490 #endif |
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|
491 |
| 1504 | 492 DicomDatasetReader reader(tags); |
| 32 | 493 |
| 494 size_t count, tmp; | |
|
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|
495 if (!tags.GetSequenceSize(count, Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE)) || |
|
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496 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE)) || |
| 32 | 497 tmp != count || |
|
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498 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE)) || |
| 32 | 499 tmp != count) |
| 0 | 500 { |
| 501 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 502 } | |
| 503 | |
| 32 | 504 structures_.resize(count); |
| 505 for (size_t i = 0; i < count; i++) | |
| 506 { | |
|
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507 structures_[i].interpretation_ = reader.GetStringValue |
|
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|
508 (Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
|
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|
509 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
|
122
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|
510 "No interpretation"); |
| 0 | 511 |
|
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512 structures_[i].name_ = reader.GetStringValue |
|
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|
513 (Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
|
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|
514 DICOM_TAG_ROI_NAME), |
|
949
32eaf4929b08
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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diff
changeset
|
515 "No name"); |
| 0 | 516 |
| 517 Vector color; | |
|
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|
518 if (FastParseVector(color, tags, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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|
519 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
| 32 | 520 color.size() == 3) |
| 0 | 521 { |
| 32 | 522 structures_[i].red_ = ConvertColor(color[0]); |
| 523 structures_[i].green_ = ConvertColor(color[1]); | |
| 524 structures_[i].blue_ = ConvertColor(color[2]); | |
| 525 } | |
| 526 else | |
| 527 { | |
| 528 structures_[i].red_ = 255; | |
| 529 structures_[i].green_ = 0; | |
| 530 structures_[i].blue_ = 0; | |
| 0 | 531 } |
| 532 | |
| 32 | 533 size_t countSlices; |
|
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|
534 if (!tags.GetSequenceSize(countSlices, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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|
535 DICOM_TAG_CONTOUR_SEQUENCE))) |
| 32 | 536 { |
|
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537 countSlices = 0; |
| 32 | 538 } |
| 0 | 539 |
|
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|
540 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ |
|
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|
541 << "\" with interpretation \"" << structures_[i].interpretation_ |
|
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542 << "\" containing " << countSlices << " slices (color: " |
|
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543 << static_cast<int>(structures_[i].red_) << "," |
|
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544 << static_cast<int>(structures_[i].green_) << "," |
|
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|
545 << static_cast<int>(structures_[i].blue_) << ")"; |
| 0 | 546 |
|
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|
547 /** |
|
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548 * These temporary variables avoid allocating many vectors in |
|
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549 * the loop below (indeed, "Orthanc::DicomPath" handles a |
|
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|
550 * "std::vector<PrefixItem>") |
|
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551 **/ |
|
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552 Orthanc::DicomPath countPointsPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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553 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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554 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS); |
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555 |
|
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556 Orthanc::DicomPath geometricTypePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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557 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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558 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE); |
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559 |
|
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560 Orthanc::DicomPath imageSequencePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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561 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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562 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); |
|
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563 |
|
981
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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564 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155) |
|
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565 Orthanc::DicomPath referencedInstancePath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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|
566 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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567 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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568 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); |
|
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569 |
|
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replaced OrthancStone::DicomPath by new class Orthanc::DicomPath from orthanc framework
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570 Orthanc::DicomPath contourDataPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
|
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571 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
|
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|
572 DICOM_TAG_CONTOUR_DATA); |
|
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|
573 |
| 32 | 574 for (size_t j = 0; j < countSlices; j++) |
| 0 | 575 { |
| 32 | 576 unsigned int countPoints; |
| 0 | 577 |
|
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578 countPointsPath.SetPrefixIndex(1, j); |
|
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|
579 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) |
| 32 | 580 { |
| 581 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 582 } | |
| 583 | |
|
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584 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
| 0 | 585 |
|
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|
586 geometricTypePath.SetPrefixIndex(1, j); |
|
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optimizing constructor of DicomStructureSet
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|
587 std::string type = reader.GetMandatoryStringValue(geometricTypePath); |
| 32 | 588 if (type != "CLOSED_PLANAR") |
| 0 | 589 { |
|
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|
590 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
|
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|
591 continue; |
| 0 | 592 } |
| 593 | |
|
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|
594 size_t size; |
|
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|
595 |
|
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optimizing constructor of DicomStructureSet
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changeset
|
596 imageSequencePath.SetPrefixIndex(1, j); |
|
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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
|
597 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1) |
|
122
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598 { |
|
981
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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parents:
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changeset
|
599 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry."; |
| 0 | 600 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
| 601 } | |
| 602 | |
|
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603 referencedInstancePath.SetPrefixIndex(1, j); |
|
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|
604 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); |
|
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|
605 |
|
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optimizing constructor of DicomStructureSet
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|
606 contourDataPath.SetPrefixIndex(1, j); |
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changeset
|
607 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); |
| 0 | 608 |
| 609 Vector points; | |
|
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changeset
|
610 |
|
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changeset
|
611 if (!GenericToolbox::FastParseVector(points, slicesData) || |
| 32 | 612 points.size() != 3 * countPoints) |
| 0 | 613 { |
| 614 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
| 615 } | |
| 616 | |
|
981
c20dbaab360c
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
|
617 // seen in real world |
|
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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changeset
|
618 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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parents:
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diff
changeset
|
619 { |
|
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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diff
changeset
|
620 LOG(ERROR) << "WARNING. The following Dicom tag (Referenced SOP Instance UID) contains an empty value : // (3006,0039)[" << i << "] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)"; |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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changeset
|
621 } |
|
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Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
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diff
changeset
|
622 |
|
122
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|
623 Polygon polygon(sopInstanceUid); |
|
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|
624 polygon.Reserve(countPoints); |
| 0 | 625 |
| 32 | 626 for (size_t k = 0; k < countPoints; k++) |
| 0 | 627 { |
| 628 Vector v(3); | |
| 629 v[0] = points[3 * k]; | |
| 630 v[1] = points[3 * k + 1]; | |
| 631 v[2] = points[3 * k + 2]; | |
|
122
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|
632 polygon.AddPoint(v); |
| 0 | 633 } |
| 634 | |
| 635 structures_[i].polygons_.push_back(polygon); | |
| 636 } | |
| 637 } | |
|
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|
638 |
|
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estimated geometry of rt-struct
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changeset
|
639 EstimateGeometry(); |
|
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changeset
|
640 |
|
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|
641 #if STONE_TIME_BLOCKING_OPS |
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changeset
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642 boost::posix_time::ptime timerEnd = boost::posix_time::microsec_clock::universal_time(); |
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|
643 boost::posix_time::time_duration duration = timerEnd - timerStart; |
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changeset
|
644 int64_t durationMs = duration.total_milliseconds(); |
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645 LOG(WARNING) << "DicomStructureSet::Setup took " << durationMs << " ms"; |
|
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changeset
|
646 #endif |
| 0 | 647 } |
| 648 | |
| 649 | |
|
1180
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changeset
|
650 #if ORTHANC_ENABLE_DCMTK == 1 |
|
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|
651 DicomStructureSet::DicomStructureSet(Orthanc::ParsedDicomFile& instance) |
|
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652 { |
|
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|
653 ParsedDicomDataset dataset(instance); |
|
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changeset
|
654 Setup(dataset); |
|
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|
655 } |
|
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|
656 #endif |
|
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|
657 |
|
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changeset
|
658 |
| 0 | 659 Vector DicomStructureSet::GetStructureCenter(size_t index) const |
| 660 { | |
| 661 const Structure& structure = GetStructure(index); | |
| 662 | |
| 663 Vector center; | |
|
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LinearAlgebra toolbox
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|
664 LinearAlgebra::AssignVector(center, 0, 0, 0); |
| 0 | 665 if (structure.polygons_.empty()) |
| 666 { | |
| 667 return center; | |
| 668 } | |
| 669 | |
| 670 double n = static_cast<double>(structure.polygons_.size()); | |
| 671 | |
| 672 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
| 673 polygon != structure.polygons_.end(); ++polygon) | |
| 674 { | |
|
122
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diff
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|
675 if (!polygon->GetPoints().empty()) |
| 0 | 676 { |
|
122
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refactoring DicomStructureSet
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parents:
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diff
changeset
|
677 center += polygon->GetPoints().front() / n; |
| 0 | 678 } |
| 679 } | |
| 680 | |
| 681 return center; | |
| 682 } | |
| 683 | |
| 684 | |
| 685 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
| 686 { | |
| 687 return GetStructure(index).name_; | |
| 688 } | |
| 689 | |
| 690 | |
| 691 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
| 692 { | |
| 693 return GetStructure(index).interpretation_; | |
| 694 } | |
| 695 | |
| 696 | |
|
804
61ba4b504e9a
PolylineSceneLayer now has one color per chain
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
794
diff
changeset
|
697 Color DicomStructureSet::GetStructureColor(size_t index) const |
|
61ba4b504e9a
PolylineSceneLayer now has one color per chain
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
794
diff
changeset
|
698 { |
|
61ba4b504e9a
PolylineSceneLayer now has one color per chain
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
794
diff
changeset
|
699 const Structure& s = GetStructure(index); |
|
61ba4b504e9a
PolylineSceneLayer now has one color per chain
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
794
diff
changeset
|
700 return Color(s.red_, s.green_, s.blue_); |
|
61ba4b504e9a
PolylineSceneLayer now has one color per chain
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
794
diff
changeset
|
701 } |
|
61ba4b504e9a
PolylineSceneLayer now has one color per chain
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
794
diff
changeset
|
702 |
|
61ba4b504e9a
PolylineSceneLayer now has one color per chain
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
794
diff
changeset
|
703 |
|
1885
ddaee6b96501
retrieving rt-struct info
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1871
diff
changeset
|
704 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) const |
| 0 | 705 { |
| 706 for (Structures::const_iterator structure = structures_.begin(); | |
| 707 structure != structures_.end(); ++structure) | |
| 708 { | |
| 709 for (Polygons::const_iterator polygon = structure->polygons_.begin(); | |
| 710 polygon != structure->polygons_.end(); ++polygon) | |
| 711 { | |
|
122
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refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
712 instances.insert(polygon->GetSopInstanceUid()); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
713 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
714 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
715 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
716 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
717 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
718 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
719 const std::string& seriesInstanceUid, |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
720 const CoordinateSystem3D& geometry, |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
721 double thickness) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
722 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
723 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
724 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
725 // This geometry is already known |
|
956
a7351ad54960
Made IsContextLost automatically set the flag by checking with the emscripten
Benjamin Golinvaux <bgo@osimis.io>
parents:
949
diff
changeset
|
726 LOG(ERROR) << "DicomStructureSet::AddReferencedSlice(): (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()). sopInstanceUid = " << sopInstanceUid; |
|
981
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
727 |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
728 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
729 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
730 else |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
731 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
732 if (thickness < 0) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
733 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
734 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
735 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
736 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
737 if (!referencedSlices_.empty()) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
738 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
739 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
740 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
741 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
| 0 | 742 { |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
743 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
744 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
745 } |
| 0 | 746 |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
747 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
748 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
749 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
750 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
751 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
752 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
753 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
754 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
| 0 | 755 |
| 131 | 756 for (Structures::iterator structure = structures_.begin(); |
| 757 structure != structures_.end(); ++structure) | |
| 758 { | |
| 759 for (Polygons::iterator polygon = structure->polygons_.begin(); | |
| 760 polygon != structure->polygons_.end(); ++polygon) | |
| 761 { | |
| 762 polygon->UpdateReferencedSlice(referencedSlices_); | |
| 763 } | |
| 764 } | |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
765 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
766 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
767 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
768 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
769 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
770 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
771 CoordinateSystem3D slice(dataset); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
772 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
773 double thickness = 1; // 1 mm by default |
| 0 | 774 |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
775 std::string s; |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
776 Vector v; |
|
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
777 if (dataset.LookupStringValue(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
|
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
137
diff
changeset
|
778 LinearAlgebra::ParseVector(v, s) && |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
779 v.size() > 0) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
780 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
781 thickness = v[0]; |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
782 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
783 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
784 std::string instance, series; |
|
994
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
785 if (dataset.LookupStringValue(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) && |
|
1f74bc3459ba
fix build due to rename in Orthanc::DicomMap
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
988
diff
changeset
|
786 dataset.LookupStringValue(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
787 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
788 AddReferencedSlice(instance, series, slice, thickness); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
789 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
790 else |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
791 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
792 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
793 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
794 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
795 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
796 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
797 void DicomStructureSet::CheckReferencedSlices() |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
798 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
799 for (Structures::iterator structure = structures_.begin(); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
800 structure != structures_.end(); ++structure) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
801 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
802 for (Polygons::iterator polygon = structure->polygons_.begin(); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
803 polygon != structure->polygons_.end(); ++polygon) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
804 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
805 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
806 { |
|
981
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
807 std::string sopInstanceUid = polygon->GetSopInstanceUid(); |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
808 if (Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "") |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
809 { |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
810 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
811 << " missing information about referenced instance " |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
812 << "(sopInstanceUid is empty!)"; |
|
981
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
813 } |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
814 else |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
815 { |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
816 LOG(ERROR) << "DicomStructureSet::CheckReferencedSlices(): " |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
817 << " missing information about referenced instance " |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
818 << "(sopInstanceUid = " << sopInstanceUid << ")"; |
|
981
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
819 } |
|
c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
Benjamin Golinvaux <bgo@osimis.io>
parents:
959
diff
changeset
|
820 //throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
| 0 | 821 } |
| 822 } | |
| 823 } | |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
824 } |
| 0 | 825 |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
826 |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
827 Vector DicomStructureSet::GetNormal() const |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
828 { |
|
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
829 if (referencedSlices_.empty()) |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
830 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
831 Vector v; |
|
158
a053ca7fa5c6
LinearAlgebra toolbox
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
137
diff
changeset
|
832 LinearAlgebra::AssignVector(v, 0, 0, 1); |
|
122
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
833 return v; |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
834 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
835 else |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
836 { |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
837 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
838 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
839 } |
|
e3433dabfb8d
refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
121
diff
changeset
|
840 |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
841 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
|
842 const Structure& structure, |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
843 const CoordinateSystem3D& cuttingPlane) const |
| 125 | 844 { |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
845 const CoordinateSystem3D cutting = CoordinateSystem3D::NormalizeCuttingPlane(cuttingPlane); |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
846 |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
847 chains.clear(); |
| 125 | 848 |
| 849 Vector normal = GetNormal(); | |
| 850 | |
| 851 bool isOpposite; | |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
852 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cutting.GetNormal())) |
| 125 | 853 { |
| 854 // This is an axial projection | |
| 855 | |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
856 chains.reserve(structure.polygons_.size()); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
857 |
| 794 | 858 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
| 125 | 859 polygon != structure.polygons_.end(); ++polygon) |
| 860 { | |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
861 const Points& points = polygon->GetPoints(); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
862 |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
863 if (polygon->IsOnSlice(cutting, GetEstimatedNormal(), GetEstimatedSliceThickness()) && |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
864 !points.empty()) |
| 125 | 865 { |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
866 chains.push_back(std::vector<ScenePoint2D>()); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
867 chains.back().reserve(points.size() + 1); |
| 125 | 868 |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
869 for (Points::const_iterator p = points.begin(); |
|
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
870 p != points.end(); ++p) |
| 125 | 871 { |
| 872 double x, y; | |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
873 cutting.ProjectPoint2(x, y, *p); |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
874 chains.back().push_back(ScenePoint2D(x, y)); |
| 125 | 875 } |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
876 |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
877 double x0, y0; |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
878 cutting.ProjectPoint2(x0, y0, points.front()); |
|
1896
b3c08e607d9f
simplified signature of DicomStructureSet::ProjectStructure()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1895
diff
changeset
|
879 chains.back().push_back(ScenePoint2D(x0, y0)); |
| 125 | 880 } |
| 881 } | |
| 882 | |
| 883 return true; | |
| 884 } | |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
885 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cutting.GetAxisX()) || |
|
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
886 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, cutting.GetAxisY())) |
| 125 | 887 { |
|
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
888 // Sagittal or coronal projection |
|
1000
50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
Benjamin Golinvaux <bgo@osimis.io>
parents:
994
diff
changeset
|
889 |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1170
diff
changeset
|
890 #if USE_BOOST_UNION_FOR_POLYGONS == 1 |
|
126
c9e88e7935a4
rt-struct projection
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
125
diff
changeset
|
891 std::vector<BoostPolygon> projected; |
|
1162
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
892 |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
893 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
894 polygon != structure.polygons_.end(); ++polygon) |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
895 { |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
896 double x1, y1, x2, y2; |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
897 |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
898 if (polygon->Project(x1, y1, x2, y2, cutting, GetEstimatedNormal(), GetEstimatedSliceThickness())) |
|
1162
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
899 { |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
900 projected.push_back(CreateRectangle(x1, y1, x2, y2)); |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
901 } |
|
709aa65aca17
recovery of USE_BOOST_UNION_FOR_POLYGONS
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1013
diff
changeset
|
902 } |
|
1897
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
903 |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
904 BoostMultiPolygon merged; |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
905 Union(merged, projected); |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
906 |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
907 chains.resize(merged.size()); |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
908 for (size_t i = 0; i < merged.size(); i++) |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
909 { |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
910 const std::vector<BoostPoint>& outer = merged[i].outer(); |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
911 |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
912 chains[i].resize(outer.size()); |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
913 for (size_t j = 0; j < outer.size(); j++) |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
914 { |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
915 chains[i][j] = ScenePoint2D(outer[j].x(), outer[j].y()); |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
916 } |
|
144f8f82c15a
added ctrl key in RtViewerWasm
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1896
diff
changeset
|
917 } |
|
1898
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
918 |
|
1908
affde38b84de
moved tentative bgo reimplementation of rt-struct into graveyard
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1905
diff
changeset
|
919 #else |
|
1898
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
920 |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
921 std::list<Extent2D> rectangles; |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
922 |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
923 for (Polygons::const_iterator polygon = structure.polygons_.begin(); |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
924 polygon != structure.polygons_.end(); ++polygon) |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
925 { |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
926 double x1, y1, x2, y2; |
|
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
927 |
|
1909
782ba9eb6f22
improved variable names
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1908
diff
changeset
|
928 if (polygon->Project(x1, y1, x2, y2, cutting, GetEstimatedNormal(), GetEstimatedSliceThickness())) |
|
1898
a5e54bd87b25
try to use UnionOfRectangles in DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1897
diff
changeset
|
929 { |
|
a5e54bd87b25
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|
930 rectangles.push_back(Extent2D(x1, y1, x2, y2)); |
|
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diff
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|
931 } |
|
a5e54bd87b25
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|
932 } |
|
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changeset
|
933 |
|
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diff
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|
934 typedef std::list< std::vector<ScenePoint2D> > Contours; |
|
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|
935 |
|
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diff
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|
936 Contours contours; |
|
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|
937 UnionOfRectangles::Apply(contours, rectangles); |
|
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changeset
|
938 |
|
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|
939 chains.reserve(contours.size()); |
|
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|
940 |
|
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|
941 for (Contours::const_iterator it = contours.begin(); it != contours.end(); ++it) |
|
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|
942 { |
|
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|
943 chains.push_back(*it); |
|
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diff
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|
944 } |
|
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|
945 |
|
1000
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diff
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|
946 #endif |
|
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|
947 |
|
126
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948 return true; |
| 125 | 949 } |
| 950 else | |
| 951 { | |
| 952 return false; | |
| 953 } | |
| 0 | 954 } |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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changeset
|
955 |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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changeset
|
956 |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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changeset
|
957 void DicomStructureSet::ProjectOntoLayer(PolylineSceneLayer& layer, |
|
1909
782ba9eb6f22
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|
958 const CoordinateSystem3D& cuttingPlane, |
|
1178
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959 size_t structureIndex, |
|
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960 const Color& color) const |
|
3c7cdbf32e2a
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changeset
|
961 { |
|
1896
b3c08e607d9f
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|
962 std::vector< std::vector<ScenePoint2D> > chains; |
|
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|
963 |
|
1909
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improved variable names
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diff
changeset
|
964 if (ProjectStructure(chains, structureIndex, cuttingPlane)) |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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changeset
|
965 { |
|
1896
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changeset
|
966 for (size_t j = 0; j < chains.size(); j++) |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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changeset
|
967 { |
|
1896
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changeset
|
968 layer.AddChain(chains[j], false, color.GetRed(), color.GetGreen(), color.GetBlue()); |
|
1178
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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|
969 } |
|
3c7cdbf32e2a
DicomStructureSet::ProjectOntoLayer()
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diff
changeset
|
970 } |
|
3c7cdbf32e2a
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|
971 } |
|
1885
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|
972 |
|
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|
973 |
|
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974 void DicomStructureSet::GetStructurePoints(std::list< std::vector<Vector> >& target, |
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975 size_t structureIndex, |
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976 const std::string& sopInstanceUid) const |
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977 { |
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978 target.clear(); |
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|
979 |
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980 const Structure& structure = GetStructure(structureIndex); |
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981 |
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982 // TODO - Could be optimized by adding a multimap on "Structure", mapping |
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983 // from SOP Instance UID to polygons |
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|
984 |
|
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985 for (Polygons::const_iterator it = structure.polygons_.begin(); |
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986 it != structure.polygons_.end(); ++it) |
|
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|
987 { |
|
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988 if (it->GetSopInstanceUid() == sopInstanceUid) |
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|
989 { |
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|
990 target.push_back(it->GetPoints()); |
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|
991 } |
|
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diff
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|
992 } |
|
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diff
changeset
|
993 } |
|
1890
6ce81914f7e4
added classes BucketAccumulator1D/2D
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changeset
|
994 |
|
6ce81914f7e4
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|
995 |
|
1892
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|
996 void DicomStructureSet::EstimateGeometry() |
|
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|
997 { |
|
1892
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998 static const double PI = boost::math::constants::pi<double>(); |
|
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999 |
|
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|
1000 BucketAccumulator2D accumulator(0, PI, 9, /* for acos() */ |
|
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1001 -PI, PI, 9, /* for atan() */ |
|
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1002 true /* store values */); |
|
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changeset
|
1003 |
|
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changeset
|
1004 unsigned int countPolygons = 0; |
|
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1005 for (size_t i = 0; i < structures_.size(); i++) |
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|
1006 { |
|
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|
1007 const Polygons& polygons = structures_[i].polygons_; |
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1008 |
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1009 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
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|
1010 { |
|
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|
1011 countPolygons++; |
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1012 |
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1013 const Points& points = it->GetPoints(); |
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1014 |
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1015 if (points.size() >= 3) |
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|
1016 { |
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1017 // Compute the normal of the polygon using 3 successive points |
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1018 Vector normal; |
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1019 bool valid = false; |
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1020 |
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1021 for (size_t i = 0; i + 2 < points.size(); i++) |
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|
1022 { |
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1023 const Vector& a = points[i]; |
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1024 const Vector& b = points[i + 1]; |
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1025 const Vector& c = points[i + 2]; |
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1026 LinearAlgebra::CrossProduct(normal, b - a, c - a); // (*) |
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1027 LinearAlgebra::NormalizeVector(normal); |
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|
1028 |
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1029 if (LinearAlgebra::IsNear(boost::numeric::ublas::norm_2(normal), 1.0)) // (**) |
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1030 { |
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1031 valid = true; |
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1032 break; |
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|
1033 } |
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1034 } |
|
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1035 |
|
1892
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|
1036 if (valid) |
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|
1037 { |
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1038 // Check that all the points of the polygon lie in the plane defined by the normal |
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1039 double d1 = GeometryToolbox::ProjectAlongNormal(points[0], normal); |
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1040 |
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1041 for (size_t i = 1; i < points.size(); i++) |
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1042 { |
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1043 double d2 = GeometryToolbox::ProjectAlongNormal(points[i], normal); |
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1044 |
|
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1045 if (!LinearAlgebra::IsNear(d1, d2)) |
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1046 { |
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1047 valid = false; |
|
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|
1048 break; |
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|
1049 } |
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|
1050 } |
|
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1051 } |
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|
1052 |
|
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1053 if (valid) |
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1054 { |
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1055 if (normal[2] < 0) |
|
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1056 { |
|
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1057 normal = -normal; |
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1058 } |
|
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|
1059 |
|
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1060 // The normal is a non-zero unit vector because of (*) and (**), so "r == 1" |
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1061 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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1062 |
|
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1063 const double theta = acos(normal[2]); |
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1064 const double phi = atan(normal[1]); |
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1065 accumulator.AddValue(theta, phi); |
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1066 } |
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1067 } |
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1068 } |
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1069 } |
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1070 |
|
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1071 size_t bestX, bestY; |
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1072 accumulator.FindBestBucket(bestX, bestY); |
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1073 |
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1074 if (accumulator.GetBucketContentSize(bestX, bestY) > 0) |
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1075 { |
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1076 double normalTheta, normalPhi; |
|
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1077 accumulator.ComputeBestMedian(normalTheta, normalPhi); |
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1078 |
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1079 // Back to (x,y,z) normal, taking "r == 1" |
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1080 // https://en.wikipedia.org/wiki/Vector_fields_in_cylindrical_and_spherical_coordinates#Vector_fields_2 |
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1081 double sinTheta = sin(normalTheta); |
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1082 estimatedNormal_ = LinearAlgebra::CreateVector(sinTheta * cos(normalPhi), sinTheta * sin(normalPhi), cos(normalTheta)); |
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1083 } |
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1084 |
|
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1085 std::vector<double> polygonsProjection; |
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1086 polygonsProjection.reserve(countPolygons); |
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1087 |
|
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1088 for (size_t i = 0; i < structures_.size(); i++) |
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1089 { |
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1090 const Polygons& polygons = structures_[i].polygons_; |
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|
1091 |
|
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1092 for (Polygons::const_iterator it = polygons.begin(); it != polygons.end(); ++it) |
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1093 { |
|
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1094 const Points& points = it->GetPoints(); |
|
1892
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1095 polygonsProjection.push_back(GeometryToolbox::ProjectAlongNormal(points[0], estimatedNormal_)); |
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1096 } |
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1097 } |
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|
1098 |
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1099 std::sort(polygonsProjection.begin(), polygonsProjection.end()); |
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1100 |
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1101 std::vector<double> deltas; |
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1102 deltas.reserve(polygonsProjection.size()); |
|
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1103 |
|
1892
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1104 for (size_t i = 0; i + 1 < polygonsProjection.size(); i++) |
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|
1105 { |
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1106 if (!LinearAlgebra::IsNear(polygonsProjection[i], polygonsProjection[i + 1])) |
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1107 { |
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1108 assert(polygonsProjection[i + 1] > polygonsProjection[i]); |
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1109 deltas.push_back(polygonsProjection[i + 1] - polygonsProjection[i]); |
|
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|
1110 } |
|
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changeset
|
1111 } |
|
1892
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|
1112 |
|
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|
1113 if (deltas.empty()) |
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|
1114 { |
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|
1115 estimatedSliceThickness_ = 1; |
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|
1116 } |
|
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changeset
|
1117 else |
|
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changeset
|
1118 { |
|
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1119 estimatedSliceThickness_ = LinearAlgebra::ComputeMedian(deltas); |
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changeset
|
1120 } |
|
1890
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changeset
|
1121 } |
| 0 | 1122 } |