Mercurial > hg > orthanc-stone

annotate Framework/Toolbox/DicomStructureSet.cpp @ 173:6b0411ac843a wasm

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fix captain rt-struct
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 08 Mar 2018 17:58:55 +0100
parents 0a73d76333db
children fccffbf99ba1
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1 /**
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2 * Stone of Orthanc
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2018 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU Affero General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * Affero General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU Affero General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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22 #include "DicomStructureSet.h"
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23
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24 #include "../Toolbox/GeometryToolbox.h"
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25 #include "../Toolbox/MessagingToolbox.h"
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27 #include <Core/Logging.h>
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28 #include <Core/OrthancException.h>
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29 #include <Plugins/Samples/Common/FullOrthancDataset.h>
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30 #include <Plugins/Samples/Common/DicomDatasetReader.h>
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31
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32 #include <limits>
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33 #include <stdio.h>
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34 #include <boost/lexical_cast.hpp>
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35 #include <boost/geometry.hpp>
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36 #include <boost/geometry/geometries/point_xy.hpp>
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37 #include <boost/geometry/geometries/polygon.hpp>
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38 #include <boost/geometry/multi/geometries/multi_polygon.hpp>
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39
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40 typedef boost::geometry::model::d2::point_xy<double> BoostPoint;
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41 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon;
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42 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon;
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44
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45 static void Union(BoostMultiPolygon& output,
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46 std::vector<BoostPolygon>& input)
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47 {
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48 for (size_t i = 0; i < input.size(); i++)
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49 {
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50 boost::geometry::correct(input[i]);
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51 }
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52
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53 if (input.size() == 0)
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54 {
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55 output.clear();
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56 }
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57 else if (input.size() == 1)
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58 {
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59 output.resize(1);
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60 output[0] = input[0];
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61 }
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62 else
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63 {
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64 boost::geometry::union_(input[0], input[1], output);
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65
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66 for (size_t i = 0; i < input.size(); i++)
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67 {
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68 BoostMultiPolygon tmp;
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69 boost::geometry::union_(output, input[i], tmp);
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70 output = tmp;
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71 }
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72 }
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73 }
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75
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76 static BoostPolygon CreateRectangle(float x1, float y1,
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77 float x2, float y2)
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78 {
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79 BoostPolygon r;
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80 boost::geometry::append(r, BoostPoint(x1, y1));
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81 boost::geometry::append(r, BoostPoint(x1, y2));
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82 boost::geometry::append(r, BoostPoint(x2, y2));
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83 boost::geometry::append(r, BoostPoint(x2, y1));
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84 return r;
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85 }
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86
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87
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89 namespace OrthancStone
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90 {
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91 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042);
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92 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016);
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93 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040);
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94 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050);
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95 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046);
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96 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155);
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97 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039);
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98 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a);
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99 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026);
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100 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4);
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101 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080);
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102 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020);
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103
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104
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105 static uint8_t ConvertColor(double v)
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106 {
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107 if (v < 0)
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108 {
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109 return 0;
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110 }
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111 else if (v >= 255)
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112 {
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113 return 255;
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114 }
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115 else
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116 {
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117 return static_cast<uint8_t>(v);
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118 }
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119 }
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122 static bool ParseVector(Vector& target,
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123 const OrthancPlugins::IDicomDataset& dataset,
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124 const OrthancPlugins::DicomPath& tag)
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125 {
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126 std::string value;
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127 return (dataset.GetStringValue(value, tag) &&
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128 LinearAlgebra::ParseVector(target, value));
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129 }
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130
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132 void DicomStructureSet::Polygon::CheckPoint(const Vector& v)
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133 {
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134 if (hasSlice_)
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135 {
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136 if (!LinearAlgebra::IsNear(GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()),
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137 projectionAlongNormal_,
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138 sliceThickness_ / 2.0 /* in mm */))
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139 {
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140 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance";
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141 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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142 }
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143 }
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144 }
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145
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146
122
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147 void DicomStructureSet::Polygon::AddPoint(const Vector& v)
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148 {
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149 CheckPoint(v);
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150 points_.push_back(v);
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151 }
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152
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153
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154 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices)
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155 {
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156 if (hasSlice_)
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157 {
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158 return true;
32
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159 }
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160 else
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161 {
122
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162 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_);
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163
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164 if (it == slices.end())
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165 {
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166 return false;
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167 }
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168 else
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169 {
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170 const CoordinateSystem3D& geometry = it->second.geometry_;
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171
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172 hasSlice_ = true;
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173 geometry_ = geometry;
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174 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal());
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175 sliceThickness_ = it->second.thickness_;
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176
131
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177 extent_.Reset();
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178
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179 for (Points::const_iterator it = points_.begin(); it != points_.end(); ++it)
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180 {
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181 CheckPoint(*it);
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182
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183 double x, y;
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184 geometry.ProjectPoint(x, y, *it);
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185 extent_.AddPoint(x, y);
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186 }
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187
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188 return true;
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189 }
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190 }
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191 }
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192
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193
122
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194 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const
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195 {
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196 bool isOpposite;
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197
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198 if (points_.empty() ||
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199 !hasSlice_ ||
131
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200 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal()))
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201 {
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202 return false;
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203 }
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204
131
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205 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal());
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206
158
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207 return (LinearAlgebra::IsNear(d, projectionAlongNormal_,
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208 sliceThickness_ / 2.0));
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209 }
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210
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211
131
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212 bool DicomStructureSet::Polygon::Project(double& x1,
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213 double& y1,
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214 double& x2,
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215 double& y2,
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216 const CoordinateSystem3D& slice) const
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217 {
132
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218 // TODO Optimize this method using a sweep-line algorithm for polygons
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219
131
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220 if (!hasSlice_ ||
132
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221 points_.size() <= 1)
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222 {
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223 return false;
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224 }
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225
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226 double x, y;
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227 geometry_.ProjectPoint(x, y, slice.GetOrigin());
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228
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229 bool isOpposite;
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230 if (GeometryToolbox::IsParallelOrOpposite
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231 (isOpposite, slice.GetNormal(), geometry_.GetAxisY()))
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232 {
132
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233 if (y < extent_.GetY1() ||
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234 y > extent_.GetY2())
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235 {
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236 // The polygon does not intersect the input slice
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237 return false;
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238 }
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239
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240 bool isFirst = true;
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241 double xmin = std::numeric_limits<double>::infinity();
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242 double xmax = -std::numeric_limits<double>::infinity();
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243
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244 double prevX, prevY;
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245 geometry_.ProjectPoint(prevX, prevY, points_[points_.size() - 1]);
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246
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247 for (size_t i = 0; i < points_.size(); i++)
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248 {
132
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249 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py
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250 double curX, curY;
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251 geometry_.ProjectPoint(curX, curY, points_[i]);
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252
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253 if ((prevY < y && curY > y) ||
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254 (prevY > y && curY < y))
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255 {
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256 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY);
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257 xmin = std::min(xmin, p);
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258 xmax = std::max(xmax, p);
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259 isFirst = false;
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260 }
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261
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262 prevX = curX;
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263 prevY = curY;
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264 }
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265
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266 if (isFirst)
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267 {
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268 return false;
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269 }
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270 else
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271 {
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272 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) +
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273 sliceThickness_ / 2.0 * geometry_.GetNormal());
132
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274 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) -
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275 sliceThickness_ / 2.0 * geometry_.GetNormal());
132
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276
131
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277 slice.ProjectPoint(x1, y1, p1);
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278 slice.ProjectPoint(x2, y2, p2);
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279 return true;
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280 }
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281 }
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282 else if (GeometryToolbox::IsParallelOrOpposite
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283 (isOpposite, slice.GetNormal(), geometry_.GetAxisX()))
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284 {
132
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285 if (x < extent_.GetX1() ||
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286 x > extent_.GetX2())
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287 {
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288 return false;
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289 }
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290
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291 bool isFirst = true;
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292 double ymin = std::numeric_limits<double>::infinity();
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293 double ymax = -std::numeric_limits<double>::infinity();
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294
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295 double prevX, prevY;
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296 geometry_.ProjectPoint(prevX, prevY, points_[points_.size() - 1]);
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297
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298 for (size_t i = 0; i < points_.size(); i++)
131
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299 {
132
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300 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py
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301 double curX, curY;
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302 geometry_.ProjectPoint(curX, curY, points_[i]);
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303
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304 if ((prevX < x && curX > x) ||
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305 (prevX > x && curX < x))
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306 {
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307 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX);
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308 ymin = std::min(ymin, p);
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309 ymax = std::max(ymax, p);
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310 isFirst = false;
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311 }
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312
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313 prevX = curX;
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314 prevY = curY;
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315 }
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316
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317 if (isFirst)
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318 {
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319 return false;
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320 }
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321 else
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322 {
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323 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) +
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324 sliceThickness_ / 2.0 * geometry_.GetNormal());
132
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325 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) -
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326 sliceThickness_ / 2.0 * geometry_.GetNormal());
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327
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328 slice.ProjectPoint(x1, y1, p1);
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329 slice.ProjectPoint(x2, y2, p2);
132
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330
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331 // TODO WHY THIS???
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332 y1 = -y1;
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333 y2 = -y2;
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334
131
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335 return true;
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336 }
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337 }
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338 else
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339 {
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340 // Should not happen
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341 return false;
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342 }
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343 }
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344
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345
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346 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const
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347 {
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348 if (index >= structures_.size())
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349 {
125
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350 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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351 }
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352
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353 return structures_[index];
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354 }
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355
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356
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357 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index)
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358 {
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359 if (index >= structures_.size())
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360 {
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361 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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362 }
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363
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364 return structures_[index];
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365 }
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366
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367
122
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368 DicomStructureSet::DicomStructureSet(const OrthancPlugins::FullOrthancDataset& tags)
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369 {
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370 using namespace OrthancPlugins;
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371
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372 DicomDatasetReader reader(tags);
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373
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374 size_t count, tmp;
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375 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) ||
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376 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) ||
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377 tmp != count ||
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378 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) ||
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379 tmp != count)
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380 {
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381 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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382 }
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383
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384 structures_.resize(count);
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385 for (size_t i = 0; i < count; i++)
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386 {
122
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387 structures_[i].interpretation_ = reader.GetStringValue
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388 (DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i,
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389 DICOM_TAG_RT_ROI_INTERPRETED_TYPE),
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390 "No interpretation");
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391
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392 structures_[i].name_ = reader.GetStringValue
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393 (DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i,
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394 DICOM_TAG_ROI_NAME),
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395 "No interpretation");
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396
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397 Vector color;
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398 if (ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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399 DICOM_TAG_ROI_DISPLAY_COLOR)) &&
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400 color.size() == 3)
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401 {
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402 structures_[i].red_ = ConvertColor(color[0]);
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403 structures_[i].green_ = ConvertColor(color[1]);
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404 structures_[i].blue_ = ConvertColor(color[2]);
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405 }
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406 else
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407 {
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408 structures_[i].red_ = 255;
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409 structures_[i].green_ = 0;
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410 structures_[i].blue_ = 0;
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411 }
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412
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413 size_t countSlices;
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414 if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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415 DICOM_TAG_CONTOUR_SEQUENCE)))
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416 {
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417 countSlices = 0;
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418 }
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419
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420 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_
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421 << "\" with interpretation \"" << structures_[i].interpretation_
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422 << "\" containing " << countSlices << " slices (color: "
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423 << static_cast<int>(structures_[i].red_) << ","
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424 << static_cast<int>(structures_[i].green_) << ","
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425 << static_cast<int>(structures_[i].blue_) << ")";
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426
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427 for (size_t j = 0; j < countSlices; j++)
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428 {
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diff changeset
429 unsigned int countPoints;
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430
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431 if (!reader.GetUnsignedIntegerValue
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432 (countPoints, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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433 DICOM_TAG_CONTOUR_SEQUENCE, j,
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434 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS)))
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435 {
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436 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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437 }
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diff changeset
438
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diff changeset
439 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices";
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440
122
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441 std::string type = reader.GetMandatoryStringValue
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diff changeset
442 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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diff changeset
443 DICOM_TAG_CONTOUR_SEQUENCE, j,
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diff changeset
444 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE));
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445 if (type != "CLOSED_PLANAR")
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446 {
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447 LOG(WARNING) << "Ignoring contour with geometry type: " << type;
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448 continue;
0
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449 }
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450
122
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diff changeset
451 size_t size;
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diff changeset
452 if (!tags.GetSequenceSize(size, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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diff changeset
453 DICOM_TAG_CONTOUR_SEQUENCE, j,
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diff changeset
454 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE)) ||
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parents: 121
diff changeset
455 size != 1)
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diff changeset
456 {
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
457 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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diff changeset
458 }
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diff changeset
459
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
460 std::string sopInstanceUid = reader.GetMandatoryStringValue
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diff changeset
461 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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diff changeset
462 DICOM_TAG_CONTOUR_SEQUENCE, j,
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diff changeset
463 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0,
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diff changeset
464 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID));
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diff changeset
465
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diff changeset
466 std::string slicesData = reader.GetMandatoryStringValue
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parents: 121
diff changeset
467 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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parents: 121
diff changeset
468 DICOM_TAG_CONTOUR_SEQUENCE, j,
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diff changeset
469 DICOM_TAG_CONTOUR_DATA));
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470
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diff changeset
471 Vector points;
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a053ca7fa5c6 LinearAlgebra toolbox
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diff changeset
472 if (!LinearAlgebra::ParseVector(points, slicesData) ||
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diff changeset
473 points.size() != 3 * countPoints)
0
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diff changeset
474 {
351ab0da0150 initial commit
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475 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
351ab0da0150 initial commit
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476 }
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parents:
diff changeset
477
122
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478 Polygon polygon(sopInstanceUid);
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diff changeset
479 polygon.Reserve(countPoints);
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parents:
diff changeset
480
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diff changeset
481 for (size_t k = 0; k < countPoints; k++)
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diff changeset
482 {
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483 Vector v(3);
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Sebastien Jodogne <s.jodogne@gmail.com>
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484 v[0] = points[3 * k];
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485 v[1] = points[3 * k + 1];
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486 v[2] = points[3 * k + 2];
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diff changeset
487 polygon.AddPoint(v);
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488 }
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diff changeset
489
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parents:
diff changeset
490 structures_[i].polygons_.push_back(polygon);
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diff changeset
491 }
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parents:
diff changeset
492 }
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parents:
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493 }
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parents:
diff changeset
494
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parents:
diff changeset
495
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diff changeset
496 Vector DicomStructureSet::GetStructureCenter(size_t index) const
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diff changeset
497 {
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498 const Structure& structure = GetStructure(index);
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parents:
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499
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diff changeset
500 Vector center;
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parents: 137
diff changeset
501 LinearAlgebra::AssignVector(center, 0, 0, 0);
0
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parents:
diff changeset
502 if (structure.polygons_.empty())
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parents:
diff changeset
503 {
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parents:
diff changeset
504 return center;
351ab0da0150 initial commit
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diff changeset
505 }
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diff changeset
506
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parents:
diff changeset
507 double n = static_cast<double>(structure.polygons_.size());
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parents:
diff changeset
508
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parents:
diff changeset
509 for (Polygons::const_iterator polygon = structure.polygons_.begin();
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parents:
diff changeset
510 polygon != structure.polygons_.end(); ++polygon)
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parents:
diff changeset
511 {
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diff changeset
512 if (!polygon->GetPoints().empty())
0
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513 {
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diff changeset
514 center += polygon->GetPoints().front() / n;
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diff changeset
515 }
351ab0da0150 initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
516 }
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parents:
diff changeset
517
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parents:
diff changeset
518 return center;
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parents:
diff changeset
519 }
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parents:
diff changeset
520
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parents:
diff changeset
521
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diff changeset
522 const std::string& DicomStructureSet::GetStructureName(size_t index) const
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parents:
diff changeset
523 {
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parents:
diff changeset
524 return GetStructure(index).name_;
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parents:
diff changeset
525 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
526
351ab0da0150 initial commit
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parents:
diff changeset
527
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parents:
diff changeset
528 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const
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parents:
diff changeset
529 {
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parents:
diff changeset
530 return GetStructure(index).interpretation_;
351ab0da0150 initial commit
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parents:
diff changeset
531 }
351ab0da0150 initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
532
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
533
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
534 void DicomStructureSet::GetStructureColor(uint8_t& red,
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parents:
diff changeset
535 uint8_t& green,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
536 uint8_t& blue,
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parents:
diff changeset
537 size_t index) const
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parents:
diff changeset
538 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
539 const Structure& s = GetStructure(index);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
540 red = s.red_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
541 green = s.green_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
542 blue = s.blue_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
543 }
351ab0da0150 initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
544
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
545
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diff changeset
546 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances)
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diff changeset
547 {
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
548 for (Structures::const_iterator structure = structures_.begin();
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
549 structure != structures_.end(); ++structure)
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
550 {
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
551 for (Polygons::const_iterator polygon = structure->polygons_.begin();
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
552 polygon != structure->polygons_.end(); ++polygon)
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parents: 121
diff changeset
553 {
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
554 instances.insert(polygon->GetSopInstanceUid());
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parents: 121
diff changeset
555 }
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
556 }
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
557 }
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
558
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
559
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
560 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid,
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
561 const std::string& seriesInstanceUid,
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
562 const CoordinateSystem3D& geometry,
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
563 double thickness)
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parents: 121
diff changeset
564 {
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
565 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end())
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parents: 121
diff changeset
566 {
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
567 // This geometry is already known
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diff changeset
568 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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parents: 121
diff changeset
569 }
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
570 else
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
571 {
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
572 if (thickness < 0)
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
573 {
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
574 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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parents: 121
diff changeset
575 }
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
576
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
577 if (!referencedSlices_.empty())
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parents: 121
diff changeset
578 {
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
579 const ReferencedSlice& reference = referencedSlices_.begin()->second;
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parents: 121
diff changeset
580
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
581 if (reference.seriesInstanceUid_ != seriesInstanceUid)
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parents: 121
diff changeset
582 {
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parents: 121
diff changeset
583 LOG(ERROR) << "This RT-STRUCT refers to several different series";
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parents: 121
diff changeset
584 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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585 }
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586
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diff changeset
587 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal()))
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diff changeset
588 {
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diff changeset
589 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel";
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590 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
591 }
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diff changeset
592 }
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diff changeset
593
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diff changeset
594 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness);
131
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595
3e6163a53b16 optimization
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
596 for (Structures::iterator structure = structures_.begin();
3e6163a53b16 optimization
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diff changeset
597 structure != structures_.end(); ++structure)
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598 {
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599 for (Polygons::iterator polygon = structure->polygons_.begin();
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diff changeset
600 polygon != structure->polygons_.end(); ++polygon)
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601 {
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diff changeset
602 polygon->UpdateReferencedSlice(referencedSlices_);
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diff changeset
603 }
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604 }
122
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diff changeset
605 }
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diff changeset
606 }
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diff changeset
607
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608
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609 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset)
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610 {
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611 CoordinateSystem3D slice(dataset);
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612
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613 double thickness = 1; // 1 mm by default
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614
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615 std::string s;
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616 Vector v;
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617 if (dataset.CopyToString(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) &&
158
a053ca7fa5c6 LinearAlgebra toolbox
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618 LinearAlgebra::ParseVector(v, s) &&
122
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619 v.size() > 0)
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620 {
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621 thickness = v[0];
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622 }
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623
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624 std::string instance, series;
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625 if (dataset.CopyToString(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) &&
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626 dataset.CopyToString(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false))
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627 {
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628 AddReferencedSlice(instance, series, slice, thickness);
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629 }
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630 else
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631 {
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632 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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633 }
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diff changeset
634 }
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diff changeset
635
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diff changeset
636
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diff changeset
637 void DicomStructureSet::CheckReferencedSlices()
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638 {
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diff changeset
639 for (Structures::iterator structure = structures_.begin();
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diff changeset
640 structure != structures_.end(); ++structure)
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diff changeset
641 {
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642 for (Polygons::iterator polygon = structure->polygons_.begin();
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diff changeset
643 polygon != structure->polygons_.end(); ++polygon)
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644 {
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645 if (!polygon->UpdateReferencedSlice(referencedSlices_))
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646 {
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diff changeset
647 LOG(ERROR) << "Missing information about referenced instance: "
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648 << polygon->GetSopInstanceUid();
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649 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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diff changeset
650 }
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diff changeset
651 }
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diff changeset
652 }
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diff changeset
653 }
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diff changeset
654
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655
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656 Vector DicomStructureSet::GetNormal() const
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657 {
126
c9e88e7935a4 rt-struct projection
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658 if (referencedSlices_.empty())
122
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diff changeset
659 {
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diff changeset
660 Vector v;
158
a053ca7fa5c6 LinearAlgebra toolbox
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parents: 137
diff changeset
661 LinearAlgebra::AssignVector(v, 0, 0, 1);
122
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662 return v;
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diff changeset
663 }
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
664 else
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parents: 121
diff changeset
665 {
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
666 return referencedSlices_.begin()->second.geometry_.GetNormal();
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
667 }
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diff changeset
668 }
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diff changeset
669
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diff changeset
670
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diff changeset
671 DicomStructureSet* DicomStructureSet::SynchronousLoad(OrthancPlugins::IOrthancConnection& orthanc,
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diff changeset
672 const std::string& instanceId)
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diff changeset
673 {
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diff changeset
674 const std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050";
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diff changeset
675 OrthancPlugins::FullOrthancDataset dataset(orthanc, uri);
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diff changeset
676
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diff changeset
677 std::auto_ptr<DicomStructureSet> result(new DicomStructureSet(dataset));
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diff changeset
678
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diff changeset
679 std::set<std::string> instances;
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diff changeset
680 result->GetReferencedInstances(instances);
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diff changeset
681
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diff changeset
682 for (std::set<std::string>::const_iterator it = instances.begin();
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diff changeset
683 it != instances.end(); ++it)
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diff changeset
684 {
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diff changeset
685 Json::Value lookup;
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diff changeset
686 MessagingToolbox::RestApiPost(lookup, orthanc, "/tools/lookup", *it);
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diff changeset
687
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diff changeset
688 if (lookup.type() != Json::arrayValue ||
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diff changeset
689 lookup.size() != 1 ||
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diff changeset
690 !lookup[0].isMember("Type") ||
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diff changeset
691 !lookup[0].isMember("Path") ||
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diff changeset
692 lookup[0]["Type"].type() != Json::stringValue ||
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
693 lookup[0]["ID"].type() != Json::stringValue ||
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diff changeset
694 lookup[0]["Type"].asString() != "Instance")
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diff changeset
695 {
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
696 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
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diff changeset
697 }
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diff changeset
698
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
699 OrthancPlugins::FullOrthancDataset slice
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diff changeset
700 (orthanc, "/instances/" + lookup[0]["ID"].asString() + "/tags");
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diff changeset
701 Orthanc::DicomMap m;
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diff changeset
702 MessagingToolbox::ConvertDataset(m, slice);
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diff changeset
703 result->AddReferencedSlice(m);
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
704 }
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diff changeset
705
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diff changeset
706 result->CheckReferencedSlices();
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diff changeset
707
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diff changeset
708 return result.release();
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diff changeset
709 }
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parents: 121
diff changeset
710
125
44fc253d4876 refactoring
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diff changeset
711
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diff changeset
712 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<PolygonPoint> >& polygons,
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diff changeset
713 Structure& structure,
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diff changeset
714 const CoordinateSystem3D& slice)
44fc253d4876 refactoring
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diff changeset
715 {
44fc253d4876 refactoring
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diff changeset
716 polygons.clear();
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diff changeset
717
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diff changeset
718 Vector normal = GetNormal();
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diff changeset
719
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diff changeset
720 bool isOpposite;
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diff changeset
721 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal()))
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722 {
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723 // This is an axial projection
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724
44fc253d4876 refactoring
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725 for (Polygons::iterator polygon = structure.polygons_.begin();
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726 polygon != structure.polygons_.end(); ++polygon)
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727 {
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728 if (polygon->IsOnSlice(slice))
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729 {
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730 polygons.push_back(std::vector<PolygonPoint>());
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731
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732 for (Points::const_iterator p = polygon->GetPoints().begin();
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diff changeset
733 p != polygon->GetPoints().end(); ++p)
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734 {
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735 double x, y;
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736 slice.ProjectPoint(x, y, *p);
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737 polygons.back().push_back(std::make_pair(x, y));
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738 }
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diff changeset
739 }
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740 }
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diff changeset
741
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742 return true;
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743 }
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744 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) ||
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745 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY()))
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746 {
132
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747 #if 1
126
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748 // Sagittal or coronal projection
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749 std::vector<BoostPolygon> projected;
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750
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751 for (Polygons::iterator polygon = structure.polygons_.begin();
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752 polygon != structure.polygons_.end(); ++polygon)
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753 {
131
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754 double x1, y1, x2, y2;
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755 if (polygon->Project(x1, y1, x2, y2, slice))
126
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756 {
131
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diff changeset
757 projected.push_back(CreateRectangle(x1, y1, x2, y2));
126
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758 }
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759 }
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760
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761 BoostMultiPolygon merged;
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762 Union(merged, projected);
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763
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diff changeset
764 polygons.resize(merged.size());
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765 for (size_t i = 0; i < merged.size(); i++)
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766 {
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767 const std::vector<BoostPoint>& outer = merged[i].outer();
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768
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769 polygons[i].resize(outer.size());
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diff changeset
770 for (size_t j = 0; j < outer.size(); j++)
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771 {
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772 polygons[i][j] = std::make_pair(outer[j].x(), outer[j].y());
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773 }
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774 }
132
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775 #else
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776 for (Polygons::iterator polygon = structure.polygons_.begin();
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diff changeset
777 polygon != structure.polygons_.end(); ++polygon)
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diff changeset
778 {
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779 double x1, y1, x2, y2;
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diff changeset
780 if (polygon->Project(x1, y1, x2, y2, slice))
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parents: 131
diff changeset
781 {
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782 std::vector<PolygonPoint> p(4);
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783 p[0] = std::make_pair(x1, y1);
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diff changeset
784 p[1] = std::make_pair(x2, y1);
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785 p[2] = std::make_pair(x2, y2);
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diff changeset
786 p[3] = std::make_pair(x1, y2);
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diff changeset
787 polygons.push_back(p);
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788 }
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789 }
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diff changeset
790 #endif
125
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791
126
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792 return true;
125
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793 }
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794 else
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diff changeset
795 {
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diff changeset
796 return false;
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diff changeset
797 }
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diff changeset
798 }
0
351ab0da0150 initial commit
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parents:
diff changeset
799 }