Mercurial > hg > orthanc-stone

annotate Framework/Toolbox/DicomStructureSet.cpp @ 148:c6a464c266dd wasm

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 24 Jan 2018 15:30:51 +0100
parents a30ff4866a1e
children a053ca7fa5c6
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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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e2fe9352f240 upgrade to year 2018
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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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20
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21
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22 #include "DicomStructureSet.h"
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24 #include "../Toolbox/MessagingToolbox.h"
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25
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26 #include <Core/Logging.h>
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27 #include <Core/OrthancException.h>
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28 #include <Plugins/Samples/Common/FullOrthancDataset.h>
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29 #include <Plugins/Samples/Common/DicomDatasetReader.h>
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31 #include <limits>
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32 #include <stdio.h>
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33 #include <boost/lexical_cast.hpp>
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34 #include <boost/geometry.hpp>
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35 #include <boost/geometry/geometries/point_xy.hpp>
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36 #include <boost/geometry/geometries/polygon.hpp>
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37 #include <boost/geometry/multi/geometries/multi_polygon.hpp>
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38
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39 typedef boost::geometry::model::d2::point_xy<double> BoostPoint;
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40 typedef boost::geometry::model::polygon<BoostPoint> BoostPolygon;
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41 typedef boost::geometry::model::multi_polygon<BoostPolygon> BoostMultiPolygon;
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43
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44 static void Union(BoostMultiPolygon& output,
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45 std::vector<BoostPolygon>& input)
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46 {
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47 for (size_t i = 0; i < input.size(); i++)
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48 {
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49 boost::geometry::correct(input[i]);
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50 }
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51
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52 if (input.size() == 0)
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53 {
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54 output.clear();
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55 }
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56 else if (input.size() == 1)
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57 {
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58 output.resize(1);
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59 output[0] = input[0];
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60 }
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61 else
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62 {
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63 boost::geometry::union_(input[0], input[1], output);
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64
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65 for (size_t i = 0; i < input.size(); i++)
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66 {
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67 BoostMultiPolygon tmp;
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68 boost::geometry::union_(output, input[i], tmp);
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69 output = tmp;
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70 }
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71 }
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72 }
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74
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75 static BoostPolygon CreateRectangle(float x1, float y1,
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76 float x2, float y2)
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77 {
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78 BoostPolygon r;
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79 boost::geometry::append(r, BoostPoint(x1, y1));
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80 boost::geometry::append(r, BoostPoint(x1, y2));
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81 boost::geometry::append(r, BoostPoint(x2, y2));
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82 boost::geometry::append(r, BoostPoint(x2, y1));
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83 return r;
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84 }
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85
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86
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87
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88 namespace OrthancStone
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89 {
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90 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042);
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91 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016);
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92 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040);
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93 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050);
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94 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046);
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95 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155);
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96 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039);
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97 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a);
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98 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026);
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99 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4);
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100 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080);
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101 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020);
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102
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103
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104 static uint8_t ConvertColor(double v)
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105 {
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106 if (v < 0)
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107 {
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108 return 0;
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109 }
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110 else if (v >= 255)
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111 {
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112 return 255;
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113 }
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114 else
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115 {
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116 return static_cast<uint8_t>(v);
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117 }
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118 }
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120
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121 static bool ParseVector(Vector& target,
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122 const OrthancPlugins::IDicomDataset& dataset,
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123 const OrthancPlugins::DicomPath& tag)
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124 {
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125 std::string value;
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126 return (dataset.GetStringValue(value, tag) &&
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127 GeometryToolbox::ParseVector(target, value));
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128 }
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129
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131 void DicomStructureSet::Polygon::CheckPoint(const Vector& v)
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132 {
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133 if (hasSlice_)
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134 {
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135 if (!GeometryToolbox::IsNear(GeometryToolbox::ProjectAlongNormal(v, geometry_.GetNormal()),
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136 projectionAlongNormal_,
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137 sliceThickness_ / 2.0 /* in mm */))
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138 {
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139 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance";
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140 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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141 }
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142 }
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143 }
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144
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145
122
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146 void DicomStructureSet::Polygon::AddPoint(const Vector& v)
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147 {
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148 CheckPoint(v);
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149 points_.push_back(v);
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150 }
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151
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152
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153 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices)
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154 {
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155 if (hasSlice_)
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156 {
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157 return true;
32
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158 }
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159 else
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160 {
122
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161 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_);
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162
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163 if (it == slices.end())
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164 {
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165 return false;
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166 }
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167 else
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168 {
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169 const CoordinateSystem3D& geometry = it->second.geometry_;
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170
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171 hasSlice_ = true;
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172 geometry_ = geometry;
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173 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), geometry.GetNormal());
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174 sliceThickness_ = it->second.thickness_;
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175
131
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176 extent_.Reset();
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177
122
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178 for (Points::const_iterator it = points_.begin(); it != points_.end(); ++it)
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179 {
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180 CheckPoint(*it);
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181
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182 double x, y;
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183 geometry.ProjectPoint(x, y, *it);
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184 extent_.AddPoint(x, y);
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185 }
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186
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187 return true;
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188 }
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189 }
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190 }
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191
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192
122
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193 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const
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194 {
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195 bool isOpposite;
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196
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197 if (points_.empty() ||
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198 !hasSlice_ ||
131
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199 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), geometry_.GetNormal()))
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200 {
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201 return false;
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202 }
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203
131
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204 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), geometry_.GetNormal());
122
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205
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206 return (GeometryToolbox::IsNear(d, projectionAlongNormal_,
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207 sliceThickness_ / 2.0));
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208 }
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209
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210
131
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211 bool DicomStructureSet::Polygon::Project(double& x1,
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212 double& y1,
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213 double& x2,
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214 double& y2,
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215 const CoordinateSystem3D& slice) const
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216 {
132
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217 // TODO Optimize this method using a sweep-line algorithm for polygons
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218
131
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219 if (!hasSlice_ ||
132
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220 points_.size() <= 1)
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221 {
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222 return false;
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223 }
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224
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225 double x, y;
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226 geometry_.ProjectPoint(x, y, slice.GetOrigin());
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227
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228 bool isOpposite;
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229 if (GeometryToolbox::IsParallelOrOpposite
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230 (isOpposite, slice.GetNormal(), geometry_.GetAxisY()))
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231 {
132
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232 if (y < extent_.GetY1() ||
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233 y > extent_.GetY2())
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234 {
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235 // The polygon does not intersect the input slice
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236 return false;
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237 }
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238
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239 bool isFirst = true;
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240 double xmin = std::numeric_limits<double>::infinity();
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241 double xmax = -std::numeric_limits<double>::infinity();
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242
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243 double prevX, prevY;
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244 geometry_.ProjectPoint(prevX, prevY, points_[points_.size() - 1]);
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245
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246 for (size_t i = 0; i < points_.size(); i++)
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247 {
132
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248 // Reference: ../../Resources/Computations/IntersectSegmentAndHorizontalLine.py
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249 double curX, curY;
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250 geometry_.ProjectPoint(curX, curY, points_[i]);
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251
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252 if ((prevY < y && curY > y) ||
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253 (prevY > y && curY < y))
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254 {
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255 double p = (curX * prevY - curY * prevX + y * (prevX - curX)) / (prevY - curY);
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256 xmin = std::min(xmin, p);
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257 xmax = std::max(xmax, p);
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258 isFirst = false;
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259 }
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260
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261 prevX = curX;
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262 prevY = curY;
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263 }
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264
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265 if (isFirst)
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266 {
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267 return false;
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268 }
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269 else
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270 {
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271 Vector p1 = (geometry_.MapSliceToWorldCoordinates(xmin, y) +
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272 sliceThickness_ / 2.0 * geometry_.GetNormal());
132
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273 Vector p2 = (geometry_.MapSliceToWorldCoordinates(xmax, y) -
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274 sliceThickness_ / 2.0 * geometry_.GetNormal());
132
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275
131
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276 slice.ProjectPoint(x1, y1, p1);
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277 slice.ProjectPoint(x2, y2, p2);
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278 return true;
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279 }
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280 }
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281 else if (GeometryToolbox::IsParallelOrOpposite
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282 (isOpposite, slice.GetNormal(), geometry_.GetAxisX()))
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283 {
132
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284 if (x < extent_.GetX1() ||
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285 x > extent_.GetX2())
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286 {
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287 return false;
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288 }
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289
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290 bool isFirst = true;
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291 double ymin = std::numeric_limits<double>::infinity();
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292 double ymax = -std::numeric_limits<double>::infinity();
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293
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294 double prevX, prevY;
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295 geometry_.ProjectPoint(prevX, prevY, points_[points_.size() - 1]);
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296
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297 for (size_t i = 0; i < points_.size(); i++)
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298 {
132
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299 // Reference: ../../Resources/Computations/IntersectSegmentAndVerticalLine.py
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300 double curX, curY;
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301 geometry_.ProjectPoint(curX, curY, points_[i]);
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302
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303 if ((prevX < x && curX > x) ||
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304 (prevX > x && curX < x))
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305 {
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306 double p = (curX * prevY - curY * prevX + x * (curY - prevY)) / (curX - prevX);
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307 ymin = std::min(ymin, p);
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308 ymax = std::max(ymax, p);
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309 isFirst = false;
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310 }
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311
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312 prevX = curX;
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313 prevY = curY;
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314 }
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315
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316 if (isFirst)
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317 {
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318 return false;
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319 }
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320 else
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321 {
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322 Vector p1 = (geometry_.MapSliceToWorldCoordinates(x, ymin) +
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323 sliceThickness_ / 2.0 * geometry_.GetNormal());
132
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324 Vector p2 = (geometry_.MapSliceToWorldCoordinates(x, ymax) -
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325 sliceThickness_ / 2.0 * geometry_.GetNormal());
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326
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327 slice.ProjectPoint(x1, y1, p1);
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328 slice.ProjectPoint(x2, y2, p2);
132
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329
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330 // TODO WHY THIS???
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331 y1 = -y1;
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332 y2 = -y2;
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333
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334 return true;
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335 }
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336 }
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337 else
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338 {
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339 // Should not happen
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340 return false;
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341 }
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342 }
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343
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344
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345 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const
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346 {
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347 if (index >= structures_.size())
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348 {
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349 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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350 }
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351
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352 return structures_[index];
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353 }
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354
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355
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356 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index)
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357 {
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358 if (index >= structures_.size())
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359 {
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360 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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361 }
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362
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363 return structures_[index];
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364 }
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365
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366
122
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367 DicomStructureSet::DicomStructureSet(const OrthancPlugins::FullOrthancDataset& tags)
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368 {
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369 using namespace OrthancPlugins;
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370
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371 DicomDatasetReader reader(tags);
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372
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373 size_t count, tmp;
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374 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) ||
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375 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) ||
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376 tmp != count ||
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377 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) ||
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378 tmp != count)
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379 {
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380 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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381 }
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382
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383 structures_.resize(count);
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384 for (size_t i = 0; i < count; i++)
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385 {
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386 structures_[i].interpretation_ = reader.GetStringValue
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387 (DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i,
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388 DICOM_TAG_RT_ROI_INTERPRETED_TYPE),
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389 "No interpretation");
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390
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391 structures_[i].name_ = reader.GetStringValue
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392 (DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i,
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393 DICOM_TAG_ROI_NAME),
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394 "No interpretation");
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395
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396 Vector color;
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397 if (ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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398 DICOM_TAG_ROI_DISPLAY_COLOR)) &&
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399 color.size() == 3)
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400 {
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401 structures_[i].red_ = ConvertColor(color[0]);
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402 structures_[i].green_ = ConvertColor(color[1]);
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403 structures_[i].blue_ = ConvertColor(color[2]);
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404 }
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405 else
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406 {
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407 structures_[i].red_ = 255;
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408 structures_[i].green_ = 0;
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409 structures_[i].blue_ = 0;
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410 }
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411
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412 size_t countSlices;
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413 if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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414 DICOM_TAG_CONTOUR_SEQUENCE)))
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415 {
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416 countSlices = 0;
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417 }
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418
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419 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_
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420 << "\" with interpretation \"" << structures_[i].interpretation_
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421 << "\" containing " << countSlices << " slices (color: "
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422 << static_cast<int>(structures_[i].red_) << ","
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423 << static_cast<int>(structures_[i].green_) << ","
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424 << static_cast<int>(structures_[i].blue_) << ")";
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425
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426 for (size_t j = 0; j < countSlices; j++)
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427 {
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428 unsigned int countPoints;
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429
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430 if (!reader.GetUnsignedIntegerValue
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431 (countPoints, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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432 DICOM_TAG_CONTOUR_SEQUENCE, j,
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433 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS)))
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434 {
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435 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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436 }
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437
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438 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices";
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439
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440 std::string type = reader.GetMandatoryStringValue
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441 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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diff changeset
442 DICOM_TAG_CONTOUR_SEQUENCE, j,
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443 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE));
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diff changeset
444 if (type != "CLOSED_PLANAR")
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445 {
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446 LOG(ERROR) << "Cannot handle contour with geometry type: " << type;
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447 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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448 }
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449
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450 size_t size;
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451 if (!tags.GetSequenceSize(size, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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diff changeset
452 DICOM_TAG_CONTOUR_SEQUENCE, j,
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diff changeset
453 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE)) ||
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diff changeset
454 size != 1)
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455 {
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456 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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diff changeset
457 }
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diff changeset
458
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diff changeset
459 std::string sopInstanceUid = reader.GetMandatoryStringValue
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diff changeset
460 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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diff changeset
461 DICOM_TAG_CONTOUR_SEQUENCE, j,
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diff changeset
462 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0,
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diff changeset
463 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID));
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diff changeset
464
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diff changeset
465 std::string slicesData = reader.GetMandatoryStringValue
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diff changeset
466 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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diff changeset
467 DICOM_TAG_CONTOUR_SEQUENCE, j,
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diff changeset
468 DICOM_TAG_CONTOUR_DATA));
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469
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470 Vector points;
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471 if (!GeometryToolbox::ParseVector(points, slicesData) ||
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diff changeset
472 points.size() != 3 * countPoints)
0
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473 {
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474 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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475 }
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476
122
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477 Polygon polygon(sopInstanceUid);
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478 polygon.Reserve(countPoints);
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479
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diff changeset
480 for (size_t k = 0; k < countPoints; k++)
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481 {
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diff changeset
482 Vector v(3);
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483 v[0] = points[3 * k];
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484 v[1] = points[3 * k + 1];
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485 v[2] = points[3 * k + 2];
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486 polygon.AddPoint(v);
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487 }
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488
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489 structures_[i].polygons_.push_back(polygon);
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490 }
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parents:
diff changeset
491 }
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parents:
diff changeset
492 }
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diff changeset
493
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parents:
diff changeset
494
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495 Vector DicomStructureSet::GetStructureCenter(size_t index) const
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496 {
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497 const Structure& structure = GetStructure(index);
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498
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diff changeset
499 Vector center;
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500 GeometryToolbox::AssignVector(center, 0, 0, 0);
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501 if (structure.polygons_.empty())
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parents:
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502 {
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503 return center;
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parents:
diff changeset
504 }
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parents:
diff changeset
505
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506 double n = static_cast<double>(structure.polygons_.size());
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507
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parents:
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508 for (Polygons::const_iterator polygon = structure.polygons_.begin();
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509 polygon != structure.polygons_.end(); ++polygon)
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510 {
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511 if (!polygon->GetPoints().empty())
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512 {
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513 center += polygon->GetPoints().front() / n;
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514 }
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parents:
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515 }
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parents:
diff changeset
516
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517 return center;
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518 }
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parents:
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519
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diff changeset
520
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diff changeset
521 const std::string& DicomStructureSet::GetStructureName(size_t index) const
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522 {
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523 return GetStructure(index).name_;
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parents:
diff changeset
524 }
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parents:
diff changeset
525
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parents:
diff changeset
526
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diff changeset
527 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const
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528 {
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diff changeset
529 return GetStructure(index).interpretation_;
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parents:
diff changeset
530 }
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parents:
diff changeset
531
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parents:
diff changeset
532
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parents:
diff changeset
533 void DicomStructureSet::GetStructureColor(uint8_t& red,
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534 uint8_t& green,
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parents:
diff changeset
535 uint8_t& blue,
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536 size_t index) const
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parents:
diff changeset
537 {
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parents:
diff changeset
538 const Structure& s = GetStructure(index);
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parents:
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539 red = s.red_;
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parents:
diff changeset
540 green = s.green_;
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parents:
diff changeset
541 blue = s.blue_;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
542 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
543
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parents:
diff changeset
544
122
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diff changeset
545 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances)
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diff changeset
546 {
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
547 for (Structures::const_iterator structure = structures_.begin();
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diff changeset
548 structure != structures_.end(); ++structure)
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diff changeset
549 {
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diff changeset
550 for (Polygons::const_iterator polygon = structure->polygons_.begin();
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diff changeset
551 polygon != structure->polygons_.end(); ++polygon)
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diff changeset
552 {
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diff changeset
553 instances.insert(polygon->GetSopInstanceUid());
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diff changeset
554 }
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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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diff changeset
558
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
559 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid,
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diff changeset
560 const std::string& seriesInstanceUid,
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diff changeset
561 const CoordinateSystem3D& geometry,
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diff changeset
562 double thickness)
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parents: 121
diff changeset
563 {
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
564 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end())
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parents: 121
diff changeset
565 {
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
566 // This geometry is already known
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diff changeset
567 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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parents: 121
diff changeset
568 }
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
569 else
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parents: 121
diff changeset
570 {
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
571 if (thickness < 0)
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parents: 121
diff changeset
572 {
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
573 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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parents: 121
diff changeset
574 }
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parents: 121
diff changeset
575
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
576 if (!referencedSlices_.empty())
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parents: 121
diff changeset
577 {
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diff changeset
578 const ReferencedSlice& reference = referencedSlices_.begin()->second;
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parents: 121
diff changeset
579
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parents: 121
diff changeset
580 if (reference.seriesInstanceUid_ != seriesInstanceUid)
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parents: 121
diff changeset
581 {
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diff changeset
582 LOG(ERROR) << "This RT-STRUCT refers to several different series";
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parents: 121
diff changeset
583 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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parents: 121
diff changeset
584 }
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diff changeset
585
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diff changeset
586 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal()))
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diff changeset
587 {
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diff changeset
588 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel";
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589 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
590 }
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parents: 121
diff changeset
591 }
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diff changeset
592
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diff changeset
593 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness);
131
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594
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diff changeset
595 for (Structures::iterator structure = structures_.begin();
3e6163a53b16 optimization
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diff changeset
596 structure != structures_.end(); ++structure)
3e6163a53b16 optimization
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597 {
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parents: 126
diff changeset
598 for (Polygons::iterator polygon = structure->polygons_.begin();
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parents: 126
diff changeset
599 polygon != structure->polygons_.end(); ++polygon)
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600 {
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parents: 126
diff changeset
601 polygon->UpdateReferencedSlice(referencedSlices_);
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parents: 126
diff changeset
602 }
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diff changeset
603 }
122
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diff changeset
604 }
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Sebastien Jodogne <s.jodogne@gmail.com>
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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 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset)
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609 {
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diff changeset
610 CoordinateSystem3D slice(dataset);
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611
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612 double thickness = 1; // 1 mm by default
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613
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Sebastien Jodogne <s.jodogne@gmail.com>
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614 std::string s;
e3433dabfb8d refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
615 Vector v;
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616 if (dataset.CopyToString(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) &&
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
617 GeometryToolbox::ParseVector(v, s) &&
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618 v.size() > 0)
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diff changeset
619 {
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diff changeset
620 thickness = v[0];
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diff changeset
621 }
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622
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diff changeset
623 std::string instance, series;
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diff changeset
624 if (dataset.CopyToString(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) &&
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diff changeset
625 dataset.CopyToString(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false))
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626 {
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diff changeset
627 AddReferencedSlice(instance, series, slice, thickness);
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628 }
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diff changeset
629 else
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diff changeset
630 {
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diff changeset
631 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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diff changeset
632 }
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parents: 121
diff changeset
633 }
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diff changeset
634
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diff changeset
635
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diff changeset
636 void DicomStructureSet::CheckReferencedSlices()
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637 {
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diff changeset
638 for (Structures::iterator structure = structures_.begin();
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diff changeset
639 structure != structures_.end(); ++structure)
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diff changeset
640 {
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diff changeset
641 for (Polygons::iterator polygon = structure->polygons_.begin();
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diff changeset
642 polygon != structure->polygons_.end(); ++polygon)
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diff changeset
643 {
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644 if (!polygon->UpdateReferencedSlice(referencedSlices_))
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diff changeset
645 {
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diff changeset
646 LOG(ERROR) << "Missing information about referenced instance: "
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diff changeset
647 << polygon->GetSopInstanceUid();
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diff changeset
648 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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diff changeset
649 }
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parents: 121
diff changeset
650 }
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
651 }
e3433dabfb8d refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 121
diff changeset
652 }
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
653
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
654
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655 Vector DicomStructureSet::GetNormal() const
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diff changeset
656 {
126
c9e88e7935a4 rt-struct projection
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diff changeset
657 if (referencedSlices_.empty())
122
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diff changeset
658 {
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diff changeset
659 Vector v;
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diff changeset
660 GeometryToolbox::AssignVector(v, 0, 0, 1);
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661 return v;
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diff changeset
662 }
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diff changeset
663 else
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diff changeset
664 {
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diff changeset
665 return referencedSlices_.begin()->second.geometry_.GetNormal();
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
666 }
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
667 }
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
668
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
669
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diff changeset
670 DicomStructureSet* DicomStructureSet::SynchronousLoad(OrthancPlugins::IOrthancConnection& orthanc,
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diff changeset
671 const std::string& instanceId)
e3433dabfb8d refactoring DicomStructureSet
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
672 {
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diff changeset
673 const std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050";
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
674 OrthancPlugins::FullOrthancDataset dataset(orthanc, uri);
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diff changeset
675
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diff changeset
676 std::auto_ptr<DicomStructureSet> result(new DicomStructureSet(dataset));
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diff changeset
677
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diff changeset
678 std::set<std::string> instances;
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
679 result->GetReferencedInstances(instances);
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diff changeset
680
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
681 for (std::set<std::string>::const_iterator it = instances.begin();
e3433dabfb8d refactoring DicomStructureSet
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parents: 121
diff changeset
682 it != instances.end(); ++it)
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
683 {
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
684 Json::Value lookup;
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
685 MessagingToolbox::RestApiPost(lookup, orthanc, "/tools/lookup", *it);
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diff changeset
686
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parents: 121
diff changeset
687 if (lookup.type() != Json::arrayValue ||
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diff changeset
688 lookup.size() != 1 ||
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
689 !lookup[0].isMember("Type") ||
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
690 !lookup[0].isMember("Path") ||
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diff changeset
691 lookup[0]["Type"].type() != Json::stringValue ||
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
692 lookup[0]["ID"].type() != Json::stringValue ||
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
693 lookup[0]["Type"].asString() != "Instance")
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
694 {
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
695 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
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diff changeset
696 }
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parents: 121
diff changeset
697
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
698 OrthancPlugins::FullOrthancDataset slice
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diff changeset
699 (orthanc, "/instances/" + lookup[0]["ID"].asString() + "/tags");
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diff changeset
700 Orthanc::DicomMap m;
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diff changeset
701 MessagingToolbox::ConvertDataset(m, slice);
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diff changeset
702 result->AddReferencedSlice(m);
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
703 }
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
704
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
705 result->CheckReferencedSlices();
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diff changeset
706
e3433dabfb8d refactoring DicomStructureSet
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diff changeset
707 return result.release();
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diff changeset
708 }
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diff changeset
709
125
44fc253d4876 refactoring
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parents: 122
diff changeset
710
44fc253d4876 refactoring
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diff changeset
711 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<PolygonPoint> >& polygons,
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diff changeset
712 Structure& structure,
44fc253d4876 refactoring
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diff changeset
713 const CoordinateSystem3D& slice)
44fc253d4876 refactoring
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diff changeset
714 {
44fc253d4876 refactoring
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diff changeset
715 polygons.clear();
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diff changeset
716
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diff changeset
717 Vector normal = GetNormal();
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diff changeset
718
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diff changeset
719 bool isOpposite;
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diff changeset
720 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal()))
44fc253d4876 refactoring
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diff changeset
721 {
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722 // This is an axial projection
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723
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724 for (Polygons::iterator polygon = structure.polygons_.begin();
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725 polygon != structure.polygons_.end(); ++polygon)
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726 {
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727 if (polygon->IsOnSlice(slice))
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728 {
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729 polygons.push_back(std::vector<PolygonPoint>());
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730
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731 for (Points::const_iterator p = polygon->GetPoints().begin();
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732 p != polygon->GetPoints().end(); ++p)
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733 {
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734 double x, y;
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735 slice.ProjectPoint(x, y, *p);
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736 polygons.back().push_back(std::make_pair(x, y));
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737 }
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738 }
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739 }
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740
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741 return true;
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742 }
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743 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) ||
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744 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY()))
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745 {
132
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746 #if 1
126
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747 // Sagittal or coronal projection
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748 std::vector<BoostPolygon> projected;
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749
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750 for (Polygons::iterator polygon = structure.polygons_.begin();
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751 polygon != structure.polygons_.end(); ++polygon)
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752 {
131
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753 double x1, y1, x2, y2;
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754 if (polygon->Project(x1, y1, x2, y2, slice))
126
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755 {
131
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756 projected.push_back(CreateRectangle(x1, y1, x2, y2));
126
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757 }
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758 }
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759
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760 BoostMultiPolygon merged;
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761 Union(merged, projected);
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762
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763 polygons.resize(merged.size());
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764 for (size_t i = 0; i < merged.size(); i++)
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765 {
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766 const std::vector<BoostPoint>& outer = merged[i].outer();
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767
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768 polygons[i].resize(outer.size());
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769 for (size_t j = 0; j < outer.size(); j++)
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770 {
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771 polygons[i][j] = std::make_pair(outer[j].x(), outer[j].y());
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772 }
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773 }
132
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774 #else
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775 for (Polygons::iterator polygon = structure.polygons_.begin();
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776 polygon != structure.polygons_.end(); ++polygon)
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777 {
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778 double x1, y1, x2, y2;
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779 if (polygon->Project(x1, y1, x2, y2, slice))
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780 {
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781 std::vector<PolygonPoint> p(4);
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782 p[0] = std::make_pair(x1, y1);
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783 p[1] = std::make_pair(x2, y1);
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784 p[2] = std::make_pair(x2, y2);
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785 p[3] = std::make_pair(x1, y2);
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786 polygons.push_back(p);
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787 }
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788 }
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789 #endif
125
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790
126
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791 return true;
125
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792 }
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793 else
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794 {
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795 return false;
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796 }
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797 }
0
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798 }