Mercurial > hg > orthanc-stone

annotate Framework/Toolbox/DicomStructureSet.cpp @ 125:44fc253d4876 wasm

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refactoring
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 08 Nov 2017 16:13:55 +0100
parents e3433dabfb8d
children c9e88e7935a4
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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 Osimis, 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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24 #include "../Toolbox/MessagingToolbox.h"
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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 <stdio.h>
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32 #include <boost/lexical_cast.hpp>
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33
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34 namespace OrthancStone
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35 {
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36 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042);
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37 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016);
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38 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040);
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39 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050);
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40 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046);
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41 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155);
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42 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039);
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43 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a);
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44 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026);
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45 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4);
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46 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080);
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47 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020);
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50 static uint8_t ConvertColor(double v)
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51 {
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52 if (v < 0)
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53 {
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54 return 0;
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55 }
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56 else if (v >= 255)
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57 {
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58 return 255;
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59 }
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60 else
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61 {
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62 return static_cast<uint8_t>(v);
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63 }
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64 }
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66
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67 static bool ParseVector(Vector& target,
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68 const OrthancPlugins::IDicomDataset& dataset,
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69 const OrthancPlugins::DicomPath& tag)
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70 {
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71 std::string value;
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72 return (dataset.GetStringValue(value, tag) &&
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73 GeometryToolbox::ParseVector(target, value));
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74 }
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77 void DicomStructureSet::Polygon::CheckPoint(const Vector& v)
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78 {
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79 if (hasSlice_)
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80 {
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81 if (!GeometryToolbox::IsNear(GeometryToolbox::ProjectAlongNormal(v, normal_),
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82 projectionAlongNormal_,
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83 sliceThickness_ / 2.0 /* in mm */))
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84 {
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85 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance";
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86 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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87 }
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88 }
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89 }
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92 void DicomStructureSet::Polygon::AddPoint(const Vector& v)
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93 {
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94 CheckPoint(v);
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95 points_.push_back(v);
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96 }
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97
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98
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99 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices)
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100 {
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101 if (hasSlice_)
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102 {
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103 return true;
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104 }
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105 else
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106 {
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107 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_);
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108
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109 if (it == slices.end())
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110 {
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111 return false;
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112 }
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113 else
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114 {
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115 const CoordinateSystem3D& geometry = it->second.geometry_;
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116
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117 hasSlice_ = true;
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118 normal_ = geometry.GetNormal();
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119 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), normal_);
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120 sliceThickness_ = it->second.thickness_;
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122 for (Points::const_iterator it = points_.begin(); it != points_.end(); ++it)
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123 {
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124 CheckPoint(*it);
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125 }
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126
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127 return true;
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128 }
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129 }
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130 }
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133 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const
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134 {
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135 bool isOpposite;
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136
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137 if (points_.empty() ||
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138 !hasSlice_ ||
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139 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), normal_))
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140 {
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141 return false;
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142 }
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143
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144 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), normal_);
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145
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146 return (GeometryToolbox::IsNear(d, projectionAlongNormal_,
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147 sliceThickness_ / 2.0));
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148 }
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149
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150
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151 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const
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152 {
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153 if (index >= structures_.size())
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154 {
125
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155 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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156 }
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157
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158 return structures_[index];
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159 }
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160
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161
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162 DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index)
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163 {
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164 if (index >= structures_.size())
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165 {
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166 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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167 }
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168
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169 return structures_[index];
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170 }
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171
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172
122
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173 DicomStructureSet::DicomStructureSet(const OrthancPlugins::FullOrthancDataset& tags)
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174 {
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175 using namespace OrthancPlugins;
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176
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177 DicomDatasetReader reader(tags);
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178
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179 size_t count, tmp;
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180 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) ||
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181 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) ||
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182 tmp != count ||
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183 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) ||
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184 tmp != count)
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185 {
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186 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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187 }
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188
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189 structures_.resize(count);
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190 for (size_t i = 0; i < count; i++)
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191 {
122
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192 structures_[i].interpretation_ = reader.GetStringValue
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193 (DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i,
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194 DICOM_TAG_RT_ROI_INTERPRETED_TYPE),
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195 "No interpretation");
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196
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197 structures_[i].name_ = reader.GetStringValue
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198 (DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i,
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199 DICOM_TAG_ROI_NAME),
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200 "No interpretation");
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201
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202 Vector color;
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203 if (ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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204 DICOM_TAG_ROI_DISPLAY_COLOR)) &&
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205 color.size() == 3)
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206 {
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207 structures_[i].red_ = ConvertColor(color[0]);
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208 structures_[i].green_ = ConvertColor(color[1]);
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209 structures_[i].blue_ = ConvertColor(color[2]);
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210 }
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211 else
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212 {
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213 structures_[i].red_ = 255;
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214 structures_[i].green_ = 0;
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215 structures_[i].blue_ = 0;
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216 }
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217
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218 size_t countSlices;
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219 if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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220 DICOM_TAG_CONTOUR_SEQUENCE)))
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221 {
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222 countSlices = 0;
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223 }
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224
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225 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_
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226 << "\" with interpretation \"" << structures_[i].interpretation_
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227 << "\" containing " << countSlices << " slices (color: "
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228 << static_cast<int>(structures_[i].red_) << ","
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229 << static_cast<int>(structures_[i].green_) << ","
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230 << static_cast<int>(structures_[i].blue_) << ")";
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231
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232 for (size_t j = 0; j < countSlices; j++)
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233 {
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234 unsigned int countPoints;
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235
122
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236 if (!reader.GetUnsignedIntegerValue
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237 (countPoints, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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238 DICOM_TAG_CONTOUR_SEQUENCE, j,
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239 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS)))
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240 {
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241 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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242 }
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243
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244 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices";
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245
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246 std::string type = reader.GetMandatoryStringValue
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247 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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248 DICOM_TAG_CONTOUR_SEQUENCE, j,
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249 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE));
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250 if (type != "CLOSED_PLANAR")
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251 {
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252 LOG(ERROR) << "Cannot handle contour with geometry type: " << type;
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253 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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254 }
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255
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256 size_t size;
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257 if (!tags.GetSequenceSize(size, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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258 DICOM_TAG_CONTOUR_SEQUENCE, j,
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259 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE)) ||
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260 size != 1)
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261 {
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262 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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263 }
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264
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265 std::string sopInstanceUid = reader.GetMandatoryStringValue
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266 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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267 DICOM_TAG_CONTOUR_SEQUENCE, j,
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268 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0,
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269 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID));
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270
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271 std::string slicesData = reader.GetMandatoryStringValue
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272 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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273 DICOM_TAG_CONTOUR_SEQUENCE, j,
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274 DICOM_TAG_CONTOUR_DATA));
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275
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276 Vector points;
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277 if (!GeometryToolbox::ParseVector(points, slicesData) ||
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278 points.size() != 3 * countPoints)
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279 {
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280 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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281 }
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282
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283 Polygon polygon(sopInstanceUid);
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284
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285 for (size_t k = 0; k < countPoints; k++)
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286 {
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287 Vector v(3);
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288 v[0] = points[3 * k];
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289 v[1] = points[3 * k + 1];
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290 v[2] = points[3 * k + 2];
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291 polygon.AddPoint(v);
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292 }
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293
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294 structures_[i].polygons_.push_back(polygon);
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295 }
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296 }
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297 }
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298
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299
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300 Vector DicomStructureSet::GetStructureCenter(size_t index) const
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301 {
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302 const Structure& structure = GetStructure(index);
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303
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304 Vector center;
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305 GeometryToolbox::AssignVector(center, 0, 0, 0);
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306 if (structure.polygons_.empty())
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307 {
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308 return center;
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309 }
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310
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311 double n = static_cast<double>(structure.polygons_.size());
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312
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313 for (Polygons::const_iterator polygon = structure.polygons_.begin();
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314 polygon != structure.polygons_.end(); ++polygon)
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315 {
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316 if (!polygon->GetPoints().empty())
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317 {
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318 center += polygon->GetPoints().front() / n;
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319 }
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320 }
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321
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322 return center;
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323 }
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324
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325
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326 const std::string& DicomStructureSet::GetStructureName(size_t index) const
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327 {
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328 return GetStructure(index).name_;
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329 }
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330
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331
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332 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const
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333 {
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334 return GetStructure(index).interpretation_;
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335 }
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336
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337
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338 void DicomStructureSet::GetStructureColor(uint8_t& red,
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339 uint8_t& green,
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340 uint8_t& blue,
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341 size_t index) const
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342 {
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343 const Structure& s = GetStructure(index);
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344 red = s.red_;
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345 green = s.green_;
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346 blue = s.blue_;
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347 }
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348
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349
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350 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances)
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351 {
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352 for (Structures::const_iterator structure = structures_.begin();
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353 structure != structures_.end(); ++structure)
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354 {
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355 for (Polygons::const_iterator polygon = structure->polygons_.begin();
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356 polygon != structure->polygons_.end(); ++polygon)
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357 {
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358 instances.insert(polygon->GetSopInstanceUid());
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359 }
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360 }
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361 }
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362
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363
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364 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid,
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365 const std::string& seriesInstanceUid,
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366 const CoordinateSystem3D& geometry,
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367 double thickness)
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368 {
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369 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end())
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370 {
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371 // This geometry is already known
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372 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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373 }
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374 else
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375 {
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376 if (thickness < 0)
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377 {
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378 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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379 }
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380
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381 if (!referencedSlices_.empty())
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382 {
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383 const ReferencedSlice& reference = referencedSlices_.begin()->second;
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384
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385 if (reference.seriesInstanceUid_ != seriesInstanceUid)
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386 {
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387 LOG(ERROR) << "This RT-STRUCT refers to several different series";
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388 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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389 }
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390
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391 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal()))
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392 {
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393 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel";
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394 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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395 }
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396 }
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397
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398 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness);
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399 }
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400 }
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401
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402
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403 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset)
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404 {
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405 CoordinateSystem3D slice(dataset);
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406
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407 double thickness = 1; // 1 mm by default
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408
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409 std::string s;
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410 Vector v;
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411 if (dataset.CopyToString(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) &&
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412 GeometryToolbox::ParseVector(v, s) &&
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413 v.size() > 0)
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414 {
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415 thickness = v[0];
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416 }
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417
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418 std::string instance, series;
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419 if (dataset.CopyToString(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) &&
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420 dataset.CopyToString(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false))
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421 {
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422 AddReferencedSlice(instance, series, slice, thickness);
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423 }
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424 else
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425 {
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426 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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427 }
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428 }
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429
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430
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431 void DicomStructureSet::CheckReferencedSlices()
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432 {
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433 for (Structures::iterator structure = structures_.begin();
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434 structure != structures_.end(); ++structure)
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435 {
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436 for (Polygons::iterator polygon = structure->polygons_.begin();
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437 polygon != structure->polygons_.end(); ++polygon)
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438 {
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439 if (!polygon->UpdateReferencedSlice(referencedSlices_))
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440 {
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441 LOG(ERROR) << "Missing information about referenced instance: "
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442 << polygon->GetSopInstanceUid();
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443 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
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444 }
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445 }
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446 }
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447 }
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448
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449
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450 Vector DicomStructureSet::GetNormal() const
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451 {
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452 if (!referencedSlices_.empty())
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453 {
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454 Vector v;
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455 GeometryToolbox::AssignVector(v, 0, 0, 1);
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456 return v;
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457 }
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458 else
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459 {
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460 return referencedSlices_.begin()->second.geometry_.GetNormal();
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461 }
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462 }
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463
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464
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465 DicomStructureSet* DicomStructureSet::SynchronousLoad(OrthancPlugins::IOrthancConnection& orthanc,
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466 const std::string& instanceId)
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467 {
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468 const std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050";
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469 OrthancPlugins::FullOrthancDataset dataset(orthanc, uri);
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470
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471 std::auto_ptr<DicomStructureSet> result(new DicomStructureSet(dataset));
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472
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473 std::set<std::string> instances;
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474 result->GetReferencedInstances(instances);
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475
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476 for (std::set<std::string>::const_iterator it = instances.begin();
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477 it != instances.end(); ++it)
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478 {
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479 Json::Value lookup;
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480 MessagingToolbox::RestApiPost(lookup, orthanc, "/tools/lookup", *it);
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481
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482 if (lookup.type() != Json::arrayValue ||
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483 lookup.size() != 1 ||
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484 !lookup[0].isMember("Type") ||
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485 !lookup[0].isMember("Path") ||
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486 lookup[0]["Type"].type() != Json::stringValue ||
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487 lookup[0]["ID"].type() != Json::stringValue ||
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488 lookup[0]["Type"].asString() != "Instance")
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489 {
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490 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
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491 }
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492
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493 OrthancPlugins::FullOrthancDataset slice
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494 (orthanc, "/instances/" + lookup[0]["ID"].asString() + "/tags");
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495 Orthanc::DicomMap m;
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496 MessagingToolbox::ConvertDataset(m, slice);
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497 result->AddReferencedSlice(m);
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498 }
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499
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500 result->CheckReferencedSlices();
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501
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502 return result.release();
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503 }
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504
125
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505
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506 bool DicomStructureSet::ProjectStructure(std::vector< std::vector<PolygonPoint> >& polygons,
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507 Structure& structure,
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508 const CoordinateSystem3D& slice)
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509 {
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510 polygons.clear();
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511
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512 Vector normal = GetNormal();
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513
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514 bool isOpposite;
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515 if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetNormal()))
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516 {
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517 // This is an axial projection
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518
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519 for (Polygons::iterator polygon = structure.polygons_.begin();
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520 polygon != structure.polygons_.end(); ++polygon)
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521 {
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522 polygon->UpdateReferencedSlice(referencedSlices_);
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523
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524 if (polygon->IsOnSlice(slice))
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525 {
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526 polygons.push_back(std::vector<PolygonPoint>());
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527
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528 for (Points::const_iterator p = polygon->GetPoints().begin();
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529 p != polygon->GetPoints().end(); ++p)
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530 {
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531 double x, y;
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532 slice.ProjectPoint(x, y, *p);
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533 polygons.back().push_back(std::make_pair(x, y));
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534 }
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535 }
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536 }
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537
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538 return true;
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539 }
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540 else if (GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisX()) ||
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541 GeometryToolbox::IsParallelOrOpposite(isOpposite, normal, slice.GetAxisY()))
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542 {
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543 // Sagittal or coronal projections
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544
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545 return false;
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546 }
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547 else
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diff changeset
548 {
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549 return false;
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550 }
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551 }
0
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parents:
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552 }