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annotate Framework/Toolbox/DicomStructureSet2.cpp @ 1478:fab6c6e795a3

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Framework/Toolbox/SortedFrames.cpp
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 18 Jun 2020 16:01:00 +0200
parents 30deba7bc8e2
children
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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) 2017-2020 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 #ifdef BGO_ENABLE_DICOMSTRUCTURESETLOADER2
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23 #include "DicomStructureSet2.h"
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24
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25 #include "../Toolbox/LinearAlgebra.h"
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26 #include "../StoneException.h"
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27
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28 #include <Logging.h>
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29 #include <OrthancException.h>
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30 #include <Toolbox.h>
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31 #include <DicomFormat/DicomTag.h>
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32
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33 #include <FullOrthancDataset.h>
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34 #include <DicomDatasetReader.h>
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36 namespace OrthancStone
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37 {
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38 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042);
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39 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016);
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40 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040);
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41 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050);
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42 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046);
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43 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155);
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44 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039);
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45 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a);
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46 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026);
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47 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4);
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48 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080);
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49 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020);
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50
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51 static inline uint8_t ConvertAndClipToByte(double v)
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52 {
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53 if (v < 0)
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54 {
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55 return 0;
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56 }
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57 else if (v >= 255)
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58 {
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59 return 255;
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60 }
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61 else
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62 {
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63 return static_cast<uint8_t>(v);
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64 }
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65 }
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66
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67 static bool ReadDicomToVector(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 LinearAlgebra::ParseVector(target, value));
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74 }
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77 void DicomPathToString(std::string& s, const OrthancPlugins::DicomPath& dicomPath)
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78 {
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79 std::stringstream tmp;
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80 for (size_t i = 0; i < dicomPath.GetPrefixLength(); ++i)
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81 {
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82 OrthancPlugins::DicomTag tag = dicomPath.GetPrefixTag(i);
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83
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84 // We use this other object to be able to use GetMainTagsName
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85 // and Format
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86 Orthanc::DicomTag tag2(tag.GetGroup(), tag.GetElement());
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87 size_t index = dicomPath.GetPrefixIndex(i);
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88 tmp << tag2.GetMainTagsName() << " (" << tag2.Format() << ") [" << index << "] / ";
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89 }
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90 const OrthancPlugins::DicomTag& tag = dicomPath.GetFinalTag();
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91 Orthanc::DicomTag tag2(tag.GetGroup(), tag.GetElement());
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92 tmp << tag2.GetMainTagsName() << " (" << tag2.Format() << ")";
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93 s = tmp.str();
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94 }
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95
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96 std::ostream& operator<<(std::ostream& s, const OrthancPlugins::DicomPath& dicomPath)
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97 {
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98 std::string tmp;
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99 DicomPathToString(tmp, dicomPath);
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100 s << tmp;
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101 return s;
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102 }
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103
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104
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105 DicomStructureSet2::DicomStructureSet2()
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106 {
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107
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108 }
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109
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111 DicomStructureSet2::~DicomStructureSet2()
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112 {
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113
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114 }
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115
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116 void DicomStructureSet2::SetContents(const OrthancPlugins::FullOrthancDataset& tags)
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117 {
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118 FillStructuresFromDataset(tags);
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119 ComputeDependentProperties();
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120 }
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121
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122 void DicomStructureSet2::ComputeDependentProperties()
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123 {
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124 for (size_t i = 0; i < structures_.size(); ++i)
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125 {
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126 structures_[i].ComputeDependentProperties();
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127 }
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128 }
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129
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130 void DicomStructureSet2::FillStructuresFromDataset(const OrthancPlugins::FullOrthancDataset& tags)
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131 {
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132 OrthancPlugins::DicomDatasetReader reader(tags);
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133
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134 // a few sanity checks
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135 size_t count = 0, tmp = 0;
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136
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137 // DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE (0x3006, 0x0080);
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138 // DICOM_TAG_ROI_CONTOUR_SEQUENCE (0x3006, 0x0039);
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139 // DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE (0x3006, 0x0020);
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140 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) ||
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141 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) ||
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142 tmp != count ||
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143 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) ||
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144 tmp != count)
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145 {
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146 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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147 }
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148
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149 // let's now parse the structures stored in the dicom file
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150 // DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE (0x3006, 0x0080)
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151 // DICOM_TAG_RT_ROI_INTERPRETED_TYPE (0x3006, 0x00a4)
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152 // DICOM_TAG_ROI_DISPLAY_COLOR (0x3006, 0x002a)
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153 // DICOM_TAG_ROI_NAME (0x3006, 0x0026)
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154 structures_.resize(count);
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155 for (size_t i = 0; i < count; i++)
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156 {
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157 // (0x3006, 0x0080)[i]/(0x3006, 0x00a4)
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158 structures_[i].interpretation_ = reader.GetStringValue
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159 (OrthancPlugins::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i,
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160 DICOM_TAG_RT_ROI_INTERPRETED_TYPE),
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161 "No interpretation");
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162
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163 // (0x3006, 0x0020)[i]/(0x3006, 0x0026)
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164 structures_[i].name_ = reader.GetStringValue
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165 (OrthancPlugins::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i,
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166 DICOM_TAG_ROI_NAME),
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167 "No name");
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168
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169 Vector color;
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170 // (0x3006, 0x0039)[i]/(0x3006, 0x002a)
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171 if (ReadDicomToVector(color, tags, OrthancPlugins::DicomPath(
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172 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_ROI_DISPLAY_COLOR))
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173 && color.size() == 3)
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174 {
998
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175 structures_[i].red_ = ConvertAndClipToByte(color[0]);
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176 structures_[i].green_ = ConvertAndClipToByte(color[1]);
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177 structures_[i].blue_ = ConvertAndClipToByte(color[2]);
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178 }
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179 else
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180 {
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181 structures_[i].red_ = 255;
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182 structures_[i].green_ = 0;
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183 structures_[i].blue_ = 0;
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184 }
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185
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186 size_t countSlices;
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187 // DICOM_TAG_ROI_CONTOUR_SEQUENCE (0x3006, 0x0039);
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188 // DICOM_TAG_CONTOUR_SEQUENCE (0x3006, 0x0040);
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189 if (!tags.GetSequenceSize(countSlices, OrthancPlugins::DicomPath(
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190 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_CONTOUR_SEQUENCE)))
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191 {
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192 LOG(WARNING) << "DicomStructureSet2::SetContents | structure \"" << structures_[i].name_ << "\" has no slices!";
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193 countSlices = 0;
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194 }
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195
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196 LOG(INFO) << "New RT structure: \"" << structures_[i].name_
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197 << "\" with interpretation \"" << structures_[i].interpretation_
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198 << "\" containing " << countSlices << " slices (color: "
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199 << static_cast<int>(structures_[i].red_) << ","
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200 << static_cast<int>(structures_[i].green_) << ","
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201 << static_cast<int>(structures_[i].blue_) << ")";
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202
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203 // These temporary variables avoid allocating many vectors in the loop below
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204
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205 // (0x3006, 0x0039)[i]/(0x3006, 0x0040)[0]/(0x3006, 0x0046)
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206 OrthancPlugins::DicomPath countPointsPath(
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207 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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208 DICOM_TAG_CONTOUR_SEQUENCE, 0,
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209 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS);
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210
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211 OrthancPlugins::DicomPath geometricTypePath(
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212 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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213 DICOM_TAG_CONTOUR_SEQUENCE, 0,
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214 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE);
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215
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216 OrthancPlugins::DicomPath imageSequencePath(
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217 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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218 DICOM_TAG_CONTOUR_SEQUENCE, 0,
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219 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE);
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220
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221 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)
998
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222 OrthancPlugins::DicomPath referencedInstancePath(
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223 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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224 DICOM_TAG_CONTOUR_SEQUENCE, 0,
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225 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0,
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226 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID);
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227
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228 OrthancPlugins::DicomPath contourDataPath(
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229 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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230 DICOM_TAG_CONTOUR_SEQUENCE, 0,
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231 DICOM_TAG_CONTOUR_DATA);
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232
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233 for (size_t j = 0; j < countSlices; j++)
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234 {
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235 unsigned int countPoints = 0;
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236
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237 countPointsPath.SetPrefixIndex(1, j);
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238 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath))
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239 {
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240 std::string s;
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241 DicomPathToString(s, countPointsPath);
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242 LOG(ERROR) << "Dicom path " << s << " is not valid (should contain an unsigned integer)";
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243 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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244 }
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245
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246 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices";
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247
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248 geometricTypePath.SetPrefixIndex(1, j);
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249 std::string type = reader.GetMandatoryStringValue(geometricTypePath);
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250 if (type != "CLOSED_PLANAR")
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251 {
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252 // TODO: support points!!
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253 LOG(WARNING) << "Ignoring contour with geometry type: " << type;
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254 continue;
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255 }
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256
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257 size_t size = 0;
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258
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259 imageSequencePath.SetPrefixIndex(1, j);
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260 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1)
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261 {
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262 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry.";
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263 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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264 }
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265
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266 referencedInstancePath.SetPrefixIndex(1, j);
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267 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath);
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268
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269 contourDataPath.SetPrefixIndex(1, j);
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270 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath);
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271
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272 Vector points;
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273 if (!LinearAlgebra::ParseVector(points, slicesData) ||
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274 points.size() != 3 * countPoints)
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275 {
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276 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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277 }
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278
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279 // seen in real world
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280 if (Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "")
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281 {
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282 LOG(ERROR) << "WARNING. The following Dicom tag (Referenced SOP Instance UID) contains an empty value : // (3006,0039)[" << i << "] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)";
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283 }
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284
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285 DicomStructurePolygon2 polygon(sopInstanceUid,type);
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286 polygon.Reserve(countPoints);
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287
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288 for (size_t k = 0; k < countPoints; k++)
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289 {
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290 Vector v(3);
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291 v[0] = points[3 * k];
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292 v[1] = points[3 * k + 1];
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293 v[2] = points[3 * k + 2];
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294 polygon.AddPoint(v);
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295 }
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296 structures_[i].AddPolygon(polygon);
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297 }
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298 }
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299 }
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300
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301
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302 void DicomStructureSet2::Clear()
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303 {
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304 structures_.clear();
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305 }
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306
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307 }
1019
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308
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309 #endif
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310 // BGO_ENABLE_DICOMSTRUCTURESETLOADER2
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311