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annotate OrthancStone/Resources/Graveyard/RTStructTentativeReimplementation-BGO/DicomStructureSet2.cpp @ 1908:affde38b84de

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moved tentative bgo reimplementation of rt-struct into graveyard
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 01 Feb 2022 08:38:32 +0100
parents OrthancStone/Sources/Toolbox/DicomStructureSet2.cpp@7053b8a0aaec
children 07964689cb0b
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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) 2017-2022 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU Lesser General Public License
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10 * as published by the Free Software Foundation, either version 3 of
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11 * the License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * Lesser General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU Lesser General Public
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19 * License along with this program. If not, see
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20 * <http://www.gnu.org/licenses/>.
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21 **/
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22
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23 #ifdef BGO_ENABLE_DICOMSTRUCTURESETLOADER2
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25 #include "DicomStructureSet2.h"
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27 #include "../Toolbox/LinearAlgebra.h"
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28 #include "../StoneException.h"
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29
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30 #include <Logging.h>
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31 #include <OrthancException.h>
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32 #include <Toolbox.h>
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33 #include <DicomFormat/DicomTag.h>
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35 #include "DicomStructure2.h"
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36 #include "GenericToolbox.h"
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37 #include "OrthancDatasets/DicomDatasetReader.h"
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39 namespace OrthancStone
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40 {
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41 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042);
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42 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016);
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43 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_SEQUENCE(0x3006, 0x0040);
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44 static const Orthanc::DicomTag DICOM_TAG_CONTOUR_DATA(0x3006, 0x0050);
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45 static const Orthanc::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046);
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46 static const Orthanc::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155);
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47 static const Orthanc::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039);
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48 static const Orthanc::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a);
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49 static const Orthanc::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026);
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50 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4);
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51 static const Orthanc::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080);
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52 static const Orthanc::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020);
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53
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54 static inline uint8_t ConvertAndClipToByte(double v)
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55 {
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56 if (v < 0)
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57 {
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58 return 0;
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59 }
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60 else if (v >= 255)
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61 {
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62 return 255;
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63 }
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64 else
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65 {
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66 return static_cast<uint8_t>(v);
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67 }
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68 }
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69
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70 static bool ReadDicomToVector(Vector& target,
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71 const IDicomDataset& dataset,
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72 const Orthanc::DicomPath& tag)
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73 {
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74 std::string value;
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75 return (dataset.GetStringValue(value, tag) &&
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76 GenericToolbox::FastParseVector(target, value));
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77 }
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79
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80 void DicomPathToString(std::string& s, const Orthanc::DicomPath& dicomPath)
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81 {
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82 std::stringstream tmp;
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83 for (size_t i = 0; i < dicomPath.GetPrefixLength(); ++i)
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84 {
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85 Orthanc::DicomTag tag = dicomPath.GetPrefixTag(i);
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86
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87 // We use this other object to be able to use Format
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88 Orthanc::DicomTag tag2(tag.GetGroup(), tag.GetElement());
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89 size_t index = dicomPath.GetPrefixIndex(i);
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90 tmp << " (" << tag2.Format() << ") [" << index << "] / ";
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91 }
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92 const Orthanc::DicomTag& tag = dicomPath.GetFinalTag();
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93 Orthanc::DicomTag tag2(tag.GetGroup(), tag.GetElement());
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94 tmp << " (" << tag2.Format() << ")";
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95 s = tmp.str();
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96 }
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97
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98 std::ostream& operator<<(std::ostream& s, const Orthanc::DicomPath& dicomPath)
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99 {
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100 std::string tmp;
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101 DicomPathToString(tmp, dicomPath);
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102 s << tmp;
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103 return s;
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104 }
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105
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106
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107 DicomStructureSet2::DicomStructureSet2()
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108 {
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109
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110 }
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111
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112
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113 DicomStructureSet2::~DicomStructureSet2()
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114 {
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115
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116 }
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117
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118 void DicomStructureSet2::SetContents(const FullOrthancDataset& tags)
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119 {
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120 FillStructuresFromDataset(tags);
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121 ComputeDependentProperties();
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122 }
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123
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124 void DicomStructureSet2::ComputeDependentProperties()
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125 {
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126 for (size_t i = 0; i < structures_.size(); ++i)
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127 {
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128 structures_[i].ComputeDependentProperties();
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129 }
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130 }
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131
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132 void DicomStructureSet2::FillStructuresFromDataset(const FullOrthancDataset& tags)
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133 {
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134 DicomDatasetReader reader(tags);
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135
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136 // a few sanity checks
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137 size_t count = 0, tmp = 0;
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138
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139 // DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE (0x3006, 0x0080);
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140 // DICOM_TAG_ROI_CONTOUR_SEQUENCE (0x3006, 0x0039);
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141 // DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE (0x3006, 0x0020);
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142 if (!tags.GetSequenceSize(count, Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE)) ||
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143 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE)) ||
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144 tmp != count ||
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145 !tags.GetSequenceSize(tmp, Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE)) ||
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146 tmp != count)
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147 {
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148 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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149 }
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150
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151 // let's now parse the structures stored in the dicom file
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152 // DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE (0x3006, 0x0080)
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153 // DICOM_TAG_RT_ROI_INTERPRETED_TYPE (0x3006, 0x00a4)
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154 // DICOM_TAG_ROI_DISPLAY_COLOR (0x3006, 0x002a)
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155 // DICOM_TAG_ROI_NAME (0x3006, 0x0026)
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156 structures_.resize(count);
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157 for (size_t i = 0; i < count; i++)
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158 {
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159 // (0x3006, 0x0080)[i]/(0x3006, 0x00a4)
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160 structures_[i].interpretation_ = reader.GetStringValue
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161 (Orthanc::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i,
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162 DICOM_TAG_RT_ROI_INTERPRETED_TYPE),
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163 "No interpretation");
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164
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165 // (0x3006, 0x0020)[i]/(0x3006, 0x0026)
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166 structures_[i].name_ = reader.GetStringValue
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167 (Orthanc::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i,
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168 DICOM_TAG_ROI_NAME),
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169 "No name");
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170
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171 Vector color;
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172 // (0x3006, 0x0039)[i]/(0x3006, 0x002a)
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173 if (ReadDicomToVector(color, tags, Orthanc::DicomPath(
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174 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_ROI_DISPLAY_COLOR))
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175 && color.size() == 3)
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176 {
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177 structures_[i].red_ = ConvertAndClipToByte(color[0]);
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178 structures_[i].green_ = ConvertAndClipToByte(color[1]);
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179 structures_[i].blue_ = ConvertAndClipToByte(color[2]);
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180 }
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181 else
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182 {
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183 structures_[i].red_ = 255;
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184 structures_[i].green_ = 0;
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185 structures_[i].blue_ = 0;
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186 }
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187
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188 size_t countSlices;
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189 // DICOM_TAG_ROI_CONTOUR_SEQUENCE (0x3006, 0x0039);
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190 // DICOM_TAG_CONTOUR_SEQUENCE (0x3006, 0x0040);
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191 if (!tags.GetSequenceSize(countSlices, Orthanc::DicomPath(
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192 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_CONTOUR_SEQUENCE)))
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193 {
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194 LOG(WARNING) << "DicomStructureSet2::SetContents | structure \"" << structures_[i].name_ << "\" has no slices!";
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195 countSlices = 0;
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196 }
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197
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198 LOG(INFO) << "New RT structure: \"" << structures_[i].name_
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199 << "\" with interpretation \"" << structures_[i].interpretation_
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200 << "\" containing " << countSlices << " slices (color: "
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201 << static_cast<int>(structures_[i].red_) << ","
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202 << static_cast<int>(structures_[i].green_) << ","
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203 << static_cast<int>(structures_[i].blue_) << ")";
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204
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205 // These temporary variables avoid allocating many vectors in the loop below
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206
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207 // (0x3006, 0x0039)[i]/(0x3006, 0x0040)[0]/(0x3006, 0x0046)
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208 Orthanc::DicomPath countPointsPath(
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209 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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210 DICOM_TAG_CONTOUR_SEQUENCE, 0,
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211 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS);
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212
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213 Orthanc::DicomPath geometricTypePath(
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214 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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215 DICOM_TAG_CONTOUR_SEQUENCE, 0,
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216 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE);
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217
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218 Orthanc::DicomPath imageSequencePath(
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219 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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220 DICOM_TAG_CONTOUR_SEQUENCE, 0,
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221 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE);
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222
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223 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)
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224 Orthanc::DicomPath referencedInstancePath(
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225 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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226 DICOM_TAG_CONTOUR_SEQUENCE, 0,
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227 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0,
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228 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID);
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229
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230 Orthanc::DicomPath contourDataPath(
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231 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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232 DICOM_TAG_CONTOUR_SEQUENCE, 0,
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233 DICOM_TAG_CONTOUR_DATA);
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234
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235 for (size_t j = 0; j < countSlices; j++)
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236 {
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237 unsigned int countPoints = 0;
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238
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239 countPointsPath.SetPrefixIndex(1, j);
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240 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath))
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241 {
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242 std::string s;
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243 DicomPathToString(s, countPointsPath);
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244 LOG(ERROR) << "Dicom path " << s << " is not valid (should contain an unsigned integer)";
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245 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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246 }
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247
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248 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices";
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249
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250 geometricTypePath.SetPrefixIndex(1, j);
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251 std::string type = reader.GetMandatoryStringValue(geometricTypePath);
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252 if (type != "CLOSED_PLANAR")
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253 {
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254 // TODO: support points!!
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255 LOG(WARNING) << "Ignoring contour with geometry type: " << type;
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256 continue;
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257 }
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258
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259 size_t size = 0;
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260
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261 imageSequencePath.SetPrefixIndex(1, j);
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262 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1)
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263 {
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264 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry.";
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265 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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266 }
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267
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268 referencedInstancePath.SetPrefixIndex(1, j);
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269 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath);
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270
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271 contourDataPath.SetPrefixIndex(1, j);
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272 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath);
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273
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274 Vector points;
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275 if (!GenericToolbox::FastParseVector(points, slicesData) ||
1834
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276 points.size() != 3 * countPoints)
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277 {
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278 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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279 }
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280
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281 // seen in real world
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282 if (Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "")
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283 {
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284 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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285 }
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286
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287 DicomStructurePolygon2 polygon(sopInstanceUid,type);
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288 polygon.Reserve(countPoints);
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289
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290 for (size_t k = 0; k < countPoints; k++)
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291 {
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292 Vector v(3);
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293 v[0] = points[3 * k];
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294 v[1] = points[3 * k + 1];
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295 v[2] = points[3 * k + 2];
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296 polygon.AddPoint(v);
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297 }
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298 structures_[i].AddPolygon(polygon);
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299 }
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300 }
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301 }
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302
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303
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304 void DicomStructureSet2::Clear()
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305 {
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306 structures_.clear();
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307 }
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308
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309 }
1019
29f5f2031310 Added a way to specificy which structures are to be initially displayed (the
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310
29f5f2031310 Added a way to specificy which structures are to be initially displayed (the
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311 #endif
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312 // BGO_ENABLE_DICOMSTRUCTURESETLOADER2
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313