Mercurial > hg > orthanc-stone

annotate Framework/Toolbox/DicomStructureSet2.cpp @ 1006:4f28d9459e31 toa2019092001

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Fixed unit tests and deprecated classes according to last API changes. UT all run ok.
author Benjamin Golinvaux <bgo@osimis.io>
date Fri, 20 Sep 2019 12:13:10 +0200
parents 38b6bb0bdd72
children efe1c44628a1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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) 2017-2019 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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21 #include "DicomStructureSet2.h"
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22
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23 #include "../Toolbox/LinearAlgebra.h"
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24 #include "../StoneException.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 <Core/Toolbox.h>
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29 #include <Core/DicomFormat/DicomTag.h>
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31 #include <Plugins/Samples/Common/FullOrthancDataset.h>
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32 #include <Plugins/Samples/Common/DicomDatasetReader.h>
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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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48
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49 static inline uint8_t ConvertAndClipToByte(double v)
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50 {
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51 if (v < 0)
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52 {
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53 return 0;
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54 }
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55 else if (v >= 255)
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56 {
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57 return 255;
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58 }
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59 else
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60 {
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61 return static_cast<uint8_t>(v);
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62 }
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63 }
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64
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65 static bool ReadDicomToVector(Vector& target,
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66 const OrthancPlugins::IDicomDataset& dataset,
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67 const OrthancPlugins::DicomPath& tag)
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68 {
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69 std::string value;
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70 return (dataset.GetStringValue(value, tag) &&
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71 LinearAlgebra::ParseVector(target, value));
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72 }
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73
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74 std::ostream& operator<<(std::ostream& s, const OrthancPlugins::DicomPath& dicomPath)
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75 {
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76 std::stringstream tmp;
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77 for (size_t i = 0; i < dicomPath.GetPrefixLength(); ++i)
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78 {
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79 OrthancPlugins::DicomTag tag = dicomPath.GetPrefixTag(i);
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80
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81 // We use this other object to be able to use GetMainTagsName
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82 // and Format
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83 Orthanc::DicomTag tag2(tag.GetGroup(), tag.GetElement());
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84 size_t index = dicomPath.GetPrefixIndex(i);
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85 tmp << tag2.GetMainTagsName() << " (" << tag2.Format() << ") [" << index << "] / ";
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86 }
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87 const OrthancPlugins::DicomTag& tag = dicomPath.GetFinalTag();
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88 Orthanc::DicomTag tag2(tag.GetGroup(), tag.GetElement());
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89 tmp << tag2.GetMainTagsName() << " (" << tag2.Format() << ")";
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90 s << tmp.str();
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91 return s;
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92 }
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93
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94
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95 DicomStructureSet2::DicomStructureSet2()
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96 {
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97
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98 }
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99
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101 DicomStructureSet2::~DicomStructureSet2()
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102 {
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103
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104 }
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105
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106 void DicomStructureSet2::SetContents(const OrthancPlugins::FullOrthancDataset& tags)
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107 {
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108 FillStructuresFromDataset(tags);
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109 ComputeDependentProperties();
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110 }
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111
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112 void DicomStructureSet2::ComputeDependentProperties()
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113 {
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114 for (size_t i = 0; i < structures_.size(); ++i)
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115 {
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116 structures_[i].ComputeDependentProperties();
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117 }
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118 }
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119
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120 void DicomStructureSet2::FillStructuresFromDataset(const OrthancPlugins::FullOrthancDataset& tags)
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121 {
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122 OrthancPlugins::DicomDatasetReader reader(tags);
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123
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124 // a few sanity checks
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125 size_t count = 0, tmp = 0;
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126
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127 // DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE (0x3006, 0x0080);
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128 // DICOM_TAG_ROI_CONTOUR_SEQUENCE (0x3006, 0x0039);
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129 // DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE (0x3006, 0x0020);
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130 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) ||
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131 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) ||
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132 tmp != count ||
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133 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) ||
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134 tmp != count)
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135 {
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136 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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137 }
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138
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139 // let's now parse the structures stored in the dicom file
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140 // DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE (0x3006, 0x0080)
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141 // DICOM_TAG_RT_ROI_INTERPRETED_TYPE (0x3006, 0x00a4)
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142 // DICOM_TAG_ROI_DISPLAY_COLOR (0x3006, 0x002a)
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143 // DICOM_TAG_ROI_NAME (0x3006, 0x0026)
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144 structures_.resize(count);
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145 for (size_t i = 0; i < count; i++)
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146 {
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147 // (0x3006, 0x0080)[i]/(0x3006, 0x00a4)
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148 structures_[i].interpretation_ = reader.GetStringValue
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149 (OrthancPlugins::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i,
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150 DICOM_TAG_RT_ROI_INTERPRETED_TYPE),
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151 "No interpretation");
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152
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153 // (0x3006, 0x0020)[i]/(0x3006, 0x0026)
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154 structures_[i].name_ = reader.GetStringValue
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155 (OrthancPlugins::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i,
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156 DICOM_TAG_ROI_NAME),
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157 "No name");
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158
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159 Vector color;
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160 // (0x3006, 0x0039)[i]/(0x3006, 0x002a)
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161 if (ReadDicomToVector(color, tags, OrthancPlugins::DicomPath(
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162 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_ROI_DISPLAY_COLOR))
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163 && color.size() == 3)
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164 {
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165 structures_[i].red_ = ConvertAndClipToByte(color[0]);
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166 structures_[i].green_ = ConvertAndClipToByte(color[1]);
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167 structures_[i].blue_ = ConvertAndClipToByte(color[2]);
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168 }
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169 else
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170 {
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171 structures_[i].red_ = 255;
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172 structures_[i].green_ = 0;
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173 structures_[i].blue_ = 0;
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174 }
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175
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176 size_t countSlices;
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177 // DICOM_TAG_ROI_CONTOUR_SEQUENCE (0x3006, 0x0039);
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178 // DICOM_TAG_CONTOUR_SEQUENCE (0x3006, 0x0040);
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179 if (!tags.GetSequenceSize(countSlices, OrthancPlugins::DicomPath(
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180 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_CONTOUR_SEQUENCE)))
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181 {
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182 LOG(WARNING) << "DicomStructureSet2::SetContents | structure \"" << structures_[i].name_ << "\" has no slices!";
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183 countSlices = 0;
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184 }
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185
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186 LOG(INFO) << "New RT structure: \"" << structures_[i].name_
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187 << "\" with interpretation \"" << structures_[i].interpretation_
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188 << "\" containing " << countSlices << " slices (color: "
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189 << static_cast<int>(structures_[i].red_) << ","
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190 << static_cast<int>(structures_[i].green_) << ","
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191 << static_cast<int>(structures_[i].blue_) << ")";
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192
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193 // These temporary variables avoid allocating many vectors in the loop below
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194
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195 // (0x3006, 0x0039)[i]/(0x3006, 0x0040)[0]/(0x3006, 0x0046)
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196 OrthancPlugins::DicomPath countPointsPath(
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197 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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198 DICOM_TAG_CONTOUR_SEQUENCE, 0,
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199 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS);
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200
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201 OrthancPlugins::DicomPath geometricTypePath(
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202 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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203 DICOM_TAG_CONTOUR_SEQUENCE, 0,
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204 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE);
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205
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206 OrthancPlugins::DicomPath imageSequencePath(
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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_CONTOUR_IMAGE_SEQUENCE);
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210
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211 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)
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212 OrthancPlugins::DicomPath referencedInstancePath(
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213 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i,
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214 DICOM_TAG_CONTOUR_SEQUENCE, 0,
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215 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0,
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216 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID);
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217
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218 OrthancPlugins::DicomPath contourDataPath(
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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_DATA);
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222
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223 for (size_t j = 0; j < countSlices; j++)
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224 {
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225 unsigned int countPoints = 0;
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226
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227 countPointsPath.SetPrefixIndex(1, j);
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228 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath))
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229 {
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230 LOG(ERROR) << "Dicom path " << countPointsPath << " is not valid (should contain an unsigned integer)";
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231 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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232 }
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233
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234 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices";
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235
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236 geometricTypePath.SetPrefixIndex(1, j);
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237 std::string type = reader.GetMandatoryStringValue(geometricTypePath);
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238 if (type != "CLOSED_PLANAR")
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239 {
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240 // TODO: support points!!
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241 LOG(WARNING) << "Ignoring contour with geometry type: " << type;
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242 continue;
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243 }
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244
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245 size_t size = 0;
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246
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247 imageSequencePath.SetPrefixIndex(1, j);
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248 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1)
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249 {
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250 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry.";
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251 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
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252 }
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253
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254 referencedInstancePath.SetPrefixIndex(1, j);
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255 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath);
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256
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257 contourDataPath.SetPrefixIndex(1, j);
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258 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath);
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259
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260 Vector points;
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261 if (!LinearAlgebra::ParseVector(points, slicesData) ||
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262 points.size() != 3 * countPoints)
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263 {
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264 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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265 }
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266
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267 // seen in real world
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268 if (Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "")
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269 {
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270 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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271 }
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272
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273 DicomStructurePolygon2 polygon(sopInstanceUid,type);
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274 polygon.Reserve(countPoints);
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275
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276 for (size_t k = 0; k < countPoints; k++)
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277 {
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278 Vector v(3);
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279 v[0] = points[3 * k];
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280 v[1] = points[3 * k + 1];
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281 v[2] = points[3 * k + 2];
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282 polygon.AddPoint(v);
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283 }
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284 structures_[i].AddPolygon(polygon);
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285 }
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286 }
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287 }
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288
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289
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290 void DicomStructureSet2::Clear()
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291 {
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292 structures_.clear();
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293 }
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294
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295 }