Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet2.cpp @ 1013:53cc787bd7bc toa2019092301
- Added an optimized ProjectPoint2 to CoordinateSystem3D. It has *not* replaced
the ProjectPoint method because more tests need to be written.
- ProjectPointOntoPlane2 is a faster version of
GeometryToolbox::ProjectPointOntoPlane. Same remark as above.
- DicomStructureSet.cpp now uses this optimized call.
author | Benjamin Golinvaux <bgo@osimis.io> |
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date | Mon, 23 Sep 2019 15:18:33 +0200 |
parents | efe1c44628a1 |
children | 29f5f2031310 |
rev | line source |
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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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20 |
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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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25 |
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26 #include <Core/Logging.h> |
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27 #include <Core/OrthancException.h> |
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28 #include <Core/Toolbox.h> |
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29 #include <Core/DicomFormat/DicomTag.h> |
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30 |
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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 |
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75 void DicomPathToString(std::string& s, const OrthancPlugins::DicomPath& dicomPath) |
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76 { |
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77 std::stringstream tmp; |
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78 for (size_t i = 0; i < dicomPath.GetPrefixLength(); ++i) |
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79 { |
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80 OrthancPlugins::DicomTag tag = dicomPath.GetPrefixTag(i); |
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81 |
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82 // We use this other object to be able to use GetMainTagsName |
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83 // and Format |
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84 Orthanc::DicomTag tag2(tag.GetGroup(), tag.GetElement()); |
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85 size_t index = dicomPath.GetPrefixIndex(i); |
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86 tmp << tag2.GetMainTagsName() << " (" << tag2.Format() << ") [" << index << "] / "; |
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87 } |
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88 const OrthancPlugins::DicomTag& tag = dicomPath.GetFinalTag(); |
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89 Orthanc::DicomTag tag2(tag.GetGroup(), tag.GetElement()); |
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90 tmp << tag2.GetMainTagsName() << " (" << tag2.Format() << ")"; |
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91 s = tmp.str(); |
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92 } |
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93 |
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94 std::ostream& operator<<(std::ostream& s, const OrthancPlugins::DicomPath& dicomPath) |
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95 { |
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96 std::string tmp; |
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97 DicomPathToString(tmp, dicomPath); |
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98 s << tmp; |
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99 return s; |
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100 } |
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101 |
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102 |
1006
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103 DicomStructureSet2::DicomStructureSet2() |
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104 { |
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105 |
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106 } |
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107 |
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108 |
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109 DicomStructureSet2::~DicomStructureSet2() |
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110 { |
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111 |
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112 } |
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113 |
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114 void DicomStructureSet2::SetContents(const OrthancPlugins::FullOrthancDataset& tags) |
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115 { |
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116 FillStructuresFromDataset(tags); |
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117 ComputeDependentProperties(); |
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118 } |
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119 |
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120 void DicomStructureSet2::ComputeDependentProperties() |
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121 { |
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122 for (size_t i = 0; i < structures_.size(); ++i) |
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123 { |
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124 structures_[i].ComputeDependentProperties(); |
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125 } |
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126 } |
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127 |
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128 void DicomStructureSet2::FillStructuresFromDataset(const OrthancPlugins::FullOrthancDataset& tags) |
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129 { |
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130 OrthancPlugins::DicomDatasetReader reader(tags); |
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131 |
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132 // a few sanity checks |
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133 size_t count = 0, tmp = 0; |
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134 |
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135 // DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE (0x3006, 0x0080); |
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136 // DICOM_TAG_ROI_CONTOUR_SEQUENCE (0x3006, 0x0039); |
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137 // DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE (0x3006, 0x0020); |
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138 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || |
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139 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || |
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140 tmp != count || |
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141 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || |
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142 tmp != count) |
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143 { |
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144 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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145 } |
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146 |
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147 // let's now parse the structures stored in the dicom file |
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148 // DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE (0x3006, 0x0080) |
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149 // DICOM_TAG_RT_ROI_INTERPRETED_TYPE (0x3006, 0x00a4) |
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150 // DICOM_TAG_ROI_DISPLAY_COLOR (0x3006, 0x002a) |
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151 // DICOM_TAG_ROI_NAME (0x3006, 0x0026) |
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152 structures_.resize(count); |
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153 for (size_t i = 0; i < count; i++) |
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154 { |
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155 // (0x3006, 0x0080)[i]/(0x3006, 0x00a4) |
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156 structures_[i].interpretation_ = reader.GetStringValue |
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157 (OrthancPlugins::DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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158 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
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159 "No interpretation"); |
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160 |
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161 // (0x3006, 0x0020)[i]/(0x3006, 0x0026) |
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162 structures_[i].name_ = reader.GetStringValue |
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163 (OrthancPlugins::DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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164 DICOM_TAG_ROI_NAME), |
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165 "No name"); |
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166 |
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167 Vector color; |
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168 // (0x3006, 0x0039)[i]/(0x3006, 0x002a) |
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169 if (ReadDicomToVector(color, tags, OrthancPlugins::DicomPath( |
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170 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_ROI_DISPLAY_COLOR)) |
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171 && color.size() == 3) |
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172 { |
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173 structures_[i].red_ = ConvertAndClipToByte(color[0]); |
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174 structures_[i].green_ = ConvertAndClipToByte(color[1]); |
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175 structures_[i].blue_ = ConvertAndClipToByte(color[2]); |
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176 } |
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177 else |
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178 { |
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179 structures_[i].red_ = 255; |
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180 structures_[i].green_ = 0; |
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181 structures_[i].blue_ = 0; |
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182 } |
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183 |
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184 size_t countSlices; |
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185 // DICOM_TAG_ROI_CONTOUR_SEQUENCE (0x3006, 0x0039); |
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186 // DICOM_TAG_CONTOUR_SEQUENCE (0x3006, 0x0040); |
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187 if (!tags.GetSequenceSize(countSlices, OrthancPlugins::DicomPath( |
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188 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, DICOM_TAG_CONTOUR_SEQUENCE))) |
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189 { |
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190 LOG(WARNING) << "DicomStructureSet2::SetContents | structure \"" << structures_[i].name_ << "\" has no slices!"; |
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191 countSlices = 0; |
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192 } |
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193 |
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194 LOG(INFO) << "New RT structure: \"" << structures_[i].name_ |
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195 << "\" with interpretation \"" << structures_[i].interpretation_ |
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196 << "\" containing " << countSlices << " slices (color: " |
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197 << static_cast<int>(structures_[i].red_) << "," |
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198 << static_cast<int>(structures_[i].green_) << "," |
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199 << static_cast<int>(structures_[i].blue_) << ")"; |
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200 |
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201 // These temporary variables avoid allocating many vectors in the loop below |
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202 |
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203 // (0x3006, 0x0039)[i]/(0x3006, 0x0040)[0]/(0x3006, 0x0046) |
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204 OrthancPlugins::DicomPath countPointsPath( |
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205 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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206 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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207 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS); |
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208 |
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209 OrthancPlugins::DicomPath geometricTypePath( |
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210 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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211 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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212 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE); |
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213 |
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214 OrthancPlugins::DicomPath imageSequencePath( |
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215 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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216 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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217 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE); |
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218 |
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219 // (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155) |
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220 OrthancPlugins::DicomPath referencedInstancePath( |
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221 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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222 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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223 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
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224 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID); |
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225 |
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226 OrthancPlugins::DicomPath contourDataPath( |
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227 DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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228 DICOM_TAG_CONTOUR_SEQUENCE, 0, |
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229 DICOM_TAG_CONTOUR_DATA); |
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230 |
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231 for (size_t j = 0; j < countSlices; j++) |
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232 { |
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233 unsigned int countPoints = 0; |
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234 |
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235 countPointsPath.SetPrefixIndex(1, j); |
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236 if (!reader.GetUnsignedIntegerValue(countPoints, countPointsPath)) |
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237 { |
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238 std::string s; |
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239 DicomPathToString(s, countPointsPath); |
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240 LOG(ERROR) << "Dicom path " << s << " is not valid (should contain an unsigned integer)"; |
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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 geometricTypePath.SetPrefixIndex(1, j); |
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247 std::string type = reader.GetMandatoryStringValue(geometricTypePath); |
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248 if (type != "CLOSED_PLANAR") |
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249 { |
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250 // TODO: support points!! |
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251 LOG(WARNING) << "Ignoring contour with geometry type: " << type; |
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252 continue; |
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253 } |
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254 |
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255 size_t size = 0; |
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256 |
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257 imageSequencePath.SetPrefixIndex(1, j); |
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258 if (!tags.GetSequenceSize(size, imageSequencePath) || size != 1) |
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259 { |
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260 LOG(ERROR) << "The ContourImageSequence sequence (tag 3006,0016) must be present and contain one entry."; |
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261 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
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262 } |
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263 |
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264 referencedInstancePath.SetPrefixIndex(1, j); |
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265 std::string sopInstanceUid = reader.GetMandatoryStringValue(referencedInstancePath); |
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266 |
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267 contourDataPath.SetPrefixIndex(1, j); |
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268 std::string slicesData = reader.GetMandatoryStringValue(contourDataPath); |
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269 |
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270 Vector points; |
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271 if (!LinearAlgebra::ParseVector(points, slicesData) || |
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272 points.size() != 3 * countPoints) |
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273 { |
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274 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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275 } |
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276 |
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277 // seen in real world |
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278 if (Orthanc::Toolbox::StripSpaces(sopInstanceUid) == "") |
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279 { |
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280 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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281 } |
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282 |
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283 DicomStructurePolygon2 polygon(sopInstanceUid,type); |
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284 polygon.Reserve(countPoints); |
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285 |
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286 for (size_t k = 0; k < countPoints; k++) |
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287 { |
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288 Vector v(3); |
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289 v[0] = points[3 * k]; |
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290 v[1] = points[3 * k + 1]; |
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291 v[2] = points[3 * k + 2]; |
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292 polygon.AddPoint(v); |
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293 } |
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294 structures_[i].AddPolygon(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 void DicomStructureSet2::Clear() |
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301 { |
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added a new set of classes that correctly handle non-convex polygons (not
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302 structures_.clear(); |
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303 } |
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Scaffolding for A/B tests with DicomStructureSet[Loader] (A/B testing)
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304 |
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Scaffolding for A/B tests with DicomStructureSet[Loader] (A/B testing)
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305 } |