Mercurial > hg > orthanc-stone
annotate Framework/Toolbox/DicomStructureSet.cpp @ 122:e3433dabfb8d wasm
refactoring DicomStructureSet
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 06 Oct 2017 17:25:08 +0200 |
parents | e66b2c757790 |
children | 44fc253d4876 |
rev | line source |
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0 | 1 /** |
2 * Stone of Orthanc | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
40
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5 * Copyright (C) 2017 Osimis, Belgium |
0 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
47 | 8 * modify it under the terms of the GNU Affero General Public License |
9 * as published by the Free Software Foundation, either version 3 of | |
10 * the License, or (at your option) any later version. | |
0 | 11 * |
12 * This program is distributed in the hope that it will be useful, but | |
13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
47 | 14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
15 * Affero General Public License for more details. | |
16 * | |
17 * You should have received a copy of the GNU Affero General Public License | |
0 | 18 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
19 **/ | |
20 | |
21 | |
22 #include "DicomStructureSet.h" | |
23 | |
35 | 24 #include "../Toolbox/MessagingToolbox.h" |
0 | 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 <Plugins/Samples/Common/FullOrthancDataset.h> |
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29 #include <Plugins/Samples/Common/DicomDatasetReader.h> |
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30 |
0 | 31 #include <stdio.h> |
32 #include <boost/lexical_cast.hpp> | |
33 | |
34 namespace OrthancStone | |
35 { | |
32 | 36 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_GEOMETRIC_TYPE(0x3006, 0x0042); |
37 static const OrthancPlugins::DicomTag DICOM_TAG_CONTOUR_IMAGE_SEQUENCE(0x3006, 0x0016); | |
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); |
32 | 40 static const OrthancPlugins::DicomTag DICOM_TAG_NUMBER_OF_CONTOUR_POINTS(0x3006, 0x0046); |
41 static const OrthancPlugins::DicomTag DICOM_TAG_REFERENCED_SOP_INSTANCE_UID(0x0008, 0x1155); | |
42 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_CONTOUR_SEQUENCE(0x3006, 0x0039); | |
43 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_DISPLAY_COLOR(0x3006, 0x002a); | |
44 static const OrthancPlugins::DicomTag DICOM_TAG_ROI_NAME(0x3006, 0x0026); | |
45 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_INTERPRETED_TYPE(0x3006, 0x00a4); | |
46 static const OrthancPlugins::DicomTag DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE(0x3006, 0x0080); | |
47 static const OrthancPlugins::DicomTag DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE(0x3006, 0x0020); | |
0 | 48 |
49 | |
50 static uint8_t ConvertColor(double v) | |
51 { | |
52 if (v < 0) | |
53 { | |
54 return 0; | |
55 } | |
56 else if (v >= 255) | |
57 { | |
58 return 255; | |
59 } | |
60 else | |
61 { | |
62 return static_cast<uint8_t>(v); | |
63 } | |
64 } | |
65 | |
66 | |
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67 static bool ParseVector(Vector& target, |
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68 const OrthancPlugins::IDicomDataset& dataset, |
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69 const OrthancPlugins::DicomPath& tag) |
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70 { |
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71 std::string value; |
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72 return (dataset.GetStringValue(value, tag) && |
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73 GeometryToolbox::ParseVector(target, value)); |
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74 } |
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75 |
0 | 76 |
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77 void DicomStructureSet::Polygon::CheckPoint(const Vector& v) |
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78 { |
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79 if (hasSlice_) |
0 | 80 { |
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81 if (!GeometryToolbox::IsNear(GeometryToolbox::ProjectAlongNormal(v, normal_), |
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82 projectionAlongNormal_, |
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83 sliceThickness_ / 2.0 /* in mm */)) |
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84 { |
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85 LOG(ERROR) << "This RT-STRUCT contains a point that is off the slice of its instance"; |
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86 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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87 } |
0 | 88 } |
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89 } |
0 | 90 |
91 | |
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92 void DicomStructureSet::Polygon::AddPoint(const Vector& v) |
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93 { |
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94 CheckPoint(v); |
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95 points_.push_back(v); |
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96 } |
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97 |
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98 |
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99 bool DicomStructureSet::Polygon::UpdateReferencedSlice(const ReferencedSlices& slices) |
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100 { |
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101 if (hasSlice_) |
0 | 102 { |
122
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103 return true; |
32 | 104 } |
105 else | |
106 { | |
122
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107 ReferencedSlices::const_iterator it = slices.find(sopInstanceUid_); |
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108 |
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109 if (it == slices.end()) |
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110 { |
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111 return false; |
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112 } |
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113 else |
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114 { |
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115 const CoordinateSystem3D& geometry = it->second.geometry_; |
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116 |
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117 hasSlice_ = true; |
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118 normal_ = geometry.GetNormal(); |
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119 projectionAlongNormal_ = GeometryToolbox::ProjectAlongNormal(geometry.GetOrigin(), normal_); |
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120 sliceThickness_ = it->second.thickness_; |
0 | 121 |
122
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122 for (Points::const_iterator it = points_.begin(); it != points_.end(); ++it) |
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123 { |
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124 CheckPoint(*it); |
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125 } |
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126 |
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127 return true; |
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128 } |
0 | 129 } |
130 } | |
131 | |
132 | |
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133 bool DicomStructureSet::Polygon::IsOnSlice(const CoordinateSystem3D& slice) const |
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134 { |
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135 bool isOpposite; |
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136 |
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137 if (points_.empty() || |
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138 !hasSlice_ || |
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139 !GeometryToolbox::IsParallelOrOpposite(isOpposite, slice.GetNormal(), normal_)) |
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140 { |
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141 return false; |
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142 } |
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143 |
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144 double d = GeometryToolbox::ProjectAlongNormal(slice.GetOrigin(), normal_); |
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145 |
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146 return (GeometryToolbox::IsNear(d, projectionAlongNormal_, |
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147 sliceThickness_ / 2.0)); |
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148 } |
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149 |
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150 |
0 | 151 const DicomStructureSet::Structure& DicomStructureSet::GetStructure(size_t index) const |
152 { | |
153 if (index >= structures_.size()) | |
154 { | |
155 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
156 } | |
157 | |
158 return structures_[index]; | |
159 } | |
160 | |
161 | |
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162 DicomStructureSet::DicomStructureSet(const OrthancPlugins::FullOrthancDataset& tags) |
0 | 163 { |
32 | 164 using namespace OrthancPlugins; |
0 | 165 |
32 | 166 DicomDatasetReader reader(tags); |
167 | |
168 size_t count, tmp; | |
169 if (!tags.GetSequenceSize(count, DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE) || | |
170 !tags.GetSequenceSize(tmp, DICOM_TAG_ROI_CONTOUR_SEQUENCE) || | |
171 tmp != count || | |
172 !tags.GetSequenceSize(tmp, DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE) || | |
173 tmp != count) | |
0 | 174 { |
175 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
176 } | |
177 | |
32 | 178 structures_.resize(count); |
179 for (size_t i = 0; i < count; i++) | |
180 { | |
122
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181 structures_[i].interpretation_ = reader.GetStringValue |
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182 (DicomPath(DICOM_TAG_RT_ROI_OBSERVATIONS_SEQUENCE, i, |
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183 DICOM_TAG_RT_ROI_INTERPRETED_TYPE), |
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184 "No interpretation"); |
0 | 185 |
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186 structures_[i].name_ = reader.GetStringValue |
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187 (DicomPath(DICOM_TAG_STRUCTURE_SET_ROI_SEQUENCE, i, |
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188 DICOM_TAG_ROI_NAME), |
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189 "No interpretation"); |
0 | 190 |
191 Vector color; | |
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192 if (ParseVector(color, tags, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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193 DICOM_TAG_ROI_DISPLAY_COLOR)) && |
32 | 194 color.size() == 3) |
0 | 195 { |
32 | 196 structures_[i].red_ = ConvertColor(color[0]); |
197 structures_[i].green_ = ConvertColor(color[1]); | |
198 structures_[i].blue_ = ConvertColor(color[2]); | |
199 } | |
200 else | |
201 { | |
202 structures_[i].red_ = 255; | |
203 structures_[i].green_ = 0; | |
204 structures_[i].blue_ = 0; | |
0 | 205 } |
206 | |
32 | 207 size_t countSlices; |
208 if (!tags.GetSequenceSize(countSlices, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, | |
209 DICOM_TAG_CONTOUR_SEQUENCE))) | |
210 { | |
121
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211 countSlices = 0; |
32 | 212 } |
0 | 213 |
214 LOG(WARNING) << "New RT structure: \"" << structures_[i].name_ | |
215 << "\" with interpretation \"" << structures_[i].interpretation_ | |
32 | 216 << "\" containing " << countSlices << " slices (color: " |
0 | 217 << static_cast<int>(structures_[i].red_) << "," |
218 << static_cast<int>(structures_[i].green_) << "," | |
219 << static_cast<int>(structures_[i].blue_) << ")"; | |
220 | |
32 | 221 for (size_t j = 0; j < countSlices; j++) |
0 | 222 { |
32 | 223 unsigned int countPoints; |
0 | 224 |
122
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225 if (!reader.GetUnsignedIntegerValue |
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226 (countPoints, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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227 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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228 DICOM_TAG_NUMBER_OF_CONTOUR_POINTS))) |
32 | 229 { |
230 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
231 } | |
232 | |
121
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233 //LOG(INFO) << "Parsing slice containing " << countPoints << " vertices"; |
0 | 234 |
122
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235 std::string type = reader.GetMandatoryStringValue |
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236 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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237 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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238 DICOM_TAG_CONTOUR_GEOMETRIC_TYPE)); |
32 | 239 if (type != "CLOSED_PLANAR") |
0 | 240 { |
32 | 241 LOG(ERROR) << "Cannot handle contour with geometry type: " << type; |
0 | 242 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); |
243 } | |
244 | |
122
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245 size_t size; |
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246 if (!tags.GetSequenceSize(size, DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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247 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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248 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE)) || |
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249 size != 1) |
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250 { |
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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 std::string sopInstanceUid = reader.GetMandatoryStringValue |
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255 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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256 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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257 DICOM_TAG_CONTOUR_IMAGE_SEQUENCE, 0, |
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258 DICOM_TAG_REFERENCED_SOP_INSTANCE_UID)); |
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259 |
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260 std::string slicesData = reader.GetMandatoryStringValue |
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261 (DicomPath(DICOM_TAG_ROI_CONTOUR_SEQUENCE, i, |
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262 DICOM_TAG_CONTOUR_SEQUENCE, j, |
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263 DICOM_TAG_CONTOUR_DATA)); |
0 | 264 |
265 Vector points; | |
266 if (!GeometryToolbox::ParseVector(points, slicesData) || | |
32 | 267 points.size() != 3 * countPoints) |
0 | 268 { |
269 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
270 } | |
271 | |
122
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272 Polygon polygon(sopInstanceUid); |
0 | 273 |
32 | 274 for (size_t k = 0; k < countPoints; k++) |
0 | 275 { |
276 Vector v(3); | |
277 v[0] = points[3 * k]; | |
278 v[1] = points[3 * k + 1]; | |
279 v[2] = points[3 * k + 2]; | |
122
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280 polygon.AddPoint(v); |
0 | 281 } |
282 | |
283 structures_[i].polygons_.push_back(polygon); | |
284 } | |
285 } | |
286 } | |
287 | |
288 | |
289 Vector DicomStructureSet::GetStructureCenter(size_t index) const | |
290 { | |
291 const Structure& structure = GetStructure(index); | |
292 | |
293 Vector center; | |
294 GeometryToolbox::AssignVector(center, 0, 0, 0); | |
295 if (structure.polygons_.empty()) | |
296 { | |
297 return center; | |
298 } | |
299 | |
300 double n = static_cast<double>(structure.polygons_.size()); | |
301 | |
302 for (Polygons::const_iterator polygon = structure.polygons_.begin(); | |
303 polygon != structure.polygons_.end(); ++polygon) | |
304 { | |
122
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305 if (!polygon->GetPoints().empty()) |
0 | 306 { |
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307 center += polygon->GetPoints().front() / n; |
0 | 308 } |
309 } | |
310 | |
311 return center; | |
312 } | |
313 | |
314 | |
315 const std::string& DicomStructureSet::GetStructureName(size_t index) const | |
316 { | |
317 return GetStructure(index).name_; | |
318 } | |
319 | |
320 | |
321 const std::string& DicomStructureSet::GetStructureInterpretation(size_t index) const | |
322 { | |
323 return GetStructure(index).interpretation_; | |
324 } | |
325 | |
326 | |
327 void DicomStructureSet::GetStructureColor(uint8_t& red, | |
328 uint8_t& green, | |
329 uint8_t& blue, | |
330 size_t index) const | |
331 { | |
332 const Structure& s = GetStructure(index); | |
333 red = s.red_; | |
334 green = s.green_; | |
335 blue = s.blue_; | |
336 } | |
337 | |
338 | |
339 void DicomStructureSet::Render(CairoContext& context, | |
122
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340 const CoordinateSystem3D& slice) |
0 | 341 { |
342 cairo_t* cr = context.GetObject(); | |
343 | |
122
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344 for (Structures::iterator structure = structures_.begin(); |
0 | 345 structure != structures_.end(); ++structure) |
346 { | |
122
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347 for (Polygons::iterator polygon = structure->polygons_.begin(); |
0 | 348 polygon != structure->polygons_.end(); ++polygon) |
349 { | |
122
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350 polygon->UpdateReferencedSlice(referencedSlices_); |
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351 |
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352 if (polygon->IsOnSlice(slice)) |
0 | 353 { |
354 context.SetSourceColor(structure->red_, structure->green_, structure->blue_); | |
355 | |
122
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356 Points::const_iterator p = polygon->GetPoints().begin(); |
0 | 357 |
358 double x, y; | |
359 slice.ProjectPoint(x, y, *p); | |
360 cairo_move_to(cr, x, y); | |
361 ++p; | |
362 | |
122
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363 while (p != polygon->GetPoints().end()) |
0 | 364 { |
365 slice.ProjectPoint(x, y, *p); | |
366 cairo_line_to(cr, x, y); | |
367 ++p; | |
368 } | |
369 | |
122
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370 slice.ProjectPoint(x, y, *polygon->GetPoints().begin()); |
0 | 371 cairo_line_to(cr, x, y); |
121
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372 |
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373 cairo_stroke(cr); |
0 | 374 } |
375 } | |
376 } | |
377 } | |
122
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378 |
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379 |
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380 void DicomStructureSet::GetReferencedInstances(std::set<std::string>& instances) |
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381 { |
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382 for (Structures::const_iterator structure = structures_.begin(); |
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383 structure != structures_.end(); ++structure) |
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384 { |
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385 for (Polygons::const_iterator polygon = structure->polygons_.begin(); |
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386 polygon != structure->polygons_.end(); ++polygon) |
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387 { |
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388 instances.insert(polygon->GetSopInstanceUid()); |
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389 } |
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390 } |
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391 } |
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392 |
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393 |
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394 void DicomStructureSet::AddReferencedSlice(const std::string& sopInstanceUid, |
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395 const std::string& seriesInstanceUid, |
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396 const CoordinateSystem3D& geometry, |
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397 double thickness) |
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398 { |
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399 if (referencedSlices_.find(sopInstanceUid) != referencedSlices_.end()) |
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400 { |
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401 // This geometry is already known |
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402 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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403 } |
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404 else |
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405 { |
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406 if (thickness < 0) |
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407 { |
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408 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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409 } |
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410 |
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411 if (!referencedSlices_.empty()) |
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412 { |
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413 const ReferencedSlice& reference = referencedSlices_.begin()->second; |
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414 |
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415 if (reference.seriesInstanceUid_ != seriesInstanceUid) |
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416 { |
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417 LOG(ERROR) << "This RT-STRUCT refers to several different series"; |
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418 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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419 } |
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420 |
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421 if (!GeometryToolbox::IsParallel(reference.geometry_.GetNormal(), geometry.GetNormal())) |
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422 { |
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423 LOG(ERROR) << "The slices in this RT-STRUCT are not parallel"; |
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424 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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425 } |
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426 } |
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427 |
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428 referencedSlices_[sopInstanceUid] = ReferencedSlice(seriesInstanceUid, geometry, thickness); |
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429 } |
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430 } |
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431 |
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432 |
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433 void DicomStructureSet::AddReferencedSlice(const Orthanc::DicomMap& dataset) |
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434 { |
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435 CoordinateSystem3D slice(dataset); |
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436 |
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437 double thickness = 1; // 1 mm by default |
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438 |
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439 std::string s; |
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440 Vector v; |
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441 if (dataset.CopyToString(s, Orthanc::DICOM_TAG_SLICE_THICKNESS, false) && |
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442 GeometryToolbox::ParseVector(v, s) && |
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443 v.size() > 0) |
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444 { |
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445 thickness = v[0]; |
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446 } |
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447 |
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448 std::string instance, series; |
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449 if (dataset.CopyToString(instance, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) && |
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450 dataset.CopyToString(series, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) |
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451 { |
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452 AddReferencedSlice(instance, series, slice, thickness); |
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453 } |
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454 else |
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455 { |
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456 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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457 } |
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458 } |
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459 |
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460 |
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461 void DicomStructureSet::CheckReferencedSlices() |
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462 { |
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463 for (Structures::iterator structure = structures_.begin(); |
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464 structure != structures_.end(); ++structure) |
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465 { |
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466 for (Polygons::iterator polygon = structure->polygons_.begin(); |
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467 polygon != structure->polygons_.end(); ++polygon) |
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468 { |
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469 if (!polygon->UpdateReferencedSlice(referencedSlices_)) |
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470 { |
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471 LOG(ERROR) << "Missing information about referenced instance: " |
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472 << polygon->GetSopInstanceUid(); |
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473 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); |
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474 } |
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475 } |
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476 } |
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477 } |
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478 |
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479 |
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480 Vector DicomStructureSet::GetNormal() const |
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481 { |
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482 if (!referencedSlices_.empty()) |
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483 { |
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484 Vector v; |
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485 GeometryToolbox::AssignVector(v, 0, 0, 1); |
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486 return v; |
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487 } |
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488 else |
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489 { |
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490 return referencedSlices_.begin()->second.geometry_.GetNormal(); |
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491 } |
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492 } |
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493 |
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494 |
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495 DicomStructureSet* DicomStructureSet::SynchronousLoad(OrthancPlugins::IOrthancConnection& orthanc, |
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496 const std::string& instanceId) |
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497 { |
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498 const std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050"; |
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499 OrthancPlugins::FullOrthancDataset dataset(orthanc, uri); |
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500 |
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501 std::auto_ptr<DicomStructureSet> result(new DicomStructureSet(dataset)); |
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502 |
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503 std::set<std::string> instances; |
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504 result->GetReferencedInstances(instances); |
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505 |
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506 for (std::set<std::string>::const_iterator it = instances.begin(); |
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507 it != instances.end(); ++it) |
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508 { |
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509 Json::Value lookup; |
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510 MessagingToolbox::RestApiPost(lookup, orthanc, "/tools/lookup", *it); |
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511 |
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512 if (lookup.type() != Json::arrayValue || |
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513 lookup.size() != 1 || |
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514 !lookup[0].isMember("Type") || |
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515 !lookup[0].isMember("Path") || |
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516 lookup[0]["Type"].type() != Json::stringValue || |
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517 lookup[0]["ID"].type() != Json::stringValue || |
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518 lookup[0]["Type"].asString() != "Instance") |
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519 { |
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520 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
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521 } |
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522 |
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523 OrthancPlugins::FullOrthancDataset slice |
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524 (orthanc, "/instances/" + lookup[0]["ID"].asString() + "/tags"); |
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525 Orthanc::DicomMap m; |
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526 MessagingToolbox::ConvertDataset(m, slice); |
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527 result->AddReferencedSlice(m); |
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528 } |
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529 |
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530 result->CheckReferencedSlices(); |
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531 |
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532 return result.release(); |
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533 } |
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534 |
0 | 535 } |