Mercurial > hg > orthanc-stone
annotate Framework/Loaders/DicomStructureSetLoader.cpp @ 1000:50e5acf5553b
changed RTSTRUCT rendering from polygons to segments
| author | Benjamin Golinvaux <bgo@osimis.io> |
|---|---|
| date | Fri, 20 Sep 2019 11:59:29 +0200 |
| parents | c20dbaab360c |
| children | 4f28d9459e31 |
| rev | line source |
|---|---|
| 815 | 1 /** |
| 2 * Stone of Orthanc | |
| 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
| 4 * Department, University Hospital of Liege, Belgium | |
| 5 * Copyright (C) 2017-2019 Osimis S.A., Belgium | |
| 6 * | |
| 7 * This program is free software: you can redistribute it and/or | |
| 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. | |
| 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 | |
| 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 | |
| 18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 19 **/ | |
| 20 | |
| 21 | |
| 22 #include "DicomStructureSetLoader.h" | |
| 23 | |
| 24 #include "../Scene2D/PolylineSceneLayer.h" | |
| 25 #include "../Toolbox/GeometryToolbox.h" | |
| 26 | |
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27 #if 0 |
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28 bool logbgo233 = false; |
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29 bool logbgo115 = false; |
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30 #endif |
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31 |
| 815 | 32 namespace OrthancStone |
| 33 { | |
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34 |
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35 #if 0 |
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36 void DumpDicomMap(std::ostream& o, const Orthanc::DicomMap& dicomMap) |
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37 { |
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38 using namespace std; |
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39 //ios_base::fmtflags state = o.flags(); |
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40 //o.flags(ios::right | ios::hex); |
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41 //o << "(" << setfill('0') << setw(4) << tag.GetGroup() |
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42 // << "," << setw(4) << tag.GetElement() << ")"; |
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43 //o.flags(state); |
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44 Json::Value val; |
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45 dicomMap.Serialize(val); |
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46 o << val; |
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47 //return o; |
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48 } |
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49 #endif |
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50 |
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51 |
| 815 | 52 class DicomStructureSetLoader::AddReferencedInstance : public LoaderStateMachine::State |
| 53 { | |
| 54 private: | |
| 55 std::string instanceId_; | |
| 56 | |
| 57 public: | |
| 58 AddReferencedInstance(DicomStructureSetLoader& that, | |
| 59 const std::string& instanceId) : | |
| 60 State(that), | |
| 61 instanceId_(instanceId) | |
| 62 { | |
| 63 } | |
| 64 | |
| 65 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
| 66 { | |
| 67 Json::Value tags; | |
| 68 message.ParseJsonBody(tags); | |
| 69 | |
| 70 Orthanc::DicomMap dicom; | |
| 71 dicom.FromDicomAsJson(tags); | |
| 72 | |
| 73 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); | |
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74 |
| 815 | 75 loader.content_->AddReferencedSlice(dicom); |
| 76 | |
| 77 loader.countProcessedInstances_ ++; | |
| 78 assert(loader.countProcessedInstances_ <= loader.countReferencedInstances_); | |
| 79 | |
| 80 if (loader.countProcessedInstances_ == loader.countReferencedInstances_) | |
| 81 { | |
| 82 // All the referenced instances have been loaded, finalize the RT-STRUCT | |
| 83 loader.content_->CheckReferencedSlices(); | |
| 84 loader.revision_++; | |
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85 loader.SetStructuresReady(); |
| 815 | 86 } |
| 87 } | |
| 88 }; | |
| 89 | |
| 90 | |
| 91 // State that converts a "SOP Instance UID" to an Orthanc identifier | |
| 92 class DicomStructureSetLoader::LookupInstance : public LoaderStateMachine::State | |
| 93 { | |
| 94 private: | |
| 95 std::string sopInstanceUid_; | |
| 96 | |
| 97 public: | |
| 98 LookupInstance(DicomStructureSetLoader& that, | |
| 99 const std::string& sopInstanceUid) : | |
| 100 State(that), | |
| 101 sopInstanceUid_(sopInstanceUid) | |
| 102 { | |
| 103 } | |
| 104 | |
| 105 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
| 106 { | |
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107 #if 0 |
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108 LOG(TRACE) << "DicomStructureSetLoader::LookupInstance::Handle() (SUCCESS)"; |
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109 #endif |
| 815 | 110 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); |
| 111 | |
| 112 Json::Value lookup; | |
| 113 message.ParseJsonBody(lookup); | |
| 114 | |
| 115 if (lookup.type() != Json::arrayValue || | |
| 116 lookup.size() != 1 || | |
| 117 !lookup[0].isMember("Type") || | |
| 118 !lookup[0].isMember("Path") || | |
| 119 lookup[0]["Type"].type() != Json::stringValue || | |
| 120 lookup[0]["ID"].type() != Json::stringValue || | |
| 121 lookup[0]["Type"].asString() != "Instance") | |
| 122 { | |
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123 std::stringstream msg; |
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124 msg << "Unknown resource! message.GetAnswer() = " << message.GetAnswer() << " message.GetAnswerHeaders() = "; |
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125 for (OrthancRestApiCommand::HttpHeaders::const_iterator it = message.GetAnswerHeaders().begin(); |
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126 it != message.GetAnswerHeaders().end(); ++it) |
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127 { |
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128 msg << "\nkey: \"" << it->first << "\" value: \"" << it->second << "\"\n"; |
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129 } |
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130 const std::string msgStr = msg.str(); |
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131 LOG(ERROR) << msgStr; |
| 815 | 132 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
| 133 } | |
| 134 | |
| 135 const std::string instanceId = lookup[0]["ID"].asString(); | |
| 136 | |
| 137 { | |
| 138 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
| 139 command->SetHttpHeader("Accept-Encoding", "gzip"); | |
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140 std::string uri = "/instances/" + instanceId + "/tags"; |
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141 command->SetUri(uri); |
| 815 | 142 command->SetPayload(new AddReferencedInstance(loader, instanceId)); |
| 143 Schedule(command.release()); | |
| 144 } | |
| 145 } | |
| 146 }; | |
| 147 | |
| 148 | |
| 149 class DicomStructureSetLoader::LoadStructure : public LoaderStateMachine::State | |
| 150 { | |
| 151 public: | |
| 152 LoadStructure(DicomStructureSetLoader& that) : | |
| 153 State(that) | |
| 154 { | |
| 155 } | |
| 156 | |
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157 |
| 815 | 158 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) |
| 159 { | |
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160 #if 0 |
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161 if (logbgo115) |
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162 LOG(TRACE) << "DicomStructureSetLoader::LoadStructure::Handle() (SUCCESS)"; |
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163 #endif |
| 815 | 164 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); |
| 165 | |
| 166 { | |
| 167 OrthancPlugins::FullOrthancDataset dicom(message.GetAnswer()); | |
| 168 loader.content_.reset(new DicomStructureSet(dicom)); | |
| 169 } | |
| 170 | |
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171 // Some (admittedly invalid) Dicom files have empty values in the |
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172 // 0008,1155 tag. We try our best to cope with this. |
| 815 | 173 std::set<std::string> instances; |
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174 std::set<std::string> nonEmptyInstances; |
| 815 | 175 loader.content_->GetReferencedInstances(instances); |
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176 for (std::set<std::string>::const_iterator |
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177 it = instances.begin(); it != instances.end(); ++it) |
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178 { |
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179 std::string instance = Orthanc::Toolbox::StripSpaces(*it); |
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180 if(instance != "") |
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181 nonEmptyInstances.insert(instance); |
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182 } |
| 815 | 183 |
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184 loader.countReferencedInstances_ = |
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185 static_cast<unsigned int>(nonEmptyInstances.size()); |
| 815 | 186 |
| 187 for (std::set<std::string>::const_iterator | |
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188 it = nonEmptyInstances.begin(); it != nonEmptyInstances.end(); ++it) |
| 815 | 189 { |
| 190 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
| 191 command->SetUri("/tools/lookup"); | |
| 192 command->SetMethod(Orthanc::HttpMethod_Post); | |
| 193 command->SetBody(*it); | |
| 194 command->SetPayload(new LookupInstance(loader, *it)); | |
| 195 Schedule(command.release()); | |
| 196 } | |
| 197 } | |
| 198 }; | |
| 199 | |
| 200 | |
| 201 class DicomStructureSetLoader::Slice : public IExtractedSlice | |
| 202 { | |
| 203 private: | |
| 204 const DicomStructureSet& content_; | |
| 205 uint64_t revision_; | |
| 206 bool isValid_; | |
| 207 | |
| 208 public: | |
| 209 Slice(const DicomStructureSet& content, | |
| 210 uint64_t revision, | |
| 211 const CoordinateSystem3D& cuttingPlane) : | |
| 212 content_(content), | |
| 213 revision_(revision) | |
| 214 { | |
| 215 bool opposite; | |
| 216 | |
| 217 const Vector normal = content.GetNormal(); | |
| 218 isValid_ = ( | |
| 219 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetNormal()) || | |
| 220 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisX()) || | |
| 221 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisY())); | |
| 222 } | |
| 223 | |
| 224 virtual bool IsValid() | |
| 225 { | |
| 226 return isValid_; | |
| 227 } | |
| 228 | |
| 229 virtual uint64_t GetRevision() | |
| 230 { | |
| 231 return revision_; | |
| 232 } | |
| 233 | |
| 234 virtual ISceneLayer* CreateSceneLayer(const ILayerStyleConfigurator* configurator, | |
| 235 const CoordinateSystem3D& cuttingPlane) | |
| 236 { | |
| 237 assert(isValid_); | |
| 238 | |
| 239 std::auto_ptr<PolylineSceneLayer> layer(new PolylineSceneLayer); | |
| 240 layer->SetThickness(2); | |
| 241 | |
| 242 for (size_t i = 0; i < content_.GetStructuresCount(); i++) | |
| 243 { | |
| 244 const Color& color = content_.GetStructureColor(i); | |
| 245 | |
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246 #ifdef USE_OLD_SJO_CUT_CODE |
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247 std::vector< std::vector<Point2D> > polygons; |
| 815 | 248 |
| 249 if (content_.ProjectStructure(polygons, i, cuttingPlane)) | |
| 250 { | |
| 251 for (size_t j = 0; j < polygons.size(); j++) | |
| 252 { | |
| 253 PolylineSceneLayer::Chain chain; | |
| 254 chain.resize(polygons[j].size()); | |
| 255 | |
| 256 for (size_t k = 0; k < polygons[j].size(); k++) | |
| 257 { | |
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258 chain[k] = ScenePoint2D(polygons[j][k].x, polygons[j][k].y); |
| 815 | 259 } |
| 260 | |
| 261 layer->AddChain(chain, true /* closed */, color); | |
| 262 } | |
| 263 } | |
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264 #else |
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265 std::vector< std::pair<Point2D, Point2D> > segments; |
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266 |
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267 if (content_.ProjectStructure(segments, i, cuttingPlane)) |
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268 { |
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269 for (size_t j = 0; j < segments.size(); j++) |
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270 { |
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271 PolylineSceneLayer::Chain chain; |
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272 chain.resize(2); |
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273 |
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274 chain[0] = ScenePoint2D(segments[j].first.x, segments[j].first.y); |
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275 chain[1] = ScenePoint2D(segments[j].second.x, segments[j].second.y); |
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276 |
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277 layer->AddChain(chain, false /* NOT closed */, color); |
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278 } |
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279 } |
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280 #endif |
| 815 | 281 } |
| 282 | |
| 283 return layer.release(); | |
| 284 } | |
| 285 }; | |
| 286 | |
| 287 | |
| 288 DicomStructureSetLoader::DicomStructureSetLoader(IOracle& oracle, | |
| 289 IObservable& oracleObservable) : | |
| 954 | 290 LoaderStateMachine(oracle, oracleObservable), |
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291 IObservable(oracleObservable.GetBroker()), |
| 815 | 292 revision_(0), |
| 293 countProcessedInstances_(0), | |
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294 countReferencedInstances_(0), |
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295 structuresReady_(false) |
| 815 | 296 { |
| 297 } | |
| 298 | |
| 299 | |
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300 DicomStructureSetLoader::~DicomStructureSetLoader() |
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301 { |
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302 LOG(TRACE) << "DicomStructureSetLoader::~DicomStructureSetLoader()"; |
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303 } |
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304 |
| 815 | 305 void DicomStructureSetLoader::LoadInstance(const std::string& instanceId) |
| 306 { | |
| 307 Start(); | |
| 308 | |
| 309 instanceId_ = instanceId; | |
| 310 | |
| 311 { | |
| 312 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
| 313 command->SetHttpHeader("Accept-Encoding", "gzip"); | |
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314 |
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315 std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050"; |
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316 |
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317 command->SetUri(uri); |
| 815 | 318 command->SetPayload(new LoadStructure(*this)); |
| 319 Schedule(command.release()); | |
| 320 } | |
| 321 } | |
| 322 | |
| 323 | |
| 324 IVolumeSlicer::IExtractedSlice* DicomStructureSetLoader::ExtractSlice(const CoordinateSystem3D& cuttingPlane) | |
| 325 { | |
| 326 if (content_.get() == NULL) | |
| 327 { | |
| 328 // Geometry is not available yet | |
| 329 return new IVolumeSlicer::InvalidSlice; | |
| 330 } | |
| 331 else | |
| 332 { | |
| 333 return new Slice(*content_, revision_, cuttingPlane); | |
| 334 } | |
| 335 } | |
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336 |
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337 void DicomStructureSetLoader::SetStructuresReady() |
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338 { |
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339 ORTHANC_ASSERT(!structuresReady_); |
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340 structuresReady_ = true; |
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341 BroadcastMessage(DicomStructureSetLoader::StructuresReady(*this)); |
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342 } |
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343 |
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344 bool DicomStructureSetLoader::AreStructuresReady() const |
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345 { |
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346 return structuresReady_; |
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347 } |
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348 |
| 815 | 349 } |