Mercurial > hg > orthanc-stone
annotate Framework/Loaders/DicomStructureSetLoader.cpp @ 981:c20dbaab360c
Ability to cope with empty "Referenced SOP Instance UID" (dicom path (3006,0039)[i] / (0x3006, 0x0040)[0] / (0x3006, 0x0016)[0] / (0x0008, 0x1155)) + better logs + code formating
author | Benjamin Golinvaux <bgo@osimis.io> |
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date | Fri, 06 Sep 2019 09:38:18 +0200 |
parents | 262a0244e9b2 |
children | 50e5acf5553b |
rev | line source |
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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 std::vector< std::vector<DicomStructureSet::PolygonPoint2D> > polygons; |
815 | 247 |
248 if (content_.ProjectStructure(polygons, i, cuttingPlane)) | |
249 { | |
250 for (size_t j = 0; j < polygons.size(); j++) | |
251 { | |
252 PolylineSceneLayer::Chain chain; | |
253 chain.resize(polygons[j].size()); | |
254 | |
255 for (size_t k = 0; k < polygons[j].size(); k++) | |
256 { | |
257 chain[k] = ScenePoint2D(polygons[j][k].first, polygons[j][k].second); | |
258 } | |
259 | |
260 layer->AddChain(chain, true /* closed */, color); | |
261 } | |
262 } | |
263 } | |
264 | |
265 return layer.release(); | |
266 } | |
267 }; | |
268 | |
269 | |
270 DicomStructureSetLoader::DicomStructureSetLoader(IOracle& oracle, | |
271 IObservable& oracleObservable) : | |
954 | 272 LoaderStateMachine(oracle, oracleObservable), |
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273 IObservable(oracleObservable.GetBroker()), |
815 | 274 revision_(0), |
275 countProcessedInstances_(0), | |
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276 countReferencedInstances_(0), |
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277 structuresReady_(false) |
815 | 278 { |
279 } | |
280 | |
281 | |
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282 DicomStructureSetLoader::~DicomStructureSetLoader() |
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283 { |
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284 LOG(TRACE) << "DicomStructureSetLoader::~DicomStructureSetLoader()"; |
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285 } |
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286 |
815 | 287 void DicomStructureSetLoader::LoadInstance(const std::string& instanceId) |
288 { | |
289 Start(); | |
290 | |
291 instanceId_ = instanceId; | |
292 | |
293 { | |
294 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
295 command->SetHttpHeader("Accept-Encoding", "gzip"); | |
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296 |
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297 std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050"; |
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298 |
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299 command->SetUri(uri); |
815 | 300 command->SetPayload(new LoadStructure(*this)); |
301 Schedule(command.release()); | |
302 } | |
303 } | |
304 | |
305 | |
306 IVolumeSlicer::IExtractedSlice* DicomStructureSetLoader::ExtractSlice(const CoordinateSystem3D& cuttingPlane) | |
307 { | |
308 if (content_.get() == NULL) | |
309 { | |
310 // Geometry is not available yet | |
311 return new IVolumeSlicer::InvalidSlice; | |
312 } | |
313 else | |
314 { | |
315 return new Slice(*content_, revision_, cuttingPlane); | |
316 } | |
317 } | |
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318 |
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319 void DicomStructureSetLoader::SetStructuresReady() |
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320 { |
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321 ORTHANC_ASSERT(!structuresReady_); |
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322 structuresReady_ = true; |
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323 BroadcastMessage(DicomStructureSetLoader::StructuresReady(*this)); |
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324 } |
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325 |
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326 bool DicomStructureSetLoader::AreStructuresReady() const |
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327 { |
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328 return structuresReady_; |
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329 } |
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330 |
815 | 331 } |