Mercurial > hg > orthanc-stone
annotate Framework/Loaders/DicomStructureSetLoader.cpp @ 1030:7014c2397b45
Empty structureNames now means NOTHING will be (initially) displayed
author | Benjamin Golinvaux <bgo@osimis.io> |
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date | Mon, 07 Oct 2019 14:05:01 +0200 |
parents | 29f5f2031310 |
children | f6be9412e42a |
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 #include <algorithm> |
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28 |
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29 #if 0 |
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30 bool logbgo233 = false; |
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31 bool logbgo115 = false; |
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32 #endif |
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33 |
815 | 34 namespace OrthancStone |
35 { | |
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36 |
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37 #if 0 |
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38 void DumpDicomMap(std::ostream& o, const Orthanc::DicomMap& dicomMap) |
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39 { |
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40 using namespace std; |
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41 //ios_base::fmtflags state = o.flags(); |
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42 //o.flags(ios::right | ios::hex); |
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43 //o << "(" << setfill('0') << setw(4) << tag.GetGroup() |
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44 // << "," << setw(4) << tag.GetElement() << ")"; |
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45 //o.flags(state); |
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46 Json::Value val; |
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47 dicomMap.Serialize(val); |
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48 o << val; |
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49 //return o; |
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50 } |
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51 #endif |
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52 |
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53 |
815 | 54 class DicomStructureSetLoader::AddReferencedInstance : public LoaderStateMachine::State |
55 { | |
56 private: | |
57 std::string instanceId_; | |
58 | |
59 public: | |
60 AddReferencedInstance(DicomStructureSetLoader& that, | |
61 const std::string& instanceId) : | |
62 State(that), | |
63 instanceId_(instanceId) | |
64 { | |
65 } | |
66 | |
67 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
68 { | |
69 Json::Value tags; | |
70 message.ParseJsonBody(tags); | |
71 | |
72 Orthanc::DicomMap dicom; | |
73 dicom.FromDicomAsJson(tags); | |
74 | |
75 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); | |
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76 |
815 | 77 loader.content_->AddReferencedSlice(dicom); |
78 | |
79 loader.countProcessedInstances_ ++; | |
80 assert(loader.countProcessedInstances_ <= loader.countReferencedInstances_); | |
81 | |
82 if (loader.countProcessedInstances_ == loader.countReferencedInstances_) | |
83 { | |
84 // All the referenced instances have been loaded, finalize the RT-STRUCT | |
85 loader.content_->CheckReferencedSlices(); | |
86 loader.revision_++; | |
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87 loader.SetStructuresReady(); |
815 | 88 } |
89 } | |
90 }; | |
91 | |
92 | |
93 // State that converts a "SOP Instance UID" to an Orthanc identifier | |
94 class DicomStructureSetLoader::LookupInstance : public LoaderStateMachine::State | |
95 { | |
96 private: | |
97 std::string sopInstanceUid_; | |
98 | |
99 public: | |
100 LookupInstance(DicomStructureSetLoader& that, | |
101 const std::string& sopInstanceUid) : | |
102 State(that), | |
103 sopInstanceUid_(sopInstanceUid) | |
104 { | |
105 } | |
106 | |
107 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
108 { | |
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109 #if 0 |
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110 LOG(TRACE) << "DicomStructureSetLoader::LookupInstance::Handle() (SUCCESS)"; |
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111 #endif |
815 | 112 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); |
113 | |
114 Json::Value lookup; | |
115 message.ParseJsonBody(lookup); | |
116 | |
117 if (lookup.type() != Json::arrayValue || | |
118 lookup.size() != 1 || | |
119 !lookup[0].isMember("Type") || | |
120 !lookup[0].isMember("Path") || | |
121 lookup[0]["Type"].type() != Json::stringValue || | |
122 lookup[0]["ID"].type() != Json::stringValue || | |
123 lookup[0]["Type"].asString() != "Instance") | |
124 { | |
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125 std::stringstream msg; |
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126 msg << "Unknown resource! message.GetAnswer() = " << message.GetAnswer() << " message.GetAnswerHeaders() = "; |
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127 for (OrthancRestApiCommand::HttpHeaders::const_iterator it = message.GetAnswerHeaders().begin(); |
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128 it != message.GetAnswerHeaders().end(); ++it) |
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129 { |
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130 msg << "\nkey: \"" << it->first << "\" value: \"" << it->second << "\"\n"; |
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131 } |
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132 const std::string msgStr = msg.str(); |
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133 LOG(ERROR) << msgStr; |
815 | 134 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
135 } | |
136 | |
137 const std::string instanceId = lookup[0]["ID"].asString(); | |
138 | |
139 { | |
140 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
141 command->SetHttpHeader("Accept-Encoding", "gzip"); | |
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142 std::string uri = "/instances/" + instanceId + "/tags"; |
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143 command->SetUri(uri); |
815 | 144 command->SetPayload(new AddReferencedInstance(loader, instanceId)); |
145 Schedule(command.release()); | |
146 } | |
147 } | |
148 }; | |
149 | |
150 | |
151 class DicomStructureSetLoader::LoadStructure : public LoaderStateMachine::State | |
152 { | |
153 public: | |
154 LoadStructure(DicomStructureSetLoader& that) : | |
155 State(that) | |
156 { | |
157 } | |
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158 |
815 | 159 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) |
160 { | |
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161 #if 0 |
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162 if (logbgo115) |
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163 LOG(TRACE) << "DicomStructureSetLoader::LoadStructure::Handle() (SUCCESS)"; |
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164 #endif |
815 | 165 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); |
166 | |
167 { | |
168 OrthancPlugins::FullOrthancDataset dicom(message.GetAnswer()); | |
169 loader.content_.reset(new DicomStructureSet(dicom)); | |
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170 size_t structureCount = loader.content_->GetStructuresCount(); |
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171 loader.structureVisibility_.resize(structureCount); |
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172 bool everythingVisible = false; |
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173 if ((loader.initiallyVisibleStructures_.size() == 1) |
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174 && (loader.initiallyVisibleStructures_[0].size() == 1) |
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175 && (loader.initiallyVisibleStructures_[0][0] == '*')) |
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176 { |
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177 everythingVisible = true; |
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178 } |
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179 |
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180 for (size_t i = 0; i < structureCount; ++i) |
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181 { |
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182 // if a single "*" string is supplied, this means we want everything |
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183 // to be visible... |
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184 if(everythingVisible) |
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185 { |
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186 loader.structureVisibility_.at(i) = true; |
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187 } |
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188 else |
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189 { |
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190 // otherwise, we only enable visibility for those structures whose |
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191 // names are mentioned in the initiallyVisibleStructures_ array |
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192 const std::string& structureName = loader.content_->GetStructureName(i); |
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193 |
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194 std::vector<std::string>::iterator foundIt = |
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195 std::find( |
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196 loader.initiallyVisibleStructures_.begin(), |
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197 loader.initiallyVisibleStructures_.end(), |
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198 structureName); |
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199 std::vector<std::string>::iterator endIt = loader.initiallyVisibleStructures_.end(); |
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200 if (foundIt != endIt) |
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201 loader.structureVisibility_.at(i) = true; |
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202 else |
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203 loader.structureVisibility_.at(i) = false; |
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204 } |
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205 } |
815 | 206 } |
207 | |
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208 // Some (admittedly invalid) Dicom files have empty values in the |
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209 // 0008,1155 tag. We try our best to cope with this. |
815 | 210 std::set<std::string> instances; |
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211 std::set<std::string> nonEmptyInstances; |
815 | 212 loader.content_->GetReferencedInstances(instances); |
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213 for (std::set<std::string>::const_iterator |
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214 it = instances.begin(); it != instances.end(); ++it) |
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215 { |
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216 std::string instance = Orthanc::Toolbox::StripSpaces(*it); |
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217 if(instance != "") |
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218 nonEmptyInstances.insert(instance); |
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219 } |
815 | 220 |
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221 loader.countReferencedInstances_ = |
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222 static_cast<unsigned int>(nonEmptyInstances.size()); |
815 | 223 |
224 for (std::set<std::string>::const_iterator | |
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225 it = nonEmptyInstances.begin(); it != nonEmptyInstances.end(); ++it) |
815 | 226 { |
227 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
228 command->SetUri("/tools/lookup"); | |
229 command->SetMethod(Orthanc::HttpMethod_Post); | |
230 command->SetBody(*it); | |
231 command->SetPayload(new LookupInstance(loader, *it)); | |
232 Schedule(command.release()); | |
233 } | |
234 } | |
235 }; | |
236 | |
237 | |
238 class DicomStructureSetLoader::Slice : public IExtractedSlice | |
239 { | |
240 private: | |
241 const DicomStructureSet& content_; | |
242 uint64_t revision_; | |
243 bool isValid_; | |
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244 std::vector<bool> visibility_; |
815 | 245 |
246 public: | |
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247 /** |
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248 The visibility vector must either: |
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249 - be empty |
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250 or |
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251 - contain the same number of items as the number of structures in the |
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252 structure set. |
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253 In the first case (empty vector), all the structures are displayed. |
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254 In the second case, the visibility of each structure is defined by the |
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255 content of the vector at the corresponding index. |
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256 */ |
815 | 257 Slice(const DicomStructureSet& content, |
258 uint64_t revision, | |
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259 const CoordinateSystem3D& cuttingPlane, |
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260 std::vector<bool> visibility = std::vector<bool>()) |
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261 : content_(content) |
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262 , revision_(revision) |
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263 , visibility_(visibility) |
815 | 264 { |
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265 ORTHANC_ASSERT((visibility_.size() == content_.GetStructuresCount()) |
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266 || (visibility_.size() == 0u)); |
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267 |
815 | 268 bool opposite; |
269 | |
270 const Vector normal = content.GetNormal(); | |
271 isValid_ = ( | |
272 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetNormal()) || | |
273 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisX()) || | |
274 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisY())); | |
275 } | |
276 | |
277 virtual bool IsValid() | |
278 { | |
279 return isValid_; | |
280 } | |
281 | |
282 virtual uint64_t GetRevision() | |
283 { | |
284 return revision_; | |
285 } | |
286 | |
287 virtual ISceneLayer* CreateSceneLayer(const ILayerStyleConfigurator* configurator, | |
288 const CoordinateSystem3D& cuttingPlane) | |
289 { | |
290 assert(isValid_); | |
291 | |
292 std::auto_ptr<PolylineSceneLayer> layer(new PolylineSceneLayer); | |
293 layer->SetThickness(2); | |
294 | |
295 for (size_t i = 0; i < content_.GetStructuresCount(); i++) | |
296 { | |
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297 if ((visibility_.size() == 0) || visibility_.at(i)) |
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298 { |
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299 const Color& color = content_.GetStructureColor(i); |
815 | 300 |
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301 #ifdef USE_BOOST_UNION_FOR_POLYGONS |
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302 std::vector< std::vector<Point2D> > polygons; |
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303 |
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304 if (content_.ProjectStructure(polygons, i, cuttingPlane)) |
815 | 305 { |
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306 for (size_t j = 0; j < polygons.size(); j++) |
815 | 307 { |
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308 PolylineSceneLayer::Chain chain; |
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309 chain.resize(polygons[j].size()); |
815 | 310 |
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311 for (size_t k = 0; k < polygons[j].size(); k++) |
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312 { |
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313 chain[k] = ScenePoint2D(polygons[j][k].x, polygons[j][k].y); |
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314 } |
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315 |
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316 layer->AddChain(chain, true /* closed */, color); |
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317 } |
815 | 318 } |
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319 #else |
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320 std::vector< std::pair<Point2D, Point2D> > segments; |
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321 |
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322 if (content_.ProjectStructure(segments, i, cuttingPlane)) |
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323 { |
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324 for (size_t j = 0; j < segments.size(); j++) |
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325 { |
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326 PolylineSceneLayer::Chain chain; |
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327 chain.resize(2); |
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328 |
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329 chain[0] = ScenePoint2D(segments[j].first.x, segments[j].first.y); |
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330 chain[1] = ScenePoint2D(segments[j].second.x, segments[j].second.y); |
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331 |
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332 layer->AddChain(chain, false /* NOT closed */, color); |
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333 } |
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334 } |
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335 #endif |
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336 } |
815 | 337 } |
338 | |
339 return layer.release(); | |
340 } | |
341 }; | |
342 | |
343 | |
344 DicomStructureSetLoader::DicomStructureSetLoader(IOracle& oracle, | |
345 IObservable& oracleObservable) : | |
954 | 346 LoaderStateMachine(oracle, oracleObservable), |
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347 IObservable(oracleObservable.GetBroker()), |
815 | 348 revision_(0), |
349 countProcessedInstances_(0), | |
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350 countReferencedInstances_(0), |
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351 structuresReady_(false) |
815 | 352 { |
353 } | |
354 | |
355 | |
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356 void DicomStructureSetLoader::SetStructureDisplayState(size_t structureIndex, bool display) |
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357 { |
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358 structureVisibility_.at(structureIndex) = display; |
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359 revision_++; |
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360 } |
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361 |
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362 DicomStructureSetLoader::~DicomStructureSetLoader() |
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363 { |
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364 LOG(TRACE) << "DicomStructureSetLoader::~DicomStructureSetLoader()"; |
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365 } |
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366 |
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367 void DicomStructureSetLoader::LoadInstance( |
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368 const std::string& instanceId, |
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369 const std::vector<std::string>& initiallyVisibleStructures) |
815 | 370 { |
371 Start(); | |
372 | |
373 instanceId_ = instanceId; | |
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374 initiallyVisibleStructures_ = initiallyVisibleStructures; |
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375 |
815 | 376 { |
377 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
378 command->SetHttpHeader("Accept-Encoding", "gzip"); | |
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379 |
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380 std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050"; |
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
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381 |
964
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Added cache-control headers for POST requests + #ifdef'd tracing logs + trace on context restored
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382 command->SetUri(uri); |
815 | 383 command->SetPayload(new LoadStructure(*this)); |
384 Schedule(command.release()); | |
385 } | |
386 } | |
387 | |
388 | |
389 IVolumeSlicer::IExtractedSlice* DicomStructureSetLoader::ExtractSlice(const CoordinateSystem3D& cuttingPlane) | |
390 { | |
391 if (content_.get() == NULL) | |
392 { | |
393 // Geometry is not available yet | |
394 return new IVolumeSlicer::InvalidSlice; | |
395 } | |
396 else | |
397 { | |
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Added a way to specificy which structures are to be initially displayed (the
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398 return new Slice(*content_, revision_, cuttingPlane, structureVisibility_); |
815 | 399 } |
400 } | |
937
86ac61a040c9
Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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401 |
86ac61a040c9
Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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402 void DicomStructureSetLoader::SetStructuresReady() |
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Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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403 { |
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Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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404 ORTHANC_ASSERT(!structuresReady_); |
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Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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405 structuresReady_ = true; |
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Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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406 BroadcastMessage(DicomStructureSetLoader::StructuresReady(*this)); |
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Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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407 } |
86ac61a040c9
Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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408 |
86ac61a040c9
Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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409 bool DicomStructureSetLoader::AreStructuresReady() const |
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Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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410 { |
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Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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411 return structuresReady_; |
86ac61a040c9
Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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412 } |
86ac61a040c9
Added getters and notifications to allow clients of the loaders (DicomStructureSetLoader, OrthancSeriesVolumeProgressiveLoader and OrthancMultiframeVolumeLoader) to know when the loading is finished + added ability for SDL event loop to execute a callback repeatedly (used to check the view loading state)
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413 |
815 | 414 } |