Mercurial > hg > orthanc-stone
annotate Framework/Loaders/DicomStructureSetLoader.cpp @ 1092:5a35688c4874
Added tag toa2019102301 for changeset 5a18e6a395bc
author | Benjamin Golinvaux <bgo@osimis.io> |
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date | Wed, 23 Oct 2019 15:34:58 +0200 |
parents | f6be9412e42a |
children | e713f1a99861 2d8ab34c8c91 |
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" | |
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25 #include "../StoneException.h" |
815 | 26 #include "../Toolbox/GeometryToolbox.h" |
27 | |
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28 #include <Core/Toolbox.h> |
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29 |
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30 #include <algorithm> |
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31 |
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32 #if 0 |
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33 bool logbgo233 = false; |
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34 bool logbgo115 = false; |
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35 #endif |
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36 |
815 | 37 namespace OrthancStone |
38 { | |
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39 |
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40 #if 0 |
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41 void DumpDicomMap(std::ostream& o, const Orthanc::DicomMap& dicomMap) |
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42 { |
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43 using namespace std; |
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44 //ios_base::fmtflags state = o.flags(); |
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45 //o.flags(ios::right | ios::hex); |
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46 //o << "(" << setfill('0') << setw(4) << tag.GetGroup() |
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47 // << "," << setw(4) << tag.GetElement() << ")"; |
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48 //o.flags(state); |
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49 Json::Value val; |
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50 dicomMap.Serialize(val); |
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51 o << val; |
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52 //return o; |
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53 } |
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54 #endif |
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55 |
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56 |
815 | 57 class DicomStructureSetLoader::AddReferencedInstance : public LoaderStateMachine::State |
58 { | |
59 private: | |
60 std::string instanceId_; | |
61 | |
62 public: | |
63 AddReferencedInstance(DicomStructureSetLoader& that, | |
64 const std::string& instanceId) : | |
65 State(that), | |
66 instanceId_(instanceId) | |
67 { | |
68 } | |
69 | |
70 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
71 { | |
72 Json::Value tags; | |
73 message.ParseJsonBody(tags); | |
74 | |
75 Orthanc::DicomMap dicom; | |
76 dicom.FromDicomAsJson(tags); | |
77 | |
78 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); | |
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79 |
815 | 80 loader.content_->AddReferencedSlice(dicom); |
81 | |
82 loader.countProcessedInstances_ ++; | |
83 assert(loader.countProcessedInstances_ <= loader.countReferencedInstances_); | |
84 | |
85 if (loader.countProcessedInstances_ == loader.countReferencedInstances_) | |
86 { | |
87 // All the referenced instances have been loaded, finalize the RT-STRUCT | |
88 loader.content_->CheckReferencedSlices(); | |
89 loader.revision_++; | |
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90 loader.SetStructuresReady(); |
815 | 91 } |
92 } | |
93 }; | |
94 | |
95 | |
96 // State that converts a "SOP Instance UID" to an Orthanc identifier | |
97 class DicomStructureSetLoader::LookupInstance : public LoaderStateMachine::State | |
98 { | |
99 private: | |
100 std::string sopInstanceUid_; | |
101 | |
102 public: | |
103 LookupInstance(DicomStructureSetLoader& that, | |
104 const std::string& sopInstanceUid) : | |
105 State(that), | |
106 sopInstanceUid_(sopInstanceUid) | |
107 { | |
108 } | |
109 | |
110 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
111 { | |
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112 #if 0 |
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113 LOG(TRACE) << "DicomStructureSetLoader::LookupInstance::Handle() (SUCCESS)"; |
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114 #endif |
815 | 115 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); |
116 | |
117 Json::Value lookup; | |
118 message.ParseJsonBody(lookup); | |
119 | |
120 if (lookup.type() != Json::arrayValue || | |
121 lookup.size() != 1 || | |
122 !lookup[0].isMember("Type") || | |
123 !lookup[0].isMember("Path") || | |
124 lookup[0]["Type"].type() != Json::stringValue || | |
125 lookup[0]["ID"].type() != Json::stringValue || | |
126 lookup[0]["Type"].asString() != "Instance") | |
127 { | |
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128 std::stringstream msg; |
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129 msg << "Unknown resource! message.GetAnswer() = " << message.GetAnswer() << " message.GetAnswerHeaders() = "; |
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130 for (OrthancRestApiCommand::HttpHeaders::const_iterator it = message.GetAnswerHeaders().begin(); |
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131 it != message.GetAnswerHeaders().end(); ++it) |
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132 { |
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133 msg << "\nkey: \"" << it->first << "\" value: \"" << it->second << "\"\n"; |
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134 } |
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135 const std::string msgStr = msg.str(); |
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136 LOG(ERROR) << msgStr; |
815 | 137 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
138 } | |
139 | |
140 const std::string instanceId = lookup[0]["ID"].asString(); | |
141 | |
142 { | |
143 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
144 command->SetHttpHeader("Accept-Encoding", "gzip"); | |
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145 std::string uri = "/instances/" + instanceId + "/tags"; |
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146 command->SetUri(uri); |
815 | 147 command->SetPayload(new AddReferencedInstance(loader, instanceId)); |
148 Schedule(command.release()); | |
149 } | |
150 } | |
151 }; | |
152 | |
153 | |
154 class DicomStructureSetLoader::LoadStructure : public LoaderStateMachine::State | |
155 { | |
156 public: | |
157 LoadStructure(DicomStructureSetLoader& that) : | |
158 State(that) | |
159 { | |
160 } | |
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161 |
815 | 162 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) |
163 { | |
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164 #if 0 |
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165 if (logbgo115) |
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166 LOG(TRACE) << "DicomStructureSetLoader::LoadStructure::Handle() (SUCCESS)"; |
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167 #endif |
815 | 168 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); |
169 | |
170 { | |
171 OrthancPlugins::FullOrthancDataset dicom(message.GetAnswer()); | |
172 loader.content_.reset(new DicomStructureSet(dicom)); | |
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173 size_t structureCount = loader.content_->GetStructuresCount(); |
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174 loader.structureVisibility_.resize(structureCount); |
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175 bool everythingVisible = false; |
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176 if ((loader.initiallyVisibleStructures_.size() == 1) |
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177 && (loader.initiallyVisibleStructures_[0].size() == 1) |
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178 && (loader.initiallyVisibleStructures_[0][0] == '*')) |
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179 { |
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180 everythingVisible = true; |
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181 } |
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182 |
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183 for (size_t i = 0; i < structureCount; ++i) |
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184 { |
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185 // if a single "*" string is supplied, this means we want everything |
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186 // to be visible... |
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187 if(everythingVisible) |
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188 { |
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189 loader.structureVisibility_.at(i) = true; |
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190 } |
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191 else |
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192 { |
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193 // otherwise, we only enable visibility for those structures whose |
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194 // names are mentioned in the initiallyVisibleStructures_ array |
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195 const std::string& structureName = loader.content_->GetStructureName(i); |
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196 |
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197 std::vector<std::string>::iterator foundIt = |
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198 std::find( |
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199 loader.initiallyVisibleStructures_.begin(), |
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200 loader.initiallyVisibleStructures_.end(), |
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201 structureName); |
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202 std::vector<std::string>::iterator endIt = loader.initiallyVisibleStructures_.end(); |
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203 if (foundIt != endIt) |
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204 loader.structureVisibility_.at(i) = true; |
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205 else |
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206 loader.structureVisibility_.at(i) = false; |
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207 } |
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208 } |
815 | 209 } |
210 | |
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211 // Some (admittedly invalid) Dicom files have empty values in the |
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212 // 0008,1155 tag. We try our best to cope with this. |
815 | 213 std::set<std::string> instances; |
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214 std::set<std::string> nonEmptyInstances; |
815 | 215 loader.content_->GetReferencedInstances(instances); |
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216 for (std::set<std::string>::const_iterator |
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217 it = instances.begin(); it != instances.end(); ++it) |
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218 { |
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219 std::string instance = Orthanc::Toolbox::StripSpaces(*it); |
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220 if(instance != "") |
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221 nonEmptyInstances.insert(instance); |
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222 } |
815 | 223 |
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224 loader.countReferencedInstances_ = |
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225 static_cast<unsigned int>(nonEmptyInstances.size()); |
815 | 226 |
227 for (std::set<std::string>::const_iterator | |
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228 it = nonEmptyInstances.begin(); it != nonEmptyInstances.end(); ++it) |
815 | 229 { |
230 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
231 command->SetUri("/tools/lookup"); | |
232 command->SetMethod(Orthanc::HttpMethod_Post); | |
233 command->SetBody(*it); | |
234 command->SetPayload(new LookupInstance(loader, *it)); | |
235 Schedule(command.release()); | |
236 } | |
237 } | |
238 }; | |
239 | |
240 | |
241 class DicomStructureSetLoader::Slice : public IExtractedSlice | |
242 { | |
243 private: | |
244 const DicomStructureSet& content_; | |
245 uint64_t revision_; | |
246 bool isValid_; | |
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247 std::vector<bool> visibility_; |
815 | 248 |
249 public: | |
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250 /** |
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251 The visibility vector must either: |
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252 - be empty |
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253 or |
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254 - contain the same number of items as the number of structures in the |
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255 structure set. |
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256 In the first case (empty vector), all the structures are displayed. |
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257 In the second case, the visibility of each structure is defined by the |
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258 content of the vector at the corresponding index. |
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259 */ |
815 | 260 Slice(const DicomStructureSet& content, |
261 uint64_t revision, | |
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262 const CoordinateSystem3D& cuttingPlane, |
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263 std::vector<bool> visibility = std::vector<bool>()) |
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264 : content_(content) |
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265 , revision_(revision) |
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266 , visibility_(visibility) |
815 | 267 { |
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268 ORTHANC_ASSERT((visibility_.size() == content_.GetStructuresCount()) |
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269 || (visibility_.size() == 0u)); |
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270 |
815 | 271 bool opposite; |
272 | |
273 const Vector normal = content.GetNormal(); | |
274 isValid_ = ( | |
275 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetNormal()) || | |
276 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisX()) || | |
277 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisY())); | |
278 } | |
279 | |
280 virtual bool IsValid() | |
281 { | |
282 return isValid_; | |
283 } | |
284 | |
285 virtual uint64_t GetRevision() | |
286 { | |
287 return revision_; | |
288 } | |
289 | |
290 virtual ISceneLayer* CreateSceneLayer(const ILayerStyleConfigurator* configurator, | |
291 const CoordinateSystem3D& cuttingPlane) | |
292 { | |
293 assert(isValid_); | |
294 | |
295 std::auto_ptr<PolylineSceneLayer> layer(new PolylineSceneLayer); | |
296 layer->SetThickness(2); | |
297 | |
298 for (size_t i = 0; i < content_.GetStructuresCount(); i++) | |
299 { | |
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300 if ((visibility_.size() == 0) || visibility_.at(i)) |
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301 { |
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302 const Color& color = content_.GetStructureColor(i); |
815 | 303 |
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304 #ifdef USE_BOOST_UNION_FOR_POLYGONS |
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305 std::vector< std::vector<Point2D> > polygons; |
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306 |
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307 if (content_.ProjectStructure(polygons, i, cuttingPlane)) |
815 | 308 { |
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309 for (size_t j = 0; j < polygons.size(); j++) |
815 | 310 { |
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311 PolylineSceneLayer::Chain chain; |
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312 chain.resize(polygons[j].size()); |
815 | 313 |
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314 for (size_t k = 0; k < polygons[j].size(); k++) |
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315 { |
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316 chain[k] = ScenePoint2D(polygons[j][k].x, polygons[j][k].y); |
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317 } |
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318 |
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319 layer->AddChain(chain, true /* closed */, color); |
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320 } |
815 | 321 } |
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322 #else |
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323 std::vector< std::pair<Point2D, Point2D> > segments; |
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324 |
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325 if (content_.ProjectStructure(segments, i, cuttingPlane)) |
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326 { |
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327 for (size_t j = 0; j < segments.size(); j++) |
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328 { |
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329 PolylineSceneLayer::Chain chain; |
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330 chain.resize(2); |
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331 |
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332 chain[0] = ScenePoint2D(segments[j].first.x, segments[j].first.y); |
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333 chain[1] = ScenePoint2D(segments[j].second.x, segments[j].second.y); |
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334 |
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335 layer->AddChain(chain, false /* NOT closed */, color); |
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336 } |
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337 } |
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338 #endif |
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339 } |
815 | 340 } |
341 | |
342 return layer.release(); | |
343 } | |
344 }; | |
345 | |
346 | |
347 DicomStructureSetLoader::DicomStructureSetLoader(IOracle& oracle, | |
348 IObservable& oracleObservable) : | |
954 | 349 LoaderStateMachine(oracle, oracleObservable), |
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350 IObservable(oracleObservable.GetBroker()), |
815 | 351 revision_(0), |
352 countProcessedInstances_(0), | |
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353 countReferencedInstances_(0), |
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354 structuresReady_(false) |
815 | 355 { |
356 } | |
357 | |
358 | |
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359 void DicomStructureSetLoader::SetStructureDisplayState(size_t structureIndex, bool display) |
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360 { |
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361 structureVisibility_.at(structureIndex) = display; |
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362 revision_++; |
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363 } |
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364 |
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365 DicomStructureSetLoader::~DicomStructureSetLoader() |
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366 { |
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367 LOG(TRACE) << "DicomStructureSetLoader::~DicomStructureSetLoader()"; |
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368 } |
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369 |
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370 void DicomStructureSetLoader::LoadInstance( |
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371 const std::string& instanceId, |
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372 const std::vector<std::string>& initiallyVisibleStructures) |
815 | 373 { |
374 Start(); | |
375 | |
376 instanceId_ = instanceId; | |
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377 initiallyVisibleStructures_ = initiallyVisibleStructures; |
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378 |
815 | 379 { |
380 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
381 command->SetHttpHeader("Accept-Encoding", "gzip"); | |
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382 |
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383 std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050"; |
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384 |
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385 command->SetUri(uri); |
815 | 386 command->SetPayload(new LoadStructure(*this)); |
387 Schedule(command.release()); | |
388 } | |
389 } | |
390 | |
391 | |
392 IVolumeSlicer::IExtractedSlice* DicomStructureSetLoader::ExtractSlice(const CoordinateSystem3D& cuttingPlane) | |
393 { | |
394 if (content_.get() == NULL) | |
395 { | |
396 // Geometry is not available yet | |
397 return new IVolumeSlicer::InvalidSlice; | |
398 } | |
399 else | |
400 { | |
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401 return new Slice(*content_, revision_, cuttingPlane, structureVisibility_); |
815 | 402 } |
403 } | |
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404 |
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405 void DicomStructureSetLoader::SetStructuresReady() |
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406 { |
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407 ORTHANC_ASSERT(!structuresReady_); |
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408 structuresReady_ = true; |
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409 BroadcastMessage(DicomStructureSetLoader::StructuresReady(*this)); |
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410 } |
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411 |
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412 bool DicomStructureSetLoader::AreStructuresReady() const |
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413 { |
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414 return structuresReady_; |
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415 } |
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416 |
815 | 417 } |