Mercurial > hg > orthanc-stone
annotate Framework/Loaders/DicomStructureSetLoader.cpp @ 925:4639d0bf6390
Added support for Grayscale16 in the multiframe loader (Victor)
| author | Benjamin Golinvaux <bgo@osimis.io> |
|---|---|
| date | Mon, 22 Jul 2019 16:00:03 +0200 |
| parents | 2b245953b44b |
| children | 401808e7ff2e |
| 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 | |
| 27 namespace OrthancStone | |
| 28 { | |
| 29 class DicomStructureSetLoader::AddReferencedInstance : public LoaderStateMachine::State | |
| 30 { | |
| 31 private: | |
| 32 std::string instanceId_; | |
| 33 | |
| 34 public: | |
| 35 AddReferencedInstance(DicomStructureSetLoader& that, | |
| 36 const std::string& instanceId) : | |
| 37 State(that), | |
| 38 instanceId_(instanceId) | |
| 39 { | |
| 40 } | |
| 41 | |
| 42 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
| 43 { | |
| 44 Json::Value tags; | |
| 45 message.ParseJsonBody(tags); | |
| 46 | |
| 47 Orthanc::DicomMap dicom; | |
| 48 dicom.FromDicomAsJson(tags); | |
| 49 | |
| 50 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); | |
| 51 loader.content_->AddReferencedSlice(dicom); | |
| 52 | |
| 53 loader.countProcessedInstances_ ++; | |
| 54 assert(loader.countProcessedInstances_ <= loader.countReferencedInstances_); | |
| 55 | |
| 56 if (loader.countProcessedInstances_ == loader.countReferencedInstances_) | |
| 57 { | |
| 58 // All the referenced instances have been loaded, finalize the RT-STRUCT | |
| 59 loader.content_->CheckReferencedSlices(); | |
| 60 loader.revision_++; | |
| 61 } | |
| 62 } | |
| 63 }; | |
| 64 | |
| 65 | |
| 66 // State that converts a "SOP Instance UID" to an Orthanc identifier | |
| 67 class DicomStructureSetLoader::LookupInstance : public LoaderStateMachine::State | |
| 68 { | |
| 69 private: | |
| 70 std::string sopInstanceUid_; | |
| 71 | |
| 72 public: | |
| 73 LookupInstance(DicomStructureSetLoader& that, | |
| 74 const std::string& sopInstanceUid) : | |
| 75 State(that), | |
| 76 sopInstanceUid_(sopInstanceUid) | |
| 77 { | |
| 78 } | |
| 79 | |
| 80 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
| 81 { | |
| 82 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); | |
| 83 | |
| 84 Json::Value lookup; | |
| 85 message.ParseJsonBody(lookup); | |
| 86 | |
| 87 if (lookup.type() != Json::arrayValue || | |
| 88 lookup.size() != 1 || | |
| 89 !lookup[0].isMember("Type") || | |
| 90 !lookup[0].isMember("Path") || | |
| 91 lookup[0]["Type"].type() != Json::stringValue || | |
| 92 lookup[0]["ID"].type() != Json::stringValue || | |
| 93 lookup[0]["Type"].asString() != "Instance") | |
| 94 { | |
|
841
266e2b0b9abc
better error reporting in DicomStructureSetLoader + fixed POST request logic
Benjamin Golinvaux <bgo@osimis.io>
parents:
828
diff
changeset
|
95 std::stringstream msg; |
|
266e2b0b9abc
better error reporting in DicomStructureSetLoader + fixed POST request logic
Benjamin Golinvaux <bgo@osimis.io>
parents:
828
diff
changeset
|
96 msg << "Unknown resource! message.GetAnswer() = " << message.GetAnswer() << " message.GetAnswerHeaders() = "; |
|
842
2b245953b44b
removed some c++11 for older compilers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
841
diff
changeset
|
97 for (OrthancRestApiCommand::HttpHeaders::const_iterator it = message.GetAnswerHeaders().begin(); |
|
2b245953b44b
removed some c++11 for older compilers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
841
diff
changeset
|
98 it != message.GetAnswerHeaders().end(); ++it) |
|
841
266e2b0b9abc
better error reporting in DicomStructureSetLoader + fixed POST request logic
Benjamin Golinvaux <bgo@osimis.io>
parents:
828
diff
changeset
|
99 { |
|
842
2b245953b44b
removed some c++11 for older compilers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
841
diff
changeset
|
100 msg << "\nkey: \"" << it->first << "\" value: \"" << it->second << "\"\n"; |
|
841
266e2b0b9abc
better error reporting in DicomStructureSetLoader + fixed POST request logic
Benjamin Golinvaux <bgo@osimis.io>
parents:
828
diff
changeset
|
101 } |
|
842
2b245953b44b
removed some c++11 for older compilers
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
841
diff
changeset
|
102 const std::string msgStr = msg.str(); |
|
841
266e2b0b9abc
better error reporting in DicomStructureSetLoader + fixed POST request logic
Benjamin Golinvaux <bgo@osimis.io>
parents:
828
diff
changeset
|
103 LOG(ERROR) << msgStr; |
| 815 | 104 throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); |
| 105 } | |
| 106 | |
| 107 const std::string instanceId = lookup[0]["ID"].asString(); | |
| 108 | |
| 109 { | |
| 110 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
| 111 command->SetHttpHeader("Accept-Encoding", "gzip"); | |
| 112 command->SetUri("/instances/" + instanceId + "/tags"); | |
| 113 command->SetPayload(new AddReferencedInstance(loader, instanceId)); | |
| 114 Schedule(command.release()); | |
| 115 } | |
| 116 } | |
| 117 }; | |
| 118 | |
| 119 | |
| 120 class DicomStructureSetLoader::LoadStructure : public LoaderStateMachine::State | |
| 121 { | |
| 122 public: | |
| 123 LoadStructure(DicomStructureSetLoader& that) : | |
| 124 State(that) | |
| 125 { | |
| 126 } | |
| 127 | |
| 128 virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) | |
| 129 { | |
| 130 DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); | |
| 131 | |
| 132 { | |
| 133 OrthancPlugins::FullOrthancDataset dicom(message.GetAnswer()); | |
| 134 loader.content_.reset(new DicomStructureSet(dicom)); | |
| 135 } | |
| 136 | |
| 137 std::set<std::string> instances; | |
| 138 loader.content_->GetReferencedInstances(instances); | |
| 139 | |
| 828 | 140 loader.countReferencedInstances_ = static_cast<unsigned int>(instances.size()); |
| 815 | 141 |
| 142 for (std::set<std::string>::const_iterator | |
| 143 it = instances.begin(); it != instances.end(); ++it) | |
| 144 { | |
| 145 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
| 146 command->SetUri("/tools/lookup"); | |
| 147 command->SetMethod(Orthanc::HttpMethod_Post); | |
| 148 command->SetBody(*it); | |
| 149 command->SetPayload(new LookupInstance(loader, *it)); | |
|
841
266e2b0b9abc
better error reporting in DicomStructureSetLoader + fixed POST request logic
Benjamin Golinvaux <bgo@osimis.io>
parents:
828
diff
changeset
|
150 //LOG(TRACE) << "About to schedule a /tools/lookup POST request. URI = " << command->GetUri() << " Body size = " << (*it).size() << " Body = " << (*it) << "\n"; |
| 815 | 151 Schedule(command.release()); |
| 152 } | |
| 153 } | |
| 154 }; | |
| 155 | |
| 156 | |
| 157 class DicomStructureSetLoader::Slice : public IExtractedSlice | |
| 158 { | |
| 159 private: | |
| 160 const DicomStructureSet& content_; | |
| 161 uint64_t revision_; | |
| 162 bool isValid_; | |
| 163 | |
| 164 public: | |
| 165 Slice(const DicomStructureSet& content, | |
| 166 uint64_t revision, | |
| 167 const CoordinateSystem3D& cuttingPlane) : | |
| 168 content_(content), | |
| 169 revision_(revision) | |
| 170 { | |
| 171 bool opposite; | |
| 172 | |
| 173 const Vector normal = content.GetNormal(); | |
| 174 isValid_ = ( | |
| 175 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetNormal()) || | |
| 176 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisX()) || | |
| 177 GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisY())); | |
| 178 } | |
| 179 | |
| 180 virtual bool IsValid() | |
| 181 { | |
| 182 return isValid_; | |
| 183 } | |
| 184 | |
| 185 virtual uint64_t GetRevision() | |
| 186 { | |
| 187 return revision_; | |
| 188 } | |
| 189 | |
| 190 virtual ISceneLayer* CreateSceneLayer(const ILayerStyleConfigurator* configurator, | |
| 191 const CoordinateSystem3D& cuttingPlane) | |
| 192 { | |
| 193 assert(isValid_); | |
| 194 | |
| 195 std::auto_ptr<PolylineSceneLayer> layer(new PolylineSceneLayer); | |
| 196 layer->SetThickness(2); | |
| 197 | |
| 198 for (size_t i = 0; i < content_.GetStructuresCount(); i++) | |
| 199 { | |
| 200 const Color& color = content_.GetStructureColor(i); | |
| 201 | |
| 202 std::vector< std::vector<DicomStructureSet::PolygonPoint> > polygons; | |
| 203 | |
| 204 if (content_.ProjectStructure(polygons, i, cuttingPlane)) | |
| 205 { | |
| 206 for (size_t j = 0; j < polygons.size(); j++) | |
| 207 { | |
| 208 PolylineSceneLayer::Chain chain; | |
| 209 chain.resize(polygons[j].size()); | |
| 210 | |
| 211 for (size_t k = 0; k < polygons[j].size(); k++) | |
| 212 { | |
| 213 chain[k] = ScenePoint2D(polygons[j][k].first, polygons[j][k].second); | |
| 214 } | |
| 215 | |
| 216 layer->AddChain(chain, true /* closed */, color); | |
| 217 } | |
| 218 } | |
| 219 } | |
| 220 | |
| 221 return layer.release(); | |
| 222 } | |
| 223 }; | |
| 224 | |
| 225 | |
| 226 DicomStructureSetLoader::DicomStructureSetLoader(IOracle& oracle, | |
| 227 IObservable& oracleObservable) : | |
| 228 LoaderStateMachine(oracle, oracleObservable), | |
| 229 revision_(0), | |
| 230 countProcessedInstances_(0), | |
| 231 countReferencedInstances_(0) | |
| 232 { | |
| 233 } | |
| 234 | |
| 235 | |
| 236 void DicomStructureSetLoader::LoadInstance(const std::string& instanceId) | |
| 237 { | |
| 238 Start(); | |
| 239 | |
| 240 instanceId_ = instanceId; | |
| 241 | |
| 242 { | |
| 243 std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); | |
| 244 command->SetHttpHeader("Accept-Encoding", "gzip"); | |
| 245 command->SetUri("/instances/" + instanceId + "/tags?ignore-length=3006-0050"); | |
| 246 command->SetPayload(new LoadStructure(*this)); | |
| 247 Schedule(command.release()); | |
| 248 } | |
| 249 } | |
| 250 | |
| 251 | |
| 252 IVolumeSlicer::IExtractedSlice* DicomStructureSetLoader::ExtractSlice(const CoordinateSystem3D& cuttingPlane) | |
| 253 { | |
| 254 if (content_.get() == NULL) | |
| 255 { | |
| 256 // Geometry is not available yet | |
| 257 return new IVolumeSlicer::InvalidSlice; | |
| 258 } | |
| 259 else | |
| 260 { | |
| 261 return new Slice(*content_, revision_, cuttingPlane); | |
| 262 } | |
| 263 } | |
| 264 } |