Mercurial > hg > orthanc-stone
view OrthancStone/Sources/Loaders/DicomStructureSetLoader.cpp @ 2174:2410a171ebfb
refactoring using DicomWebDataset and OrthancNativeDataset
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 22 Oct 2024 21:52:34 +0200 |
parents | 16c01cc201e7 |
children |
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/** * Stone of Orthanc * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, Belgium * Copyright (C) 2017-2023 Osimis S.A., Belgium * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium * * This program is free software: you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public License * as published by the Free Software Foundation, either version 3 of * the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public * License along with this program. If not, see * <http://www.gnu.org/licenses/>. **/ #include "DicomStructureSetLoader.h" #include "../Scene2D/PolylineSceneLayer.h" #include "../StoneException.h" #include "../Toolbox/GeometryToolbox.h" #include <Toolbox.h> #if STONE_TIME_BLOCKING_OPS # include <boost/date_time/posix_time/posix_time.hpp> #endif #include <algorithm> namespace OrthancStone { #if 0 void DumpDicomMap(std::ostream& o, const Orthanc::DicomMap& dicomMap) { using namespace std; //ios_base::fmtflags state = o.flags(); //o.flags(ios::right | ios::hex); //o << "(" << setfill('0') << setw(4) << tag.GetGroup() // << "," << setw(4) << tag.GetElement() << ")"; //o.flags(state); Json::Value val; dicomMap.Serialize(val); o << val; //return o; } #endif // implementation of IInstanceLookupHandler that uses Orthanc REST API calls to retrive the // geometry of referenced instances class DicomStructureSetLoader::RestInstanceLookupHandler : public DicomStructureSetLoader::IInstanceLookupHandler, public LoaderStateMachine { public: static boost::shared_ptr<RestInstanceLookupHandler > Create(DicomStructureSetLoader& loader) { boost::shared_ptr<RestInstanceLookupHandler> obj(new RestInstanceLookupHandler(loader)); obj->LoaderStateMachine::PostConstructor(); return obj; } protected: explicit RestInstanceLookupHandler(DicomStructureSetLoader& loader) : LoaderStateMachine(loader.loadersContext_), loader_(loader) { } virtual void RetrieveReferencedSlices(const std::set<std::string>& nonEmptyInstances) ORTHANC_OVERRIDE; private: // these subclasses hold the loading state class AddReferencedInstance; // 2nd state class LookupInstance; // 1st state DicomStructureSetLoader& loader_; }; class DicomStructureSetLoader::RestInstanceLookupHandler::AddReferencedInstance : public LoaderStateMachine::State { private: std::string instanceId_; public: AddReferencedInstance(DicomStructureSetLoader& that, const std::string& instanceId) : State(that), instanceId_(instanceId) { } virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) ORTHANC_OVERRIDE { Json::Value tags; message.ParseJsonBody(tags); Orthanc::DicomMap dicom; dicom.FromDicomAsJson(tags); DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); loader.AddReferencedSlice(dicom); } }; // State that converts a "SOP Instance UID" to an Orthanc identifier class DicomStructureSetLoader::RestInstanceLookupHandler::LookupInstance : public LoaderStateMachine::State { private: std::string sopInstanceUid_; public: LookupInstance(DicomStructureSetLoader& that, const std::string& sopInstanceUid) : State(that), sopInstanceUid_(sopInstanceUid) { } virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) ORTHANC_OVERRIDE { DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); Json::Value lookup; message.ParseJsonBody(lookup); if (lookup.type() != Json::arrayValue || lookup.size() != 1 || !lookup[0].isMember("Type") || !lookup[0].isMember("Path") || lookup[0]["Type"].type() != Json::stringValue || lookup[0]["ID"].type() != Json::stringValue || lookup[0]["Type"].asString() != "Instance") { std::stringstream msg; msg << "Unknown resource! message.GetAnswer() = " << message.GetAnswer() << " message.GetAnswerHeaders() = "; for (OrthancRestApiCommand::HttpHeaders::const_iterator it = message.GetAnswerHeaders().begin(); it != message.GetAnswerHeaders().end(); ++it) { msg << "\nkey: \"" << it->first << "\" value: \"" << it->second << "\"\n"; } const std::string msgStr = msg.str(); LOG(ERROR) << msgStr; throw Orthanc::OrthancException(Orthanc::ErrorCode_BadJson); } const std::string instanceId = lookup[0]["ID"].asString(); { std::unique_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); command->SetCallerName("DicomStructureSetLoader::RestInstanceLookupHandler::LookupInstance"); command->SetHttpHeader("Accept-Encoding", "gzip"); std::string uri = "/instances/" + instanceId + "/tags"; command->SetUri(uri); command->AcquirePayload(new AddReferencedInstance(loader, instanceId)); Schedule(command.release()); } } }; void DicomStructureSetLoader::RestInstanceLookupHandler::RetrieveReferencedSlices( const std::set<std::string>& nonEmptyInstances) { for (std::set<std::string>::const_iterator it = nonEmptyInstances.begin(); it != nonEmptyInstances.end(); ++it) { std::unique_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); command->SetCallerName("DicomStructureSetLoader::RestInstanceLookupHandler"); command->SetUri("/tools/lookup"); command->SetMethod(Orthanc::HttpMethod_Post); command->SetBody(*it); command->AcquirePayload(new LookupInstance(loader_, *it)); Schedule(command.release()); } } class DicomStructureSetLoader::LoadStructure : public LoaderStateMachine::State { public: explicit LoadStructure(DicomStructureSetLoader& that) : State(that) { } virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) ORTHANC_OVERRIDE { #if STONE_TIME_BLOCKING_OPS boost::posix_time::ptime timerStart = boost::posix_time::microsec_clock::universal_time(); #endif DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); // Set the actual structure set content { FullOrthancDataset dicom(message.GetAnswer()); loader.content_.reset(new DicomStructureSet(dicom)); } // initialize visibility flags SetDefaultStructureVisibility(); // retrieve the (non-empty) referenced instances (the CT slices containing the corresponding structures) // Some (admittedly invalid) Dicom files have empty values in the // 0008,1155 tag. We try our best to cope with this. // this is why we use `nonEmptyInstances` and not `instances` std::set<std::string> instances; std::set<std::string> nonEmptyInstances; // this traverses the polygon collection for all structures and retrieve the SOPInstanceUID of // the referenced instances loader.content_->GetReferencedInstances(instances); for (std::set<std::string>::const_iterator it = instances.begin(); it != instances.end(); ++it) { std::string instance = Orthanc::Toolbox::StripSpaces(*it); if(instance != "") nonEmptyInstances.insert(instance); } loader.RetrieveReferencedSlices(nonEmptyInstances); #if STONE_TIME_BLOCKING_OPS boost::posix_time::ptime timerEnd = boost::posix_time::microsec_clock::universal_time(); boost::posix_time::time_duration duration = timerEnd - timerStart; int64_t durationMs = duration.total_milliseconds(); LOG(WARNING) << "DicomStructureSetLoader::LoadStructure::Handle took " << durationMs << " ms"; #endif } void SetDefaultStructureVisibility() { DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); size_t structureCount = loader.content_->GetStructuresCount(); loader.structureVisibility_.resize(structureCount); bool everythingVisible = false; if ((loader.initiallyVisibleStructures_.size() == 1) && (loader.initiallyVisibleStructures_[0].size() == 1) && (loader.initiallyVisibleStructures_[0][0] == '*')) { everythingVisible = true; } for (size_t i = 0; i < structureCount; ++i) { // if a single "*" string is supplied, this means we want everything // to be visible... if (everythingVisible) { loader.structureVisibility_.at(i) = true; } else { // otherwise, we only enable visibility for those structures whose // names are mentioned in the initiallyVisibleStructures_ array const std::string& structureName = loader.content_->GetStructureName(i); std::vector<std::string>::iterator foundIt = std::find( loader.initiallyVisibleStructures_.begin(), loader.initiallyVisibleStructures_.end(), structureName); std::vector<std::string>::iterator endIt = loader.initiallyVisibleStructures_.end(); if (foundIt != endIt) loader.structureVisibility_.at(i) = true; else loader.structureVisibility_.at(i) = false; } } } private: }; class DicomStructureSetLoader::Slice : public IExtractedSlice { private: const DicomStructureSet& content_; uint64_t revision_; bool isValid_; std::vector<bool> visibility_; public: /** The visibility vector must either: - be empty or - contain the same number of items as the number of structures in the structure set. In the first case (empty vector), all the structures are displayed. In the second case, the visibility of each structure is defined by the content of the vector at the corresponding index. */ Slice(const DicomStructureSet& content, uint64_t revision, const CoordinateSystem3D& cuttingPlane, const std::vector<bool>& visibility) : content_(content), revision_(revision), visibility_(visibility) { ORTHANC_ASSERT((visibility_.size() == content_.GetStructuresCount()) || (visibility_.size() == 0u)); bool opposite; const Vector normal = content.GetNormal(); isValid_ = ( GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetNormal()) || GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisX()) || GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisY())); } virtual bool IsValid() ORTHANC_OVERRIDE { return isValid_; } virtual uint64_t GetRevision() ORTHANC_OVERRIDE { return revision_; } virtual ISceneLayer* CreateSceneLayer( const ILayerStyleConfigurator* configurator, const CoordinateSystem3D& cuttingPlane) ORTHANC_OVERRIDE { assert(isValid_); std::unique_ptr<PolylineSceneLayer> layer(new PolylineSceneLayer); layer->SetThickness(2); #if 0 // For testing - This displays a cross at the origin of the 3D // cutting plane in the 2D viewport { PolylineSceneLayer::Chain chain; chain.push_back(ScenePoint2D(-100, 0)); chain.push_back(ScenePoint2D(100, 0)); layer->AddChain(chain, false, Color(255, 0, 0)); } { PolylineSceneLayer::Chain chain; chain.push_back(ScenePoint2D(0, -100)); chain.push_back(ScenePoint2D(0, 100)); layer->AddChain(chain, false, Color(255, 0, 0)); } #endif for (size_t i = 0; i < content_.GetStructuresCount(); i++) { if (visibility_.size() == 0 || visibility_.at(i)) { content_.ProjectOntoLayer(*layer, cuttingPlane, i, content_.GetStructureColor(i)); } } return layer.release(); } }; DicomStructureSetLoader::DicomStructureSetLoader( ILoadersContext& loadersContext) : LoaderStateMachine(loadersContext) , loadersContext_(loadersContext) , revision_(0) , countProcessedInstances_(0) , countReferencedInstances_(0) , structuresReady_(false) { // the default handler to retrieve slice geometry is RestInstanceLookupHandler instanceLookupHandler_ = RestInstanceLookupHandler::Create(*this); } boost::shared_ptr<DicomStructureSetLoader> DicomStructureSetLoader::Create(ILoadersContext& loadersContext) { boost::shared_ptr<DicomStructureSetLoader> obj( new DicomStructureSetLoader( loadersContext)); obj->LoaderStateMachine::PostConstructor(); return obj; } void DicomStructureSetLoader::AddReferencedSlice(const Orthanc::DicomMap& dicom) { content_->AddReferencedSlice(dicom); countProcessedInstances_ ++; assert(countProcessedInstances_ <= countReferencedInstances_); revision_++; SetStructuresUpdated(); if (countProcessedInstances_ == countReferencedInstances_) { // All the referenced instances have been loaded, finalize the RT-STRUCT content_->CheckReferencedSlices(); revision_++; SetStructuresReady(); } } void DicomStructureSetLoader::RetrieveReferencedSlices(const std::set<std::string>& nonEmptyInstances) { // we set the number of referenced instances. This allows to know, in the method above, when we're done countReferencedInstances_ = static_cast<unsigned int>(nonEmptyInstances.size()); instanceLookupHandler_->RetrieveReferencedSlices(nonEmptyInstances); } void DicomStructureSetLoader::SetStructureDisplayState(size_t structureIndex, bool display) { structureVisibility_.at(structureIndex) = display; revision_++; } DicomStructureSetLoader::~DicomStructureSetLoader() { LOG(TRACE) << "DicomStructureSetLoader::~DicomStructureSetLoader()"; } void DicomStructureSetLoader::LoadInstance( const std::string& instanceId, const std::vector<std::string>& initiallyVisibleStructures) { Start(); instanceId_ = instanceId; initiallyVisibleStructures_ = initiallyVisibleStructures; { std::unique_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); command->SetCallerName("DicomStructureSetLoader::LoadInstance"); command->SetHttpHeader("Accept-Encoding", "gzip"); std::string uri = "/instances/" + instanceId + "/tags?ignore-length=3006-0050"; command->SetUri(uri); command->AcquirePayload(new LoadStructure(*this)); Schedule(command.release()); } } void DicomStructureSetLoader::LoadInstanceFullVisibility(const std::string& instanceId) { std::vector<std::string> initiallyVisibleStructures; initiallyVisibleStructures.push_back("*"); // wildcard to make all structure sets visible LoadInstance(instanceId, initiallyVisibleStructures); } IVolumeSlicer::IExtractedSlice* DicomStructureSetLoader::ExtractSlice(const CoordinateSystem3D& cuttingPlane) { if (content_.get() == NULL) { // Geometry is not available yet return new IVolumeSlicer::InvalidSlice; } else { return new Slice(*content_, revision_, cuttingPlane, structureVisibility_); } } void DicomStructureSetLoader::SetStructuresUpdated() { BroadcastMessage(DicomStructureSetLoader::StructuresUpdated(*this)); } void DicomStructureSetLoader::SetStructuresReady() { ORTHANC_ASSERT(!structuresReady_); structuresReady_ = true; BroadcastMessage(DicomStructureSetLoader::StructuresReady(*this)); } bool DicomStructureSetLoader::AreStructuresReady() const { return structuresReady_; } }