Mercurial > hg > orthanc-stone
diff OrthancStone/Sources/Loaders/DicomStructureSetLoader.cpp @ 1512:244ad1e4e76a
reorganization of folders
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Tue, 07 Jul 2020 16:21:02 +0200 |
parents | Framework/Loaders/DicomStructureSetLoader.cpp@d8af188ab545 |
children | 85e117739eca |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancStone/Sources/Loaders/DicomStructureSetLoader.cpp Tue Jul 07 16:21:02 2020 +0200 @@ -0,0 +1,495 @@ +/** + * Stone of Orthanc + * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics + * Department, University Hospital of Liege, Belgium + * Copyright (C) 2017-2020 Osimis S.A., Belgium + * + * This program is free software: you can redistribute it and/or + * modify it under the terms of the GNU Affero 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 + * Affero General Public License for more details. + * + * You should have received a copy of the GNU Affero 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> + +#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: + 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 OrthancStone::OrthancRestApiCommand::SuccessMessage& message) + { + 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 OrthancStone::OrthancRestApiCommand::SuccessMessage& message) + { + 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 (OrthancStone::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_UnknownResource); + } + + const std::string instanceId = lookup[0]["ID"].asString(); + + { + std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); + 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<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); + 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: + LoadStructure(DicomStructureSetLoader& that) : + State(that) + { + } + + virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message) + { + DicomStructureSetLoader& loader = GetLoader<DicomStructureSetLoader>(); + + // Set the actual structure set content + { + FullOrthancDataset dicom(message.GetAnswer()); + + loader.content_.reset(new OrthancStone::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); + } + + 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 OrthancStone::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 OrthancStone::DicomStructureSet& content, + uint64_t revision, + const OrthancStone::CoordinateSystem3D& cuttingPlane, + std::vector<bool> visibility = std::vector<bool>()) + : content_(content) + , revision_(revision) + , visibility_(visibility) + { + ORTHANC_ASSERT((visibility_.size() == content_.GetStructuresCount()) + || (visibility_.size() == 0u)); + + bool opposite; + + const OrthancStone::Vector normal = content.GetNormal(); + isValid_ = ( + OrthancStone::GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetNormal()) || + OrthancStone::GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisX()) || + OrthancStone::GeometryToolbox::IsParallelOrOpposite(opposite, normal, cuttingPlane.GetAxisY())); + } + + virtual bool IsValid() + { + return isValid_; + } + + virtual uint64_t GetRevision() + { + return revision_; + } + + virtual OrthancStone::ISceneLayer* CreateSceneLayer( + const OrthancStone::ILayerStyleConfigurator* configurator, + const OrthancStone::CoordinateSystem3D& cuttingPlane) + { + assert(isValid_); + + std::unique_ptr<OrthancStone::PolylineSceneLayer> layer(new OrthancStone::PolylineSceneLayer); + layer->SetThickness(2); + + for (size_t i = 0; i < content_.GetStructuresCount(); i++) + { + if ((visibility_.size() == 0) || visibility_.at(i)) + { + const OrthancStone::Color& color = content_.GetStructureColor(i); + +#ifdef USE_BOOST_UNION_FOR_POLYGONS + std::vector< std::vector<OrthancStone::Point2D> > polygons; + + if (content_.ProjectStructure(polygons, i, cuttingPlane)) + { + for (size_t j = 0; j < polygons.size(); j++) + { + PolylineSceneLayer::Chain chain; + chain.resize(polygons[j].size()); + + for (size_t k = 0; k < polygons[j].size(); k++) + { + chain[k] = ScenePoint2D(polygons[j][k].x, polygons[j][k].y); + } + + layer->AddChain(chain, true /* closed */, color); + } + } +#else + std::vector< std::pair<OrthancStone::Point2D, OrthancStone::Point2D> > segments; + + if (content_.ProjectStructure(segments, i, cuttingPlane)) + { + for (size_t j = 0; j < segments.size(); j++) + { + OrthancStone::PolylineSceneLayer::Chain chain; + chain.resize(2); + + chain[0] = OrthancStone::ScenePoint2D(segments[j].first.x, segments[j].first.y); + chain[1] = OrthancStone::ScenePoint2D(segments[j].second.x, segments[j].second.y); + + layer->AddChain(chain, false /* NOT closed */, color); + } + } +#endif + } + } + + return layer.release(); + } + }; + + + DicomStructureSetLoader::DicomStructureSetLoader( + OrthancStone::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<OrthancStone::DicomStructureSetLoader> DicomStructureSetLoader::Create(OrthancStone::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<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); + 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); + } + + OrthancStone::IVolumeSlicer::IExtractedSlice* DicomStructureSetLoader::ExtractSlice(const OrthancStone::CoordinateSystem3D& cuttingPlane) + { + if (content_.get() == NULL) + { + // Geometry is not available yet + return new OrthancStone::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_; + } + +}