Mercurial > hg > orthanc-stone
view OrthancStone/Sources/Loaders/SeriesFramesLoader.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 | fe5406abd43f |
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 "SeriesFramesLoader.h" #include "../Oracle/ParseDicomFromFileCommand.h" #include "../Oracle/ParseDicomFromWadoCommand.h" #if ORTHANC_ENABLE_DCMTK == 1 # include <DicomParsing/ParsedDicomFile.h> #endif #include <DicomFormat/DicomInstanceHasher.h> #include <Images/Image.h> #include <Images/ImageProcessing.h> #include <Images/JpegReader.h> #include <boost/algorithm/string/predicate.hpp> namespace OrthancStone { class SeriesFramesLoader::Payload : public Orthanc::IDynamicObject { private: DicomSource source_; size_t seriesIndex_; std::string sopInstanceUid_; // Only used for debug purpose unsigned int quality_; bool hasWindowing_; Windowing windowing_; std::unique_ptr<Orthanc::IDynamicObject> userPayload_; public: Payload(const DicomSource& source, size_t seriesIndex, const std::string& sopInstanceUid, unsigned int quality, Orthanc::IDynamicObject* userPayload) : source_(source), seriesIndex_(seriesIndex), sopInstanceUid_(sopInstanceUid), quality_(quality), hasWindowing_(false), userPayload_(userPayload) { } size_t GetSeriesIndex() const { return seriesIndex_; } const std::string& GetSopInstanceUid() const { return sopInstanceUid_; } unsigned int GetQuality() const { return quality_; } void SetWindowing(const Windowing& windowing) { hasWindowing_ = true; windowing_ = windowing; } bool HasWindowing() const { return hasWindowing_; } const Windowing& GetWindowing() const { if (hasWindowing_) { return windowing_; } else { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); } } const DicomSource& GetSource() const { return source_; } Orthanc::IDynamicObject* GetUserPayload() const { return userPayload_.get(); } }; SeriesFramesLoader::SeriesFramesLoader(ILoadersContext& context, LoadedDicomResources& instances, const std::string& dicomDirPath, boost::shared_ptr<LoadedDicomResources> dicomDir) : context_(context), frames_(instances), dicomDirPath_(dicomDirPath), dicomDir_(dicomDir) { } void SeriesFramesLoader::EmitMessage(const Payload& payload, const Orthanc::ImageAccessor& image) { const DicomInstanceParameters& parameters = frames_.GetInstanceParameters(payload.GetSeriesIndex()); const Orthanc::DicomMap& instance = frames_.GetInstance(payload.GetSeriesIndex()); size_t frameIndex = frames_.GetFrameIndex(payload.GetSeriesIndex()); if (frameIndex >= parameters.GetImageInformation().GetNumberOfFrames() || payload.GetSopInstanceUid() != parameters.GetSopInstanceUid()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } LOG(TRACE) << "Decoded instance " << payload.GetSopInstanceUid() << ", frame " << frameIndex << ": " << image.GetWidth() << "x" << image.GetHeight() << ", " << Orthanc::EnumerationToString(image.GetFormat()) << ", quality " << payload.GetQuality(); FrameLoadedMessage message(*this, frameIndex, payload.GetQuality(), image, instance, parameters, payload.GetUserPayload()); BroadcastMessage(message); } #if ORTHANC_ENABLE_DCMTK == 1 void SeriesFramesLoader::HandleDicom(const Payload& payload, const Orthanc::ParsedDicomFile& dicom) { size_t frameIndex = frames_.GetFrameIndex(payload.GetSeriesIndex()); std::unique_ptr<Orthanc::ImageAccessor> decoded; decoded.reset(dicom.DecodeFrame(static_cast<unsigned int>(frameIndex))); if (decoded.get() == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); } EmitMessage(payload, *decoded); } #endif void SeriesFramesLoader::HandleDicomWebRendered(const Payload& payload, const std::string& body, const std::map<std::string, std::string>& headers) { assert(payload.GetSource().IsDicomWeb() && payload.HasWindowing()); bool ok = false; for (std::map<std::string, std::string>::const_iterator it = headers.begin(); it != headers.end(); ++it) { if (boost::iequals("content-type", it->first) && boost::iequals(Orthanc::MIME_JPEG, it->second)) { ok = true; break; } } if (!ok) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol, "The WADO-RS server has not generated a JPEG image on /rendered"); } Orthanc::JpegReader reader; reader.ReadFromMemory(body); switch (reader.GetFormat()) { case Orthanc::PixelFormat_RGB24: EmitMessage(payload, reader); break; case Orthanc::PixelFormat_Grayscale8: { const DicomInstanceParameters& parameters = frames_.GetInstanceParameters(payload.GetSeriesIndex()); Orthanc::Image scaled(parameters.GetExpectedPixelFormat(), reader.GetWidth(), reader.GetHeight(), false); Orthanc::ImageProcessing::Convert(scaled, reader); float w = static_cast<float>(payload.GetWindowing().GetWidth()); if (w <= 0.01f) { w = 0.01f; // Prevent division by zero } const float c = static_cast<float>(payload.GetWindowing().GetCenter()); const float scaling = w / 255.0f; const float offset = (c - w / 2.0f) / scaling; Orthanc::ImageProcessing::ShiftScale(scaled, offset, scaling, false /* truncation to speed up */); EmitMessage(payload, scaled); break; } default: throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } } #if ORTHANC_ENABLE_DCMTK == 1 void SeriesFramesLoader::Handle(const ParseDicomSuccessMessage& message) { assert(message.GetOrigin().HasPayload()); const Payload& payload = dynamic_cast<const Payload&>(message.GetOrigin().GetPayload()); if ((payload.GetSource().IsDicomDir() || payload.GetSource().IsDicomWeb()) && message.HasPixelData()) { HandleDicom(dynamic_cast<const Payload&>(message.GetOrigin().GetPayload()), message.GetDicom()); } else { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } } #endif void SeriesFramesLoader::Handle(const GetOrthancImageCommand::SuccessMessage& message) { assert(message.GetOrigin().HasPayload()); const Payload& payload = dynamic_cast<const Payload&>(message.GetOrigin().GetPayload()); assert(payload.GetSource().IsOrthanc()); EmitMessage(payload, message.GetImage()); } void SeriesFramesLoader::Handle(const GetOrthancWebViewerJpegCommand::SuccessMessage& message) { assert(message.GetOrigin().HasPayload()); const Payload& payload = dynamic_cast<const Payload&>(message.GetOrigin().GetPayload()); assert(payload.GetSource().IsOrthanc()); EmitMessage(payload, message.GetImage()); } void SeriesFramesLoader::Handle(const OrthancRestApiCommand::SuccessMessage& message) { // This is to handle "/rendered" in DICOMweb assert(message.GetOrigin().HasPayload()); HandleDicomWebRendered(dynamic_cast<const Payload&>(message.GetOrigin().GetPayload()), message.GetAnswer(), message.GetAnswerHeaders()); } void SeriesFramesLoader::Handle(const HttpCommand::SuccessMessage& message) { // This is to handle "/rendered" in DICOMweb assert(message.GetOrigin().HasPayload()); HandleDicomWebRendered(dynamic_cast<const Payload&>(message.GetOrigin().GetPayload()), message.GetAnswer(), message.GetAnswerHeaders()); } Orthanc::IDynamicObject& SeriesFramesLoader::FrameLoadedMessage::GetUserPayload() const { if (userPayload_) { return *userPayload_; } else { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); } } void SeriesFramesLoader::Factory::SetDicomDir(const std::string& dicomDirPath, boost::shared_ptr<LoadedDicomResources> dicomDir) { dicomDirPath_ = dicomDirPath; dicomDir_ = dicomDir; } boost::shared_ptr<IObserver> SeriesFramesLoader::Factory::Create(ILoadersContext::ILock& stone) { boost::shared_ptr<SeriesFramesLoader> loader( new SeriesFramesLoader(stone.GetContext(), instances_, dicomDirPath_, dicomDir_)); loader->Register<GetOrthancImageCommand::SuccessMessage>(stone.GetOracleObservable(), &SeriesFramesLoader::Handle); loader->Register<GetOrthancWebViewerJpegCommand::SuccessMessage>(stone.GetOracleObservable(), &SeriesFramesLoader::Handle); loader->Register<HttpCommand::SuccessMessage>(stone.GetOracleObservable(), &SeriesFramesLoader::Handle); loader->Register<OrthancRestApiCommand::SuccessMessage>(stone.GetOracleObservable(), &SeriesFramesLoader::Handle); #if ORTHANC_ENABLE_DCMTK == 1 loader->Register<ParseDicomSuccessMessage>(stone.GetOracleObservable(), &SeriesFramesLoader::Handle); #endif return loader; } void SeriesFramesLoader::ScheduleLoadFrame(int priority, const DicomSource& source, size_t index, unsigned int quality, Orthanc::IDynamicObject* userPayload) { std::unique_ptr<Orthanc::IDynamicObject> protection(userPayload); if (index >= frames_.GetFramesCount() || quality >= source.GetQualityCount()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); } const Orthanc::DicomMap& instance = frames_.GetInstance(index); std::string sopInstanceUid; if (!instance.LookupStringValue(sopInstanceUid, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false)) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "Missing SOPInstanceUID in a DICOM instance"); } if (source.IsDicomDir()) { if (dicomDir_.get() == NULL) { // Should have been set in the factory throw Orthanc::OrthancException( Orthanc::ErrorCode_BadSequenceOfCalls, "SeriesFramesLoader::Factory::SetDicomDir() should have been called"); } assert(quality == 0); std::string file; if (dicomDir_->LookupStringValue(file, sopInstanceUid, Orthanc::DICOM_TAG_REFERENCED_FILE_ID)) { std::unique_ptr<ParseDicomFromFileCommand> command(new ParseDicomFromFileCommand(source, dicomDirPath_, file)); command->SetPixelDataIncluded(true); command->AcquirePayload(new Payload(source, index, sopInstanceUid, quality, protection.release())); { std::unique_ptr<ILoadersContext::ILock> lock(context_.Lock()); lock->Schedule(GetSharedObserver(), priority, command.release()); } } else { LOG(WARNING) << "Missing tag ReferencedFileID in a DICOMDIR entry"; } } else if (source.IsDicomWeb()) { std::string studyInstanceUid, seriesInstanceUid; if (!instance.LookupStringValue(studyInstanceUid, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) || !instance.LookupStringValue(seriesInstanceUid, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "Missing StudyInstanceUID or SeriesInstanceUID in a DICOM instance"); } const std::string uri = ("/studies/" + studyInstanceUid + "/series/" + seriesInstanceUid + "/instances/" + sopInstanceUid); if (source.HasDicomWebRendered() && quality == 0) { const DicomInstanceParameters& parameters = frames_.GetInstanceParameters(index); Windowing windowing = parameters.GetWindowingPresetsUnion(); std::map<std::string, std::string> arguments, headers; arguments["window"] = (boost::lexical_cast<std::string>(windowing.GetCenter()) + "," + boost::lexical_cast<std::string>(windowing.GetWidth()) + ",linear"); headers["Accept"] = "image/jpeg"; std::unique_ptr<Payload> payload(new Payload(source, index, sopInstanceUid, quality, protection.release())); payload->SetWindowing(windowing); { std::unique_ptr<ILoadersContext::ILock> lock(context_.Lock()); lock->Schedule(GetSharedObserver(), priority, source.CreateDicomWebCommand(uri + "/rendered", arguments, headers, payload.release())); } } else { assert((source.HasDicomWebRendered() && quality == 1) || (!source.HasDicomWebRendered() && quality == 0)); #if ORTHANC_ENABLE_DCMTK == 1 std::unique_ptr<Payload> payload(new Payload(source, index, sopInstanceUid, quality, protection.release())); const std::map<std::string, std::string> empty; std::unique_ptr<ParseDicomFromWadoCommand> command( new ParseDicomFromWadoCommand(source, sopInstanceUid, false /* no server-side transcoding */, Orthanc::DicomTransferSyntax_LittleEndianExplicit /* dummy value */, source.CreateDicomWebCommand(uri, empty, empty, NULL))); command->AcquirePayload(payload.release()); { std::unique_ptr<ILoadersContext::ILock> lock(context_.Lock()); lock->Schedule(GetSharedObserver(), priority, command.release()); } #else throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "DCMTK is not enabled, cannot parse a DICOM instance"); #endif } } else if (source.IsOrthanc()) { std::string orthancId; { std::string patientId, studyInstanceUid, seriesInstanceUid; if (!instance.LookupStringValue(patientId, Orthanc::DICOM_TAG_PATIENT_ID, false) || !instance.LookupStringValue(studyInstanceUid, Orthanc::DICOM_TAG_STUDY_INSTANCE_UID, false) || !instance.LookupStringValue(seriesInstanceUid, Orthanc::DICOM_TAG_SERIES_INSTANCE_UID, false)) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "Missing StudyInstanceUID or SeriesInstanceUID in a DICOM instance"); } Orthanc::DicomInstanceHasher hasher(patientId, studyInstanceUid, seriesInstanceUid, sopInstanceUid); orthancId = hasher.HashInstance(); } const DicomInstanceParameters& parameters = frames_.GetInstanceParameters(index); if (quality == 0 && source.HasOrthancWebViewer1()) { std::unique_ptr<GetOrthancWebViewerJpegCommand> command(new GetOrthancWebViewerJpegCommand); command->SetInstance(orthancId); command->SetExpectedPixelFormat(parameters.GetExpectedPixelFormat()); command->AcquirePayload(new Payload(source, index, sopInstanceUid, quality, protection.release())); { std::unique_ptr<ILoadersContext::ILock> lock(context_.Lock()); lock->Schedule(GetSharedObserver(), priority, command.release()); } } else if (quality == 0 && source.HasOrthancAdvancedPreview()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } else { assert(quality <= 1); assert(quality == 0 || source.HasOrthancWebViewer1() || source.HasOrthancAdvancedPreview()); std::unique_ptr<GetOrthancImageCommand> command(new GetOrthancImageCommand); command->SetFrameUri(orthancId, frames_.GetFrameIndex(index), parameters.GetExpectedPixelFormat()); command->SetExpectedPixelFormat(parameters.GetExpectedPixelFormat()); command->SetHttpHeader("Accept", Orthanc::MIME_PAM); command->AcquirePayload(new Payload(source, index, sopInstanceUid, quality, protection.release())); { std::unique_ptr<ILoadersContext::ILock> lock(context_.Lock()); lock->Schedule(GetSharedObserver(), priority, command.release()); } } } else { throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } } }