Mercurial > hg > orthanc-stone
changeset 762:26f4345e771e
creation of OrthancMultiframeVolumeLoader
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Thu, 23 May 2019 11:27:11 +0200 |
parents | 1181e1ad98ec |
children | 53167294d870 |
files | Framework/Toolbox/DicomInstanceParameters.cpp Samples/Sdl/Loader.cpp |
diffstat | 2 files changed, 261 insertions(+), 66 deletions(-) [+] |
line wrap: on
line diff
--- a/Framework/Toolbox/DicomInstanceParameters.cpp Wed May 22 18:34:06 2019 +0200 +++ b/Framework/Toolbox/DicomInstanceParameters.cpp Thu May 23 11:27:11 2019 +0200 @@ -62,12 +62,7 @@ { if (frameOffsets_.size() >= 2) { - thickness_ = frameOffsets_[1] - frameOffsets_[0]; - - if (thickness_ < 0) - { - thickness_ = -thickness_; - } + thickness_ = std::abs(frameOffsets_[1] - frameOffsets_[0]); } } }
--- a/Samples/Sdl/Loader.cpp Wed May 22 18:34:06 2019 +0200 +++ b/Samples/Sdl/Loader.cpp Thu May 23 11:27:11 2019 +0200 @@ -39,12 +39,14 @@ #include "../../Framework/Volumes/VolumeImageGeometry.h" // From Orthanc framework +#include <Core/DicomFormat/DicomArray.h> #include <Core/Images/Image.h> #include <Core/Images/ImageProcessing.h> #include <Core/Images/PngWriter.h> #include <Core/Logging.h> #include <Core/OrthancException.h> #include <Core/SystemToolbox.h> +#include <Core/Toolbox.h> namespace OrthancStone @@ -193,7 +195,7 @@ class DicomSeriesVolumeImage : public boost::noncopyable { public: - class ExtractedSlice : public DicomVolumeImageOrthogonalSlice + class ExtractedOrthogonalSlice : public DicomVolumeImageOrthogonalSlice { private: const DicomSeriesVolumeImage& that_; @@ -221,8 +223,8 @@ } public: - ExtractedSlice(const DicomSeriesVolumeImage& that, - const CoordinateSystem3D& plane) : + ExtractedOrthogonalSlice(const DicomSeriesVolumeImage& that, + const CoordinateSystem3D& plane) : DicomVolumeImageOrthogonalSlice(that.GetImage(), that.GetGeometry(), plane), that_(that) { @@ -478,8 +480,7 @@ class OrthancSeriesVolumeProgressiveLoader : - public IObserver, - public IVolumeSlicer + public IObserver { private: static const unsigned int LOW_QUALITY = 0; @@ -623,7 +624,55 @@ std::auto_ptr<IFetchingItemsSorter::IFactory> sorter_; std::auto_ptr<IFetchingStrategy> strategy_; + + IVolumeSlicer::ExtractedSlice* ExtractOrthogonalSlice(const CoordinateSystem3D& cuttingPlane) const + { + if (volume_.HasGeometry() && + volume_.GetSlicesCount() != 0) + { + std::auto_ptr<DicomVolumeImageOrthogonalSlice> slice + (new DicomSeriesVolumeImage::ExtractedOrthogonalSlice(volume_, cuttingPlane)); + + assert(slice.get() != NULL && + strategy_.get() != NULL); + + if (slice->GetProjection() == VolumeProjection_Axial) + { + strategy_->SetCurrent(slice->GetSliceIndex()); + } + + return slice.release(); + } + else + { + return new InvalidExtractedSlice; + } + } + + public: + class MPRSlicer : public IVolumeSlicer + { + private: + boost::shared_ptr<OrthancSeriesVolumeProgressiveLoader> that_; + + public: + MPRSlicer(const boost::shared_ptr<OrthancSeriesVolumeProgressiveLoader>& that) : + that_(that) + { + } + + virtual IVolumeSlicer::ExtractedSlice* ExtractSlice(const CoordinateSystem3D& cuttingPlane) const + { + return that_->ExtractOrthogonalSlice(cuttingPlane); + } + + const DicomSeriesVolumeImage& GetVolume() const + { + return that_->GetVolume(); + } + }; + OrthancSeriesVolumeProgressiveLoader(IOracle& oracle, IObservable& oracleObservable) : IObserver(oracleObservable.GetBroker()), @@ -683,64 +732,213 @@ { return volume_; } + }; + + + + class OrthancMultiframeVolumeLoader : public IObserver + { + private: + class Handler : public Orthanc::IDynamicObject + { + private: + OrthancMultiframeVolumeLoader& that_; + std::string instanceId_; + + protected: + void Schedule(OrthancRestApiCommand* command) const + { + that_.oracle_.Schedule(that_, command); + } + + const std::string& GetInstanceId() const + { + return instanceId_; + } + + OrthancMultiframeVolumeLoader& GetTarget() const + { + return that_; + } + + public: + Handler(OrthancMultiframeVolumeLoader& that, + const std::string& instanceId) : + that_(that), + instanceId_(instanceId) + { + } + + Handler(const Handler& previous) : + that_(previous.that_), + instanceId_(previous.instanceId_) + { + } + + virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) const = 0; + }; + + void Handle(const OrthancRestApiCommand::SuccessMessage& message) + { + dynamic_cast<const Handler&>(message.GetOrigin().GetPayload()).Handle(message); + } - virtual IVolumeSlicer::ExtractedSlice* ExtractSlice(const CoordinateSystem3D& cuttingPlane) const + class LoadRTDoseGeometry : public Handler { - if (volume_.HasGeometry() && - volume_.GetSlicesCount() != 0) + private: + std::auto_ptr<Orthanc::DicomMap> dicom_; + + public: + LoadRTDoseGeometry(const Handler& previous, + Orthanc::DicomMap* dicom) : + Handler(previous), + dicom_(dicom) + { + if (dicom == NULL) + { + throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); + } + } + + virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) const { - std::auto_ptr<DicomVolumeImageOrthogonalSlice> slice - (new DicomSeriesVolumeImage::ExtractedSlice(volume_, cuttingPlane)); + // Complete the DICOM tags with just-received "Grid Frame Offset Vector" + std::string s = Orthanc::Toolbox::StripSpaces(message.GetAnswer()); + dicom_->SetValue(Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR, s, false); + + GetTarget().SetGeometry(*dicom_); + } + }; + - assert(slice.get() != NULL && - strategy_.get() != NULL); + class LoadGeometry : public Handler + { + public: + LoadGeometry(OrthancMultiframeVolumeLoader& that, + const std::string& instanceId) : + Handler(that, instanceId) + { + } + + virtual void Handle(const OrthancRestApiCommand::SuccessMessage& message) const + { + Json::Value body; + message.ParseJsonBody(body); + + if (body.type() != Json::objectValue) + { + throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); + } - if (slice->GetProjection() == VolumeProjection_Axial) + std::auto_ptr<Orthanc::DicomMap> dicom(new Orthanc::DicomMap); + dicom->FromDicomAsJson(body); + + std::string s; + if (!dicom->CopyToString(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false)) { - strategy_->SetCurrent(slice->GetSliceIndex()); + throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, + "DICOM file without SOP class UID"); } - return slice.release(); + if (StringToSopClassUid(s) == SopClassUid_RTDose) + { + // Download the "Grid Frame Offset Vector" DICOM tag, that is + // mandatory for RT-DOSE, but is too long to be returned by default + + std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); + command->SetUri("/instances/" + GetInstanceId() + "/content/" + + Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR.Format()); + command->SetPayload(new LoadRTDoseGeometry(*this, dicom.release())); + + Schedule(command.release()); + } + else + { + GetTarget().SetGeometry(*dicom); + } + } + }; + + + + IOracle& oracle_; + bool active_; + + std::auto_ptr<ImageBuffer3D> image_; + std::auto_ptr<DicomInstanceParameters> dicom_; + std::auto_ptr<VolumeImageGeometry> geometry_; + + + void SetGeometry(const Orthanc::DicomMap& dicom) + { + dicom_.reset(new DicomInstanceParameters(dicom)); + + Orthanc::PixelFormat format; + if (!dicom_->GetImageInformation().ExtractPixelFormat(format, true)) + { + throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); + } + + const unsigned int width = dicom_->GetImageInformation().GetWidth(); + const unsigned int height = dicom_->GetImageInformation().GetHeight(); + const unsigned int depth = dicom_->GetImageInformation().GetNumberOfFrames(); + + geometry_.reset(new VolumeImageGeometry); + geometry_->SetSize(width, height, depth); + geometry_->SetAxialGeometry(dicom_->GetGeometry()); + geometry_->SetVoxelDimensions(dicom_->GetPixelSpacingX(), + dicom_->GetPixelSpacingY(), + dicom_->GetThickness()); + + image_.reset(new ImageBuffer3D(format, width, height, depth, + false /* don't compute range */)); + + { + Orthanc::DicomArray a(dicom); + a.Print(stdout); + } + } + + + public: + OrthancMultiframeVolumeLoader(IOracle& oracle, + IObservable& oracleObservable) : + IObserver(oracleObservable.GetBroker()), + oracle_(oracle), + active_(false) + { + oracleObservable.RegisterObserverCallback( + new Callable<OrthancMultiframeVolumeLoader, OrthancRestApiCommand::SuccessMessage> + (*this, &OrthancMultiframeVolumeLoader::Handle)); + } + + void LoadInstance(const std::string& instanceId) + { + if (active_) + { + throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); } else { - return new InvalidExtractedSlice; + active_ = true; + + std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); + command->SetUri("/instances/" + instanceId + "/tags"); + command->SetPayload(new LoadGeometry(*this, instanceId)); + + oracle_.Schedule(*this, command.release()); } } }; -#if 0 - void LoadInstance(const std::string& instanceId) - { - if (active_) - { - throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); - } - - active_ = true; - - // Tag "3004-000c" is "Grid Frame Offset Vector", which is - // mandatory to read RT DOSE, but is too long to be returned by default - - // TODO => Should be part of a second call if needed - - std::auto_ptr<OrthancRestApiCommand> command(new OrthancRestApiCommand); - command->SetUri("/instances/" + instanceId + "/tags?ignore-length=3004-000c"); - command->SetPayload(new LoadInstanceGeometryHandler(*this)); - - oracle_.Schedule(*this, command.release()); - } -#endif - - - class SceneVolumeSlicer : public boost::noncopyable + class VolumeSceneLayerSource : public boost::noncopyable { private: int layerDepth_; - std::auto_ptr<IVolumeSlicer> volume_; + boost::shared_ptr<IVolumeSlicer> slicer_; bool linearInterpolation_; std::auto_ptr<CoordinateSystem3D> lastPlane_; uint64_t lastRevision_; @@ -754,13 +952,13 @@ } public: - SceneVolumeSlicer(int layerDepth, - IVolumeSlicer* volume) : // Takes ownership + VolumeSceneLayerSource(int layerDepth, + IVolumeSlicer* slicer) : // Takes ownership layerDepth_(layerDepth), - volume_(volume), + slicer_(slicer), linearInterpolation_(false) { - if (volume == NULL) + if (slicer == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); } @@ -768,7 +966,7 @@ const IVolumeSlicer& GetSlicer() const { - return *volume_; + return *slicer_; } void SetLinearInterpolation(bool enabled) @@ -784,8 +982,8 @@ void Update(Scene2D& scene, const CoordinateSystem3D& plane) { - assert(volume_.get() != NULL); - std::auto_ptr<IVolumeSlicer::ExtractedSlice> slice(volume_->ExtractSlice(plane)); + assert(slicer_.get() != NULL); + std::auto_ptr<IVolumeSlicer::ExtractedSlice> slice(slicer_->ExtractSlice(plane)); if (slice.get() == NULL) { @@ -908,7 +1106,7 @@ private: OrthancStone::IOracle& oracle_; OrthancStone::Scene2D scene_; - std::auto_ptr<OrthancStone::SceneVolumeSlicer> slicer_; + std::auto_ptr<OrthancStone::VolumeSceneLayerSource> source_; void Handle(const OrthancStone::SleepOracleCommand::TimeoutMessage& message) { @@ -920,12 +1118,12 @@ { printf("TIMEOUT\n"); - if (slicer_.get() != NULL) + if (source_.get() != NULL) { OrthancStone::CoordinateSystem3D plane; - const OrthancStone::OrthancSeriesVolumeProgressiveLoader& loader = - dynamic_cast<const OrthancStone::OrthancSeriesVolumeProgressiveLoader&>(slicer_->GetSlicer()); + const OrthancStone::OrthancSeriesVolumeProgressiveLoader::MPRSlicer& loader = + dynamic_cast<const OrthancStone::OrthancSeriesVolumeProgressiveLoader::MPRSlicer&>(source_->GetSlicer()); if (loader.GetVolume().HasGeometry()) { @@ -933,7 +1131,7 @@ plane.SetOrigin(loader.GetVolume().GetGeometry().GetCoordinates(0.5f, 0.5f, 0.5f)); } - slicer_->Update(scene_, plane); + source_->Update(scene_, plane); scene_.FitContent(1024, 768); { @@ -1023,7 +1221,7 @@ void SetVolume(int depth, OrthancStone::IVolumeSlicer* volume) { - slicer_.reset(new OrthancStone::SceneVolumeSlicer(0, volume)); + source_.reset(new OrthancStone::VolumeSceneLayerSource(0, volume)); } }; @@ -1031,14 +1229,16 @@ void Run(OrthancStone::NativeApplicationContext& context, OrthancStone::IOracle& oracle) { - std::auto_ptr<Toto> toto; - std::auto_ptr<OrthancStone::OrthancSeriesVolumeProgressiveLoader> loader1, loader2; + boost::shared_ptr<Toto> toto; + boost::shared_ptr<OrthancStone::OrthancSeriesVolumeProgressiveLoader> loader1, loader2; + boost::shared_ptr<OrthancStone::OrthancMultiframeVolumeLoader> loader3; { OrthancStone::NativeApplicationContext::WriterLock lock(context); toto.reset(new Toto(oracle, lock.GetOracleObservable())); loader1.reset(new OrthancStone::OrthancSeriesVolumeProgressiveLoader(oracle, lock.GetOracleObservable())); loader2.reset(new OrthancStone::OrthancSeriesVolumeProgressiveLoader(oracle, lock.GetOracleObservable())); + loader3.reset(new OrthancStone::OrthancMultiframeVolumeLoader(oracle, lock.GetOracleObservable())); } oracle.Schedule(*toto, new OrthancStone::SleepOracleCommand(100)); @@ -1120,14 +1320,14 @@ // 2017-11-17-Anonymized //loader1->LoadSeries("cb3ea4d1-d08f3856-ad7b6314-74d88d77-60b05618"); // CT - //loader2->LoadInstance("41029085-71718346-811efac4-420e2c15-d39f99b6"); // RT-DOSE + loader3->LoadInstance("41029085-71718346-811efac4-420e2c15-d39f99b6"); // RT-DOSE // Delphine //loader1->LoadSeries("5990e39c-51e5f201-fe87a54c-31a55943-e59ef80e"); // CT - loader1->LoadSeries("67f1b334-02c16752-45026e40-a5b60b6b-030ecab5"); // Lung 1/10mm + //loader1->LoadSeries("67f1b334-02c16752-45026e40-a5b60b6b-030ecab5"); // Lung 1/10mm - toto->SetVolume(0, loader1.release()); + toto->SetVolume(0, new OrthancStone::OrthancSeriesVolumeProgressiveLoader::MPRSlicer(loader1)); LOG(WARNING) << "...Waiting for Ctrl-C..."; Orthanc::SystemToolbox::ServerBarrier();