Mercurial > hg > orthanc-stone
view OrthancStone/Sources/Loaders/OrthancMultiframeVolumeLoader.cpp @ 1543:4cfdaf4ef3fe
fixing paths
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 11 Aug 2020 14:08:51 +0200 |
parents | 244ad1e4e76a |
children | 85e117739eca |
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/** * 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 "OrthancMultiframeVolumeLoader.h" #include <Endianness.h> #include <Toolbox.h> namespace OrthancStone { class OrthancMultiframeVolumeLoader::LoadRTDoseGeometry : public LoaderStateMachine::State { private: std::unique_ptr<Orthanc::DicomMap> dicom_; public: LoadRTDoseGeometry(OrthancMultiframeVolumeLoader& that, Orthanc::DicomMap* dicom) : State(that), dicom_(dicom) { if (dicom == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); } } virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message) { // 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); GetLoader<OrthancMultiframeVolumeLoader>().SetGeometry(*dicom_); } }; static std::string GetSopClassUid(const Orthanc::DicomMap& dicom) { std::string s; if (!dicom.LookupStringValue(s, Orthanc::DICOM_TAG_SOP_CLASS_UID, false)) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "DICOM file without SOP class UID"); } else { return s; } } class OrthancMultiframeVolumeLoader::LoadGeometry : public State { public: LoadGeometry(OrthancMultiframeVolumeLoader& that) : State(that) { } virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message) { OrthancMultiframeVolumeLoader& loader = GetLoader<OrthancMultiframeVolumeLoader>(); Json::Value body; message.ParseJsonBody(body); if (body.type() != Json::objectValue) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol); } std::unique_ptr<Orthanc::DicomMap> dicom(new Orthanc::DicomMap); dicom->FromDicomAsJson(body); if (OrthancStone::StringToSopClassUid(GetSopClassUid(*dicom)) == OrthancStone::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::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); command->SetUri("/instances/" + loader.GetInstanceId() + "/content/" + Orthanc::DICOM_TAG_GRID_FRAME_OFFSET_VECTOR.Format()); command->AcquirePayload(new LoadRTDoseGeometry(loader, dicom.release())); Schedule(command.release()); } else { loader.SetGeometry(*dicom); } } }; class OrthancMultiframeVolumeLoader::LoadTransferSyntax : public State { public: LoadTransferSyntax(OrthancMultiframeVolumeLoader& that) : State(that) { } virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message) { GetLoader<OrthancMultiframeVolumeLoader>().SetTransferSyntax(message.GetAnswer()); } }; class OrthancMultiframeVolumeLoader::LoadUncompressedPixelData : public State { public: LoadUncompressedPixelData(OrthancMultiframeVolumeLoader& that) : State(that) { } virtual void Handle(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message) { GetLoader<OrthancMultiframeVolumeLoader>().SetUncompressedPixelData(message.GetAnswer()); } }; const std::string& OrthancMultiframeVolumeLoader::GetInstanceId() const { if (IsActive()) { return instanceId_; } else { LOG(ERROR) << "OrthancMultiframeVolumeLoader::GetInstanceId(): (!IsActive())"; throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); } } void OrthancMultiframeVolumeLoader::ScheduleFrameDownloads() { if (transferSyntaxUid_.empty() || !volume_->HasGeometry()) { return; } /* 1.2.840.10008.1.2 Implicit VR Endian: Default Transfer Syntax for DICOM 1.2.840.10008.1.2.1 Explicit VR Little Endian 1.2.840.10008.1.2.2 Explicit VR Big Endian See https://www.dicomlibrary.com/dicom/transfer-syntax/ */ if (transferSyntaxUid_ == "1.2.840.10008.1.2" || transferSyntaxUid_ == "1.2.840.10008.1.2.1" || transferSyntaxUid_ == "1.2.840.10008.1.2.2") { std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); command->SetHttpHeader("Accept-Encoding", "gzip"); command->SetUri("/instances/" + instanceId_ + "/content/" + Orthanc::DICOM_TAG_PIXEL_DATA.Format() + "/0"); command->AcquirePayload(new LoadUncompressedPixelData(*this)); Schedule(command.release()); } else { throw Orthanc::OrthancException( Orthanc::ErrorCode_NotImplemented, "No support for multiframe instances with transfer syntax: " + transferSyntaxUid_); } } void OrthancMultiframeVolumeLoader::SetTransferSyntax(const std::string& transferSyntax) { transferSyntaxUid_ = Orthanc::Toolbox::StripSpaces(transferSyntax); ScheduleFrameDownloads(); } void OrthancMultiframeVolumeLoader::SetGeometry(const Orthanc::DicomMap& dicom) { OrthancStone::DicomInstanceParameters parameters(dicom); volume_->SetDicomParameters(parameters); Orthanc::PixelFormat format; if (!parameters.GetImageInformation().ExtractPixelFormat(format, true)) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } double spacingZ; switch (parameters.GetSopClassUid()) { case OrthancStone::SopClassUid_RTDose: spacingZ = parameters.GetThickness(); break; default: throw Orthanc::OrthancException( Orthanc::ErrorCode_NotImplemented, "No support for multiframe instances with SOP class UID: " + GetSopClassUid(dicom)); } const unsigned int width = parameters.GetImageInformation().GetWidth(); const unsigned int height = parameters.GetImageInformation().GetHeight(); const unsigned int depth = parameters.GetImageInformation().GetNumberOfFrames(); { OrthancStone::VolumeImageGeometry geometry; geometry.SetSizeInVoxels(width, height, depth); geometry.SetAxialGeometry(parameters.GetGeometry()); geometry.SetVoxelDimensions(parameters.GetPixelSpacingX(), parameters.GetPixelSpacingY(), spacingZ); volume_->Initialize(geometry, format, true /* Do compute range */); } volume_->GetPixelData().Clear(); ScheduleFrameDownloads(); BroadcastMessage(OrthancStone::DicomVolumeImage::GeometryReadyMessage(*volume_)); } ORTHANC_FORCE_INLINE static void CopyPixel(uint32_t& target, const void* source) { // TODO - check alignement? target = le32toh(*reinterpret_cast<const uint32_t*>(source)); } ORTHANC_FORCE_INLINE static void CopyPixel(uint16_t& target, const void* source) { // TODO - check alignement? target = le16toh(*reinterpret_cast<const uint16_t*>(source)); } ORTHANC_FORCE_INLINE static void CopyPixel(int16_t& target, const void* source) { // byte swapping is the same for unsigned and signed integers // (the sign bit is always stored with the MSByte) uint16_t* targetUp = reinterpret_cast<uint16_t*>(&target); CopyPixel(*targetUp, source); } template <typename T> void OrthancMultiframeVolumeLoader::CopyPixelDataAndComputeDistribution( const std::string& pixelData, std::map<T,uint64_t>& distribution) { OrthancStone::ImageBuffer3D& target = volume_->GetPixelData(); const unsigned int bpp = target.GetBytesPerPixel(); const unsigned int width = target.GetWidth(); const unsigned int height = target.GetHeight(); const unsigned int depth = target.GetDepth(); if (pixelData.size() != bpp * width * height * depth) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat, "The pixel data has not the proper size"); } if (pixelData.empty()) { return; } // first pass to initialize map { const uint8_t* source = reinterpret_cast<const uint8_t*>(pixelData.c_str()); for (unsigned int z = 0; z < depth; z++) { for (unsigned int y = 0; y < height; y++) { for (unsigned int x = 0; x < width; x++) { T value; CopyPixel(value, source); distribution[value] = 0; source += bpp; } } } } { const uint8_t* source = reinterpret_cast<const uint8_t*>(pixelData.c_str()); for (unsigned int z = 0; z < depth; z++) { OrthancStone::ImageBuffer3D::SliceWriter writer(target, OrthancStone::VolumeProjection_Axial, z); assert(writer.GetAccessor().GetWidth() == width && writer.GetAccessor().GetHeight() == height); #if 0 for (unsigned int y = 0; y < height; y++) { assert(sizeof(T) == Orthanc::GetBytesPerPixel(target.GetFormat())); T* target = reinterpret_cast<T*>(writer.GetAccessor().GetRow(y)); for (unsigned int x = 0; x < width; x++) { CopyPixel(*target, source); distribution[*target] += 1; target++; source += bpp; } } #else // optimized version (fixed) as of 2020-04-15 unsigned int pitch = writer.GetAccessor().GetPitch(); T* targetAddrLine = reinterpret_cast<T*>(writer.GetAccessor().GetRow(0)); assert(sizeof(T) == Orthanc::GetBytesPerPixel(target.GetFormat())); for (unsigned int y = 0; y < height; y++) { T* targetAddrPix = targetAddrLine; for (unsigned int x = 0; x < width; x++) { CopyPixel(*targetAddrPix, source); distribution[*targetAddrPix] += 1; targetAddrPix++; source += bpp; } uint8_t* targetAddrLineBytes = reinterpret_cast<uint8_t*>(targetAddrLine) + pitch; targetAddrLine = reinterpret_cast<T*>(targetAddrLineBytes); } #endif } } } template <typename T> void OrthancMultiframeVolumeLoader::ComputeMinMaxWithOutlierRejection( const std::map<T, uint64_t>& distribution) { if (distribution.size() == 0) { LOG(ERROR) << "ComputeMinMaxWithOutlierRejection -- Volume image empty."; } else { OrthancStone::ImageBuffer3D& target = volume_->GetPixelData(); const uint64_t width = target.GetWidth(); const uint64_t height = target.GetHeight(); const uint64_t depth = target.GetDepth(); const uint64_t voxelCount = width * height * depth; // now that we have distribution[pixelValue] == numberOfPixelsWithValue // compute number of values and check (assertion) that it is equal to // width * height * depth { typename std::map<T, uint64_t>::const_iterator it = distribution.begin(); uint64_t totalCount = 0; distributionRawMin_ = static_cast<float>(it->first); while (it != distribution.end()) { T pixelValue = it->first; uint64_t count = it->second; totalCount += count; it++; if (it == distribution.end()) distributionRawMax_ = static_cast<float>(pixelValue); } LOG(INFO) << "Volume image. First distribution value = " << static_cast<float>(distributionRawMin_) << " | Last distribution value = " << static_cast<float>(distributionRawMax_); if (totalCount != voxelCount) { LOG(ERROR) << "Internal error in dose distribution computation. TC (" << totalCount << ") != VoxC (" << voxelCount; throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } } // compute the number of voxels to reject at each end of the distribution uint64_t endRejectionCount = static_cast<uint64_t>( outliersHalfRejectionRate_ * voxelCount); if (endRejectionCount > voxelCount) { LOG(ERROR) << "Internal error in dose distribution computation." << " endRejectionCount = " << endRejectionCount << " | voxelCount = " << voxelCount; throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } // this will contain the actual distribution minimum after outlier // rejection T resultMin = 0; // then start from start and remove pixel values up to // endRejectionCount voxels rejected { typename std::map<T, uint64_t>::const_iterator it = distribution.begin(); uint64_t currentCount = 0; while (it != distribution.end()) { T pixelValue = it->first; uint64_t count = it->second; // if this pixelValue crosses the rejection threshold, let's set it // and exit the loop if ((currentCount <= endRejectionCount) && (currentCount + count > endRejectionCount)) { resultMin = pixelValue; break; } else { currentCount += count; } // and continue walking along the distribution it++; } } // this will contain the actual distribution maximum after outlier // rejection T resultMax = 0; // now start from END and remove pixel values up to // endRejectionCount voxels rejected { typename std::map<T, uint64_t>::const_reverse_iterator it = distribution.rbegin(); uint64_t currentCount = 0; while (it != distribution.rend()) { T pixelValue = it->first; uint64_t count = it->second; if ((currentCount <= endRejectionCount) && (currentCount + count > endRejectionCount)) { resultMax = pixelValue; break; } else { currentCount += count; } // and continue walking along the distribution it++; } } if (resultMin > resultMax) { LOG(ERROR) << "Internal error in dose distribution computation! " << "resultMin (" << resultMin << ") > resultMax (" << resultMax << ")"; throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } computedDistributionMin_ = static_cast<float>(resultMin); computedDistributionMax_ = static_cast<float>(resultMax); } } template <typename T> void OrthancMultiframeVolumeLoader::CopyPixelDataAndComputeMinMax( const std::string& pixelData) { std::map<T, uint64_t> distribution; CopyPixelDataAndComputeDistribution(pixelData, distribution); ComputeMinMaxWithOutlierRejection(distribution); } void OrthancMultiframeVolumeLoader::SetUncompressedPixelData(const std::string& pixelData) { switch (volume_->GetPixelData().GetFormat()) { case Orthanc::PixelFormat_Grayscale32: CopyPixelDataAndComputeMinMax<uint32_t>(pixelData); break; case Orthanc::PixelFormat_Grayscale16: CopyPixelDataAndComputeMinMax<uint16_t>(pixelData); break; case Orthanc::PixelFormat_SignedGrayscale16: CopyPixelDataAndComputeMinMax<int16_t>(pixelData); break; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } volume_->IncrementRevision(); pixelDataLoaded_ = true; BroadcastMessage(OrthancStone::DicomVolumeImage::ContentUpdatedMessage(*volume_)); } bool OrthancMultiframeVolumeLoader::HasGeometry() const { return volume_->HasGeometry(); } const OrthancStone::VolumeImageGeometry& OrthancMultiframeVolumeLoader::GetImageGeometry() const { return volume_->GetGeometry(); } OrthancMultiframeVolumeLoader::OrthancMultiframeVolumeLoader( OrthancStone::ILoadersContext& loadersContext, boost::shared_ptr<OrthancStone::DicomVolumeImage> volume, float outliersHalfRejectionRate) : LoaderStateMachine(loadersContext) , volume_(volume) , pixelDataLoaded_(false) , outliersHalfRejectionRate_(outliersHalfRejectionRate) , distributionRawMin_(0) , distributionRawMax_(0) , computedDistributionMin_(0) , computedDistributionMax_(0) { if (volume.get() == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); } } boost::shared_ptr<OrthancMultiframeVolumeLoader> OrthancMultiframeVolumeLoader::Create( OrthancStone::ILoadersContext& loadersContext, boost::shared_ptr<OrthancStone::DicomVolumeImage> volume, float outliersHalfRejectionRate /*= 0.0005*/) { boost::shared_ptr<OrthancMultiframeVolumeLoader> obj( new OrthancMultiframeVolumeLoader( loadersContext, volume, outliersHalfRejectionRate)); obj->LoaderStateMachine::PostConstructor(); return obj; } OrthancMultiframeVolumeLoader::~OrthancMultiframeVolumeLoader() { LOG(TRACE) << "OrthancMultiframeVolumeLoader::~OrthancMultiframeVolumeLoader()"; } void OrthancMultiframeVolumeLoader::GetDistributionMinMax (float& minValue, float& maxValue) const { if (distributionRawMin_ == 0 && distributionRawMax_ == 0) { LOG(WARNING) << "GetDistributionMinMaxWithOutliersRejection called before computation!"; } minValue = distributionRawMin_; maxValue = distributionRawMax_; } void OrthancMultiframeVolumeLoader::GetDistributionMinMaxWithOutliersRejection (float& minValue, float& maxValue) const { if (computedDistributionMin_ == 0 && computedDistributionMax_ == 0) { LOG(WARNING) << "GetDistributionMinMaxWithOutliersRejection called before computation!"; } minValue = computedDistributionMin_; maxValue = computedDistributionMax_; } void OrthancMultiframeVolumeLoader::LoadInstance(const std::string& instanceId) { Start(); instanceId_ = instanceId; { std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); command->SetHttpHeader("Accept-Encoding", "gzip"); command->SetUri("/instances/" + instanceId + "/tags"); command->AcquirePayload(new LoadGeometry(*this)); Schedule(command.release()); } { std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand); command->SetUri("/instances/" + instanceId + "/metadata/TransferSyntax"); command->AcquirePayload(new LoadTransferSyntax(*this)); Schedule(command.release()); } } }