--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Framework/Loaders/OrthancSeriesVolumeProgressiveLoader.cpp	Fri Apr 03 16:13:06 2020 +0200
@@ -0,0 +1,577 @@
+/**
+ * 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 "OrthancSeriesVolumeProgressiveLoader.h"
+
+#include "../../StoneException.h"
+#include "../../Loaders/ILoadersContext.h"
+#include "../../Loaders/BasicFetchingItemsSorter.h"
+#include "../../Loaders/BasicFetchingStrategy.h"
+#include "../../Toolbox/GeometryToolbox.h"
+#include "../../Volumes/DicomVolumeImageMPRSlicer.h"
+
+#include <Core/Images/ImageProcessing.h>
+#include <Core/OrthancException.h>
+
+namespace OrthancStone
+{
+  using OrthancStone::ILoadersContext;
+
+  class OrthancSeriesVolumeProgressiveLoader::ExtractedSlice : public OrthancStone::DicomVolumeImageMPRSlicer::Slice
+  {
+  private:
+    const OrthancSeriesVolumeProgressiveLoader&  that_;
+
+  public:
+    ExtractedSlice(const OrthancSeriesVolumeProgressiveLoader& that,
+                   const OrthancStone::CoordinateSystem3D& plane) :
+      OrthancStone::DicomVolumeImageMPRSlicer::Slice(*that.volume_, plane),
+      that_(that)
+    {
+      if (IsValid())
+      {
+        if (GetProjection() == OrthancStone::VolumeProjection_Axial)
+        {
+          // For coronal and sagittal projections, we take the global
+          // revision of the volume because even if a single slice changes,
+          // this means the projection will yield a different result --> 
+          // we must increase the revision as soon as any slice changes 
+          SetRevision(that_.seriesGeometry_.GetSliceRevision(GetSliceIndex()));
+        }
+      
+        if (that_.strategy_.get() != NULL &&
+            GetProjection() == OrthancStone::VolumeProjection_Axial)
+        {
+          that_.strategy_->SetCurrent(GetSliceIndex());
+        }
+      }
+    }
+  };
+    
+  void OrthancSeriesVolumeProgressiveLoader::SeriesGeometry::CheckSlice(
+    size_t index, const OrthancStone::DicomInstanceParameters& reference) const
+  {
+    const OrthancStone::DicomInstanceParameters& slice = *slices_[index];
+      
+    if (!OrthancStone::GeometryToolbox::IsParallel(
+          reference.GetGeometry().GetNormal(),
+          slice.GetGeometry().GetNormal()))
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadGeometry,
+                                      "A slice in the volume image is not parallel to the others");
+    }
+
+    if (reference.GetExpectedPixelFormat() != slice.GetExpectedPixelFormat())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat,
+                                      "The pixel format changes across the slices of the volume image");
+    }
+
+    if (reference.GetImageInformation().GetWidth() != slice.GetImageInformation().GetWidth() ||
+        reference.GetImageInformation().GetHeight() != slice.GetImageInformation().GetHeight())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageSize,
+                                      "The width/height of slices are not constant in the volume image");
+    }
+
+    if (!OrthancStone::LinearAlgebra::IsNear(reference.GetPixelSpacingX(), slice.GetPixelSpacingX()) ||
+        !OrthancStone::LinearAlgebra::IsNear(reference.GetPixelSpacingY(), slice.GetPixelSpacingY()))
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadGeometry,
+                                      "The pixel spacing of the slices change across the volume image");
+    }
+  }
+
+    
+  void OrthancSeriesVolumeProgressiveLoader::SeriesGeometry::CheckVolume() const
+  {
+    for (size_t i = 0; i < slices_.size(); i++)
+    {
+      assert(slices_[i] != NULL);
+      if (slices_[i]->GetImageInformation().GetNumberOfFrames() != 1)
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_BadGeometry,
+                                        "This class does not support multi-frame images");
+      }
+    }
+
+    if (slices_.size() != 0)
+    {
+      const OrthancStone::DicomInstanceParameters& reference = *slices_[0];
+
+      for (size_t i = 1; i < slices_.size(); i++)
+      {
+        CheckSlice(i, reference);
+      }
+    }
+  }
+
+
+  void OrthancSeriesVolumeProgressiveLoader::SeriesGeometry::Clear()
+  {
+    for (size_t i = 0; i < slices_.size(); i++)
+    {
+      assert(slices_[i] != NULL);
+      delete slices_[i];
+    }
+
+    slices_.clear();
+    slicesRevision_.clear();
+  }
+
+
+  void OrthancSeriesVolumeProgressiveLoader::SeriesGeometry::CheckSliceIndex(size_t index) const
+  {
+    if (!HasGeometry())
+    {
+      LOG(ERROR) << "OrthancSeriesVolumeProgressiveLoader::SeriesGeometry::CheckSliceIndex(size_t index): (!HasGeometry())";
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+    else if (index >= slices_.size())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+    else
+    {
+      assert(slices_.size() == GetImageGeometry().GetDepth() &&
+             slices_.size() == slicesRevision_.size());
+    }
+  }
+
+
+  // WARNING: The payload of "slices" must be of class "DicomInstanceParameters"
+  // (called with the slices created in LoadGeometry)
+  void OrthancSeriesVolumeProgressiveLoader::SeriesGeometry::ComputeGeometry(OrthancStone::SlicesSorter& slices)
+  {
+    Clear();
+      
+    if (!slices.Sort())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange,
+                                      "Cannot sort the 3D slices of a DICOM series");          
+    }
+
+    if (slices.GetSlicesCount() == 0)
+    {
+      geometry_.reset(new OrthancStone::VolumeImageGeometry);
+    }
+    else
+    {
+      slices_.reserve(slices.GetSlicesCount());
+      slicesRevision_.resize(slices.GetSlicesCount(), 0);
+
+      for (size_t i = 0; i < slices.GetSlicesCount(); i++)
+      {
+        const OrthancStone::DicomInstanceParameters& slice =
+          dynamic_cast<const OrthancStone::DicomInstanceParameters&>(slices.GetSlicePayload(i));
+        slices_.push_back(new OrthancStone::DicomInstanceParameters(slice));
+      }
+
+      CheckVolume();
+
+      double spacingZ;
+
+      if (slices.ComputeSpacingBetweenSlices(spacingZ))
+      {
+        LOG(TRACE) << "Computed spacing between slices: " << spacingZ << "mm";
+      
+        const OrthancStone::DicomInstanceParameters& parameters = *slices_[0];
+
+        geometry_.reset(new OrthancStone::VolumeImageGeometry);
+        geometry_->SetSizeInVoxels(parameters.GetImageInformation().GetWidth(),
+                                   parameters.GetImageInformation().GetHeight(),
+                                   static_cast<unsigned int>(slices.GetSlicesCount()));
+        geometry_->SetAxialGeometry(slices.GetSliceGeometry(0));
+        geometry_->SetVoxelDimensions(parameters.GetPixelSpacingX(),
+                                      parameters.GetPixelSpacingY(), spacingZ);
+      }
+      else
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_BadGeometry,
+                                        "The origins of the slices of a volume image are not regularly spaced");
+     }
+    }
+  }
+
+
+  const OrthancStone::VolumeImageGeometry& OrthancSeriesVolumeProgressiveLoader::SeriesGeometry::GetImageGeometry() const
+  {
+    if (!HasGeometry())
+    {
+      LOG(ERROR) << "OrthancSeriesVolumeProgressiveLoader::SeriesGeometry::GetImageGeometry(): (!HasGeometry())";
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      assert(slices_.size() == geometry_->GetDepth());
+      return *geometry_;
+    }
+  }
+
+
+  const OrthancStone::DicomInstanceParameters& OrthancSeriesVolumeProgressiveLoader::SeriesGeometry::GetSliceParameters(size_t index) const
+  {
+    CheckSliceIndex(index);
+    return *slices_[index];
+  }
+
+
+  uint64_t OrthancSeriesVolumeProgressiveLoader::SeriesGeometry::GetSliceRevision(size_t index) const
+  {
+    CheckSliceIndex(index);
+    return slicesRevision_[index];
+  }
+
+
+  void OrthancSeriesVolumeProgressiveLoader::SeriesGeometry::IncrementSliceRevision(size_t index)
+  {
+    CheckSliceIndex(index);
+    slicesRevision_[index] ++;
+  }
+
+
+  static unsigned int GetSliceIndexPayload(const OrthancStone::OracleCommandBase& command)
+  {
+    assert(command.HasPayload());
+    return dynamic_cast< const Orthanc::SingleValueObject<unsigned int>& >(command.GetPayload()).GetValue();
+  }
+
+
+  void OrthancSeriesVolumeProgressiveLoader::ScheduleNextSliceDownload()
+  {
+    assert(strategy_.get() != NULL);
+      
+    unsigned int sliceIndex = 0, quality = 0;
+      
+    if (strategy_->GetNext(sliceIndex, quality))
+    {
+      if (!progressiveQuality_)
+      {
+        ORTHANC_ASSERT(quality == QUALITY_00, "INTERNAL ERROR. quality != QUALITY_00 in "
+                       << "OrthancSeriesVolumeProgressiveLoader::ScheduleNextSliceDownload");
+      }
+
+      const OrthancStone::DicomInstanceParameters& slice = seriesGeometry_.GetSliceParameters(sliceIndex);
+          
+      const std::string& instance = slice.GetOrthancInstanceIdentifier();
+      if (instance.empty())
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+      }
+
+      std::unique_ptr<OrthancStone::OracleCommandBase> command;
+        
+      if (!progressiveQuality_ || quality == QUALITY_02)
+      {
+        std::unique_ptr<OrthancStone::GetOrthancImageCommand> tmp(new OrthancStone::GetOrthancImageCommand);
+        // TODO: review the following comment. 
+        // - Commented out by bgo on 2019-07-19 | reason: Alain has seen cases 
+        //   where gzipping the uint16 image took 11 sec to produce 5mb. 
+        //   The unzipped request was much much faster.
+        // - Re-enabled on 2019-07-30. Reason: in Web Assembly, the browser 
+        //   does not use the Accept-Encoding header and always requests
+        //   compression. Furthermore, NOT 
+        tmp->SetHttpHeader("Accept-Encoding", "gzip");
+        tmp->SetHttpHeader("Accept", std::string(Orthanc::EnumerationToString(Orthanc::MimeType_Pam)));
+        tmp->SetInstanceUri(instance, slice.GetExpectedPixelFormat());
+        tmp->SetExpectedPixelFormat(slice.GetExpectedPixelFormat());
+        //LOG(INFO) 
+        //  << "OrthancSeriesVolumeProgressiveLoader.ScheduleNextSliceDownload()"
+        //  << " sliceIndex = " << sliceIndex << " slice quality = " << quality 
+        //  << " URI = " << tmp->GetUri();
+        command.reset(tmp.release());
+      }
+      else // progressive mode is true AND quality is not final (different from QUALITY_02
+      {
+        std::unique_ptr<OrthancStone::GetOrthancWebViewerJpegCommand> tmp(
+          new OrthancStone::GetOrthancWebViewerJpegCommand);
+
+        // TODO: review the following comment. Commented out by bgo on 2019-07-19
+        // (gzip for jpeg seems overkill)
+        //tmp->SetHttpHeader("Accept-Encoding", "gzip");
+        tmp->SetInstance(instance);
+        tmp->SetQuality((quality == 0 ? 50 : 90)); // QUALITY_00 is Jpeg50 while QUALITY_01 is Jpeg90
+        tmp->SetExpectedPixelFormat(slice.GetExpectedPixelFormat());
+        LOG(TRACE)
+          << "OrthancSeriesVolumeProgressiveLoader.ScheduleNextSliceDownload()"
+          << " sliceIndex = " << sliceIndex << " slice quality = " << quality;
+        command.reset(tmp.release());
+      }
+
+      command->AcquirePayload(new Orthanc::SingleValueObject<unsigned int>(sliceIndex));
+      
+      {
+        std::unique_ptr<OrthancStone::ILoadersContext::ILock> lock(loadersContext_.Lock());
+        boost::shared_ptr<IObserver> observer(GetSharedObserver());
+        lock->Schedule(observer, 0, command.release()); // TODO: priority!
+      }
+    }
+    else
+    {
+      // loading is finished!
+      volumeImageReadyInHighQuality_ = true;
+      BroadcastMessage(OrthancSeriesVolumeProgressiveLoader::VolumeImageReadyInHighQuality(*this));
+    }
+  }
+
+/**
+   This is called in response to GET "/series/XXXXXXXXXXXXX/instances-tags"
+*/
+  void OrthancSeriesVolumeProgressiveLoader::LoadGeometry(const OrthancStone::OrthancRestApiCommand::SuccessMessage& message)
+  {
+    Json::Value body;
+    message.ParseJsonBody(body);
+      
+    if (body.type() != Json::objectValue)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_NetworkProtocol);
+    }
+
+    {
+      Json::Value::Members instances = body.getMemberNames();
+
+      OrthancStone::SlicesSorter slices;
+        
+      for (size_t i = 0; i < instances.size(); i++)
+      {
+        Orthanc::DicomMap dicom;
+        dicom.FromDicomAsJson(body[instances[i]]);
+
+        std::unique_ptr<OrthancStone::DicomInstanceParameters> instance(new OrthancStone::DicomInstanceParameters(dicom));
+        instance->SetOrthancInstanceIdentifier(instances[i]);
+
+        // the 3D plane corresponding to the slice
+        OrthancStone::CoordinateSystem3D geometry = instance->GetGeometry();
+        slices.AddSlice(geometry, instance.release());
+      }
+
+      seriesGeometry_.ComputeGeometry(slices);
+    }
+
+    size_t slicesCount = seriesGeometry_.GetImageGeometry().GetDepth();
+
+    if (slicesCount == 0)
+    {
+      volume_->Initialize(seriesGeometry_.GetImageGeometry(), Orthanc::PixelFormat_Grayscale8);
+    }
+    else
+    {
+      const OrthancStone::DicomInstanceParameters& parameters = seriesGeometry_.GetSliceParameters(0);
+        
+      volume_->Initialize(seriesGeometry_.GetImageGeometry(), parameters.GetExpectedPixelFormat());
+      volume_->SetDicomParameters(parameters);
+      volume_->GetPixelData().Clear();
+
+      // If we are in progressive mode, the Fetching strategy will first request QUALITY_00, then QUALITY_01, then
+      // QUALITY_02... Otherwise, it's only QUALITY_00
+      unsigned int maxQuality = QUALITY_00;
+      if (progressiveQuality_)
+        maxQuality = QUALITY_02;
+
+      strategy_.reset(new OrthancStone::BasicFetchingStrategy(
+        sorter_->CreateSorter(static_cast<unsigned int>(slicesCount)),
+        maxQuality));
+
+      assert(simultaneousDownloads_ != 0);
+      for (unsigned int i = 0; i < simultaneousDownloads_; i++)
+      {
+        ScheduleNextSliceDownload();
+      }
+    }
+
+    slicesQuality_.resize(slicesCount, 0);
+
+    BroadcastMessage(OrthancStone::DicomVolumeImage::GeometryReadyMessage(*volume_));
+  }
+
+
+  void OrthancSeriesVolumeProgressiveLoader::SetSliceContent(unsigned int sliceIndex,
+                                                             const Orthanc::ImageAccessor& image,
+                                                             unsigned int quality)
+  {
+    ORTHANC_ASSERT(sliceIndex < slicesQuality_.size() &&
+           slicesQuality_.size() == volume_->GetPixelData().GetDepth());
+      
+    if (!progressiveQuality_)
+    {
+      ORTHANC_ASSERT(quality                    == QUALITY_00);
+      ORTHANC_ASSERT(slicesQuality_[sliceIndex] == QUALITY_00);
+    }
+
+    if (quality >= slicesQuality_[sliceIndex])
+    {
+      {
+        OrthancStone::ImageBuffer3D::SliceWriter writer(volume_->GetPixelData(), 
+                                                        OrthancStone::VolumeProjection_Axial, 
+                                                        sliceIndex);
+        
+        Orthanc::ImageProcessing::Copy(writer.GetAccessor(), image);
+      }
+
+      volume_->IncrementRevision();
+      seriesGeometry_.IncrementSliceRevision(sliceIndex);
+      slicesQuality_[sliceIndex] = quality;
+
+      BroadcastMessage(OrthancStone::DicomVolumeImage::ContentUpdatedMessage(*volume_));
+    }
+    LOG(TRACE) << "SetSliceContent sliceIndex = " << sliceIndex << " -- will "
+      << " now call ScheduleNextSliceDownload()";
+    ScheduleNextSliceDownload();
+  }
+
+  void OrthancSeriesVolumeProgressiveLoader::LoadBestQualitySliceContent(
+    const OrthancStone::GetOrthancImageCommand::SuccessMessage& message)
+  {
+    unsigned int quality = QUALITY_00;
+    if (progressiveQuality_)
+      quality = QUALITY_02;
+
+    SetSliceContent(GetSliceIndexPayload(message.GetOrigin()), 
+                                         message.GetImage(),
+                                         quality);
+  }
+
+  void OrthancSeriesVolumeProgressiveLoader::LoadJpegSliceContent(
+    const OrthancStone::GetOrthancWebViewerJpegCommand::SuccessMessage& message)
+  {
+    ORTHANC_ASSERT(progressiveQuality_, "INTERNAL ERROR: OrthancSeriesVolumeProgressiveLoader::LoadJpegSliceContent"
+                   << " called while progressiveQuality_ is false!");
+
+    LOG(TRACE) << "OrthancSeriesVolumeProgressiveLoader::LoadJpegSliceContent";
+    unsigned int quality;
+      
+    switch (dynamic_cast<const OrthancStone::GetOrthancWebViewerJpegCommand&>(message.GetOrigin()).GetQuality())
+    {
+      case 50:
+        quality = QUALITY_00;
+        break;
+
+      case 90:
+        quality = QUALITY_01;
+        break;
+
+      default:
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+    }
+      
+    SetSliceContent(GetSliceIndexPayload(message.GetOrigin()), message.GetImage(), quality);
+  }
+
+  OrthancSeriesVolumeProgressiveLoader::OrthancSeriesVolumeProgressiveLoader(
+    OrthancStone::ILoadersContext& loadersContext,
+    boost::shared_ptr<OrthancStone::DicomVolumeImage> volume,
+    bool progressiveQuality)
+    : loadersContext_(loadersContext)
+    , active_(false)
+    , progressiveQuality_(progressiveQuality)
+    , simultaneousDownloads_(4)
+    , volume_(volume)
+    , sorter_(new OrthancStone::BasicFetchingItemsSorter::Factory)
+    , volumeImageReadyInHighQuality_(false)
+  {
+  }
+
+  boost::shared_ptr<OrthancSeriesVolumeProgressiveLoader> 
+    OrthancSeriesVolumeProgressiveLoader::Create(
+      OrthancStone::ILoadersContext& loadersContext,
+      boost::shared_ptr<OrthancStone::DicomVolumeImage> volume,
+      bool progressiveQuality)
+  {
+    std::auto_ptr<OrthancStone::ILoadersContext::ILock> lock(loadersContext.Lock());
+
+    boost::shared_ptr<OrthancSeriesVolumeProgressiveLoader> obj(
+        new OrthancSeriesVolumeProgressiveLoader(
+          loadersContext, volume, progressiveQuality));
+
+    obj->Register<OrthancStone::OrthancRestApiCommand::SuccessMessage>(
+      lock->GetOracleObservable(),
+      &OrthancSeriesVolumeProgressiveLoader::LoadGeometry);
+
+    obj->Register<OrthancStone::GetOrthancImageCommand::SuccessMessage>(
+      lock->GetOracleObservable(),
+      &OrthancSeriesVolumeProgressiveLoader::LoadBestQualitySliceContent);
+
+    obj->Register<OrthancStone::GetOrthancWebViewerJpegCommand::SuccessMessage>(
+      lock->GetOracleObservable(),
+      &OrthancSeriesVolumeProgressiveLoader::LoadJpegSliceContent);
+
+    return obj;
+  }
+
+
+  OrthancSeriesVolumeProgressiveLoader::~OrthancSeriesVolumeProgressiveLoader()
+  {
+    LOG(TRACE) << "OrthancSeriesVolumeProgressiveLoader::~OrthancSeriesVolumeProgressiveLoader()";
+  }
+
+  void OrthancSeriesVolumeProgressiveLoader::SetSimultaneousDownloads(unsigned int count)
+  {
+    if (active_)
+    {
+      LOG(ERROR) << "OrthancSeriesVolumeProgressiveLoader::SetSimultaneousDownloads(): (active_)";
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+    else if (count == 0)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);        
+    }
+    else
+    {
+      simultaneousDownloads_ = count;
+    }
+  }
+
+
+  void OrthancSeriesVolumeProgressiveLoader::LoadSeries(const std::string& seriesId)
+  {
+    if (active_)
+    {
+      LOG(ERROR) << "OrthancSeriesVolumeProgressiveLoader::LoadSeries(const std::string& seriesId): (active_)";
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      active_ = true;
+
+      std::unique_ptr<OrthancStone::OrthancRestApiCommand> command(new OrthancStone::OrthancRestApiCommand);
+      command->SetUri("/series/" + seriesId + "/instances-tags");
+      {
+        std::unique_ptr<OrthancStone::ILoadersContext::ILock> lock(loadersContext_.Lock());
+        boost::shared_ptr<IObserver> observer(GetSharedObserver());
+        lock->Schedule(observer, 0, command.release()); //TODO: priority!
+      }
+    }
+  }
+  
+
+  OrthancStone::IVolumeSlicer::IExtractedSlice* 
+  OrthancSeriesVolumeProgressiveLoader::ExtractSlice(const OrthancStone::CoordinateSystem3D& cuttingPlane)
+  {
+    if (volume_->HasGeometry())
+    {
+      return new ExtractedSlice(*this, cuttingPlane);
+    }
+    else
+    {
+      return new IVolumeSlicer::InvalidSlice;
+    }
+  }
+}