--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Framework/Volumes/VolumeImage.cpp	Fri Oct 14 15:34:11 2016 +0200
@@ -0,0 +1,412 @@
+/**
+ * Stone of Orthanc
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ *
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * In addition, as a special exception, the copyright holders of this
+ * program give permission to link the code of its release with the
+ * OpenSSL project's "OpenSSL" library (or with modified versions of it
+ * that use the same license as the "OpenSSL" library), and distribute
+ * the linked executables. You must obey the GNU General Public License
+ * in all respects for all of the code used other than "OpenSSL". If you
+ * modify file(s) with this exception, you may extend this exception to
+ * your version of the file(s), but you are not obligated to do so. If
+ * you do not wish to do so, delete this exception statement from your
+ * version. If you delete this exception statement from all source files
+ * in the program, then also delete it here.
+ * 
+ * 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
+ * General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+#include "VolumeImage.h"
+
+#include "../Orthanc/Core/Logging.h"
+#include "../Layers/FrameRenderer.h"
+
+namespace OrthancStone
+{
+  void VolumeImage::StoreUpdateTime()
+  {
+    lastUpdate_ = MessagingToolbox::Timestamp();
+  }
+
+
+  void VolumeImage::NotifyChange(bool force)
+  {
+    bool go = false;
+
+    if (force)
+    {
+      go = true;
+    }
+    else
+    {
+      // Don't notify the observers more than 5 times per second
+      MessagingToolbox::Timestamp now;
+      go = (now.GetMillisecondsSince(lastUpdate_) > 200);
+    }
+
+    if (go)
+    {
+      StoreUpdateTime();
+      observers_.NotifyChange(this);
+    }
+  }
+
+
+  void VolumeImage::LoadThread(VolumeImage* that)
+  {
+    while (that->continue_)
+    {
+      bool complete = false;
+      bool done = that->policy_->DownloadStep(complete);
+
+      if (complete)
+      {
+        that->loadingComplete_ = true;
+      }
+
+      if (done)
+      {
+        break;
+      }
+      else
+      {
+        that->NotifyChange(false);
+      }
+    }
+
+    that->NotifyChange(true);
+  }
+
+
+  VolumeImage::VolumeImage(ISeriesLoader* loader) :   // Takes ownership
+    loader_(loader),
+    threads_(1),
+    started_(false),
+    continue_(false),
+    loadingComplete_(false)
+  {
+    if (loader == NULL)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+    }
+
+    const size_t depth = loader_->GetGeometry().GetSliceCount();
+      
+    if (depth < 2)
+    {
+      // Empty or flat series
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+    }
+
+    // TODO Check pixel spacing, slice thickness, and windowing are
+    // constant across slices
+    referenceDataset_.reset(loader->DownloadDicom(0));
+
+    double spacingZ;
+
+    {
+      // Project the origin of the first and last slices onto the normal
+      const SliceGeometry& s1 = loader_->GetGeometry().GetSlice(0);
+      const SliceGeometry& s2 = loader_->GetGeometry().GetSlice(depth - 1);
+      const Vector& normal = loader_->GetGeometry().GetNormal();
+
+      double p1 = boost::numeric::ublas::inner_prod(s1.GetOrigin(), normal);
+      double p2 = boost::numeric::ublas::inner_prod(s2.GetOrigin(), normal);
+
+      spacingZ = fabs(p2 - p1) / static_cast<double>(depth);
+
+      // TODO Check that all slices are evenly distributed
+    }      
+
+    buffer_.reset(new ImageBuffer3D(loader_->GetPixelFormat(), 
+                                    loader_->GetWidth(), 
+                                    loader_->GetHeight(),
+                                    depth));
+    buffer_->Clear();
+    buffer_->SetAxialGeometry(loader_->GetGeometry().GetSlice(0));
+
+    double spacingX, spacingY;
+    referenceDataset_->GetPixelSpacing(spacingX, spacingY);
+    buffer_->SetVoxelDimensions(spacingX, spacingY, spacingZ);
+
+    // These 3 values are only used to speed up the LayerFactory
+    axialGeometry_.reset(buffer_->GetGeometry(VolumeProjection_Axial));
+    coronalGeometry_.reset(buffer_->GetGeometry(VolumeProjection_Coronal));
+    sagittalGeometry_.reset(buffer_->GetGeometry(VolumeProjection_Sagittal));
+  }
+
+
+  VolumeImage::~VolumeImage()
+  {
+    Stop();
+      
+    for (size_t i = 0; i < threads_.size(); i++)
+    {
+      if (threads_[i] != NULL)
+      {
+        delete threads_[i];
+      }
+    }
+  }
+
+
+  void VolumeImage::SetDownloadPolicy(IDownloadPolicy* policy)   // Takes ownership
+  {
+    if (started_)
+    {
+      LOG(ERROR) << "Cannot change the number of threads after a call to Start()";
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+
+    policy_.reset(policy);
+  }
+
+
+  void VolumeImage::SetThreadCount(size_t count)
+  {
+    if (started_)
+    {
+      LOG(ERROR) << "Cannot change the number of threads after a call to Start()";
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+
+    if (count <= 0)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+
+    threads_.resize(count);
+  }
+
+
+  void VolumeImage::Register(IChangeObserver& observer)
+  {
+    observers_.Register(observer);
+  }
+
+
+  void VolumeImage::Unregister(IChangeObserver& observer)
+  {
+    observers_.Unregister(observer);
+  }
+
+
+  void VolumeImage::Start()
+  {
+    if (started_)
+    {
+      LOG(ERROR) << "Cannot call Start() twice";
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+
+    started_ = true;
+    StoreUpdateTime();
+
+    if (policy_.get() != NULL &&
+        threads_.size() > 0)
+    {
+      continue_ = true;
+      policy_->Initialize(*buffer_, *loader_);
+
+      for (size_t i = 0; i < threads_.size(); i++)
+      {
+        assert(threads_[i] == NULL);
+        threads_[i] = new boost::thread(LoadThread, this);
+      }
+    }
+  }
+
+
+  void VolumeImage::Stop()
+  {
+    if (!started_)
+    {
+      LOG(ERROR) << "Cannot call Stop() without calling Start() beforehand";
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+
+    if (continue_)
+    {
+      continue_ = false;
+
+      for (size_t i = 0; i < threads_.size(); i++)
+      {
+        if (threads_[i]->joinable())
+        {
+          threads_[i]->join();
+        }
+      }
+
+      assert(policy_.get() != NULL);
+      policy_->Finalize();
+    }
+  }
+
+
+  ParallelSlices* VolumeImage::GetGeometry(VolumeProjection projection,
+                                           bool reverse)
+  {
+    std::auto_ptr<ParallelSlices> slices(buffer_->GetGeometry(projection));
+
+    if (reverse)
+    {
+      return slices->Reverse();
+    }
+    else
+    {
+      return slices.release();
+    }
+  }
+
+
+  bool VolumeImage::DetectProjection(VolumeProjection& projection,
+                                     bool& reverse,
+                                     const SliceGeometry& viewportSlice)
+  {
+    if (GeometryToolbox::IsParallelOrOpposite(reverse, viewportSlice.GetNormal(), axialGeometry_->GetNormal()))
+    {
+      projection = VolumeProjection_Axial;
+      return true;
+    }
+    else if (GeometryToolbox::IsParallelOrOpposite(reverse, viewportSlice.GetNormal(), sagittalGeometry_->GetNormal()))
+    {
+      projection = VolumeProjection_Sagittal;
+      return true;
+    }
+    else if (GeometryToolbox::IsParallelOrOpposite(reverse, viewportSlice.GetNormal(), coronalGeometry_->GetNormal()))
+    {
+      projection = VolumeProjection_Coronal;
+      return true;
+    }
+    else
+    {
+      return false;
+    }
+  }
+
+
+  const ParallelSlices& VolumeImage::GetGeometryInternal(VolumeProjection projection)
+  {
+    switch (projection)
+    {
+      case VolumeProjection_Axial:
+        return *axialGeometry_;
+
+      case VolumeProjection_Sagittal:
+        return *sagittalGeometry_;
+
+      case VolumeProjection_Coronal:
+        return *coronalGeometry_;
+
+      default:
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+  }
+
+
+  bool VolumeImage::LayerFactory::GetExtent(double& x1,
+                                            double& y1,
+                                            double& x2,
+                                            double& y2,
+                                            const SliceGeometry& viewportSlice)
+  {
+    VolumeProjection projection;
+    bool reverse;
+
+    if (that_.buffer_->GetWidth() == 0 ||
+        that_.buffer_->GetHeight() == 0 ||
+        that_.buffer_->GetDepth() == 0 ||
+        !that_.DetectProjection(projection, reverse, viewportSlice))
+    {
+      return false;
+    }
+    else
+    {
+      Vector spacing = that_.GetVoxelDimensions(projection);
+
+      unsigned int width, height;
+      that_.buffer_->GetSliceSize(width, height, projection);
+
+      // As the slices of the volumic image are arranged in a box,
+      // we only consider one single reference slice (the one with index 0).
+      const SliceGeometry& volumeSlice = that_.GetGeometryInternal(projection).GetSlice(0);
+
+      return FrameRenderer::ComputeFrameExtent(x1, y1, x2, y2, 
+                                               viewportSlice, volumeSlice,
+                                               width, height,
+                                               spacing[0], spacing[1]);
+    }
+  }
+
+
+  ILayerRenderer* VolumeImage::LayerFactory::CreateLayerRenderer(const SliceGeometry& viewportSlice)
+  {
+    VolumeProjection projection;
+    bool reverse;
+    
+    if (that_.buffer_->GetWidth() == 0 ||
+        that_.buffer_->GetHeight() == 0 ||
+        that_.buffer_->GetDepth() == 0 ||
+        !that_.DetectProjection(projection, reverse, viewportSlice))
+    {
+      return NULL;
+    }
+
+    const ParallelSlices& geometry = that_.GetGeometryInternal(projection);
+
+    size_t closest;
+    double distance;
+
+    const Vector spacing = that_.GetVoxelDimensions(projection);
+    const double sliceThickness = spacing[2];
+
+    if (geometry.ComputeClosestSlice(closest, distance, viewportSlice.GetOrigin()) &&
+        distance <= sliceThickness / 2.0)
+    {
+      bool isFullQuality;
+
+      if (projection == VolumeProjection_Axial &&
+          that_.policy_.get() != NULL)
+      {
+        isFullQuality = that_.policy_->IsFullQualityAxial(closest);
+      }
+      else
+      {
+        isFullQuality = that_.IsLoadingComplete();
+      }
+
+      std::auto_ptr<Orthanc::Image> frame;
+      SliceGeometry frameSlice = geometry.GetSlice(closest);
+
+      {
+        ImageBuffer3D::SliceReader reader(*that_.buffer_, projection, closest);
+        frame.reset(Orthanc::Image::Clone(reader.GetAccessor()));
+      }
+
+      return FrameRenderer::CreateRenderer(frame.release(), 
+                                           viewportSlice, 
+                                           frameSlice, 
+                                           *that_.referenceDataset_, 
+                                           spacing[0], spacing[1],
+                                           isFullQuality);
+    }
+    else
+    {
+      return NULL;
+    }
+  }
+}