--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Framework/Loaders/SeriesOrderedFrames.cpp	Mon Dec 09 13:58:37 2019 +0100
@@ -0,0 +1,343 @@
+/**
+ * Stone of Orthanc
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2019 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 "../Toolbox/SlicesSorter.h"
+#include "SeriesOrderedFrames.h"
+
+#include <Core/OrthancException.h>
+
+namespace OrthancStone
+{
+  class SeriesOrderedFrames::Instance : public boost::noncopyable
+  {
+  private:
+    std::auto_ptr<Orthanc::DicomMap>  dicom_;
+    DicomInstanceParameters           parameters_;
+
+  public:
+    Instance(const Orthanc::DicomMap& dicom) :
+      dicom_(dicom.Clone()),
+      parameters_(dicom)
+    {
+    }
+    
+    const Orthanc::DicomMap& GetInstance() const
+    {
+      return *dicom_;
+    }
+    
+    const DicomInstanceParameters& GetInstanceParameters() const
+    {
+      return parameters_;
+    }
+
+    bool Lookup3DGeometry(CoordinateSystem3D& target) const
+    {
+      try
+      {
+        std::string imagePositionPatient, imageOrientationPatient;
+        if (dicom_->LookupStringValue(imagePositionPatient, Orthanc::DICOM_TAG_IMAGE_POSITION_PATIENT, false) &&
+            dicom_->LookupStringValue(imageOrientationPatient, Orthanc::DICOM_TAG_IMAGE_ORIENTATION_PATIENT, false))
+        {
+          target = CoordinateSystem3D(imagePositionPatient, imageOrientationPatient);
+          return true;
+        }
+      }
+      catch (Orthanc::OrthancException&)
+      {
+      }
+
+      return false;
+    }
+
+    bool LookupIndexInSeries(int& target) const
+    {
+      std::string value;
+
+      if (dicom_->LookupStringValue(value, Orthanc::DICOM_TAG_INSTANCE_NUMBER, false) ||
+          dicom_->LookupStringValue(value, Orthanc::DICOM_TAG_IMAGE_INDEX, false))
+      {
+        try
+        {
+          target = boost::lexical_cast<int>(value);
+          return true;
+        }
+        catch (boost::bad_lexical_cast&)
+        {
+        }
+      }
+
+      return false;
+    }
+  };
+
+
+  class SeriesOrderedFrames::Frame : public boost::noncopyable
+  {
+  private:
+    const Instance*  instance_;
+    unsigned int     frameIndex_;
+
+  public:
+    Frame(const Instance& instance,
+          unsigned int frameIndex) :
+      instance_(&instance),
+      frameIndex_(frameIndex)
+    {
+      if (frameIndex_ >= instance.GetInstanceParameters().GetImageInformation().GetNumberOfFrames())
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+      }
+    }
+
+    const Orthanc::DicomMap& GetInstance() const
+    {
+      assert(instance_ != NULL);
+      return instance_->GetInstance();
+    }
+    
+    const DicomInstanceParameters& GetInstanceParameters() const
+    {
+      assert(instance_ != NULL);
+      return instance_->GetInstanceParameters();
+    }
+
+    unsigned int GetFrameIndex() const
+    {
+      return frameIndex_;
+    }
+  };
+
+
+  class SeriesOrderedFrames::InstanceWithIndexInSeries
+  {
+  private:
+    const Instance* instance_;  // Don't use a reference to make "std::sort()" happy
+    int             index_;
+
+  public:
+    InstanceWithIndexInSeries(const Instance& instance) :
+    instance_(&instance)
+    {
+      if (!instance_->LookupIndexInSeries(index_))
+      {
+        index_ = std::numeric_limits<int>::max();
+      }
+    }
+
+    const Instance& GetInstance() const
+    {
+      return *instance_;
+    }
+
+    int GetIndexInSeries() const
+    {
+      return index_;
+    }
+
+    bool operator< (const InstanceWithIndexInSeries& other) const
+    {
+      return (index_ < other.index_);
+    }
+  };
+
+
+  void SeriesOrderedFrames::Clear()
+  {
+    for (size_t i = 0; i < instances_.size(); i++)
+    {
+      assert(instances_[i] != NULL);
+      delete instances_[i];
+    }
+
+    for (size_t i = 0; i < orderedFrames_.size(); i++)
+    {
+      assert(orderedFrames_[i] != NULL);
+      delete orderedFrames_[i];
+    }
+
+    instances_.clear();
+    orderedFrames_.clear();
+  }
+
+
+  bool SeriesOrderedFrames::Sort3DVolume()
+  {
+    SlicesSorter sorter;
+    sorter.Reserve(instances_.size());
+
+    for (size_t i = 0; i < instances_.size(); i++)
+    {
+      CoordinateSystem3D geometry;
+      if (instances_[i]->Lookup3DGeometry(geometry))
+      {
+        sorter.AddSlice(geometry, new Orthanc::SingleValueObject<Instance*>(instances_[i]));
+      }
+      else
+      {
+        return false;   // Not a 3D volume
+      }
+    }
+
+    if (!sorter.Sort() ||
+        sorter.GetSlicesCount() != instances_.size() ||
+        !sorter.AreAllSlicesDistinct())
+    {
+      return false;
+    }
+    else
+    {
+      for (size_t i = 0; i < sorter.GetSlicesCount(); i++)
+      {
+        assert(sorter.HasSlicePayload(i));
+
+        const Orthanc::SingleValueObject<Instance*>& payload =
+          dynamic_cast<const Orthanc::SingleValueObject<Instance*>&>(sorter.GetSlicePayload(i));
+              
+        assert(payload.GetValue() != NULL);
+              
+        for (size_t j = 0; j < payload.GetValue()->GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++)
+        {
+          orderedFrames_.push_back(new Frame(*payload.GetValue(), j));
+        }
+      }
+
+      isRegular_ = sorter.ComputeSpacingBetweenSlices(spacingBetweenSlices_);
+      return true;
+    }
+  }
+
+
+  void SeriesOrderedFrames::SortIndexInSeries()
+  {
+    std::vector<InstanceWithIndexInSeries> tmp;
+    tmp.reserve(instances_.size());      
+        
+    for (size_t i = 0; i < instances_.size(); i++)
+    {
+      assert(instances_[i] != NULL);
+      tmp.push_back(InstanceWithIndexInSeries(*instances_[i]));
+    }
+
+    std::sort(tmp.begin(), tmp.end());
+
+    for (size_t i = 0; i < tmp.size(); i++)
+    {
+      for (size_t j = 0; j < tmp[i].GetInstance().GetInstanceParameters().GetImageInformation().GetNumberOfFrames(); j++)
+      {
+        orderedFrames_.push_back(new Frame(tmp[i].GetInstance(), j));
+      }
+    }
+  }
+
+
+  const SeriesOrderedFrames::Frame& SeriesOrderedFrames::GetFrame(size_t seriesIndex) const
+  {
+    if (seriesIndex >= orderedFrames_.size())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+    else
+    {
+      assert(orderedFrames_[seriesIndex] != NULL);
+      return *(orderedFrames_[seriesIndex]);
+    }
+  }
+  
+
+  SeriesOrderedFrames::SeriesOrderedFrames(LoadedDicomResources& instances) :
+    isVolume_(false),
+    isRegular_(false),
+    spacingBetweenSlices_(0)
+  {
+    instances_.reserve(instances.GetSize());
+
+    size_t numberOfFrames = 0;
+      
+    for (size_t i = 0; i < instances.GetSize(); i++)
+    {
+      try
+      {
+        std::auto_ptr<Instance> instance(new Instance(instances.GetResource(i)));
+        numberOfFrames += instance->GetInstanceParameters().GetImageInformation().GetNumberOfFrames();
+        instances_.push_back(instance.release());
+      }
+      catch (Orthanc::OrthancException&)
+      {
+        // The instance has not all the required DICOM tags, skip it
+      }
+    }
+
+    orderedFrames_.reserve(numberOfFrames);
+      
+    if (Sort3DVolume())
+    {
+      isVolume_ = true;
+
+      if (isRegular_)
+      {
+        LOG(INFO) << "Regular 3D volume detected";
+      }
+      else
+      {
+        LOG(INFO) << "Non-regular 3D volume detected";
+      }
+    }
+    else
+    {
+      LOG(INFO) << "Series is not a 3D volume, sorting by index";
+      SortIndexInSeries();
+    }
+
+    LOG(INFO) << "Number of frames: " << orderedFrames_.size();
+  }
+
+
+  unsigned int SeriesOrderedFrames::GetFrameIndex(size_t seriesIndex) const
+  {
+    return GetFrame(seriesIndex).GetFrameIndex();
+  }
+
+
+  const Orthanc::DicomMap& SeriesOrderedFrames::GetInstance(size_t seriesIndex) const
+  {
+    return GetFrame(seriesIndex).GetInstance();
+  }
+
+
+  const DicomInstanceParameters& SeriesOrderedFrames::GetInstanceParameters(size_t seriesIndex) const
+  {
+    return GetFrame(seriesIndex).GetInstanceParameters();
+  }
+
+
+  double SeriesOrderedFrames::GetSpacingBetweenSlices() const
+  {
+    if (IsRegular3DVolume())
+    {
+      return spacingBetweenSlices_;
+    }
+    else
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+  }
+}