itkTimeSeriesDatabase.h

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#ifndef itkTimeSeriesDatabase_h
#define itkTimeSeriesDatabase_h

#include <itkImage.h>
#include <itkArray.h>
#include <itkImageSource.h>
#include <iostream>
#include <fstream>
#include <itkTimeSeriesDatabaseHelper.h>

#define TimeSeriesBlockSize 16
#define TimeSeriesBlockSizeP2 TimeSeriesBlockSize*TimeSeriesBlockSize
#define TimeSeriesBlockSizeP3 TimeSeriesBlockSize*TimeSeriesBlockSize*TimeSeriesBlockSize
#define TimeSeriesVolumeBlockSize TimeSeriesBlockSize*TimeSeriesBlockSize*TimeSeriesBlockSize
#define TimeSeriesVolumeBlockSizeP3 TimeSeriesVolumeBlockSize*TimeSeriesVolumeBlockSize*TimeSeriesVolumeBlockSize

namespace itk
{

template <class TPixel> class TimeSeriesDatabase : public ImageSource<Image<TPixel,3> > {
public:

  typedef TimeSeriesDatabase            Self;
  typedef ImageSource<Image<TPixel,3> > Superclass;
  typedef SmartPointer<Self>            Pointer;
  typedef SmartPointer<const Self>      ConstPointer;
  typedef WeakPointer<const Self>       ConstWeakPointer;

  itkNewMacro(Self);

  itkTypeMacro(TimeSeriesDatabase, ImageSource);

  typedef Image<TPixel, 3>                  OutputImageType;
  typedef typename OutputImageType::Pointer OutputImageTypePointer;
  typedef Image<TPixel, 2>                  OutputSliceType;
  typedef typename OutputSliceType::Pointer OutputSliceTypePointer;
  typedef Array<TPixel>                     ArrayType;

  void Connect ( const char* filename );

  void Disconnect();

  static void CreateFromFileArchetype ( const char* filename, const char* archetype );
  static void CreateFromFileArchetype ( const char* filename, const char* archetype, unsigned long BlocksPerFile );

  itkSetMacro ( CurrentImage, unsigned int );
  itkGetMacro ( CurrentImage, unsigned int );

  int GetNumberOfVolumes() { return this->m_Dimensions[3]; };
  itkGetMacro ( OutputSpacing, typename OutputImageType::SpacingType );
  itkGetMacro ( OutputRegion, typename OutputImageType::RegionType );
  itkGetMacro ( OutputOrigin, typename OutputImageType::PointType );
  itkGetMacro ( OutputDirection, typename OutputImageType::DirectionType );

  void GenerateOutputInformation() override;
  void GenerateData() override;

  void GetVoxelTimeSeries ( typename OutputImageType::IndexType idx, ArrayType& array );

  void SetCacheSizeInMiB ( float sz );
  float GetCacheSizeInMiB ();


protected:
  TimeSeriesDatabase();
  ~TimeSeriesDatabase() override;
  void PrintSelf(std::ostream& os, Indent indent) const override;

  Array<unsigned int> m_Dimensions;
  Array<unsigned int> m_BlocksPerImage;

  typename OutputImageType::SpacingType   m_OutputSpacing;
  typename OutputImageType::RegionType    m_OutputRegion;
  typename OutputImageType::PointType     m_OutputOrigin;
  typename OutputImageType::DirectionType m_OutputDirection;

  typedef itk::TimeSeriesDatabaseHelper::counted_ptr<std::fstream> StreamPtr;

  static std::streampos CalculatePosition ( unsigned long index, unsigned long BlocksPerFile );

  unsigned int CalculateFileIndex ( unsigned long Index );
  static unsigned int CalculateFileIndex ( unsigned long Index, unsigned long BlocksPerFile );

  unsigned long CalculateIndex ( Size<3> Position, int ImageCount );
  static unsigned long CalculateIndex ( Size<3> Position, int ImageCount, unsigned int BlocksPerImage[3] );
  bool CalculateIntersection ( Size<3> BlockIndex, typename OutputImageType::RegionType RequestedRegion,
                               typename OutputImageType::RegionType& BlockRegion,
                               typename OutputImageType::RegionType& ImageRegion );
  bool IsOpen() const;

  Array<unsigned int> m_PixelRemainder;

  std::string  m_Filename;
  unsigned int m_CurrentImage{0};

  std::vector<StreamPtr>   m_DatabaseFiles;
  std::vector<std::string> m_DatabaseFileNames;
  unsigned long            m_BlocksPerFile{0};

  struct CacheBlock
  {
    TPixel data[TimeSeriesBlockSize*TimeSeriesBlockSize*TimeSeriesBlockSize];
  };
  TimeSeriesDatabaseHelper::LRUCache<unsigned long, CacheBlock> m_Cache;
  CacheBlock* GetCacheBlock ( unsigned long index );
};

} // end namespace itk
# include "itkTimeSeriesDatabase.txx"

#endif