#ifndef __itkMultipleUnlabeledImagesToLabeledImageFilter_h
#define __itkMultipleUnlabeledImagesToLabeledImageFilter_h

#include "itkImageToImageFilter.h"
#include "itkConceptChecking.h"
#include "itkThresholdImageFilter.h"
#include "itkAddImageFilter.h"

namespace itk
{
/** \class MultipleUnlabeledImagesToLabeledImageFilter
 * \brief This class takes as takes as input a vector of input images 
 * and outputs a single image with the "interesting" input voxels (as determined by
 * an intensity threshold) uniquely labeled.
 *
 * TODO: The input images are combined into a single image with
 * the AddImageFilter. In cases where voxels have multiple labels,
 * the resulting label with be the addition of these labels. This
 * filter needs an elegant way to handle voxels with multiple labels, e.g.,
 * assign overlapping regions a new label.
 *
 * \author Robert Tamburo
 *
 * \ingroup ImageToImageFilter Singlethreaded
 */
 
template <class TImage>
class ITK_EXPORT MultipleUnlabeledImagesToLabeledImageFilter : public ImageToImageFilter<TImage, TImage>
{
public:
  /** Standard class typedefs. */
  typedef MultipleUnlabeledImagesToLabeledImageFilter Self;
  typedef ImageToImageFilter<TImage, TImage> Superclass;
  typedef SmartPointer<Self> Pointer;
  typedef SmartPointer<const Self> ConstPointer;

  /** Method for creation through the object factory. */
  itkNewMacro(Self);  

  /** Run-time type information (and related methods). */
  itkTypeMacro(MultipleUnlabeledImagesToLabeledImageFilter, ImageToImageFilter);

  /** Image type information. */
  typedef TImage ImageType;
  typedef typename ImageType::Pointer ImagePointerType;
  typedef typename ImageType::PixelType PixelType;
  
  /** Filter typedefs. */
  typedef ThresholdImageFilter<ImageType> ThresholdFilterType;
  typedef AddImageFilter<ImageType, ImageType, ImageType> AddFilterType;
    
  /** Typedef for vector of values of type PixelType. */
  typedef std::vector<PixelType> * PixelVectorType;
  
  /** Typedef for vector of image pointers. */
  typedef std::vector<typename ImageType::Pointer> ImageVectorType;
  
  /** Set intensity thresholds. */
  itkSetMacro(IntensityThresholds, PixelVectorType);
  
  /** Set flag to use or not use the intensity thresholds as a lower threshold. */
  itkSetMacro(UseLowerThreshold, bool);
  
  /** Set list of input images. */
  void SetInputImageList(ImageVectorType imageVector) {m_InputImageList = imageVector;}

  /** Return the output image of this filter. */  
  ImagePointerType GetOutput() {return m_OutputImage;}
  
protected:
  MultipleUnlabeledImagesToLabeledImageFilter();
  virtual ~MultipleUnlabeledImagesToLabeledImageFilter() {};

  /** Print member variables. */
  void PrintSelf(std::ostream& os, Indent indent) const;
  
  /** This method implements the actual split of the image. */
  void GenerateData(void);

private:
  MultipleUnlabeledImagesToLabeledImageFilter(const Self&); // purposely not implemented
  void operator=(const Self&); // purposely not implemented
  
  PixelVectorType m_IntensityThresholds; // intensity thresholds
  ImageVectorType m_InputImageList; // input image list
  
  ImagePointerType m_OutputImage; // output image
  bool m_UseLowerThreshold; // flag for using thresholds as lower thresholds
    
};

} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkMultipleUnlabeledImagesToLabeledImageFilter.txx"
#endif
  
#endif