/*=========================================================================

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: itkJointDomainImageToListAdaptor.h,v $
  Language:  C++
  Date:      $Date: 2009-03-04 15:23:50 $
  Version:   $Revision: 1.15 $

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even 
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
     PURPOSE.  See the above copyright notices for more information.

=========================================================================*/
#ifndef __itkJointDomainImageToListAdaptor_h
#define __itkJointDomainImageToListAdaptor_h

#include "itkMacro.h"
#include "itkFixedArray.h"
#include "itkPoint.h"
#include "itkPixelTraits.h"
#include "itkImageToListAdaptor.h"
#include "itkImageRegionConstIteratorWithIndex.h"
#include "itkEuclideanDistance.h"
#include "itkListSample.h"

namespace itk { 
namespace Statistics {

/** \class ImageJointDomainTraits
 *  \brief This class provides the type defintion for the measurement
 *  vector in the joint domain (range domain -- pixel values + spatial
 *  domain -- pixel's physical coordinates).
 *
 * \sa JointDomainImageToListAdaptor
 */
template< class TImage >
struct ImageJointDomainTraits
{
  typedef ImageJointDomainTraits                     Self;
  typedef PixelTraits< typename TImage::PixelType >  PixelTraitsType;
  typedef typename PixelTraitsType::ValueType        RangeDomainMeasurementType;
  typedef typename TImage::IndexType::IndexValueType IndexValueType;

  itkStaticConstMacro(ImageDimension, unsigned int, TImage::ImageDimension);
  itkStaticConstMacro(Dimension, 
                      unsigned int, 
                      TImage::ImageDimension +
                      PixelTraitsType::Dimension );

  typedef float                              CoordinateRepType;
  typedef Point< CoordinateRepType, itkGetStaticConstMacro(ImageDimension) > 
                                             PointType;
  typedef JoinTraits< RangeDomainMeasurementType, CoordinateRepType > 
                                             JoinTraitsType;
  typedef typename JoinTraitsType::ValueType MeasurementType;
  typedef FixedArray< MeasurementType, itkGetStaticConstMacro(Dimension) >
                                             MeasurementVectorType;
}; // end of ImageJointDomainTraits

/** \class JointDomainImageToListAdaptor
 *  \brief This adaptor returns measurement vectors composed of an
 *  image pixel's range domain value (pixel value) and spatial domain
 *  value (pixel's physical coordiantes).
 *
 * This class is a derived class of the ImageToListAdaptor. This class
 * overrides the GetMeasurementVector method. The GetMeasurementVector
 * returns a measurement vector that consist of a pixel's physical
 * coordinates and intensity value. For example, if the image
 * dimension is 3, and the pixel value is two component vector, the
 * measurement vector is a 5 component vector. The first three
 * component will be x, y, z physical coordinates (not index) and the
 * rest two component is the pixel values. The type of component is
 * float or which is determined by the ImageJointDomainTraits
 * class. When the pixel value type is double, the component value
 * type of a measurement vector is double. In other case, the
 * component value type is float becase the physical coordinate value
 * type is float. Since the measurment vector is a composition of
 * spatial domain and range domain, for many statistical analysis, we
 * want to normalize the values from both domains. For this purpose,
 * there is the SetNormalizationFactors method. With the above example
 * (5 component measurement vector), you can specify a 5 component
 * normalization factor array. With such factors, the
 * GetMeasurementVector method returns a measurement vector whose each
 * component is divided by the corresponding component of the factor array. 
 *
 * \sa Sample, ListSampleBase, ImageToListAdaptor
 */

template < class TImage >
class ITK_EXPORT JointDomainImageToListAdaptor 
  : public ImageToListAdaptor< 
  TImage, 
  typename ImageJointDomainTraits< TImage >::MeasurementVectorType >
{
public:
  typedef ImageJointDomainTraits< TImage >    ImageJointDomainTraitsType;
  typedef typename ImageJointDomainTraitsType::MeasurementVectorType
                                              MeasurementVectorType;
  typedef typename ImageJointDomainTraitsType::MeasurementType
                                              MeasurementType;
  typedef typename ImageJointDomainTraitsType::RangeDomainMeasurementType
                                              RangeDomainMeasurementType;
  typedef typename ImageJointDomainTraitsType::PointType
                                              PointType;
  typedef typename ImageJointDomainTraitsType::CoordinateRepType 
                                              CoordinateRepType;
  /** Standard class typedefs */
  typedef JointDomainImageToListAdaptor       Self;
  typedef ImageToListAdaptor< TImage, MeasurementVectorType > 
                                              Superclass;
  typedef SmartPointer< Self >                Pointer;
  typedef SmartPointer<const Self>            ConstPointer;
  
  /** Run-time type information (and related methods). */
  itkTypeMacro(JointDomainImageToListAdaptor, ImageToListAdaptor);
  
  /** Method for creation through the object factory. */
  itkNewMacro(Self);
  
  /** the number of components in a measurement vector */
  itkStaticConstMacro(MeasurementVectorSize, 
                      unsigned int, 
                      ImageJointDomainTraitsType::Dimension);
  
  typedef typename Superclass::MeasurementVectorSizeType MeasurementVectorSizeType;

  virtual void SetMeasurementVectorSize( const MeasurementVectorSizeType s ) 
    {
    // Measurement vector size for this class is fixed as the pixel's 
    // dimension. This method should have no effect
    if( s != MeasurementVectorSize )
      {
      itkExceptionMacro( << "Cannot set measurement vector size of "
          << " JointDomainImageToListAdaptor to " << s );
      }
    }

  MeasurementVectorSizeType GetMeasurementVectorSize() const
    {
    return MeasurementVectorSize;
    } 
 
  /** typedefs for Measurement vector, measurement, 
   * Instance Identifier, frequency, size, size element value */
  typedef typename Superclass::FrequencyType      FrequencyType;
  typedef typename Superclass::InstanceIdentifier InstanceIdentifier;

  typedef typename TImage::IndexType                  ImageIndexType;
  typedef typename TImage::IndexType::IndexValueType  ImageIndexValueType;
  typedef typename TImage::SizeType                   ImageSizeType;
  typedef typename TImage::RegionType                 ImageRegionType;
  typedef ImageRegionConstIteratorWithIndex< TImage > ImageIteratorType;

  typedef MeasurementVectorType ValueType;
 
  itkStaticConstMacro(RangeDomainDimension, 
                      unsigned int, 
                      itk::PixelTraits< 
                      typename TImage::PixelType >::Dimension);

  typedef FixedArray< RangeDomainMeasurementType, 
                      itkGetStaticConstMacro( RangeDomainDimension ) > 
  RangeDomainMeasurementVectorType;

  typedef std::vector< InstanceIdentifier > InstanceIdentifierVectorType; 

  typedef FixedArray< float, itkGetStaticConstMacro(MeasurementVectorSize) >
  NormalizationFactorsType;

  /** Sets the normalization factors */
  void SetNormalizationFactors(NormalizationFactorsType& factors);

  /** Gets the measurement vector specified by the instance
   * identifier. This method overrides superclass method. */
  inline const MeasurementVectorType & GetMeasurementVector(const InstanceIdentifier &id) const;

  /** Computes the image region (rectangular) that enclose the ball
   * defined by the mv (center) and the radius. */
  inline void ComputeRegion(const MeasurementVectorType& mv, 
                            const double radius,
                            ImageRegionType& region) const;

  /** Fills he result id vectors with instances that fall within a
   * ball specified by the mv (center) and radius. This method utilizes
   * the ComputRegion */
  inline void Search(const MeasurementVectorType& mv, 
                     const double radius, 
                     InstanceIdentifierVectorType& result) const;

protected:
  JointDomainImageToListAdaptor();
  virtual ~JointDomainImageToListAdaptor() {}
  void PrintSelf(std::ostream& os, Indent indent) const;  

private:
  JointDomainImageToListAdaptor(const Self&); //purposely not implemented
  void operator=(const Self&); //purposely not implemented

  NormalizationFactorsType m_NormalizationFactors;

  mutable MeasurementVectorType            m_TempVector;
  mutable PointType                        m_TempPoint;
  mutable ImageIndexType                   m_TempIndex;
  mutable RangeDomainMeasurementVectorType m_TempRangeVector;
}; // end of class JointDomainImageToListAdaptor

template < class TImage >
inline const typename JointDomainImageToListAdaptor< TImage >::MeasurementVectorType &
JointDomainImageToListAdaptor< TImage >
::GetMeasurementVector(const InstanceIdentifier &id) const
{
  m_TempIndex = this->GetImage()->ComputeIndex( id );
  
  this->GetImage()->TransformIndexToPhysicalPoint( m_TempIndex, m_TempPoint );
  
  for ( unsigned int i = 0; i < TImage::ImageDimension; ++i )
    {
    m_TempVector[i] = m_TempPoint[i] / m_NormalizationFactors[i];
    }
  
  if( this->GetUseBuffer() )
    {
    m_TempRangeVector =  
      *(reinterpret_cast<const RangeDomainMeasurementVectorType* >
        (&(*this->GetPixelContainer())[id]));
    }
  else
    {
    m_TempRangeVector = 
      *(reinterpret_cast< const RangeDomainMeasurementVectorType* >
        (&(this->GetImage()->GetPixel( m_TempIndex ) ) ) );
    }
  
  for ( unsigned int i = TImage::ImageDimension; i < MeasurementVectorType::Length; ++i )
    {
    m_TempVector[i] = m_TempRangeVector[i - TImage::ImageDimension] 
      / m_NormalizationFactors[i];
    }
  
  return m_TempVector;
}

template < class TImage >
inline void
JointDomainImageToListAdaptor< TImage >
::ComputeRegion(const MeasurementVectorType& mv, 
                const double radius,
                ImageRegionType& region) const
{
  ImageIndexType beginIndex;
  ImageSizeType size;

  for ( unsigned int i = 0; i < TImage::ImageDimension; ++i )
    {
    m_TempPoint[i] = m_NormalizationFactors[i] * (mv[i] - radius);
    size[i] = (unsigned long)(2.0 * m_NormalizationFactors[i] * radius 
                              / this->GetImage()->GetSpacing()[i]);
    }

  this->GetImage()->TransformPhysicalPointToIndex(m_TempPoint , beginIndex );

  for ( unsigned int i = 0; i < TImage::ImageDimension; ++i )
    {
    if ( beginIndex[i] < this->GetImageBeginIndex()[i] )
      {
      beginIndex[i] = this->GetImageBeginIndex()[i];
      size[i] -= (this->GetImageBeginIndex()[i] - beginIndex[i]);
      }

    if ( static_cast<typename ImageIndexType::IndexValueType>(beginIndex[i] + size[i] - 1) > this->GetImageEndIndex()[i] )
      {
      size[i] = this->GetImageEndIndex()[i] - beginIndex[i] + 1;
      }
    }
  
  region.SetIndex( beginIndex );
  region.SetSize( size );
}

template < class TImage >
inline void
JointDomainImageToListAdaptor< TImage >
::Search(const MeasurementVectorType& mv,
         const double radius,
         InstanceIdentifierVectorType& result) const
{
  ImageRegionType region;
  this->ComputeRegion( mv, radius, region );

  result.clear();
  ImageIteratorType iter( this->GetImage(), region );
  iter.GoToBegin();
  double squaredRadius = radius * radius;
  InstanceIdentifier instanceID;
  while ( !iter.IsAtEnd() )
    {
    instanceID  = this->GetImage()->ComputeOffset(iter.GetIndex());
    m_TempVector = this->GetMeasurementVector( instanceID );
    bool isWithinRange = true;
    double sum = 0.0;
    for ( unsigned int i = 0; i < MeasurementVectorSize; ++i )
      {
      const double temp = (m_TempVector[i] - mv[i]);
      sum += temp * temp;
      if ( sum > squaredRadius )
        {
        isWithinRange = false;
        break;
        }
      }

    if ( isWithinRange )
      {
      result.push_back(instanceID);
      }
    ++iter;
    }
}

} // end of namespace Statistics
} // end of namespace itk

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

#endif