#ifndef __gsGSAffine3DTransform_h
#define __gsGSAffine3DTransform_h

#include <iostream>
#include "itkRigid3DTransform.h"
#include "vnl/vnl_quaternion.h"

namespace itk
{

/** \brief GSAffine3DTransform of a vector space (e.g. space coordinates).
 *
 * This transform applies a rotation and translation to the space
 *
 * \ingroup Transforms
 */
template < class TScalarType=double >    // Data type for scalars (float or double)
class ITK_EXPORT GSAffine3DTransform :
          public MatrixOffsetTransformBase< TScalarType, 3, 3>
  //        public Rigid3DTransform< TScalarType > 
{
public:
  /** Standard class typedefs.   */
  typedef GSAffine3DTransform            Self;
//  typedef Rigid3DTransform< TScalarType >     Superclass;
  typedef MatrixOffsetTransformBase< TScalarType, 3, 3 >   Superclass;
  typedef SmartPointer<Self>                  Pointer;
  typedef SmartPointer<const Self>            ConstPointer;
  
  /** New macro for creation of through a Smart Pointer   */
  itkNewMacro( Self );

  /** Run-time type information (and related methods).   */
  // itkTypeMacro( GSAffine3DTransform, Rigid3DTransform );
  itkTypeMacro( GSAffine3DTransform, MatrixOffsetTransformBase );

  /** Dimension of parameters   */
  itkStaticConstMacro(InputSpaceDimension, unsigned int, 3);
  itkStaticConstMacro(OutputSpaceDimension, unsigned int, 3);
  itkStaticConstMacro(SpaceDimension, unsigned int, 3);
  itkStaticConstMacro(ParametersDimension, unsigned int, 13);

  /** Parameters Type   */
  typedef typename Superclass::ParametersType         ParametersType;
  typedef typename Superclass::JacobianType           JacobianType;
  typedef typename Superclass::ScalarType             ScalarType;
  typedef typename Superclass::InputPointType         InputPointType;
  typedef typename Superclass::OutputPointType        OutputPointType;
  typedef typename Superclass::InputVectorType        InputVectorType;
  typedef typename Superclass::OutputVectorType       OutputVectorType;
  typedef typename Superclass::InputVnlVectorType     InputVnlVectorType;
  typedef typename Superclass::OutputVnlVectorType    OutputVnlVectorType;
  typedef typename Superclass::InputCovariantVectorType 
                                                      InputCovariantVectorType;
  typedef typename Superclass::OutputCovariantVectorType      
                                                      OutputCovariantVectorType;
  typedef typename Superclass::MatrixType             MatrixType;
  typedef typename Superclass::InverseMatrixType      InverseMatrixType;
  typedef typename Superclass::CenterType             CenterType;
  typedef typename Superclass::OffsetType             OffsetType;
  typedef typename Superclass::TranslationType        TranslationType;


  /** VnlQuaternion type.  */
  typedef vnl_quaternion<TScalarType>           VnlQuaternionType;

  /** Compute the Jacobian Matrix of the transformation at one point */
  /** Set the rotation of the rigid transform.
   * This method sets the rotation of a GSAffine3DTransform to a
   * value specified by the user. */
  void SetRotation(const VnlQuaternionType &rotation);
  void SetS1(const TScalarType S1);
  void SetS2(const TScalarType S2);
  void SetS3(const TScalarType S3);
  void SetK1(const TScalarType K1);
  void SetK2(const TScalarType K2);
  void SetK3(const TScalarType K3);


  /** Get the rotation from an GSAffine3DTransform.
   * This method returns the value of the rotation of the
   * GSAffine3DTransform.   **/
   const VnlQuaternionType & GetRotation(void) const 
     { return m_Rotation; } 

  MatrixType ComputeMyRotationMatrix();

  itkGetConstReferenceMacro( S1, TScalarType );
  itkGetConstReferenceMacro( S2, TScalarType );
  itkGetConstReferenceMacro( S3, TScalarType );
  itkGetConstReferenceMacro( K1, TScalarType );
  itkGetConstReferenceMacro( K2, TScalarType );
  itkGetConstReferenceMacro( K3, TScalarType );



  /** Set the parameters to the IdentityTransform */
  virtual void SetIdentity(void);

  /** Set the transformation from a container of parameters.
   * This is typically used by optimizers.
   * There are 7 parameters. The first four represents the
   * quaternion and the last three represents the
   * offset. */
  void SetParameters( const ParametersType & parameters );
  virtual const ParametersType & GetParameters() const;

  /** Compute the Jacobian of the transformation.
   * This method computes the Jacobian matrix of the transformation.
   * given point or vector, returning the transformed point or
   * vector. The rank of the Jacobian will also indicate if the transform
   * is invertible at this point. */
  const JacobianType & GetJacobian(const InputPointType  &point ) const;

protected:
/*   GSAffine3DTransform(const MatrixType &matrix, */
/*                            const OutputVectorType &offset); */
  GSAffine3DTransform(unsigned int outputDims,
                           unsigned int paramDims);
  GSAffine3DTransform();
  ~GSAffine3DTransform(){};

  void ComputeMatrix();

//  void ComputeMatrixParameters();

  void SetVarRotation(const VnlQuaternionType & rotation)
    { m_Rotation = rotation; };

//  const InverseMatrixType & GetInverseMatrix( void ) const;

  void PrintSelf(std::ostream &os, Indent indent) const;

private:
  GSAffine3DTransform(const Self&); //purposely not implemented
  void operator=(const Self&); //purposely not implemented

  /** Rotation of the transformation. */
  VnlQuaternionType   m_Rotation;

  /** added affine parameters **/
  TScalarType m_S1;
  TScalarType m_S2;
  TScalarType m_S3;
  TScalarType m_K1;
  TScalarType m_K2;
  TScalarType m_K3;

}; //class GSAffine3DTransform


}  // namespace itk


#ifndef ITK_MANUAL_INSTANTIATION
#include "gsGSAffine3DTransform.txx"
#endif

#endif /* __gsGSAffine3DTransform_h */
