itkStackTransform.h

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

This file is part of the elastix software.

Copyright (c) University Medical Center Utrecht. All rights reserved.
See src/CopyrightElastix.txt or http://elastix.isi.uu.nl/legal.php 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 __itkStackTransform_h
#define __itkStackTransform_h

#include "itkAdvancedTransform.h"
#include "itkIndex.h"

namespace itk
{

template< class TScalarType,
unsigned int NInputDimensions  = 3,
unsigned int NOutputDimensions = 3 >
class StackTransform :
  public AdvancedTransform< TScalarType, NInputDimensions, NOutputDimensions >
{
public:

  typedef StackTransform Self;
  typedef AdvancedTransform< TScalarType,
    NInputDimensions,
    NOutputDimensions >               Superclass;
  typedef SmartPointer< Self >       Pointer;
  typedef SmartPointer< const Self > ConstPointer;

  itkNewMacro( Self );

  itkTypeMacro( StackTransform, AdvancedTransform );

  itkStaticConstMacro( InputSpaceDimension, unsigned int, NInputDimensions );
  itkStaticConstMacro( OutputSpaceDimension, unsigned int, NOutputDimensions );
  itkStaticConstMacro( ReducedInputSpaceDimension, unsigned int, NInputDimensions - 1 );
  itkStaticConstMacro( ReducedOutputSpaceDimension, unsigned int, NOutputDimensions - 1 );

  typedef typename Superclass::ScalarType     ScalarType;
  typedef typename Superclass::ParametersType ParametersType;
  typedef typename Superclass::NumberOfParametersType
    NumberOfParametersType;
  typedef typename Superclass::ParametersValueType ParametersValueType;
  typedef typename Superclass::JacobianType        JacobianType;
  typedef typename Superclass::SpatialJacobianType SpatialJacobianType;
  typedef typename Superclass::JacobianOfSpatialJacobianType
    JacobianOfSpatialJacobianType;
  typedef typename Superclass::SpatialHessianType SpatialHessianType;
  typedef typename Superclass::JacobianOfSpatialHessianType
    JacobianOfSpatialHessianType;
  typedef typename
    Superclass::NonZeroJacobianIndicesType NonZeroJacobianIndicesType;
  typedef typename Superclass::InputPointType      InputPointType;
  typedef typename Superclass::InputVectorType     InputVectorType;
  typedef typename Superclass::OutputVectorType    OutputVectorType;
  typedef typename Superclass::InputVnlVectorType  InputVnlVectorType;
  typedef typename Superclass::OutputVnlVectorType OutputVnlVectorType;
  typedef typename Superclass::OutputCovariantVectorType
    OutputCovariantVectorType;
  typedef typename Superclass::InputCovariantVectorType
    InputCovariantVectorType;
  typedef typename Superclass::OutputPointType       OutputPointType;
  typedef typename Superclass::OutputVectorPixelType OutputVectorPixelType;
  typedef typename Superclass::InputVectorPixelType  InputVectorPixelType;

  typedef AdvancedTransform< TScalarType,
    itkGetStaticConstMacro( ReducedInputSpaceDimension ),
    itkGetStaticConstMacro( ReducedOutputSpaceDimension ) >  SubTransformType;
  typedef typename SubTransformType::Pointer      SubTransformPointer;
  typedef std::vector< SubTransformPointer  >     SubTransformContainerType;
  typedef typename SubTransformType::JacobianType SubTransformJacobianType;

  typedef typename SubTransformType::InputPointType  SubTransformInputPointType;
  typedef typename SubTransformType::OutputPointType SubTransformOutputPointType;

  typedef typename ParametersType::ArrayType ParametersArrayType;

  virtual OutputPointType TransformPoint( const InputPointType & ipp ) const;

  virtual OutputVectorType TransformVector( const InputVectorType & ) const
  {
    itkExceptionMacro(
        << "TransformVector(const InputVectorType &) is not implemented "
        << "for StackTransform" );
  }


  virtual OutputVnlVectorType TransformVector( const InputVnlVectorType & ) const
  {
    itkExceptionMacro(
        << "TransformVector(const InputVnlVectorType &) is not implemented "
        << "for StackTransform" );
  }


  virtual OutputCovariantVectorType TransformCovariantVector( const InputCovariantVectorType & ) const
  {
    itkExceptionMacro(
        << "TransformCovariantVector(const InputCovariantVectorType &) is not implemented "
        << "for StackTransform" );
  }


  virtual void GetJacobian(
    const InputPointType & ipp,
    JacobianType & jac,
    NonZeroJacobianIndicesType & nzji ) const;

  virtual void SetParameters( const ParametersType & param );

  virtual const ParametersType & GetParameters( void ) const;

  virtual void SetFixedParameters( const ParametersType & )
  {
    // \todo: to be implemented by Coert
  }


  virtual const ParametersType & GetFixedParameters( void ) const
  {
    // \todo: to be implemented by Coert: check this:
    return this->m_FixedParameters;
  }


  virtual NumberOfParametersType GetNumberOfParameters( void ) const
  {
    if( this->m_SubTransformContainer.size() == 0 )
    {
      return 0;
    }
    else
    {
      return this->m_SubTransformContainer.size() * m_SubTransformContainer[ 0 ]->GetNumberOfParameters();
    }
  }


  virtual void SetNumberOfSubTransforms( const unsigned int num )
  {
    if( this->m_NumberOfSubTransforms != num )
    {
      this->m_NumberOfSubTransforms = num;
      this->m_SubTransformContainer.clear();
      this->m_SubTransformContainer.resize( num );
      this->Modified();
    }
  }


  itkGetMacro( NumberOfSubTransforms, unsigned int );

  itkSetMacro( StackSpacing, TScalarType );
  itkGetConstMacro( StackSpacing, TScalarType );
  itkSetMacro( StackOrigin, TScalarType );
  itkGetConstMacro( StackOrigin, TScalarType );

  virtual void SetSubTransform( unsigned int i, SubTransformType * transform )
  {
    this->m_SubTransformContainer[ i ] = transform;
    this->Modified();
  }


  virtual void SetAllSubTransforms( SubTransformType * transform )
  {
    for( unsigned int t = 0; t < this->m_NumberOfSubTransforms; ++t )
    {
      // Copy transform
      SubTransformPointer transformcopy = dynamic_cast< SubTransformType * >( transform->CreateAnother().GetPointer() );
      transformcopy->SetFixedParameters( transform->GetFixedParameters() );
      transformcopy->SetParameters( transform->GetParameters() );
      // Set sub transform
      this->m_SubTransformContainer[ t ] = transformcopy;
    }
  }


  virtual SubTransformPointer GetSubTransform( unsigned int i )
  {
    return this->m_SubTransformContainer[ i ];
  }


  virtual NumberOfParametersType GetNumberOfNonZeroJacobianIndices( void ) const;

  virtual void GetSpatialJacobian(
    const InputPointType & ipp, SpatialJacobianType & sj ) const
  {
    itkExceptionMacro( << "Not implemented for StackTransform" );
  }


  virtual void GetSpatialHessian(
    const InputPointType & ipp, SpatialHessianType & sh ) const
  {
    itkExceptionMacro( << "Not implemented for StackTransform" );
  }


  virtual void GetJacobianOfSpatialJacobian(
    const InputPointType & ipp, JacobianOfSpatialJacobianType & jsj,
    NonZeroJacobianIndicesType & nonZeroJacobianIndices ) const
  {
    itkExceptionMacro( << "Not implemented for StackTransform" );
  }


  virtual void GetJacobianOfSpatialJacobian(
    const InputPointType & ipp, SpatialJacobianType & sj,
    JacobianOfSpatialJacobianType & jsj,
    NonZeroJacobianIndicesType & nonZeroJacobianIndices ) const
  {
    itkExceptionMacro( << "Not implemented for StackTransform" );
  }


  virtual void GetJacobianOfSpatialHessian(
    const InputPointType & ipp, JacobianOfSpatialHessianType & jsh,
    NonZeroJacobianIndicesType & nonZeroJacobianIndices ) const
  {
    itkExceptionMacro( << "Not implemented for StackTransform" );
  }


  virtual void GetJacobianOfSpatialHessian(
    const InputPointType & ipp, SpatialHessianType & sh,
    JacobianOfSpatialHessianType & jsh,
    NonZeroJacobianIndicesType & nonZeroJacobianIndices ) const
  {
    itkExceptionMacro( << "Not implemented for StackTransform" );
  }


protected:

  StackTransform();
  virtual ~StackTransform() {}

private:

  StackTransform( const Self & );  // purposely not implemented
  void operator=( const Self & );  // purposely not implemented

  // Number of transforms and transform container
  unsigned int              m_NumberOfSubTransforms;
  SubTransformContainerType m_SubTransformContainer;

  // Stack spacing and origin of last dimension
  TScalarType m_StackSpacing, m_StackOrigin;

};

} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkStackTransform.hxx"
#endif

#endif