libinsighttoolkit4-dev 4.5.0-3 / usr / include / ITK-4.5 / itkBSplineBaseTransform.h

/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef __itkBSplineBaseTransform_h
#define __itkBSplineBaseTransform_h

#include <iostream>
#include "itkTransform.h"
#include "itkImage.h"
#include "itkBSplineInterpolationWeightFunction.h"

namespace itk
{
/** \class BSplineBaseTransform
 * \brief A base class with common elements of BSplineTransform and BSplineDeformableTransform
 *
 * \ingroup ITKTransform
 */
template <typename TScalar = double, unsigned int NDimensions = 3,
          unsigned int VSplineOrder = 3>
class BSplineBaseTransform :
  public Transform<TScalar, NDimensions, NDimensions>
{
public:
  /** Standard class typedefs. */
  typedef BSplineBaseTransform                         Self;
  typedef Transform<TScalar, NDimensions, NDimensions> Superclass;
  typedef SmartPointer<Self>                           Pointer;
  typedef SmartPointer<const Self>                     ConstPointer;

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

  /** Dimension of the domain space. */
  itkStaticConstMacro( SpaceDimension, unsigned int, NDimensions );

  /** The BSpline order. */
  itkStaticConstMacro( SplineOrder, unsigned int, VSplineOrder );

  /** implement type-specific clone method*/
  itkCloneMacro(Self);

  /** Standard scalar type for this class. */
  typedef typename Superclass::ScalarType ScalarType;

  /** Standard parameters container. */
  typedef typename Superclass::ParametersType ParametersType;

  /** Standard Jacobian container. */
  typedef typename Superclass::JacobianType JacobianType;

  /** Transform category type. */
  typedef typename Superclass::TransformCategoryType TransformCategoryType;

  /** The number of parameters defininig this transform. */
  typedef typename Superclass::NumberOfParametersType NumberOfParametersType;

  /** Standard vector type for this class. */
  typedef Vector<TScalar, itkGetStaticConstMacro( SpaceDimension )> InputVectorType;
  typedef Vector<TScalar, itkGetStaticConstMacro( SpaceDimension )> OutputVectorType;

  /** Standard covariant vector type for this class. */
  typedef CovariantVector<TScalar, itkGetStaticConstMacro( SpaceDimension )> InputCovariantVectorType;
  typedef CovariantVector<TScalar, itkGetStaticConstMacro( SpaceDimension )> OutputCovariantVectorType;

  /** Standard vnl_vector type for this class. */
  typedef vnl_vector_fixed<TScalar, SpaceDimension> InputVnlVectorType;
  typedef vnl_vector_fixed<TScalar, SpaceDimension> OutputVnlVectorType;

  /** Standard coordinate point type for this class. */
  typedef Point <TScalar, itkGetStaticConstMacro( SpaceDimension )> InputPointType;
  typedef Point <TScalar, itkGetStaticConstMacro( SpaceDimension )> OutputPointType;

  /** This method sets the parameters of the transform.
   * For a BSpline deformation transform, the parameters are the BSpline
   * coefficients on a sparse grid.
   *
   * The parameters are N number of N-D grid of coefficients. Each N-D grid
   * is represented as a flat array of scalars (in the same configuration as
   * an itk::Image). The N arrays are then concatenated to form one parameter
   * array.
   *
   * For efficiency, this transform does not make a copy of the parameters.
   * It only keeps a pointer to the input parameters. It assumes that the memory
   * is managed by the caller. Use SetParametersByValue to force the transform
   * to call copy the parameters.
   *
   * This method wraps each grid as itk::Image's using the user specified
   * fixed parameters.
   * NOTE: The transform domain must be set first.
   *
   */
  void SetParameters( const ParametersType & parameters );

  /** This method sets the fixed parameters of the transform.
   * For a BSpline deformation transform, the fixed parameters are the
   * following: grid size, grid origin, grid spacing, and grid direction.
   * However, all of these are set via the much more intuitive
   * SetTransformDomainXXX() functions
   *
   * The fixed parameters are the three times the size of the templated
   * dimensions.  This function has the effect of make the following non-
   * existing functional calls:
   *   transform->SetGridSpacing( spacing );
   *   transform->SetGridOrigin( origin );
   *   transform->SetGridDirection( direction );
   *   transform->SetGridRegion( bsplineRegion );
   *
   * With recent updates to this transform, however, all these parameters
   * are set indirectly by setting the transform domain parameters unless
   * the user sets them with SetFixedParameters().
   *
   * This function was added to allow the transform to work with the
   * itkTransformReader/Writer I/O filters.
   *
   */
  virtual void SetFixedParameters( const ParametersType & parameters ) = 0;

  /** This method sets the parameters of the transform.
   * For a BSpline deformation transform, the parameters are the BSpline
   * coefficients on a sparse grid.
   *
   * The parameters are N number of N-D grid of coefficients. Each N-D grid
   * is represented as a flat array of doubles
   * (in the same configuration as an itk::Image).
   * The N arrays are then concatenated to form one parameter array.
   *
   * This methods makes a copy of the parameters while for
   * efficiency the SetParameters method does not.
   *
   * This method wraps each grid as itk::Image's using the user specified
   * fixed parameters.
   * NOTE: The fixed parameters must be set first.
   */
  void SetParametersByValue( const ParametersType & parameters );

  /** This method can ONLY be invoked AFTER calling SetParameters().
   *  This restriction is due to the fact that the BSplineBaseTransform
   *  does not copy the array of parameters internally, instead it keeps a
   *  pointer to the user-provided array of parameters. This method is also
   *  in violation of the const-correctness of the parameters since the
   *  parameter array has been passed to the transform on a 'const' basis but
   *  the values get modified when the user invokes SetIdentity().
   */
  void SetIdentity();

  /** Get the Transformation Parameters. */
  virtual const ParametersType & GetParameters() const;

  /** Get the Transformation Fixed Parameters. */
  virtual const ParametersType & GetFixedParameters() const;

  /** Parameters as SpaceDimension number of images. */
  typedef typename ParametersType::ValueType           ParametersValueType;
  typedef Image<ParametersValueType, itkGetStaticConstMacro( SpaceDimension )> ImageType;
  typedef typename ImageType::Pointer                  ImagePointer;
  typedef FixedArray<ImagePointer, NDimensions>        CoefficientImageArray;

  /** Set the array of coefficient images.
   *
   * This is an alternative API for setting the BSpline coefficients
   * as an array of SpaceDimension images. The fixed parameters are
   * taken from the first image. It is assumed that
   * the buffered region of all the subsequent images are the same
   * as the first image. Note that no error checking is done.
   *
   * Warning: use either the SetParameters() or SetCoefficientImages()
   * API. Mixing the two modes may results in unexpected results.
   */
  virtual void SetCoefficientImages( const CoefficientImageArray & images ) = 0;

  /** Get the array of coefficient images. */
  const CoefficientImageArray GetCoefficientImages() const
  {
    return this->m_CoefficientImages;
  }

  typedef typename Superclass::DerivativeType DerivativeType;

  /** Update the transform's parameters by the adding values in \c update
   * to current parameter values.
   * We assume \c update is of the same length as Parameters. Throw
   * exception otherwise.
   * \c factor is a scalar multiplier for each value in update.
   * SetParameters is called at the end of this method, to allow transforms
   * to perform any required operations on the update parameters, typically
   * a converion to member variables for use in TransformPoint.
   * Derived classes should override to provide specialized behavior.
   */
  virtual void UpdateTransformParameters( const DerivativeType & update, TScalar factor = 1.0 );

  /** Typedefs for specifying the extent of the grid. */
  typedef ImageRegion<itkGetStaticConstMacro( SpaceDimension )> RegionType;

  typedef typename RegionType::IndexType    IndexType;
  typedef typename RegionType::SizeType     SizeType;
  typedef typename ImageType::SpacingType   SpacingType;
  typedef typename ImageType::DirectionType DirectionType;
  typedef typename ImageType::PointType     OriginType;

  /** Transform points by a BSpline deformable transformation. */
  OutputPointType  TransformPoint( const InputPointType & point ) const;

  /** Interpolation weights function type. */
  typedef BSplineInterpolationWeightFunction<ScalarType,
    itkGetStaticConstMacro( SpaceDimension ),
     itkGetStaticConstMacro( SplineOrder )> WeightsFunctionType;

  typedef typename WeightsFunctionType::WeightsType         WeightsType;
  typedef typename WeightsFunctionType::ContinuousIndexType ContinuousIndexType;

  /** Parameter index array type. */
  typedef Array<unsigned long> ParameterIndexArrayType;

  /**
   * Transform points by a BSpline deformable transformation.
   * On return, weights contains the interpolation weights used to compute the
   * deformation and indices of the x (zeroth) dimension coefficient parameters
   * in the support region used to compute the deformation.
   * Parameter indices for the i-th dimension can be obtained by adding
   * ( i * this->GetNumberOfParametersPerDimension() ) to the indices array.
   */
  virtual void TransformPoint( const InputPointType & inputPoint, OutputPointType & outputPoint,
    WeightsType & weights, ParameterIndexArrayType & indices, bool & inside ) const = 0;

  /** Get number of weights. */
  unsigned long GetNumberOfWeights() const
  {
    return m_WeightsFunction->GetNumberOfWeights();
  }

  /** Method to transform a vector -
   *  not applicable for this type of transform. */
  using Superclass::TransformVector;
  virtual OutputVectorType TransformVector( const InputVectorType & ) const
  {
    itkExceptionMacro( << "Method not applicable for deformable transform." );
    return OutputVectorType();
  }

  /** Method to transform a vnl_vector -
   *  not applicable for this type of transform */
  virtual OutputVnlVectorType TransformVector( const InputVnlVectorType & ) const
  {
    itkExceptionMacro( << "Method not applicable for deformable transform. " );
    return OutputVnlVectorType();
  }

  /** Method to transform a CovariantVector -
   *  not applicable for this type of transform */
  using Superclass::TransformCovariantVector;
  virtual OutputCovariantVectorType TransformCovariantVector(
    const InputCovariantVectorType & ) const
  {
    itkExceptionMacro( << "Method not applicable for deformable transfrom. " );
    return OutputCovariantVectorType();
  }

  /** Get Jacobian at a point. A very specialized function just for BSplines */
  void ComputeJacobianFromBSplineWeightsWithRespectToPosition(
    const InputPointType &, WeightsType &, ParameterIndexArrayType & ) const;

  virtual void ComputeJacobianWithRespectToParameters( const InputPointType &, JacobianType & ) const = 0;

  virtual void ComputeJacobianWithRespectToPosition( const InputPointType &, JacobianType & ) const
  {
    itkExceptionMacro( << "ComputeJacobianWithRespectToPosition not yet implemented "
                       "for " << this->GetNameOfClass() );
  }

  /** Return the number of parameters that completely define the Transfom */
  virtual NumberOfParametersType GetNumberOfParameters() const = 0;

  /** Return the number of parameters per dimension */
  virtual NumberOfParametersType GetNumberOfParametersPerDimension() const = 0;

  virtual TransformCategoryType GetTransformCategory() const
  {
    return Self::BSpline;
  }

  unsigned int GetNumberOfAffectedWeights() const;

  typedef typename ImageType::SpacingType   PhysicalDimensionsType;
  typedef typename ImageType::PixelType     PixelType;

  typedef SizeType MeshSizeType;

  /** Return the number of local parameters */
  virtual NumberOfParametersType GetNumberOfLocalParameters() const
  {
    return this->GetNumberOfParameters();
  }

protected:
  /** Print contents of an BSplineBaseTransform. */
  void PrintSelf( std::ostream & os, Indent indent ) const;

  BSplineBaseTransform();
  virtual ~BSplineBaseTransform();

  /** Get/Set to allow subclasses to access and manipulate the weights function. */
  itkSetObjectMacro( WeightsFunction, WeightsFunctionType );
  itkGetModifiableObjectMacro(WeightsFunction, WeightsFunctionType );

  /** Wrap flat array into images of coefficients. */
  void WrapAsImages();

protected:
  /** Construct control point grid from transform domain information */
  void SetFixedParametersFromTransformDomainInformation() const;

  /** Construct control point grid size from transform domain information */
  virtual void SetFixedParametersGridSizeFromTransformDomainInformation() const = 0;

  /** Construct control point grid origin from transform domain information */
  virtual void SetFixedParametersGridOriginFromTransformDomainInformation() const = 0;

  /** Construct control point grid spacing from transform domain information */
  virtual void SetFixedParametersGridSpacingFromTransformDomainInformation() const = 0;

  /** Construct control point grid direction from transform domain information */
  virtual void SetFixedParametersGridDirectionFromTransformDomainInformation() const = 0;

  /** Construct control point grid size from transform domain information */
  virtual void SetCoefficientImageInformationFromFixedParameters() =0;

  /** Check if a continuous index is inside the valid region. */
  virtual bool InsideValidRegion( ContinuousIndexType & ) const = 0;

  // NOTE:  There is a natural duality between the
  //       two representations of of the coefficients
  //       whereby the m_InternalParametersBuffer is
  //       needed to fit into the optimization framework
  //       and the m_CoefficientImages is needed for
  //       the Jacobian computations.  This implementation
  //       is an attempt to remove as much redundancy as possible
  //       and share as much information between the two
  //       instances as possible.
  //
  /** Array of images representing the B-spline coefficients
   *  in each dimension wrapped from the flat parameters in
   *  m_InternalParametersBuffer
   */
  CoefficientImageArray m_CoefficientImages;

  /** Internal parameters buffer. */
  ParametersType m_InternalParametersBuffer;

  /** Pointer to function used to compute Bspline interpolation weights. */
  typename WeightsFunctionType::Pointer m_WeightsFunction;

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

  CoefficientImageArray ArrayOfImagePointerGeneratorHelper() const;
}; // class BSplineBaseTransform
}  // namespace itk

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

#endif /* __itkBSplineBaseTransform_h */