/*=========================================================================
 *
 *  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 itkMatrixOffsetTransformBase_h
#define itkMatrixOffsetTransformBase_h


#include "itkMacro.h"
#include "itkMatrix.h"
#include "itkTransform.h"

#include <iostream>

namespace itk
{

/* MatrixOrthogonalityTolerance is a utility to
 * allow setting the tolerance limits used for
 * checking if a matrix meet the orthogonality
 * constraints of being a rigid rotation matrix.
 * The tolerance needs to be different for
 * matricies of type float vs. double.
 */
template<typename T>
class MatrixOrthogonalityTolerance;

template <>
class ITK_TEMPLATE_EXPORT MatrixOrthogonalityTolerance<double>
{
public:
  static double GetTolerance() { return 1e-10; }
};

template <>
class ITK_TEMPLATE_EXPORT MatrixOrthogonalityTolerance<float>
{
public:
  static float GetTolerance() { return 1e-5f; }
};

/** \class MatrixOffsetTransformBase
 * \brief Matrix and Offset transformation of a vector space (e.g. space coordinates)
 *
 * This class serves as a base class for transforms that can be expressed
 * as a linear transformation plus a constant offset (e.g., affine, similarity
 * and rigid transforms).   This base class also provides the concept of
 * using a center of rotation and a translation instead of an offset.
 *
 * As derived instances of this class are specializations of an affine
 * transform, any two of these transformations may be composed and the result
 * is an affine transformation.  However, the order is important.
 * Given two affine transformations T1 and T2, we will say that
 * "precomposing T1 with T2" yields the transformation which applies
 * T1 to the source, and then applies T2 to that result to obtain the
 * target.  Conversely, we will say that "postcomposing T1 with T2"
 * yields the transformation which applies T2 to the source, and then
 * applies T1 to that result to obtain the target.  (Whether T1 or T2
 * comes first lexicographically depends on whether you choose to
 * write mappings from right-to-left or vice versa; we avoid the whole
 * problem by referring to the order of application rather than the
 * textual order.)
 *
 * \tparam TParametersValueType The type to be used for scalar numeric values.  Either
 *    float or double.
 *
 * \tparam NInputDimensions   The number of dimensions of the input vector space.
 *
 * \tparam NOutputDimensions  The number of dimensions of the output vector space.
 *
 * This class provides several methods for setting the matrix and offset
 * defining the transform. To support the registration framework, the
 * transform parameters can also be set as an Array<TParametersValueType> of size
 * (NInputDimension + 1) * NOutputDimension using method SetParameters().
 * The first (NOutputDimension x NInputDimension) parameters defines the
 * matrix in row-major order (where the column index varies the fastest).
 * The last NOutputDimension parameters defines the translation
 * in each dimensions.
 *
 * \ingroup ITKTransform
 */

template<typename TParametersValueType=double,
         unsigned int NInputDimensions = 3,
         unsigned int NOutputDimensions = 3>
class ITK_TEMPLATE_EXPORT MatrixOffsetTransformBase :
  public Transform<TParametersValueType, NInputDimensions, NOutputDimensions>
{
public:
  /** Standard type alias   */
  using Self = MatrixOffsetTransformBase;
  using Superclass = Transform<TParametersValueType,
                    NInputDimensions,
                    NOutputDimensions>;

  using Pointer = SmartPointer<Self>;
  using ConstPointer = SmartPointer<const Self>;

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

  /** New macro for creation of through a Smart Pointer   */
  itkNewMacro(Self);

  /** Dimension of the domain space. */
  static constexpr unsigned int InputSpaceDimension = NInputDimensions;
  static constexpr unsigned int OutputSpaceDimension = NOutputDimensions;
  static constexpr unsigned int ParametersDimension = NOutputDimensions * ( NInputDimensions + 1 );

  /** Parameters Type   */
  using FixedParametersType = typename Superclass::FixedParametersType;
  using FixedParametersValueType = typename Superclass::FixedParametersValueType;
  using ParametersType = typename Superclass::ParametersType;
  using ParametersValueType = typename Superclass::ParametersValueType;

  /** Jacobian Types   */
  using JacobianType = typename Superclass::JacobianType;
  using JacobianPositionType = typename Superclass::JacobianPositionType;
  using InverseJacobianPositionType = typename Superclass::InverseJacobianPositionType;

  /** Transform category type. */
  using TransformCategoryType = typename Superclass::TransformCategoryType;

  /** Standard scalar type for this class */
  using ScalarType = typename Superclass::ScalarType;

  /** Standard vector type for this class   */
  using InputVectorType = Vector<TParametersValueType,
                 Self::InputSpaceDimension>;
  using OutputVectorType = Vector<TParametersValueType,
                 Self::OutputSpaceDimension>;
  using OutputVectorValueType = typename OutputVectorType::ValueType;

  /** Standard covariant vector type for this class   */
  using InputCovariantVectorType = CovariantVector<TParametersValueType,
                          Self::InputSpaceDimension>;
  using OutputCovariantVectorType = CovariantVector<TParametersValueType,
                          Self::OutputSpaceDimension>;

  using InputVectorPixelType = typename Superclass::InputVectorPixelType;
  using OutputVectorPixelType = typename Superclass::OutputVectorPixelType;

  /** Standard diffusion tensor type for this class */
  using InputDiffusionTensor3DType = typename Superclass::InputDiffusionTensor3DType;
  using OutputDiffusionTensor3DType = typename Superclass::OutputDiffusionTensor3DType;

  /** Standard tensor type for this class */
  using InputSymmetricSecondRankTensorType = typename Superclass::InputSymmetricSecondRankTensorType;
  using OutputSymmetricSecondRankTensorType = typename Superclass::OutputSymmetricSecondRankTensorType;

  using InputTensorEigenVectorType =
      CovariantVector<TParametersValueType, InputDiffusionTensor3DType::Dimension>;

  /** Standard vnl_vector type for this class   */
  using InputVnlVectorType = vnl_vector_fixed<TParametersValueType,
                           Self::InputSpaceDimension>;
  using OutputVnlVectorType = vnl_vector_fixed<TParametersValueType,
                           Self::OutputSpaceDimension>;

  /** Standard coordinate point type for this class   */
  using InputPointType = Point<TParametersValueType,
                Self::InputSpaceDimension>;
  using InputPointValueType = typename InputPointType::ValueType;
  using OutputPointType = Point<TParametersValueType,
                Self::OutputSpaceDimension>;
  using OutputPointValueType = typename OutputPointType::ValueType;

  /** Standard matrix type for this class   */
  using MatrixType = Matrix<TParametersValueType, Self::OutputSpaceDimension,
                 Self::InputSpaceDimension>;
  using MatrixValueType = typename MatrixType::ValueType;

  /** Standard inverse matrix type for this class   */
  using InverseMatrixType = Matrix<TParametersValueType, Self::InputSpaceDimension,
                 Self::OutputSpaceDimension>;

  using CenterType = InputPointType;

  using OffsetType = OutputVectorType;
  using OffsetValueType = typename OffsetType::ValueType;

  using TranslationType = OutputVectorType;

  using TranslationValueType = typename TranslationType::ValueType;

  /** Base inverse transform type. This type should not be changed to the
   * concrete inverse transform type or inheritance would be lost. */
  using InverseTransformBaseType = typename Superclass::InverseTransformBaseType;
  using InverseTransformBasePointer = typename InverseTransformBaseType::Pointer;

  /** Set the transformation to an Identity
   *
   * This sets the matrix to identity and the Offset to null. */
  virtual void SetIdentity();

  /** Indicates the category transform.
   *  e.g. an affine transform, or a local one, e.g. a deformation field.
   */
  TransformCategoryType GetTransformCategory() const override
  {
    return Self::Linear;
  }

  /** Set matrix of an MatrixOffsetTransformBase
   *
   * This method sets the matrix of an MatrixOffsetTransformBase to a
   * value specified by the user.
   *
   * This updates the Offset wrt to current translation
   * and center.  See the warning regarding offset-versus-translation
   * in the documentation for SetCenter.
   *
   * To define an affine transform, you must set the matrix,
   * center, and translation OR the matrix and offset */
  virtual void SetMatrix(const MatrixType & matrix)
  {
    m_Matrix = matrix; this->ComputeOffset();
    this->ComputeMatrixParameters();
    m_MatrixMTime.Modified(); this->Modified(); return;
  }

  /** Get matrix of an MatrixOffsetTransformBase
   *
   * This method returns the value of the matrix of the
   * MatrixOffsetTransformBase.
   * To define an affine transform, you must set the matrix,
   * center, and translation OR the matrix and offset */

  virtual const MatrixType & GetMatrix() const
  {
    return m_Matrix;
  }

  /** Set offset (origin) of an MatrixOffset TransformBase.
   *
   * This method sets the offset of an MatrixOffsetTransformBase to a
   * value specified by the user.
   * This updates Translation wrt current center.  See the warning regarding
   * offset-versus-translation in the documentation for SetCenter.
   * To define an affine transform, you must set the matrix,
   * center, and translation OR the matrix and offset */
  void SetOffset(const OutputVectorType & offset)
  {
    m_Offset = offset; this->ComputeTranslation();
    this->Modified(); return;
  }

  /** Get offset of an MatrixOffsetTransformBase
   *
   * This method returns the offset value of the MatrixOffsetTransformBase.
   * To define an affine transform, you must set the matrix,
   * center, and translation OR the matrix and offset */
  const OutputVectorType & GetOffset() const
  {
    return m_Offset;
  }

  /** Set center of rotation of an MatrixOffsetTransformBase
   *
   * This method sets the center of rotation of an MatrixOffsetTransformBase
   * to a fixed point - for most transforms derived from this class,
   * this point is not a "parameter" of the transform - the exception is that
   * "centered" transforms have center as a parameter during optimization.
   *
   * This method updates offset wrt to current translation and matrix.
   * That is, changing the center changes the transform!
   *
   * WARNING: When using the Center, we strongly recommend only changing the
   * matrix and translation to define a transform.   Changing a transform's
   * center, changes the mapping between spaces - specifically, translation is
   * not changed with respect to that new center, and so the offset is updated
   * to * maintain the consistency with translation.   If a center is not used,
   * or is set before the matrix and the offset, then it is safe to change the
   * offset directly.
   *        As a rule of thumb, if you wish to set the center explicitly, set
   * before Offset computations are done.
   *
   * To define an affine transform, you must set the matrix,
   * center, and translation OR the matrix and offset */
  void SetCenter(const InputPointType & center)
  {
    m_Center = center; this->ComputeOffset();
    this->Modified(); return;
  }

  /** Get center of rotation of the MatrixOffsetTransformBase
   *
   * This method returns the point used as the fixed
   * center of rotation for the MatrixOffsetTransformBase.
   * To define an affine transform, you must set the matrix,
   * center, and translation OR the matrix and offset */
  const InputPointType & GetCenter() const
  {
    return m_Center;
  }

  /** Set translation of an MatrixOffsetTransformBase
   *
   * This method sets the translation of an MatrixOffsetTransformBase.
   * This updates Offset to reflect current translation.
   * To define an affine transform, you must set the matrix,
   * center, and translation OR the matrix and offset */
  void SetTranslation(const OutputVectorType & translation)
  {
    m_Translation = translation; this->ComputeOffset();
    this->Modified(); return;
  }

  /** Get translation component of the MatrixOffsetTransformBase
   *
   * This method returns the translation used after rotation
   * about the center point.
   * To define an affine transform, you must set the matrix,
   * center, and translation OR the matrix and offset */
  const OutputVectorType & GetTranslation() const
  {
    return m_Translation;
  }

  /** Set the transformation from a container of parameters.
   * The first (NOutputDimension x NInputDimension) parameters define the
   * matrix and the last NOutputDimension parameters the translation.
   * Offset is updated based on current center. */
  void SetParameters(const ParametersType & parameters) override;

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

  /** Set the fixed parameters and update internal transformation. */
  void SetFixedParameters(const FixedParametersType &) override;

  /** Get the Fixed Parameters. */
  const FixedParametersType & GetFixedParameters() const override;

  /** Compose with another MatrixOffsetTransformBase
   *
   * This method composes self with another MatrixOffsetTransformBase of the
   * same dimension, modifying self to be the composition of self
   * and other.  If the argument pre is true, then other is
   * precomposed with self; that is, the resulting transformation
   * consists of first applying other to the source, followed by
   * self.  If pre is false or omitted, then other is post-composed
   * with self; that is the resulting transformation consists of
   * first applying self to the source, followed by other.
   * This updates the Translation based on current center. */
  void Compose(const Self *other, bool pre = false);

  /** Transform by an affine transformation
   *
   * This method applies the affine transform given by self to a
   * given point or vector, returning the transformed point or
   * vector.  The TransformPoint method transforms its argument as
   * an affine point, whereas the TransformVector method transforms
   * its argument as a vector. */

  OutputPointType       TransformPoint(const InputPointType & point) const override;

  using Superclass::TransformVector;

  OutputVectorType      TransformVector(const InputVectorType & vector) const override;

  OutputVnlVectorType   TransformVector(const InputVnlVectorType & vector) const override;

  OutputVectorPixelType TransformVector(const InputVectorPixelType & vector) const override;

  using Superclass::TransformCovariantVector;

  OutputCovariantVectorType TransformCovariantVector(const InputCovariantVectorType & vector) const override;

  OutputVectorPixelType TransformCovariantVector(const InputVectorPixelType & vector) const override;

  using Superclass::TransformDiffusionTensor3D;

  OutputDiffusionTensor3DType TransformDiffusionTensor3D(const InputDiffusionTensor3DType & tensor) const override;

  OutputVectorPixelType TransformDiffusionTensor3D(const InputVectorPixelType & tensor ) const override;

  using Superclass::TransformSymmetricSecondRankTensor;
  OutputSymmetricSecondRankTensorType TransformSymmetricSecondRankTensor( const InputSymmetricSecondRankTensorType & tensor ) const override;

  OutputVectorPixelType TransformSymmetricSecondRankTensor( const InputVectorPixelType & tensor ) const override;


  /** 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.
   * Get local Jacobian for the given point
   * \c j will sized properly as needed.
   */
  void ComputeJacobianWithRespectToParameters(const InputPointType  & x, JacobianType & j) const override;


  /** Get the jacobian with respect to position. This simply returns
   * the current Matrix. jac will be resized as needed, but it's
   * more efficient if it's already properly sized. */
  void ComputeJacobianWithRespectToPosition(const InputPointType  & x, JacobianPositionType & jac) const override;
  using Superclass::ComputeJacobianWithRespectToPosition;

  /** Get the jacobian with respect to position. This simply returns
   * the inverse of the current Matrix. jac will be resized as needed, but it's
   * more efficient if it's already properly sized. */
  void ComputeInverseJacobianWithRespectToPosition(const InputPointType  & x,
                                                   InverseJacobianPositionType & jac) const override;
  using Superclass::ComputeInverseJacobianWithRespectToPosition;

  /** Create inverse of an affine transformation
   *
   * This populates the parameters an affine transform such that
   * the transform is the inverse of self. If self is not invertible,
   * an exception is thrown.
   * Note that by default the inverese transform is centered at
   * the origin. If you need to compute the inverse centered at a point, p,
   *
     \code
     transform2->SetCenter( p );
     transform1->GetInverse( transform2 );
     \endcode
   *
   * transform2 will now contain the inverse of transform1 and will
   * with its center set to p. Flipping the two statements will produce an
   * incorrect transform.
   *
   */
  bool GetInverse(Self *inverse) const;

  /** Return an inverse of this transform. */
  InverseTransformBasePointer GetInverseTransform() const override;

  /** Indicates that this transform is linear. That is, given two
   * points P and Q, and scalar coefficients a and b, then
   *
   *           T( a*P + b*Q ) = a * T(P) + b * T(Q)
   */
  bool IsLinear() const override
  {
    return true;
  }

protected:
  /** \deprecated Use GetInverse for public API instead.
   * Method will eventually be made a protected member function */
  const InverseMatrixType & GetInverseMatrix() const;

protected:
  /** Construct an MatrixOffsetTransformBase object
   *
   * This method constructs a new MatrixOffsetTransformBase object and
   * initializes the matrix and offset parts of the transformation
   * to values specified by the caller.  If the arguments are
   * omitted, then the MatrixOffsetTransformBase is initialized to an identity
   * transformation in the appropriate number of dimensions. */
  MatrixOffsetTransformBase(const MatrixType & matrix, const OutputVectorType & offset);
  MatrixOffsetTransformBase(unsigned int paramDims);
  MatrixOffsetTransformBase();

  /** Destroy an MatrixOffsetTransformBase object */
  ~MatrixOffsetTransformBase() override = default;

  /** Print contents of an MatrixOffsetTransformBase */
  void PrintSelf(std::ostream & s, Indent indent) const override;

  const InverseMatrixType & GetVarInverseMatrix() const
  {
    return m_InverseMatrix;
  }
  void SetVarInverseMatrix(const InverseMatrixType & matrix) const
  {
    m_InverseMatrix = matrix; m_InverseMatrixMTime.Modified();
  }
  bool InverseMatrixIsOld() const
  {
    if( m_MatrixMTime != m_InverseMatrixMTime )
      {
      return true;
      }
    else
      {
      return false;
      }
  }

  virtual void ComputeMatrixParameters();

  virtual void ComputeMatrix();

  void SetVarMatrix(const MatrixType & matrix)
  {
    m_Matrix = matrix; m_MatrixMTime.Modified();
  }

  virtual void ComputeTranslation();

  void SetVarTranslation(const OutputVectorType & translation)
  {
    m_Translation = translation;
  }

  virtual void ComputeOffset();

  void SetVarOffset(const OutputVectorType & offset)
  {
    m_Offset = offset;
  }

  void SetVarCenter(const InputPointType & center)
  {
    m_Center = center;
  }

  itkGetConstMacro(Singular, bool);
private:

  MatrixOffsetTransformBase(const Self & other) = delete;
  const Self & operator=(const Self &) = delete;

  MatrixType                m_Matrix;           // Matrix of the transformation
  OutputVectorType          m_Offset;           // Offset of the transformation
  mutable InverseMatrixType m_InverseMatrix;    // Inverse of the matrix
  mutable bool              m_Singular;         // Is m_Inverse singular?

  InputPointType   m_Center;
  OutputVectorType m_Translation;

  /** To avoid recomputation of the inverse if not needed */
  TimeStamp         m_MatrixMTime;
  mutable TimeStamp m_InverseMatrixMTime;
}; // class MatrixOffsetTransformBase
}  // namespace itk

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

#endif /* itkMatrixOffsetTransformBase_h */
