/*=========================================================================
 *
 *  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 itkDisplacementFieldTransform_hxx
#define itkDisplacementFieldTransform_hxx

#include "itkDisplacementFieldTransform.h"
#include "itkVectorLinearInterpolateImageFunction.h"
#include "itkImageToImageFilter.h"

#include "itkImageRegionIteratorWithIndex.h"
#include "vnl/algo/vnl_symmetric_eigensystem.h"
#include "vnl/algo/vnl_matrix_inverse.h"

namespace itk
{

/**
 * Constructor
 */
template<typename TParametersValueType, unsigned int NDimensions>
DisplacementFieldTransform<TParametersValueType, NDimensions>::DisplacementFieldTransform()
: Superclass( 0 ),
  m_CoordinateTolerance(ImageToImageFilterCommon::GetGlobalDefaultCoordinateTolerance()),
  m_DirectionTolerance(ImageToImageFilterCommon::GetGlobalDefaultDirectionTolerance())
{
  this->m_DisplacementField = ITK_NULLPTR;
  this->m_InverseDisplacementField = ITK_NULLPTR;

  this->m_FixedParameters.SetSize( NDimensions * ( NDimensions + 3 ) );
  this->m_FixedParameters.Fill( 0.0 );

  // Setup and assign default interpolator
  typedef VectorLinearInterpolateImageFunction< DisplacementFieldType, ScalarType> DefaultInterpolatorType;
  typename DefaultInterpolatorType::Pointer interpolator = DefaultInterpolatorType::New();
  this->m_Interpolator = interpolator;

  typename DefaultInterpolatorType::Pointer inverseInterpolator = DefaultInterpolatorType::New();
  this->m_InverseInterpolator = inverseInterpolator;

  // Setup and assign parameter helper. This will hold the displacement field
  // for access through the common OptimizerParameters interface.
  OptimizerParametersHelperType* helper = new OptimizerParametersHelperType;
  // After assigning this, m_Parametes will manage this,
  // deleting when appropriate.
  this->m_Parameters.SetHelper( helper );

  m_DisplacementFieldSetTime = 0;

  /* Initialize the identity jacobian. */
  m_IdentityJacobian.SetSize( NDimensions, NDimensions );
  m_IdentityJacobian.Fill(0.0);
  for( unsigned int dim = 0; dim < NDimensions; dim++ )
    {
    m_IdentityJacobian[dim][dim] = 1.0;
    }
}

/**
 * Destructor
 */
template<typename TParametersValueType, unsigned int NDimensions>
DisplacementFieldTransform<TParametersValueType, NDimensions>::
~DisplacementFieldTransform()
{
}

/**
 * Transform point
 */
template<typename TParametersValueType, unsigned int NDimensions>
typename DisplacementFieldTransform<TParametersValueType, NDimensions>::OutputPointType
DisplacementFieldTransform<TParametersValueType, NDimensions>
::TransformPoint( const InputPointType& inputPoint ) const
{
  if( !this->m_DisplacementField )
    {
    itkExceptionMacro( "No displacement field is specified." );
    }
  if( !this->m_Interpolator )
    {
    itkExceptionMacro( "No interpolator is specified." );
    }

  typename InterpolatorType::ContinuousIndexType cidx;
  typename InterpolatorType::PointType point;
  point.CastFrom( inputPoint );

  OutputPointType outputPoint;
  outputPoint.CastFrom( inputPoint );

  if( this->m_Interpolator->IsInsideBuffer( point ) )
    {
    this->m_DisplacementField->TransformPhysicalPointToContinuousIndex( point, cidx );
    typename InterpolatorType::OutputType displacement = this->m_Interpolator->EvaluateAtContinuousIndex( cidx );
    for( unsigned int ii = 0; ii < NDimensions; ++ii )
      {
      outputPoint[ii] += displacement[ii];
      }
    }
  // else
  // simply return inputPoint

  return outputPoint;
}

/**
 * return an inverse transformation
 */
template<typename TParametersValueType, unsigned int NDimensions>
bool DisplacementFieldTransform<TParametersValueType, NDimensions>
::GetInverse( Self *inverse ) const
{
  if( !inverse || !this->m_InverseDisplacementField )
    {
    return false;
    }
  else
    {
    inverse->SetFixedParameters(this->GetFixedParameters());
    inverse->SetDisplacementField( this->m_InverseDisplacementField );
    inverse->SetInverseDisplacementField( this->m_DisplacementField );
    inverse->SetInterpolator( this->m_InverseInterpolator );
    inverse->SetInverseInterpolator( this->m_Interpolator );

    return true;
    }
}

// Return an inverse of this transform
template<typename TParametersValueType, unsigned int NDimensions>
typename DisplacementFieldTransform<TParametersValueType, NDimensions>::InverseTransformBasePointer
DisplacementFieldTransform<TParametersValueType, NDimensions>
::GetInverseTransform() const
{
  Pointer inverseTransform = New();

  if( this->GetInverse( inverseTransform ) )
    {
    return inverseTransform.GetPointer();
    }
  else
    {
    return ITK_NULLPTR;
    }
}

template<typename TParametersValueType, unsigned int NDimensions>
void
DisplacementFieldTransform<TParametersValueType, NDimensions>
::SetIdentity(void)
{
  if (!this->m_DisplacementField.IsNull())
    {
    this->m_DisplacementField->FillBuffer(OutputVectorType(0.0));
    }
  if (!this->m_InverseDisplacementField.IsNull())
    {
    this->m_InverseDisplacementField->FillBuffer(OutputVectorType(0.0));
    }
}


/*
 * ComputeJacobianWithRespectToParameters methods
 */

template<typename TParametersValueType, unsigned int NDimensions>
void
DisplacementFieldTransform<TParametersValueType, NDimensions>
::ComputeJacobianWithRespectToPosition( const InputPointType & point,
                                        JacobianType & jacobian )
const
{
  IndexType idx;

  this->m_DisplacementField->TransformPhysicalPointToIndex( point, idx );
  this->ComputeJacobianWithRespectToPosition( idx, jacobian );
}

template<typename TParametersValueType, unsigned int NDimensions>
void
DisplacementFieldTransform<TParametersValueType, NDimensions>
::ComputeJacobianWithRespectToPosition( const IndexType & index,
                                        JacobianType & jacobian )
const
{
  this->ComputeJacobianWithRespectToPositionInternal( index, jacobian, false );
}

template<typename TParametersValueType, unsigned int NDimensions>
void
DisplacementFieldTransform<TParametersValueType, NDimensions>
::ComputeInverseJacobianWithRespectToPosition( const InputPointType & point,
                                        JacobianType & jacobian )
const
{
  IndexType idx;
  this->m_DisplacementField->TransformPhysicalPointToIndex(point, idx);
  this->ComputeJacobianWithRespectToPositionInternal( idx, jacobian, true );
}

template<typename TParametersValueType, unsigned int NDimensions>
void
DisplacementFieldTransform<TParametersValueType, NDimensions>
::GetInverseJacobianOfForwardFieldWithRespectToPosition(
  const InputPointType & point,
  JacobianType & jacobian,
  bool useSVD )
const
{
  IndexType idx;

  this->m_DisplacementField->TransformPhysicalPointToIndex( point, idx );
  this->GetInverseJacobianOfForwardFieldWithRespectToPosition( idx, jacobian,
                                                               useSVD );
}

template<typename TParametersValueType, unsigned int NDimensions>
void
DisplacementFieldTransform<TParametersValueType, NDimensions>
::GetInverseJacobianOfForwardFieldWithRespectToPosition(
  const IndexType & index,
  JacobianType & jacobian,
  bool useSVD )
const
{
  if( useSVD )
    {
    this->ComputeJacobianWithRespectToPositionInternal( index, jacobian, false );
    vnl_svd<typename JacobianType::ValueType> svd( jacobian );
    for( unsigned int i = 0; i < jacobian.rows(); i++ )
      {
      for( unsigned int j = 0; j < jacobian.cols(); j++ )
        {
        jacobian(i, j) = svd.inverse() (i, j);
        }
      }
    }
  else
    {
    this->ComputeJacobianWithRespectToPositionInternal( index, jacobian, true );
    }
}

/*
 * ComputeJacobianWithRespectToPositionInternal. Worker method.
 */
template<typename TParametersValueType, unsigned int NDimensions>
void
DisplacementFieldTransform<TParametersValueType, NDimensions>
::ComputeJacobianWithRespectToPositionInternal( const IndexType & index,
                                                JacobianType & jacobian,
                                                bool doInverseJacobian )
const
{
  jacobian.SetSize(NDimensions, NDimensions);

  typename DisplacementFieldType::SizeType size =
    this->m_DisplacementField->GetLargestPossibleRegion().GetSize();
  typename DisplacementFieldType::SpacingType spacing =
    this->m_DisplacementField->GetSpacing();

  IndexType ddrindex;
  IndexType ddlindex;
  IndexType difIndex[NDimensions][2];

  // index offset
  unsigned int posoff = NumericTraits<unsigned int>::OneValue();

  // space between indices
  TParametersValueType space = NumericTraits<TParametersValueType>::OneValue();

  // minimum distance between neighbors
  TParametersValueType mindist = NumericTraits<TParametersValueType>::OneValue();

  // flag indicating a valid location for jacobian calculation
  bool oktosample = true;

  // multiplier for getting inverse jacobian
  TParametersValueType dPixSign = NumericTraits<TParametersValueType>::OneValue();
  dPixSign = doInverseJacobian ? -dPixSign : dPixSign;
  for( unsigned int row = 0; row < NDimensions; row++ )
    {
    TParametersValueType dist = fabs( (float)index[row]);
    if( dist < mindist )
      {
      oktosample = false;
      }
    dist = fabs( (TParametersValueType)size[row] - (TParametersValueType)index[row]);
    if( dist < mindist )
      {
      oktosample = false;
      }
    }

  if( oktosample )
    {
    OutputVectorType cpix = this->m_DisplacementField->GetPixel(index);
    m_DisplacementField->TransformLocalVectorToPhysicalVector( cpix, cpix );
    // cpix = directionRaw->TransformVector( cpix );
    // itkCentralDifferenceImageFunction does not support 4th order so
    // do manually here
    for( unsigned int row = 0; row < NDimensions; row++ )
      {
      difIndex[row][0] = index;
      difIndex[row][1] = index;
      ddrindex = index;
      ddlindex = index;
      if( (int) index[row] < (int)(size[row] - 2) )
        {
        difIndex[row][0][row] = index[row] + posoff;
        ddrindex[row] = index[row] + posoff * 2;
        }
      if( index[row] > 1 )
        {
        difIndex[row][1][row] = index[row] - 1;
        ddlindex[row] = index[row] - 2;
        }

      OutputVectorType rpix = m_DisplacementField->GetPixel( difIndex[row][1] );
      OutputVectorType lpix = m_DisplacementField->GetPixel( difIndex[row][0] );
      OutputVectorType rrpix = m_DisplacementField->GetPixel( ddrindex );
      OutputVectorType llpix = m_DisplacementField->GetPixel( ddlindex );

      m_DisplacementField->TransformLocalVectorToPhysicalVector( rpix, rpix );
      m_DisplacementField->TransformLocalVectorToPhysicalVector( rrpix, rrpix );
      m_DisplacementField->TransformLocalVectorToPhysicalVector( lpix, lpix );
      m_DisplacementField->TransformLocalVectorToPhysicalVector( llpix, llpix );

      // 4th order centered difference
      OutputVectorType dPix =
        ( lpix * 8.0 + llpix - rrpix - rpix * 8.0 ) * space / (12.0) * dPixSign;

      // typename DisplacementFieldType::PixelType dPix=
      //      ( lpix - rpix )*space/(2.0*h); //2nd order centered difference
      for( unsigned int col = 0; col < NDimensions; col++ )
        {
        TParametersValueType val = dPix[col] / spacing[col];
        if( row == col )
          {
          val += 1.0;
          }
        jacobian(col, row) = val;
        // Verify it's a real number
        if( !itk::Math::isfinite( val) )
          {
          oktosample = false;
          break;
          }
        }
      } // for row
    }   // if oktosample

  if( !oktosample )
    {
    jacobian.Fill(0.0);
    for( unsigned int i = 0; i < NDimensions; i++ )
      {
      jacobian(i, i) = 1.0;
      }
    }
}

template<typename TParametersValueType, unsigned int NDimensions>
void
DisplacementFieldTransform<TParametersValueType, NDimensions>
::UpdateTransformParameters( const DerivativeType & update, ScalarType factor)
{
  // This simply adds the values.
  // TODO: This should be multi-threaded probably, via image add filter.
  Superclass::UpdateTransformParameters( update, factor );
}

template<typename TParametersValueType, unsigned int NDimensions>
void DisplacementFieldTransform<TParametersValueType, NDimensions>
::SetDisplacementField( DisplacementFieldType* field )
{
  itkDebugMacro("setting DisplacementField to " << field);
  if( this->m_DisplacementField != field )
    {
    this->m_DisplacementField = field;

    if( !this->m_InverseDisplacementField.IsNull() )
      {
      this->m_InverseDisplacementField = ITK_NULLPTR;
      }
    this->Modified();
    /* Store this separately for use in smoothing because we only want
     * to know when the displacement field object has changed, not just
     * its contents. */
    this->m_DisplacementFieldSetTime = this->GetMTime();
    if( !this->m_Interpolator.IsNull() && !this->m_DisplacementField.IsNull() )
      {
      this->m_Interpolator->SetInputImage( this->m_DisplacementField );
      }
    // Assign to parameters object
    this->m_Parameters.SetParametersObject( this->m_DisplacementField );
    }
  this->SetFixedParametersFromDisplacementField();
}

template<typename TParametersValueType, unsigned int NDimensions>
void DisplacementFieldTransform<TParametersValueType, NDimensions>
::SetInverseDisplacementField( DisplacementFieldType* inverseField )
{
  itkDebugMacro( "setting InverseDisplacementField to " << inverseField );
  if( this->m_InverseDisplacementField != inverseField )
    {
    this->m_InverseDisplacementField = inverseField;
    if( !this->m_DisplacementField.IsNull() && inverseField )
      {
      this->VerifyFixedParametersInformation();
      }
    if( !this->m_InverseInterpolator.IsNull() && !this->m_InverseDisplacementField.IsNull() )
      {
      this->m_InverseInterpolator->SetInputImage( this->m_InverseDisplacementField );
      }
    this->Modified();
    }
}

template<typename TParametersValueType, unsigned int NDimensions>
void
DisplacementFieldTransform<TParametersValueType, NDimensions>
::VerifyFixedParametersInformation()
{
  if( !this->m_DisplacementField.IsNull() && !this->m_InverseDisplacementField.IsNull() )
    {
    // check to see if the candidate inverse displacement field has the
    // same fixed parameters as the displacement field.

    SizeType inverseFieldSize = this->m_InverseDisplacementField->GetLargestPossibleRegion().GetSize();
    PointType inverseFieldOrigin = this->m_InverseDisplacementField->GetOrigin();
    SpacingType inverseFieldSpacing = this->m_InverseDisplacementField->GetSpacing();
    DirectionType inverseFieldDirection = this->m_InverseDisplacementField->GetDirection();

    SizeType fieldSize = this->m_DisplacementField->GetLargestPossibleRegion().GetSize();
    PointType fieldOrigin = this->m_DisplacementField->GetOrigin();
    SpacingType fieldSpacing = this->m_DisplacementField->GetSpacing();
    DirectionType fieldDirection = this->m_DisplacementField->GetDirection();

    // tolerance for origin and spacing depends on the size of pixel
    // tolerance for directions a fraction of the unit cube.
    const double coordinateTolerance = m_CoordinateTolerance * fieldSpacing[0];
    const double directionTolerance =  m_DirectionTolerance;

    std::ostringstream sizeString;
    std::ostringstream originString;
    std::ostringstream spacingString;
    std::ostringstream directionString;

    bool unequalSizes = false;
    bool unequalOrigins = false;
    bool unequalSpacings = false;
    bool unequalDirections = false;

    if( inverseFieldSize != fieldSize )
      {
      unequalSizes = true;
      sizeString << "InverseDisplacementField Size: " << inverseFieldSize
                   << ", DisplacementField Size: " << fieldSize << std::endl;

      }
    if( !inverseFieldOrigin.GetVnlVector().is_equal( fieldOrigin.GetVnlVector(), coordinateTolerance ) )
      {
      unequalOrigins = true;
      originString << "InverseDisplacementField Origin: " << inverseFieldOrigin
                   << ", DisplacementField Origin: " << fieldOrigin << std::endl;

      }
    if( !inverseFieldSpacing.GetVnlVector().is_equal( fieldSpacing.GetVnlVector(), coordinateTolerance ) )
      {
      unequalSpacings = false;
      originString << "InverseDisplacementField Spacing: " << inverseFieldSpacing
                   << ", DisplacementField Spacing: " << fieldSpacing << std::endl;

      }
    if( !inverseFieldDirection.GetVnlMatrix().as_ref().is_equal( fieldDirection.GetVnlMatrix(), directionTolerance ) )
      {
      unequalDirections = true;
      originString << "InverseDisplacementField Direction: " << inverseFieldDirection
                   << ", DisplacementField Direction: " << fieldDirection << std::endl;

      }
    if( unequalSizes || unequalOrigins || unequalSpacings || unequalDirections )
      {
      itkExceptionMacro( "The inverse and displacement fields do not have the same fixed parameters: "
                        << std::endl << sizeString.str() << originString.str() << spacingString.str() << directionString.str() );
      }
    }
}

template<typename TParametersValueType, unsigned int NDimensions>
void
DisplacementFieldTransform<TParametersValueType, NDimensions>
::SetInterpolator( InterpolatorType* interpolator )
{
  itkDebugMacro("setting Interpolator to " << interpolator);
  if( this->m_Interpolator != interpolator )
    {
    this->m_Interpolator = interpolator;
    this->Modified();
    if( !this->m_DisplacementField.IsNull() && !this->m_Interpolator.IsNull() )
      {
      this->m_Interpolator->SetInputImage( this->m_DisplacementField );
      }
    }
}

template<typename TParametersValueType, unsigned int NDimensions>
void
DisplacementFieldTransform<TParametersValueType, NDimensions>
::SetInverseInterpolator( InterpolatorType* interpolator )
{
  itkDebugMacro("setting InverseInterpolator to " << interpolator);
  if( this->m_InverseInterpolator != interpolator )
    {
    this->m_InverseInterpolator = interpolator;
    this->Modified();
    if( !this->m_InverseDisplacementField.IsNull() && !this->m_InverseInterpolator.IsNull() )
      {
      this->m_InverseInterpolator->SetInputImage( this->m_InverseDisplacementField );
      }
    }
}

template<typename TParametersValueType, unsigned int NDimensions>
void
DisplacementFieldTransform<TParametersValueType, NDimensions>
::SetFixedParameters( const FixedParametersType & fixedParameters )
{
  if( fixedParameters.Size() != NDimensions * ( NDimensions + 3 ) )
    {
    itkExceptionMacro( "The fixed parameters are not the right size." );
    }

  bool nullState = true;
  for ( unsigned int i = 0; i < fixedParameters.Size() && nullState; ++i )
    {
    nullState = (fixedParameters[i] == 0.0);
    }
  if ( nullState )
    {
    this->SetDisplacementField( ITK_NULLPTR );
    this->SetInverseDisplacementField( ITK_NULLPTR );
    return;
    }

  SizeType size;
  for( unsigned int d = 0; d < NDimensions; d++ )
    {
    size[d] = static_cast<SizeValueType>( fixedParameters[d] );
    }

  PointType origin;
  for( unsigned int d = 0; d < NDimensions; d++ )
    {
    origin[d] = fixedParameters[d + NDimensions];
    }

  SpacingType spacing;
  for( unsigned int d = 0; d < NDimensions; d++ )
    {
    spacing[d] = fixedParameters[d + 2 * NDimensions];
    }

  DirectionType direction;
  for( unsigned int di = 0; di < NDimensions; di++ )
    {
    for( unsigned int dj = 0; dj < NDimensions; dj++ )
      {
      direction[di][dj] = fixedParameters[3 * NDimensions + ( di * NDimensions + dj )];
      }
    }

  PixelType zeroDisplacement;
  zeroDisplacement.Fill( 0.0 );

  typename DisplacementFieldType::Pointer displacementField = DisplacementFieldType::New();
  displacementField->SetSpacing( spacing );
  displacementField->SetOrigin( origin );
  displacementField->SetDirection( direction );
  displacementField->SetRegions( size );
  displacementField->Allocate();
  displacementField->FillBuffer( zeroDisplacement );

  this->SetDisplacementField( displacementField );

  if( !this->m_InverseDisplacementField.IsNull() )
    {
    typename DisplacementFieldType::Pointer inverseDisplacementField = DisplacementFieldType::New();
    inverseDisplacementField->SetSpacing( spacing );
    inverseDisplacementField->SetOrigin( origin );
    inverseDisplacementField->SetDirection( direction );
    inverseDisplacementField->SetRegions( size );
    inverseDisplacementField->Allocate();
    inverseDisplacementField->FillBuffer( zeroDisplacement );

    this->SetInverseDisplacementField( inverseDisplacementField );
    }
}

template<typename TParametersValueType, unsigned int NDimensions>
void
DisplacementFieldTransform<TParametersValueType, NDimensions>
::SetFixedParametersFromDisplacementField() const
  {
  this->m_FixedParameters.SetSize( NDimensions * ( NDimensions + 3 ) );

  if ( this->m_DisplacementField.IsNull() )
    {
    this->m_FixedParameters.Fill( 0.0 );
    return;
    }

  const typename DisplacementFieldType::RegionType & fieldRegion =
    this->m_DisplacementField->GetLargestPossibleRegion();

  // Set the field size parameters
  SizeType fieldSize = fieldRegion.GetSize();
  for( unsigned int i = 0; i < NDimensions; i++ )
    {
    this->m_FixedParameters[i] = static_cast<FixedParametersValueType>( fieldSize[i] );
    }

  // Set the origin parameters
  PointType fieldOrigin = this->m_DisplacementField->GetOrigin();
  for( unsigned int i = 0; i < NDimensions; i++ )
    {
    this->m_FixedParameters[NDimensions + i] = fieldOrigin[i];
    }

  // Set the spacing parameters
  SpacingType fieldSpacing = this->m_DisplacementField->GetSpacing();
  for( unsigned int i = 0; i < NDimensions; i++ )
    {
    this->m_FixedParameters[2 * NDimensions + i] = static_cast<FixedParametersValueType>( fieldSpacing[i] );
    }

  // Set the direction parameters
  DirectionType fieldDirection = this->m_DisplacementField->GetDirection();
  for( unsigned int di = 0; di < NDimensions; di++ )
    {
    for( unsigned int dj = 0; dj < NDimensions; dj++ )
      {
      this->m_FixedParameters[3 * NDimensions + ( di * NDimensions + dj )] =
        static_cast<FixedParametersValueType>( fieldDirection[di][dj] );
      }
    }
}

template<typename TParametersValueType, unsigned int NDimensions>
void
DisplacementFieldTransform<TParametersValueType, NDimensions>
::PrintSelf( std::ostream& os, Indent indent ) const
{
  Superclass::PrintSelf( os, indent );

  itkPrintSelfObjectMacro( Interpolator );
  itkPrintSelfObjectMacro( InverseInterpolator );
  itkPrintSelfObjectMacro( DisplacementField );
  itkPrintSelfObjectMacro( InverseDisplacementField )
}

} // namespace itk

#endif
