/*=========================================================================
 *
 *  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 itkDiffeomorphicDemonsRegistrationWithMaskFilter_hxx
#define itkDiffeomorphicDemonsRegistrationWithMaskFilter_hxx

#include "itkDiffeomorphicDemonsRegistrationWithMaskFilter.h"
#include "itkSmoothingRecursiveGaussianImageFilter.h"

namespace itk
{
/**
 * Default constructor
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::DiffeomorphicDemonsRegistrationWithMaskFilter():
  m_UseFirstOrderExp(false)
{
  typename DemonsRegistrationFunctionType::Pointer drfp;
  drfp = DemonsRegistrationFunctionType::New();

  this->SetDifferenceFunction( drfp.GetPointer() );

  m_Multiplier = MultiplyByConstantType::New();
  m_Multiplier->InPlaceOn();

  m_Exponentiator = FieldExponentiatorType::New();

  m_Warper = VectorWarperType::New();
  FieldInterpolatorPointer VectorInterpolator =
    FieldInterpolatorType::New();
  m_Warper->SetInterpolator(VectorInterpolator);

  m_Adder = AdderType::New();
  m_Adder->InPlaceOn();
}

/**
 * Checks whether the DifferenceFunction is of type DemonsRegistrationFunction.
 * It throws and exception, if it is not.
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
typename DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage,
                                                TDisplacementField >::DemonsRegistrationFunctionType *
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::DownCastDifferenceFunctionType()
{
  DemonsRegistrationFunctionType *drfp =
    dynamic_cast< DemonsRegistrationFunctionType * >
    ( this->GetDifferenceFunction().GetPointer() );

  if ( !drfp )
    {
    itkExceptionMacro(
      << "Could not cast difference function to SymmetricDemonsRegistrationFunction");
    }

  return drfp;
}

/**
 * Checks whether the DifferenceFunction is of type DemonsRegistrationFunction.
 * It throws and exception, if it is not.
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
const typename DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage,
                                                      TDisplacementField >::DemonsRegistrationFunctionType *
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::DownCastDifferenceFunctionType() const
{
  const DemonsRegistrationFunctionType *drfp =
    dynamic_cast< const DemonsRegistrationFunctionType * >
    ( this->GetDifferenceFunction().GetPointer() );

  if ( !drfp )
    {
    itkExceptionMacro(
      << "Could not cast difference function to SymmetricDemonsRegistrationFunction");
    }

  return drfp;
}

/**
 * Set the function state values before each iteration
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::InitializeIteration()
{
  // update variables in the equation object
  DemonsRegistrationFunctionType *f = this->DownCastDifferenceFunctionType();

  f->SetDisplacementField( this->GetDisplacementField() );

  // call the superclass  implementation ( initializes f )
  Superclass::InitializeIteration();
}

/*
 * Get the metric value from the difference function
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
double
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::GetMetric() const
{
  const DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();

  return drfp->GetMetric();
}

/**
 *  Get Intensity Difference Threshold
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
double
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::GetIntensityDifferenceThreshold() const
{
  const DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();

  return drfp->GetIntensityDifferenceThreshold();
}

/**
 *  Set Intensity Difference Threshold
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::SetIntensityDifferenceThreshold(double threshold)
{
  DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();

  drfp->SetIntensityDifferenceThreshold(threshold);
}

/**
 *  Get Maximum Update Step Length
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
double
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::GetMaximumUpdateStepLength() const
{
  const DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();

  return drfp->GetMaximumUpdateStepLength();
}

/**
 *  Set Maximum Update Step Length
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::SetMaximumUpdateStepLength(double threshold)
{
  DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();

  drfp->SetMaximumUpdateStepLength(threshold);
}

/**
 * Get the metric value from the difference function
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
const double &
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::GetRMSChange() const
{
  const DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();

  return drfp->GetRMSChange();
}

/**
 *
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
typename DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::GradientType
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::GetUseGradientType() const
{
  const DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();

  return drfp->GetUseGradientType();
}

/**
 *
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::SetUseGradientType(GradientType gtype)
{
  DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();

  drfp->SetUseGradientType(gtype);
}

/**
 *
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::AllocateUpdateBuffer()
{
  // The update buffer looks just like the output.
  DisplacementFieldPointer output = this->GetOutput();
  DisplacementFieldPointer upbuf = this->GetUpdateBuffer();

  upbuf->SetLargestPossibleRegion( output->GetLargestPossibleRegion() );
  upbuf->SetRequestedRegion( output->GetRequestedRegion() );
  upbuf->SetBufferedRegion( output->GetBufferedRegion() );
  upbuf->SetOrigin( output->GetOrigin() );
  upbuf->SetSpacing( output->GetSpacing() );
  upbuf->SetDirection( output->GetDirection() );
  upbuf->Allocate();
}

/**
 * Get the metric value from the difference function
 */
template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::ApplyUpdate(const TimeStepType& dt)
{
  // If we smooth the update buffer before applying it, then the are
  // approximating a viscuous problem as opposed to an elastic problem
  if ( this->GetSmoothUpdateField() )
    {
    this->SmoothUpdateField();
    }

  // Use time step if necessary. In many cases
  // the time step is one so this will be skipped
  if ( std::fabs(dt - 1.0) > 1.0e-4 )
    {
    itkDebugMacro("Using timestep: " << dt);
    m_Multiplier->SetInput2(dt);
    m_Multiplier->SetInput( this->GetUpdateBuffer() );
    m_Multiplier->GraftOutput( this->GetUpdateBuffer() );
    // in place update
    m_Multiplier->Update();
    // graft output back to this->GetUpdateBuffer()
    this->GetUpdateBuffer()->Graft( m_Multiplier->GetOutput() );
    }

  if ( this->m_UseFirstOrderExp )
    {
    // use s <- s o (Id +u)

    // skip exponential and compose the vector fields
    m_Warper->SetOutputOrigin( this->GetUpdateBuffer()->GetOrigin() );
    m_Warper->SetOutputSpacing( this->GetUpdateBuffer()->GetSpacing() );
    m_Warper->SetOutputDirection( this->GetUpdateBuffer()->GetDirection() );
    m_Warper->SetInput( this->GetOutput() );
    m_Warper->SetDisplacementField( this->GetUpdateBuffer() );

    m_Adder->SetInput1( m_Warper->GetOutput() );
    m_Adder->SetInput2( this->GetUpdateBuffer() );

    m_Adder->GetOutput()->SetRequestedRegion(
      this->GetOutput()->GetRequestedRegion() );
    }
  else
    {
    // use s <- s o exp(u)

    // compute the exponential
    m_Exponentiator->SetInput( this->GetUpdateBuffer() );

    const double imposedMaxUpStep = this->GetMaximumUpdateStepLength();
    if ( imposedMaxUpStep > 0.0 )
      {
      // max(norm(Phi))/2^N <= 0.25*pixelspacing
      const double numiterfloat = 2.0 + std::log(imposedMaxUpStep) / itk::Math::ln2;
      unsigned int numiter = 0;
      if ( numiterfloat > 0.0 )
        {
        numiter = Math::Ceil< unsigned int >(numiterfloat);
        }

      m_Exponentiator->AutomaticNumberOfIterationsOff();
      m_Exponentiator->SetMaximumNumberOfIterations(numiter);
      }
    else
      {
      m_Exponentiator->AutomaticNumberOfIterationsOn();
      // just set a high value so that automatic number of step
      // is not thresholded
      m_Exponentiator->SetMaximumNumberOfIterations(2000u);
      }

    m_Exponentiator->GetOutput()->SetRequestedRegion(
      this->GetOutput()->GetRequestedRegion() );

    m_Exponentiator->Update();

    // compose the vector fields
    m_Warper->SetOutputOrigin( this->GetUpdateBuffer()->GetOrigin() );
    m_Warper->SetOutputSpacing( this->GetUpdateBuffer()->GetSpacing() );
    m_Warper->SetOutputDirection( this->GetUpdateBuffer()->GetDirection() );
    m_Warper->SetInput( this->GetOutput() );
    m_Warper->SetDisplacementField( m_Exponentiator->GetOutput() );

    m_Warper->Update();

    m_Adder->SetInput1( m_Warper->GetOutput() );
    m_Adder->SetInput2( m_Exponentiator->GetOutput() );

    m_Adder->GetOutput()->SetRequestedRegion(
      this->GetOutput()->GetRequestedRegion() );
    }

  // Triggers update
  m_Adder->Update();

  // Region passing stuff
  this->GraftOutput( m_Adder->GetOutput() );

  DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();

  this->SetRMSChange( drfp->GetRMSChange() );

  /**
   * Smooth the deformation field
   */
  if ( this->GetSmoothDisplacementField() )
    {
    this->SmoothDisplacementField();
    }
}

template< typename TFixedImage, typename TMovingImage, typename TDisplacementField >
void
DiffeomorphicDemonsRegistrationWithMaskFilter< TFixedImage, TMovingImage, TDisplacementField >
::PrintSelf(std::ostream & os, Indent indent) const
{
  Superclass::PrintSelf(os, indent);
  os << indent << "Intensity difference threshold: "
     << this->GetIntensityDifferenceThreshold() << std::endl;
  os << indent << "Use First Order exponential: "
     << this->m_UseFirstOrderExp << std::endl;
}
} // end namespace itk

#endif
