/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  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 itkFastSymmetricForcesDemonsRegistrationFunction_hxx
#define itkFastSymmetricForcesDemonsRegistrationFunction_hxx

#include "itkFastSymmetricForcesDemonsRegistrationFunction.h"
#include "itkMacro.h"
#include "itkMath.h"

namespace itk
{
/**
 * Default constructor
 */
template <typename TFixedImage, typename TMovingImage, typename TDisplacementField>
FastSymmetricForcesDemonsRegistrationFunction<TFixedImage, TMovingImage, TDisplacementField>::
  FastSymmetricForcesDemonsRegistrationFunction()
{
  RadiusType   r;
  unsigned int j;

  for (j = 0; j < ImageDimension; j++)
  {
    r[j] = 0;
  }
  this->SetRadius(r);

  m_TimeStep = 1.0;
  m_DenominatorThreshold = 1e-9;
  m_IntensityDifferenceThreshold = 0.001;
  this->SetMovingImage(nullptr);
  this->SetFixedImage(nullptr);
  m_Normalizer = 0.0;
  m_FixedImageGradientCalculator = GradientCalculatorType::New();

  typename DefaultInterpolatorType::Pointer interp = DefaultInterpolatorType::New();

  m_MovingImageInterpolator = static_cast<InterpolatorType *>(interp.GetPointer());

  m_WarpedMovingImageGradientCalculator = MovingGradientCalculatorType::New();
  m_MovingImageWarper = WarperType::New();
  m_MovingImageWarper->SetInterpolator(m_MovingImageInterpolator);

  m_Metric = NumericTraits<double>::max();
  m_SumOfSquaredDifference = 0.0;
  m_NumberOfPixelsProcessed = 0L;
  m_RMSChange = NumericTraits<double>::max();
  m_SumOfSquaredChange = 0.0;
}

/**
 * Standard "PrintSelf" method.
 */
template <typename TFixedImage, typename TMovingImage, typename TDisplacementField>
void
FastSymmetricForcesDemonsRegistrationFunction<TFixedImage, TMovingImage, TDisplacementField>::PrintSelf(
  std::ostream & os,
  Indent         indent) const
{
  Superclass::PrintSelf(os, indent);

  os << indent << "MovingImageIterpolator: ";
  os << m_MovingImageInterpolator.GetPointer() << std::endl;
  os << indent << "FixedImageGradientCalculator: ";
  os << m_FixedImageGradientCalculator.GetPointer() << std::endl;
  os << indent << "DenominatorThreshold: ";
  os << m_DenominatorThreshold << std::endl;
  os << indent << "IntensityDifferenceThreshold: ";
  os << m_IntensityDifferenceThreshold << std::endl;

  os << indent << "Metric: ";
  os << m_Metric << std::endl;
  os << indent << "SumOfSquaredDifference: ";
  os << m_SumOfSquaredDifference << std::endl;
  os << indent << "NumberOfPixelsProcessed: ";
  os << m_NumberOfPixelsProcessed << std::endl;
  os << indent << "RMSChange: ";
  os << m_RMSChange << std::endl;
  os << indent << "SumOfSquaredChange: ";
  os << m_SumOfSquaredChange << std::endl;
}

/**
 *
 */
template <typename TFixedImage, typename TMovingImage, typename TDisplacementField>
void
FastSymmetricForcesDemonsRegistrationFunction<TFixedImage, TMovingImage, TDisplacementField>::
  SetIntensityDifferenceThreshold(double threshold)
{
  m_IntensityDifferenceThreshold = threshold;
}

/**
 *
 */
template <typename TFixedImage, typename TMovingImage, typename TDisplacementField>
double
FastSymmetricForcesDemonsRegistrationFunction<TFixedImage, TMovingImage, TDisplacementField>::
  GetIntensityDifferenceThreshold() const
{
  return m_IntensityDifferenceThreshold;
}

/**
 * Set the function state values before each iteration
 */
template <typename TFixedImage, typename TMovingImage, typename TDisplacementField>
void
FastSymmetricForcesDemonsRegistrationFunction<TFixedImage, TMovingImage, TDisplacementField>::InitializeIteration()
{
  if (!this->GetMovingImage() || !this->GetFixedImage() || !m_MovingImageInterpolator)
  {
    itkExceptionMacro(<< "MovingImage, FixedImage and/or Interpolator not set");
  }

  // cache fixed image information
  const PixelType fixedImageSpacing = this->GetFixedImage()->GetSpacing();

  // compute the normalizer
  m_Normalizer = 0.0;
  for (unsigned int k = 0; k < ImageDimension; k++)
  {
    m_Normalizer += fixedImageSpacing[k] * fixedImageSpacing[k];
  }
  m_Normalizer /= static_cast<double>(ImageDimension);

  // setup gradient calculator
  m_FixedImageGradientCalculator->SetInputImage(this->GetFixedImage());

  m_MovingImageWarper->SetOutputOrigin(this->GetFixedImage()->GetOrigin());
  m_MovingImageWarper->SetOutputSpacing(this->GetFixedImage()->GetSpacing());
  m_MovingImageWarper->SetOutputDirection(this->GetFixedImage()->GetDirection());
  m_MovingImageWarper->SetInput(this->GetMovingImage());
  m_MovingImageWarper->SetDisplacementField(this->GetDisplacementField());
  m_MovingImageWarper->Update();
  m_WarpedMovingImageGradientCalculator->SetInputImage(this->m_MovingImageWarper->GetOutput());

  // setup moving image interpolator for further access
  m_MovingImageInterpolator->SetInputImage(this->GetMovingImage());

  // initialize metric computation variables
  m_SumOfSquaredDifference = 0.0;
  m_NumberOfPixelsProcessed = 0L;
  m_SumOfSquaredChange = 0.0;
}

/**
 * Compute update at a non boundary neighbourhood
 */
template <typename TFixedImage, typename TMovingImage, typename TDisplacementField>
typename FastSymmetricForcesDemonsRegistrationFunction<TFixedImage, TMovingImage, TDisplacementField>::PixelType
FastSymmetricForcesDemonsRegistrationFunction<TFixedImage, TMovingImage, TDisplacementField>::ComputeUpdate(
  const NeighborhoodType & it,
  void *                   gd,
  const FloatOffsetType &  itkNotUsed(offset))
{
  auto *          globalData = (GlobalDataStruct *)gd;
  const IndexType FirstIndex = this->GetFixedImage()->GetLargestPossibleRegion().GetIndex();
  const IndexType LastIndex = this->GetFixedImage()->GetLargestPossibleRegion().GetIndex() +
                              this->GetFixedImage()->GetLargestPossibleRegion().GetSize();

  const IndexType index = it.GetIndex();

  // Get fixed image related information
  // Note: no need to check the index is within
  // fixed image buffer. This is done by the external filter.
  const auto                fixedValue = (double)this->GetFixedImage()->GetPixel(index);
  const CovariantVectorType fixedGradient = m_FixedImageGradientCalculator->EvaluateAtIndex(index);

  // Get moving image related information
  // use warped moving image to get moving value and gradient fast(er).
  const auto                movingValue = (double)m_MovingImageWarper->GetOutput()->GetPixel(index);
  const CovariantVectorType movingGradient = m_WarpedMovingImageGradientCalculator->EvaluateAtIndex(index);

  // unfortunately (since it's a little redundant) we still need the mapped
  // center point coordinates
  PointType mappedCenterPoint;

  this->GetFixedImage()->TransformIndexToPhysicalPoint(index, mappedCenterPoint);
  for (unsigned int dim = 0; dim < ImageDimension; dim++)
  {
    mappedCenterPoint[dim] += it.GetCenterPixel()[dim];
  }

  /**
   * Compute Update.
   * In the original equation the denominator is defined as
   *
   *         (g-f)^2 + (moving_grad+fixed_grad)_mag^2
   *
   * However there is a mismatch in units between the two terms.
   * The units for the second term is intensity^2/mm^2 while the
   * units for the first term is intensity^2. This mismatch is particularly
   * problematic when the fixed image does not have unit spacing.
   * In this implementation, we normalize the first term by a factor K,
   * such that denominator = (g-f)^2/K + grad_mag^2
   * where K = mean square spacing to compensate for the mismatch in units.
   */
  double fixedPlusMovingGradientSquaredMagnitude = 0;
  for (unsigned int dim = 0; dim < ImageDimension; dim++)
  {
    fixedPlusMovingGradientSquaredMagnitude += itk::Math::sqr(fixedGradient[dim] + movingGradient[dim]);
  }

  const double speedValue = fixedValue - movingValue;
  const double denominator = itk::Math::sqr(speedValue) / m_Normalizer + fixedPlusMovingGradientSquaredMagnitude;

  PixelType update;
  if (itk::Math::abs(speedValue) < m_IntensityDifferenceThreshold || denominator < m_DenominatorThreshold)
  {
    update.Fill(0.0);
  }
  else
  {
    for (unsigned int j = 0; j < ImageDimension; j++)
    {
      update[j] = 2 * speedValue * (movingGradient[j] + fixedGradient[j]) / denominator;
    }
  }

  // update the squared change value
  PointType newMappedCenterPoint;
  bool      IsOutsideRegion = false;
  for (unsigned int j = 0; j < ImageDimension; j++)
  {
    if (globalData)
    {
      globalData->m_SumOfSquaredChange += itk::Math::sqr(update[j]);
      newMappedCenterPoint[j] = mappedCenterPoint[j] + update[j];
      if (index[j] < (FirstIndex[j] + 2) || index[j] > (LastIndex[j] - 3))
      {
        IsOutsideRegion = true;
      }
    }
  }

  // update the metric with the latest deformable field
  double newMovingValue = 0;
  if (globalData)
  {
    // do not consider voxel on the border (2 voxels) as there are often
    // artefacts
    // which falsify the metric
    if (!IsOutsideRegion)
    {
      if (m_MovingImageInterpolator->IsInsideBuffer(newMappedCenterPoint))
      {
        newMovingValue = m_MovingImageInterpolator->Evaluate(newMappedCenterPoint);
      }
      else
      {
        newMovingValue = 0;
      }
      globalData->m_SumOfSquaredDifference += itk::Math::sqr(fixedValue - newMovingValue);
      globalData->m_NumberOfPixelsProcessed += 1;
    }
  }
  return update;
}

/**
 * Update the metric and release the per-thread-global data.
 */
template <typename TFixedImage, typename TMovingImage, typename TDisplacementField>
void
FastSymmetricForcesDemonsRegistrationFunction<TFixedImage, TMovingImage, TDisplacementField>::ReleaseGlobalDataPointer(
  void * gd) const
{
  auto * globalData = (GlobalDataStruct *)gd;

  m_MetricCalculationLock.lock();
  m_SumOfSquaredDifference += globalData->m_SumOfSquaredDifference;
  m_NumberOfPixelsProcessed += globalData->m_NumberOfPixelsProcessed;
  m_SumOfSquaredChange += globalData->m_SumOfSquaredChange;
  if (m_NumberOfPixelsProcessed)
  {
    m_Metric = m_SumOfSquaredDifference / static_cast<double>(m_NumberOfPixelsProcessed);
    m_RMSChange = std::sqrt(m_SumOfSquaredChange / static_cast<double>(m_NumberOfPixelsProcessed));
  }
  m_MetricCalculationLock.unlock();

  delete globalData;
}
} // end namespace itk

#endif