/*=========================================================================
 *
 *  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
 *
 *         https://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 itkGaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform_hxx
#define itkGaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform_hxx


#include "itkImageAlgorithm.h"
#include "itkImageDuplicator.h"
#include "itkImageRegionConstIteratorWithIndex.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkImportImageFilter.h"
#include "itkVectorNeighborhoodOperatorImageFilter.h"
#include "itkGaussianOperator.h"

namespace itk
{

template <typename TParametersValueType, unsigned int VDimension>
GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform<TParametersValueType, VDimension>::
  GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform()
  : m_GaussianSpatialSmoothingVarianceForTheUpdateField(3.0)
  , m_GaussianSpatialSmoothingVarianceForTheTotalField(0.5)
  , m_GaussianTemporalSmoothingVarianceForTheUpdateField(0.25)
  , m_GaussianTemporalSmoothingVarianceForTheTotalField(0.0)
{}

template <typename TParametersValueType, unsigned int VDimension>
void
GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform<TParametersValueType, VDimension>::UpdateTransformParameters(
  const DerivativeType & update,
  ScalarType             factor)
{
  TimeVaryingVelocityFieldPointer velocityField = this->GetModifiableVelocityField();

  const typename VelocityFieldType::RegionType & bufferedRegion = velocityField->GetBufferedRegion();
  const SizeValueType                            numberOfPixels = bufferedRegion.GetNumberOfPixels();

  using ImporterType = ImportImageFilter<DisplacementVectorType, VDimension + 1>;
  const bool importFilterWillReleaseMemory = false;

  //
  // Smooth the update field
  //
  bool smoothUpdateField = true;
  if (this->m_GaussianSpatialSmoothingVarianceForTheUpdateField <= 0.0 &&
      this->m_GaussianTemporalSmoothingVarianceForTheUpdateField <= 0.0)
  {
    itkDebugMacro("Not smooothing the update field.");
    smoothUpdateField = false;
  }
  if (smoothUpdateField)
  {
    itkDebugMacro("Smooothing the update field.");

    auto * updateFieldPointer =
      reinterpret_cast<DisplacementVectorType *>(const_cast<DerivativeType &>(update).data_block());

    auto importer = ImporterType::New();
    importer->SetImportPointer(updateFieldPointer, numberOfPixels, importFilterWillReleaseMemory);
    importer->SetRegion(velocityField->GetBufferedRegion());
    importer->SetOrigin(velocityField->GetOrigin());
    importer->SetSpacing(velocityField->GetSpacing());
    importer->SetDirection(velocityField->GetDirection());

    TimeVaryingVelocityFieldPointer updateField = importer->GetOutput();
    updateField->Update();
    updateField->DisconnectPipeline();

    TimeVaryingVelocityFieldPointer updateSmoothField =
      this->GaussianSmoothTimeVaryingVelocityField(updateField,
                                                   this->m_GaussianSpatialSmoothingVarianceForTheUpdateField,
                                                   this->m_GaussianTemporalSmoothingVarianceForTheUpdateField);

    ImageAlgorithm::Copy<VelocityFieldType, VelocityFieldType>(
      updateSmoothField, updateField, updateSmoothField->GetBufferedRegion(), updateField->GetBufferedRegion());
  }

  //
  // Add the update field to the current total field before (optionally)
  // smoothing the total field
  //
  Superclass::UpdateTransformParameters(update, factor);

  //
  // Smooth the total field
  //
  bool smoothTotalField = true;
  if (this->m_GaussianSpatialSmoothingVarianceForTheTotalField <= 0.0 &&
      this->m_GaussianTemporalSmoothingVarianceForTheTotalField <= 0.0)
  {
    itkDebugMacro("Not smooothing the total field.");
    smoothTotalField = false;
  }
  if (smoothTotalField)
  {
    itkDebugMacro("Smooothing the total field.");

    auto importer = ImporterType::New();
    importer->SetImportPointer(velocityField->GetBufferPointer(), numberOfPixels, importFilterWillReleaseMemory);
    importer->SetRegion(velocityField->GetBufferedRegion());
    importer->SetOrigin(velocityField->GetOrigin());
    importer->SetSpacing(velocityField->GetSpacing());
    importer->SetDirection(velocityField->GetDirection());

    TimeVaryingVelocityFieldPointer totalField = importer->GetOutput();
    totalField->Update();
    totalField->DisconnectPipeline();

    TimeVaryingVelocityFieldPointer totalSmoothField =
      this->GaussianSmoothTimeVaryingVelocityField(totalField,
                                                   this->m_GaussianSpatialSmoothingVarianceForTheTotalField,
                                                   this->m_GaussianTemporalSmoothingVarianceForTheTotalField);

    ImageAlgorithm::Copy<VelocityFieldType, VelocityFieldType>(
      totalSmoothField, velocityField, totalSmoothField->GetBufferedRegion(), velocityField->GetBufferedRegion());
  }

  this->IntegrateVelocityField();
}

template <typename TParametersValueType, unsigned int VDimension>
typename GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform<TParametersValueType,
                                                                    VDimension>::TimeVaryingVelocityFieldPointer
GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform<TParametersValueType, VDimension>::
  GaussianSmoothTimeVaryingVelocityField(VelocityFieldType * field,
                                         ScalarType          spatialVariance,
                                         ScalarType          temporalVariance)
{
  if (spatialVariance <= 0.0 && temporalVariance <= 0.0)
  {
    return field;
  }

  using DuplicatorType = ImageDuplicator<VelocityFieldType>;
  auto duplicator = DuplicatorType::New();
  duplicator->SetInputImage(field);
  duplicator->Update();

  TimeVaryingVelocityFieldPointer smoothField = duplicator->GetOutput();

  using SmootherType = VectorNeighborhoodOperatorImageFilter<VelocityFieldType, VelocityFieldType>;
  auto smoother = SmootherType::New();

  for (unsigned int d = 0; d < TimeVaryingVelocityFieldDimension; ++d)
  {
    using GaussianType = GaussianOperator<DisplacementVectorValueType, VDimension + 1>;
    GaussianType gaussian;
    if (d < VDimension)
    {
      gaussian.SetVariance(spatialVariance);
    }
    else
    {
      gaussian.SetVariance(temporalVariance);
    }

    if (gaussian.GetVariance() > 0.0)
    {
      gaussian.SetMaximumError(0.001);
      gaussian.SetDirection(d);
      gaussian.SetMaximumKernelWidth(smoothField->GetRequestedRegion().GetSize()[d]);
      gaussian.CreateDirectional();

      smoother->SetOperator(gaussian);
      smoother->SetInput(smoothField);

      smoothField = smoother->GetOutput();
      smoothField->Update();
      smoothField->DisconnectPipeline();
    }
  }

  // make sure boundary does not move

  constexpr DisplacementVectorType zeroVector{};

  ScalarType weight1 = 1.0;
  if (spatialVariance < 0.5)
  {
    weight1 = 1.0 - 1.0 * (spatialVariance / 0.5);
  }
  ScalarType weight2 = 1.0 - weight1;

  using TimeVaryingVelocityFieldSizeType = typename VelocityFieldType::SizeType;
  using TimeVaryingVelocityFieldIndexType = typename VelocityFieldType::IndexType;

  TimeVaryingVelocityFieldSizeType  size = field->GetLargestPossibleRegion().GetSize();
  TimeVaryingVelocityFieldIndexType startIndex = field->GetLargestPossibleRegion().GetIndex();

  ImageRegionIteratorWithIndex<VelocityFieldType>      fieldIt(field, field->GetLargestPossibleRegion());
  ImageRegionConstIteratorWithIndex<VelocityFieldType> smoothedFieldIt(smoothField,
                                                                       smoothField->GetLargestPossibleRegion());
  for (fieldIt.GoToBegin(), smoothedFieldIt.GoToBegin(); !fieldIt.IsAtEnd(); ++fieldIt, ++smoothedFieldIt)
  {
    TimeVaryingVelocityFieldIndexType index = fieldIt.GetIndex();

    bool isOnBoundary = false;
    for (unsigned int d = 0; d < VDimension; ++d)
    {
      if (index[d] == startIndex[d] || index[d] == static_cast<IndexValueType>(size[d]) - startIndex[d] - 1)
      {
        isOnBoundary = true;
        break;
      }
    }
    if (isOnBoundary)
    {
      fieldIt.Set(zeroVector);
    }
    else
    {
      fieldIt.Set(smoothedFieldIt.Get() * weight1 + fieldIt.Get() * weight2);
    }
  }

  return field;
}

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

  os << indent << "Gaussian smoothing parameters: " << std::endl
     << indent << "Gaussian spatial smoothing variance for the update field: "
     << this->m_GaussianSpatialSmoothingVarianceForTheUpdateField << std::endl
     << indent << "Gaussian temporal smoothing variance for the update field: "
     << this->m_GaussianTemporalSmoothingVarianceForTheUpdateField << std::endl
     << indent << "Gaussian spatial smoothing variance for the total field: "
     << this->m_GaussianSpatialSmoothingVarianceForTheTotalField << std::endl
     << indent << "Gaussian temporal smoothing variance for the total field: "
     << this->m_GaussianTemporalSmoothingVarianceForTheTotalField << std::endl
     << std::endl;
}
} // namespace itk

#endif