/*=========================================================================
 *
 *  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 itkWeightedCovarianceSampleFilter_hxx
#define itkWeightedCovarianceSampleFilter_hxx

#include "itkWeightedMeanSampleFilter.h"

namespace itk
{
namespace Statistics
{
template <typename TSample>
WeightedCovarianceSampleFilter<TSample>::WeightedCovarianceSampleFilter()
{
  this->ProcessObject::SetNthInput(1, nullptr);
}

template <typename TSample>
inline void
WeightedCovarianceSampleFilter<TSample>::GenerateData()
{
  // if weighting function is specified, use it to compute the mean
  const InputWeightingFunctionObjectType * functionObject = this->GetWeightingFunctionInput();

  if (functionObject != nullptr)
  {
    this->ComputeCovarianceMatrixWithWeightingFunction();
    return;
  }

  // if weight array is specified use it to compute the covariance
  const InputWeightArrayObjectType * weightArrayObject = this->GetWeightsInput();

  if (weightArrayObject != nullptr)
  {
    this->ComputeCovarianceMatrixWithWeights();
    return;
  }

  // Otherwise compute the regular covariance matrix ( without weight
  // coefficients)
  Superclass::GenerateData();
}

template <typename TSample>
inline void
WeightedCovarianceSampleFilter<TSample>::ComputeCovarianceMatrixWithWeightingFunction()
{
  // set up input / output
  const SampleType * input = this->GetInput();

  MeasurementVectorSizeType measurementVectorSize = input->GetMeasurementVectorSize();

  auto * decoratedOutput = itkDynamicCastInDebugMode<MatrixDecoratedType *>(this->ProcessObject::GetOutput(0));

  MatrixType output = decoratedOutput->Get();
  output.SetSize(measurementVectorSize, measurementVectorSize);
  output.Fill(typename MatrixType::ValueType{});

  auto * decoratedMeanOutput =
    itkDynamicCastInDebugMode<MeasurementVectorDecoratedType *>(this->ProcessObject::GetOutput(1));

  // calculate mean
  const WeightingFunctionType * const weightingFunction = this->GetWeightingFunction();

  using WeightedMeanFilterType = WeightedMeanSampleFilter<SampleType>;
  auto meanFilter = WeightedMeanFilterType::New();

  meanFilter->SetInput(input);
  meanFilter->SetWeightingFunction(weightingFunction);
  meanFilter->Update();

  const typename WeightedMeanFilterType::MeasurementVectorRealType mean = meanFilter->GetMean();
  decoratedMeanOutput->Set(mean);

  // covariance algorithm
  MeasurementVectorRealType diff;
  NumericTraits<MeasurementVectorRealType>::SetLength(diff, measurementVectorSize);

  WeightValueType totalWeight{};

  WeightValueType totalSquaredWeight{};

  typename SampleType::ConstIterator       iter = input->Begin();
  const typename SampleType::ConstIterator end = input->End();

  // fills the lower triangle and the diagonal cells in the covariance matrix
  for (; iter != end; ++iter)
  {
    const MeasurementVectorType & measurement = iter.GetMeasurementVector();

    const typename SampleType::AbsoluteFrequencyType frequency = iter.GetFrequency();

    const WeightValueType rawWeight = weightingFunction->Evaluate(measurement);

    const WeightValueType weight = (rawWeight * static_cast<WeightValueType>(frequency));
    totalWeight += weight;
    totalSquaredWeight += (weight * weight);

    for (unsigned int dim = 0; dim < measurementVectorSize; ++dim)
    {
      const auto component = static_cast<MeasurementRealType>(measurement[dim]);

      diff[dim] = (component - mean[dim]);
    }

    // updates the covariance matrix
    for (unsigned int row = 0; row < measurementVectorSize; ++row)
    {
      for (unsigned int col = 0; col < row + 1; ++col)
      {
        output(row, col) += (static_cast<MeasurementRealType>(weight) * diff[row] * diff[col]);
      }
    }
  }

  // fills the upper triangle using the lower triangle
  for (unsigned int row = 1; row < measurementVectorSize; ++row)
  {
    for (unsigned int col = 0; col < row; ++col)
    {
      output(col, row) = output(row, col);
    }
  }

  const double normalizationFactor = (totalWeight - (totalSquaredWeight / totalWeight));

  if (normalizationFactor > itk::Math::eps)
  {
    const double inverseNormalizationFactor = 1.0 / normalizationFactor;

    output *= inverseNormalizationFactor;
  }
  else
  {
    itkExceptionMacro("Normalization factor was too close to zero. Value = " << normalizationFactor);
  }

  decoratedOutput->Set(output);
}

template <typename TSample>
inline void
WeightedCovarianceSampleFilter<TSample>::ComputeCovarianceMatrixWithWeights()
{
  // set up input / output
  const SampleType * input = this->GetInput();

  MeasurementVectorSizeType measurementVectorSize = input->GetMeasurementVectorSize();

  auto * decoratedOutput = itkDynamicCastInDebugMode<MatrixDecoratedType *>(this->ProcessObject::GetOutput(0));

  MatrixType output = decoratedOutput->Get();
  output.SetSize(measurementVectorSize, measurementVectorSize);
  output.Fill(typename MatrixType::ValueType{});

  auto * decoratedMeanOutput =
    itkDynamicCastInDebugMode<MeasurementVectorDecoratedType *>(this->ProcessObject::GetOutput(1));

  // calculate mean
  const WeightArrayType & weightsArray = this->GetWeights();

  using WeightedMeanFilterType = WeightedMeanSampleFilter<SampleType>;
  auto meanFilter = WeightedMeanFilterType::New();

  meanFilter->SetInput(input);
  meanFilter->SetWeights(weightsArray);
  meanFilter->Update();

  const typename WeightedMeanFilterType::MeasurementVectorRealType mean = meanFilter->GetMean();
  decoratedMeanOutput->Set(mean);

  // covariance algorithm
  MeasurementVectorRealType diff;
  NumericTraits<MeasurementVectorRealType>::SetLength(diff, measurementVectorSize);

  WeightValueType totalWeight{};

  WeightValueType totalSquaredWeight{};

  typename SampleType::ConstIterator       iter = input->Begin();
  const typename SampleType::ConstIterator end = input->End();

  // fills the lower triangle and the diagonal cells in the covariance matrix
  for (unsigned int sampleVectorIndex = 0; iter != end; ++iter, ++sampleVectorIndex)
  {
    const MeasurementVectorType & measurement = iter.GetMeasurementVector();

    const typename SampleType::AbsoluteFrequencyType frequency = iter.GetFrequency();

    const WeightValueType rawWeight = weightsArray[sampleVectorIndex];

    const WeightValueType weight = (rawWeight * static_cast<WeightValueType>(frequency));
    totalWeight += weight;
    totalSquaredWeight += (weight * weight);

    for (unsigned int dim = 0; dim < measurementVectorSize; ++dim)
    {
      const auto component = static_cast<MeasurementRealType>(measurement[dim]);

      diff[dim] = (component - mean[dim]);
    }

    // updates the covariance matrix
    for (unsigned int row = 0; row < measurementVectorSize; ++row)
    {
      for (unsigned int col = 0; col < row + 1; ++col)
      {
        output(row, col) += (static_cast<MeasurementRealType>(weight) * diff[row] * diff[col]);
      }
    }
  }

  // fills the upper triangle using the lower triangle
  for (unsigned int row = 1; row < measurementVectorSize; ++row)
  {
    for (unsigned int col = 0; col < row; ++col)
    {
      output(col, row) = output(row, col);
    }
  }

  const double normalizationFactor = (totalWeight - (totalSquaredWeight / totalWeight));

  if (normalizationFactor > itk::Math::eps)
  {
    const double inverseNormalizationFactor = 1.0 / normalizationFactor;

    output *= inverseNormalizationFactor;
  }
  else
  {
    itkExceptionMacro("Normalization factor was too close to zero. Value = " << normalizationFactor);
  }

  decoratedOutput->Set(output);
}
} // end of namespace Statistics
} // end of namespace itk

#endif
