/*=========================================================================
 *
 *  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 itkGaussianMixtureModelComponent_hxx
#define itkGaussianMixtureModelComponent_hxx

#include <iostream>

#include "itkMath.h"

namespace itk
{
namespace Statistics
{
template <typename TSample>
GaussianMixtureModelComponent<TSample>::GaussianMixtureModelComponent()
{
  m_MeanEstimator = MeanEstimatorType::New();
  m_CovarianceEstimator = CovarianceEstimatorType::New();
  m_GaussianMembershipFunction = NativeMembershipFunctionType::New();
  this->SetMembershipFunction((MembershipFunctionType *)m_GaussianMembershipFunction.GetPointer());
  m_Mean.Fill(0.0);
  m_Covariance.SetIdentity();
}

template <typename TSample>
void
GaussianMixtureModelComponent<TSample>::PrintSelf(std::ostream & os, Indent indent) const
{
  Superclass::PrintSelf(os, indent);

  os << indent << "Mean: " << m_Mean << std::endl;
  os << indent << "Covariance: " << m_Covariance << std::endl;
  os << indent << "Mean Estimator: " << m_MeanEstimator << std::endl;
  os << indent << "Covariance Estimator: " << m_CovarianceEstimator << std::endl;
  os << indent << "GaussianMembershipFunction: " << m_GaussianMembershipFunction << std::endl;
}

template <typename TSample>
void
GaussianMixtureModelComponent<TSample>::SetSample(const TSample * sample)
{
  Superclass::SetSample(sample);

  m_MeanEstimator->SetInput(sample);
  m_CovarianceEstimator->SetInput(sample);

  const MeasurementVectorSizeType measurementVectorLength = sample->GetMeasurementVectorSize();
  m_GaussianMembershipFunction->SetMeasurementVectorSize(measurementVectorLength);

  NumericTraits<MeasurementVectorType>::SetLength(m_Mean, measurementVectorLength);
  m_Covariance.SetSize(measurementVectorLength, measurementVectorLength);

  m_Mean.Fill(0.0);

  m_Covariance.Fill(0.0);

  typename NativeMembershipFunctionType::MeanVectorType mean;

  NumericTraits<typename NativeMembershipFunctionType::MeanVectorType>::SetLength(mean, measurementVectorLength);

  for (unsigned int i = 0; i < measurementVectorLength; ++i)
  {
    mean[i] = m_Mean[i];
  }

  m_GaussianMembershipFunction->SetMean(mean);
}

template <typename TSample>
void
GaussianMixtureModelComponent<TSample>::SetParameters(const ParametersType & parameters)
{
  Superclass::SetParameters(parameters);

  unsigned int paramIndex = 0;
  unsigned int i, j;

  bool changed = false;

  MeasurementVectorSizeType measurementVectorSize = this->GetSample()->GetMeasurementVectorSize();

  for (i = 0; i < measurementVectorSize; ++i)
  {
    if (Math::NotExactlyEquals(m_Mean[i], parameters[paramIndex]))
    {
      m_Mean[i] = parameters[paramIndex];
      changed = true;
    }

    ++paramIndex;
  }

  typename NativeMembershipFunctionType::MeanVectorType mean;

  NumericTraits<typename NativeMembershipFunctionType::MeanVectorType>::SetLength(mean, measurementVectorSize);

  for (i = 0; i < measurementVectorSize; ++i)
  {
    mean[i] = m_Mean[i];
  }

  m_GaussianMembershipFunction->SetMean(mean);

  for (i = 0; i < measurementVectorSize; ++i)
  {
    for (j = 0; j < measurementVectorSize; ++j)
    {
      if (Math::NotExactlyEquals(m_Covariance.GetVnlMatrix().get(i, j), parameters[paramIndex]))
      {
        m_Covariance.GetVnlMatrix().put(i, j, parameters[paramIndex]);
        changed = true;
      }
      ++paramIndex;
    }
  }
  m_GaussianMembershipFunction->SetCovariance(m_Covariance);

  this->AreParametersModified(changed);
}

template <typename TSample>
double
GaussianMixtureModelComponent<TSample>::CalculateParametersChange()
{
  unsigned int i, j;

  typename MeanVectorType::MeasurementVectorType meanEstimate = m_MeanEstimator->GetMean();

  CovarianceMatrixType                                 covEstimateDecoratedObject = m_CovarianceEstimator->GetOutput();
  typename CovarianceMatrixType::MeasurementVectorType covEstimate = covEstimateDecoratedObject->et();

  double                    temp;
  double                    changes = 0.0;
  MeasurementVectorSizeType measurementVectorSize = this->GetSample()->GetMeasurementVectorSize();

  for (i = 0; i < measurementVectorSize; ++i)
  {
    temp = m_Mean[i] - meanEstimate[i];
    changes += temp * temp;
  }

  for (i = 0; i < measurementVectorSize; ++i)
  {
    for (j = 0; j < measurementVectorSize; ++j)
    {
      temp = m_Covariance.GetVnlMatrix().get(i, j) - covEstimate.GetVnlMatrix().get(i, j);
      changes += temp * temp;
    }
  }

  changes = std::sqrt(changes);
  return changes;
}

template <typename TSample>
void
GaussianMixtureModelComponent<TSample>::GenerateData()
{
  MeasurementVectorSizeType measurementVectorSize = this->GetSample()->GetMeasurementVectorSize();

  this->AreParametersModified(false);

  const WeightArrayType & weights = this->GetWeights();

  typename TSample::ConstIterator iter = this->GetSample()->Begin();
  typename TSample::ConstIterator end = this->GetSample()->End();

  typename TSample::MeasurementVectorType measurements;

  // why these lines???
  while (iter != end)
  {
    measurements = iter.GetMeasurementVector();
    ++iter;
  }

  m_MeanEstimator->SetWeights(weights);
  m_MeanEstimator->Update();

  MeasurementVectorSizeType i, j;
  double                    temp;
  double                    changes;
  bool                      changed = false;
  ParametersType            parameters = this->GetFullParameters();
  MeasurementVectorSizeType paramIndex = 0;

  typename MeanEstimatorType::MeasurementVectorType meanEstimate = m_MeanEstimator->GetMean();
  for (i = 0; i < measurementVectorSize; ++i)
  {
    changes = itk::Math::abs(m_Mean[i] - meanEstimate[i]);

    if (changes > this->GetMinimalParametersChange())
    {
      changed = true;
      break;
    }
  }

  if (changed)
  {
    m_Mean = meanEstimate;
    for (paramIndex = 0; paramIndex < measurementVectorSize; ++paramIndex)
    {
      parameters[paramIndex] = meanEstimate[paramIndex];
    }
    this->AreParametersModified(true);
  }
  else
  {
    paramIndex = measurementVectorSize;
  }

  m_CovarianceEstimator->SetWeights(weights);
  m_CovarianceEstimator->Update();
  typename CovarianceEstimatorType::MatrixType covEstimate = m_CovarianceEstimator->GetCovarianceMatrix();

  changed = false;
  for (i = 0; i < measurementVectorSize; ++i)
  {
    if (!changed)
    {
      for (j = 0; j < measurementVectorSize; ++j)
      {
        temp = m_Covariance.GetVnlMatrix().get(i, j) - covEstimate.GetVnlMatrix().get(i, j);
        changes = itk::Math::abs(temp);
        if (changes > this->GetMinimalParametersChange())
        {
          changed = true;
          break;
        }
      }
    }
  }

  if (changed)
  {
    m_Covariance = covEstimate;
    for (i = 0; i < measurementVectorSize; ++i)
    {
      for (j = 0; j < measurementVectorSize; ++j)
      {
        parameters[paramIndex] = covEstimate.GetVnlMatrix().get(i, j);
        ++paramIndex;
      }
    }
    this->AreParametersModified(true);
  }

  // THIS IS NEEDED TO update m_Mean and m_Covariance.SHOULD BE REMOVED
  paramIndex = 0;
  for (i = 0; i < measurementVectorSize; ++i)
  {
    m_Mean[i] = parameters[paramIndex];
    ++paramIndex;
  }

  typename NativeMembershipFunctionType::MeanVectorType mean;
  NumericTraits<typename NativeMembershipFunctionType::MeanVectorType>::SetLength(mean, measurementVectorSize);

  for (i = 0; i < measurementVectorSize; ++i)
  {
    mean[i] = m_Mean[i];
  }
  m_GaussianMembershipFunction->SetMean(mean);

  for (i = 0; i < measurementVectorSize; ++i)
  {
    for (j = 0; j < measurementVectorSize; ++j)
    {
      m_Covariance.GetVnlMatrix().put(i, j, parameters[paramIndex]);
      ++paramIndex;
    }
  }
  m_GaussianMembershipFunction->SetCovariance(m_Covariance);

  Superclass::SetParameters(parameters);
}
} // end of namespace Statistics
} // end of namespace itk

#endif
