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 *
 *  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 itkStandardDeviationPerComponentSampleFilter_hxx
#define itkStandardDeviationPerComponentSampleFilter_hxx

#include "itkStandardDeviationPerComponentSampleFilter.h"
#include "itkMeasurementVectorTraits.h"
#include "itkMath.h"

namespace itk
{
namespace Statistics
{
template< typename TSample >
StandardDeviationPerComponentSampleFilter< TSample >
::StandardDeviationPerComponentSampleFilter()
{
  this->ProcessObject::SetNumberOfRequiredInputs(1);
  this->ProcessObject::SetNumberOfRequiredOutputs(2);

  this->ProcessObject::SetNthOutput( 0, this->MakeOutput(0) );
  this->ProcessObject::SetNthOutput( 1, this->MakeOutput(1) );
}

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

template< typename TSample >
void
StandardDeviationPerComponentSampleFilter< TSample >
::SetInput(const SampleType *sample)
{
  this->ProcessObject::SetNthInput( 0, const_cast< SampleType * >( sample ) );
}

template< typename TSample >
const TSample *
StandardDeviationPerComponentSampleFilter< TSample >
::GetInput() const
{
  return itkDynamicCastInDebugMode< const SampleType * >( this->GetPrimaryInput() );
}

template< typename TSample >
typename StandardDeviationPerComponentSampleFilter< TSample >::DataObjectPointer
StandardDeviationPerComponentSampleFilter< TSample >
::MakeOutput(DataObjectPointerArraySizeType index)
{
  if ( index == 0 )
    {
    using ValueType = typename MeasurementVectorTraitsTypes< MeasurementVectorType >::ValueType;
    MeasurementVectorType standardDeviation;
    NumericTraits<MeasurementVectorType>::SetLength( standardDeviation,
      this->GetMeasurementVectorSize() );
    standardDeviation.Fill(NumericTraits< ValueType >::ZeroValue());
    typename MeasurementVectorRealDecoratedType::Pointer decoratedStandardDeviation =
      MeasurementVectorRealDecoratedType::New();
    decoratedStandardDeviation->Set(standardDeviation);
    return decoratedStandardDeviation.GetPointer();
    }

  if ( index == 1 )
    {
    using ValueType = typename MeasurementVectorTraitsTypes< MeasurementVectorType >::ValueType;
    MeasurementVectorType mean;
    NumericTraits<MeasurementVectorType>::SetLength(mean, this->GetMeasurementVectorSize());
    mean.Fill(NumericTraits< ValueType >::ZeroValue());
    typename MeasurementVectorRealDecoratedType::Pointer decoratedStandardDeviation =
      MeasurementVectorRealDecoratedType::New();
    decoratedStandardDeviation->Set(mean);
    return decoratedStandardDeviation.GetPointer();
    }

  itkExceptionMacro("Trying to create output of index " << index << " larger than the number of output");
}

template< typename TSample >
typename StandardDeviationPerComponentSampleFilter< TSample >::MeasurementVectorSizeType
StandardDeviationPerComponentSampleFilter< TSample >
::GetMeasurementVectorSize() const
{
  const SampleType *input = this->GetInput();

  if ( input )
    {
    return input->GetMeasurementVectorSize();
    }

  // Test if the Vector type knows its length
  MeasurementVectorType     vector;
  MeasurementVectorSizeType measurementVectorSize =
    NumericTraits<MeasurementVectorType>::GetLength(vector);

  if ( measurementVectorSize )
    {
    return measurementVectorSize;
    }

  measurementVectorSize = 1; // Otherwise set it to an innocuous value

  return measurementVectorSize;
}

template< typename TSample >
inline void
StandardDeviationPerComponentSampleFilter< TSample >
::GenerateData()
{
  const SampleType *input = this->GetInput();

  MeasurementVectorSizeType measurementVectorSize = input->GetMeasurementVectorSize();

  auto * decoratedStandardDeviationOutput = itkDynamicCastInDebugMode< MeasurementVectorRealDecoratedType * >(
      this->ProcessObject::GetOutput(0) );

  auto * decoratedMean = itkDynamicCastInDebugMode< MeasurementVectorRealDecoratedType * >(
      this->ProcessObject::GetOutput(1) );

  MeasurementVectorRealType sum;
  MeasurementVectorRealType sumOfSquares;
  MeasurementVectorRealType mean;
  MeasurementVectorRealType standardDeviation;

  NumericTraits<MeasurementVectorRealType>::SetLength(sum, measurementVectorSize);
  NumericTraits<MeasurementVectorRealType>::SetLength(mean, measurementVectorSize);
  NumericTraits<MeasurementVectorRealType>::SetLength(sumOfSquares, measurementVectorSize);
  NumericTraits<MeasurementVectorRealType>::SetLength(standardDeviation, measurementVectorSize);

  sum.Fill(0.0);
  mean.Fill(0.0);
  sumOfSquares.Fill(0.0);
  standardDeviation.Fill(0.0);

  typename TSample::AbsoluteFrequencyType frequency;

  using TotalAbsoluteFrequencyType = typename TSample::TotalAbsoluteFrequencyType;
  TotalAbsoluteFrequencyType totalFrequency =
    itk::NumericTraits< TotalAbsoluteFrequencyType >::ZeroValue();

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

  MeasurementVectorType diff;
  MeasurementVectorType measurements;

  NumericTraits<MeasurementVectorType>::SetLength(diff, measurementVectorSize);
  NumericTraits<MeasurementVectorType>::SetLength(measurements, measurementVectorSize);

  //Compute the mean first
  while ( iter != end )
    {
    frequency = iter.GetFrequency();
    totalFrequency += frequency;
    measurements = iter.GetMeasurementVector();

    for ( unsigned int i = 0; i < measurementVectorSize; ++i )
      {
      double value = measurements[i];
      sum[i] += frequency * value;
      sumOfSquares[i] += frequency * value * value;
      }
    ++iter;
    }

  for ( unsigned int i = 0; i < measurementVectorSize; ++i )
    {
    const double meanValue = sum[i] / totalFrequency;
    mean[i] = meanValue;
    const double variance =
      ( sumOfSquares[i] - meanValue * meanValue * totalFrequency ) / ( totalFrequency - 1.0 );
    standardDeviation[i] = std::sqrt(variance);
    }

  decoratedStandardDeviationOutput->Set(standardDeviation);
  decoratedMean->Set(mean);
}

template< typename TSample >
const typename StandardDeviationPerComponentSampleFilter< TSample >::MeasurementVectorRealDecoratedType *
StandardDeviationPerComponentSampleFilter< TSample >
::GetStandardDeviationPerComponentOutput() const
{
  return static_cast< const MeasurementVectorRealDecoratedType * >( this->ProcessObject::GetOutput(0) );
}

template< typename TSample >
const typename StandardDeviationPerComponentSampleFilter< TSample >::MeasurementVectorRealType
StandardDeviationPerComponentSampleFilter< TSample >
::GetStandardDeviationPerComponent() const
{
  return this->GetStandardDeviationPerComponentOutput()->Get();
}

template< typename TSample >
const typename StandardDeviationPerComponentSampleFilter< TSample >::MeasurementVectorRealDecoratedType *
StandardDeviationPerComponentSampleFilter< TSample >
::GetMeanPerComponentOutput() const
{
  return static_cast< const MeasurementVectorRealDecoratedType * >( this->ProcessObject::GetOutput(1) );
}

template< typename TSample >
const typename StandardDeviationPerComponentSampleFilter< TSample >::MeasurementVectorRealType
StandardDeviationPerComponentSampleFilter< TSample >
::GetMeanPerComponent() const
{
  return this->GetMeanPerComponentOutput()->Get();
}
} // end of namespace Statistics
} // end of namespace itk

#endif
