/*=========================================================================
 *
 *  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 __itkHistogramToRunLengthFeaturesFilter_hxx
#define __itkHistogramToRunLengthFeaturesFilter_hxx

#include "itkHistogramToRunLengthFeaturesFilter.h"

#include "itkNumericTraits.h"
#include "vnl/vnl_math.h"

namespace itk {
namespace Statistics {

//constructor
template<typename THistogram>
HistogramToRunLengthFeaturesFilter<THistogram>
::HistogramToRunLengthFeaturesFilter()
{
  this->ProcessObject::SetNumberOfRequiredInputs( 1 );

  // allocate the data objects for the outputs which are
  // just decorators real types
  for( unsigned int i = 0; i < 10; i++ )
    {
    this->ProcessObject::SetNthOutput( i, this->MakeOutput( i ) );
    }
}

template<typename THistogram>
void
HistogramToRunLengthFeaturesFilter< THistogram>
::SetInput( const HistogramType *histogram )
{
  this->ProcessObject::SetNthInput( 0, const_cast<HistogramType*>( histogram ) );
}

template<typename THistogram>
const typename
HistogramToRunLengthFeaturesFilter<THistogram>::HistogramType *
HistogramToRunLengthFeaturesFilter< THistogram>
::GetInput() const
{
  if ( this->GetNumberOfInputs() < 1 )
    {
    return ITK_NULLPTR;
    }
  return itkDynamicCastInDebugMode<const HistogramType *>(this->ProcessObject::GetInput( 0 ) );
}

template<typename THistogram>
typename
HistogramToRunLengthFeaturesFilter<THistogram>::DataObjectPointer
HistogramToRunLengthFeaturesFilter<THistogram>
::MakeOutput( DataObjectPointerArraySizeType itkNotUsed( idx ) )
{
  return MeasurementObjectType::New().GetPointer();
}

template<typename THistogram>
void
HistogramToRunLengthFeaturesFilter< THistogram>::
GenerateData( void )
{
  const HistogramType * inputHistogram = this->GetInput();

  this->m_TotalNumberOfRuns = static_cast<unsigned long>
    ( inputHistogram->GetTotalFrequency() );

  MeasurementType shortRunEmphasis = NumericTraits<MeasurementType>::Zero;
  MeasurementType longRunEmphasis = NumericTraits<MeasurementType>::Zero;
  MeasurementType greyLevelNonuniformity = NumericTraits<MeasurementType>::Zero;
  MeasurementType runLengthNonuniformity = NumericTraits<MeasurementType>::Zero;
  MeasurementType lowGreyLevelRunEmphasis = NumericTraits<MeasurementType>::Zero;
  MeasurementType highGreyLevelRunEmphasis =
    NumericTraits<MeasurementType>::Zero;
  MeasurementType shortRunLowGreyLevelEmphasis =
    NumericTraits<MeasurementType>::Zero;
  MeasurementType shortRunHighGreyLevelEmphasis =
    NumericTraits<MeasurementType>::Zero;
  MeasurementType longRunLowGreyLevelEmphasis =
    NumericTraits<MeasurementType>::Zero;
  MeasurementType longRunHighGreyLevelEmphasis =
    NumericTraits<MeasurementType>::Zero;

  vnl_vector<double> greyLevelNonuniformityVector(
    inputHistogram->GetSize()[0], 0.0 );
  vnl_vector<double> runLengthNonuniformityVector(
    inputHistogram->GetSize()[1], 0.0 );

  typedef typename HistogramType::ConstIterator HistogramIterator;
  for ( HistogramIterator hit = inputHistogram->Begin();
          hit != inputHistogram->End(); ++hit )
    {
    MeasurementType frequency = hit.GetFrequency();
    if ( frequency == 0 )
      {
      continue;
      }
    MeasurementVectorType measurement = hit.GetMeasurementVector();
    IndexType index =
      inputHistogram->GetIndex( hit.GetInstanceIdentifier() );

    double i2 = static_cast<double>( ( index[0] + 1 ) * ( index[0] + 1 ) );
    double j2 = static_cast<double>( ( index[1] + 1 ) * ( index[1] + 1 ) );

    // Traditional measures
    shortRunEmphasis += ( frequency / j2 );
    longRunEmphasis += ( frequency * j2 );

    greyLevelNonuniformityVector[index[0]] += frequency;
    runLengthNonuniformityVector[index[1]] += frequency;

    // measures from Chu et al.
    lowGreyLevelRunEmphasis += ( frequency / i2 );
    highGreyLevelRunEmphasis += ( frequency * i2 );

    // measures from Dasarathy and Holder
    shortRunLowGreyLevelEmphasis += ( frequency / ( i2 * j2 ) );
    shortRunHighGreyLevelEmphasis += ( frequency * i2 / j2 );
    longRunLowGreyLevelEmphasis += ( frequency * j2 / i2 );
    longRunHighGreyLevelEmphasis += ( frequency * i2 * j2 );
    }
  greyLevelNonuniformity =
    greyLevelNonuniformityVector.squared_magnitude();
  runLengthNonuniformity =
    runLengthNonuniformityVector.squared_magnitude();

  // Normalize all measures by the total number of runs

  shortRunEmphasis       /=
    static_cast<double>( this->m_TotalNumberOfRuns );
  longRunEmphasis        /=
    static_cast<double>( this->m_TotalNumberOfRuns );
  greyLevelNonuniformity /=
    static_cast<double>( this->m_TotalNumberOfRuns );
  runLengthNonuniformity /=
    static_cast<double>( this->m_TotalNumberOfRuns );

  lowGreyLevelRunEmphasis /=
    static_cast<double>( this->m_TotalNumberOfRuns );
  highGreyLevelRunEmphasis /=
    static_cast<double>( this->m_TotalNumberOfRuns );

  shortRunLowGreyLevelEmphasis /=
    static_cast<double>( this->m_TotalNumberOfRuns );
  shortRunHighGreyLevelEmphasis /=
    static_cast<double>( this->m_TotalNumberOfRuns );
  longRunLowGreyLevelEmphasis /=
    static_cast<double>( this->m_TotalNumberOfRuns );
  longRunHighGreyLevelEmphasis /=
    static_cast<double>( this->m_TotalNumberOfRuns );

  MeasurementObjectType* shortRunEmphasisOutputObject =
    static_cast<MeasurementObjectType*>( this->ProcessObject::GetOutput( 0 ) );
  shortRunEmphasisOutputObject->Set( shortRunEmphasis );

  MeasurementObjectType* longRunEmphasisOutputObject =
    static_cast<MeasurementObjectType*>( this->ProcessObject::GetOutput( 1 ) );
  longRunEmphasisOutputObject->Set( longRunEmphasis );

  MeasurementObjectType* greyLevelNonuniformityOutputObject =
    static_cast<MeasurementObjectType*>( this->ProcessObject::GetOutput( 2 ) );
  greyLevelNonuniformityOutputObject->Set( greyLevelNonuniformity );

  MeasurementObjectType* runLengthNonuniformityOutputObject =
    static_cast<MeasurementObjectType*>( this->ProcessObject::GetOutput( 3 ) );
  runLengthNonuniformityOutputObject->Set( runLengthNonuniformity );

  MeasurementObjectType* lowGreyLevelRunEmphasisOutputObject =
    static_cast<MeasurementObjectType*>( this->ProcessObject::GetOutput( 4 ) );
  lowGreyLevelRunEmphasisOutputObject->Set( lowGreyLevelRunEmphasis );

  MeasurementObjectType* highGreyLevelRunEmphasisOutputObject =
    static_cast<MeasurementObjectType*>( this->ProcessObject::GetOutput( 5 ) );
  highGreyLevelRunEmphasisOutputObject->Set( highGreyLevelRunEmphasis );

  MeasurementObjectType* shortRunLowGreyLevelEmphasisOutputObject =
    static_cast<MeasurementObjectType*>( this->ProcessObject::GetOutput( 6 ) );
  shortRunLowGreyLevelEmphasisOutputObject->Set( shortRunLowGreyLevelEmphasis );

  MeasurementObjectType* shortRunHighGreyLevelEmphasisOutputObject =
    static_cast<MeasurementObjectType*>( this->ProcessObject::GetOutput( 7 ) );
  shortRunHighGreyLevelEmphasisOutputObject->Set(
    shortRunHighGreyLevelEmphasis );

  MeasurementObjectType* longRunLowGreyLevelEmphasisOutputObject =
    static_cast<MeasurementObjectType*>( this->ProcessObject::GetOutput( 8 ) );
  longRunLowGreyLevelEmphasisOutputObject->Set( longRunLowGreyLevelEmphasis );

  MeasurementObjectType* longRunHighGreyLevelEmphasisOutputObject =
    static_cast<MeasurementObjectType*>( this->ProcessObject::GetOutput( 9 ) );
  longRunHighGreyLevelEmphasisOutputObject->Set( longRunHighGreyLevelEmphasis );
}

template<typename THistogram>
const
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementObjectType*
HistogramToRunLengthFeaturesFilter<THistogram>
::GetShortRunEmphasisOutput() const
{
  return itkDynamicCastInDebugMode<const MeasurementObjectType*>(this->ProcessObject::GetOutput( 0 ) );
}

template<typename THistogram>
const
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementObjectType*
HistogramToRunLengthFeaturesFilter<THistogram>
::GetLongRunEmphasisOutput() const
{
  return itkDynamicCastInDebugMode<const MeasurementObjectType*>( this->ProcessObject::GetOutput( 1 ) );
}

template<typename THistogram>
const
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementObjectType*
HistogramToRunLengthFeaturesFilter<THistogram>
::GetGreyLevelNonuniformityOutput() const
{
  return itkDynamicCastInDebugMode<const MeasurementObjectType*>(this->ProcessObject::GetOutput( 2 ) );
}

template<typename THistogram>
const
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementObjectType*
HistogramToRunLengthFeaturesFilter<THistogram>
::GetRunLengthNonuniformityOutput() const
{
  return itkDynamicCastInDebugMode<const MeasurementObjectType*>(this->ProcessObject::GetOutput( 3 ) );
}

template<typename THistogram>
const
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementObjectType*
HistogramToRunLengthFeaturesFilter<THistogram>
::GetLowGreyLevelRunEmphasisOutput() const
{
  return itkDynamicCastInDebugMode<const MeasurementObjectType*>( this->ProcessObject::GetOutput( 4 ) );
}

template<typename THistogram>
const
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementObjectType*
HistogramToRunLengthFeaturesFilter<THistogram>
::GetHighGreyLevelRunEmphasisOutput() const
{
  return itkDynamicCastInDebugMode<const MeasurementObjectType*>( this->ProcessObject::GetOutput( 5 ) );
}

template<typename THistogram>
const
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementObjectType*
HistogramToRunLengthFeaturesFilter<THistogram>
::GetShortRunLowGreyLevelEmphasisOutput() const
{
  return itkDynamicCastInDebugMode<const MeasurementObjectType*>( this->ProcessObject::GetOutput( 6 ) );
}

template<typename THistogram>
const
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementObjectType*
HistogramToRunLengthFeaturesFilter<THistogram>
::GetShortRunHighGreyLevelEmphasisOutput() const
{
  return itkDynamicCastInDebugMode<const MeasurementObjectType*>( this->ProcessObject::GetOutput( 7 ) );
}

template<typename THistogram>
const
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementObjectType*
HistogramToRunLengthFeaturesFilter<THistogram>
::GetLongRunLowGreyLevelEmphasisOutput() const
{
  return itkDynamicCastInDebugMode<const MeasurementObjectType*>( this->ProcessObject::GetOutput( 8 ) );
}

template<typename THistogram>
const
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementObjectType*
HistogramToRunLengthFeaturesFilter<THistogram>
::GetLongRunHighGreyLevelEmphasisOutput() const
{
  return itkDynamicCastInDebugMode<const MeasurementObjectType*>( this->ProcessObject::GetOutput( 9 ) );
}

template<typename THistogram>
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementType
HistogramToRunLengthFeaturesFilter<THistogram>
::GetShortRunEmphasis() const
{
  return this->GetShortRunEmphasisOutput()->Get();
}

template<typename THistogram>
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementType
HistogramToRunLengthFeaturesFilter<THistogram>
::GetLongRunEmphasis() const
{
  return this->GetLongRunEmphasisOutput()->Get();
}

template<typename THistogram>
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementType
HistogramToRunLengthFeaturesFilter<THistogram>
::GetGreyLevelNonuniformity() const
{
  return this->GetGreyLevelNonuniformityOutput()->Get();
}

template<typename THistogram>
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementType
HistogramToRunLengthFeaturesFilter<THistogram>
::GetRunLengthNonuniformity() const
{
  return this->GetRunLengthNonuniformityOutput()->Get();
}

template<typename THistogram>
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementType
HistogramToRunLengthFeaturesFilter<THistogram>
::GetLowGreyLevelRunEmphasis() const
{
  return this->GetLowGreyLevelRunEmphasisOutput()->Get();
}
template<typename THistogram>
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementType
HistogramToRunLengthFeaturesFilter<THistogram>
::GetHighGreyLevelRunEmphasis() const
{
  return this->GetHighGreyLevelRunEmphasisOutput()->Get();
}
template<typename THistogram>
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementType
HistogramToRunLengthFeaturesFilter<THistogram>
::GetShortRunLowGreyLevelEmphasis() const
{
  return this->GetShortRunLowGreyLevelEmphasisOutput()->Get();
}
template<typename THistogram>
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementType
HistogramToRunLengthFeaturesFilter<THistogram>
::GetShortRunHighGreyLevelEmphasis() const
{
  return this->GetShortRunHighGreyLevelEmphasisOutput()->Get();
}
template<typename THistogram>
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementType
HistogramToRunLengthFeaturesFilter<THistogram>
::GetLongRunLowGreyLevelEmphasis() const
{
  return this->GetLongRunLowGreyLevelEmphasisOutput()->Get();
}
template<typename THistogram>
typename HistogramToRunLengthFeaturesFilter<THistogram>::MeasurementType
HistogramToRunLengthFeaturesFilter<THistogram>
::GetLongRunHighGreyLevelEmphasis() const
{
  return this->GetLongRunHighGreyLevelEmphasisOutput()->Get();
}

template<typename THistogram>
typename HistogramToRunLengthFeaturesFilter< THistogram>::MeasurementType
HistogramToRunLengthFeaturesFilter<THistogram>
::GetFeature( RunLengthFeatureName feature )
{
  switch( feature )
    {
    case ShortRunEmphasis:
      return this->GetShortRunEmphasis();
    case LongRunEmphasis:
      return this->GetLongRunEmphasis();
    case GreyLevelNonuniformity:
      return this->GetGreyLevelNonuniformity();
    case RunLengthNonuniformity:
      return this->GetRunLengthNonuniformity();
    case LowGreyLevelRunEmphasis:
      return this->GetLowGreyLevelRunEmphasis();
    case HighGreyLevelRunEmphasis:
      return this->GetHighGreyLevelRunEmphasis();
    case ShortRunLowGreyLevelEmphasis:
      return this->GetShortRunLowGreyLevelEmphasis();
    case ShortRunHighGreyLevelEmphasis:
      return this->GetShortRunHighGreyLevelEmphasis();
    case LongRunLowGreyLevelEmphasis:
      return this->GetLongRunLowGreyLevelEmphasis();
    case LongRunHighGreyLevelEmphasis:
      return this->GetLongRunHighGreyLevelEmphasis();
    default:
      return 0;
    }
}

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

} // end of namespace Statistics
} // end of namespace itk


#endif
