/*=========================================================================
 *
 *  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 itkScalarImageToRunLengthFeaturesFilter_hxx
#define itkScalarImageToRunLengthFeaturesFilter_hxx

#include "itkScalarImageToRunLengthFeaturesFilter.h"
#include "itkNeighborhood.h"
#include "itkMath.h"

namespace itk
{
namespace Statistics
{
template<typename TImage, typename THistogramFrequencyContainer>
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::ScalarImageToRunLengthFeaturesFilter()
{
  this->SetNumberOfRequiredInputs( 1 );
  this->SetNumberOfRequiredOutputs( 1 );

  for( int i = 0; i < 2; ++i )
    {
    this->ProcessObject::SetNthOutput( i, this->MakeOutput( i ) );
    }

  this->m_RunLengthMatrixGenerator = RunLengthMatrixFilterType::New();
  this->m_FeatureMeans = FeatureValueVector::New();
  this->m_FeatureStandardDeviations = FeatureValueVector::New();

  // Set the requested features to the default value:
  // {Energy, Entropy, InverseDifferenceMoment, Inertia, ClusterShade,
  // ClusterProminence}
  FeatureNameVectorPointer requestedFeatures = FeatureNameVector::New();
  // can't directly set this->m_RequestedFeatures since it is const!

  requestedFeatures->push_back( RunLengthFeaturesFilterType::ShortRunEmphasis );
  requestedFeatures->push_back( RunLengthFeaturesFilterType::LongRunEmphasis );
  requestedFeatures->push_back(
    RunLengthFeaturesFilterType::GreyLevelNonuniformity );
  requestedFeatures->push_back(
    RunLengthFeaturesFilterType::RunLengthNonuniformity );
  requestedFeatures->push_back(
    RunLengthFeaturesFilterType::LowGreyLevelRunEmphasis );
  requestedFeatures->push_back(
    RunLengthFeaturesFilterType::HighGreyLevelRunEmphasis );
  requestedFeatures->push_back(
    RunLengthFeaturesFilterType::ShortRunLowGreyLevelEmphasis );
  requestedFeatures->push_back(
    RunLengthFeaturesFilterType::ShortRunHighGreyLevelEmphasis );
  requestedFeatures->push_back(
    RunLengthFeaturesFilterType::LongRunLowGreyLevelEmphasis );
  requestedFeatures->push_back(
    RunLengthFeaturesFilterType::LongRunHighGreyLevelEmphasis );

  this->SetRequestedFeatures( requestedFeatures );

  // Set the offset directions to their defaults: half of all the possible
  // directions 1 pixel away. (The other half is included by symmetry.)
  // We use a neighborhood iterator to calculate the appropriate offsets.
  typedef Neighborhood<typename ImageType::PixelType,
    ImageType::ImageDimension> NeighborhoodType;
  NeighborhoodType hood;
  hood.SetRadius( 1 );

  // select all "previous" neighbors that are face+edge+vertex
  // connected to the current pixel. do not include the center pixel.
  unsigned int centerIndex = hood.GetCenterNeighborhoodIndex();
  OffsetVectorPointer offsets = OffsetVector::New();
  for( unsigned int d = 0; d < centerIndex; d++ )
    {
    OffsetType offset = hood.GetOffset( d );
    offsets->push_back( offset );
    }
  this->SetOffsets( offsets );
  this->m_FastCalculations = false;
}

template<typename TImage, typename THistogramFrequencyContainer>
typename
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::DataObjectPointer
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::MakeOutput( DataObjectPointerArraySizeType itkNotUsed(idx) )
{
  return FeatureValueVectorDataObjectType::New().GetPointer();
}

template<typename TImage, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::GenerateData(void)
{
  if ( this->m_FastCalculations )
    {
    this->FastCompute();
    }
  else
    {
    this->FullCompute();
    }
}

template<typename TImage, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::FullCompute()
{
  size_t numOffsets = this->m_Offsets->size();
  size_t numFeatures = this->m_RequestedFeatures->size();
  double **features;

  features = new double *[numOffsets];
  for( size_t i = 0; i < numOffsets; i++ )
    {
    features[i] = new double[numFeatures];
    }

  // For each offset, calculate each feature
  typename OffsetVector::ConstIterator offsetIt;
  size_t offsetNum, featureNum;
  typedef typename RunLengthFeaturesFilterType::RunLengthFeatureName
    InternalRunLengthFeatureName;

  for( offsetIt = this->m_Offsets->Begin(), offsetNum = 0;
    offsetIt != this->m_Offsets->End(); offsetIt++, offsetNum++ )
    {
    this->m_RunLengthMatrixGenerator->SetOffset( offsetIt.Value() );
    this->m_RunLengthMatrixGenerator->Update();
    typename RunLengthFeaturesFilterType::Pointer runLengthMatrixCalculator =
      RunLengthFeaturesFilterType::New();
    runLengthMatrixCalculator->SetInput(
      this->m_RunLengthMatrixGenerator->GetOutput() );
    runLengthMatrixCalculator->Update();

    typename FeatureNameVector::ConstIterator fnameIt;
    for( fnameIt = this->m_RequestedFeatures->Begin(), featureNum = 0;
      fnameIt != this->m_RequestedFeatures->End(); fnameIt++, featureNum++ )
      {
      features[offsetNum][featureNum] = runLengthMatrixCalculator->GetFeature(
        ( InternalRunLengthFeatureName )fnameIt.Value() );
      }
    }

  // Now get the mean and deviaton of each feature across the offsets.
  this->m_FeatureMeans->clear();
  this->m_FeatureStandardDeviations->clear();
  double *tempFeatureMeans = new double[numFeatures];
  double *tempFeatureDevs = new double[numFeatures];

  /*Compute incremental mean and SD, a la Knuth, "The  Art of Computer
    Programming, Volume 2: Seminumerical Algorithms",  section 4.2.2.
    Compute mean and standard deviation using the recurrence relation:
    M(1) = x(1), M(k) = M(k-1) + (x(k) - M(k-1) ) / k
    S(1) = 0, S(k) = S(k-1) + (x(k) - M(k-1)) * (x(k) - M(k))
    for 2 <= k <= n, then
    sigma = std::sqrt(S(n) / n) (or divide by n-1 for sample SD instead of
    population SD).
  */

  // Set up the initial conditions (k = 1)
  for( featureNum = 0; featureNum < numFeatures; featureNum++ )
    {
    tempFeatureMeans[featureNum] = features[0][featureNum];
    tempFeatureDevs[featureNum] = 0;
    }
  // Run through the recurrence (k = 2 ... N)
  for( offsetNum = 1; offsetNum < numOffsets; offsetNum++ )
    {
    int k = offsetNum + 1;
    for( featureNum = 0; featureNum < numFeatures; featureNum++ )
      {
      double M_k_minus_1 = tempFeatureMeans[featureNum];
      double S_k_minus_1 = tempFeatureDevs[featureNum];
      double x_k = features[offsetNum][featureNum];

      double M_k = M_k_minus_1 + ( x_k - M_k_minus_1 ) / k;
      double S_k = S_k_minus_1 + ( x_k - M_k_minus_1 ) * ( x_k - M_k );

      tempFeatureMeans[featureNum] = M_k;
      tempFeatureDevs[featureNum] = S_k;
      }
    }
  for( featureNum = 0; featureNum < numFeatures; featureNum++ )
    {
    tempFeatureDevs[featureNum] = std::sqrt( tempFeatureDevs[featureNum] /
      numOffsets );

    this->m_FeatureMeans->push_back( tempFeatureMeans[featureNum] );
    this->m_FeatureStandardDeviations->push_back( tempFeatureDevs[featureNum] );
    }

  FeatureValueVectorDataObjectType *meanOutputObject =
    itkDynamicCastInDebugMode<FeatureValueVectorDataObjectType *>( this->ProcessObject::GetOutput( 0 ) );
  meanOutputObject->Set( this->m_FeatureMeans );

  FeatureValueVectorDataObjectType *standardDeviationOutputObject =
    itkDynamicCastInDebugMode<FeatureValueVectorDataObjectType *>( this->ProcessObject::GetOutput( 1 ) );
  standardDeviationOutputObject->Set( this->m_FeatureStandardDeviations );

  delete[] tempFeatureMeans;
  delete[] tempFeatureDevs;
  for( size_t i = 0; i < numOffsets; i++ )
    {
    delete[] features[i];
    }
  delete[] features;
}

template<typename TImage, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::FastCompute()
{
  // Compute the feature for the first offset
  typename OffsetVector::ConstIterator offsetIt = this->m_Offsets->Begin();
  this->m_RunLengthMatrixGenerator->SetOffset( offsetIt.Value() );

  this->m_RunLengthMatrixGenerator->Update();
  typename RunLengthFeaturesFilterType::Pointer runLengthMatrixCalculator =
    RunLengthFeaturesFilterType::New();
  runLengthMatrixCalculator->SetInput(
    this->m_RunLengthMatrixGenerator->GetOutput() );
  runLengthMatrixCalculator->Update();

  typedef typename RunLengthFeaturesFilterType::RunLengthFeatureName
    InternalRunLengthFeatureName;
  this->m_FeatureMeans->clear();
  this->m_FeatureStandardDeviations->clear();
  typename FeatureNameVector::ConstIterator fnameIt;
  for( fnameIt = this->m_RequestedFeatures->Begin();
    fnameIt != this->m_RequestedFeatures->End(); fnameIt++ )
    {
    this->m_FeatureMeans->push_back( runLengthMatrixCalculator->GetFeature(
      ( InternalRunLengthFeatureName )fnameIt.Value() ) );
    this->m_FeatureStandardDeviations->push_back( 0.0 );
    }

  FeatureValueVectorDataObjectType *meanOutputObject =
    itkDynamicCastInDebugMode<FeatureValueVectorDataObjectType *>( this->ProcessObject::GetOutput( 0 ) );
  meanOutputObject->Set( this->m_FeatureMeans );

  FeatureValueVectorDataObjectType *standardDeviationOutputObject =
    itkDynamicCastInDebugMode<FeatureValueVectorDataObjectType *>( this->ProcessObject::GetOutput( 1 ) );
  standardDeviationOutputObject->Set( this->m_FeatureStandardDeviations );
}

template<typename TImage, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::SetInput( const ImageType *image )
{
  // Process object is not const-correct so the const_cast is required here
  this->ProcessObject::SetNthInput( 0,
    const_cast<ImageType *>( image ) );

  this->m_RunLengthMatrixGenerator->SetInput( image );
}

template<typename TImage, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::SetNumberOfBinsPerAxis( unsigned int numberOfBins )
{
  itkDebugMacro( "setting NumberOfBinsPerAxis to " << numberOfBins );
  this->m_RunLengthMatrixGenerator->SetNumberOfBinsPerAxis( numberOfBins );
  this->Modified();
}

template<typename TImage, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::SetPixelValueMinMax( PixelType min, PixelType max )
{
  itkDebugMacro( "setting Min to " << min << "and Max to " << max );
  this->m_RunLengthMatrixGenerator->SetPixelValueMinMax( min, max );
  this->Modified();
}

template<typename TImage, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::SetDistanceValueMinMax( double min, double max )
{
  itkDebugMacro( "setting Min to " << min << "and Max to " << max );
  this->m_RunLengthMatrixGenerator->SetDistanceValueMinMax( min, max );
  this->Modified();
}

template<typename TImage, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::SetMaskImage( const ImageType *image )
{
  // Process object is not const-correct so the const_cast is required here
  this->ProcessObject::SetNthInput( 1,
    const_cast< ImageType * >( image ) );

  this->m_RunLengthMatrixGenerator->SetMaskImage( image );
}

template<typename TImage, typename THistogramFrequencyContainer>
const TImage *
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::GetInput() const
{
  if ( this->GetNumberOfInputs() < 1 )
    {
    return ITK_NULLPTR;
    }
  return static_cast<const ImageType *>( this->ProcessObject::GetInput( 0 ) );
}

template<typename TImage, typename THistogramFrequencyContainer>
const typename
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::FeatureValueVectorDataObjectType *
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::GetFeatureMeansOutput() const
{
  return itkDynamicCastInDebugMode<const FeatureValueVectorDataObjectType *>
    (this->ProcessObject::GetOutput( 0 ) );
}

template<typename TImage, typename THistogramFrequencyContainer>
const typename
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::FeatureValueVectorDataObjectType *
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::GetFeatureStandardDeviationsOutput() const
{
  return itkDynamicCastInDebugMode< const FeatureValueVectorDataObjectType * >
    ( this->ProcessObject::GetOutput( 1 ) );
}

template<typename TImage, typename THistogramFrequencyContainer>
const TImage *
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::GetMaskImage() const
{
  if ( this->GetNumberOfInputs() < 2 )
    {
    return ITK_NULLPTR;
    }
  return static_cast< const ImageType *>( this->ProcessObject::GetInput( 1 ) );
}

template<typename TImage, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::SetInsidePixelValue( PixelType insidePixelValue )
{
  itkDebugMacro( "setting InsidePixelValue to " << insidePixelValue );
  this->m_RunLengthMatrixGenerator->SetInsidePixelValue( insidePixelValue );
  this->Modified();
}

template<typename TImage, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthFeaturesFilter<TImage, THistogramFrequencyContainer>
::PrintSelf(std::ostream & os, Indent indent) const
{
  Superclass::PrintSelf(os, indent);
  os << indent << "RequestedFeatures: "
     << this->GetRequestedFeatures() << std::endl;
  os << indent << "FeatureStandardDeviations: "
     << this->GetFeatureStandardDeviations() << std::endl;
  os << indent << "FastCalculations: "
     << this->GetFastCalculations() << std::endl;
  os << indent << "Offsets: " << this->GetOffsets() << std::endl;
  os << indent << "FeatureMeans: " << this->GetFeatureMeans() << std::endl;
}
} // end of namespace Statistics
} // end of namespace itk

#endif