/*=========================================================================
 *
 *  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 __itkScalarImageToTextureFeaturesFilter_hxx
#define __itkScalarImageToTextureFeaturesFilter_hxx

#include "itkScalarImageToTextureFeaturesFilter.h"
#include "itkNeighborhood.h"
#include "vnl/vnl_math.h"

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

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

  this->m_GLCMGenerator = CooccurrenceMatrixFilterType::New();
  this->m_GLCMCalculator = TextureFeaturesFilterType::New();
  this->m_GLCMCalculator->SetInput( this->m_GLCMGenerator->GetOutput() );
  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 m_RequestedFeatures since it is const!
  requestedFeatures->push_back(TextureFeaturesFilterType::Energy);
  requestedFeatures->push_back(TextureFeaturesFilterType::Entropy);
  requestedFeatures->push_back(TextureFeaturesFilterType::InverseDifferenceMoment);
  requestedFeatures->push_back(TextureFeaturesFilterType::Inertia);
  requestedFeatures->push_back(TextureFeaturesFilterType::ClusterShade);
  requestedFeatures->push_back(TextureFeaturesFilterType::ClusterProminence);
  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();
  OffsetType          offset;
  OffsetVectorPointer offsets = OffsetVector::New();
  for ( unsigned int d = 0; d < centerIndex; d++ )
    {
    offset = hood.GetOffset(d);
    offsets->push_back(offset);
    }
  this->SetOffsets(offsets);
  m_FastCalculations = false;
}

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

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

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

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

  // For each offset, calculate each feature
  typename OffsetVector::ConstIterator offsetIt;
  int offsetNum, featureNum;
  typedef typename TextureFeaturesFilterType::TextureFeatureName InternalTextureFeatureName;

  for ( offsetIt = m_Offsets->Begin(), offsetNum = 0;
        offsetIt != m_Offsets->End(); offsetIt++, offsetNum++ )
    {
    this->m_GLCMGenerator->SetOffset( offsetIt.Value() );
    this->m_GLCMCalculator->Update();

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

  // Now get the mean and deviaton of each feature across the offsets.
  m_FeatureMeans->clear();
  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);

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

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

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

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

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

  typedef typename TextureFeaturesFilterType::TextureFeatureName InternalTextureFeatureName;
  m_FeatureMeans->clear();
  m_FeatureStandardDeviations->clear();
  typename FeatureNameVector::ConstIterator fnameIt;
  for ( fnameIt = m_RequestedFeatures->Begin();
        fnameIt != m_RequestedFeatures->End(); fnameIt++ )
    {
    m_FeatureMeans->push_back( this->m_GLCMCalculator->GetFeature( (InternalTextureFeatureName)fnameIt.Value() ) );
    m_FeatureStandardDeviations->push_back(0.0);
    }

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

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

template< typename TImage, typename THistogramFrequencyContainer >
void
ScalarImageToTextureFeaturesFilter< 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 ) );

  m_GLCMGenerator->SetInput(image);
}

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

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

template< typename TImage, typename THistogramFrequencyContainer >
void
ScalarImageToTextureFeaturesFilter< 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 ) );

  m_GLCMGenerator->SetMaskImage(image);
}

template< typename TImage, typename THistogramFrequencyContainer >
const TImage *
ScalarImageToTextureFeaturesFilter< TImage, THistogramFrequencyContainer >
::GetInput() const
{
  return itkDynamicCastInDebugMode< const ImageType * >( this->GetPrimaryInput() );
}

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

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

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

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

template< typename TImage, typename THistogramFrequencyContainer >
void
ScalarImageToTextureFeaturesFilter< 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
