/*=========================================================================
 *
 *  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 itkLabelOverlapMeasuresImageFilter_hxx
#define itkLabelOverlapMeasuresImageFilter_hxx

#include "itkLabelOverlapMeasuresImageFilter.h"

#include "itkImageRegionConstIterator.h"
#include "itkProgressReporter.h"

namespace itk {

template<typename TLabelImage>
LabelOverlapMeasuresImageFilter<TLabelImage>
::LabelOverlapMeasuresImageFilter()
{
  // this filter requires two input images
  this->SetNumberOfRequiredInputs( 2 );
}

template<typename TLabelImage>
void
LabelOverlapMeasuresImageFilter<TLabelImage>
::EnlargeOutputRequestedRegion( DataObject *data )
{
  Superclass::EnlargeOutputRequestedRegion( data );
  data->SetRequestedRegionToLargestPossibleRegion();
}


template<typename TLabelImage>
void
LabelOverlapMeasuresImageFilter<TLabelImage>
::AllocateOutputs()
{
  // Pass the source through as the output
  LabelImagePointer image =
    const_cast<TLabelImage *>( this->GetSourceImage() );
  this->GraftOutput(image);
}

template<typename TLabelImage>
void
LabelOverlapMeasuresImageFilter<TLabelImage>
::BeforeThreadedGenerateData()
{
  ThreadIdType numberOfThreads = this->GetNumberOfThreads();

  // Resize the thread temporaries
  this->m_LabelSetMeasuresPerThread.resize( numberOfThreads );

  // Initialize the temporaries
  for( ThreadIdType n = 0; n < numberOfThreads; n++ )
    {
    this->m_LabelSetMeasuresPerThread[n].clear();
    }

  // Initialize the final map
  this->m_LabelSetMeasures.clear();
}

template<typename TLabelImage>
void
LabelOverlapMeasuresImageFilter<TLabelImage>
::AfterThreadedGenerateData()
{
  // Run through the map for each thread and accumulate the set measures.
  for( ThreadIdType n = 0; n < this->GetNumberOfThreads(); n++ )
    {
    // iterate over the map for this thread
    for( MapConstIterator threadIt = this->m_LabelSetMeasuresPerThread[n].begin();
         threadIt != this->m_LabelSetMeasuresPerThread[n].end();
         ++threadIt )
      {
      // does this label exist in the cumulative structure yet?
      MapIterator mapIt = this->m_LabelSetMeasures.find( ( *threadIt ).first );
      if( mapIt == this->m_LabelSetMeasures.end() )
        {
        // create a new entry
        typedef typename MapType::value_type MapValueType;
        mapIt = this->m_LabelSetMeasures.insert( MapValueType(
                                                   (*threadIt).first, LabelSetMeasures() ) ).first;
        }

      // accumulate the information from this thread
      (*mapIt).second.m_Source += (*threadIt).second.m_Source;
      (*mapIt).second.m_Target += (*threadIt).second.m_Target;
      (*mapIt).second.m_Union += (*threadIt).second.m_Union;
      (*mapIt).second.m_Intersection +=
        (*threadIt).second.m_Intersection;
      (*mapIt).second.m_SourceComplement +=
        (*threadIt).second.m_SourceComplement;
      (*mapIt).second.m_TargetComplement +=
        (*threadIt).second.m_TargetComplement;
      } // end of thread map iterator loop
    } // end of thread loop
}

template<typename TLabelImage>
void
LabelOverlapMeasuresImageFilter<TLabelImage>
::ThreadedGenerateData( const RegionType& outputRegionForThread,
                        ThreadIdType threadId )
{
  ImageRegionConstIterator<LabelImageType> itS( this->GetSourceImage(),
                                                outputRegionForThread );
  ImageRegionConstIterator<LabelImageType> itT( this->GetTargetImage(),
                                                outputRegionForThread );

  // support progress methods/callbacks
  ProgressReporter progress( this, threadId,
                             2*outputRegionForThread.GetNumberOfPixels() );

  for( itS.GoToBegin(), itT.GoToBegin(); !itS.IsAtEnd(); ++itS, ++itT )
    {
    LabelType sourceLabel = itS.Get();
    LabelType targetLabel = itT.Get();

    // is the label already in this thread?
    MapIterator mapItS =
      this->m_LabelSetMeasuresPerThread[threadId].find( sourceLabel );
    MapIterator mapItT =
      this->m_LabelSetMeasuresPerThread[threadId].find( targetLabel );

    if( mapItS == this->m_LabelSetMeasuresPerThread[threadId].end() )
      {
      // create a new label set measures object
      typedef typename MapType::value_type MapValueType;
      mapItS = this->m_LabelSetMeasuresPerThread[threadId].insert(
        MapValueType( sourceLabel, LabelSetMeasures() ) ).first;
      }

    if( mapItT == this->m_LabelSetMeasuresPerThread[threadId].end() )
      {
      // create a new label set measures object
      typedef typename MapType::value_type MapValueType;
      mapItT = this->m_LabelSetMeasuresPerThread[threadId].insert(
        MapValueType( targetLabel, LabelSetMeasures() ) ).first;
      }

    (*mapItS).second.m_Source++;
    (*mapItT).second.m_Target++;

    if( sourceLabel == targetLabel )
      {
      (*mapItS).second.m_Intersection++;
      (*mapItS).second.m_Union++;
      }
    else
      {
      (*mapItS).second.m_Union++;
      (*mapItT).second.m_Union++;

      (*mapItS).second.m_SourceComplement++;
      (*mapItT).second.m_TargetComplement++;
      }

    progress.CompletedPixel();
    }
}

/**
 *  measures
 */
template<typename TLabelImage>
typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
LabelOverlapMeasuresImageFilter<TLabelImage>
::GetTotalOverlap() const
{
  RealType numerator = 0.0;
  RealType denominator = 0.0;
  for( MapConstIterator mapIt = this->m_LabelSetMeasures.begin();
       mapIt != this->m_LabelSetMeasures.end(); ++mapIt )
    {
    // Do not include the background in the final value.
    if( (*mapIt).first == NumericTraits<LabelType>::ZeroValue() )
      {
      continue;
      }
    numerator += static_cast<RealType>( (*mapIt).second.m_Intersection );
    denominator += static_cast<RealType>( (*mapIt).second.m_Target );
    }

  if( Math::ExactlyEquals(denominator,0.0) )
    {
    return NumericTraits<RealType>::max();
    }
  else
    {
    return ( numerator / denominator );
    }
}

template<typename TLabelImage>
typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
LabelOverlapMeasuresImageFilter<TLabelImage>
::GetTargetOverlap( LabelType label ) const
{
  MapConstIterator mapIt = this->m_LabelSetMeasures.find( label );
  if( mapIt == this->m_LabelSetMeasures.end() )
    {
    itkWarningMacro( "Label " << label << " not found." );
    return 0.0;
    }

  //std::cout << "GetTargetOverlap ::: 001" << std::endl;
  RealType value;

  if((*mapIt).second.m_Target == 0)
    {
    value = NumericTraits<RealType>::max();
    }
  else
    {
    value=
      static_cast<RealType>( (*mapIt).second.m_Intersection ) /
      static_cast<RealType>( (*mapIt).second.m_Target );
    }
  return value;
}

template<typename TLabelImage>
typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
LabelOverlapMeasuresImageFilter<TLabelImage>
::GetUnionOverlap() const
{
  RealType numerator = 0.0;
  RealType denominator = 0.0;
  for( MapConstIterator mapIt = this->m_LabelSetMeasures.begin();
       mapIt != this->m_LabelSetMeasures.end(); ++mapIt )
    {
    // Do not include the background in the final value.
    if( (*mapIt).first == NumericTraits<LabelType>::ZeroValue() )
      {
      continue;
      }
    numerator += static_cast<RealType>( (*mapIt).second.m_Intersection );
    denominator += static_cast<RealType>( (*mapIt).second.m_Union );
    }

  if( Math::ExactlyEquals(denominator,0.0) )
    {
    return NumericTraits<RealType>::max();
    }
  else
    {
    return ( numerator / denominator );
    }
}

template<typename TLabelImage>
typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
LabelOverlapMeasuresImageFilter<TLabelImage>
::GetUnionOverlap( LabelType label ) const
{
  MapConstIterator mapIt = this->m_LabelSetMeasures.find( label );
  if( mapIt == this->m_LabelSetMeasures.end() )
    {
    itkWarningMacro( "Label " << label << " not found." );
    return 0.0;
    }

  RealType value;
  if(Math::ExactlyEquals((*mapIt).second.m_Union, 0.0))
    {
    value = NumericTraits<RealType>::max();
    }
  else
    {
    value =
      static_cast<RealType>( (*mapIt).second.m_Intersection ) /
      static_cast<RealType>( (*mapIt).second.m_Union );
    }

  return value;
}

template<typename TLabelImage>
typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
LabelOverlapMeasuresImageFilter<TLabelImage>
::GetMeanOverlap() const
{
  RealType uo = this->GetUnionOverlap();
  return ( 2.0 * uo / ( 1.0 + uo ) );
}

template<typename TLabelImage>
typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
LabelOverlapMeasuresImageFilter<TLabelImage>
::GetMeanOverlap( LabelType label ) const
{
  RealType uo = this->GetUnionOverlap( label );
  return ( 2.0 * uo / ( 1.0 + uo ) );
}

template<typename TLabelImage>
typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
LabelOverlapMeasuresImageFilter<TLabelImage>
::GetVolumeSimilarity() const
{
  RealType numerator = 0.0;
  RealType denominator = 0.0;
  for( MapConstIterator mapIt = this->m_LabelSetMeasures.begin();
       mapIt != this->m_LabelSetMeasures.end(); ++mapIt )
    {
    // Do not include the background in the final value.
    if( (*mapIt).first == NumericTraits<LabelType>::ZeroValue() )
      {
      continue;
      }
    numerator += ( ( static_cast<RealType>( (*mapIt).second.m_Source ) -
                     static_cast<RealType>( (*mapIt).second.m_Target ) ) );
    denominator += ( ( static_cast<RealType>( (*mapIt).second.m_Source ) +
                       static_cast<RealType>( (*mapIt).second.m_Target ) ) );
    }

  if( Math::ExactlyEquals(denominator,0.0) )
    {
    return NumericTraits<RealType>::max();
    }
  else
    {
    return ( 2.0 * numerator / denominator );
    }
}

template<typename TLabelImage>
typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
LabelOverlapMeasuresImageFilter<TLabelImage>
::GetVolumeSimilarity( LabelType label ) const
{
  MapConstIterator mapIt = this->m_LabelSetMeasures.find( label );
  if( mapIt == this->m_LabelSetMeasures.end() )
    {
    itkWarningMacro( "Label " << label << " not found." );
    return 0.0;
    }
  RealType value = 2.0 *
    ( static_cast<RealType>( (*mapIt).second.m_Source ) -
      static_cast<RealType>( (*mapIt).second.m_Target ) ) /
    ( static_cast<RealType>( (*mapIt).second.m_Source ) +
      static_cast<RealType>( (*mapIt).second.m_Target ) );
  return value;
}

template<typename TLabelImage>
typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
LabelOverlapMeasuresImageFilter<TLabelImage>
::GetFalseNegativeError() const
{
  RealType numerator = 0.0;
  RealType denominator = 0.0;
  for( MapConstIterator mapIt = this->m_LabelSetMeasures.begin();
       mapIt != this->m_LabelSetMeasures.end(); ++mapIt )
    {
    // Do not include the background in the final value.
    if( (*mapIt).first == NumericTraits<LabelType>::ZeroValue() )
      {
      continue;
      }
    numerator += static_cast<RealType>( (*mapIt).second.m_TargetComplement );
    denominator += static_cast<RealType>( (*mapIt).second.m_Target );
    }

  if( Math::ExactlyEquals(denominator,0.0) )
    {
    return NumericTraits<RealType>::max();
    }
  else
    {
    return ( numerator / denominator );
    }
}

template<typename TLabelImage>
typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
LabelOverlapMeasuresImageFilter<TLabelImage>
::GetFalseNegativeError( LabelType label ) const
{
  MapConstIterator mapIt = this->m_LabelSetMeasures.find( label );
  if( mapIt == this->m_LabelSetMeasures.end() )
    {
    itkWarningMacro( "Label " << label << " not found." );
    return 0.0;
    }

  RealType value;
  if(Math::ExactlyEquals((*mapIt).second.m_Target, 0.0))
    {
    value = NumericTraits<RealType>::max();
    }
  else
    {
    value =
      static_cast<RealType>( (*mapIt).second.m_TargetComplement ) /
      static_cast<RealType>( (*mapIt).second.m_Target );
    }

  return value;
}

template<typename TLabelImage>
typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
LabelOverlapMeasuresImageFilter<TLabelImage>
::GetFalsePositiveError() const
{
  RealType numerator = 0.0;
  RealType denominator = 0.0;
  for( MapConstIterator mapIt = this->m_LabelSetMeasures.begin();
       mapIt != this->m_LabelSetMeasures.end(); ++mapIt )
    {
    // Do not include the background in the final value.
    if( (*mapIt).first == NumericTraits<LabelType>::ZeroValue() )
      {
      continue;
      }
    numerator += static_cast<RealType>( (*mapIt).second.m_SourceComplement );
    denominator += static_cast<RealType>( (*mapIt).second.m_Source );
    }

  if( Math::ExactlyEquals(denominator,0.0) )
    {
    return NumericTraits<RealType>::max();
    }
  else
    {
    return ( numerator / denominator );
    }
}

template<typename TLabelImage>
typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
LabelOverlapMeasuresImageFilter<TLabelImage>
::GetFalsePositiveError( LabelType label ) const
{
  MapConstIterator mapIt = this->m_LabelSetMeasures.find( label );
  if( mapIt == this->m_LabelSetMeasures.end() )
    {
    itkWarningMacro( "Label " << label << " not found." );
    return 0.0;
    }

  RealType value;
  if(Math::ExactlyEquals((*mapIt).second.m_Source, 0.0))
    {
    value = NumericTraits<RealType>::max();
    }
  else
    {
    value =
      static_cast<RealType>( (*mapIt).second.m_SourceComplement ) /
      static_cast<RealType>( (*mapIt).second.m_Source );
    }

  return value;
}

template<typename TLabelImage>
void
LabelOverlapMeasuresImageFilter<TLabelImage>
::PrintSelf( std::ostream& os, Indent indent ) const
{
  // todo!!!
  Superclass::PrintSelf( os, indent );
}


}// end namespace itk
#endif
