/*=========================================================================
 *
 *  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 __itkRelabelComponentImageFilter_hxx
#define __itkRelabelComponentImageFilter_hxx

#include "itkRelabelComponentImageFilter.h"
#include "itkImageRegionIterator.h"
#include "itkNumericTraits.h"
#include "itkProgressReporter.h"
#include "itksys/hash_map.hxx"
#include <map>

namespace itk
{
template< class TInputImage, class TOutputImage >
void
RelabelComponentImageFilter< TInputImage, TOutputImage >
::GenerateInputRequestedRegion()
{
  // call the superclass' implementation of this method
  Superclass::GenerateInputRequestedRegion();

  // We need all the input.
  InputImagePointer input = const_cast< InputImageType * >( this->GetInput() );
  if ( input )
    {
    input->SetRequestedRegion( input->GetLargestPossibleRegion() );
    }
}

template< class TInputImage, class TOutputImage >
void
RelabelComponentImageFilter< TInputImage, TOutputImage >
::GenerateData()
{
  SizeValueType i;

  // Use a map to keep track of the size of each object.  Object
  // number -> ObjectType (which has Object number and the two sizes)
  typedef itksys::hash_map< LabelType, RelabelComponentObjectType > MapType;
  MapType sizeMap;
  typename MapType::iterator mapIt;
  typedef typename MapType::value_type MapValueType;

  // Get the input and the output
  typename TInputImage::ConstPointer input = this->GetInput();
  typename TOutputImage::Pointer output = this->GetOutput();

  // Setup a progress reporter.  We have 2 stages to the algorithm so
  // use the total number of pixels accessed. We walk the entire input
  // in the first pass, then walk just the output requested region in
  // the second pass.
  ProgressReporter progress( this, 0,
                             input->GetRequestedRegion().GetNumberOfPixels()
                             + output->GetRequestedRegion().GetNumberOfPixels() );

  // Calculate the size of pixel
  float physicalPixelSize = 1.0;
  for ( i = 0; i < TInputImage::ImageDimension; ++i )
    {
    physicalPixelSize *= input->GetSpacing()[i];
    }

  RelabelComponentObjectType initialSize;
  initialSize.m_SizeInPixels = 1;
  initialSize.m_SizeInPhysicalUnits = physicalPixelSize;

  // First pass: walk the entire input image and determine what
  // labels are used and the number of pixels used in each label.
  //

  // walk the input
  ImageRegionConstIterator< InputImageType > it( input, input->GetRequestedRegion() );
  it.GoToBegin();

  while ( !it.IsAtEnd() )
    {
    // Get the input pixel value
    const LabelType inputValue = static_cast< LabelType >( it.Get() );

    // if the input pixel is not the background
    if ( inputValue != NumericTraits< LabelType >::Zero )
      {
      // Does this label already exist
      mapIt = sizeMap.find(inputValue);
      if ( mapIt == sizeMap.end() )
        {
        // label is not currently in the map
        initialSize.m_ObjectNumber = inputValue;
        sizeMap.insert( MapValueType(inputValue, initialSize) );
        }
      else
        {
        // label is already in the map, update the values
        ( *mapIt ).second.m_SizeInPixels++;
        ( *mapIt ).second.m_SizeInPhysicalUnits += physicalPixelSize;
        }
      }

    // increment the iterators
    ++it;
    progress.CompletedPixel();
    }

  // Now we need to reorder the labels. Use the m_SortByObjectSize
  // to determine how to sort the objects. Define a map for converting
  // input labels to output labels.
  //
  typedef std::vector< RelabelComponentObjectType > VectorType;
  VectorType sizeVector;
  typename VectorType::iterator vit;

  typedef std::map< LabelType, LabelType >    RelabelMapType;
  typedef typename RelabelMapType::value_type RelabelMapValueType;
  RelabelMapType relabelMap;

  // copy the original object map to a vector so we can sort it
  for ( mapIt = sizeMap.begin(); mapIt != sizeMap.end(); ++mapIt )
    {
    sizeVector.push_back( ( *mapIt ).second );
    }

  // sort the objects (by size or number) and define the map to use to relabel the image
  std::sort( sizeVector.begin(), sizeVector.end(),
      RelabelComponentSizeInPixelsComparator(m_SortByObjectSize) );

  // create a lookup table to map the input label to the output label.
  // cache the object sizes for later access by the user
  m_NumberOfObjects = sizeVector.size();
  m_OriginalNumberOfObjects = sizeVector.size();
  m_SizeOfObjectsInPixels.clear();
  m_SizeOfObjectsInPixels.resize(m_NumberOfObjects);
  m_SizeOfObjectsInPhysicalUnits.clear();
  m_SizeOfObjectsInPhysicalUnits.resize(m_NumberOfObjects);
  int NumberOfObjectsRemoved = 0;
  for ( i = 0, vit = sizeVector.begin(); vit != sizeVector.end(); ++vit, ++i )
    {
    // if we find an object smaller than the minimum size, we
    // terminate the loop.
    if ( m_MinimumObjectSize > 0 && ( *vit ).m_SizeInPixels < m_MinimumObjectSize )
      {
      // map small objects to the background
      NumberOfObjectsRemoved++;
      relabelMap.insert( RelabelMapValueType( ( *vit ).m_ObjectNumber, 0 ) );
      }
    else
      {
      // map for input labels to output labels (Note we use i+1 in the
      // map since index 0 is the background)
      relabelMap.insert( RelabelMapValueType( ( *vit ).m_ObjectNumber, i + 1 ) );

      // cache object sizes for later access by the user
      m_SizeOfObjectsInPixels[i] = ( *vit ).m_SizeInPixels;
      m_SizeOfObjectsInPhysicalUnits[i] = ( *vit ).m_SizeInPhysicalUnits;
      }
    }

  // update number of objects and resize cache vectors if we have removed small
  // objects
  m_NumberOfObjects -= NumberOfObjectsRemoved;
  if ( NumberOfObjectsRemoved > 0 )
    {
    m_SizeOfObjectsInPixels.resize(m_NumberOfObjects);
    m_SizeOfObjectsInPhysicalUnits.resize(m_NumberOfObjects);
    }

  // Second pass: walk just the output requested region and relabel
  // the necessary pixels.
  //

  // Allocate the output
  this->AllocateOutputs();

  // Remap the labels.  Note we only walk the region of the output
  // that was requested.  This may be a subset of the input image.
  OutputPixelType                        outputValue;
  ImageRegionIterator< OutputImageType > oit;
  oit = ImageRegionIterator< OutputImageType >( output,
                                                output->GetRequestedRegion() );
  it = ImageRegionConstIterator< InputImageType >( input,
                                                   output->GetRequestedRegion() );

  it.GoToBegin();
  oit.GoToBegin();
  while ( !oit.IsAtEnd() )
    {
    const LabelType inputValue = static_cast< LabelType >( it.Get() );

    if ( inputValue != NumericTraits< LabelType >::Zero )
      {
      // lookup the mapped label
      outputValue = static_cast< OutputPixelType >( relabelMap[inputValue] );
      oit.Set(outputValue);
      }
    else
      {
      oit.Set(inputValue);
      }

    // increment the iterators
    ++it;
    ++oit;
    progress.CompletedPixel();
    }
}

template< class TInputImage, class TOutputImage >
void
RelabelComponentImageFilter< TInputImage, TOutputImage >
::PrintSelf(std::ostream & os, Indent indent) const
{
  Superclass::PrintSelf(os, indent);

  os << indent << "NumberOfObjects: " << m_NumberOfObjects << std::endl;
  os << indent << "OriginalNumberOfObjects: " << m_OriginalNumberOfObjects << std::endl;
  os << indent << "NumberOfObjectsToPrint: "
     << m_NumberOfObjectsToPrint << std::endl;
  os << indent << "MinimumObjectSize: " << m_MinimumObjectSize << std::endl;
  os << indent << "SortByObjectSize: " << m_SortByObjectSize << std::endl;

  typename ObjectSizeInPixelsContainerType::const_iterator it;
  ObjectSizeInPhysicalUnitsContainerType::const_iterator   fit;
  LabelType                                                i;

  // limit the number of objects to print
  LabelType numPrint = m_NumberOfObjectsToPrint;
  if ( numPrint > m_SizeOfObjectsInPixels.size() )
    {
    numPrint = m_SizeOfObjectsInPixels.size();
    }

  for ( i = 0, it = m_SizeOfObjectsInPixels.begin(),
        fit = m_SizeOfObjectsInPhysicalUnits.begin();
        i < numPrint; ++it, ++fit, ++i )
    {
    os << indent << "Object #" << i + 1 << ": " << *it << " pixels, "
       << *fit << " physical units" << std::endl;
    }
  if ( numPrint < m_SizeOfObjectsInPixels.size() )
    {
    os << indent << "..." << std::endl;
    }
}
} // end namespace itk

#endif
