#include <ctime>
#include <iostream>
#include <string>

#include <itkConstNeighborhoodIterator.h>
#include <itkDanielssonDistanceMapImageFilter.h>
#include <itkImage.h>
#include <itkImageFileReader.h>
#include <itkImageFileWriter.h>
#include <itkImageToVTKImageFilter.h>

#include <vtkImageMarchingCubes.h>

#include <fpa/Image/RegionGrowWithMultipleThresholds.h>
#include <fpa/Image/DijkstraWithSphereBacktracking.h>
#include <fpa/VTK/ImageMPR.h>
#include <fpa/VTK/Image3DObserver.h>

// -------------------------------------------------------------------------
const unsigned int Dim = 3;
typedef short                                TPixel;
typedef float                                TScalar;
typedef itk::Image< TPixel, Dim >            TImage;
typedef itk::Image< TScalar, Dim >           TDistanceMap;
typedef itk::ImageToVTKImageFilter< TImage > TVTKImage;
typedef itk::ImageToVTKImageFilter< TDistanceMap > TVTKDistanceMap;

typedef itk::ImageFileReader< TImage >                       TImageReader;
typedef itk::ImageFileWriter< TImage >                       TImageWriter;
typedef itk::ImageFileWriter< TDistanceMap >           TDistanceMapWriter;
typedef fpa::Image::RegionGrowWithMultipleThresholds< TImage > TSegmentor;
typedef
itk::DanielssonDistanceMapImageFilter< TImage, TDistanceMap >
TDistanceFilter;
typedef
fpa::Image::DijkstraWithSphereBacktracking< TDistanceMap, TScalar >
TDijkstra;

typedef fpa::VTK::ImageMPR TMPR;
typedef fpa::VTK::Image3DObserver< TSegmentor, vtkRenderWindow > TSegmentorObs;
typedef fpa::VTK::Image3DObserver< TDijkstra, vtkRenderWindow > TDijkstraObs;

// -------------------------------------------------------------------------
int main( int argc, char* argv[] )
{
  if( argc < 8 )
  {
    std::cerr
      << "Usage: " << argv[ 0 ]
      << " input_image thr_0 thr_1 step"
      << " output_segmentation output_distancemap output_dijkstra"
      << " visual_debug"
      << std::endl;
    return( 1 );

  } // fi
  std::string input_image_fn = argv[ 1 ];
  TPixel thr_0 = TPixel( std::atof( argv[ 2 ] ) );
  TPixel thr_1 = TPixel( std::atof( argv[ 3 ] ) );
  unsigned int step = std::atoi( argv[ 4 ] );
  std::string output_segmentation_fn = argv[ 5 ];
  std::string output_distancemap_fn = argv[ 6 ];
  std::string output_dijkstra_fn = argv[ 7 ];
  bool visual_debug = false;
  if( argc > 8 )
    visual_debug = ( std::atoi( argv[ 8 ] ) == 1 );

  // Read image
  TImageReader::Pointer input_image_reader = TImageReader::New( );
  input_image_reader->SetFileName( input_image_fn );
  try
  {
    input_image_reader->Update( );
  }
  catch( itk::ExceptionObject& err )
  {
    std::cerr << "Error caught: " << err << std::endl;
    return( 1 );

  } // yrt
  TImage::ConstPointer input_image = input_image_reader->GetOutput( );

  // Show image
  TVTKImage::Pointer vtk_image = TVTKImage::New( );
  vtk_image->SetInput( input_image );
  vtk_image->Update( );

  TMPR view;
  view.SetBackground( 0.3, 0.2, 0.8 );
  view.SetSize( 800, 800 );
  view.SetImage( vtk_image->GetOutput( ) );

  // Wait for a seed to be given
  while( view.GetNumberOfSeeds( ) == 0 )
    view.Start( );

  // Get seed from user
  double seed[ 3 ];
  view.GetSeed( 0, seed );
  TImage::PointType seed_pnt;
  seed_pnt[ 0 ] = seed[ 0 ];
  seed_pnt[ 1 ] = seed[ 1 ];
  seed_pnt[ 2 ] = seed[ 2 ];
  TImage::IndexType seed_idx;
  input_image->TransformPhysicalPointToIndex( seed_pnt, seed_idx );

  // Segment input image
  TSegmentor::Pointer segmentor = TSegmentor::New( );
  segmentor->AddThresholds( thr_0, thr_1, step );
  segmentor->AddSeed( seed_idx, 0 );
  segmentor->SetInput( input_image );
  segmentor->SetNeighborhoodOrder( 1 );
  segmentor->SetDifferenceThreshold( double( 3 ) );
  segmentor->SetInsideValue( TPixel( 0 ) );  // WARNING: This is to optimize
  segmentor->SetOutsideValue( TPixel( 1 ) ); // distance map calculation
  if( visual_debug )
  {
    // Configure observer
    TSegmentorObs::Pointer obs = TSegmentorObs::New( );
    obs->SetRenderWindow( view.GetWindow( ) );
    segmentor->AddObserver( itk::AnyEvent( ), obs );
    segmentor->ThrowEventsOn( );
  }
  else
    segmentor->ThrowEventsOff( );
  std::clock_t start = std::clock( );
  segmentor->Update( );
  std::clock_t end = std::clock( );
  double seconds = double( end - start ) / double( CLOCKS_PER_SEC );
  std::cout << "Segmentation time = " << seconds << std::endl;

  // Extract distance map
  TDistanceFilter::Pointer distanceMap = TDistanceFilter::New( );
  distanceMap->SetInput( segmentor->GetOutput( ) );
  distanceMap->InputIsBinaryOn( );
  distanceMap->SquaredDistanceOn( );
  distanceMap->UseImageSpacingOn( );
  start = std::clock( );
  distanceMap->Update( );
  end = std::clock( );
  seconds = double( end - start ) / double( CLOCKS_PER_SEC );
  std::cout << "Distance map time = " << seconds << std::endl;

  TVTKDistanceMap::Pointer vtk_distanceMap = TVTKDistanceMap::New( );
  vtk_distanceMap->SetInput( distanceMap->GetOutput( ) );
  vtk_distanceMap->Update( );

  vtkSmartPointer< vtkImageMarchingCubes > mc =
    vtkSmartPointer< vtkImageMarchingCubes >::New( );
  mc->SetInputData( vtk_distanceMap->GetOutput( ) );
  mc->SetValue( 0, 1e-2 );
  mc->Update( );
  view.AddPolyData( mc->GetOutput( ), 1, 1, 1, 0.4 );
  view.Render( );

  // Extract paths
  TDijkstra::Pointer paths = TDijkstra::New( );
  paths->AddSeed( segmentor->GetSeed( 0 ), TScalar( 0 ) );
  paths->SetInput( distanceMap->GetOutput( ) );
  paths->SetNeighborhoodOrder( 2 );

  if( visual_debug )
  {
    // Configure observer
    TDijkstraObs::Pointer obs = TDijkstraObs::New( );
    obs->SetRenderWindow( view.GetWindow( ) );
    paths->AddObserver( itk::AnyEvent( ), obs );
    paths->ThrowEventsOn( );
  }
  else
    paths->ThrowEventsOff( );
  start = std::clock( );
  paths->Update( );
  end = std::clock( );
  seconds = double( end - start ) / double( CLOCKS_PER_SEC );
  std::cout << "Paths extraction time = " << seconds << std::endl;

  std::cout << "Final seed: " << paths->GetSeed( 0 ) << std::endl;

  // Create polydata
  vtkSmartPointer< vtkPoints > points =
    vtkSmartPointer< vtkPoints >::New( );
  vtkSmartPointer< vtkCellArray > cells =
    vtkSmartPointer< vtkCellArray >::New( );
  vtkSmartPointer< vtkFloatArray > scalars =
    vtkSmartPointer< vtkFloatArray >::New( );

  const TDijkstra::TVertices& endpoints = paths->GetEndPoints( );
  const TDijkstra::TTree& tree = paths->GetFinalTree( );
  TDijkstra::TVertices::const_iterator epIt = endpoints.begin( );
  for( unsigned int epId = 0; epIt != endpoints.end( ); ++epIt, ++epId )
  {
    double pd = double( epId ) / double( endpoints.size( ) - 1 );

    TDijkstra::TVertex idx = *epIt;
    do
    {
      TImage::PointType pnt;
      input_image->TransformIndexToPhysicalPoint( idx, pnt );

      points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
      scalars->InsertNextTuple1( pd );
      if( idx != *epIt )
      {
        cells->InsertNextCell( 2 );
        cells->InsertCellPoint( points->GetNumberOfPoints( ) - 2 );
        cells->InsertCellPoint( points->GetNumberOfPoints( ) - 1 );

      } // fi
      idx = tree.find( idx )->second;

    } while( idx != tree.find( idx )->second );

  } // rof

  vtkSmartPointer< vtkPolyData > vtk_tree =
    vtkSmartPointer< vtkPolyData >::New( );
  vtk_tree->SetPoints( points );
  vtk_tree->SetLines( cells );
  vtk_tree->GetPointData( )->SetScalars( scalars );

  view.AddPolyData( vtk_tree );
  view.Render( );
  view.Start( );

  itk::ImageFileWriter< TImage >::Pointer segmentation_writer =
    itk::ImageFileWriter< TImage >::New( );
  segmentation_writer->SetInput( segmentor->GetOutput( ) );
  segmentation_writer->SetFileName( output_segmentation_fn );

  itk::ImageFileWriter< TDistanceMap >::Pointer dmap_writer =
    itk::ImageFileWriter< TDistanceMap >::New( );
  dmap_writer->SetInput( distanceMap->GetOutput( ) );
  dmap_writer->SetFileName( output_distancemap_fn );

  itk::ImageFileWriter< TDistanceMap >::Pointer dijk_writer =
    itk::ImageFileWriter< TDistanceMap >::New( );
  dijk_writer->SetInput( paths->GetOutput( ) );
  dijk_writer->SetFileName( output_dijkstra_fn );

  try
  {
    segmentation_writer->Update( );
    dmap_writer->Update( );
    dijk_writer->Update( );
  }
  catch( itk::ExceptionObject& err )
  {
    std::cerr << "Error caught: " << err << std::endl;
    return( -1 );

  } // yrt

  return( 0 );
}

// eof - $RCSfile$