appli/examples/example_ImageAlgorithm_Skeletonization.cxx

   1 #include <ctime>
   2 #include <iostream>
   3 #include <string>
   4
   5 #include <itkConstNeighborhoodIterator.h>
   6 #include <itkDanielssonDistanceMapImageFilter.h>
   7 #include <itkImage.h>
   8 #include <itkImageFileReader.h>
   9 #include <itkImageFileWriter.h>
  10 #include <itkImageToVTKImageFilter.h>
  11
  12 #include <vtkImageMarchingCubes.h>
  13
  14 #include <fpa/Image/RegionGrowWithMultipleThresholds.h>
  15 #include <fpa/Image/DijkstraWithSphereBacktracking.h>
  16 #include <fpa/VTK/ImageMPR.h>
  17 #include <fpa/VTK/Image3DObserver.h>
  18
  19 // -------------------------------------------------------------------------
  20 const unsigned int Dim = 3;
  21 typedef short                                TPixel;
  22 typedef float                                TScalar;
  23 typedef itk::Image< TPixel, Dim >            TImage;
  24 typedef itk::Image< TScalar, Dim >           TDistanceMap;
  25 typedef itk::ImageToVTKImageFilter< TImage > TVTKImage;
  26 typedef itk::ImageToVTKImageFilter< TDistanceMap > TVTKDistanceMap;
  27
  28 typedef itk::ImageFileReader< TImage >                       TImageReader;
  29 typedef itk::ImageFileWriter< TImage >                       TImageWriter;
  30 typedef itk::ImageFileWriter< TDistanceMap >           TDistanceMapWriter;
  31 typedef fpa::Image::RegionGrowWithMultipleThresholds< TImage > TSegmentor;
  32 typedef
  33 itk::DanielssonDistanceMapImageFilter< TImage, TDistanceMap >
  34 TDistanceFilter;
  35 typedef
  36 fpa::Image::DijkstraWithSphereBacktracking< TDistanceMap, TScalar >
  37 TDijkstra;
  38
  39 typedef fpa::VTK::ImageMPR TMPR;
  40 typedef fpa::VTK::Image3DObserver< TSegmentor, vtkRenderWindow > TSegmentorObs;
  41 typedef fpa::VTK::Image3DObserver< TDijkstra, vtkRenderWindow > TDijkstraObs;
  42
  43 // -------------------------------------------------------------------------
  44 int main( int argc, char* argv[] )
  45 {
  46   if( argc < 8 )
  47   {
  48     std::cerr
  49       << "Usage: " << argv[ 0 ]
  50       << " input_image thr_0 thr_1 step"
  51       << " output_segmentation output_distancemap output_dijkstra"
  52       << " visual_debug"
  53       << std::endl;
  54     return( 1 );
  55
  56   } // fi
  57   std::string input_image_fn = argv[ 1 ];
  58   TPixel thr_0 = TPixel( std::atof( argv[ 2 ] ) );
  59   TPixel thr_1 = TPixel( std::atof( argv[ 3 ] ) );
  60   unsigned int step = std::atoi( argv[ 4 ] );
  61   std::string output_segmentation_fn = argv[ 5 ];
  62   std::string output_distancemap_fn = argv[ 6 ];
  63   std::string output_dijkstra_fn = argv[ 7 ];
  64   bool visual_debug = false;
  65   if( argc > 8 )
  66     visual_debug = ( std::atoi( argv[ 8 ] ) == 1 );
  67
  68   // Read image
  69   TImageReader::Pointer input_image_reader = TImageReader::New( );
  70   input_image_reader->SetFileName( input_image_fn );
  71   try
  72   {
  73     input_image_reader->Update( );
  74   }
  75   catch( itk::ExceptionObject& err )
  76   {
  77     std::cerr << "Error caught: " << err << std::endl;
  78     return( 1 );
  79
  80   } // yrt
  81   TImage::ConstPointer input_image = input_image_reader->GetOutput( );
  82
  83   // Show image
  84   TVTKImage::Pointer vtk_image = TVTKImage::New( );
  85   vtk_image->SetInput( input_image );
  86   vtk_image->Update( );
  87
  88   TMPR view;
  89   view.SetBackground( 0.3, 0.2, 0.8 );
  90   view.SetSize( 800, 800 );
  91   view.SetImage( vtk_image->GetOutput( ) );
  92
  93   // Wait for a seed to be given
  94   while( view.GetNumberOfSeeds( ) == 0 )
  95     view.Start( );
  96
  97   // Get seed from user
  98   double seed[ 3 ];
  99   view.GetSeed( 0, seed );
 100   TImage::PointType seed_pnt;
 101   seed_pnt[ 0 ] = seed[ 0 ];
 102   seed_pnt[ 1 ] = seed[ 1 ];
 103   seed_pnt[ 2 ] = seed[ 2 ];
 104   TImage::IndexType seed_idx;
 105   input_image->TransformPhysicalPointToIndex( seed_pnt, seed_idx );
 106
 107   // Segment input image
 108   TSegmentor::Pointer segmentor = TSegmentor::New( );
 109   segmentor->AddThresholds( thr_0, thr_1, step );
 110   segmentor->AddSeed( seed_idx, 0 );
 111   segmentor->SetInput( input_image );
 112   segmentor->SetNeighborhoodOrder( 1 );
 113   segmentor->SetDifferenceThreshold( double( 3 ) );
 114   segmentor->SetInsideValue( TPixel( 0 ) );  // WARNING: This is to optimize
 115   segmentor->SetOutsideValue( TPixel( 1 ) ); // distance map calculation
 116   if( visual_debug )
 117   {
 118     // Configure observer
 119     TSegmentorObs::Pointer obs = TSegmentorObs::New( );
 120     obs->SetRenderWindow( view.GetWindow( ) );
 121     segmentor->AddObserver( itk::AnyEvent( ), obs );
 122     segmentor->ThrowEventsOn( );
 123   }
 124   else
 125     segmentor->ThrowEventsOff( );
 126   std::clock_t start = std::clock( );
 127   segmentor->Update( );
 128   std::clock_t end = std::clock( );
 129   double seconds = double( end - start ) / double( CLOCKS_PER_SEC );
 130   std::cout << "Segmentation time = " << seconds << std::endl;
 131
 132   // Extract distance map
 133   TDistanceFilter::Pointer distanceMap = TDistanceFilter::New( );
 134   distanceMap->SetInput( segmentor->GetOutput( ) );
 135   distanceMap->InputIsBinaryOn( );
 136   distanceMap->SquaredDistanceOn( );
 137   distanceMap->UseImageSpacingOn( );
 138   start = std::clock( );
 139   distanceMap->Update( );
 140   end = std::clock( );
 141   seconds = double( end - start ) / double( CLOCKS_PER_SEC );
 142   std::cout << "Distance map time = " << seconds << std::endl;
 143
 144   TVTKDistanceMap::Pointer vtk_distanceMap = TVTKDistanceMap::New( );
 145   vtk_distanceMap->SetInput( distanceMap->GetOutput( ) );
 146   vtk_distanceMap->Update( );
 147
 148   vtkSmartPointer< vtkImageMarchingCubes > mc =
 149     vtkSmartPointer< vtkImageMarchingCubes >::New( );
 150   mc->SetInputData( vtk_distanceMap->GetOutput( ) );
 151   mc->SetValue( 0, 1e-2 );
 152   mc->Update( );
 153   view.AddPolyData( mc->GetOutput( ), 1, 1, 1, 0.4 );
 154   view.Render( );
 155
 156   // Extract paths
 157   TDijkstra::Pointer paths = TDijkstra::New( );
 158   paths->AddSeed( segmentor->GetSeed( 0 ), TScalar( 0 ) );
 159   paths->SetInput( distanceMap->GetOutput( ) );
 160   paths->SetNeighborhoodOrder( 2 );
 161
 162   if( visual_debug )
 163   {
 164     // Configure observer
 165     TDijkstraObs::Pointer obs = TDijkstraObs::New( );
 166     obs->SetRenderWindow( view.GetWindow( ) );
 167     paths->AddObserver( itk::AnyEvent( ), obs );
 168     paths->ThrowEventsOn( );
 169   }
 170   else
 171     paths->ThrowEventsOff( );
 172   start = std::clock( );
 173   paths->Update( );
 174   end = std::clock( );
 175   seconds = double( end - start ) / double( CLOCKS_PER_SEC );
 176   std::cout << "Paths extraction time = " << seconds << std::endl;
 177
 178   std::cout << "Final seed: " << paths->GetSeed( 0 ) << std::endl;
 179
 180   // Create polydata
 181   vtkSmartPointer< vtkPoints > points =
 182     vtkSmartPointer< vtkPoints >::New( );
 183   vtkSmartPointer< vtkCellArray > cells =
 184     vtkSmartPointer< vtkCellArray >::New( );
 185   vtkSmartPointer< vtkFloatArray > scalars =
 186     vtkSmartPointer< vtkFloatArray >::New( );
 187
 188   const TDijkstra::TVertices& endpoints = paths->GetEndPoints( );
 189   const TDijkstra::TTree& tree = paths->GetFinalTree( );
 190   TDijkstra::TVertices::const_iterator epIt = endpoints.begin( );
 191   for( unsigned int epId = 0; epIt != endpoints.end( ); ++epIt, ++epId )
 192   {
 193     double pd = double( epId ) / double( endpoints.size( ) - 1 );
 194
 195     TDijkstra::TVertex idx = *epIt;
 196     do
 197     {
 198       TImage::PointType pnt;
 199       input_image->TransformIndexToPhysicalPoint( idx, pnt );
 200
 201       points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
 202       scalars->InsertNextTuple1( pd );
 203       if( idx != *epIt )
 204       {
 205         cells->InsertNextCell( 2 );
 206         cells->InsertCellPoint( points->GetNumberOfPoints( ) - 2 );
 207         cells->InsertCellPoint( points->GetNumberOfPoints( ) - 1 );
 208
 209       } // fi
 210       idx = tree.find( idx )->second;
 211
 212     } while( idx != tree.find( idx )->second );
 213
 214   } // rof
 215
 216   vtkSmartPointer< vtkPolyData > vtk_tree =
 217     vtkSmartPointer< vtkPolyData >::New( );
 218   vtk_tree->SetPoints( points );
 219   vtk_tree->SetLines( cells );
 220   vtk_tree->GetPointData( )->SetScalars( scalars );
 221
 222   view.AddPolyData( vtk_tree );
 223   view.Render( );
 224   view.Start( );
 225
 226   itk::ImageFileWriter< TImage >::Pointer segmentation_writer =
 227     itk::ImageFileWriter< TImage >::New( );
 228   segmentation_writer->SetInput( segmentor->GetOutput( ) );
 229   segmentation_writer->SetFileName( output_segmentation_fn );
 230
 231   itk::ImageFileWriter< TDistanceMap >::Pointer dmap_writer =
 232     itk::ImageFileWriter< TDistanceMap >::New( );
 233   dmap_writer->SetInput( distanceMap->GetOutput( ) );
 234   dmap_writer->SetFileName( output_distancemap_fn );
 235
 236   itk::ImageFileWriter< TDistanceMap >::Pointer dijk_writer =
 237     itk::ImageFileWriter< TDistanceMap >::New( );
 238   dijk_writer->SetInput( paths->GetOutput( ) );
 239   dijk_writer->SetFileName( output_dijkstra_fn );
 240
 241   try
 242   {
 243     segmentation_writer->Update( );
 244     dmap_writer->Update( );
 245     dijk_writer->Update( );
 246   }
 247   catch( itk::ExceptionObject& err )
 248   {
 249     std::cerr << "Error caught: " << err << std::endl;
 250     return( -1 );
 251
 252   } // yrt
 253
 254   return( 0 );
 255 }
 256
 257 // eof - $RCSfile$