appli/examples/example_ImageAlgorithmDijkstra_03.cxx

   1 #include <cmath>
   2 #include <ctime>
   3 #include <deque>
   4 #include <iostream>
   5 #include <limits>
   6 #include <map>
   7 #include <string>
   8
   9 #include <itkConstNeighborhoodIterator.h>
  10 #include <itkNeighborhoodIterator.h>
  11 #include <itkDanielssonDistanceMapImageFilter.h>
  12 #include <itkImage.h>
  13 #include <itkImageFileReader.h>
  14 #include <itkImageFileWriter.h>
  15 #include <itkImageToVTKImageFilter.h>
  16
  17 #include <itkMinimumMaximumImageCalculator.h>
  18 #include <itkInvertIntensityImageFilter.h>
  19
  20 #include <vtkPoints.h>
  21 #include <vtkCellArray.h>
  22 #include <vtkFloatArray.h>
  23 #include <vtkPolyData.h>
  24 #include <vtkSmartPointer.h>
  25 #include <vtkImageMarchingCubes.h>
  26
  27 #include <fpa/Image/DijkstraWithSphereBacktracking.h>
  28 #include <fpa/VTK/ImageMPR.h>
  29 #include <fpa/VTK/Image3DObserver.h>
  30
  31 // -------------------------------------------------------------------------
  32 const unsigned int Dim = 3;
  33 typedef float                                TPixel;
  34 typedef float                                TScalar;
  35 typedef itk::Image< TPixel, Dim >            TImage;
  36 typedef itk::ImageToVTKImageFilter< TImage > TVTKImage;
  37
  38 typedef itk::ImageFileReader< TImage >          TImageReader;
  39 typedef itk::ImageFileWriter< TImage >    TImageWriter;
  40 typedef fpa::Image::DijkstraWithSphereBacktracking< TImage, TScalar > TDijkstra;
  41
  42 typedef fpa::VTK::ImageMPR TMPR;
  43 typedef fpa::VTK::Image3DObserver< TDijkstra, vtkRenderWindow > TDijkstraObs;
  44
  45 // -------------------------------------------------------------------------
  46 int main( int argc, char* argv[] )
  47 {
  48   if( argc < 6 )
  49   {
  50     std::cerr
  51       << "Usage: " << argv[ 0 ]
  52       << " input_image x y z output_image"
  53       << " visual_debug"
  54       << std::endl;
  55     return( 1 );
  56
  57   } // fi
  58   std::string input_image_fn = argv[ 1 ];
  59   TImage::PointType seed_pnt;
  60   seed_pnt[ 0 ] = std::atof( argv[ 2 ] );
  61   seed_pnt[ 1 ] = std::atof( argv[ 3 ] );
  62   seed_pnt[ 2 ] = std::atof( argv[ 4 ] );
  63   std::string output_image_fn = argv[ 5 ];
  64   bool visual_debug = false;
  65   if( argc > 6 )
  66     visual_debug = ( std::atoi( argv[ 6 ] ) == 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   vtkSmartPointer< vtkImageMarchingCubes > mc =
  94     vtkSmartPointer< vtkImageMarchingCubes >::New( );
  95   mc->SetInputData( vtk_image->GetOutput( ) );
  96   mc->SetValue( 0, 1e-2 );
  97   mc->Update( );
  98   view.AddPolyData( mc->GetOutput( ), 1, 1, 1, 0.4 );
  99
 100   // Allow some interaction
 101   view.Render( );
 102   view.Start( );
 103
 104   TImage::IndexType seed_idx;
 105   input_image->TransformPhysicalPointToIndex( seed_pnt, seed_idx );
 106   std::cout << seed_idx << " " << seed_pnt << std::endl;
 107   seed_idx[ 0 ] = 256;
 108   seed_idx[ 1 ] = 313;
 109   seed_idx[ 2 ] = 381;
 110
 111   // Extract paths
 112   TDijkstra::Pointer paths = TDijkstra::New( );
 113   paths->AddSeed( seed_idx, TScalar( 0 ) );
 114   paths->SetInput( input_image );
 115   paths->SetNeighborhoodOrder( 2 );
 116
 117   if( visual_debug )
 118   {
 119     // Configure observer
 120     TDijkstraObs::Pointer obs = TDijkstraObs::New( );
 121     obs->SetRenderWindow( view.GetWindow( ) );
 122     paths->AddObserver( itk::AnyEvent( ), obs );
 123     paths->ThrowEventsOn( );
 124   }
 125   else
 126     paths->ThrowEventsOff( );
 127   std::clock_t start = std::clock( );
 128   paths->Update( );
 129   std::clock_t end = std::clock( );
 130   double seconds = double( end - start ) / double( CLOCKS_PER_SEC );
 131   std::cout << "Paths extraction time = " << seconds << std::endl;
 132
 133   // Create polydata
 134   vtkSmartPointer< vtkPoints > points =
 135     vtkSmartPointer< vtkPoints >::New( );
 136   vtkSmartPointer< vtkCellArray > cells =
 137     vtkSmartPointer< vtkCellArray >::New( );
 138   vtkSmartPointer< vtkFloatArray > scalars =
 139     vtkSmartPointer< vtkFloatArray >::New( );
 140
 141   const TDijkstra::TVertices& endpoints = paths->GetEndPoints( );
 142   const TDijkstra::TTree& tree = paths->GetFinalTree( );
 143   TDijkstra::TVertices::const_iterator epIt = endpoints.begin( );
 144   for( unsigned int epId = 0; epIt != endpoints.end( ); ++epIt, ++epId )
 145   {
 146     double pd = double( epId ) / double( endpoints.size( ) - 1 );
 147
 148     TDijkstra::TVertex idx = *epIt;
 149     do
 150     {
 151       TImage::PointType pnt;
 152       input_image->TransformIndexToPhysicalPoint( idx, pnt );
 153
 154       points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
 155       scalars->InsertNextTuple1( pd );
 156       if( idx != *epIt )
 157       {
 158         cells->InsertNextCell( 2 );
 159         cells->InsertCellPoint( points->GetNumberOfPoints( ) - 2 );
 160         cells->InsertCellPoint( points->GetNumberOfPoints( ) - 1 );
 161
 162       } // fi
 163       idx = tree.find( idx )->second;
 164
 165     } while( idx != tree.find( idx )->second );
 166
 167   } // rof
 168
 169   vtkSmartPointer< vtkPolyData > vtk_tree =
 170     vtkSmartPointer< vtkPolyData >::New( );
 171   vtk_tree->SetPoints( points );
 172   vtk_tree->SetLines( cells );
 173   vtk_tree->GetPointData( )->SetScalars( scalars );
 174
 175   view.AddPolyData( vtk_tree );
 176   view.Render( );
 177   view.Start( );
 178
 179   /* TODO
 180      TImageWriter::Pointer dijkstra_writer =
 181      TImageWriter::New( );
 182      dijkstra_writer->SetInput( paths->GetOutput( ) );
 183      dijkstra_writer->SetFileName( "dijkstra.mhd" );
 184      dijkstra_writer->Update( );
 185   */
 186
 187   return( 0 );
 188 }
 189
 190 // eof - $RCSfile$