9 #include <itkConstNeighborhoodIterator.h>
10 #include <itkNeighborhoodIterator.h>
11 #include <itkDanielssonDistanceMapImageFilter.h>
13 #include <itkImageFileReader.h>
14 #include <itkImageFileWriter.h>
15 #include <itkImageToVTKImageFilter.h>
17 #include <vtkPoints.h>
18 #include <vtkCellArray.h>
19 #include <vtkFloatArray.h>
20 #include <vtkPolyData.h>
21 #include <vtkSmartPointer.h>
23 #include <fpa/Image/DijkstraWithSphereBacktracking.h>
24 #include <fpa/VTK/ImageMPR.h>
25 #include <fpa/VTK/Image3DObserver.h>
27 // -------------------------------------------------------------------------
28 const unsigned int Dim = 3;
29 typedef double TPixel;
30 typedef double TScalar;
31 typedef itk::Image< TPixel, Dim > TImage;
32 typedef itk::ImageToVTKImageFilter< TImage > TVTKImage;
34 typedef itk::ImageFileReader< TImage > TImageReader;
35 typedef itk::ImageFileWriter< TImage > TImageWriter;
36 typedef fpa::Image::DijkstraWithSphereBacktracking< TImage, TScalar > TDijkstra;
38 typedef fpa::VTK::ImageMPR TMPR;
39 typedef fpa::VTK::Image3DObserver< TDijkstra, vtkRenderWindow > TDijkstraObs;
41 // -------------------------------------------------------------------------
42 int main( int argc, char* argv[] )
47 << "Usage: " << argv[ 0 ]
48 << " input_image output_image"
49 << " neighborhood_order"
55 std::string input_image_fn = argv[ 1 ];
56 std::string output_image_fn = argv[ 2 ];
57 unsigned int neighborhood_order = std::atoi( argv[ 3 ] );
58 bool visual_debug = false;
60 visual_debug = ( std::atoi( argv[ 4 ] ) == 1 );
63 TImageReader::Pointer input_image_reader = TImageReader::New( );
64 input_image_reader->SetFileName( input_image_fn );
67 input_image_reader->Update( );
69 catch( itk::ExceptionObject& err )
71 std::cerr << "Error caught: " << err << std::endl;
75 TImage::ConstPointer input_image = input_image_reader->GetOutput( );
78 TVTKImage::Pointer vtk_image = TVTKImage::New( );
79 vtk_image->SetInput( input_image );
83 view.SetBackground( 0.3, 0.2, 0.8 );
84 view.SetSize( 800, 800 );
85 view.SetImage( vtk_image->GetOutput( ) );
87 // Wait for a seed to be given
88 while( view.GetNumberOfSeeds( ) == 0 )
93 view.GetSeed( 0, seed );
94 TImage::PointType seed_pnt;
95 seed_pnt[ 0 ] = seed[ 0 ];
96 seed_pnt[ 1 ] = seed[ 1 ];
97 seed_pnt[ 2 ] = seed[ 2 ];
98 TImage::IndexType seed_idx;
99 input_image->TransformPhysicalPointToIndex( seed_pnt, seed_idx );
102 TDijkstra::Pointer paths = TDijkstra::New( );
103 paths->AddSeed( seed_idx, TScalar( 0 ) );
104 paths->SetInput( input_image );
105 paths->SetNeighborhoodOrder( neighborhood_order );
109 // Configure observer
110 TDijkstraObs::Pointer obs = TDijkstraObs::New( );
111 obs->SetRenderWindow( view.GetWindow( ) );
112 paths->AddObserver( itk::AnyEvent( ), obs );
113 paths->ThrowEventsOn( );
116 paths->ThrowEventsOff( );
117 std::clock_t start = std::clock( );
119 std::clock_t end = std::clock( );
120 double seconds = double( end - start ) / double( CLOCKS_PER_SEC );
121 std::cout << "Paths extraction time = " << seconds << std::endl;
124 vtkSmartPointer< vtkPoints > points =
125 vtkSmartPointer< vtkPoints >::New( );
126 vtkSmartPointer< vtkCellArray > cells =
127 vtkSmartPointer< vtkCellArray >::New( );
128 vtkSmartPointer< vtkFloatArray > scalars =
129 vtkSmartPointer< vtkFloatArray >::New( );
131 const TDijkstra::TVertices& endpoints = paths->GetEndPoints( );
132 const TDijkstra::TTree& tree = paths->GetFinalTree( );
133 TDijkstra::TVertices::const_iterator epIt = endpoints.begin( );
134 for( unsigned int epId = 0; epIt != endpoints.end( ); ++epIt, ++epId )
136 double pd = double( epId ) / double( endpoints.size( ) - 1 );
138 TDijkstra::TVertex idx = *epIt;
141 TImage::PointType pnt;
142 input_image->TransformIndexToPhysicalPoint( idx, pnt );
144 points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
145 scalars->InsertNextTuple1( pd );
148 cells->InsertNextCell( 2 );
149 cells->InsertCellPoint( points->GetNumberOfPoints( ) - 2 );
150 cells->InsertCellPoint( points->GetNumberOfPoints( ) - 1 );
153 idx = tree.find( idx )->second;
155 } while( idx != tree.find( idx )->second );
159 vtkSmartPointer< vtkPolyData > vtk_tree =
160 vtkSmartPointer< vtkPolyData >::New( );
161 vtk_tree->SetPoints( points );
162 vtk_tree->SetLines( cells );
163 vtk_tree->GetPointData( )->SetScalars( scalars );
165 view.AddPolyData( vtk_tree );
170 TImageWriter::Pointer dijkstra_writer =
171 TImageWriter::New( );
172 dijkstra_writer->SetInput( paths->GetOutput( ) );
173 dijkstra_writer->SetFileName( "dijkstra.mhd" );
174 dijkstra_writer->Update( );