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 x y z output_image"
54 std::string input_image_fn = argv[ 1 ];
55 TImage::IndexType seed_idx;
56 seed_idx[ 0 ] = std::atoi( argv[ 2 ] );
57 seed_idx[ 1 ] = std::atoi( argv[ 3 ] );
58 seed_idx[ 2 ] = std::atoi( argv[ 4 ] );
59 std::string output_image_fn = argv[ 5 ];
60 bool visual_debug = false;
62 visual_debug = ( std::atoi( argv[ 6 ] ) == 1 );
65 TImageReader::Pointer input_image_reader = TImageReader::New( );
66 input_image_reader->SetFileName( input_image_fn );
69 input_image_reader->Update( );
71 catch( itk::ExceptionObject& err )
73 std::cerr << "Error caught: " << err << std::endl;
77 TImage::ConstPointer input_image = input_image_reader->GetOutput( );
80 TVTKImage::Pointer vtk_image = TVTKImage::New( );
81 vtk_image->SetInput( input_image );
85 view.SetBackground( 0.3, 0.2, 0.8 );
86 view.SetSize( 800, 800 );
87 view.SetImage( vtk_image->GetOutput( ) );
89 // Allow some interaction
93 TDijkstra::Pointer paths = TDijkstra::New( );
94 paths->AddSeed( seed_idx, TScalar( 0 ) );
95 paths->SetInput( input_image );
96 paths->SetNeighborhoodOrder( 1 );
100 // Configure observer
101 TDijkstraObs::Pointer obs = TDijkstraObs::New( );
102 obs->SetRenderWindow( view.GetWindow( ) );
103 paths->AddObserver( itk::AnyEvent( ), obs );
104 paths->ThrowEventsOn( );
107 paths->ThrowEventsOff( );
108 std::clock_t start = std::clock( );
110 std::clock_t end = std::clock( );
111 double seconds = double( end - start ) / double( CLOCKS_PER_SEC );
112 std::cout << "Paths extraction time = " << seconds << std::endl;
115 vtkSmartPointer< vtkPoints > points =
116 vtkSmartPointer< vtkPoints >::New( );
117 vtkSmartPointer< vtkCellArray > cells =
118 vtkSmartPointer< vtkCellArray >::New( );
119 vtkSmartPointer< vtkFloatArray > scalars =
120 vtkSmartPointer< vtkFloatArray >::New( );
122 const TDijkstra::TVertices& endpoints = paths->GetEndPoints( );
123 const TDijkstra::TTree& tree = paths->GetFinalTree( );
124 TDijkstra::TVertices::const_iterator epIt = endpoints.begin( );
125 for( unsigned int epId = 0; epIt != endpoints.end( ); ++epIt, ++epId )
127 double pd = double( epId ) / double( endpoints.size( ) - 1 );
129 TDijkstra::TVertex idx = *epIt;
132 TImage::PointType pnt;
133 input_image->TransformIndexToPhysicalPoint( idx, pnt );
135 points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
136 scalars->InsertNextTuple1( pd );
139 cells->InsertNextCell( 2 );
140 cells->InsertCellPoint( points->GetNumberOfPoints( ) - 2 );
141 cells->InsertCellPoint( points->GetNumberOfPoints( ) - 1 );
144 idx = tree.find( idx )->second;
146 } while( idx != tree.find( idx )->second );
150 vtkSmartPointer< vtkPolyData > vtk_tree =
151 vtkSmartPointer< vtkPolyData >::New( );
152 vtk_tree->SetPoints( points );
153 vtk_tree->SetLines( cells );
154 vtk_tree->GetPointData( )->SetScalars( scalars );
156 view.AddPolyData( vtk_tree );
161 TImageWriter::Pointer dijkstra_writer =
162 TImageWriter::New( );
163 dijkstra_writer->SetInput( paths->GetOutput( ) );
164 dijkstra_writer->SetFileName( "dijkstra.mhd" );
165 dijkstra_writer->Update( );