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 <itkMinimumMaximumImageCalculator.h>
18 #include <itkInvertIntensityImageFilter.h>
20 #include <vtkPoints.h>
21 #include <vtkCellArray.h>
22 #include <vtkFloatArray.h>
23 #include <vtkPolyData.h>
24 #include <vtkSmartPointer.h>
26 #include <fpa/Image/DijkstraWithSphereBacktracking.h>
27 #include <fpa/VTK/ImageMPR.h>
28 #include <fpa/VTK/Image3DObserver.h>
30 // -------------------------------------------------------------------------
31 const unsigned int Dim = 3;
33 typedef float TScalar;
34 typedef itk::Image< TPixel, Dim > TImage;
35 typedef itk::ImageToVTKImageFilter< TImage > TVTKImage;
37 typedef itk::ImageFileReader< TImage > TImageReader;
38 typedef itk::ImageFileWriter< TImage > TImageWriter;
39 typedef fpa::Image::DijkstraWithSphereBacktracking< TImage, TScalar > TDijkstra;
41 typedef fpa::VTK::ImageMPR TMPR;
42 typedef fpa::VTK::Image3DObserver< TDijkstra, vtkRenderWindow > TDijkstraObs;
44 // -------------------------------------------------------------------------
45 int main( int argc, char* argv[] )
50 << "Usage: " << argv[ 0 ]
51 << " input_image x y z output_image"
57 std::string input_image_fn = argv[ 1 ];
58 TImage::PointType seed_pnt;
59 seed_pnt[ 0 ] = std::atof( argv[ 2 ] );
60 seed_pnt[ 1 ] = std::atof( argv[ 3 ] );
61 seed_pnt[ 2 ] = std::atof( argv[ 4 ] );
62 std::string output_image_fn = argv[ 5 ];
63 bool visual_debug = false;
65 visual_debug = ( std::atoi( argv[ 6 ] ) == 1 );
68 TImageReader::Pointer input_image_reader = TImageReader::New( );
69 input_image_reader->SetFileName( input_image_fn );
72 input_image_reader->Update( );
74 catch( itk::ExceptionObject& err )
76 std::cerr << "Error caught: " << err << std::endl;
80 TImage::ConstPointer input_image = input_image_reader->GetOutput( );
83 TVTKImage::Pointer vtk_image = TVTKImage::New( );
84 vtk_image->SetInput( input_image );
88 view.SetBackground( 0.3, 0.2, 0.8 );
89 view.SetSize( 800, 800 );
90 view.SetImage( vtk_image->GetOutput( ) );
92 // Allow some interaction
95 TImage::IndexType seed_idx;
96 input_image->TransformPhysicalPointToIndex( seed_pnt, seed_idx );
97 std::cout << seed_idx << " " << seed_pnt << std::endl;
103 TDijkstra::Pointer paths = TDijkstra::New( );
104 paths->AddSeed( seed_idx, TScalar( 0 ) );
105 paths->SetInput( input_image );
106 paths->SetNeighborhoodOrder( 2 );
110 // Configure observer
111 TDijkstraObs::Pointer obs = TDijkstraObs::New( );
112 obs->SetRenderWindow( view.GetWindow( ) );
113 paths->AddObserver( itk::AnyEvent( ), obs );
114 paths->ThrowEventsOn( );
117 paths->ThrowEventsOff( );
118 std::clock_t start = std::clock( );
120 std::clock_t end = std::clock( );
121 double seconds = double( end - start ) / double( CLOCKS_PER_SEC );
122 std::cout << "Paths extraction time = " << seconds << std::endl;
125 vtkSmartPointer< vtkPoints > points =
126 vtkSmartPointer< vtkPoints >::New( );
127 vtkSmartPointer< vtkCellArray > cells =
128 vtkSmartPointer< vtkCellArray >::New( );
129 vtkSmartPointer< vtkFloatArray > scalars =
130 vtkSmartPointer< vtkFloatArray >::New( );
132 const TDijkstra::TVertices& endpoints = paths->GetEndPoints( );
133 const TDijkstra::TTree& tree = paths->GetFinalTree( );
134 TDijkstra::TVertices::const_iterator epIt = endpoints.begin( );
135 for( unsigned int epId = 0; epIt != endpoints.end( ); ++epIt, ++epId )
137 double pd = double( epId ) / double( endpoints.size( ) - 1 );
139 TDijkstra::TVertex idx = *epIt;
142 TImage::PointType pnt;
143 input_image->TransformIndexToPhysicalPoint( idx, pnt );
145 points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
146 scalars->InsertNextTuple1( pd );
149 cells->InsertNextCell( 2 );
150 cells->InsertCellPoint( points->GetNumberOfPoints( ) - 2 );
151 cells->InsertCellPoint( points->GetNumberOfPoints( ) - 1 );
154 idx = tree.find( idx )->second;
156 } while( idx != tree.find( idx )->second );
160 vtkSmartPointer< vtkPolyData > vtk_tree =
161 vtkSmartPointer< vtkPolyData >::New( );
162 vtk_tree->SetPoints( points );
163 vtk_tree->SetLines( cells );
164 vtk_tree->GetPointData( )->SetScalars( scalars );
166 view.AddPolyData( vtk_tree );
171 TImageWriter::Pointer dijkstra_writer =
172 TImageWriter::New( );
173 dijkstra_writer->SetInput( paths->GetOutput( ) );
174 dijkstra_writer->SetFileName( "dijkstra.mhd" );
175 dijkstra_writer->Update( );