+++ /dev/null
-#include <ctime>
-#include <iostream>
-#include <string>
-
-#include <itkConstNeighborhoodIterator.h>
-#include <itkDanielssonDistanceMapImageFilter.h>
-#include <itkImage.h>
-#include <itkImageFileReader.h>
-#include <itkImageFileWriter.h>
-#include <itkImageToVTKImageFilter.h>
-
-#include <vtkImageMarchingCubes.h>
-
-#include <fpa/Image/RegionGrowWithMultipleThresholds.h>
-#include <fpa/Image/DijkstraWithSphereBacktracking.h>
-#include <fpa/VTK/ImageMPR.h>
-#include <fpa/VTK/Image3DObserver.h>
-
-// -------------------------------------------------------------------------
-const unsigned int Dim = 3;
-typedef short TPixel;
-typedef float TScalar;
-typedef itk::Image< TPixel, Dim > TImage;
-typedef itk::Image< TScalar, Dim > TDistanceMap;
-typedef itk::ImageToVTKImageFilter< TImage > TVTKImage;
-typedef itk::ImageToVTKImageFilter< TDistanceMap > TVTKDistanceMap;
-
-typedef itk::ImageFileReader< TImage > TImageReader;
-typedef itk::ImageFileWriter< TImage > TImageWriter;
-typedef itk::ImageFileWriter< TDistanceMap > TDistanceMapWriter;
-typedef fpa::Image::RegionGrowWithMultipleThresholds< TImage > TSegmentor;
-typedef
-itk::DanielssonDistanceMapImageFilter< TImage, TDistanceMap >
-TDistanceFilter;
-typedef
-fpa::Image::DijkstraWithSphereBacktracking< TDistanceMap, TScalar >
-TDijkstra;
-
-typedef fpa::VTK::ImageMPR TMPR;
-typedef fpa::VTK::Image3DObserver< TSegmentor, vtkRenderWindow > TSegmentorObs;
-typedef fpa::VTK::Image3DObserver< TDijkstra, vtkRenderWindow > TDijkstraObs;
-
-// -------------------------------------------------------------------------
-int main( int argc, char* argv[] )
-{
- if( argc < 8 )
- {
- std::cerr
- << "Usage: " << argv[ 0 ]
- << " input_image thr_0 thr_1 step"
- << " output_segmentation output_distancemap output_dijkstra"
- << " visual_debug"
- << std::endl;
- return( 1 );
-
- } // fi
- std::string input_image_fn = argv[ 1 ];
- TPixel thr_0 = TPixel( std::atof( argv[ 2 ] ) );
- TPixel thr_1 = TPixel( std::atof( argv[ 3 ] ) );
- unsigned int step = std::atoi( argv[ 4 ] );
- std::string output_segmentation_fn = argv[ 5 ];
- std::string output_distancemap_fn = argv[ 6 ];
- std::string output_dijkstra_fn = argv[ 7 ];
- bool visual_debug = false;
- if( argc > 8 )
- visual_debug = ( std::atoi( argv[ 8 ] ) == 1 );
-
- // Read image
- TImageReader::Pointer input_image_reader = TImageReader::New( );
- input_image_reader->SetFileName( input_image_fn );
- try
- {
- input_image_reader->Update( );
- }
- catch( itk::ExceptionObject& err )
- {
- std::cerr << "Error caught: " << err << std::endl;
- return( 1 );
-
- } // yrt
- TImage::ConstPointer input_image = input_image_reader->GetOutput( );
-
- // Show image
- TVTKImage::Pointer vtk_image = TVTKImage::New( );
- vtk_image->SetInput( input_image );
- vtk_image->Update( );
-
- TMPR view;
- view.SetBackground( 0.3, 0.2, 0.8 );
- view.SetSize( 800, 800 );
- view.SetImage( vtk_image->GetOutput( ) );
-
- // Wait for a seed to be given
- while( view.GetNumberOfSeeds( ) == 0 )
- view.Start( );
-
- // Get seed from user
- double seed[ 3 ];
- view.GetSeed( 0, seed );
- TImage::PointType seed_pnt;
- seed_pnt[ 0 ] = seed[ 0 ];
- seed_pnt[ 1 ] = seed[ 1 ];
- seed_pnt[ 2 ] = seed[ 2 ];
- TImage::IndexType seed_idx;
- input_image->TransformPhysicalPointToIndex( seed_pnt, seed_idx );
-
- // Segment input image
- TSegmentor::Pointer segmentor = TSegmentor::New( );
- segmentor->AddThresholds( thr_0, thr_1, step );
- segmentor->AddSeed( seed_idx, 0 );
- segmentor->SetInput( input_image );
- segmentor->SetNeighborhoodOrder( 1 );
- segmentor->SetDifferenceThreshold( double( 3 ) );
- segmentor->SetInsideValue( TPixel( 0 ) ); // WARNING: This is to optimize
- segmentor->SetOutsideValue( TPixel( 1 ) ); // distance map calculation
- if( visual_debug )
- {
- // Configure observer
- TSegmentorObs::Pointer obs = TSegmentorObs::New( );
- obs->SetRenderWindow( view.GetWindow( ) );
- segmentor->AddObserver( itk::AnyEvent( ), obs );
- segmentor->ThrowEventsOn( );
- }
- else
- segmentor->ThrowEventsOff( );
- std::clock_t start = std::clock( );
- segmentor->Update( );
- std::clock_t end = std::clock( );
- double seconds = double( end - start ) / double( CLOCKS_PER_SEC );
- std::cout << "Segmentation time = " << seconds << std::endl;
-
- // Extract distance map
- TDistanceFilter::Pointer distanceMap = TDistanceFilter::New( );
- distanceMap->SetInput( segmentor->GetOutput( ) );
- distanceMap->InputIsBinaryOn( );
- distanceMap->SquaredDistanceOn( );
- distanceMap->UseImageSpacingOn( );
- start = std::clock( );
- distanceMap->Update( );
- end = std::clock( );
- seconds = double( end - start ) / double( CLOCKS_PER_SEC );
- std::cout << "Distance map time = " << seconds << std::endl;
-
- TVTKDistanceMap::Pointer vtk_distanceMap = TVTKDistanceMap::New( );
- vtk_distanceMap->SetInput( distanceMap->GetOutput( ) );
- vtk_distanceMap->Update( );
-
- vtkSmartPointer< vtkImageMarchingCubes > mc =
- vtkSmartPointer< vtkImageMarchingCubes >::New( );
- mc->SetInputData( vtk_distanceMap->GetOutput( ) );
- mc->SetValue( 0, 1e-2 );
- mc->Update( );
- view.AddPolyData( mc->GetOutput( ), 1, 1, 1, 0.4 );
- view.Render( );
-
- // Extract paths
- TDijkstra::Pointer paths = TDijkstra::New( );
- paths->AddSeed( segmentor->GetSeed( 0 ), TScalar( 0 ) );
- paths->SetInput( distanceMap->GetOutput( ) );
- paths->SetNeighborhoodOrder( 2 );
-
- if( visual_debug )
- {
- // Configure observer
- TDijkstraObs::Pointer obs = TDijkstraObs::New( );
- obs->SetRenderWindow( view.GetWindow( ) );
- paths->AddObserver( itk::AnyEvent( ), obs );
- paths->ThrowEventsOn( );
- }
- else
- paths->ThrowEventsOff( );
- start = std::clock( );
- paths->Update( );
- end = std::clock( );
- seconds = double( end - start ) / double( CLOCKS_PER_SEC );
- std::cout << "Paths extraction time = " << seconds << std::endl;
-
- std::cout << "Final seed: " << paths->GetSeed( 0 ) << std::endl;
-
- // Create polydata
- vtkSmartPointer< vtkPoints > points =
- vtkSmartPointer< vtkPoints >::New( );
- vtkSmartPointer< vtkCellArray > cells =
- vtkSmartPointer< vtkCellArray >::New( );
- vtkSmartPointer< vtkFloatArray > scalars =
- vtkSmartPointer< vtkFloatArray >::New( );
-
- const TDijkstra::TVertices& endpoints = paths->GetEndPoints( );
- const TDijkstra::TTree& tree = paths->GetFullTree( );
- TDijkstra::TVertices::const_iterator epIt = endpoints.begin( );
- for( unsigned int epId = 0; epIt != endpoints.end( ); ++epIt, ++epId )
- {
- double pd = double( epId ) / double( endpoints.size( ) - 1 );
-
- TDijkstra::TVertex idx = *epIt;
- do
- {
- TImage::PointType pnt;
- input_image->TransformIndexToPhysicalPoint( idx, pnt );
-
- points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
- scalars->InsertNextTuple1( pd );
- if( idx != *epIt )
- {
- cells->InsertNextCell( 2 );
- cells->InsertCellPoint( points->GetNumberOfPoints( ) - 2 );
- cells->InsertCellPoint( points->GetNumberOfPoints( ) - 1 );
-
- } // fi
- idx = tree.find( idx )->second.first;
-
- } while( idx != tree.find( idx )->second.first );
-
- } // rof
-
- vtkSmartPointer< vtkPolyData > vtk_tree =
- vtkSmartPointer< vtkPolyData >::New( );
- vtk_tree->SetPoints( points );
- vtk_tree->SetLines( cells );
- vtk_tree->GetPointData( )->SetScalars( scalars );
-
- view.AddPolyData( vtk_tree );
- view.Render( );
- view.Start( );
-
- itk::ImageFileWriter< TImage >::Pointer segmentation_writer =
- itk::ImageFileWriter< TImage >::New( );
- segmentation_writer->SetInput( segmentor->GetOutput( ) );
- segmentation_writer->SetFileName( output_segmentation_fn );
-
- itk::ImageFileWriter< TDistanceMap >::Pointer dmap_writer =
- itk::ImageFileWriter< TDistanceMap >::New( );
- dmap_writer->SetInput( distanceMap->GetOutput( ) );
- dmap_writer->SetFileName( output_distancemap_fn );
-
- itk::ImageFileWriter< TDistanceMap >::Pointer dijk_writer =
- itk::ImageFileWriter< TDistanceMap >::New( );
- dijk_writer->SetInput( paths->GetOutput( ) );
- dijk_writer->SetFileName( output_dijkstra_fn );
-
- try
- {
- segmentation_writer->Update( );
- dmap_writer->Update( );
- dijk_writer->Update( );
- }
- catch( itk::ExceptionObject& err )
- {
- std::cerr << "Error caught: " << err << std::endl;
- return( -1 );
-
- } // yrt
-
- return( 0 );
-}
-
-// eof - $RCSfile$
git://git.creatis.insa-lyon.fr / FrontAlgorithms.git / blobdiff