#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 double TScalar;
+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::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 < 7 )
+ if( argc < 8 )
{
std::cerr
<< "Usage: " << argv[ 0 ]
<< " input_image thr_0 thr_1 step"
- << " output_segmentation output_distancemap"
+ << " output_segmentation output_distancemap output_dijkstra"
<< " visual_debug"
<< std::endl;
return( 1 );
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 > 7 )
- visual_debug = ( std::atoi( argv[ 7 ] ) == 1 );
+ if( argc > 8 )
+ visual_debug = ( std::atoi( argv[ 8 ] ) == 1 );
// Read image
TImageReader::Pointer input_image_reader = TImageReader::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;
- std::cout << "Final seed: " << seed_idx << 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 );
- TDistanceMapWriter::Pointer distancemap_writer =
- TDistanceMapWriter::New( );
- distancemap_writer->SetInput( distanceMap->GetOutput( ) );
- distancemap_writer->SetFileName( output_distancemap_fn );
- distancemap_writer->Update( );
+ } // rof
- TImageWriter::Pointer segmentation_writer =
- TImageWriter::New( );
+ 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 );
- segmentation_writer->Update( );
- // Show result
- /*
- TVTKImage::Pointer output_image_vtk = TVTKImage::New( );
- output_image_vtk->SetInput( segmentor->GetOutput( ) );
- output_image_vtk->Update( );
+ itk::ImageFileWriter< TDistanceMap >::Pointer dmap_writer =
+ itk::ImageFileWriter< TDistanceMap >::New( );
+ dmap_writer->SetInput( distanceMap->GetOutput( ) );
+ dmap_writer->SetFileName( output_distancemap_fn );
- vtkSmartPointer< vtkImageMarchingCubes > mc =
- vtkSmartPointer< vtkImageMarchingCubes >::New( );
- mc->SetInputData( output_image_vtk->GetOutput( ) );
- mc->SetValue(
- 0,
- double( segmentor->GetInsideValue( ) ) * double( 0.95 )
- );
- mc->Update( );
-
- // Let some interaction and close program
- view.AddPolyData( mc->GetOutput( ), 0.1, 0.6, 0.8, 0.5 );
- view.Start( );
+ itk::ImageFileWriter< TDistanceMap >::Pointer dijk_writer =
+ itk::ImageFileWriter< TDistanceMap >::New( );
+ dijk_writer->SetInput( paths->GetOutput( ) );
+ dijk_writer->SetFileName( output_dijkstra_fn );
- // Write resulting image
- TImageWriter::Pointer output_image_writer = TImageWriter::New( );
- output_image_writer->SetInput( segmentor->GetOutput( ) );
- output_image_writer->SetFileName( output_image_fn );
- try
- {
- output_image_writer->Update( );
- }
- catch( itk::ExceptionObject& err )
- {
+ try
+ {
+ segmentation_writer->Update( );
+ dmap_writer->Update( );
+ dijk_writer->Update( );
+ }
+ catch( itk::ExceptionObject& err )
+ {
std::cerr << "Error caught: " << err << std::endl;
- return( 1 );
+ return( -1 );
+
+ } // yrt
- } // yrt
- */
return( 0 );
}
git://git.creatis.insa-lyon.fr / FrontAlgorithms.git / blobdiff