#include <iostream>
#include <string>
+#include <itkConstNeighborhoodIterator.h>
#include <itkDanielssonDistanceMapImageFilter.h>
#include <itkImage.h>
#include <itkImageFileReader.h>
+#include <itkImageFileWriter.h>
#include <itkImageToVTKImageFilter.h>
-#include <fpa/Base/Functors/InvertCostFunction.h>
-#include <fpa/Image/Dijkstra.h>
+#include <vtkImageMarchingCubes.h>
+
#include <fpa/Image/RegionGrowWithMultipleThresholds.h>
+#include <fpa/Image/DijkstraWithSphereBacktracking.h>
#include <fpa/VTK/ImageMPR.h>
#include <fpa/VTK/Image3DObserver.h>
-/*
- #include <limits>
- #include <set>
-
- #include <itkImageFileWriter.h>
-
-
- #include <vtkImageActor.h>
- #include <vtkImageMarchingCubes.h>
- #include <vtkProperty.h>
- #include <vtkRenderer.h>
- #include <vtkRenderWindow.h>
- #include <vtkRenderWindowInteractor.h>
- #include <vtkSmartPointer.h>
- #include <vtkSphereSource.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::ImageFileWriter< TDistanceMap > TDistanceMapWriter;
+typedef fpa::Image::RegionGrowWithMultipleThresholds< TImage > TSegmentor;
+typedef
+itk::DanielssonDistanceMapImageFilter< TImage, TDistanceMap >
+TDistanceFilter;
+typedef
+fpa::Image::DijkstraWithSphereBacktracking< TDistanceMap, TScalar >
+TDijkstra;
-/*
- typedef itk::ImageToVTKImageFilter< TImage > TVTKImage;
- typedef itk::ImageFileReader< TImage > TImageReader;
- typedef itk::ImageFileWriter< TImage > TImageWriter;
- typedef
- fpa::Image::RegionGrowWithMultipleThresholds< TImage >
- TSegmentor;
- typedef
-
- TObserver;
-*/
+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 < 6 )
+ if( argc < 8 )
{
std::cerr
<< "Usage: " << argv[ 0 ]
- << " input_image thr_0 thr_1 step output_image"
+ << " input_image thr_0 thr_1 step"
+ << " output_segmentation output_distancemap output_dijkstra"
<< " visual_debug"
<< std::endl;
return( 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_image_fn = argv[ 5 ];
+ 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 > 6 )
- visual_debug = ( std::atoi( argv[ 6 ] ) == 1 );
+ if( argc > 8 )
+ visual_debug = ( std::atoi( argv[ 8 ] ) == 1 );
// Read image
- itk::ImageFileReader< TImage >::Pointer input_image_reader =
- itk::ImageFileReader< TImage >::New( );
+ TImageReader::Pointer input_image_reader = TImageReader::New( );
input_image_reader->SetFileName( input_image_fn );
try
{
TImage::ConstPointer input_image = input_image_reader->GetOutput( );
// Show image
- itk::ImageToVTKImageFilter< TImage >::Pointer vtk_image =
- itk::ImageToVTKImageFilter< TImage >::New( );
+ TVTKImage::Pointer vtk_image = TVTKImage::New( );
vtk_image->SetInput( input_image );
vtk_image->Update( );
- fpa::VTK::ImageMPR view;
+ TMPR view;
view.SetBackground( 0.3, 0.2, 0.8 );
view.SetSize( 800, 800 );
view.SetImage( vtk_image->GetOutput( ) );
input_image->TransformPhysicalPointToIndex( seed_pnt, seed_idx );
// Segment input image
- fpa::Image::RegionGrowWithMultipleThresholds< TImage >::Pointer segmentor =
- fpa::Image::RegionGrowWithMultipleThresholds< TImage >::New( );
+ TSegmentor::Pointer segmentor = TSegmentor::New( );
segmentor->AddThresholds( thr_0, thr_1, step );
segmentor->AddSeed( seed_idx, 0 );
segmentor->SetInput( input_image );
if( visual_debug )
{
// Configure observer
- fpa::VTK::Image3DObserver< fpa::Image::RegionGrowWithMultipleThresholds< TImage >, vtkRenderWindow >::Pointer obs =
- fpa::VTK::Image3DObserver< fpa::Image::RegionGrowWithMultipleThresholds< TImage >, vtkRenderWindow >::New( );
- obs->SetImage( input_image, view.GetWindow( ) );
+ TSegmentorObs::Pointer obs = TSegmentorObs::New( );
+ obs->SetRenderWindow( view.GetWindow( ) );
segmentor->AddObserver( itk::AnyEvent( ), obs );
segmentor->ThrowEventsOn( );
}
std::cout << "Segmentation time = " << seconds << std::endl;
// Extract distance map
- itk::DanielssonDistanceMapImageFilter< TImage, TDistanceMap >::Pointer
- distanceMap =
- itk::DanielssonDistanceMapImageFilter< TImage, TDistanceMap >::New( );
+ 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
- fpa::Image::Dijkstra< TDistanceMap, TScalar >::Pointer paths =
- fpa::Image::Dijkstra< TDistanceMap, TScalar >::New( );
+ TDijkstra::Pointer paths = TDijkstra::New( );
paths->AddSeed( segmentor->GetSeed( 0 ), TScalar( 0 ) );
paths->SetInput( distanceMap->GetOutput( ) );
- paths->SetNeighborhoodOrder( 1 );
-
- // Associate an inversion cost function
- fpa::Base::Functors::InvertCostFunction< TScalar >::Pointer
- cost_function =
- fpa::Base::Functors::InvertCostFunction< TScalar >::New( );
- paths->SetCostConversion( cost_function );
+ paths->SetNeighborhoodOrder( 2 );
if( visual_debug )
{
// Configure observer
- fpa::VTK::Image3DObserver< fpa::Image::Dijkstra< TDistanceMap, TScalar >, vtkRenderWindow >::Pointer obs =
- fpa::VTK::Image3DObserver< fpa::Image::Dijkstra< TDistanceMap, TScalar >, vtkRenderWindow >::New( );
- obs->SetImage( distanceMap->GetOutput( ), view.GetWindow( ) );
+ TDijkstraObs::Pointer obs = TDijkstraObs::New( );
+ obs->SetRenderWindow( view.GetWindow( ) );
paths->AddObserver( itk::AnyEvent( ), obs );
paths->ThrowEventsOn( );
}
seconds = double( end - start ) / double( CLOCKS_PER_SEC );
std::cout << "Paths extraction time = " << seconds << std::endl;
- // Show result
- /*
- TVTKImage::Pointer output_image_vtk = TVTKImage::New( );
- output_image_vtk->SetInput( segmentor->GetOutput( ) );
- output_image_vtk->Update( );
+ std::cout << "Final seed: " << paths->GetSeed( 0 ) << std::endl;
- 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( );
+ // Create polydata
+ vtkSmartPointer< vtkPoints > points =
+ vtkSmartPointer< vtkPoints >::New( );
+ vtkSmartPointer< vtkCellArray > cells =
+ vtkSmartPointer< vtkCellArray >::New( );
+ vtkSmartPointer< vtkFloatArray > scalars =
+ vtkSmartPointer< vtkFloatArray >::New( );
- // 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 )
+ 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 );
+ return( -1 );
+
+ } // yrt
- } // yrt
- */
return( 0 );
}
git://git.creatis.insa-lyon.fr / FrontAlgorithms.git / blobdiff