--- /dev/null
+#include <ctime>
+#include <iostream>
+#include <limits>
+#include <map>
+#include <string>
+#include <deque>
+
+#include <itkConstNeighborhoodIterator.h>
+#include <itkDanielssonDistanceMapImageFilter.h>
+#include <itkImage.h>
+#include <itkImageFileReader.h>
+#include <itkImageFileWriter.h>
+#include <itkImageToVTKImageFilter.h>
+
+#include <vtkPoints.h>
+#include <vtkCellArray.h>
+#include <vtkPolyData.h>
+#include <vtkSmartPointer.h>
+
+#include <fpa/Base/Functors/InvertCostFunction.h>
+#include <fpa/Image/Dijkstra.h>
+#include <fpa/Image/RegionGrowWithMultipleThresholds.h>
+#include <fpa/VTK/ImageMPR.h>
+#include <fpa/VTK/Image3DObserver.h>
+
+// -------------------------------------------------------------------------
+const unsigned int Dim = 3;
+typedef double TPixel;
+typedef double TScalar;
+typedef itk::Image< TPixel, Dim > TImage;
+typedef itk::ImageToVTKImageFilter< TImage > TVTKImage;
+
+typedef itk::ImageFileReader< TImage > TImageReader;
+typedef itk::ImageFileWriter< TImage > TImageWriter;
+typedef fpa::Image::Dijkstra< TImage, TScalar > TBaseDijkstra;
+
+typedef fpa::VTK::ImageMPR TMPR;
+typedef fpa::VTK::Image3DObserver< TBaseDijkstra, vtkRenderWindow > TDijkstraObs;
+
+// -------------------------------------------------------------------------
+class TDijkstra
+ : public TBaseDijkstra
+{
+public:
+ typedef TDijkstra Self;
+ typedef TBaseDijkstra Superclass;
+ typedef itk::SmartPointer< Self > Pointer;
+ typedef itk::SmartPointer< const Self > ConstPointer;
+
+ typedef Superclass::TCost TCost;
+ typedef Superclass::TVertex TVertex;
+ typedef Superclass::InputImageType TImage;
+ typedef std::deque< TVertex > TVertices;
+
+protected:
+ typedef std::pair< TCost, TVertex > _TCandidate;
+ typedef std::multimap< TCost, TVertex > _TCandidates;
+ typedef Superclass::_TNode _TNode;
+
+public:
+ itkNewMacro( Self );
+ itkTypeMacro( TDijkstra, TBaseDijkstra );
+
+protected:
+ TDijkstra( )
+ : Superclass( )
+ { }
+ virtual ~TDijkstra( )
+ { }
+
+ virtual void _BeforeMainLoop( )
+ {
+ const TImage* img = this->GetInput( );
+
+ // Correct seeds
+ TImage::SizeType radius;
+ radius.Fill( 3 );
+ itk::ConstNeighborhoodIterator< TImage > it(
+ radius, img, img->GetRequestedRegion( )
+ );
+ for( unsigned int s = 0; s < this->m_Seeds.size( ); ++s )
+ {
+ _TNode seed = this->m_Seeds[ s ];
+ it.SetLocation( seed.Vertex );
+
+ TImage::SizeType size = it.GetSize( );
+ unsigned int nN = 1;
+ for( unsigned int d = 0; d < TImage::ImageDimension; ++d )
+ nN *= size[ d ];
+ TImage::PixelType max_value = img->GetPixel( seed.Vertex );
+ for( unsigned int i = 0; i < nN; ++i )
+ {
+ if( it.GetPixel( i ) > max_value )
+ {
+ seed.Vertex = it.GetIndex( i );
+ seed.Parent = seed.Vertex;
+ max_value = it.GetPixel( i );
+
+ } // fi
+
+ } // rof
+ this->m_Seeds[ s ] = seed;
+
+ } // rof
+
+ // End initialization
+ this->Superclass::_BeforeMainLoop( );
+ this->m_Candidates.clear( );
+ }
+
+ virtual void _AfterMainLoop( )
+ {
+ this->Superclass::_AfterMainLoop( );
+ if( this->m_Candidates.size( ) == 0 )
+ return;
+
+ this->m_Axes = vtkSmartPointer< vtkPolyData >::New( );
+ vtkSmartPointer< vtkPoints > points =
+ vtkSmartPointer< vtkPoints >::New( );
+ vtkSmartPointer< vtkCellArray > lines =
+ vtkSmartPointer< vtkCellArray >::New( );
+
+ _TCandidates::const_reverse_iterator cIt =
+ this->m_Candidates.rbegin( );
+
+ TVertices pS;
+ TVertex vIt = cIt->second;
+ TVertex parent = this->_Parent( vIt );
+ while( parent != vIt )
+ {
+ pS.push_front( vIt );
+ vIt = parent;
+ parent = this->_Parent( vIt );
+
+ TImage::PointType pnt;
+ this->GetInput( )->TransformIndexToPhysicalPoint( vIt, pnt );
+ points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
+ if( points->GetNumberOfPoints( ) > 1 )
+ {
+ lines->InsertNextCell( 2 );
+ lines->InsertCellPoint( points->GetNumberOfPoints( ) - 2 );
+ lines->InsertCellPoint( points->GetNumberOfPoints( ) - 1 );
+
+ } // fi
+
+ } // elihw
+ pS.push_front( vIt );
+ TImage::PointType pnt;
+ this->GetInput( )->TransformIndexToPhysicalPoint( vIt, pnt );
+ points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
+ if( points->GetNumberOfPoints( ) > 1 )
+ {
+ lines->InsertNextCell( 2 );
+ lines->InsertCellPoint( points->GetNumberOfPoints( ) - 2 );
+ lines->InsertCellPoint( points->GetNumberOfPoints( ) - 1 );
+
+ } // fi
+
+ this->m_Axes->SetPoints( points );
+ this->m_Axes->SetLines( lines );
+ }
+
+ virtual bool _UpdateNeigh( _TNode& nn, const _TNode& n )
+ {
+ TCost nc = this->_Cost( nn.Vertex, n.Vertex );
+ if( TCost( 0 ) < nc )
+ {
+ nn.Cost = n.Cost + ( TCost( 1 ) / nc );
+ nn.Result = nn.Cost;
+ return( true );
+ }
+ else
+ return( false );
+ }
+
+ virtual bool _UpdateResult( _TNode& n )
+ {
+ bool ret = this->Superclass::_UpdateResult( n );
+ if( ret )
+ {
+ TCost nc = this->_Cost( n.Vertex, n.Parent );
+ if( TCost( 0 ) < nc )
+ {
+ n.Result = n.Cost / ( nc * nc );
+ this->GetOutput( )->SetPixel( n.Vertex, n.Result );
+ this->m_Candidates.insert( _TCandidate( n.Result, n.Vertex ) );
+
+ } // fi
+
+ } // fi
+ return( ret );
+ }
+
+private:
+ TDijkstra( const Self& other );
+ Self& operator=( const Self& other );
+
+protected:
+ _TCandidates m_Candidates;
+public:
+ vtkSmartPointer< vtkPolyData > m_Axes;
+};
+
+// -------------------------------------------------------------------------
+int main( int argc, char* argv[] )
+{
+ if( argc < 6 )
+ {
+ std::cerr
+ << "Usage: " << argv[ 0 ]
+ << " input_image x y z output_image"
+ << " visual_debug"
+ << std::endl;
+ return( 1 );
+
+ } // fi
+ std::string input_image_fn = argv[ 1 ];
+ TImage::IndexType seed_idx;
+ seed_idx[ 0 ] = std::atoi( argv[ 2 ] );
+ seed_idx[ 1 ] = std::atoi( argv[ 3 ] );
+ seed_idx[ 2 ] = std::atoi( argv[ 4 ] );
+ std::string output_image_fn = argv[ 5 ];
+ bool visual_debug = false;
+ if( argc > 6 )
+ visual_debug = ( std::atoi( argv[ 6 ] ) == 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( ) );
+
+ // Allow some interaction
+ view.Start( );
+
+ // Extract paths
+ TDijkstra::Pointer paths = TDijkstra::New( );
+ paths->AddSeed( seed_idx, TScalar( 0 ) );
+ paths->SetInput( input_image );
+ paths->SetNeighborhoodOrder( 1 );
+
+ if( visual_debug )
+ {
+ // Configure observer
+ TDijkstraObs::Pointer obs = TDijkstraObs::New( );
+ obs->SetImage( input_image, view.GetWindow( ) );
+ paths->AddObserver( itk::AnyEvent( ), obs );
+ paths->ThrowEventsOn( );
+ }
+ else
+ paths->ThrowEventsOff( );
+ std::clock_t start = std::clock( );
+ paths->Update( );
+ std::clock_t end = std::clock( );
+ double seconds = double( end - start ) / double( CLOCKS_PER_SEC );
+ std::cout << "Paths extraction time = " << seconds << std::endl;
+
+ view.AddPolyData( paths->m_Axes, 1, 0, 0 );
+ view.Start( );
+
+ TImageWriter::Pointer dijkstra_writer =
+ TImageWriter::New( );
+ dijkstra_writer->SetInput( paths->GetOutput( ) );
+ dijkstra_writer->SetFileName( "dijkstra.mhd" );
+ dijkstra_writer->Update( );
+
+ // Show result
+ /*
+ TVTKImage::Pointer output_image_vtk = TVTKImage::New( );
+ output_image_vtk->SetInput( segmentor->GetOutput( ) );
+ output_image_vtk->Update( );
+
+ 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( );
+
+ // 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 )
+ {
+ std::cerr << "Error caught: " << err << std::endl;
+ return( 1 );
+
+ } // yrt
+ */
+ return( 0 );
+}
+
+// eof - $RCSfile$
#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 <fpa/Image/RegionGrowWithMultipleThresholds.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 itk::Image< TPixel, Dim > TImage;
typedef itk::Image< TScalar, Dim > TDistanceMap;
+typedef itk::ImageToVTKImageFilter< TImage > TVTKImage;
+
+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 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;
// -------------------------------------------------------------------------
int main( int argc, char* argv[] )
{
- if( argc < 6 )
+ if( argc < 7 )
{
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"
<< " 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 ];
bool visual_debug = false;
- if( argc > 6 )
- visual_debug = ( std::atoi( argv[ 6 ] ) == 1 );
+ if( argc > 7 )
+ visual_debug = ( std::atoi( argv[ 7 ] ) == 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( );
+ TSegmentorObs::Pointer obs = TSegmentorObs::New( );
obs->SetImage( input_image, 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( );
start = std::clock( );
seconds = double( end - start ) / double( CLOCKS_PER_SEC );
std::cout << "Distance map time = " << seconds << std::endl;
- // Extract paths
- fpa::Image::Dijkstra< TDistanceMap, TScalar >::Pointer paths =
- fpa::Image::Dijkstra< TDistanceMap, TScalar >::New( );
- paths->AddSeed( segmentor->GetSeed( 0 ), TScalar( 0 ) );
- paths->SetInput( distanceMap->GetOutput( ) );
- paths->SetNeighborhoodOrder( 1 );
+ std::cout << "Final seed: " << seed_idx << std::endl;
- // Associate an inversion cost function
- fpa::Base::Functors::InvertCostFunction< TScalar >::Pointer
- cost_function =
- fpa::Base::Functors::InvertCostFunction< TScalar >::New( );
- paths->SetCostConversion( cost_function );
+ TDistanceMapWriter::Pointer distancemap_writer =
+ TDistanceMapWriter::New( );
+ distancemap_writer->SetInput( distanceMap->GetOutput( ) );
+ distancemap_writer->SetFileName( output_distancemap_fn );
+ distancemap_writer->Update( );
- 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( ) );
- 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;
+ TImageWriter::Pointer segmentation_writer =
+ TImageWriter::New( );
+ segmentation_writer->SetInput( segmentor->GetOutput( ) );
+ segmentation_writer->SetFileName( output_segmentation_fn );
+ segmentation_writer->Update( );
// Show result
/*
git://git.creatis.insa-lyon.fr / FrontAlgorithms.git / commitdiff