+++ /dev/null
-#include <cmath>
-#include <ctime>
-#include <deque>
-#include <fstream>
-#include <iostream>
-#include <iomanip>
-#include <limits>
-#include <map>
-#include <string>
-
-#include <itkConstNeighborhoodIterator.h>
-#include <itkNeighborhoodIterator.h>
-#include <itkDanielssonDistanceMapImageFilter.h>
-#include <itkImage.h>
-#include <itkImageFileReader.h>
-#include <itkImageFileWriter.h>
-#include <itkImageToVTKImageFilter.h>
-
-#include <itkMinimumMaximumImageCalculator.h>
-#include <itkInvertIntensityImageFilter.h>
-
-#include <vtkPoints.h>
-#include <vtkCellArray.h>
-#include <vtkFloatArray.h>
-#include <vtkPolyData.h>
-#include <vtkPolyDataWriter.h>
-#include <vtkSmartPointer.h>
-#include <vtkImageMarchingCubes.h>
-#include <vtkLookupTable.h>
-
-#include <fpa/Image/DijkstraWithSphereBacktracking.h>
-#include <fpa/VTK/ImageMPR.h>
-#include <fpa/VTK/Image3DObserver.h>
-
-// -------------------------------------------------------------------------
-const unsigned int Dim = 3;
-typedef float TPixel;
-typedef float 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::DijkstraWithSphereBacktracking< TImage, TScalar > TDijkstra;
-
-typedef fpa::VTK::ImageMPR TMPR;
-typedef fpa::VTK::Image3DObserver< TDijkstra, vtkRenderWindow > TDijkstraObs;
-
-struct TBranch
-{
- double Length;
- TImage::PointType::VectorType V1;
- TImage::PointType::VectorType V2;
-
- bool operator<( const TBranch& other ) const
- {
- return( other.Length < this->Length );
- }
-};
-typedef std::multiset< TBranch > TBranches;
-
-// -------------------------------------------------------------------------
-int main( int argc, char* argv[] )
-{
- if( argc < 8 )
- {
- std::cerr
- << "Usage: " << argv[ 0 ]
- << " input_image x y z output_image output_imagej output_vtk"
- << " visual_debug"
- << std::endl;
- return( 1 );
-
- } // fi
- std::string input_image_fn = argv[ 1 ];
- TImage::PointType seed_pnt;
- seed_pnt[ 0 ] = std::atof( argv[ 2 ] );
- seed_pnt[ 1 ] = std::atof( argv[ 3 ] );
- seed_pnt[ 2 ] = std::atof( argv[ 4 ] );
- std::string output_image_fn = argv[ 5 ];
- std::string output_imagej_fn = argv[ 6 ];
- std::string output_vtk_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( ) );
-
- /* TODO
- vtkSmartPointer< vtkImageMarchingCubes > mc =
- vtkSmartPointer< vtkImageMarchingCubes >::New( );
- mc->SetInputData( vtk_image->GetOutput( ) );
- mc->SetValue( 0, 1e-2 );
- mc->Update( );
- view.AddPolyData( mc->GetOutput( ), 1, 1, 1, 0.4 );
- */
-
- // Allow some interaction
- view.Render( );
- if( visual_debug )
- view.Start( );
-
- TImage::IndexType seed_idx;
- input_image->TransformPhysicalPointToIndex( seed_pnt, seed_idx );
- /* TODO
- std::cout << seed_idx << " " << seed_pnt << std::endl;
- seed_idx[ 0 ] = 256;
- seed_idx[ 1 ] = 313;
- seed_idx[ 2 ] = 381;
- */
-
- // Extract paths
- TDijkstra::Pointer paths = TDijkstra::New( );
- paths->AddSeed( seed_idx, TScalar( 0 ) );
- paths->SetInput( input_image );
- 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( );
- 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;
-
- // Create polydata
- vtkSmartPointer< vtkPoints > points =
- vtkSmartPointer< vtkPoints >::New( );
- vtkSmartPointer< vtkCellArray > cells =
- vtkSmartPointer< vtkCellArray >::New( );
- vtkSmartPointer< vtkFloatArray > scalars =
- vtkSmartPointer< vtkFloatArray >::New( );
-
- TDijkstra::TMarkImage::Pointer new_marks = TDijkstra::TMarkImage::New( );
- new_marks->SetLargestPossibleRegion( input_image->GetLargestPossibleRegion( ) );
- new_marks->SetRequestedRegion( input_image->GetRequestedRegion( ) );
- new_marks->SetBufferedRegion( input_image->GetBufferedRegion( ) );
- new_marks->SetOrigin( input_image->GetOrigin( ) );
- new_marks->SetSpacing( input_image->GetSpacing( ) );
- new_marks->SetDirection( input_image->GetDirection( ) );
- new_marks->Allocate( );
- new_marks->FillBuffer( 0 );
-
- const TDijkstra::TMarkImage* marks = paths->GetOutputMarkImage( );
- TDijkstra::TMark max_mark = paths->GetNumberOfBranches( );
- const TDijkstra::TVertices& endpoints = paths->GetEndPoints( );
- const TDijkstra::TVertices& bifurcations = paths->GetBifurcationPoints( );
- const TDijkstra::TTree& tree = paths->GetFullTree( );
- const TDijkstra::TTree& reduced_tree = paths->GetReducedTree( );
- TDijkstra::TVertices::const_iterator epIt = endpoints.begin( );
-
- TBranches branches;
- TImage::PointType ori = input_image->GetOrigin( );
-
- TDijkstra::TTree::const_iterator rIt = reduced_tree.begin( );
- for( ; rIt != reduced_tree.end( ); ++rIt )
- {
- TDijkstra::TTree::const_iterator tIt = tree.find( rIt->first );
-
- // Prepare branch "a la ImageJ"
- TBranch branch;
- TImage::PointType p1, p2;
- input_image->TransformIndexToPhysicalPoint( rIt->second.first, p1 );
- input_image->TransformIndexToPhysicalPoint( rIt->first, p2 );
- branch.V1 = p1 - ori;
- branch.V2 = p2 - ori;
- branch.Length = double( 0 );
-
- double pd =
- ( double( tIt->second.second ) - double( 1 ) ) /
- ( double( max_mark ) - double( 1 ) );
- bool start = true;
- TImage::PointType prev;
- do
- {
- TDijkstra::TVertex idx = tIt->first;
- new_marks->SetPixel( idx, 255 );
- TImage::PointType pnt;
- input_image->TransformIndexToPhysicalPoint( idx, pnt );
- points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
- scalars->InsertNextTuple1( pd );
- if( !start )
- {
- cells->InsertNextCell( 2 );
- cells->InsertCellPoint( points->GetNumberOfPoints( ) - 2 );
- cells->InsertCellPoint( points->GetNumberOfPoints( ) - 1 );
- branch.Length += prev.EuclideanDistanceTo( pnt );
-
- } // fi
- start = false;
- prev = pnt;
- tIt = tree.find( tIt->second.first );
-
- } while( tIt->first != rIt->second.first );
-
- // Last point
- TDijkstra::TVertex idx = tIt->first;
- new_marks->SetPixel( idx, 255 );
- TImage::PointType pnt;
- input_image->TransformIndexToPhysicalPoint( idx, pnt );
- points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
- scalars->InsertNextTuple1( pd );
- if( !start )
- {
- cells->InsertNextCell( 2 );
- cells->InsertCellPoint( points->GetNumberOfPoints( ) - 2 );
- cells->InsertCellPoint( points->GetNumberOfPoints( ) - 1 );
- branch.Length += prev.EuclideanDistanceTo( pnt );
-
- } // fi
- branches.insert( branch );
-
- } // rof
-
- std::ofstream bout( output_imagej_fn.c_str( ) );
- if( !bout )
- {
- std::cerr << "Error: could not open " << output_imagej_fn << std::endl;
- return( 1 );
-
- } // fi
- int i = 1;
- for( TBranches::const_iterator bIt = branches.begin( ); bIt != branches.end( ); ++bIt, ++i )
- {
- bout
- << std::setiosflags( std::ios::fixed) << std::setprecision( 3 )
- << i << "\t1.000\t"
- << bIt->Length << "\t"
- << bIt->V1[ 0 ] << "\t"
- << bIt->V1[ 1 ] << "\t"
- << bIt->V1[ 2 ] << "\t"
- << bIt->V2[ 0 ] << "\t"
- << bIt->V2[ 1 ] << "\t"
- << bIt->V2[ 2 ] << "\t"
- << ( bIt->V2 - bIt->V1 ).GetNorm( )
- << std::endl;
-
- } // rof
- bout.close( );
-
- 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( );
- if( visual_debug )
- view.Start( );
-
- vtkSmartPointer< vtkPolyDataWriter > writer =
- vtkSmartPointer< vtkPolyDataWriter >::New( );
- writer->SetInputData( vtk_tree );
- writer->SetFileName( output_vtk_fn.c_str( ) );
- writer->Update( );
-
- itk::ImageFileWriter< TDijkstra::TMarkImage >::Pointer marks_writer =
- itk::ImageFileWriter< TDijkstra::TMarkImage >::New( );
- marks_writer->SetInput( new_marks );
- marks_writer->SetFileName( output_image_fn );
- marks_writer->Update( );
-
- TImageWriter::Pointer dijkstra_writer =
- TImageWriter::New( );
- dijkstra_writer->SetInput( paths->GetOutput( ) );
- dijkstra_writer->SetFileName( "dijkstra.mhd" );
- dijkstra_writer->Update( );
-
- return( 0 );
-}
-
-// eof - $RCSfile$
git://git.creatis.insa-lyon.fr / FrontAlgorithms.git / blobdiff