+#include <ctime>
#include <iostream>
#include <limits>
#include <set>
#include <itkImage.h>
#include <itkImageFileReader.h>
+#include <itkImageFileWriter.h>
#include <itkImageToVTKImageFilter.h>
#include <vtkImageActor.h>
+#include <vtkImageMarchingCubes.h>
#include <vtkProperty.h>
#include <vtkRenderer.h>
#include <vtkRenderWindow.h>
typedef itk::ImageToVTKImageFilter< TImage > TVTKImage;
typedef itk::ImageFileReader< TImage > TImageReader;
+typedef itk::ImageFileWriter< TImage > TImageWriter;
typedef
fpa::Image::RegionGrowWithMultipleThresholds< TImage >
// -------------------------------------------------------------------------
int main( int argc, char* argv[] )
{
- if( argc < 8 )
+ if( argc < 6 )
{
std::cerr
<< "Usage: " << argv[ 0 ]
- << " input_image s_x s_y s_z thr_0 thr_1 n_samples" << std::endl;
+ << " input_image thr_0 thr_1 step output_image"
+ << " 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 ] );
- TPixel thr_0 = TPixel( std::atof( argv[ 5 ] ) );
- TPixel thr_1 = TPixel( std::atof( argv[ 6 ] ) );
- unsigned int n_samples = std::atoi( argv[ 7 ] );
+ 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 ];
+ bool visual_debug = false;
+ if( argc > 6 )
+ visual_debug = ( std::atoi( argv[ 6 ] ) == 1 );
// Read image
TImageReader::Pointer input_image_reader = TImageReader::New( );
vtk_image->SetInput( input_image );
vtk_image->Update( );
- vtkSmartPointer< vtkSphereSource > seed =
- vtkSmartPointer< vtkSphereSource >::New( );
- seed->SetCenter( seed_pnt[ 0 ], seed_pnt[ 1 ], seed_pnt[ 2 ] );
- seed->SetRadius( min_spac * double( 5 ) );
- seed->Update( );
-
fpa::VTK::ImageMPR view;
view.SetBackground( 0.3, 0.2, 0.8 );
view.SetSize( 800, 800 );
view.SetImage( vtk_image->GetOutput( ) );
- view.AddPolyData( seed->GetOutput( ), 1, 0, 0 );
- view.Start( );
- // Configure observer
- TObserver::Pointer obs = TObserver::New( );
- obs->SetImage( input_image, view.GetWindow( ) );
-
- // Configure algorithm
- TFrontAlgorithm::Pointer algorithm = TFrontAlgorithm::New( );
- algorithm->AddThresholds( thr_0, thr_1, n_samples );
+ // Wait for a seed to be given
+ while( view.GetNumberOfSeeds( ) == 0 )
+ view.Start( );
+ // Convert seed
+ 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 );
- algorithm->AddSeed( seed_idx, 0 );
- algorithm->AddObserver( itk::AnyEvent( ), obs );
- algorithm->ThrowEventsOn( );
+ // Configure algorithm
+ TFrontAlgorithm::Pointer algorithm = TFrontAlgorithm::New( );
+ algorithm->AddThresholds( thr_0, thr_1, step );
+ algorithm->AddSeed( seed_idx, 0 );
algorithm->SetInput( input_image );
algorithm->SetNeighborhoodOrder( 1 );
- algorithm->SetDerivativeThreshold( double( 3 ) );
- algorithm->Update( );
+ algorithm->SetDifferenceThreshold( double( 3 ) );
+ algorithm->SetInsideValue( 0 );
+ algorithm->SetOutsideValue( 1 );
+ if( visual_debug )
+ {
+ // Configure observer
+ TObserver::Pointer obs = TObserver::New( );
+ obs->SetImage( input_image, view.GetWindow( ) );
+ algorithm->AddObserver( itk::AnyEvent( ), obs );
+ algorithm->ThrowEventsOn( );
+ }
+ else
+ algorithm->ThrowEventsOff( );
+
+ std::clock_t start = std::clock( );
+ algorithm->Update( );
+ std::clock_t end = std::clock( );
+ double seconds = double( end - start ) / double( CLOCKS_PER_SEC );
+ std::cout << "Execution time = " << seconds << std::endl;
+
+ // Show result
+ TVTKImage::Pointer output_image_vtk = TVTKImage::New( );
+ output_image_vtk->SetInput( algorithm->GetOutput( ) );
+ output_image_vtk->Update( );
+
+ vtkSmartPointer< vtkImageMarchingCubes > mc =
+ vtkSmartPointer< vtkImageMarchingCubes >::New( );
+ mc->SetInputData( output_image_vtk->GetOutput( ) );
+ mc->SetValue(
+ 0,
+ double( algorithm->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( algorithm->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 );
}