Complete skeletonization application added

diff --git a/appli/examples/CMakeLists.txt b/appli/examples/CMakeLists.txt
index dff8fe08b5ebc9e7adc02a6b31f869a8396f5d63..520a4a3eede926705f4592a4c7c767e66f49f56a 100644 (file)
--- a/appli/examples/CMakeLists.txt
+++ b/appli/examples/CMakeLists.txt
@@ -19,6 +19,7 @@ IF(BUILD_EXAMPLES)
       example_ImageAlgorithmDijkstra_01
       example_ImageAlgorithmDijkstra_02
       example_ImageAlgorithmFastMarching_01
+      example_ImageAlgorithm_Skeletonization
       )
 
     FOREACH(APP ${vtk_APPLIS})

diff --git a/appli/examples/example_ImageAlgorithmRegionGrow_MultipleThresholds.cxx b/appli/examples/example_ImageAlgorithmRegionGrow_MultipleThresholds.cxx
index e9b06cc7238e475e0ac725120740153abc752cde..0216bed6753465cafa38910bfb5421e1286cacf4 100644 (file)
--- a/appli/examples/example_ImageAlgorithmRegionGrow_MultipleThresholds.cxx
+++ b/appli/examples/example_ImageAlgorithmRegionGrow_MultipleThresholds.cxx
@@ -110,6 +110,8 @@ int main( int argc, char* argv[] )
   algorithm->SetInput( input_image );
   algorithm->SetNeighborhoodOrder( 1 );
   algorithm->SetDifferenceThreshold( double( 3 ) );
+  algorithm->SetInsideValue( 0 );
+  algorithm->SetOutsideValue( 1 );
 
   if( visual_debug )
   {

diff --git a/appli/examples/example_ImageAlgorithm_Skeletonization.cxx b/appli/examples/example_ImageAlgorithm_Skeletonization.cxx
new file mode 100644 (file)
index 0000000..156469e
--- /dev/null
+++ b/appli/examples/example_ImageAlgorithm_Skeletonization.cxx
@@ -0,0 +1,222 @@
+#include <ctime>
+#include <iostream>
+#include <string>
+
+#include <itkDanielssonDistanceMapImageFilter.h>
+#include <itkImage.h>
+#include <itkImageFileReader.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
+  fpa::Image::RegionGrowWithMultipleThresholds< TImage >
+  TSegmentor;
+  typedef
+  
+  TObserver;
+*/
+
+// -------------------------------------------------------------------------
+int main( int argc, char* argv[] )
+{
+  if( argc < 6 )
+  {
+    std::cerr
+      << "Usage: " << argv[ 0 ]
+      << " input_image thr_0 thr_1 step output_image"
+      << " visual_debug"
+      << std::endl;
+    return( 1 );
+
+  } // fi
+  std::string input_image_fn = argv[ 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 ];
+  bool visual_debug = false;
+  if( argc > 6 )
+    visual_debug = ( std::atoi( argv[ 6 ] ) == 1 );
+
+  // Read image
+  itk::ImageFileReader< TImage >::Pointer input_image_reader =
+    itk::ImageFileReader< TImage >::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
+  itk::ImageToVTKImageFilter< TImage >::Pointer vtk_image =
+    itk::ImageToVTKImageFilter< TImage >::New( );
+  vtk_image->SetInput( input_image );
+  vtk_image->Update( );
+
+  fpa::VTK::ImageMPR view;
+  view.SetBackground( 0.3, 0.2, 0.8 );
+  view.SetSize( 800, 800 );
+  view.SetImage( vtk_image->GetOutput( ) );
+
+  // Wait for a seed to be given
+  while( view.GetNumberOfSeeds( ) == 0 )
+    view.Start( );
+
+  // Get seed from user
+  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 );
+
+  // Segment input image
+  fpa::Image::RegionGrowWithMultipleThresholds< TImage >::Pointer segmentor =
+    fpa::Image::RegionGrowWithMultipleThresholds< TImage >::New( );
+  segmentor->AddThresholds( thr_0, thr_1, step );
+  segmentor->AddSeed( seed_idx, 0 );
+  segmentor->SetInput( input_image );
+  segmentor->SetNeighborhoodOrder( 1 );
+  segmentor->SetDifferenceThreshold( double( 3 ) );
+  segmentor->SetInsideValue( TPixel( 0 ) );  // WARNING: This is to optimize
+  segmentor->SetOutsideValue( TPixel( 1 ) ); // distance map calculation
+  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( ) );
+    segmentor->AddObserver( itk::AnyEvent( ), obs );
+    segmentor->ThrowEventsOn( );
+  }
+  else
+    segmentor->ThrowEventsOff( );
+  std::clock_t start = std::clock( );
+  segmentor->Update( );
+  std::clock_t end = std::clock( );
+  double seconds = double( end - start ) / double( CLOCKS_PER_SEC );
+  std::cout << "Segmentation time = " << seconds << std::endl;
+
+  // Extract distance map
+  itk::DanielssonDistanceMapImageFilter< TImage, TDistanceMap >::Pointer
+    distanceMap =
+    itk::DanielssonDistanceMapImageFilter< TImage, TDistanceMap >::New( );
+  distanceMap->SetInput( segmentor->GetOutput( ) );
+  distanceMap->InputIsBinaryOn( );
+  start = std::clock( );
+  distanceMap->Update( );
+  end = 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 );
+
+  // Associate an inversion cost function
+  fpa::Base::Functors::InvertCostFunction< TScalar >::Pointer
+    cost_function =
+    fpa::Base::Functors::InvertCostFunction< TScalar >::New( );
+  paths->SetCostConversion( cost_function );
+
+  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;
+
+  // 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 - $RCSfile$

diff --git a/lib/fpa/Base/Functors/InvertCostFunction.h b/lib/fpa/Base/Functors/InvertCostFunction.h
index faf4fb2dbea2027c58874f75d77f9ff2df8fbb73..278ae557ed7dd9374d09bfae1dc5f9e7ecb7d15d 100644 (file)
--- a/lib/fpa/Base/Functors/InvertCostFunction.h
+++ b/lib/fpa/Base/Functors/InvertCostFunction.h
@@ -29,7 +29,7 @@ namespace fpa
       public:
         virtual C Evaluate( const C& input ) const
           {
-            return( C( 1 ) / ( C( 1 ) + C( input ) ) );
+            return( C( 1 ) / ( C( 0 ) + C( input ) ) );
           }
 
       protected: