#include <fpa/VTK/ImageMPR.h>
#include <fpa/VTK/Image3DObserver.h>
-/*
- #include <itkMinimumMaximumImageCalculator.h>
- #include <itkInvertIntensityImageFilter.h>
- #include <itkDanielssonDistanceMapImageFilter.h>
- #include <itkImageFileWriter.h>
-
- #include <vtkCamera.h>
- #include <vtkImageActor.h>
- #include <vtkInteractorStyleImage.h>
- #include <vtkPointHandleRepresentation3D.h>
- #include <vtkProperty.h>
- #include <vtkRenderer.h>
- #include <vtkRenderWindow.h>
- #include <vtkRenderWindowInteractor.h>
- #include <vtkSeedRepresentation.h>
- #include <vtkSeedWidget.h>
- #include <vtkSmartPointer.h>
-
- #include <fpa/Image/Dijkstra.h>
-*/
+#include <fpa/IO/MinimumSpanningTreeWriter.h>
+#include <fpa/IO/UniqueValuesContainerWriter.h>
+#include <fpa/IO/MatrixValuesContainerWriter.h>
+
+#include <vtkCellArray.h>
+#include <vtkFloatArray.h>
+#include <vtkImageMarchingCubes.h>
+#include <vtkPoints.h>
+#include <vtkPolyData.h>
+#include <vtkSmartPointer.h>
// -------------------------------------------------------------------------
const unsigned int Dim = 3;
template< class I >
void ReadImage( typename I::Pointer& image, const std::string& filename );
+template< class I >
+void SaveImage( const I* image, const std::string& filename );
+
template< class I, class O >
void DistanceMap(
const typename I::Pointer& input, typename O::Pointer& output
// -------------------------------------------------------------------------
int main( int argc, char* argv[] )
{
- if( argc < 2 )
+ if( argc < 9 )
{
std::cerr
- << "Usage: " << argv[ 0 ]
- << " input_image"
+ << "Usage: " << argv[ 0 ] << std::endl
+ << " input_image" << std::endl
+ << " output_distancemap" << std::endl
+ << " output_costmap" << std::endl
+ << " output_labels" << std::endl
+ << " output_minimum_spanning_tree" << std::endl
+ << " output_endpoints" << std::endl
+ << " output_bifurcations" << std::endl
+ << " output_branches" << std::endl
<< std::endl;
return( 1 );
} // fi
std::string input_image_fn = argv[ 1 ];
+ std::string distancemap_fn = argv[ 2 ];
+ std::string output_costmap_fn = argv[ 3 ];
+ std::string output_labels_fn = argv[ 4 ];
+ std::string mst_output_fn = argv[ 5 ];
+ std::string endpoints_output_fn = argv[ 6 ];
+ std::string bifurcations_output_fn = argv[ 7 ];
+ std::string branches_output_fn = argv[ 8 ];
// Read image
TImage::Pointer input_image;
return( 1 );
} // yrt
+
TVTKInputImage::Pointer vtk_input_image = TVTKInputImage::New( );
vtk_input_image->SetInput( input_image );
vtk_input_image->Update( );
view.SetSize( 800, 800 );
view.SetImage( vtk_input_image->GetOutput( ) );
+ vtkSmartPointer< vtkImageMarchingCubes > mc =
+ vtkSmartPointer< vtkImageMarchingCubes >::New( );
+ mc->SetInputData( vtk_input_image->GetOutput( ) );
+ mc->SetValue( 0, 1e-1 );
+ mc->Update( );
+ view.AddPolyData( mc->GetOutput( ), 1, 1, 1, 0.4 );
+
// Allow some interaction and wait for, at least, one seed
view.Render( );
while( view.GetNumberOfSeeds( ) == 0 )
<< std::difftime( end, start )
<< " s." << std::endl;
- /* TODO
- // Save final total cost map
- itk::ImageFileWriter< TOutputImage >::Pointer output_image_writer =
- itk::ImageFileWriter< TOutputImage >::New( );
- output_image_writer->SetFileName( output_image_fn );
- output_image_writer->SetInput( filter->GetOutput( ) );
- try
+ // Outputs
+ const TFilter::TOutputImage* accumulated_costs = filter->GetOutput( );
+ const TFilter::TLabelImage* labeled_image = filter->GetLabelImage( );
+ const TFilter::TMinimumSpanningTree* mst = filter->GetMinimumSpanningTree( );
+ const TFilter::TUniqueVertices* endpoints = filter->GetEndPoints( );
+ const TFilter::TUniqueVertices* bifurcations = filter->GetBifurcations( );
+ const TFilter::TBranches* branches = filter->GetBranches( );
+ unsigned long nBranches = filter->GetNumberOfBranches( );
+
+ // Save outputs
+ SaveImage( dmap.GetPointer( ), distancemap_fn );
+ SaveImage( accumulated_costs, output_costmap_fn );
+ SaveImage( labeled_image, output_labels_fn );
+
+ fpa::IO::MinimumSpanningTreeWriter< TFilter::TMinimumSpanningTree >::Pointer
+ mst_writer =
+ fpa::IO::MinimumSpanningTreeWriter< TFilter::TMinimumSpanningTree >::New( );
+ mst_writer->SetInput( mst );
+ mst_writer->SetFileName( mst_output_fn );
+ mst_writer->Update( );
+
+ fpa::IO::UniqueValuesContainerWriter< TFilter::TUniqueVertices >::Pointer
+ endpoints_writer =
+ fpa::IO::UniqueValuesContainerWriter< TFilter::TUniqueVertices >::New( );
+ endpoints_writer->SetInput( endpoints );
+ endpoints_writer->SetFileName( endpoints_output_fn );
+ endpoints_writer->Update( );
+
+ fpa::IO::UniqueValuesContainerWriter< TFilter::TUniqueVertices >::Pointer
+ bifurcations_writer =
+ fpa::IO::UniqueValuesContainerWriter< TFilter::TUniqueVertices >::New( );
+ bifurcations_writer->SetInput( bifurcations );
+ bifurcations_writer->SetFileName( bifurcations_output_fn );
+ bifurcations_writer->Update( );
+
+ fpa::IO::MatrixValuesContainerWriter< TFilter::TBranches >::Pointer
+ branches_writer =
+ fpa::IO::MatrixValuesContainerWriter< TFilter::TBranches >::New( );
+ branches_writer->SetInput( branches );
+ branches_writer->SetFileName( branches_output_fn );
+ branches_writer->Update( );
+
+ // Show endpoints
+ vtkSmartPointer< vtkPoints > endpoints_points =
+ vtkSmartPointer< vtkPoints >::New( );
+ vtkSmartPointer< vtkCellArray > endpoints_cells =
+ vtkSmartPointer< vtkCellArray >::New( );
+ for(
+ TFilter::TUniqueVertices::ConstIterator epIt = endpoints->Begin( );
+ epIt != endpoints->End( );
+ ++epIt
+ )
{
- output_image_writer->Update( );
- }
- catch( itk::ExceptionObject& err )
+ TImage::PointType pnt;
+ input_image->TransformIndexToPhysicalPoint( *epIt, pnt );
+ endpoints_points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
+ endpoints_cells->InsertNextCell( 1 );
+ endpoints_cells->
+ InsertCellPoint( endpoints_points->GetNumberOfPoints( ) - 1 );
+
+ } // rof
+ vtkSmartPointer< vtkPolyData > endpoints_polydata =
+ vtkSmartPointer< vtkPolyData >::New( );
+ endpoints_polydata->SetPoints( endpoints_points );
+ endpoints_polydata->SetVerts( endpoints_cells );
+ view.AddPolyData( endpoints_polydata, 0, 0, 1, 1 );
+
+ // Show bifurcations
+ vtkSmartPointer< vtkPoints > bifurcations_points =
+ vtkSmartPointer< vtkPoints >::New( );
+ vtkSmartPointer< vtkCellArray > bifurcations_cells =
+ vtkSmartPointer< vtkCellArray >::New( );
+ for(
+ TFilter::TUniqueVertices::ConstIterator bfIt = bifurcations->Begin( );
+ bfIt != bifurcations->End( );
+ ++bfIt
+ )
{
- std::cerr
- << "Error while writing image to " << output_image_fn << ": "
- << err << std::endl;
- return( 1 );
+ TImage::PointType pnt;
+ input_image->TransformIndexToPhysicalPoint( *bfIt, pnt );
+ bifurcations_points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
+ bifurcations_cells->InsertNextCell( 1 );
+ bifurcations_cells->
+ InsertCellPoint( bifurcations_points->GetNumberOfPoints( ) - 1 );
+
+ } // rof
+ vtkSmartPointer< vtkPolyData > bifurcations_polydata =
+ vtkSmartPointer< vtkPolyData >::New( );
+ bifurcations_polydata->SetPoints( bifurcations_points );
+ bifurcations_polydata->SetVerts( bifurcations_cells );
+ view.AddPolyData( bifurcations_polydata, 0, 1, 0, 1 );
+
+ // Show branches (simple and detailed)
+ vtkSmartPointer< vtkPoints > simple_branches_points =
+ vtkSmartPointer< vtkPoints >::New( );
+ vtkSmartPointer< vtkCellArray > simple_branches_cells =
+ vtkSmartPointer< vtkCellArray >::New( );
+
+ vtkSmartPointer< vtkPoints > detailed_branches_points =
+ vtkSmartPointer< vtkPoints >::New( );
+ vtkSmartPointer< vtkCellArray > detailed_branches_cells =
+ vtkSmartPointer< vtkCellArray >::New( );
+ vtkSmartPointer< vtkFloatArray > detailed_branches_scalars =
+ vtkSmartPointer< vtkFloatArray >::New( );
+
+ TFilter::TBranches::ConstIterator brIt = branches->Begin( );
+ for( ; brIt != branches->End( ); ++brIt )
+ {
+ // Branch's first point
+ TImage::PointType first_point;
+ input_image->TransformIndexToPhysicalPoint( brIt->first, first_point );
+ unsigned long first_id = simple_branches_points->GetNumberOfPoints( );
+ simple_branches_points->InsertNextPoint(
+ first_point[ 0 ], first_point[ 1 ], first_point[ 2 ]
+ );
+
+ TFilter::TBranches::ConstRowIterator brRowIt = branches->Begin( brIt );
+ for( ; brRowIt != branches->End( brIt ); ++brRowIt )
+ {
+ // Branch's second point
+ TImage::PointType second_point;
+ input_image->
+ TransformIndexToPhysicalPoint( brRowIt->first, second_point );
+ unsigned long second_id = simple_branches_points->GetNumberOfPoints( );
+ simple_branches_points->InsertNextPoint(
+ second_point[ 0 ], second_point[ 1 ], second_point[ 2 ]
+ );
+ simple_branches_cells->InsertNextCell( 2 );
+ simple_branches_cells->InsertCellPoint( first_id );
+ simple_branches_cells->InsertCellPoint( second_id );
+
+ // Detailed path
+ double pathId = double( brRowIt->second - 1 ) / double( nBranches - 1 );
+ TFilter::TVertices path;
+ mst->GetPath( path, brIt->first, brRowIt->first );
+ TFilter::TVertices::const_iterator pIt = path.begin( );
+ for( ; pIt != path.end( ); ++pIt )
+ {
+ TImage::PointType path_point;
+ input_image->TransformIndexToPhysicalPoint( *pIt, path_point );
+ detailed_branches_points->InsertNextPoint(
+ path_point[ 0 ], path_point[ 1 ], path_point[ 2 ]
+ );
+ detailed_branches_scalars->InsertNextTuple1( pathId );
+ if( pIt != path.begin( ) )
+ {
+ unsigned long nPoints =
+ detailed_branches_points->GetNumberOfPoints( );
+ detailed_branches_cells->InsertNextCell( 2 );
+ detailed_branches_cells->InsertCellPoint( nPoints - 2 );
+ detailed_branches_cells->InsertCellPoint( nPoints - 1 );
+
+ } // fi
+
+ } // rof
+
+ } // rof
+
+ } // rof
+ vtkSmartPointer< vtkPolyData > simple_branches_polydata =
+ vtkSmartPointer< vtkPolyData >::New( );
+ simple_branches_polydata->SetPoints( simple_branches_points );
+ simple_branches_polydata->SetLines( simple_branches_cells );
+ view.AddPolyData( simple_branches_polydata, 1, 0, 1, 1 );
+
+ vtkSmartPointer< vtkPolyData > detailed_branches_polydata =
+ vtkSmartPointer< vtkPolyData >::New( );
+ detailed_branches_polydata->SetPoints( detailed_branches_points );
+ detailed_branches_polydata->SetLines( detailed_branches_cells );
+ detailed_branches_polydata->
+ GetPointData( )->SetScalars( detailed_branches_scalars );
+ view.AddPolyData( detailed_branches_polydata, 1 );
+
+ // Let some more interaction
+ view.Render( );
+ view.Start( );
- } // yrt
- */
return( 0 );
}
image->DisconnectPipeline( );
}
+// -------------------------------------------------------------------------
+template< class I >
+void SaveImage( const I* image, const std::string& filename )
+{
+ typename itk::ImageFileWriter< I >::Pointer writer =
+ itk::ImageFileWriter< I >::New( );
+ writer->SetInput( image );
+ writer->SetFileName( filename );
+ try
+ {
+ writer->Update( );
+ }
+ catch( itk::ExceptionObject& err )
+ {
+ std::cerr
+ << "Error saving \"" << filename << "\": " << err
+ << std::endl;
+
+ } // yrt
+}
+
// -------------------------------------------------------------------------
template< class I, class O >
void DistanceMap(
git://git.creatis.insa-lyon.fr / FrontAlgorithms.git / blobdiff