#include <cmath>
#include <ctime>
#include <deque>
+#include <fstream>
#include <iostream>
+#include <iomanip>
#include <limits>
#include <map>
#include <string>
#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>
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 < 6 )
+ if( argc < 8 )
{
std::cerr
<< "Usage: " << argv[ 0 ]
- << " input_image x y z output_image"
+ << " input_image x y z output_image output_imagej output_vtk"
<< " visual_debug"
<< std::endl;
return( 1 );
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 > 6 )
- visual_debug = ( std::atoi( argv[ 6 ] ) == 1 );
+ if( argc > 8 )
+ visual_debug = ( std::atoi( argv[ 8 ] ) == 1 );
// Read image
TImageReader::Pointer input_image_reader = TImageReader::New( );
view.SetSize( 800, 800 );
view.SetImage( vtk_image->GetOutput( ) );
- 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 );
+ /* 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( );
- view.Start( );
+ if( visual_debug )
+ view.Start( );
TImage::IndexType seed_idx;
input_image->TransformPhysicalPointToIndex( seed_pnt, seed_idx );
- std::cout << seed_idx << " " << seed_pnt << std::endl;
- seed_idx[ 0 ] = 256;
- seed_idx[ 1 ] = 313;
- seed_idx[ 2 ] = 381;
+ /* 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( );
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::TTree& tree = paths->GetFinalTree( );
+ 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( );
- for( unsigned int epId = 0; epIt != endpoints.end( ); ++epIt, ++epId )
+
+ TBranches branches;
+ TImage::PointType ori = input_image->GetOrigin( );
+
+ TDijkstra::TTree::const_iterator rIt = reduced_tree.begin( );
+ for( ; rIt != reduced_tree.end( ); ++rIt )
{
- double pd = double( epId ) / double( endpoints.size( ) - 1 );
+ TDijkstra::TTree::const_iterator tIt = tree.find( rIt->first );
- TDijkstra::TVertex idx = *epIt;
+ // 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( idx != *epIt )
+ if( !start )
{
cells->InsertNextCell( 2 );
cells->InsertCellPoint( points->GetNumberOfPoints( ) - 2 );
cells->InsertCellPoint( points->GetNumberOfPoints( ) - 1 );
+ branch.Length += prev.EuclideanDistanceTo( pnt );
} // fi
- idx = tree.find( idx )->second;
+ 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 );
- } while( idx != tree.find( idx )->second );
+ } // 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 );
view.AddPolyData( vtk_tree );
view.Render( );
- view.Start( );
+ if( visual_debug )
+ view.Start( );
- /* TODO
- TImageWriter::Pointer dijkstra_writer =
- TImageWriter::New( );
- dijkstra_writer->SetInput( paths->GetOutput( ) );
- dijkstra_writer->SetFileName( "dijkstra.mhd" );
- dijkstra_writer->Update( );
- */
+ 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 );
}
git://git.creatis.insa-lyon.fr / FrontAlgorithms.git / blobdiff