#include <vector>
#include <set>
#include <itkImageRegionConstIteratorWithIndex.h>
+#include <itkImageRegionIteratorWithIndex.h>
// -------------------------------------------------------------------------
template< class I, class O >
this->GraftNthOutput( this->m_LabelImageIndex, lbl );
}
+
+
+
+// -------------------------------------------------------------------------
+template< class I, class O >
+typename fpa::Image::DijkstraWithEndPointDetection< I, O >::
+TUniqueVertices* fpa::Image::DijkstraWithEndPointDetection< I, O >::
+GetEndPoints( )
+{
+ return(
+ dynamic_cast< TUniqueVertices* >(
+ this->itk::ProcessObject::GetOutput( this->m_EndPointsIndex )
+ )
+ );
+}
+
+// -------------------------------------------------------------------------
+template< class I, class O >
+const typename fpa::Image::DijkstraWithEndPointDetection< I, O >::
+TUniqueVertices* fpa::Image::DijkstraWithEndPointDetection< I, O >::
+GetEndPoints( ) const
+{
+ return(
+ dynamic_cast< const TUniqueVertices* >(
+ this->itk::ProcessObject::GetOutput( this->m_EndPointsIndex )
+ )
+ );
+}
+
+// -------------------------------------------------------------------------
+template< class I, class O >
+void fpa::Image::DijkstraWithEndPointDetection< I, O >::
+GraftEndPoints( itk::DataObject* obj )
+{
+ TUniqueVertices* lbl =
+ dynamic_cast< TUniqueVertices* >(
+ this->itk::ProcessObject::GetOutput( this->m_EndPointsIndex )
+ );
+ if( lbl != NULL )
+ this->GraftNthOutput( this->m_EndPointsIndex, lbl );
+}
+
+// -------------------------------------------------------------------------
+template< class I, class O >
+typename fpa::Image::DijkstraWithEndPointDetection< I, O >::
+TUniqueVertices* fpa::Image::DijkstraWithEndPointDetection< I, O >::
+GetBifurcations( )
+{
+ return(
+ dynamic_cast< TUniqueVertices* >(
+ this->itk::ProcessObject::GetOutput( this->m_BifurcationsIndex )
+ )
+ );
+}
+
+// -------------------------------------------------------------------------
+template< class I, class O >
+const typename fpa::Image::DijkstraWithEndPointDetection< I, O >::
+TUniqueVertices* fpa::Image::DijkstraWithEndPointDetection< I, O >::
+GetBifurcations( ) const
+{
+ return(
+ dynamic_cast< const TUniqueVertices* >(
+ this->itk::ProcessObject::GetOutput( this->m_BifurcationsIndex )
+ )
+ );
+}
+
+// -------------------------------------------------------------------------
+template< class I, class O >
+void fpa::Image::DijkstraWithEndPointDetection< I, O >::
+GraftBifurcations( itk::DataObject* obj )
+{
+ TUniqueVertices* lbl =
+ dynamic_cast< TUniqueVertices* >(
+ this->itk::ProcessObject::GetOutput( this->m_BifurcationsIndex )
+ );
+ if( lbl != NULL )
+ this->GraftNthOutput( this->m_BifurcationsIndex, lbl );
+}
+
+
+// -------------------------------------------------------------------------
+template< class I, class O >
+typename fpa::Image::DijkstraWithEndPointDetection< I, O >::
+TBranches* fpa::Image::DijkstraWithEndPointDetection< I, O >::
+GetBranches( )
+{
+ return(
+ dynamic_cast< TBranches* >(
+ this->itk::ProcessObject::GetOutput( this->m_BranchesIndex )
+ )
+ );
+}
+
+// -------------------------------------------------------------------------
+template< class I, class O >
+const typename fpa::Image::DijkstraWithEndPointDetection< I, O >::
+TBranches* fpa::Image::DijkstraWithEndPointDetection< I, O >::
+GetBranches( ) const
+{
+ return(
+ dynamic_cast< const TBranches* >(
+ this->itk::ProcessObject::GetOutput( this->m_BranchesIndex )
+ )
+ );
+}
+
+// -------------------------------------------------------------------------
+template< class I, class O >
+void fpa::Image::DijkstraWithEndPointDetection< I, O >::
+GraftBranches( itk::DataObject* obj )
+{
+ TBranches* lbl =
+ dynamic_cast< TBranches* >(
+ this->itk::ProcessObject::GetOutput( this->m_BranchesIndex )
+ );
+ if( lbl != NULL )
+ this->GraftNthOutput( this->m_BranchesIndex, lbl );
+}
+
// -------------------------------------------------------------------------
template< class I, class O >
fpa::Image::DijkstraWithEndPointDetection< I, O >::
: Superclass( )
{
this->m_LabelImageIndex = this->GetNumberOfRequiredOutputs( );
- this->SetNumberOfRequiredOutputs( this->m_LabelImageIndex + 1 );
+ this->m_EndPointsIndex = this->m_LabelImageIndex + 1;
+ this->m_BifurcationsIndex = this->m_LabelImageIndex + 2;
+ this->m_BranchesIndex = this->m_LabelImageIndex + 3;
+ this->SetNumberOfRequiredOutputs( this->m_LabelImageIndex + 4 );
this->itk::ProcessObject::SetNthOutput(
this->m_LabelImageIndex, TLabelImage::New( )
);
+ this->itk::ProcessObject::SetNthOutput(
+ this->m_EndPointsIndex, TUniqueVertices::New( )
+ );
+ this->itk::ProcessObject::SetNthOutput(
+ this->m_BifurcationsIndex, TUniqueVertices::New( )
+ );
+ this->itk::ProcessObject::SetNthOutput(
+ this->m_BranchesIndex, TBranches::New( )
+ );
}
// -------------------------------------------------------------------------
void fpa::Image::DijkstraWithEndPointDetection< I, O >::
_BeforeGenerateData( )
{
+ const I* input = this->GetInput( );
+ typename I::SpacingType spac = input->GetSpacing( );
+ double max_spac = double( spac[ 0 ] );
+ for( unsigned int d = 1; d < I::ImageDimension; ++d )
+ max_spac =
+ ( double( spac[ d ] ) > max_spac )? double( spac[ d ] ): max_spac;
+ max_spac *= double( 3 );
+
// Correct seeds
- /* TODO
- for( unsigned int s = 0; s < this->m_Seeds.size( ); ++s )
- {
- _TNode seed = this->m_Seeds[ s ];
- _TRegion region = this->_Region( seed.Vertex, max_spac );
- itk::ImageRegionConstIteratorWithIndex< I > iIt( img, region );
-
- iIt.GoToBegin( );
- _TPixel max_value = iIt.Get( );
- for( ++iIt; !iIt.IsAtEnd( ); ++iIt )
- {
- if( iIt.Get( ) > max_value )
- {
- seed.Vertex = iIt.GetIndex( );
- seed.Parent = seed.Vertex;
- max_value = iIt.Get( );
+ for( unsigned int s = 0; s < this->m_SeedVertices.size( ); ++s )
+ {
+ TVertex seed = this->m_SeedVertices[ s ];
+ _TNode n = this->m_Seeds[ seed ];
+ _TRegion region = this->_Region( seed, max_spac );
+ itk::ImageRegionConstIteratorWithIndex< I > iIt( input, region );
+
+ iIt.GoToBegin( );
+ _TPixel max_value = iIt.Get( );
+ for( ++iIt; !iIt.IsAtEnd( ); ++iIt )
+ {
+ if( iIt.Get( ) > max_value )
+ {
+ this->m_SeedVertices[ s ] = iIt.GetIndex( );
+ max_value = iIt.Get( );
- } // fi
+ } // fi
- } // rof
- this->m_Seeds[ s ] = seed;
+ } // rof
+ this->m_Seeds.erase( seed );
+ n.Parent = this->m_SeedVertices[ s ];
+ this->m_Seeds[ this->m_SeedVertices[ s ] ] = n;
- } // rof
- */
+ } // rof
// End initialization
this->Superclass::_BeforeGenerateData( );
// Finish base algorithm
this->Superclass::_AfterGenerateData( );
- // Prepare backtracking objects
- this->m_EndPoints.clear( );
- this->m_BifurcationPoints.clear( );
+ // Check if backtracking has any sense
if( this->m_Candidates.size( ) == 0 )
return;
this->InvokeEvent( TEndEvent( ) );
this->InvokeEvent( TStartBacktrackingEvent( ) );
- // Get some input values
- const I* input = this->GetInput( );
- typename I::SpacingType spac = input->GetSpacing( );
- double ms = double( spac[ 0 ] );
- for( unsigned int d = 1; d < I::ImageDimension; ++d )
- ms =( ms < double( spac[ d ] ) )? double( spac[ d ] ): ms;
+ // Detect endpoints and bifurcations
+ this->_EndPointsAndBifurcations( );
- // Prepare labels
- TLabelImage* label = this->GetLabelImage( );
- label->FillBuffer( 0 );
+ // Find branches
+ this->_FindBranches( );
+
+ // Label pixels and branches
+ this->_LabelAll( );
+}
+
+// -------------------------------------------------------------------------
+template< class I, class O >
+void fpa::Image::DijkstraWithEndPointDetection< I, O >::
+_SetResult( const TVertex& v, const _TNode& n )
+{
+ this->Superclass::_SetResult( v, n );
+ this->m_Candidates.insert( _TCandidate( n.Result, v ) );
+}
+
+// -------------------------------------------------------------------------
+template< class I, class O >
+void fpa::Image::DijkstraWithEndPointDetection< I, O >::
+_EndPointsAndBifurcations( )
+{
+ // Prepare backtracking objects
+ TUniqueVertices* endpoints = this->GetEndPoints( );
+ TUniqueVertices* bifurcations = this->GetBifurcations( );
+ endpoints->Clear( );
+ bifurcations->Clear( );
- // Object to hold marks
- std::set< TVertex, TVertexCompare > tree_marks;
+ // Get some input values
+ TVertex seed = this->GetSeed( 0 );
+ const I* input = this->GetInput( );
+ const TMinimumSpanningTree* mst = this->GetMinimumSpanningTree( );
- // Object to hold all branches
- this->m_Branches.clear( );
+ // Prepare a pixel marks structure
+ typedef std::map< TVertex, bool, TVertexCompare > _TPixelMarks;
+ _TPixelMarks pixel_marks;
- // First label
- this->m_NumberOfBranches = 1;
+ // Object to hold tree-nodes marks
+ typedef std::set< TVertex, TVertexCompare > _TTreeMarks;
+ _TTreeMarks tree_marks;
// Iterate over the candidates, starting from the candidates that
- // are near thin branches
+ // are near thin branches (high accumulated cost)
typename _TCandidates::const_reverse_iterator cIt =
this->m_Candidates.rbegin( );
for( ; cIt != this->m_Candidates.rend( ); ++cIt )
{
- // If pixel has been already labelled, pass
+ // If pixel has already been visited, pass
TVertex v = cIt->second;
- if( label->GetPixel( v ) != 0 )
+ if( pixel_marks[ v ] )
continue;
- // Compute nearest start candidate
- TVertex endpoint =
- this->_MaxInRegion(
- input, v,
- double( std::sqrt( input->GetPixel( v ) ) ) * double( 1.5 )
- );
+ // Correct it to nearest start candidate (high distance value)
+ double vr = std::sqrt( double( input->GetPixel( v ) ) );
+ v = this->_MaxInRegion( input, v, vr * double( 1.5 ) );
- // Re-check labelling
- if( this->_Node( endpoint ).Label == Self::FarLabel )
+ // Now, check for real marking conditions
+ // 1. Has it been visited by dijkstra?
+ if( this->_Node( v ).Label == Self::FarLabel )
continue;
- if( label->GetPixel( endpoint ) != 0 )
+ // 2. Is it already marked?
+ if( pixel_marks[ v ] )
continue;
- if( this->m_EndPoints.find( endpoint ) != this->m_EndPoints.end( ) )
+ // 3. Is it already an endpoint?
+ if( endpoints->Find( v ) )
continue;
- this->m_EndPoints.insert( endpoint );
- std::cout << "endpoint " << endpoint << " inserted " << this->m_EndPoints.size( ) << std::endl;
-
- // Get the path all the way to seed
- std::vector< TVertex > path;
- this->GetMinimumSpanningTree( )->
- GetPath( path, endpoint, this->GetSeed( 0 ) );
-
- // Mark branches
- bool start = true;
- bool change = false;
- TVertex last_start = endpoint;
- typename std::vector< TVertex >::const_iterator pIt = path.begin( );
- for( ; pIt != path.end( ); ++pIt )
+ // 4. Ok, it is completely new!
+ endpoints->Insert( v );
+
+ // Get the path all the way to global seed
+ TVertices path;
+ mst->GetPath( path, v, seed );
+
+ // Backtracking to find endpoints and bifurcations
+ bool adding_new_points = true;
+ typename TVertices::const_iterator pIt = path.begin( );
+ for( ; pIt != path.end( ) && adding_new_points; ++pIt )
{
- this->InvokeEvent(
- TBacktrackingEvent( *pIt, this->m_NumberOfBranches )
- );
- if( start )
+ this->InvokeEvent( TBacktrackingEvent( *pIt, 1 ) );
+ if( tree_marks.find( *pIt ) == tree_marks.end( ) )
{
- if( tree_marks.find( *pIt ) == tree_marks.end( ) )
+ // Mark current point as a tree point
+ tree_marks.insert( *pIt );
+
+ // Mark a region around current point as visited
+ vr = std::sqrt( double( input->GetPixel( *pIt ) ) );
+ _TRegion region = this->_Region( *pIt, vr );
+ if( region.GetNumberOfPixels( ) > 0 )
{
- // Mark a region around current point as visited
- tree_marks.insert( *pIt );
- this->_Label( *pIt, TLabel( this->m_NumberOfBranches ) );
+ itk::ImageRegionConstIteratorWithIndex< I > iIt( input, region );
+ for( iIt.GoToBegin( ); !iIt.IsAtEnd( ); ++iIt )
+ pixel_marks[ iIt.GetIndex( ) ] = true;
}
else
- {
- // A bifurcation point has been reached!
- if( *pIt != this->GetSeed( 0 ) )
- {
- this->m_Branches[ *pIt ][ last_start ] = this->m_NumberOfBranches;
- last_start = *pIt;
- this->m_BifurcationPoints.insert( *pIt );
- std::cout << "bifurcation = " << *pIt << " " << this->GetSeed( 0 ) << std::endl;
- this->m_NumberOfBranches++;
- start = false;
-
- } // fi
-
- } // fi
+ pixel_marks[ *pIt ] = true;
}
else
{
- if(
- std::find(
- this->m_BifurcationPoints.begin( ),
- this->m_BifurcationPoints.end( ),
- *pIt
- ) == this->m_BifurcationPoints.end( )
- )
+ // A bifurcation point has been reached!
+ if( *pIt != seed )
{
- // Mark a sphere around current point as visited
- this->_Label( *pIt, TLabel( this->m_NumberOfBranches ) );
- change = true;
- }
- else
- {
- // A bifurcation point has been reached!
- if( *pIt != this->GetSeed( 0 ) )
- {
- this->m_Branches[ *pIt ][ last_start ] = this->m_NumberOfBranches;
- last_start = *pIt;
- this->m_NumberOfBranches++;
-
- } // fi
+ bifurcations->Insert( *pIt );
+ adding_new_points = false;
} // fi
} // fi
} // rof
- if( start || change )
- this->m_NumberOfBranches++;
this->InvokeEvent( TEndBacktrackingEvent( ) );
} // rof
+}
- typename TBranches::const_iterator bIt = this->m_Branches.begin( );
- unsigned int leo = 0;
- for( ; bIt != this->m_Branches.end( ); ++bIt )
+// -------------------------------------------------------------------------
+template< class I, class O >
+void fpa::Image::DijkstraWithEndPointDetection< I, O >::
+_FindBranches( )
+{
+ // Configure and obtain inputs
+ TVertex seed = this->GetSeed( 0 );
+ const TMinimumSpanningTree* mst = this->GetMinimumSpanningTree( );
+ const TUniqueVertices* endpoints = this->GetEndPoints( );
+ const TUniqueVertices* bifurcations = this->GetBifurcations( );
+ TBranches* branches = this->GetBranches( );
+ branches->Clear( );
+
+ // Reconstruct pixels
+ typename TUniqueVertices::ConstIterator eIt = endpoints->Begin( );
+ for( ; eIt != endpoints->End( ); ++eIt )
{
- typename TBranch::const_iterator brIt = bIt->second.begin( );
- for( ; brIt != bIt->second.end( ); ++brIt )
+ // Get the path all the way to global seed
+ TVertices path;
+ mst->GetPath( path, *eIt, seed );
+
+ TVertex start_vertex = *eIt;
+ typename TVertices::const_iterator pIt = path.begin( );
+ for( ; pIt != path.end( ); ++pIt )
{
- std::cout << bIt->first << " " << brIt->first << std::endl;
- leo++;
- }
- }
-
- // Re-enumerate labels
- std::map< TLabel, unsigned long > histo;
- for(
- typename std::set< TVertex, TVertexCompare >::iterator treeIt = tree_marks.begin( );
- treeIt != tree_marks.end( );
- ++treeIt
- )
- histo[ label->GetPixel( *treeIt ) ]++;
-
- std::map< TLabel, TLabel > changes;
- TLabel last_change = 1;
- for( TLabel i = 1; i <= this->m_NumberOfBranches; ++i )
- {
- if( histo[ i ] != 0 )
- changes[ i ] = last_change++;
+ if( bifurcations->Find( *pIt ) )
+ {
+ branches->SetValue( start_vertex, *pIt, 1 );
+ start_vertex = *pIt;
- } // rof
- this->m_NumberOfBranches = changes.size( );
+ } // fi
- std::cout << leo << " - " << this->m_EndPoints.size( ) << " - " << this->m_BifurcationPoints.size( ) << " - " << this->m_NumberOfBranches << std::endl;
+ } // rof
- /*
- for(
- typename TTree::iterator treeIt = this->m_FullTree.begin( );
- treeIt != this->m_FullTree.end( );
- ++treeIt
- )
- {
- TMark old = treeIt->second.second;
- treeIt->second.second = changes[ old ];
+ // Finish with branches to global seed
+ branches->SetValue( start_vertex, seed, 1 );
- } // fi
+ } // rof
+}
- // Construct reduced tree
- for(
- typename TVertices::const_iterator eIt = this->m_EndPoints.begin( );
- eIt != this->m_EndPoints.end( );
- ++eIt
- )
- {
- typename TTree::const_iterator tIt = this->m_FullTree.find( *eIt );
- if( tIt != this->m_FullTree.end( ) )
- {
- TMark id = tIt->second.second;
- do
+// -------------------------------------------------------------------------
+template< class I, class O >
+void fpa::Image::DijkstraWithEndPointDetection< I, O >::
+_LabelAll( )
+{
+ // Configure and obtain inputs
+ const I* input = this->GetInput( );
+ const TMinimumSpanningTree* mst = this->GetMinimumSpanningTree( );
+ TBranches* branches = this->GetBranches( );
+ TLabelImage* label = this->GetLabelImage( );
+ label->FillBuffer( 0 );
+
+ // Label branches
+ typename TBranches::Iterator bIt = branches->Begin( );
+ TLabel actual_label = 0;
+ for( ; bIt != branches->End( ); ++bIt )
+ {
+ typename TBranches::RowIterator brIt = branches->Begin( bIt );
+ for( ; brIt != branches->End( bIt ); ++brIt )
{
- tIt = this->m_FullTree.find( tIt->second.first );
- if( tIt == this->m_FullTree.end( ) )
- break;
+ actual_label++;
+ brIt->second = actual_label;
- } while( tIt->second.second == id );
- this->m_ReducedTree[ *eIt ] = TTreeNode( tIt->first, id );
+ TVertices path;
+ mst->GetPath( path, bIt->first, brIt->first );
+ typename TVertices::const_iterator pIt = path.begin( );
+ for( ; pIt != path.end( ); ++pIt )
+ {
+ double d = std::sqrt( double( input->GetPixel( *pIt ) ) );
+ _TRegion region = this->_Region( *pIt, d );
+ itk::ImageRegionConstIteratorWithIndex< I > iIt( input, region );
+ itk::ImageRegionIteratorWithIndex< TLabelImage > lIt( label, region );
+ iIt.GoToBegin( );
+ lIt.GoToBegin( );
+ for( ; !iIt.IsAtEnd( ); ++iIt, ++lIt )
+ {
+ // Mask real input image
+ if(
+ !( iIt.Get( ) < ( typename I::PixelType )( 0 ) ) &&
+ lIt.Get( ) == TLabel( 0 )
+ )
+ lIt.Set( actual_label );
+
+ } // rof
- } // fi
+ } // rof
} // rof
- for(
- typename TVertices::const_iterator bIt = this->m_BifurcationPoints.begin( );
- bIt != this->m_BifurcationPoints.end( );
- ++bIt
- )
- {
- typename TTree::const_iterator tIt = this->m_FullTree.find( *bIt );
- if( tIt != this->m_FullTree.end( ) )
- {
- TMark id = tIt->second.second;
- do
- {
- tIt = this->m_FullTree.find( tIt->second.first );
- if( tIt == this->m_FullTree.end( ) )
- break;
+ } // rof
+ this->m_NumberOfBranches = actual_label;
- } while( tIt->second.second == id );
- this->m_ReducedTree[ *bIt ] = TTreeNode( tIt->first, id );
+ // Label bifurcations
+ /* TODO: Is this necessary?
+ typename TUniqueVertices::const_iterator bifIt =
+ this->m_Bifurcations.begin( );
+ for( ; bifIt != this->m_Bifurcations.end( ); ++bifIt )
+ {
+ actual_label++;
+ double d = std::sqrt( double( input->GetPixel( *bifIt ) ) );
+ _TRegion region = this->_Region( *bifIt, d );
+ itk::ImageRegionConstIteratorWithIndex< I > iIt( input, region );
+ itk::ImageRegionIteratorWithIndex< TLabelImage > lIt( label, region );
+ iIt.GoToBegin( );
+ lIt.GoToBegin( );
+ for( ; !iIt.IsAtEnd( ); ++iIt, ++lIt )
+ {
+ // Mask real input image
+ if( !( iIt.Get( ) < ( typename I::PixelType )( 0 ) ) )
+ lIt.Set( actual_label );
- } // fi
+ } // rof
- } // rof
+ } // rof
*/
}
-// -------------------------------------------------------------------------
-template< class I, class O >
-void fpa::Image::DijkstraWithEndPointDetection< I, O >::
-_SetResult( const TVertex& v, const _TNode& n )
-{
- this->Superclass::_SetResult( v, n );
- this->m_Candidates.insert( _TCandidate( n.Result, v ) );
-}
-
// -------------------------------------------------------------------------
template< class I, class O >
typename fpa::Image::DijkstraWithEndPointDetection< I, O >::
_TSize size;
for( unsigned int d = 0; d < I::ImageDimension; ++d )
{
+ // NOTE: 3 is a minimum neighborhood size
long s = long( std::ceil( r / double( spac[ d ] ) ) ) + 3;
i0[ d ] = c[ d ] - s;
i1[ d ] = c[ d ] + s;
return( max_vertex );
}
-// -------------------------------------------------------------------------
-template< class I, class O >
-void fpa::Image::DijkstraWithEndPointDetection< I, O >::
-_Label( const TVertex& v, const TLabel& l )
-{
- typedef itk::ImageRegionIteratorWithIndex< TLabelImage > _TIt;
-
- double d = std::sqrt( double( this->GetInput( )->GetPixel( v ) ) );
- _TRegion region = this->_Region( v, d );
- if( region.GetNumberOfPixels( ) > 0 )
- {
- _TIt lIt( this->GetLabelImage( ), region );
- for( lIt.GoToBegin( ); !lIt.IsAtEnd( ); ++lIt )
- lIt.Set( l );
- }
- else
- this->GetLabelImage( )->SetPixel( v, l );
-}
-
#endif // __FPA__IMAGE__DIJKSTRAWITHENDPOINTDETECTION__HXX__
// eof - $RCSfile$
git://git.creatis.insa-lyon.fr / FrontAlgorithms.git / blobdiff