1 // =========================================================================
2 // @author Leonardo Florez Valencia
3 // @email florez-l@javeriana.edu.co
4 // =========================================================================
6 #ifndef __fpa__Image__SkeletonFilter__hxx__
7 #define __fpa__Image__SkeletonFilter__hxx__
10 #include <itkImageRegionIteratorWithIndex.h>
11 #include <itkMinimumMaximumImageCalculator.h>
12 #include <fpa/Image/Functors/Dijkstra/Invert.h>
14 // -------------------------------------------------------------------------
15 template< class _TInputImage, class _TDistanceMap >
16 fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::_TDijkstra::
20 // Prepare weight function
21 typedef fpa::Image::Functors::Dijkstra::Invert< TOutputImage, TScalar > _TWeight;
22 typename _TWeight::Pointer weight = _TWeight::New( );
23 weight->SetAlpha( 1 );
25 this->SetWeightFunction( weight );
28 // -------------------------------------------------------------------------
29 template< class _TInputImage, class _TDistanceMap >
30 fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::_TDijkstra::
35 // -------------------------------------------------------------------------
36 template< class _TInputImage, class _TDistanceMap >
37 void fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::_TDijkstra::
38 _BeforeGenerateData( )
40 this->Superclass::_BeforeGenerateData( );
41 this->m_SkeletonQueue.clear( );
44 // -------------------------------------------------------------------------
45 template< class _TInputImage, class _TDistanceMap >
46 void fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::_TDijkstra::
47 _UpdateOutputValue( TNode& n )
49 typedef typename _TSkeletonQueue::value_type _TSkeletonQueueValue;
51 this->Superclass::_UpdateOutputValue( n );
52 double d = double( this->GetInput( )->GetPixel( n.Vertex ) );
53 if( d >= double( 0 ) )
55 // Update skeleton candidates
57 double v = double( n.Value ) / ( d * d );
58 this->m_SkeletonQueue.insert( _TSkeletonQueueValue( v, n.Vertex ) );
63 // -------------------------------------------------------------------------
64 template< class _TInputImage, class _TDistanceMap >
66 fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
69 itk::ModifiedTimeType t = this->Superclass::GetMTime( );
70 itk::ModifiedTimeType q = this->m_DistanceMap->GetMTime( );
71 return( ( q < t )? q: t );
74 // -------------------------------------------------------------------------
75 template< class _TInputImage, class _TDistanceMap >
76 void fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
77 SetInput( TInputImage* input )
79 this->Superclass::SetNthInput( 0, input );
82 // -------------------------------------------------------------------------
83 template< class _TInputImage, class _TDistanceMap >
84 typename fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
85 TInputImage* fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
88 return( dynamic_cast< TInputImage* >( this->Superclass::GetInput( 0 ) ) );
91 // -------------------------------------------------------------------------
92 template< class _TInputImage, class _TDistanceMap >
93 const typename fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
94 TInputImage* fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
98 dynamic_cast< const TInputImage* >( this->Superclass::GetInput( 0 ) )
102 // -------------------------------------------------------------------------
103 template< class _TInputImage, class _TDistanceMap >
104 typename fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
105 TSkeleton* fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
108 return( dynamic_cast< TSkeleton* >( this->Superclass::GetOutput( 0 ) ) );
111 // -------------------------------------------------------------------------
112 template< class _TInputImage, class _TDistanceMap >
113 const typename fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
114 TSkeleton* fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
118 dynamic_cast< const TSkeleton* >( this->Superclass::GetOutput( 0 ) )
122 // -------------------------------------------------------------------------
123 template< class _TInputImage, class _TDistanceMap >
124 fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
127 m_SeedFromMaximumDistance( false )
129 this->SetNumberOfRequiredInputs( 1 );
130 this->SetNumberOfRequiredOutputs( 1 );
131 this->SetNthOutput( 0, TSkeleton::New( ) );
133 this->m_DistanceMap = TDistanceMap::New( );
136 // -------------------------------------------------------------------------
137 template< class _TInputImage, class _TDistanceMap >
138 fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
143 // -------------------------------------------------------------------------
144 template< class _TInputImage, class _TDistanceMap >
145 void fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
148 // Update distance map
149 this->m_DistanceMap->SetInput( this->GetInput( ) );
150 this->m_DistanceMap->Update( );
153 if( this->m_SeedFromMaximumDistance )
155 typedef itk::MinimumMaximumImageCalculator< TOutputImage > _TMinMax;
156 typename _TMinMax::Pointer minmax = _TMinMax::New( );
157 minmax->SetImage( this->m_DistanceMap->GetOutput( ) );
159 this->m_Seed = minmax->GetIndexOfMaximum( );
164 typename _TDijkstra::Pointer dijkstra = _TDijkstra::New( );
165 dijkstra->SetInput( this->m_DistanceMap->GetOutput( ) );
166 dijkstra->AddSeed( this->m_Seed );
169 // Compute end-points
170 const _TMST* mst = dijkstra->GetMinimumSpanningTree( );
171 std::vector< TIndex > end_points;
173 end_points, this->m_DistanceMap->GetOutput( ),
174 mst, dijkstra->GetSkeletonQueue( )
177 // Compute symbolic branches
178 typedef std::map< TIndex, TIndex, typename TIndex::LexicographicCompare > _TTags;
179 _TTags tags, branches;
180 typename std::vector< TIndex >::const_iterator eIt = end_points.begin( );
181 for( ; eIt != end_points.end( ); ++eIt )
185 TIndex p = mst->GetParent( it );
186 typename _TTags::iterator bIt = tags.end( );
187 while( it != p && bIt == tags.end( ) )
189 typename _TTags::iterator tIt = tags.find( it );
190 if( tIt != tags.end( ) )
192 // Ok, a bifurcation point has been found
193 // branch1: tIt->second <-> it (ok)
194 branches[ tIt->second ] = it;
196 // branch2: *eit <-> it (ok)
197 branches[ *eIt ] = it;
199 // branch3: it <-> until next bifurcation
205 p = mst->GetParent( it );
208 if( bIt != tags.end( ) )
210 TIndex pTag = bIt->second;
211 TIndex nTag = bIt->first;
214 while( tags[ it ] == pTag )
218 it = mst->GetParent( it );
222 branches[ bIt->first ] = p;
227 branches[ *eIt ] = it;
233 // Fill full branches
234 typedef typename _TMST::TVertices _TVertices;
235 typedef typename TSkeleton::TPath _TPath;
237 TSkeleton* sk = this->GetOutput( );
238 typename _TTags::const_iterator bIt = branches.begin( );
239 for( ; bIt != branches.end( ); ++bIt )
241 _TVertices v = mst->GetPath( bIt->first, bIt->second );
242 typename _TPath::Pointer path = _TPath::New( );
243 path->SetReferenceImage( this->GetInput( ) );
244 typename _TVertices::const_reverse_iterator vIt = v.rbegin( );
245 for( ; vIt != v.rend( ); ++vIt )
246 path->AddVertex( *vIt );
247 sk->AddBranch( path );
252 // -------------------------------------------------------------------------
253 template< class _TInputImage, class _TDistanceMap >
254 template< class _TMarksPointer >
255 void fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
257 _TMarksPointer& marks, const TOutputImage* dmap, const TIndex& center
260 typedef typename _TMarksPointer::ObjectType _TMarks;
261 typedef itk::ImageRegionIteratorWithIndex< _TMarks > _TMarksIt;
263 static const double _eps = std::sqrt( double( Self::Dimension + 1 ) );
264 typename _TMarks::SpacingType spac = dmap->GetSpacing( );
265 typename _TMarks::RegionType region = dmap->GetRequestedRegion( );
267 typename _TMarks::PointType cnt;
268 dmap->TransformIndexToPhysicalPoint( center, cnt );
269 double r = double( dmap->GetPixel( center ) ) * _eps;
272 for( unsigned int d = 0; d < Self::Dimension; ++d )
274 long off = long( std::ceil( r / double( spac[ d ] ) ) );
277 i0[ d ] = center[ d ] - off;
278 i1[ d ] = center[ d ] + off;
280 if( i0[ d ] < region.GetIndex( )[ d ] )
281 i0[ d ] = region.GetIndex( )[ d ];
283 if( i1[ d ] >= region.GetIndex( )[ d ] + region.GetSize( )[ d ] )
284 i1[ d ] = region.GetIndex( )[ d ] + region.GetSize( )[ d ] - 1;
288 typename _TMarks::SizeType size;
289 for( unsigned int d = 0; d < Self::Dimension; ++d )
290 size[ d ] = i1[ d ] - i0[ d ] + 1;
292 typename _TMarks::RegionType neighRegion;
293 neighRegion.SetIndex( i0 );
294 neighRegion.SetSize( size );
296 _TMarksIt mIt( marks, neighRegion );
297 for( mIt.GoToBegin( ); !mIt.IsAtEnd( ); ++mIt )
301 // -------------------------------------------------------------------------
302 template< class _TInputImage, class _TDistanceMap >
303 void fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::
305 std::vector< TIndex >& end_points,
306 const TOutputImage* dmap,
308 const _TSkeletonQueue& queue
311 typedef typename _TSkeletonQueue::value_type _TSkeletonQueueValue;
314 typedef itk::Image< bool, Self::Dimension > _TMarks;
315 typename _TMarks::Pointer marks = _TMarks::New( );
316 marks->SetLargestPossibleRegion( mst->GetLargestPossibleRegion( ) );
317 marks->SetRequestedRegion( mst->GetRequestedRegion( ) );
318 marks->SetBufferedRegion( mst->GetBufferedRegion( ) );
319 marks->SetSpacing( mst->GetSpacing( ) );
320 marks->SetOrigin( mst->GetOrigin( ) );
321 marks->SetDirection( mst->GetDirection( ) );
323 marks->FillBuffer( false );
325 // Get candidates in maximum to minimum iteration
326 typename _TSkeletonQueue::const_reverse_iterator nIt = queue.rbegin( );
327 for( ; nIt != queue.rend( ); ++nIt )
329 // Mark it and update end-points
330 if( !( marks->GetPixel( nIt->second ) ) )
332 marks->SetPixel( nIt->second, true );
333 end_points.push_back( nIt->second );
336 TIndex it = nIt->second;
337 TIndex p = mst->GetParent( it );
340 this->_MarkSphere( marks, dmap, it );
342 p = mst->GetParent( it );
345 this->_MarkSphere( marks, dmap, it );
352 #endif // __fpa__Image__SkeletonFilter__hxx__