1 // =========================================================================
2 // @author Leonardo Florez Valencia
3 // @email florez-l@javeriana.edu.co
4 // =========================================================================
5 #ifndef __fpa__Filters__Image__ExtractSkeleton__hxx__
6 #define __fpa__Filters__Image__ExtractSkeleton__hxx__
9 #include <itkImageRegionIteratorWithIndex.h>
10 #include <itkMinimumMaximumImageCalculator.h>
11 #include <fpa/Functors/Dijkstra/Invert.h>
13 // -------------------------------------------------------------------------
14 template< class _TInputImage, class _TDistanceMap >
15 fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
16 _TDijkstra::_TDijkstra( )
19 // Prepare weight function
20 typedef fpa::Functors::Dijkstra::Invert< TScalar > _TWeight;
21 typename _TWeight::Pointer weight = _TWeight::New( );
22 weight->SetAlpha( 1 );
24 this->SetWeightFunction( weight );
27 // -------------------------------------------------------------------------
28 template< class _TInputImage, class _TDistanceMap >
29 fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
30 _TDijkstra::~_TDijkstra( )
34 // -------------------------------------------------------------------------
35 template< class _TInputImage, class _TDistanceMap >
36 void fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
37 _TDijkstra::_BeforeGenerateData( )
39 this->Superclass::_BeforeGenerateData( );
40 this->m_SkeletonQueue.clear( );
43 // -------------------------------------------------------------------------
44 template< class _TInputImage, class _TDistanceMap >
45 void fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
46 _TDijkstra::_PostComputeOutputValue( TNode& n )
48 typedef typename _TSkeletonQueue::value_type _TSkeletonQueueValue;
50 this->Superclass::_PostComputeOutputValue( n );
51 double d = double( this->GetInput( )->GetPixel( n.Vertex ) );
52 if( d >= double( 0 ) )
54 // Update skeleton candidates
56 double v = double( n.Value ) / ( d * d );
57 this->m_SkeletonQueue.insert( _TSkeletonQueueValue( v, n.Vertex ) );
62 // -------------------------------------------------------------------------
63 template< class _TInputImage, class _TDistanceMap >
65 fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
68 itk::ModifiedTimeType t = this->Superclass::GetMTime( );
69 itk::ModifiedTimeType q = this->m_DistanceMap->GetMTime( );
70 return( ( q < t )? q: t );
73 // -------------------------------------------------------------------------
74 template< class _TInputImage, class _TDistanceMap >
75 void fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
76 SetInput( TInputImage* input )
78 this->Superclass::SetNthInput( 0, input );
81 // -------------------------------------------------------------------------
82 template< class _TInputImage, class _TDistanceMap >
83 typename fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
84 TInputImage* fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
87 return( dynamic_cast< TInputImage* >( this->Superclass::GetInput( 0 ) ) );
90 // -------------------------------------------------------------------------
91 template< class _TInputImage, class _TDistanceMap >
92 const typename fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
93 TInputImage* fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
97 dynamic_cast< const TInputImage* >( this->Superclass::GetInput( 0 ) )
101 // -------------------------------------------------------------------------
102 template< class _TInputImage, class _TDistanceMap >
103 typename fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
104 TSkeleton* fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
107 return( dynamic_cast< TSkeleton* >( this->Superclass::GetOutput( 0 ) ) );
110 // -------------------------------------------------------------------------
111 template< class _TInputImage, class _TDistanceMap >
112 const typename fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
113 TSkeleton* fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
117 dynamic_cast< const TSkeleton* >( this->Superclass::GetOutput( 0 ) )
121 // -------------------------------------------------------------------------
122 template< class _TInputImage, class _TDistanceMap >
123 fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
126 m_SeedFromMaximumDistance( false )
128 this->SetNumberOfRequiredInputs( 1 );
129 this->SetNumberOfRequiredOutputs( 1 );
130 this->SetNthOutput( 0, TSkeleton::New( ) );
132 this->m_DistanceMap = TDistanceMap::New( );
135 // -------------------------------------------------------------------------
136 template< class _TInputImage, class _TDistanceMap >
137 fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
142 // -------------------------------------------------------------------------
143 template< class _TInputImage, class _TDistanceMap >
144 void fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
147 // Update distance map
148 this->m_DistanceMap->SetInput( this->GetInput( ) );
149 this->m_DistanceMap->Update( );
152 if( this->m_SeedFromMaximumDistance )
154 typedef itk::MinimumMaximumImageCalculator< TOutputImage > _TMinMax;
155 typename _TMinMax::Pointer minmax = _TMinMax::New( );
156 minmax->SetImage( this->m_DistanceMap->GetOutput( ) );
158 this->m_Seed = minmax->GetIndexOfMaximum( );
162 std::cout << int( this->GetInput( )->GetPixel( this->m_Seed ) ) << std::endl;
163 std::cout << this->m_DistanceMap->GetOutput( )->GetPixel( this->m_Seed ) << std::endl;
166 typename _TDijkstra::Pointer dijkstra = _TDijkstra::New( );
167 dijkstra->SetInput( this->m_DistanceMap->GetOutput( ) );
168 dijkstra->AddSeed( this->m_Seed );
171 // Compute end-points
172 const _TMST* mst = dijkstra->GetMinimumSpanningTree( );
173 std::vector< TIndex > end_points;
175 end_points, this->m_DistanceMap->GetOutput( ),
176 mst, dijkstra->GetSkeletonQueue( )
178 this->m_EndPoints = end_points;
180 // Compute symbolic branches
182 typedef std::map< TIndex, TIndex, typename TIndex::LexicographicCompare > _TTags;
183 _TTags tags, branches;
184 typename std::vector< TIndex >::const_iterator eIt = end_points.begin( );
185 for( ; eIt != end_points.end( ); ++eIt )
189 TIndex p = mst->GetParent( it );
190 typename _TTags::iterator bIt = tags.end( );
191 while( it != p && bIt == tags.end( ) )
193 typename _TTags::iterator tIt = tags.find( it );
194 if( tIt != tags.end( ) )
196 // Ok, a bifurcation point has been found
197 // branch1: tIt->second <-> it (ok)
198 branches[ tIt->second ] = it;
200 // branch2: *eit <-> it (ok)
201 branches[ *eIt ] = it;
203 // branch3: it <-> until next bifurcation
209 p = mst->GetParent( it );
212 if( bIt != tags.end( ) )
214 TIndex pTag = bIt->second;
215 TIndex nTag = bIt->first;
218 while( tags[ it ] == pTag )
222 it = mst->GetParent( it );
226 branches[ bIt->first ] = p;
231 branches[ *eIt ] = it;
237 // Fill full branches
238 typedef typename _TMST::TVertices _TVertices;
239 typedef typename TSkeleton::TPath _TPath;
241 TSkeleton* sk = this->GetOutput( );
242 typename _TTags::const_iterator bIt = branches.begin( );
243 for( ; bIt != branches.end( ); ++bIt )
245 _TVertices v = mst->GetAxis( bIt->first, bIt->second );
246 typename _TPath::Pointer path = _TPath::New( );
247 path->SetReferenceImage( this->GetInput( ) );
248 typename _TVertices::const_reverse_iterator vIt = v.rbegin( );
249 for( ; vIt != v.rend( ); ++vIt )
250 path->AddVertex( *vIt );
251 sk->AddBranch( path );
257 // -------------------------------------------------------------------------
258 template< class _TInputImage, class _TDistanceMap >
259 template< class _TMarksPointer >
260 void fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
262 _TMarksPointer& marks, const TOutputImage* dmap, const TIndex& center
265 typedef typename _TMarksPointer::ObjectType _TMarks;
266 typedef itk::ImageRegionIteratorWithIndex< _TMarks > _TMarksIt;
268 static const double _eps = std::sqrt( double( Self::Dimension + 1 ) );
269 typename _TMarks::SpacingType spac = dmap->GetSpacing( );
270 typename _TMarks::RegionType region = dmap->GetRequestedRegion( );
272 typename _TMarks::PointType cnt;
273 dmap->TransformIndexToPhysicalPoint( center, cnt );
274 double r = double( dmap->GetPixel( center ) ) * _eps;
277 for( unsigned int d = 0; d < Self::Dimension; ++d )
279 long off = long( std::ceil( r / double( spac[ d ] ) ) );
282 i0[ d ] = center[ d ] - off;
283 i1[ d ] = center[ d ] + off;
285 if( i0[ d ] < region.GetIndex( )[ d ] )
286 i0[ d ] = region.GetIndex( )[ d ];
288 if( i1[ d ] >= region.GetIndex( )[ d ] + region.GetSize( )[ d ] )
289 i1[ d ] = region.GetIndex( )[ d ] + region.GetSize( )[ d ] - 1;
293 typename _TMarks::SizeType size;
294 for( unsigned int d = 0; d < Self::Dimension; ++d )
295 size[ d ] = i1[ d ] - i0[ d ] + 1;
297 typename _TMarks::RegionType neighRegion;
298 neighRegion.SetIndex( i0 );
299 neighRegion.SetSize( size );
301 _TMarksIt mIt( marks, neighRegion );
302 for( mIt.GoToBegin( ); !mIt.IsAtEnd( ); ++mIt )
306 // -------------------------------------------------------------------------
307 template< class _TInputImage, class _TDistanceMap >
308 void fpa::Filters::Image::ExtractSkeleton< _TInputImage, _TDistanceMap >::
310 std::vector< TIndex >& end_points,
311 const TOutputImage* dmap,
313 const _TSkeletonQueue& queue
316 typedef typename _TSkeletonQueue::value_type _TSkeletonQueueValue;
319 typedef itk::Image< bool, Self::Dimension > _TMarks;
320 typename _TMarks::Pointer marks = _TMarks::New( );
321 marks->SetLargestPossibleRegion( mst->GetLargestPossibleRegion( ) );
322 marks->SetRequestedRegion( mst->GetRequestedRegion( ) );
323 marks->SetBufferedRegion( mst->GetBufferedRegion( ) );
324 marks->SetSpacing( mst->GetSpacing( ) );
325 marks->SetOrigin( mst->GetOrigin( ) );
326 marks->SetDirection( mst->GetDirection( ) );
328 marks->FillBuffer( false );
330 // Get candidates in maximum to minimum iteration
331 typename _TSkeletonQueue::const_reverse_iterator nIt = queue.rbegin( );
332 for( ; nIt != queue.rend( ); ++nIt )
334 // Mark it and update end-points
335 if( !( marks->GetPixel( nIt->second ) ) )
337 marks->SetPixel( nIt->second, true );
338 end_points.push_back( nIt->second );
341 TIndex it = nIt->second;
342 TIndex p = mst->GetParent( it );
345 this->_MarkSphere( marks, dmap, it );
347 p = mst->GetParent( it );
350 this->_MarkSphere( marks, dmap, it );
357 #endif // __fpa__Filters__Image__ExtractSkeleton__hxx__