X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=lib%2Ffpa%2FImage%2FSkeletonFilter.hxx;h=d8dc66a1f0841216b02c7ddeeeba8ee941a5ddac;hb=e9083d9f5f381f258f994fa9bbbe39a897f97c5b;hp=069eea071af885b3ae432a8edebfa66d327e9ec1;hpb=7955ba9683b8032e8cd3ca7aa361568fdbb218d2;p=FrontAlgorithms.git

diff --git a/lib/fpa/Image/SkeletonFilter.hxx b/lib/fpa/Image/SkeletonFilter.hxx
index 069eea0..d8dc66a 100644
--- a/lib/fpa/Image/SkeletonFilter.hxx
+++ b/lib/fpa/Image/SkeletonFilter.hxx
@@ -93,36 +93,32 @@ _AfterGenerateData( )
 {
   this->Superclass::_AfterGenerateData( );
 
+  _TAdjacencies A;
   std::vector< TIndex > end_points;
-  this->_EndPoints( end_points );
-  this->_Skeleton( end_points );
+  this->_EndPoints( end_points, A );
+  this->_Skeleton( end_points, A );
 }
 
 // -------------------------------------------------------------------------
 template< class _TImage >
 void fpa::Image::SkeletonFilter< _TImage >::
-_EndPoints( std::vector< TIndex >& end_points )
+_EndPoints( std::vector< TIndex >& end_points, _TAdjacencies& A )
 {
-  typedef itk::ImageRegionIteratorWithIndex< TMarks > _TMarksIt;
-
-  static const double _eps = std::sqrt( double( Self::Dimension + 1 ) );
-  auto input = this->GetInput( );
-  auto mst = this->GetMinimumSpanningTree( );
   auto marks = this->GetMarks( );
+  auto mst = this->GetMinimumSpanningTree( );
+  auto spac = marks->GetSpacing( );
 
   // Some values
-  marks->SetLargestPossibleRegion( input->GetLargestPossibleRegion( ) );
-  marks->SetRequestedRegion( input->GetRequestedRegion( ) );
-  marks->SetBufferedRegion( input->GetBufferedRegion( ) );
-  marks->SetSpacing( input->GetSpacing( ) );
-  marks->SetOrigin( input->GetOrigin( ) );
-  marks->SetDirection( input->GetDirection( ) );
+  marks->SetLargestPossibleRegion( mst->GetLargestPossibleRegion( ) );
+  marks->SetRequestedRegion( mst->GetRequestedRegion( ) );
+  marks->SetBufferedRegion( mst->GetBufferedRegion( ) );
+  marks->SetSpacing( mst->GetSpacing( ) );
+  marks->SetOrigin( mst->GetOrigin( ) );
+  marks->SetDirection( mst->GetDirection( ) );
   marks->Allocate( );
   marks->FillBuffer( 0 );
-  auto spac = marks->GetSpacing( );
 
   // BFS from maximum queue
-  auto region = input->GetRequestedRegion( );
   while( this->m_SkeletonQueue.size( ) > 0 )
   {
     // Get node
@@ -136,66 +132,20 @@ _EndPoints( std::vector< TIndex >& end_points )
       continue;
     marks->SetPixel( n.second, 1 );
     end_points.push_back( n.second );
+    std::cout << this->m_SkeletonQueue.size( ) << std::endl;
 
     // Mark path
     TIndex it = n.second;
     TIndex p = mst->GetParent( it );
     while( it != p )
     {
-      // TODO: tags->SetPixel( it, tags->GetPixel( it ) + 1 );
+      this->_MarkSphere( it );
       it = p;
       p = mst->GetParent( it );
 
     } // elihw
-    // TODO: tags->SetPixel( it, tags->GetPixel( it ) + 1 );
-
-    /* TODO: use mst directly rather than computing paths
-       typename TMST::TPath::Pointer path;
-       mst->GetPath( path, n.second );
-       for( unsigned long i = 0; i < path->GetSize( ); ++i )
-       {
-       TIndex idx = path->GetVertex( i );
-       typename _TImage::PointType cnt;
-       input->TransformIndexToPhysicalPoint( idx, cnt );
-       double r = double( input->GetPixel( idx ) ) * _eps;
-
-       TIndex i0, i1;
-       for( unsigned int d = 0; d < Self::Dimension; ++d )
-       {
-       long off = long( std::ceil( r / double( spac[ d ] ) ) );
-       if( off < 3 )
-       off = 3;
-       i0[ d ] = idx[ d ] - off;
-       i1[ d ] = idx[ d ] + off;
-
-       if( i0[ d ] < region.GetIndex( )[ d ] )
-       i0[ d ] = region.GetIndex( )[ d ];
-
-       if( i1[ d ] >= region.GetIndex( )[ d ] + region.GetSize( )[ d ] )
-       i1[ d ] = region.GetIndex( )[ d ] + region.GetSize( )[ d ] - 1;
-
-       } // rof
-
-       typename _TImage::SizeType size;
-       for( unsigned int d = 0; d < Self::Dimension; ++d )
-       size[ d ] = i1[ d ] - i0[ d ] + 1;
-
-       typename _TImage::RegionType neighRegion;
-       neighRegion.SetIndex( i0 );
-       neighRegion.SetSize( size );
-
-       _TMarksIt mIt( marks, neighRegion );
-       for( mIt.GoToBegin( ); !mIt.IsAtEnd( ); ++mIt )
-       {
-       TIndex w = mIt.GetIndex( );
-       typename _TImage::PointType p;
-       marks->TransformIndexToPhysicalPoint( w, p );
-       mIt.Set( 1 );
-
-       } // rof
-
-       } // rof
-    */
+    this->_MarkSphere( it );
+    A[ n.second ] = it;
 
   } // elihw
 }
@@ -203,67 +153,124 @@ _EndPoints( std::vector< TIndex >& end_points )
 // -------------------------------------------------------------------------
 template< class _TImage >
 void fpa::Image::SkeletonFilter< _TImage >::
-_Skeleton( const std::vector< TIndex >& end_points )
+_Skeleton( const std::vector< TIndex >& end_points, _TAdjacencies& A )
 {
-  typedef itk::Image< unsigned long, Self::Dimension > _TTagsImage;
-  typedef typename TMST::TPath _TPath;
+  std::cout << end_points.size( ) << " " << A.size( ) << std::endl;
+
+  /* TODO
+     typedef itk::Image< unsigned long, Self::Dimension > _TTagsImage;
+     typedef typename TMST::TPath _TPath;
+
+     auto mst = this->GetMinimumSpanningTree( );
+     auto skeleton = this->GetSkeleton( );
+
+     // Tag branches
+     typename _TTagsImage::Pointer tags = _TTagsImage::New( );
+     tags->SetLargestPossibleRegion( mst->GetLargestPossibleRegion( ) );
+     tags->SetRequestedRegion( mst->GetRequestedRegion( ) );
+     tags->SetBufferedRegion( mst->GetBufferedRegion( ) );
+     tags->Allocate( );
+     tags->FillBuffer( 0 );
+     for( auto eIt = end_points.begin( ); eIt != end_points.end( ); ++eIt )
+     {
+     TIndex it = *eIt;
+     TIndex p = mst->GetParent( it );
+     while( it != p )
+     {
+     tags->SetPixel( it, tags->GetPixel( it ) + 1 );
+     it = p;
+     p = mst->GetParent( it );
+
+     } // elihw
+     tags->SetPixel( it, tags->GetPixel( it ) + 1 );
+
+     } // rof
+
+     // Build paths (branches)
+     for( auto eIt = end_points.begin( ); eIt != end_points.end( ); ++eIt )
+     {
+     TIndex it = *eIt;
+     TIndex p = mst->GetParent( it );
+     TIndex sIdx = *eIt;
+     typename _TPath::Pointer path = _TPath::New( );
+     path->SetReferenceImage( mst );
+     while( it != p )
+     {
+     if( tags->GetPixel( sIdx ) != tags->GetPixel( it ) )
+     {
+     // Ok, a new branch has been added
+     path->AddVertex( it );
+     skeleton->AddBranch( path );
+
+     // Update a new starting index
+     path = _TPath::New( );
+     path->SetReferenceImage( mst );
+     sIdx = it;
+     }
+     else
+     path->AddVertex( it );
+     it = p;
+     p = mst->GetParent( it );
+
+     } // elihw
+
+     // Finally, add last branch
+     path->AddVertex( it );
+     skeleton->AddBranch( path );
+
+     } // rof
+  */
+}
 
-  auto mst = this->GetMinimumSpanningTree( );
-  auto skeleton = this->GetSkeleton( );
-
-  // Tag branches
-  typename _TTagsImage::Pointer tags = _TTagsImage::New( );
-  tags->SetLargestPossibleRegion( mst->GetLargestPossibleRegion( ) );
-  tags->SetRequestedRegion( mst->GetRequestedRegion( ) );
-  tags->SetBufferedRegion( mst->GetBufferedRegion( ) );
-  tags->Allocate( );
-  tags->FillBuffer( 0 );
-  for( auto eIt = end_points.begin( ); eIt != end_points.end( ); ++eIt )
+// -------------------------------------------------------------------------
+template< class _TImage >
+void fpa::Image::SkeletonFilter< _TImage >::
+_MarkSphere( const TIndex& idx )
+{
+  typedef itk::ImageRegionIteratorWithIndex< TMarks > _TMarksIt;
+
+  static const double _eps = std::sqrt( double( Self::Dimension + 1 ) );
+  auto input = this->GetInput( );
+  auto marks = this->GetMarks( );
+  auto spac = input->GetSpacing( );
+  auto region = input->GetRequestedRegion( );
+
+  typename _TImage::PointType cnt;
+  input->TransformIndexToPhysicalPoint( idx, cnt );
+  double r = double( input->GetPixel( idx ) ) * _eps;
+
+  TIndex i0, i1;
+  for( unsigned int d = 0; d < Self::Dimension; ++d )
   {
-    TIndex it = *eIt;
-    TIndex p = mst->GetParent( it );
-    while( it != p )
-    {
-      tags->SetPixel( it, tags->GetPixel( it ) + 1 );
-      it = p;
-      p = mst->GetParent( it );
+    long off = long( std::ceil( r / double( spac[ d ] ) ) );
+    if( off < 3 )
+      off = 3;
+    i0[ d ] = idx[ d ] - off;
+    i1[ d ] = idx[ d ] + off;
 
-    } // elihw
-    tags->SetPixel( it, tags->GetPixel( it ) + 1 );
+    if( i0[ d ] < region.GetIndex( )[ d ] )
+      i0[ d ] = region.GetIndex( )[ d ];
+
+    if( i1[ d ] >= region.GetIndex( )[ d ] + region.GetSize( )[ d ] )
+      i1[ d ] = region.GetIndex( )[ d ] + region.GetSize( )[ d ] - 1;
 
   } // rof
 
-  // Build paths (branches)
-  for( auto eIt = end_points.begin( ); eIt != end_points.end( ); ++eIt )
-  {
-    TIndex it = *eIt;
-    TIndex p = mst->GetParent( it );
-    TIndex sIdx = *eIt;
-    typename _TPath::Pointer path = _TPath::New( );
-    path->SetReferenceImage( mst );
-    while( it != p )
-    {
-      if( tags->GetPixel( sIdx ) != tags->GetPixel( it ) )
-      {
-        // Ok, a new branch has been added
-        path->AddVertex( it );
-        skeleton->AddBranch( path );
-
-        // Update a new starting index
-        path = _TPath::New( );
-        path->SetReferenceImage( mst );
-        sIdx = it;
-      }
-      else
-        path->AddVertex( it );
-      it = p;
-      p = mst->GetParent( it );
+  typename _TImage::SizeType size;
+  for( unsigned int d = 0; d < Self::Dimension; ++d )
+    size[ d ] = i1[ d ] - i0[ d ] + 1;
 
-    } // elihw
+  typename _TImage::RegionType neighRegion;
+  neighRegion.SetIndex( i0 );
+  neighRegion.SetSize( size );
 
-    // Finally, add last branch
-    path->AddVertex( it );
-    skeleton->AddBranch( path );
+  _TMarksIt mIt( marks, neighRegion );
+  for( mIt.GoToBegin( ); !mIt.IsAtEnd( ); ++mIt )
+  {
+    TIndex w = mIt.GetIndex( );
+    typename _TImage::PointType p;
+    marks->TransformIndexToPhysicalPoint( w, p );
+    mIt.Set( 1 );
 
   } // rof
 }