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[FrontAlgorithms.git] / lib / fpa / Common / Image / SkeletonReader.hxx

diff --git a/lib/fpa/Common/Image/SkeletonReader.hxx b/lib/fpa/Common/Image/SkeletonReader.hxx
new file mode 100644 (file)
index 0000000..ee886c5
--- /dev/null
+++ b/lib/fpa/Common/Image/SkeletonReader.hxx
@@ -0,0 +1,208 @@
+// =========================================================================
+// @author Leonardo Florez Valencia
+// @email florez-l@javeriana.edu.co
+// =========================================================================
+#ifndef __fpa__Common__Image__SkeletonReader__hxx__
+#define __fpa__Common__Image__SkeletonReader__hxx__
+
+// -------------------------------------------------------------------------
+template< class _TSkeleton >
+_TSkeleton* fpa::Common::Image::SkeletonReader< _TSkeleton >::
+GetOutput( )
+{
+  return(
+    itkDynamicCastInDebugMode< TSkeleton* >( this->GetPrimaryOutput( ) )
+    );
+}
+
+// -------------------------------------------------------------------------
+template< class _TSkeleton >
+_TSkeleton* fpa::Common::Image::SkeletonReader< _TSkeleton >::
+GetOutput( unsigned int i )
+{
+  return(
+    itkDynamicCastInDebugMode< TSkeleton* >(
+      this->itk::ProcessObject::GetOutput( i )
+      )
+    );
+}
+
+// -------------------------------------------------------------------------
+template< class _TSkeleton >
+void fpa::Common::Image::SkeletonReader< _TSkeleton >::
+GraftOutput( itk::DataObject* out )
+{
+  this->GraftNthOutput( 0, out );
+}
+
+// -------------------------------------------------------------------------
+template< class _TSkeleton >
+void fpa::Common::Image::SkeletonReader< _TSkeleton >::
+GraftOutput(
+  const typename Superclass::DataObjectIdentifierType& key,
+  itk::DataObject* out
+  )
+{
+  if( out == NULL )
+  {
+    itkExceptionMacro(
+      << "Requested to graft output that is a NULL pointer"
+      );
+
+  } // fi
+  itk::DataObject* output = this->itk::ProcessObject::GetOutput( key );
+  output->Graft( out );
+}
+
+// -------------------------------------------------------------------------
+template< class _TSkeleton >
+void fpa::Common::Image::SkeletonReader< _TSkeleton >::
+GraftNthOutput( unsigned int i, itk::DataObject* out )
+{
+  if( i >= this->GetNumberOfIndexedOutputs( ) )
+  {
+    itkExceptionMacro(
+      << "Requested to graft output " << i
+      << " but this filter only has "
+      << this->GetNumberOfIndexedOutputs( )
+      << " indexed Outputs."
+      );
+
+  } // fi
+  this->GraftOutput( this->MakeNameFromOutputIndex( i ), out );
+}
+
+// -------------------------------------------------------------------------
+template< class _TSkeleton >
+itk::DataObject::Pointer
+fpa::Common::Image::SkeletonReader< _TSkeleton >::
+MakeOutput( itk::ProcessObject::DataObjectPointerArraySizeType i )
+{
+  return( TSkeleton::New( ).GetPointer( ) );
+}
+
+// -------------------------------------------------------------------------
+template< class _TSkeleton >
+fpa::Common::Image::SkeletonReader< _TSkeleton >::
+SkeletonReader( )
+  : Superclass( )
+{
+  typename TSkeleton::Pointer out =
+    static_cast< TSkeleton* >( this->MakeOutput( 0 ).GetPointer( ) );
+  this->itk::ProcessObject::SetNumberOfRequiredInputs( 0 );
+  this->itk::ProcessObject::SetNumberOfRequiredOutputs( 1 );
+  this->itk::ProcessObject::SetNthOutput( 0, out.GetPointer( ) );
+}
+
+// -------------------------------------------------------------------------
+template< class _TSkeleton >
+fpa::Common::Image::SkeletonReader< _TSkeleton >::
+~SkeletonReader( )
+{
+}
+
+// -------------------------------------------------------------------------
+template< class _TSkeleton >
+void fpa::Common::Image::SkeletonReader< _TSkeleton >::
+GenerateData( )
+{
+  typedef typename TSkeleton::TPath   _TPath;
+  typedef typename _TPath::TIndex     _TIndex;
+  typedef typename _TPath::TSpacing   _TSpacing;
+  typedef typename _TPath::TPoint     _TPoint;
+  typedef typename _TPath::TDirection _TDirection;
+
+  std::string buffer;
+  std::ifstream file_stream( this->m_FileName.c_str( ) );
+  if( !file_stream )
+  {
+    itkExceptionMacro(
+      << "Error reading skeleton from \"" << this->m_FileName << "\""
+      );
+    return;
+
+  } // fi
+  file_stream.seekg( 0, std::ios::end );
+  buffer.reserve( ( unsigned int )( file_stream.tellg( ) ) );
+  file_stream.seekg( 0, std::ios::beg );
+  buffer.assign(
+    ( std::istreambuf_iterator< char >( file_stream ) ),
+    std::istreambuf_iterator< char >( )
+    );
+  file_stream.close( );
+
+  std::istringstream in( buffer );
+  unsigned int dim;
+  in >> dim;
+  if( dim != TSkeleton::Dimension )
+  {
+    itkExceptionMacro(
+      << "Mismatched skeletons dimension: " << dim
+      << " != " << TSkeleton::Dimension
+      );
+    return;
+
+  } // fi
+
+  // Read spatial parameters
+  _TSpacing spa;
+  _TDirection dir;
+  _TPoint ori;
+  for( unsigned int d = 0; d < dim; ++d )
+    in >> spa[ d ];
+  for( unsigned int d = 0; d < dim; ++d )
+    for( unsigned int e = 0; e < dim; ++e )
+      in >> dir[ d ][ e ];
+  for( unsigned int d = 0; d < dim; ++d )
+    in >> ori[ d ];
+
+  // Read end-points, just to ignore
+  unsigned int n;
+  in >> n;
+  for( unsigned int i = 0; i < n; ++i )
+  {
+    _TIndex idx;
+    for( unsigned int d = 0; d < dim; ++d )
+      in >> idx[ d ];
+
+  } // rof
+
+  // Read bifurcations, just to ignore
+  in >> n;
+  for( unsigned int i = 0; i < n; ++i )
+  {
+    _TIndex idx;
+    for( unsigned int d = 0; d < dim; ++d )
+      in >> idx[ d ];
+
+  } // rof
+
+  // Read paths
+  TSkeleton* out = this->GetOutput( );
+  unsigned int nPaths;
+  in >> nPaths;
+  for( unsigned int p = 0; p < nPaths; ++p )
+  {
+    typename _TPath::Pointer path = _TPath::New( );
+    path->SetSpacing( spa );
+    path->SetOrigin( ori );
+    path->SetDirection( dir );
+
+    unsigned long pathSize;
+    in >> pathSize;
+    for( unsigned long id = 0; id < pathSize; ++id )
+    {
+      _TIndex idx;
+      for( unsigned int d = 0; d < dim; ++d )
+        in >> idx[ d ];
+      path->AddVertex( idx );
+
+    } // rof
+    out->AddBranch( path );
+
+  } // rof
+}
+
+#endif // __fpa__Common__Image__SkeletonReader__hxx__
+
+// eof - $RCSfile$