From: Leonardo Flórez-Valencia Date: Thu, 17 Aug 2017 02:25:21 +0000 (-0500) Subject: ... X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?p=FrontAlgorithms.git;a=commitdiff_plain;h=3c639e5da479c7216a0a302ffa156ac6762caeed ... --- diff --git a/CMakeLists.txt b/CMakeLists.txt index b098f7a..13e90cb 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,3 +1,8 @@ +## ========================================================================= +## @author Leonardo Florez Valencia +## @email florez-l@javeriana.edu.co +## ========================================================================= + cmake_minimum_required(VERSION 3.0) ## ======================== @@ -91,7 +96,12 @@ mark_as_advanced( ## == Find needed packages and dependencies == ## =========================================== -find_package(ivq CONFIG REQUIRED) +find_package(ITK CONFIG REQUIRED) +include(${ITK_USE_FILE}) +if(ITKVtkGlue_LOADED) + find_package(VTK CONFIG REQUIRED) + include(${VTK_USE_FILE}) +endif(ITKVtkGlue_LOADED) ## ========================= ## == Installation values == @@ -109,7 +119,7 @@ set(namespace "${PROJECT_NAME}::") ## == Build different parts == ## =========================== -subdirs(appli lib tests) +subdirs(lib tests) ## =============================== ## == Global installation rules == diff --git a/cmake/fpaConfig.cmake.in b/cmake/fpaConfig.cmake.in index f019632..67047bb 100644 --- a/cmake/fpaConfig.cmake.in +++ b/cmake/fpaConfig.cmake.in @@ -1,3 +1,8 @@ +## ========================================================================= +## @author Leonardo Florez Valencia +## @email florez-l@javeriana.edu.co +## ========================================================================= + @PACKAGE_INIT@ include("${CMAKE_CURRENT_LIST_DIR}/@targets_export_name@.cmake") @@ -7,6 +12,13 @@ check_required_components("@PROJECT_NAME@") ## == Find needed packages and dependencies == ## =========================================== -find_package(ivq CONFIG REQUIRED) +set(ITK_DIR @ITK_DIR@) +find_package(ITK CONFIG REQUIRED) +include(${ITK_USE_FILE}) +if(ITKVtkGlue_LOADED) + set(VTK_DIR @VTK_DIR@) + find_package(VTK CONFIG REQUIRED) + include(${VTK_USE_FILE}) +endif(ITKVtkGlue_LOADED) ## eof - $RCSfile$ diff --git a/lib/CMakeLists.txt b/lib/CMakeLists.txt deleted file mode 100644 index f4c0955..0000000 --- a/lib/CMakeLists.txt +++ /dev/null @@ -1,8 +0,0 @@ - -include_directories( - ${CMAKE_CURRENT_SOURCE_DIR} - ${CMAKE_CURRENT_BINARY_DIR} - ) -subdirs(fpa) - -## eof - $RCSfile$ diff --git a/lib/fpa/Base/Algorithm.h b/lib/fpa/Base/Algorithm.h deleted file mode 100644 index 785b818..0000000 --- a/lib/fpa/Base/Algorithm.h +++ /dev/null @@ -1,128 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__Algorithm__h__ -#define __fpa__Base__Algorithm__h__ - -#include - -#include -#include - -namespace fpa -{ - namespace Base - { - /** - */ - template< class _TTraits > - class Algorithm - : public _TTraits::TFilter, - public _TTraits::TMarksInterface, - public _TTraits::TSeedsInterface - { - public: - typedef _TTraits TTraits; - typedef typename TTraits::TFilter Superclass; - typedef typename TTraits::TMarksInterface TMarksInterface; - typedef typename TTraits::TSeedsInterface TSeedsInterface; - typedef Algorithm Self; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef typename TTraits::TInputValue TInputValue; - typedef typename TTraits::TOutputValue TOutputValue; - typedef typename TTraits::TNeighborhood TNeighborhood; - typedef typename TTraits::TNode TNode; - typedef typename TTraits::TNodes TNodes; - typedef typename TTraits::TSeeds TSeeds; - typedef typename TTraits::TVertex TVertex; - - /** - */ - class TEvent - : public itk::EventObject - { - public: - typedef TEvent Self; - typedef itk::EventObject Superclass; - - public: - TEvent( ); - TEvent( const TVertex& v, unsigned long fid, bool intoq ); - virtual ~TEvent( ); - virtual const char* GetEventName( ) const override; - virtual bool CheckEvent( const itk::EventObject* e ) const override; - virtual itk::EventObject* MakeObject( ) const override; - - private: - // Purposely not implemented. - Self& operator=( const Self& other ); - - public: - TVertex Vertex; - unsigned long FrontId; - bool IntoQueue; - }; - - public: - itkTypeMacro( fpa::Base::Algorithm, _TFilter ); - - itkBooleanMacro( VisualDebug ); - - itkGetConstMacro( InitValue, TOutputValue ); - itkGetConstMacro( VisualDebug, bool ); - - itkSetMacro( InitValue, TOutputValue ); - itkSetMacro( VisualDebug, bool ); - - public: - virtual void InvokeEvent( const itk::EventObject& e ); - virtual void InvokeEvent( const itk::EventObject& e ) const; - - protected: - Algorithm( ); - virtual ~Algorithm( ); - - virtual void GenerateData( ) override; - virtual void _BeforeGenerateData( ); - virtual void _AfterGenerateData( ); - virtual void _FinishOneLoop( ); - - virtual void _QueueInit( ); - - virtual void _ConfigureOutput( const TOutputValue& v ) = 0; - virtual TNeighborhood _GetNeighbors( const TVertex& v ) const = 0; - virtual TInputValue _GetInputValue( const TVertex& v ) const = 0; - virtual TOutputValue _GetOutputValue( const TVertex& v ) const = 0; - - virtual void _ComputeOutputValue( TNode& n ) = 0; - virtual void _UpdateOutputValue( TNode& n ) = 0; - virtual void _QueueClear( ) = 0; - virtual void _QueuePush( const TNode& node ) = 0; - virtual unsigned long _QueueSize( ) const = 0; - virtual TNode _QueuePop( ) = 0; - - private: - // Purposely not implemented - Algorithm( const Self& other ); - Self& operator=( const Self& other ); - - protected: - bool m_VisualDebug; - TOutputValue m_InitValue; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Base__Algorithm__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/Algorithm.hxx b/lib/fpa/Base/Algorithm.hxx deleted file mode 100644 index 68296be..0000000 --- a/lib/fpa/Base/Algorithm.hxx +++ /dev/null @@ -1,220 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__Algorithm__hxx__ -#define __fpa__Base__Algorithm__hxx__ - -// ------------------------------------------------------------------------- -template< class _TTraits > -fpa::Base::Algorithm< _TTraits >::TEvent:: -TEvent( ) - : Superclass( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -fpa::Base::Algorithm< _TTraits >::TEvent:: -TEvent( const TVertex& v, unsigned long fid, bool intoq ) - : Superclass( ), - Vertex( v ), - FrontId( fid ), - IntoQueue( intoq ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -fpa::Base::Algorithm< _TTraits >::TEvent:: -~TEvent( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -const char* fpa::Base::Algorithm< _TTraits >::TEvent:: -GetEventName( ) const -{ - return( "fpa::Base::Algorithm< _TTraits >::TEvent" ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -bool fpa::Base::Algorithm< _TTraits >::TEvent:: -CheckEvent( const itk::EventObject* e ) const -{ - return( dynamic_cast< const Self* >( e ) != NULL ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -itk::EventObject* fpa::Base::Algorithm< _TTraits >::TEvent:: -MakeObject( ) const -{ - return( new Self ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -void fpa::Base::Algorithm< _TTraits >:: -InvokeEvent( const itk::EventObject& e ) -{ - TEvent a; - if( a.CheckEvent( &e ) ) - { - if( this->m_VisualDebug ) - this->Superclass::InvokeEvent( e ); - } - else - this->Superclass::InvokeEvent( e ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -void fpa::Base::Algorithm< _TTraits >:: -InvokeEvent( const itk::EventObject& e ) const -{ - TEvent a; - if( a.CheckEvent( &e ) ) - { - if( this->m_VisualDebug ) - this->Superclass::InvokeEvent( e ); - } - else - this->Superclass::InvokeEvent( e ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -fpa::Base::Algorithm< _TTraits >:: -Algorithm( ) - : Superclass( ), - TMarksInterface( this ), - TSeedsInterface( this ), - m_VisualDebug( false ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -fpa::Base::Algorithm< _TTraits >:: -~Algorithm( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -void fpa::Base::Algorithm< _TTraits >:: -GenerateData( ) -{ - this->InvokeEvent( itk::StartEvent( ) ); - - // Init objects - this->_BeforeGenerateData( ); - this->_ConfigureOutput( this->m_InitValue ); - this->_InitMarks( this->GetSeeds( ).size( ) ); - TNodes seeds = this->_UnifySeeds( ); - this->_PrepareSeeds( seeds ); - - // Init queue - this->_QueueInit( ); - typename TNodes::const_iterator sIt = seeds.begin( ); - for( ; sIt != seeds.end( ); ++sIt ) - { - this->_QueuePush( *sIt ); - this->InvokeEvent( TEvent( sIt->Vertex, sIt->FrontId, true ) ); - - } // rof - - // Main loop - while( this->_QueueSize( ) > 0 ) - { - // Get next candidate - TNode node = this->_QueuePop( ); - this->InvokeEvent( TEvent( node.Vertex, node.FrontId, false ) ); - if( !( this->_IsMarked( node.Vertex ) ) ) - { - // Update output value and mark vertex - this->_UpdateOutputValue( node ); - this->_Mark( node.Vertex, node.FrontId ); - - // The actual node was effectively marked? - if( node.FrontId > 0 ) - { - // Add neighborhood - TNeighborhood neighbors = this->_GetNeighbors( node.Vertex ); - typename TNeighborhood::const_iterator nIt = neighbors.begin( ); - bool coll = false; - while( nIt != neighbors.end( ) && !coll ) - { - if( this->_IsMarked( *nIt ) ) - { - // Invoke stop at collisions - if( this->_Collisions( node.Vertex, *nIt ) ) - { - this->_QueueClear( ); - coll = true; - - } // fi - } - else - { - TNode nnode; - nnode.Vertex = *nIt; - nnode.Parent = node.Vertex; - nnode.FrontId = node.FrontId; - this->_ComputeOutputValue( nnode ); - this->_QueuePush( nnode ); - this->InvokeEvent( TEvent( nnode.Vertex, nnode.FrontId, true ) ); - - } // fi - ++nIt; - - } // elihw - - } // fi - - } // fi - this->_FinishOneLoop( ); - - } // elihw - - // Finish - this->_AfterGenerateData( ); - this->InvokeEvent( itk::EndEvent( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -void fpa::Base::Algorithm< _TTraits >:: -_BeforeGenerateData( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -void fpa::Base::Algorithm< _TTraits >:: -_AfterGenerateData( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -void fpa::Base::Algorithm< _TTraits >:: -_FinishOneLoop( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -void fpa::Base::Algorithm< _TTraits >:: -_QueueInit( ) -{ - this->_QueueClear( ); -} - -#endif // __fpa__Base__Algorithm__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/Dijkstra.h b/lib/fpa/Base/Dijkstra.h deleted file mode 100644 index 11f5538..0000000 --- a/lib/fpa/Base/Dijkstra.h +++ /dev/null @@ -1,71 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__Dijkstra__h__ -#define __fpa__Base__Dijkstra__h__ - -#include - -namespace fpa -{ - namespace Base - { - /** - */ - template< class _TAlgorithm, class _TMST > - class Dijkstra - : public fpa::Base::DijkstraBase< _TAlgorithm > - { - public: - typedef Dijkstra Self; - typedef fpa::Base::DijkstraBase< _TAlgorithm > Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef _TMST TMST; - - typedef typename Superclass::TNode TNode; - typedef typename Superclass::TNodes TNodes; - typedef typename Superclass::TInputValue TInputValue; - typedef typename Superclass::TOutputValue TOutputValue; - typedef typename Superclass::TFrontId TFrontId; - typedef typename Superclass::TVertex TVertex; - typedef typename Superclass::TSeeds TSeeds; - - typedef typename Superclass::TQueue TQueue; - typedef typename Superclass::TQueueOrder TQueueOrder; - typedef typename Superclass::TWeightFunction TWeightFunction; - - public: - TMST* GetMinimumSpanningTree( ); - const TMST* GetMinimumSpanningTree( ) const; - - protected: - Dijkstra( ); - virtual ~Dijkstra( ); - - virtual void _AfterGenerateData( ) override; - virtual void _UpdateOutputValue( TNode& n ) override; - - private: - // Purposely not implemented. - Dijkstra( const Self& other ); - Self& operator=( const Self& other ); - - protected: - unsigned int m_MSTIdx; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Base__Dijkstra__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/Dijkstra.hxx b/lib/fpa/Base/Dijkstra.hxx deleted file mode 100644 index 9de7912..0000000 --- a/lib/fpa/Base/Dijkstra.hxx +++ /dev/null @@ -1,85 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__Dijkstra__hxx__ -#define __fpa__Base__Dijkstra__hxx__ - -// ------------------------------------------------------------------------- -template< class _TAlgorithm, class _TMST > -typename fpa::Base::Dijkstra< _TAlgorithm, _TMST >:: -TMST* fpa::Base::Dijkstra< _TAlgorithm, _TMST >:: -GetMinimumSpanningTree( ) -{ - return( - dynamic_cast< TMST* >( - this->itk::ProcessObject::GetOutput( this->m_MSTIdx ) - ) - ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm, class _TMST > -const typename fpa::Base::Dijkstra< _TAlgorithm, _TMST >:: -TMST* fpa::Base::Dijkstra< _TAlgorithm, _TMST >:: -GetMinimumSpanningTree( ) const -{ - return( - dynamic_cast< const TMST* >( - this->itk::ProcessObject::GetOutput( this->m_MSTIdx ) - ) - ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm, class _TMST > -fpa::Base::Dijkstra< _TAlgorithm, _TMST >:: -Dijkstra( ) - : Superclass( ) -{ - this->m_MSTIdx = this->GetNumberOfRequiredOutputs( ); - this->itk::ProcessObject::SetNumberOfRequiredOutputs( this->m_MSTIdx + 1 ); - this->SetNthOutput( this->m_MSTIdx, TMST::New( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm, class _TMST > -fpa::Base::Dijkstra< _TAlgorithm, _TMST >:: -~Dijkstra( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm, class _TMST > -void fpa::Base::Dijkstra< _TAlgorithm, _TMST >:: -_AfterGenerateData( ) -{ - this->Superclass::_AfterGenerateData( ); - - TMST* mst = this->GetMinimumSpanningTree( ); - mst->ClearSeeds( ); - mst->SetCollisions( this->m_Collisions ); - - const TSeeds& seeds = this->GetSeeds( ); - typename TSeeds::const_iterator sIt = seeds.begin( ); - for( ; sIt != seeds.end( ); ++sIt ) - { - if( sIt->IsUnified ) - mst->AddSeed( sIt->Vertex ); - - } // rof -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm, class _TMST > -void fpa::Base::Dijkstra< _TAlgorithm, _TMST >:: -_UpdateOutputValue( TNode& n ) -{ - this->Superclass::_UpdateOutputValue( n ); - this->GetMinimumSpanningTree( )->SetParent( n.Vertex, n.Parent ); -} - -#endif // __fpa__Base__Dijkstra__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/DijkstraBase.h b/lib/fpa/Base/DijkstraBase.h deleted file mode 100644 index 4f08eb9..0000000 --- a/lib/fpa/Base/DijkstraBase.h +++ /dev/null @@ -1,92 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__DijkstraBase__h__ -#define __fpa__Base__DijkstraBase__h__ - -#include - -#include -#include - -namespace fpa -{ - namespace Base - { - /** - */ - template< class _TAlgorithm > - class DijkstraBase - : public _TAlgorithm - { - public: - typedef DijkstraBase Self; - typedef _TAlgorithm Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef typename _TAlgorithm::TNode TNode; - typedef typename _TAlgorithm::TNodes TNodes; - typedef typename _TAlgorithm::TInputValue TInputValue; - typedef typename _TAlgorithm::TOutputValue TOutputValue; - typedef typename _TAlgorithm::TVertex TVertex; - - typedef std::vector< TNode > TQueue; - struct TQueueOrder - { - bool operator()( const TNode& a, const TNode& b ) const - { - return( b.Value < a.Value ); - } - }; - typedef fpa::Base::Functors::Dijkstra::Function< TVertex, TOutputValue > TWeightFunction; - - public: - itkConceptMacro( - Check_TOutputValue, - ( itk::Concept::IsFloatingPoint< TOutputValue > ) - ); - - public: - itkGetObjectMacro( WeightFunction, TWeightFunction ); - itkSetObjectMacro( WeightFunction, TWeightFunction ); - - public: - virtual itk::ModifiedTimeType GetMTime( ) const override; - - protected: - DijkstraBase( ); - virtual ~DijkstraBase( ); - - virtual void _ComputeOutputValue( TNode& n ) override; - virtual void _QueueClear( ) override; - virtual TNode _QueuePop( ) override; - virtual void _QueuePush( const TNode& node ) override; - virtual unsigned long _QueueSize( ) const override; - virtual void _PrepareSeeds( TNodes& nodes ) override; - - private: - // Purposely not implemented. - DijkstraBase( const Self& other ); - Self& operator=( const Self& other ); - - protected: - typename TWeightFunction::Pointer m_WeightFunction; - - TQueue m_Queue; - TQueueOrder m_QueueOrder; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Base__DijkstraBase__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/DijkstraBase.hxx b/lib/fpa/Base/DijkstraBase.hxx deleted file mode 100644 index d04ecf5..0000000 --- a/lib/fpa/Base/DijkstraBase.hxx +++ /dev/null @@ -1,111 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__DijkstraBase__hxx__ -#define __fpa__Base__DijkstraBase__hxx__ - -#include -#include - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -itk::ModifiedTimeType fpa::Base::DijkstraBase< _TAlgorithm >:: -GetMTime( ) const -{ - itk::ModifiedTimeType t = this->Superclass::GetMTime( ); - if( this->m_WeightFunction.IsNotNull( ) ) - { - itk::ModifiedTimeType q = this->m_WeightFunction->GetMTime( ); - t = ( q < t )? q: t; - - } // fi - return( t ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -fpa::Base::DijkstraBase< _TAlgorithm >:: -DijkstraBase( ) - : Superclass( ) -{ - this->SetInitValue( std::numeric_limits< TOutputValue >::max( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -fpa::Base::DijkstraBase< _TAlgorithm >:: -~DijkstraBase( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::DijkstraBase< _TAlgorithm >:: -_ComputeOutputValue( TNode& n ) -{ - TOutputValue c = this->m_WeightFunction->Evaluate( n.Vertex, n.Parent ); - n.Value = c + this->_GetOutputValue( n.Parent ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::DijkstraBase< _TAlgorithm >:: -_QueueClear( ) -{ - this->m_Queue.clear( ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -typename fpa::Base::DijkstraBase< _TAlgorithm >:: -TNode fpa::Base::DijkstraBase< _TAlgorithm >:: -_QueuePop( ) -{ - std::pop_heap( - this->m_Queue.begin( ), this->m_Queue.end( ), this->m_QueueOrder - ); - TNode n = this->m_Queue.back( ); - this->m_Queue.pop_back( ); - return( n ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::DijkstraBase< _TAlgorithm >:: -_QueuePush( const TNode& node ) -{ - bool push_needed = ( node.Parent == node.Vertex ); - push_needed |= !( node.Value < this->_GetOutputValue( node.Parent ) ); - if( push_needed ) - { - this->m_Queue.push_back( node ); - std::push_heap( - this->m_Queue.begin( ), this->m_Queue.end( ), this->m_QueueOrder - ); - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -unsigned long fpa::Base::DijkstraBase< _TAlgorithm >:: -_QueueSize( ) const -{ - return( this->m_Queue.size( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::DijkstraBase< _TAlgorithm >:: -_PrepareSeeds( TNodes& nodes ) -{ - typename TNodes::iterator nIt = nodes.begin( ); - for( ; nIt != nodes.end( ); ++nIt ) - nIt->Value = TOutputValue( 0 ); -} - -#endif // __fpa__Base__DijkstraBase__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/Functors/Dijkstra/Function.h b/lib/fpa/Base/Functors/Dijkstra/Function.h deleted file mode 100644 index 013cb99..0000000 --- a/lib/fpa/Base/Functors/Dijkstra/Function.h +++ /dev/null @@ -1,64 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__Functors__Dijkstra__Function__h__ -#define __fpa__Base__Functors__Dijkstra__Function__h__ - -#include - -namespace fpa -{ - namespace Base - { - namespace Functors - { - namespace Dijkstra - { - /** - */ - template< class _TVertex, class _TOutputValue > - class Function - : public itk::Object - { - public: - typedef Function Self; - typedef itk::Object Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - public: - itkTypeMacro( fpa::Base::Functors::Dijkstra::Function, itk::Object ); - - public: - virtual _TOutputValue Evaluate( - const _TVertex& v, const _TVertex& p - ) const = 0; - - protected: - Function( ) - : Superclass( ) - { - } - virtual ~Function( ) - { - } - - private: - // Purposely not implemented - Function( const Self& other ); - Self& operator=( const Self& other ); - }; - - } // ecapseman - - } // ecapseman - - } // ecapseman - -} // ecapseman - -#endif // __fpa__Base__Functors__Dijkstra__Function__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/Functors/RegionGrow/BinaryThreshold.h b/lib/fpa/Base/Functors/RegionGrow/BinaryThreshold.h deleted file mode 100644 index 0ac4618..0000000 --- a/lib/fpa/Base/Functors/RegionGrow/BinaryThreshold.h +++ /dev/null @@ -1,95 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__Functors__RegionGrow__BinaryThreshold__h__ -#define __fpa__Base__Functors__RegionGrow__BinaryThreshold__h__ - -#include -#include - -namespace fpa -{ - namespace Base - { - namespace Functors - { - namespace RegionGrow - { - /** - */ - template< class _TValue > - class BinaryThreshold - : public itk::FunctionBase< _TValue, bool > - { - public: - typedef BinaryThreshold Self; - typedef itk::FunctionBase< _TValue, bool > Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - public: - itkNewMacro( Self ); - itkTypeMacro( - fpa::Base::Functors::RegionGrow::BinaryThreshold, - itk::FunctionBase - ); - - itkBooleanMacro( Strict ); - - itkGetConstMacro( Lower, _TValue ); - itkGetConstMacro( Upper, _TValue ); - itkGetConstMacro( Strict, bool ); - - itkSetMacro( Lower, _TValue ); - itkSetMacro( Upper, _TValue ); - itkSetMacro( Strict, bool ); - - public: - virtual bool Evaluate( const _TValue& input ) const override - { - if( this->m_Strict ) - return( this->m_Lower < input && input < this->m_Upper ); - else - return( this->m_Lower <= input && input <= this->m_Upper ); - } - - protected: - BinaryThreshold( ) - : Superclass( ), - m_Strict( true ) - { - this->m_Upper = std::numeric_limits< _TValue >::max( ); - if( std::numeric_limits< _TValue >::is_integer ) - this->m_Lower = std::numeric_limits< _TValue >::min( ); - else - this->m_Lower = -this->m_Upper; - } - - virtual ~BinaryThreshold( ) - { - } - - private: - // Purposely not implemented - BinaryThreshold( const Self& other ); - Self& operator=( const Self& other ); - - protected: - _TValue m_Lower; - _TValue m_Upper; - bool m_Strict; - }; - - } // ecapseman - - } // ecapseman - - } // ecapseman - -} // ecapseman - -#endif // __fpa__Base__Functors__RegionGrow__BinaryThreshold__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/Functors/RegionGrow/Tautology.h b/lib/fpa/Base/Functors/RegionGrow/Tautology.h deleted file mode 100644 index a024b59..0000000 --- a/lib/fpa/Base/Functors/RegionGrow/Tautology.h +++ /dev/null @@ -1,69 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__Functors__RegionGrow__Tautology__h__ -#define __fpa__Base__Functors__RegionGrow__Tautology__h__ - -#include - -namespace fpa -{ - namespace Base - { - namespace Functors - { - namespace RegionGrow - { - /** - */ - template< class _TValue > - class Tautology - : public itk::FunctionBase< _TValue, bool > - { - public: - typedef Tautology Self; - typedef itk::FunctionBase< _TValue, bool > Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - public: - itkNewMacro( Self ); - itkTypeMacro( - fpa::Base::Functors::RegionGrow::Tautology, - itk::FunctionBase - ); - - public: - virtual bool Evaluate( const _TValue& input ) const override - { - return( true ); - } - - protected: - Tautology( ) - : Superclass( ) - { - } - virtual ~Tautology( ) - { - } - - private: - // Purposely not implemented - Tautology( const Self& other ); - Self& operator=( const Self& other ); - }; - - } // ecapseman - - } // ecapseman - - } // ecapseman - -} // ecapseman - -#endif // __fpa__Base__Functors__RegionGrow__Tautology__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/Graph.h b/lib/fpa/Base/Graph.h deleted file mode 100644 index 41b2fb9..0000000 --- a/lib/fpa/Base/Graph.h +++ /dev/null @@ -1,170 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__Graph__h__ -#define __fpa__Base__Graph__h__ - -#include -#include -#include -#include -#include - -namespace fpa -{ - namespace Base - { - /** \brief A generic graph with templated index types. - * - * @param _TVertex Vertex type. - * @param _TCost Cost type. - * @param _TIndex Index type (it should be a strict weak ordering type). - */ - template< class _TVertex, class _TCost, class _TIndex = unsigned long, class _TIndexCompare = std::less< _TIndex > > - class Graph - : public itk::DataObject - { - public: - typedef Graph Self; - typedef itk::DataObject Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef _TVertex TVertex; - typedef _TCost TCost; - typedef _TIndex TIndex; - typedef _TIndexCompare TIndexCompare; - - // Base types - typedef std::map< TIndex, TVertex, TIndexCompare > TVertices; - typedef std::vector< TCost > TEdges; - typedef std::map< TIndex, TEdges, TIndexCompare > TMatrixRow; - typedef std::map< TIndex, TMatrixRow, TIndexCompare > TMatrix; - - public: - itkNewMacro( Self ); - itkTypeMacro( Graph, itk::DataObject ); - - public: - /*! \brief Iterators over vertices. - * These allow you to iterate over all of graph's vertices. - * - * Typical iteration should be done as: - * - * TGraph g; - * ... - * TGraph::TVertices::[const_]iterator vIt = g.BeginVertices( ); - * for( ; vIt != g.EndVertices( ); ++vIt ) - * { - * vIt->first; --> this is the vertex's index <-- - * vIt->second; --> this is the vertex's value <-- - * } - */ - inline typename TVertices::iterator BeginVertices( ) - { return( this->m_Vertices.begin( ) ); } - inline typename TVertices::iterator EndVertices( ) - { return( this->m_Vertices.end( ) ); } - inline typename TVertices::const_iterator BeginVertices( ) const - { return( this->m_Vertices.begin( ) ); } - inline typename TVertices::const_iterator EndVertices( ) const - { return( this->m_Vertices.end( ) ); } - - /*! \brief Iterators over edges. - * These allow you to iterate over all of graph's edges. - * - * Typical iteration should be done as: - * - * TGraph g; - * ... - * TGraph::TMatrix::[const_]iterator mIt = g.BeginEdgesRows( ); - * for( ; mIt != g.EndEdgesRows( ); ++mIt ) - * { - * mIt->first; --> this is the row index. <-- - * TGraph::TMatrixRow::[const_]iterator rIt = mIt->second.begin( ); - * for( ; rIt != mIt->second.end( ); ++rIt ) - * { - * rIt->first; --> this is the column index. - * TGraph::TEdges::[const_]iterator eIt = rIt->second.begin( ); - * for( ; eIt != rIt->second.end( ); ++eIt ) - * *eIt; --> this is the cost between mIt->first and rIt->first - * } - * } - */ - inline typename TMatrix::iterator BeginEdgesRows( ) - { return( this->m_Matrix.begin( ) ); } - inline typename TMatrix::iterator EndEdgetsRows( ) - { return( this->m_Matrix.end( ) ); } - inline typename TMatrix::const_iterator BeginEdgesRows( ) const - { return( this->m_Matrix.begin( ) ); } - inline typename TMatrix::const_iterator EndEdgesRows( ) const - { return( this->m_Matrix.end( ) ); } - - /*! \brief Clear all vertices and edges. - */ - void Clear( ); - - /*! \brief Clear all edges. - */ - inline void ClearEdges( ) - { this->m_Matrix.clear( ); } - - /*! \brief Vertex manipulation methods. - * Names are self-explanatory. - */ - inline bool HasVertexIndex( const TIndex& i ) const - { return( this->m_Vertices.find( i ) != this->m_Vertices.end( ) ); } - inline void SetVertex( const TIndex& index, TVertex& vertex ) - { this->m_Vertices[ index ] = vertex; } - inline TVertex& GetVertex( const TIndex& index ) - { return( this->m_Vertices[ index ] ); } - inline const TVertex& GetVertex( const TIndex& index ) const - { return( this->m_Vertices[ index ] ); } - bool RenameVertex( const TIndex& old_index, const TIndex& new_index ); - void RemoveVertex( const TIndex& index ); - - /*! \brief Edge manipulation methods. - * Names are self-explanatory. - */ - inline void AddEdge( const TIndex& orig, const TIndex& dest, const TCost& cost ) - { this->m_Matrix[ orig ][ dest ].push_back( cost ); } - TEdges& GetEdges( const TIndex& orig, const TIndex& dest ); - const TEdges& GetEdges( const TIndex& orig, const TIndex& dest ) const; - bool HasEdge( const TIndex& orig, const TIndex& dest ) const; - void RemoveEdge( const TIndex& orig, const TIndex& dest, const TCost& cost ); - void RemoveEdges( const TIndex& orig, const TIndex& dest ); - - /*! \brief Returns graph's sinks. - * - * A sink is a special vertex which does not have any "exiting" edges. - * - * @return Sinks ordered by their index. - */ - std::set< TIndex, TIndexCompare > GetSinks( ) const; - - protected: - Graph( ); - virtual ~Graph( ); - - private: - // Purposely not implemented - Graph( const Self& other ); - Self& operator=( const Self& other ); - - protected: - TVertices m_Vertices; - TMatrix m_Matrix; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Base__Graph__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/Graph.hxx b/lib/fpa/Base/Graph.hxx deleted file mode 100644 index 03f85a8..0000000 --- a/lib/fpa/Base/Graph.hxx +++ /dev/null @@ -1,272 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__Graph__hxx__ -#define __fpa__Base__Graph__hxx__ - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TCost, class _TIndex, class _TIndexCompare > -void fpa::Base::Graph< _TVertex, _TCost, _TIndex, _TIndexCompare >:: -Clear( ) -{ - this->m_Vertices.clear( ); - this->m_Matrix.clear( ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TCost, class _TIndex, class _TIndexCompare > -bool fpa::Base::Graph< _TVertex, _TCost, _TIndex, _TIndexCompare >:: -RenameVertex( const TIndex& old_index, const TIndex& new_index ) -{ - typename TVertices::iterator old_v = this->m_Vertices.find( old_index ); - typename TVertices::iterator new_v = this->m_Vertices.find( new_index ); - if( old_v != this->m_Vertices.end( ) && new_v == this->m_Vertices.end( ) ) - { - // Replace vertex - this->m_Vertices[ new_index ] = old_v->second; - this->m_Vertices.erase( old_index ); - - // Duplicate edges - typename TMatrix::iterator mIt = this->m_Matrix.begin( ); - typename TMatrix::iterator found_row = this->m_Matrix.end( ); - for( ; mIt != this->m_Matrix.end( ); ++mIt ) - { - if( mIt->first == old_index ) - found_row = mIt; - - typename TMatrixRow::iterator rIt = mIt->second.begin( ); - for( ; rIt != mIt->second.end( ); ++rIt ) - { - if( mIt->first == old_index ) - this->m_Matrix[ new_index ][ rIt->first ] = rIt->second; - else if( rIt->first == old_index ) - this->m_Matrix[ mIt->first ][ new_index ] = rIt->second; - - } // rof - - } // rof - - // Delete old edges - if( found_row != this->m_Matrix.end( ) ) - this->m_Matrix.erase( found_row ); - - mIt = this->m_Matrix.begin( ); - for( ; mIt != this->m_Matrix.end( ); ++mIt ) - { - typename TMatrixRow::iterator rIt = mIt->second.begin( ); - while( rIt != mIt->second.end( ) ) - { - if( rIt->first == old_index ) - { - mIt->second.erase( rIt ); - rIt = mIt->second.begin( ); - } - else - ++rIt; - - } // elihw - - } // rof - return( true ); - } - else - return( false ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TCost, class _TIndex, class _TIndexCompare > -void fpa::Base::Graph< _TVertex, _TCost, _TIndex, _TIndexCompare >:: -RemoveVertex( const TIndex& index ) -{ - typename TVertices::iterator i = this->m_Vertices.find( index ); - if( i != this->m_Vertices.end( ) ) - { - // Delete vertex - this->m_Vertices.erase( i ); - - // Delete edges starting from given vertex - typename TMatrix::iterator mIt = this->m_Matrix.find( index ); - if( mIt != this->m_Matrix.end( ) ) - this->m_Matrix.erase( mIt ); - - // Delete edges arriving to given vertex - mIt = this->m_Matrix.begin( ); - for( ; mIt != this->m_Matrix.end( ); ++mIt ) - { - typename TMatrixRow::iterator rIt = mIt->second.begin( ); - while( rIt != mIt->second.end( ) ) - { - if( rIt->first == index ) - { - mIt->second.erase( rIt ); - rIt = mIt->second.begin( ); - } - else - ++rIt; - - } // elihw - - } // rof - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TCost, class _TIndex, class _TIndexCompare > -typename -fpa::Base::Graph< _TVertex, _TCost, _TIndex, _TIndexCompare >:: -TEdges& -fpa::Base::Graph< _TVertex, _TCost, _TIndex, _TIndexCompare >:: -GetEdges( const TIndex& orig, const TIndex& dest ) -{ - static TEdges null_edges; - typename TMatrix::iterator o = this->m_Matrix.find( orig ); - if( o != this->m_Matrix.find( orig ) ) - { - typename TMatrixRow::iterator d = o->second.find( dest ); - if( d == o->second.end( ) ) - { - null_edges.clear( ); - return( null_edges ); - } - else - return( d->second ); - } - else - { - null_edges.clear( ); - return( null_edges ); - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TCost, class _TIndex, class _TIndexCompare > -const typename -fpa::Base::Graph< _TVertex, _TCost, _TIndex, _TIndexCompare >:: -TEdges& -fpa::Base::Graph< _TVertex, _TCost, _TIndex, _TIndexCompare >:: -GetEdges( const TIndex& orig, const TIndex& dest ) const -{ - static const TEdges null_edges; - typename TMatrix::iterator o = this->m_Matrix.find( orig ); - if( o != this->m_Matrix.find( orig ) ) - { - typename TMatrixRow::iterator d = o->second.find( dest ); - if( d == o->second.end( ) ) - return( null_edges ); - else - return( d->second ); - } - else - return( null_edges ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TCost, class _TIndex, class _TIndexCompare > -bool fpa::Base::Graph< _TVertex, _TCost, _TIndex, _TIndexCompare >:: -HasEdge( const TIndex& orig, const TIndex& dest ) const -{ - typename TMatrix::const_iterator mIt = this->m_Matrix.find( orig ); - if( mIt != this->m_Matrix.end( ) ) - return( mIt->second.find( dest ) != mIt->second.end( ) ); - else - return( false ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TCost, class _TIndex, class _TIndexCompare > -void fpa::Base::Graph< _TVertex, _TCost, _TIndex, _TIndexCompare >:: -RemoveEdge( const TIndex& orig, const TIndex& dest, const TCost& cost ) -{ - typename TMatrix::iterator m = this->m_Matrix.find( orig ); - if( m != this->m_Matrix.end( ) ) - { - typename TMatrixRow::iterator r = m->second.find( dest ); - if( r != m->second.end( ) ) - { - typename TEdges::iterator e = r->second.end( ); - for( - typename TEdges::iterator i = r->second.begin( ); - i != r->second.end( ) && e == r->second.end( ); - ++i - ) - if( *i == cost ) - e = i; - if( e != r->second.end( ) ) - { - r->second.erase( e ); - if( r->second.size( ) == 0 ) - { - m->second.erase( r ); - if( m->second.size( ) == 0 ) - this->m_Matrix.erase( m ); - - } // fi - - } // fi - - } // fi - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TCost, class _TIndex, class _TIndexCompare > -void fpa::Base::Graph< _TVertex, _TCost, _TIndex, _TIndexCompare >:: -RemoveEdges( const TIndex& orig, const TIndex& dest ) -{ - typename TMatrix::iterator m = this->m_Matrix.find( orig ); - if( m != this->m_Matrix.end( ) ) - { - typename TMatrixRow::iterator r = m->second.find( dest ); - if( r != m->second.end( ) ) - { - m->second.erase( r ); - if( m->second.size( ) == 0 ) - this->m_Matrix.erase( m ); - - } // fi - - } // fi - -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TCost, class _TIndex, class _TIndexCompare > -std::set< _TIndex, _TIndexCompare > -fpa::Base::Graph< _TVertex, _TCost, _TIndex, _TIndexCompare >:: -GetSinks( ) const -{ - std::set< _TIndex, _TIndexCompare > sinks; - - typename TVertices::iterator vIt = this->m_Vertices.begin( ); - for( ; vIt != this->m_Vertices.end( ); ++vIt ) - sinks.insert( vIt->first ); - typename TMatrix::iterator mIt = this->m_Matrix.begin( ); - for( ; mIt != this->m_Matrix.end( ); ++mIt ) - sinks.erase( mIt->first ); - - return( sinks ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TCost, class _TIndex, class _TIndexCompare > -fpa::Base::Graph< _TVertex, _TCost, _TIndex, _TIndexCompare >:: -Graph( ) - : Superclass( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TCost, class _TIndex, class _TIndexCompare > -fpa::Base::Graph< _TVertex, _TCost, _TIndex, _TIndexCompare >:: -~Graph( ) -{ -} - -#endif // __fpa__Base__Graph__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/MarksInterface.h b/lib/fpa/Base/MarksInterface.h deleted file mode 100644 index 9644457..0000000 --- a/lib/fpa/Base/MarksInterface.h +++ /dev/null @@ -1,50 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__MarksInterface__h__ -#define __fpa__Base__MarksInterface__h__ - -#include - -namespace fpa -{ - namespace Base - { - /** - */ - template< class _TVertex > - class MarksInterface - { - public: - typedef _TVertex TVertex; - typedef MarksInterface Self; - - protected: - MarksInterface( itk::ProcessObject* filter ); - virtual ~MarksInterface( ); - - virtual bool _IsMarked( const TVertex& v ) const = 0; - virtual unsigned long _GetMark( const TVertex& v ) const = 0; - virtual void _Mark( const TVertex& v, unsigned long frontId ) = 0; - - virtual void _InitMarks( unsigned long nSeeds ); - virtual bool _Collisions( const TVertex& a, const TVertex& b ); - - protected: - unsigned int m_NumberOfSeeds; - itk::ProcessObject* m_Filter; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Base__MarksInterface__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/MarksInterface.hxx b/lib/fpa/Base/MarksInterface.hxx deleted file mode 100644 index cd37eb5..0000000 --- a/lib/fpa/Base/MarksInterface.hxx +++ /dev/null @@ -1,43 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__MarksInterface__hxx__ -#define __fpa__Base__MarksInterface__hxx__ - -// ------------------------------------------------------------------------- -template< class _TVertex > -fpa::Base::MarksInterface< _TVertex >:: -MarksInterface( itk::ProcessObject* filter ) - : m_NumberOfSeeds( 0 ), - m_Filter( filter ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TVertex > -fpa::Base::MarksInterface< _TVertex >:: -~MarksInterface( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TVertex > -void fpa::Base::MarksInterface< _TVertex >:: -_InitMarks( unsigned long nSeeds ) -{ - this->m_NumberOfSeeds = nSeeds; -} - -// ------------------------------------------------------------------------- -template< class _TVertex > -bool fpa::Base::MarksInterface< _TVertex >:: -_Collisions( const TVertex& a, const TVertex& b ) -{ - return( false ); -} - -#endif // __fpa__Base__MarksInterface__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/MarksInterfaceWithCollisions.h b/lib/fpa/Base/MarksInterfaceWithCollisions.h deleted file mode 100644 index 3d6f10e..0000000 --- a/lib/fpa/Base/MarksInterfaceWithCollisions.h +++ /dev/null @@ -1,62 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__MarksInterfaceWithCollisions__h__ -#define __fpa__Base__MarksInterfaceWithCollisions__h__ - -#include -#include -#include - -namespace fpa -{ - namespace Base - { - /** - */ - template< class _TVertex > - class MarksInterfaceWithCollisions - : public fpa::Base::MarksInterface< _TVertex > - { - public: - typedef _TVertex TVertex; - typedef MarksInterfaceWithCollisions Self; - typedef fpa::Base::MarksInterface< TVertex > Superclass; - - // Minigraph to represent collisions - typedef std::pair< TVertex, bool > TCollision; - typedef std::vector< TCollision > TCollisionsRow; - typedef std::vector< TCollisionsRow > TCollisions; - - public: - bool StopAtOneFront( ) const; - void StopAtOneFrontOn( ); - void StopAtOneFrontOff( ); - void SetStopAtOneFront( bool v ); - - protected: - MarksInterfaceWithCollisions( itk::ProcessObject* filter ); - virtual ~MarksInterfaceWithCollisions( ); - - virtual void _InitMarks( unsigned long nSeeds ) override; - virtual bool _Collisions( const TVertex& a, const TVertex& b ) override; - - protected: - bool m_StopAtOneFront; - TCollisions m_Collisions; - unsigned int m_NumberOfFronts; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Base__MarksInterfaceWithCollisions__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/MarksInterfaceWithCollisions.hxx b/lib/fpa/Base/MarksInterfaceWithCollisions.hxx deleted file mode 100644 index 1230931..0000000 --- a/lib/fpa/Base/MarksInterfaceWithCollisions.hxx +++ /dev/null @@ -1,133 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__MarksInterfaceWithCollisions__hxx__ -#define __fpa__Base__MarksInterfaceWithCollisions__hxx__ - -#include - -// ------------------------------------------------------------------------- -template< class _TVertex > -bool fpa::Base::MarksInterfaceWithCollisions< _TVertex >:: -StopAtOneFront( ) const -{ - return( this->m_StopAtOneFront ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex > -void fpa::Base::MarksInterfaceWithCollisions< _TVertex >:: -StopAtOneFrontOn( ) -{ - this->SetStopAtOneFront( true ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex > -void fpa::Base::MarksInterfaceWithCollisions< _TVertex >:: -StopAtOneFrontOff( ) -{ - this->SetStopAtOneFront( false ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex > -void fpa::Base::MarksInterfaceWithCollisions< _TVertex >:: -SetStopAtOneFront( bool v ) -{ - if( this->m_StopAtOneFront != v ) - { - this->m_StopAtOneFront = v; - if( this->m_Filter != NULL ) - this->m_Filter->Modified( ); - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TVertex > -fpa::Base::MarksInterfaceWithCollisions< _TVertex >:: -MarksInterfaceWithCollisions( itk::ProcessObject* filter ) - : Superclass( filter ), - m_StopAtOneFront( false ), - m_NumberOfFronts( 0 ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TVertex > -fpa::Base::MarksInterfaceWithCollisions< _TVertex >:: -~MarksInterfaceWithCollisions( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TVertex > -void fpa::Base::MarksInterfaceWithCollisions< _TVertex >:: -_InitMarks( unsigned long nSeeds ) -{ - this->Superclass::_InitMarks( nSeeds ); - this->m_NumberOfFronts = nSeeds; - TCollision coll( TVertex( ), false ); - TCollisionsRow row( this->m_NumberOfFronts, coll ); - this->m_Collisions.clear( ); - this->m_Collisions.resize( this->m_NumberOfFronts, row ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex > -bool fpa::Base::MarksInterfaceWithCollisions< _TVertex >:: -_Collisions( const TVertex& a, const TVertex& b ) -{ - unsigned long ma = this->_GetMark( a ); - unsigned long mb = this->_GetMark( b ); - if( ma == mb || ma == 0 || mb == 0 ) - return( false ); - - // Mark collision, if it is new - ma--; mb--; - bool ret = false; - bool exists = this->m_Collisions[ ma ][ mb ].second; - exists &= this->m_Collisions[ mb ][ ma ].second; - if( !exists ) - { - this->m_Collisions[ ma ][ mb ].first = a; - this->m_Collisions[ ma ][ mb ].second = true; - this->m_Collisions[ mb ][ ma ].first = b; - this->m_Collisions[ mb ][ ma ].second = true; - - // Update number of fronts - unsigned long count = 0; - std::vector< bool > m( this->m_NumberOfSeeds, false ); - std::queue< unsigned long > q; - q.push( 0 ); - while( !q.empty( ) ) - { - unsigned long f = q.front( ); - q.pop( ); - - if( m[ f ] ) - continue; - m[ f ] = true; - count++; - - for( unsigned int n = 0; n < this->m_NumberOfSeeds; ++n ) - if( this->m_Collisions[ f ][ n ].second && !m[ n ] ) - q.push( n ); - - } // elihw - this->m_NumberOfFronts = this->m_NumberOfSeeds - count + 1; - - } // fi - return( - this->m_StopAtOneFront && - this->m_NumberOfSeeds > 1 && - this->m_NumberOfFronts == 1 - ); -} - -#endif // __fpa__Base__MarksInterfaceWithCollisions__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/MinimumSpanningTree.h b/lib/fpa/Base/MinimumSpanningTree.h deleted file mode 100644 index 35cb6e4..0000000 --- a/lib/fpa/Base/MinimumSpanningTree.h +++ /dev/null @@ -1,77 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__MinimumSpanningTree__h__ -#define __fpa__Base__MinimumSpanningTree__h__ - -#include - -namespace fpa -{ - namespace Base - { - /** - */ - template< class _TVertex, class _Superclass > - class MinimumSpanningTree - : public _Superclass - { - public: - typedef MinimumSpanningTree Self; - typedef _Superclass Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef _TVertex TVertex; - typedef std::pair< TVertex, bool > TCollision; - typedef std::vector< TCollision > TCollisionsRow; - typedef std::vector< TCollisionsRow > TCollisions; - typedef std::vector< TVertex > TVertices; - - protected: - typedef std::vector< unsigned long > _TRow; - typedef std::vector< _TRow > _TMatrix; - - public: - itkTypeMacro( fpa::Base::MinimumSpanningTree, _Superclass ); - - public: - const TCollisions& GetCollisions( ) const; - void SetCollisions( const TCollisions& collisions ); - - void ClearSeeds( ); - void AddSeed( const TVertex& seed ); - - virtual TVertex GetParent( const TVertex& v ) const = 0; - virtual void SetParent( const TVertex& v, const TVertex& p ) = 0; - - virtual TVertices GetPath( const TVertex& a ) const; - virtual TVertices GetPath( const TVertex& a, const TVertex& b ) const; - - protected: - MinimumSpanningTree( ); - virtual ~MinimumSpanningTree( ); - - private: - MinimumSpanningTree( const Self& other ); - Self& operator=( const Self& other ); - - protected: - TCollisions m_Collisions; - _TMatrix m_FrontPaths; - std::vector< TVertex > m_Seeds; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Base__MinimumSpanningTree__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/MinimumSpanningTree.hxx b/lib/fpa/Base/MinimumSpanningTree.hxx deleted file mode 100644 index d04cd36..0000000 --- a/lib/fpa/Base/MinimumSpanningTree.hxx +++ /dev/null @@ -1,237 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__MinimumSpanningTree__hxx__ -#define __fpa__Base__MinimumSpanningTree__hxx__ - -// ------------------------------------------------------------------------- -template< class _TVertex, class _Superclass > -const typename fpa::Base::MinimumSpanningTree< _TVertex, _Superclass >:: -TCollisions& fpa::Base::MinimumSpanningTree< _TVertex, _Superclass >:: -GetCollisions( ) const -{ - return( this->m_Collisions ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _Superclass > -void fpa::Base::MinimumSpanningTree< _TVertex, _Superclass >:: -SetCollisions( const TCollisions& collisions ) -{ - static const unsigned long _inf = - std::numeric_limits< unsigned long >::max( ); - if( this->m_Collisions == collisions ) - return; - - this->m_Collisions = collisions; - - // Prepare a front graph - unsigned long N = this->m_Collisions.size( ); - _TMatrix dist( N, _TRow( N, _inf ) ); - this->m_FrontPaths = dist; - for( unsigned long i = 0; i < N; ++i ) - { - for( unsigned long j = 0; j < N; ++j ) - { - if( this->m_Collisions[ i ][ j ].second ) - { - dist[ i ][ j ] = 1; - dist[ j ][ i ] = 1; - this->m_FrontPaths[ i ][ j ] = j; - this->m_FrontPaths[ j ][ i ] = i; - - } // fi - - } // rof - dist[ i ][ i ] = 0; - this->m_FrontPaths[ i ][ i ] = i; - - } // rof - - // Use Floyd-Warshall to compute all possible paths between fronts - for( unsigned long k = 0; k < N; ++k ) - { - for( unsigned long i = 0; i < N; ++i ) - { - for( unsigned long j = 0; j < N; ++j ) - { - // WARNING: you don't want a numeric overflow!!! - unsigned long dik = dist[ i ][ k ]; - unsigned long dkj = dist[ k ][ j ]; - unsigned long sum = _inf; - if( dik < _inf && dkj < _inf ) - sum = dik + dkj; - - // Ok, continue Floyd-Warshall - if( sum < dist[ i ][ j ] ) - { - dist[ i ][ j ] = sum; - this->m_FrontPaths[ i ][ j ] = this->m_FrontPaths[ i ][ k ]; - - } // fi - - } // rof - - } // rof - - } // rof - this->Modified( ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _Superclass > -void fpa::Base::MinimumSpanningTree< _TVertex, _Superclass >:: -ClearSeeds( ) -{ - this->m_Seeds.clear( ); - this->Modified( ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _Superclass > -void fpa::Base::MinimumSpanningTree< _TVertex, _Superclass >:: -AddSeed( const _TVertex& seed ) -{ - this->m_Seeds.push_back( seed ); - this->Modified( ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _Superclass > -typename fpa::Base::MinimumSpanningTree< _TVertex, _Superclass >:: -TVertices fpa::Base::MinimumSpanningTree< _TVertex, _Superclass >:: -GetPath( const _TVertex& a ) const -{ - TVertices vertices; - _TVertex it = a; - _TVertex p = this->GetParent( it ); - while( it != p ) - { - vertices.push_back( it ); - it = p; - p = this->GetParent( it ); - - } // elihw - vertices.push_back( it ); - return( vertices ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _Superclass > -typename fpa::Base::MinimumSpanningTree< _TVertex, _Superclass >:: -TVertices fpa::Base::MinimumSpanningTree< _TVertex, _Superclass >:: -GetPath( const _TVertex& a, const _TVertex& b ) const -{ - static const unsigned long _inf = - std::numeric_limits< unsigned long >::max( ); - - TVertices vertices; - TVertices pa = this->GetPath( a ); - TVertices pb = this->GetPath( b ); - if( pa.size( ) > 0 && pb.size( ) > 0 ) - { - // Find front identifiers - unsigned long ia = _inf, ib = _inf; - unsigned long N = this->m_Seeds.size( ); - for( unsigned long i = 0; i < N; ++i ) - { - if( this->m_Seeds[ i ] == pa[ pa.size( ) - 1 ] ) - ia = i; - if( this->m_Seeds[ i ] == pb[ pb.size( ) - 1 ] ) - ib = i; - - } // rof - - // Check if there is a front-jump between given seeds - if( ia != ib ) - { - // Compute front path - std::vector< long > fpath; - fpath.push_back( ia ); - while( ia != ib ) - { - ia = this->m_FrontPaths[ ia ][ ib ]; - fpath.push_back( ia ); - - } // elihw - - // Continue only if both fronts are connected - unsigned int N = fpath.size( ); - if( N > 0 ) - { - // First path: from start vertex to first collision - vertices = this->GetPath( - a, this->m_Collisions[ fpath[ 0 ] ][ fpath[ 1 ] ].first - ); - - // Intermediary paths - for( unsigned int i = 1; i < N - 1; ++i ) - { - TVertices ipath = - this->GetPath( - this->m_Collisions[ fpath[ i - 1 ] ][ fpath[ i ] ].first, - this->m_Collisions[ fpath[ i + 1 ] ][ fpath[ i ] ].first - ); - for( long id = 0; id < ipath.size( ); ++id ) - vertices.push_back( ipath[ id ] ); - - } // rof - - // Final path: from last collision to end point - TVertices lpath = - this->GetPath( - this->m_Collisions[ fpath[ N - 1 ] ][ fpath[ N - 2 ] ].first, b - ); - for( long id = 0; id < lpath.size( ); ++id ) - vertices.push_back( lpath[ id ] ); - - } // fi - } - else - { - // Ignore common part: find common ancestor - long aIt = pa.size( ) - 1; - long bIt = pb.size( ) - 1; - bool cont = true; - while( aIt >= 0 && bIt >= 0 && cont ) - { - cont = ( pa[ aIt ] == pb[ bIt ] ); - aIt--; - bIt--; - - } // elihw - aIt++; - bIt++; - - // Glue both parts - for( long cIt = 0; cIt <= aIt; ++cIt ) - vertices.push_back( pa[ cIt ] ); - for( ; bIt >= 0; --bIt ) - vertices.push_back( pb[ bIt ] ); - - } // fi - - } // fi - return( vertices ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _Superclass > -fpa::Base::MinimumSpanningTree< _TVertex, _Superclass >:: -MinimumSpanningTree( ) - : Superclass( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _Superclass > -fpa::Base::MinimumSpanningTree< _TVertex, _Superclass >:: -~MinimumSpanningTree( ) -{ -} - -#endif // __fpa__Base__MinimumSpanningTree__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/Mori.h b/lib/fpa/Base/Mori.h deleted file mode 100644 index 27f6915..0000000 --- a/lib/fpa/Base/Mori.h +++ /dev/null @@ -1,132 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__Mori__h__ -#define __fpa__Base__Mori__h__ - -#include -#include -#include -#include - -#include -#include - -namespace fpa -{ - namespace Base - { - /** - */ - template< class _TAlgorithm > - class Mori - : public _TAlgorithm - { - public: - typedef Mori Self; - typedef _TAlgorithm Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef typename _TAlgorithm::TNode TNode; - typedef typename _TAlgorithm::TNodes TNodes; - typedef typename _TAlgorithm::TInputValue TInputValue; - typedef typename _TAlgorithm::TOutputValue TOutputValue; - typedef typename _TAlgorithm::TFrontId TFrontId; - typedef typename _TAlgorithm::TVertex TVertex; - - typedef std::deque< TNode > TQueue; - typedef std::set< TInputValue > TThresholds; - - typedef ivq::ITK::PeakDetector TPeakDetector; - typedef TPeakDetector::TPeak TPeak; - - typedef fpa::Base::Functors::RegionGrow::BinaryThreshold< TInputValue > TPredicate; - - public: - itkConceptMacro( - Check_TOutputValue, - ( itk::Concept::IsUnsignedInteger< TOutputValue > ) - ); - - itkGetConstMacro( InsideValue, TOutputValue ); - itkSetMacro( InsideValue, TOutputValue ); - - itkGetConstMacro( MinimumThreshold, TInputValue ); - itkSetMacro( MinimumThreshold, TInputValue ); - - public: - virtual itk::ModifiedTimeType GetMTime( ) const override; - - TOutputValue GetOutsideValue( ) const; - void SetOutsideValue( const TOutputValue& v ); - - unsigned long GetSignalKernelSize( ) const; - double GetSignalThreshold( ) const; - double GetSignalInfluence( ) const; - - void SetSignalKernelSize( unsigned long k ); - void SetSignalThreshold( double t ); - void SetSignalInfluence( double i ); - - void ClearThresholds( ); - void AddThreshold( const TInputValue& thr ); - void SetThresholds( - const TInputValue& init, - const TInputValue& end, - const TInputValue& delta - ); - const TThresholds& GetThresholds( ) const; - unsigned long GetNumberOfEvaluatedThresholds( ) const; - TInputValue GetOptimumThreshold( ) const; - void GetSignalValues( - unsigned long i, double& x, double& y, TPeak& p - ) const; - - protected: - Mori( ); - virtual ~Mori( ); - - virtual void _BeforeGenerateData( ) override; - virtual void _FinishOneLoop( ) override; - virtual void _ComputeOutputValue( TNode& n ) override; - virtual void _UpdateOutputValue( TNode& n ) override; - virtual void _QueueClear( ) override; - virtual TNode _QueuePop( ) override; - virtual void _QueuePush( const TNode& node ) override; - virtual unsigned long _QueueSize( ) const override; - virtual void _PrepareSeeds( TNodes& nodes ) override; - - private: - // Purposely not implemented. - Mori( const Self& other ); - Self& operator=( const Self& other ); - - protected: - typename TPredicate::Pointer m_Predicate; - - TOutputValue m_InsideValue; - TInputValue m_MinimumThreshold; - TThresholds m_Thresholds; - typename TThresholds::const_iterator m_CurrThr; - - TQueue m_Queues[ 2 ]; - unsigned int m_CurrQueue; - double m_CurrCount; - - TPeakDetector m_PeakDetector; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Base__Mori__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/Mori.hxx b/lib/fpa/Base/Mori.hxx deleted file mode 100644 index 723e6fa..0000000 --- a/lib/fpa/Base/Mori.hxx +++ /dev/null @@ -1,321 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__Mori__hxx__ -#define __fpa__Base__Mori__hxx__ - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -itk::ModifiedTimeType fpa::Base::Mori< _TAlgorithm >:: -GetMTime( ) const -{ - itk::ModifiedTimeType t = this->Superclass::GetMTime( ); - itk::ModifiedTimeType q = this->m_Predicate->GetMTime( ); - return( ( q < t )? q: t ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -typename fpa::Base::Mori< _TAlgorithm >:: -TOutputValue fpa::Base::Mori< _TAlgorithm >:: -GetOutsideValue( ) const -{ - return( this->GetInitValue( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -SetOutsideValue( const TOutputValue& v ) -{ - this->SetInitValue( v ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -unsigned long fpa::Base::Mori< _TAlgorithm >:: -GetSignalKernelSize( ) const -{ - return( this->m_PeakDetector.GetKernelSize( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -double fpa::Base::Mori< _TAlgorithm >:: -GetSignalThreshold( ) const -{ - return( this->m_PeakDetector.GetThreshold( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -double fpa::Base::Mori< _TAlgorithm >:: -GetSignalInfluence( ) const -{ - return( this->m_PeakDetector.GetInfluence( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -SetSignalKernelSize( unsigned long k ) -{ - this->m_PeakDetector.SetKernelSize( k ); - this->Modified( ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -SetSignalThreshold( double t ) -{ - this->m_PeakDetector.SetThreshold( t ); - this->Modified( ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -SetSignalInfluence( double i ) -{ - this->m_PeakDetector.SetInfluence( i ); - this->Modified( ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -ClearThresholds( ) -{ - this->m_Thresholds.clear( ); - this->Modified( ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -AddThreshold( const TInputValue& thr ) -{ - if( this->m_Thresholds.insert( thr ).second ) - this->Modified( ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -SetThresholds( - const TInputValue& init, - const TInputValue& end, - const TInputValue& delta - ) -{ - for( TInputValue thr = init; thr <= end; thr += delta ) - this->AddThreshold( thr ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -const typename fpa::Base::Mori< _TAlgorithm >:: -TThresholds& fpa::Base::Mori< _TAlgorithm >:: -GetThresholds( ) const -{ - return( this->m_Thresholds ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -unsigned long fpa::Base::Mori< _TAlgorithm >:: -GetNumberOfEvaluatedThresholds( ) const -{ - return( this->m_PeakDetector.GetNumberOfSamples( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -typename fpa::Base::Mori< _TAlgorithm >:: -TInputValue fpa::Base::Mori< _TAlgorithm >:: -GetOptimumThreshold( ) const -{ - TInputValue thr = TInputValue( 0 ); - unsigned long n = this->m_PeakDetector.GetNumberOfSamples( ); - if( n > 1 ) - thr = TInputValue( this->m_PeakDetector.GetXValues( )[ n - 2 ] ); - return( thr ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -GetSignalValues( unsigned long i, double& x, double& y, TPeak& p ) const -{ - if( i < this->m_PeakDetector.GetNumberOfSamples( ) ) - { - x = this->m_PeakDetector.GetXValues( )[ i ]; - y = this->m_PeakDetector.GetYValues( )[ i ]; - p = this->m_PeakDetector.GetPeaks( )[ i ]; - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -fpa::Base::Mori< _TAlgorithm >:: -Mori( ) - : Superclass( ), - m_InsideValue( TOutputValue( 1 ) ) -{ - this->SetInitValue( TOutputValue( 0 ) ); - this->m_Predicate = TPredicate::New( ); - this->m_Predicate->StrictOff( ); - if( std::numeric_limits< TInputValue >::is_integer ) - this->m_MinimumThreshold = std::numeric_limits< TInputValue >::min( ); - else - this->m_MinimumThreshold = -std::numeric_limits< TInputValue >::max( ); - this->m_PeakDetector.SetKernelSize( 20 ); - this->m_PeakDetector.SetThreshold( 500 ); - this->m_PeakDetector.SetInfluence( 0.5 ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -fpa::Base::Mori< _TAlgorithm >:: -~Mori( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -_BeforeGenerateData( ) -{ - this->Superclass::_BeforeGenerateData( ); - - // Prepare queues - this->_QueueClear( ); - this->m_CurrQueue = 0; - - // Prepare iteration over all thresholds - this->m_CurrThr = this->m_Thresholds.begin( ); - this->m_Predicate->SetLower( *( this->m_CurrThr ) ); - this->m_CurrThr++; - this->m_Predicate->SetUpper( *( this->m_CurrThr ) ); - - // Prepare counting signal - this->m_CurrCount = double( 0 ); - this->m_PeakDetector.Clear( ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -_FinishOneLoop( ) -{ - if( this->m_Queues[ this->m_CurrQueue ].size( ) == 0 ) - { - // Update peak detector - TPeak p = this->m_PeakDetector.AddValue( - *this->m_CurrThr, this->m_CurrCount - ); - this->m_CurrThr++; - this->m_CurrQueue = ( this->m_CurrQueue + 1 ) % 2; - if( this->m_CurrThr != this->m_Thresholds.end( ) ) - { - // Update predicate and counting value - this->m_Predicate->SetUpper( *( this->m_CurrThr ) ); - this->m_CurrCount = double( 0 ); - - // Peak detected? -> stop! - if( - p == TPeakDetector::PosPeak && - this->m_MinimumThreshold < *( this->m_CurrThr ) - ) - this->_QueueClear( ); - } - else - this->_QueueClear( ); - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -_ComputeOutputValue( TNode& n ) -{ - // Do nothing!!! -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -_UpdateOutputValue( TNode& n ) -{ - TInputValue value = this->_GetInputValue( n.Vertex ); - bool inside = this->m_Predicate->Evaluate( value ); - if( !inside ) - { - n.Value = this->m_InitValue; - n.FrontId++; - this->m_Queues[ ( this->m_CurrQueue + 1 ) % 2 ].push_back( n ); - n.FrontId = 0; - } - else - { - n.Value = this->m_InsideValue; - this->m_CurrCount += double( 1 ); - - } // fi - this->Superclass::_UpdateOutputValue( n ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -_QueueClear( ) -{ - this->m_Queues[ 0 ].clear( ); - this->m_Queues[ 1 ].clear( ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -typename fpa::Base::Mori< _TAlgorithm >:: -TNode fpa::Base::Mori< _TAlgorithm >:: -_QueuePop( ) -{ - TNode n = this->m_Queues[ this->m_CurrQueue ].front( ); - this->m_Queues[ this->m_CurrQueue ].pop_front( ); - return( n ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -_QueuePush( const TNode& node ) -{ - this->m_Queues[ this->m_CurrQueue ].push_back( node ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -unsigned long fpa::Base::Mori< _TAlgorithm >:: -_QueueSize( ) const -{ - return( this->m_Queues[ this->m_CurrQueue ].size( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::Mori< _TAlgorithm >:: -_PrepareSeeds( TNodes& nodes ) -{ - typename TNodes::iterator nIt = nodes.begin( ); - for( ; nIt != nodes.end( ); ++nIt ) - nIt->Value = this->m_InitValue; -} - -#endif // __fpa__Base__Mori__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/RegionGrow.h b/lib/fpa/Base/RegionGrow.h deleted file mode 100644 index 8d7439f..0000000 --- a/lib/fpa/Base/RegionGrow.h +++ /dev/null @@ -1,98 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__RegionGrow__h__ -#define __fpa__Base__RegionGrow__h__ - -#include - -#include -#include - -namespace fpa -{ - namespace Base - { - /** - */ - template< class _TAlgorithm > - class RegionGrow - : public _TAlgorithm - { - public: - typedef RegionGrow Self; - typedef _TAlgorithm Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef typename _TAlgorithm::TNode TNode; - typedef typename _TAlgorithm::TNodes TNodes; - typedef typename _TAlgorithm::TInputValue TInputValue; - typedef typename _TAlgorithm::TOutputValue TOutputValue; - typedef typename _TAlgorithm::TFrontId TFrontId; - typedef typename _TAlgorithm::TVertex TVertex; - - typedef std::deque< TNode > TQueue; - typedef itk::FunctionBase< TInputValue, bool > TValuePredicate; - typedef itk::FunctionBase< TVertex, bool > TVertexPredicate; - - public: - itkConceptMacro( - Check_TOutputValue, - ( itk::Concept::IsUnsignedInteger< TOutputValue > ) - ); - - public: - itkGetObjectMacro( ValuePredicate, TValuePredicate ); - itkGetObjectMacro( VertexPredicate, TVertexPredicate ); - itkGetConstMacro( InsideValue, TOutputValue ); - - itkSetMacro( InsideValue, TOutputValue ); - - public: - virtual itk::ModifiedTimeType GetMTime( ) const override; - virtual TOutputValue GetOutsideValue( ) const; - virtual void SetOutsideValue( const TOutputValue& v ); - - void SetPredicate( TValuePredicate* p ); - void SetPredicate( TVertexPredicate* p ); - - protected: - RegionGrow( ); - virtual ~RegionGrow( ); - - virtual void _ComputeOutputValue( TNode& n ) override; - virtual void _UpdateOutputValue( TNode& n ) override; - virtual void _QueueClear( ) override; - virtual TNode _QueuePop( ) override; - virtual void _QueuePush( const TNode& node ) override; - virtual unsigned long _QueueSize( ) const override; - virtual void _PrepareSeeds( TNodes& nodes ) override; - - private: - // Purposely not implemented. - RegionGrow( const Self& other ); - Self& operator=( const Self& other ); - - protected: - typename TValuePredicate::Pointer m_ValuePredicate; - typename TVertexPredicate::Pointer m_VertexPredicate; - - TOutputValue m_InsideValue; - - TQueue m_Queue; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Base__RegionGrow__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/RegionGrow.hxx b/lib/fpa/Base/RegionGrow.hxx deleted file mode 100644 index bf0a862..0000000 --- a/lib/fpa/Base/RegionGrow.hxx +++ /dev/null @@ -1,167 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__RegionGrow__hxx__ -#define __fpa__Base__RegionGrow__hxx__ - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -itk::ModifiedTimeType fpa::Base::RegionGrow< _TAlgorithm >:: -GetMTime( ) const -{ - itk::ModifiedTimeType t = this->Superclass::GetMTime( ); - if( this->m_ValuePredicate.IsNotNull( ) ) - { - itk::ModifiedTimeType q = this->m_ValuePredicate->GetMTime( ); - t = ( q < t )? q: t; - - } // fi - if( this->m_VertexPredicate.IsNotNull( ) ) - { - itk::ModifiedTimeType q = this->m_VertexPredicate->GetMTime( ); - t = ( q < t )? q: t; - - } // fi - - return( t ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -typename fpa::Base::RegionGrow< _TAlgorithm >:: -TOutputValue fpa::Base::RegionGrow< _TAlgorithm >:: -GetOutsideValue( ) const -{ - return( this->GetInitValue( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::RegionGrow< _TAlgorithm >:: -SetOutsideValue( const TOutputValue& v ) -{ - this->SetInitValue( v ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::RegionGrow< _TAlgorithm >:: -SetPredicate( TValuePredicate* p ) -{ - if( this->m_ValuePredicate.GetPointer( ) != p ) - { - this->m_ValuePredicate = p; - this->Modified( ); - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::RegionGrow< _TAlgorithm >:: -SetPredicate( TVertexPredicate* p ) -{ - if( this->m_VertexPredicate.GetPointer( ) != p ) - { - this->m_VertexPredicate = p; - this->Modified( ); - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -fpa::Base::RegionGrow< _TAlgorithm >:: -RegionGrow( ) - : Superclass( ), - m_InsideValue( TOutputValue( 1 ) ) -{ - this->SetInitValue( TOutputValue( 0 ) ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -fpa::Base::RegionGrow< _TAlgorithm >:: -~RegionGrow( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::RegionGrow< _TAlgorithm >:: -_ComputeOutputValue( TNode& n ) -{ - // Do nothing!!! -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::RegionGrow< _TAlgorithm >:: -_UpdateOutputValue( TNode& n ) -{ - TInputValue value = this->_GetInputValue( n.Vertex ); - bool inside = false; - if( this->m_ValuePredicate.IsNotNull( ) ) - inside = this->m_ValuePredicate->Evaluate( value ); - if( this->m_VertexPredicate.IsNotNull( ) ) - inside &= this->m_VertexPredicate->Evaluate( n.Vertex ); - if( !inside ) - { - n.Value = this->m_InitValue; - n.FrontId = 0; - } - else - n.Value = this->m_InsideValue; - this->Superclass::_UpdateOutputValue( n ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::RegionGrow< _TAlgorithm >:: -_QueueClear( ) -{ - this->m_Queue.clear( ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -typename fpa::Base::RegionGrow< _TAlgorithm >:: -TNode fpa::Base::RegionGrow< _TAlgorithm >:: -_QueuePop( ) -{ - TNode n = this->m_Queue.front( ); - this->m_Queue.pop_front( ); - return( n ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::RegionGrow< _TAlgorithm >:: -_QueuePush( const TNode& node ) -{ - this->m_Queue.push_back( node ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -unsigned long fpa::Base::RegionGrow< _TAlgorithm >:: -_QueueSize( ) const -{ - return( this->m_Queue.size( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TAlgorithm > -void fpa::Base::RegionGrow< _TAlgorithm >:: -_PrepareSeeds( TNodes& nodes ) -{ - typename TNodes::iterator nIt = nodes.begin( ); - for( ; nIt != nodes.end( ); ++nIt ) - nIt->Value = this->m_InitValue; -} - -#endif // __fpa__Base__RegionGrow__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/SeedsInterface.h b/lib/fpa/Base/SeedsInterface.h deleted file mode 100644 index 61860cc..0000000 --- a/lib/fpa/Base/SeedsInterface.h +++ /dev/null @@ -1,103 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__SeedsInterface__h__ -#define __fpa__Base__SeedsInterface__h__ - -#include -#include -#include - -#include -#include - -namespace fpa -{ - namespace Base - { - /** - */ - template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare = std::greater< _TVertex > > - class SeedsInterface - { - public: - itkConceptMacro( - Check_TFrontId, - ( itk::Concept::IsUnsignedInteger< _TFrontId > ) - ); - - public: - typedef _TVertex TVertex; - typedef _TPoint TPoint; - typedef _TInputValue TInputValue; - typedef _TOutputValue TOutputValue; - typedef _TFrontId TFrontId; - typedef _TCompare TCompare; - typedef SeedsInterface Self; - - struct TSeed - { - TVertex Vertex; - TPoint Point; - bool IsPoint; - bool IsUnified; - TFrontId FrontId; - TSeed( ) - : IsUnified( false ), - FrontId( TFrontId( 0 ) ) - { } - }; - typedef std::vector< TSeed > TSeeds; - - struct TNode - { - TVertex Vertex; - TVertex Parent; - TFrontId FrontId; - - // Hack to hide the fact that seed values need to be initialized - mutable TOutputValue Value; - }; - struct TNodeCompare - { - bool operator()( const TNode& a, const TNode& b ) const - { - TCompare cmp; - return( cmp( a.Vertex, b.Vertex ) ); - } - }; - typedef std::set< TNode, TNodeCompare > TNodes; - - public: - TSeeds& GetSeeds( ); - const TSeeds& GetSeeds( ) const; - - virtual void AddSeed( const TVertex& seed ); - virtual void AddSeed( const TPoint& seed ); - virtual void ClearSeeds( ); - - protected: - SeedsInterface( itk::ProcessObject* filter ); - virtual ~SeedsInterface( ); - - virtual TNodes _UnifySeeds( ) = 0; - virtual void _PrepareSeeds( TNodes& nodes ) = 0; - - protected: - TSeeds m_Seeds; - itk::ProcessObject* m_Filter; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Base__SeedsInterface__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/SeedsInterface.hxx b/lib/fpa/Base/SeedsInterface.hxx deleted file mode 100644 index 5bfd16a..0000000 --- a/lib/fpa/Base/SeedsInterface.hxx +++ /dev/null @@ -1,92 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__SeedsInterface__hxx__ -#define __fpa__Base__SeedsInterface__hxx__ - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -typename -fpa::Base::SeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -TSeeds& -fpa::Base::SeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -GetSeeds( ) -{ - return( this->m_Seeds ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -const typename -fpa::Base::SeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -TSeeds& -fpa::Base::SeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -GetSeeds( ) const -{ - return( this->m_Seeds ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -void -fpa::Base::SeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -AddSeed( const TVertex& seed ) -{ - TSeed s; - s.Vertex = seed; - s.IsPoint = false; - this->m_Seeds.push_back( s ); - if( this->m_Filter != NULL ) - this->m_Filter->Modified( ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -void -fpa::Base::SeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -AddSeed( const TPoint& seed ) -{ - TSeed s; - s.Point = seed; - s.IsPoint = true; - this->m_Seeds.push_back( s ); - if( this->m_Filter != NULL ) - this->m_Filter->Modified( ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -void -fpa::Base::SeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -ClearSeeds( ) -{ - if( this->m_Seeds.size( ) > 0 ) - { - this->m_Seeds.clear( ); - if( this->m_Filter != NULL ) - this->m_Filter->Modified( ); - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -fpa::Base::SeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -SeedsInterface( itk::ProcessObject* filter ) - : m_Filter( filter ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -fpa::Base::SeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -~SeedsInterface( ) -{ - this->m_Seeds.clear( ); -} - -#endif // __fpa__Base__SeedsInterface__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/SingleSeedInterface.h b/lib/fpa/Base/SingleSeedInterface.h deleted file mode 100644 index 0b2147b..0000000 --- a/lib/fpa/Base/SingleSeedInterface.h +++ /dev/null @@ -1,102 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__SingleSeedInterface__h__ -#define __fpa__Base__SingleSeedInterface__h__ - -#include -#include -#include - -#include -#include - -namespace fpa -{ - namespace Base - { - /** - */ - template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare = std::greater< _TVertex > > - class SingleSeedInterface - { - public: - itkConceptMacro( - Check_TFrontId, - ( itk::Concept::IsUnsignedInteger< _TFrontId > ) - ); - - public: - typedef _TVertex TVertex; - typedef _TPoint TPoint; - typedef _TInputValue TInputValue; - typedef _TOutputValue TOutputValue; - typedef _TFrontId TFrontId; - typedef _TCompare TCompare; - typedef SingleSeedInterface Self; - - struct TSeed - { - TVertex Vertex; - TPoint Point; - bool IsPoint; - bool IsUnified; - TFrontId FrontId; - TSeed( ) - : IsUnified( false ), - FrontId( TFrontId( 0 ) ) - { } - }; - typedef std::vector< TSeed > TSeeds; - - struct TNode - { - TVertex Vertex; - TVertex Parent; - TFrontId FrontId; - - // Hack to hide the fact that seed values need to be initialized - mutable TOutputValue Value; - }; - struct TNodeCompare - { - bool operator()( const TNode& a, const TNode& b ) const - { - TCompare cmp; - return( cmp( a.Vertex, b.Vertex ) ); - } - }; - typedef std::set< TNode, TNodeCompare > TNodes; - - public: - TSeeds& GetSeeds( ); - const TSeeds& GetSeeds( ) const; - - virtual void SetSeed( const TVertex& seed ); - virtual void SetSeed( const TPoint& seed ); - - protected: - SingleSeedInterface( itk::ProcessObject* filter ); - virtual ~SingleSeedInterface( ); - - virtual TNodes _UnifySeeds( ) = 0; - virtual void _PrepareSeeds( TNodes& nodes ) = 0; - - protected: - TSeeds m_Seeds; - itk::ProcessObject* m_Filter; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Base__SingleSeedInterface__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Base/SingleSeedInterface.hxx b/lib/fpa/Base/SingleSeedInterface.hxx deleted file mode 100644 index c669618..0000000 --- a/lib/fpa/Base/SingleSeedInterface.hxx +++ /dev/null @@ -1,78 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Base__SingleSeedInterface__hxx__ -#define __fpa__Base__SingleSeedInterface__hxx__ - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -typename -fpa::Base::SingleSeedInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -TSeeds& -fpa::Base::SingleSeedInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -GetSeeds( ) -{ - return( this->m_Seeds ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -const typename -fpa::Base::SingleSeedInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -TSeeds& -fpa::Base::SingleSeedInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -GetSeeds( ) const -{ - return( this->m_Seeds ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -void -fpa::Base::SingleSeedInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -SetSeed( const TVertex& seed ) -{ - TSeed s; - s.Vertex = seed; - s.IsPoint = false; - this->m_Seeds[ 0 ] = s; - if( this->m_Filter != NULL ) - this->m_Filter->Modified( ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -void -fpa::Base::SingleSeedInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -SetSeed( const TPoint& seed ) -{ - TSeed s; - s.Point = seed; - s.IsPoint = true; - this->m_Seeds[ 0 ] = s; - if( this->m_Filter != NULL ) - this->m_Filter->Modified( ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -fpa::Base::SingleSeedInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -SingleSeedInterface( itk::ProcessObject* filter ) - : m_Filter( filter ) -{ - this->m_Seeds = TSeeds( 1 ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -fpa::Base::SingleSeedInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -~SingleSeedInterface( ) -{ - this->m_Seeds.clear( ); -} - -#endif // __fpa__Base__SingleSeedInterface__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/CMakeLists.txt b/lib/fpa/CMakeLists.txt deleted file mode 100644 index e57fdbd..0000000 --- a/lib/fpa/CMakeLists.txt +++ /dev/null @@ -1,78 +0,0 @@ - -## ===================== -## == Get source code == -## ===================== - -configure_file(Version.cxx.in "${CMAKE_CURRENT_BINARY_DIR}/Version.cxx" @ONLY) -configure_file(Config.h.in "${CMAKE_CURRENT_BINARY_DIR}/Config.h" @ONLY) -file(GLOB_RECURSE _base_src "${CMAKE_CURRENT_SOURCE_DIR}/Base/*.cxx") -file(GLOB_RECURSE _base_hdr "${CMAKE_CURRENT_SOURCE_DIR}/Base/*.h") -file(GLOB_RECURSE _base_hrc "${CMAKE_CURRENT_SOURCE_DIR}/Base/*.hxx") -file(GLOB_RECURSE _image_src "${CMAKE_CURRENT_SOURCE_DIR}/Image/*.cxx") -file(GLOB_RECURSE _image_hdr "${CMAKE_CURRENT_SOURCE_DIR}/Image/*.h") -file(GLOB_RECURSE _image_hrc "${CMAKE_CURRENT_SOURCE_DIR}/Image/*.hxx") - -file(GLOB_RECURSE _generic_src "${CMAKE_CURRENT_SOURCE_DIR}/Generic/*.cxx") -file(GLOB_RECURSE _generic_hdr "${CMAKE_CURRENT_SOURCE_DIR}/Generic/*.h") -file(GLOB_RECURSE _generic_hrc "${CMAKE_CURRENT_SOURCE_DIR}/Generic/*.hxx") - - -set(_src - ${_base_src} ${_image_src} ${_generic_src} - "${CMAKE_CURRENT_BINARY_DIR}/Version.cxx" - ) -set( - _hdr - ${_base_hdr} ${_image_hdr} ${_generic_hdr} - "${CMAKE_CURRENT_BINARY_DIR}/Config.h" - ) -set(_hrc ${_base_hrc} ${_image_hrc} ${_generic_hrc}) - -## ===================== -## == Compile library == -## ===================== - -add_library(fpa SHARED ${_src} ${_hdr} ${_hrc}) -generate_export_header(fpa) -set_property(TARGET fpa PROPERTY VERSION ${prj_VERSION}) -set_property(TARGET fpa PROPERTY SOVERSION ${prj_SHORT_VERSION}) -set_property( - TARGET fpa PROPERTY INTERFACE_fpa_MAJOR_VERSION ${prj_MAJ_VERSION} - ) -set_property( - TARGET fpa APPEND PROPERTY COMPATIBLE_INTERFACE_STRING ${prj_MAJ_VERSION} - ) -target_link_libraries(fpa PUBLIC ${VTK_LIBRARIES} ${ITK_LIBRARIES}) - -## ======================== -## == Installation rules == -## ======================== - -install( - TARGETS fpa - EXPORT "${targets_export_name}" - LIBRARY DESTINATION "lib" - ARCHIVE DESTINATION "lib" - RUNTIME DESTINATION "bin" - INCLUDES DESTINATION "${include_install_dir}" - ) -install( - DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}" - DESTINATION "${include_install_dir}" - FILES_MATCHING PATTERN "*.h" - ) -install( - DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}" - DESTINATION "${include_install_dir}" - FILES_MATCHING PATTERN "*.hxx" - ) -install( - FILES "${CMAKE_CURRENT_BINARY_DIR}/fpa_export.h" - DESTINATION "${include_install_dir}/fpa" - ) -install( - FILES "${CMAKE_CURRENT_BINARY_DIR}/Config.h" - DESTINATION "${include_install_dir}/fpa" - ) - -## eof - $RCSfile$ diff --git a/lib/fpa/Config.h.in b/lib/fpa/Config.h.in deleted file mode 100644 index 708dec1..0000000 --- a/lib/fpa/Config.h.in +++ /dev/null @@ -1,25 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Config__h__ -#define __fpa__Config__h__ - -#define VTK_FOUND @VTK_FOUND@ -#if VTK_FOUND == 1 -# define USE_VTK -#else -# undef USE_VTK -#endif - -#define ivq_FOUND @ivq_FOUND@ -#if ivq_FOUND == 1 -# define USE_ivq -#else -# undef USE_ivq -#endif - -#endif // __fpa__Config__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/Algorithm.h b/lib/fpa/Image/Algorithm.h deleted file mode 100644 index 1c84a72..0000000 --- a/lib/fpa/Image/Algorithm.h +++ /dev/null @@ -1,110 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__Algorithm__h__ -#define __fpa__Image__Algorithm__h__ - -#include -#include - -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TTraits > - class Algorithm - : public fpa::Base::Algorithm< _TTraits > - { - public: - typedef _TTraits TTraits; - typedef fpa::Base::Algorithm< _TTraits > Superclass; - typedef Algorithm Self; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef typename TTraits::TFrontId TFrontId; - typedef typename TTraits::TInputImage TInputImage; - typedef typename TTraits::TInputValue TInputValue; - typedef typename TTraits::TNeighborhood TNeighborhood; - typedef typename TTraits::TNode TNode; - typedef typename TTraits::TNodes TNodes; - typedef typename TTraits::TOutputImage TOutputImage; - typedef typename TTraits::TOutputValue TOutputValue; - typedef typename TTraits::TSeeds TSeeds; - typedef typename TTraits::TVertex TVertex; - - typedef itk::Image< TFrontId, TTraits::Dimension > TMarks; - - /* TODO - typedef _TMarksInterface TMarksInterface; - typedef _TSeedsInterface TSeedsInterface; - - typedef typename TSeedsInterface::TTraits TTraits; - typedef typename TTraits::TInputImage TInputImage; - typedef typename TTraits::TOutputImage TOutputImage; - typedef typename TTraits::TInputValue TInputValue; - typedef typename TTraits::TOutputValue TOutputValue; - typedef typename TTraits::TFrontId TFrontId; - typedef typename TTraits::TNeighborhood TNeighborhood; - typedef typename TTraits::TNode TNode; - typedef typename TTraits::TNodes TNodes; - typedef typename TTraits::TSeeds TSeeds; - typedef typename TTraits::TVertex TVertex; - typedef typename TTraits::TPoint TPoint; - - typedef itk::ImageToImageFilter< TInputImage, TOutputImage > TFilter; - typedef fpa::Base::Algorithm< TFilter, TMarksInterface, TSeedsInterface > Superclass; - typedef Algorithm Self; - */ - - public: - itkTypeMacro( fpa::Image::Algorithm, fpa::Base::Algorithm ); - - itkGetConstMacro( NeigborhoodOrder, unsigned int ); - itkSetMacro( NeigborhoodOrder, unsigned int ); - - public: - TMarks* GetMarks( ); - const TMarks* GetMarks( ) const; - - protected: - Algorithm( ); - virtual ~Algorithm( ); - - virtual TNodes _UnifySeeds( ) override; - virtual void _ConfigureOutput( const TOutputValue& v ) override; - virtual TNeighborhood _GetNeighbors( const TVertex& v ) const override; - virtual TInputValue _GetInputValue( const TVertex& v ) const override; - virtual TOutputValue _GetOutputValue( const TVertex& v ) const override; - virtual void _UpdateOutputValue( TNode& n ) override; - virtual bool _IsMarked( const TVertex& v ) const override; - virtual unsigned long _GetMark( const TVertex& v ) const override; - virtual void _Mark( const TVertex& v, unsigned long frontId ) override; - - private: - // Purposely not implemented. - Algorithm( const Self& other ); - Self& operator=( const Self& other ); - - protected: - unsigned long m_MarksIdx; - unsigned int m_NeigborhoodOrder; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__Algorithm__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/Algorithm.hxx b/lib/fpa/Image/Algorithm.hxx deleted file mode 100644 index 43ebeb0..0000000 --- a/lib/fpa/Image/Algorithm.hxx +++ /dev/null @@ -1,204 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__Algorithm__hxx__ -#define __fpa__Image__Algorithm__hxx__ - -// ------------------------------------------------------------------------- -template< class _TTraits > -typename fpa::Image::Algorithm< _TTraits >::TMarks* -fpa::Image::Algorithm< _TTraits >:: -GetMarks( ) -{ - return( - dynamic_cast< TMarks* >( - this->itk::ProcessObject::GetOutput( this->m_MarksIdx ) - ) - ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -const typename fpa::Image::Algorithm< _TTraits >::TMarks* -fpa::Image::Algorithm< _TTraits >:: -GetMarks( ) const -{ - return( - dynamic_cast< const TMarks* >( - this->itk::ProcessObject::GetOutput( this->m_MarksIdx ) - ) - ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -fpa::Image::Algorithm< _TTraits >:: -Algorithm( ) - : Superclass( ), - m_NeigborhoodOrder( 1 ) -{ - this->m_MarksIdx = this->GetNumberOfRequiredOutputs( ); - this->itk::ProcessObject::SetNumberOfRequiredOutputs( this->m_MarksIdx + 1 ); - this->SetNthOutput( this->m_MarksIdx, TMarks::New( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -fpa::Image::Algorithm< _TTraits >:: -~Algorithm( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -typename fpa::Image::Algorithm< _TTraits >::TNodes -fpa::Image::Algorithm< _TTraits >:: -_UnifySeeds( ) -{ - const TInputImage* input = this->GetInput( ); - typename TInputImage::RegionType region = input->GetRequestedRegion( ); - TSeeds& seeds = this->GetSeeds( ); - TNodes nodes; - - typename TSeeds::iterator sIt = seeds.begin( ); - for( ; sIt != seeds.end( ); ++sIt ) - { - TNode node; - if( sIt->IsPoint ) - input->TransformPhysicalPointToIndex( sIt->Point, sIt->Vertex ); - else - input->TransformIndexToPhysicalPoint( sIt->Vertex, sIt->Point ); - if( region.IsInside( sIt->Vertex ) ) - { - sIt->IsUnified = true; - node.Vertex = sIt->Vertex; - node.Parent = node.Vertex; - if( sIt->FrontId == 0 ) - node.FrontId = nodes.size( ) + 1; - else - node.FrontId = sIt->FrontId; - nodes.insert( node ); - } - else - sIt->IsUnified = false; - - } // rof - - return( nodes ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -void fpa::Image::Algorithm< _TTraits >:: -_ConfigureOutput( const TOutputValue& v ) -{ - const TInputImage* in = this->GetInput( ); - - TOutputImage* out = this->GetOutput( ); - out->SetLargestPossibleRegion( in->GetLargestPossibleRegion( ) ); - out->SetRequestedRegion( in->GetRequestedRegion( ) ); - out->SetBufferedRegion( in->GetBufferedRegion( ) ); - out->SetSpacing( in->GetSpacing( ) ); - out->SetOrigin( in->GetOrigin( ) ); - out->SetDirection( in->GetDirection( ) ); - out->Allocate( ); - out->FillBuffer( v ); - - TMarks* marks = this->GetMarks( ); - marks->SetLargestPossibleRegion( in->GetLargestPossibleRegion( ) ); - marks->SetRequestedRegion( in->GetRequestedRegion( ) ); - marks->SetBufferedRegion( in->GetBufferedRegion( ) ); - marks->SetSpacing( in->GetSpacing( ) ); - marks->SetOrigin( in->GetOrigin( ) ); - marks->SetDirection( in->GetDirection( ) ); - marks->Allocate( ); - marks->FillBuffer( TFrontId( 0 ) ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -typename fpa::Image::Algorithm< _TTraits >::TNeighborhood -fpa::Image::Algorithm< _TTraits >:: -_GetNeighbors( const TVertex& v ) const -{ - typename TInputImage::RegionType region = - this->GetInput( )->GetRequestedRegion( ); - TNeighborhood neighborhood; - if( this->m_NeigborhoodOrder != 1 ) - { - // TODO - } - else - { - for( unsigned int d = 0; d < TInputImage::ImageDimension; ++d ) - { - for( int s = -1; s <= 1; s += 2 ) - { - TVertex n = v; - n[ d ] += s; - if( region.IsInside( n ) ) - neighborhood.push_back( n ); - - } // rof - - } // rof - - } // fi - return( neighborhood ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -typename fpa::Image::Algorithm< _TTraits >::TInputValue -fpa::Image::Algorithm< _TTraits >:: -_GetInputValue( const TVertex& v ) const -{ - return( this->GetInput( )->GetPixel( v ) ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -typename fpa::Image::Algorithm< _TTraits >::TOutputValue -fpa::Image::Algorithm< _TTraits >:: -_GetOutputValue( const TVertex& v ) const -{ - return( this->GetOutput( )->GetPixel( v ) ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -void fpa::Image::Algorithm< _TTraits >:: -_UpdateOutputValue( TNode& n ) -{ - this->GetOutput( )->SetPixel( n.Vertex, n.Value ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -bool fpa::Image::Algorithm< _TTraits >:: -_IsMarked( const TVertex& v ) const -{ - return( this->GetMarks( )->GetPixel( v ) > 0 ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -unsigned long fpa::Image::Algorithm< _TTraits >:: -_GetMark( const TVertex& v ) const -{ - return( ( unsigned long )( this->GetMarks( )->GetPixel( v ) ) ); -} - -// ------------------------------------------------------------------------- -template< class _TTraits > -void fpa::Image::Algorithm< _TTraits >:: -_Mark( const TVertex& v, unsigned long frontId ) -{ - this->GetMarks( )->SetPixel( v, TFrontId( frontId ) ); -} - -#endif // __fpa__Image__Algorithm__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/DefaultTraits.h b/lib/fpa/Image/DefaultTraits.h deleted file mode 100644 index c2b8295..0000000 --- a/lib/fpa/Image/DefaultTraits.h +++ /dev/null @@ -1,69 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__DefaultTraits__h__ -#define __fpa__Image__DefaultTraits__h__ - -#include -#include -#include - -#include -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TInputImage, class _TOutputImage, class _TFrontId > - class DefaultTraits - { - public: - typedef DefaultTraits Self; - typedef _TInputImage TInputImage; - typedef _TOutputImage TOutputImage; - typedef _TFrontId TFrontId; - itkStaticConstMacro( Dimension, unsigned int, TInputImage::ImageDimension ); - - typedef typename TInputImage::IndexType TVertex; - typedef typename TInputImage::PixelType TInputValue; - typedef typename TInputImage::PointType TPoint; - typedef typename TOutputImage::PixelType TOutputValue; - typedef typename TVertex::LexicographicCompare TCompare; - - typedef std::vector< TVertex > TNeighborhood; - - typedef fpa::Base::SeedsInterface< TVertex, TPoint, TInputValue, TOutputValue, TFrontId, TCompare > TSeedsInterface; - typedef fpa::Base::MarksInterfaceWithCollisions< TVertex > TMarksInterface; - typedef itk::ImageToImageFilter< TInputImage, TOutputImage > TFilter; - - typedef typename TSeedsInterface::TNode TNode; - typedef typename TSeedsInterface::TNodes TNodes; - typedef typename TSeedsInterface::TSeed TSeed; - typedef typename TSeedsInterface::TSeeds TSeeds; - - public: - itkConceptMacro( - Check_SameDimension, - ( itk::Concept::SameDimension< TInputImage::ImageDimension, TOutputImage::ImageDimension > ) - ); - - private: - // Purposely not implemented. - DefaultTraits( ); - DefaultTraits( const Self& other ); - virtual ~DefaultTraits( ); - Self& operator=( const Self& other ); - }; - - } // ecapseman - -} // ecapseman - -#endif // __fpa__Image__DefaultTraits__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/Dijkstra.h b/lib/fpa/Image/Dijkstra.h deleted file mode 100644 index 24c0643..0000000 --- a/lib/fpa/Image/Dijkstra.h +++ /dev/null @@ -1,70 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__Dijkstra__h__ -#define __fpa__Image__Dijkstra__h__ - -#include -#include -#include -#include -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TInputImage, class _TOutputImage, class _TFrontId = unsigned char > - class Dijkstra - : public fpa::Base::Dijkstra< fpa::Image::Algorithm< fpa::Image::DefaultTraits< _TInputImage, _TOutputImage, _TFrontId > >, fpa::Image::MinimumSpanningTree< _TInputImage::ImageDimension > > - { - public: - typedef _TInputImage TInputImage; - typedef _TOutputImage TOutputImage; - typedef _TFrontId TFrontId; - typedef fpa::Image::MinimumSpanningTree< _TInputImage::ImageDimension > TMST; - - typedef fpa::Image::DefaultTraits< TInputImage, TOutputImage, TFrontId > TTraits; - typedef fpa::Image::Algorithm< TTraits > TAlgorithm; - typedef fpa::Base::Dijkstra< TAlgorithm, TMST > Superclass; - typedef Dijkstra Self; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef typename Superclass::TOutputValue TOutputValue; - typedef typename Superclass::TVertex TVertex; - - typedef fpa::Image::Functors::Dijkstra::Function< TInputImage, TOutputValue > TWeightFunction; - - public: - itkNewMacro( Self ); - itkTypeMacro( fpa::Image::Dijkstra, fpa::Base::Dijkstra ); - - protected: - Dijkstra( ); - virtual ~Dijkstra( ); - - virtual void _BeforeGenerateData( ) override; - virtual void _ConfigureOutput( const TOutputValue& v ) override; - - private: - // Purposely not implemented. - Dijkstra( const Self& other ); - Self& operator=( const Self& other ); - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__Dijkstra__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/Dijkstra.hxx b/lib/fpa/Image/Dijkstra.hxx deleted file mode 100644 index b0780de..0000000 --- a/lib/fpa/Image/Dijkstra.hxx +++ /dev/null @@ -1,60 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__Dijkstra__hxx__ -#define __fpa__Image__Dijkstra__hxx__ - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TOutputImage, class _TFrontId > -fpa::Image::Dijkstra< _TInputImage, _TOutputImage, _TFrontId >:: -Dijkstra( ) - : Superclass( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TOutputImage, class _TFrontId > -fpa::Image::Dijkstra< _TInputImage, _TOutputImage, _TFrontId >:: -~Dijkstra( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TOutputImage, class _TFrontId > -void fpa::Image::Dijkstra< _TInputImage, _TOutputImage, _TFrontId >:: -_BeforeGenerateData( ) -{ - this->Superclass::_BeforeGenerateData( ); - TWeightFunction* wf = - dynamic_cast< TWeightFunction* >( this->GetWeightFunction( ) ); - if( wf != NULL ) - wf->SetImage( this->GetInput( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TOutputImage, class _TFrontId > -void fpa::Image::Dijkstra< _TInputImage, _TOutputImage, _TFrontId >:: -_ConfigureOutput( const TOutputValue& v ) -{ - this->Superclass::_ConfigureOutput( v ); - - const TInputImage* in = this->GetInput( ); - TMST* mst = this->GetMinimumSpanningTree( ); - mst->SetLargestPossibleRegion( in->GetLargestPossibleRegion( ) ); - mst->SetRequestedRegion( in->GetRequestedRegion( ) ); - mst->SetBufferedRegion( in->GetBufferedRegion( ) ); - mst->SetSpacing( in->GetSpacing( ) ); - mst->SetOrigin( in->GetOrigin( ) ); - mst->SetDirection( in->GetDirection( ) ); - mst->Allocate( ); - - typename TVertex::OffsetType o; - o.Fill( 0 ); - mst->FillBuffer( o ); -} - -#endif // __fpa__Image__Dijkstra__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/ExtractAxisFilter.h b/lib/fpa/Image/ExtractAxisFilter.h deleted file mode 100644 index 5c65916..0000000 --- a/lib/fpa/Image/ExtractAxisFilter.h +++ /dev/null @@ -1,105 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__ExtractAxisFilter__h__ -#define __fpa__Image__ExtractAxisFilter__h__ - -#include -#include - -#include -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TInputImage, class _TScalar > - class ExtractAxisFilter - : public itk::ProcessObject - { - public: - typedef ExtractAxisFilter Self; - typedef itk::ProcessObject Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef _TInputImage TInputImage; - typedef _TScalar TScalar; - typedef typename TInputImage::IndexType TIndex; - typedef typename TInputImage::PointType TPoint; - - itkStaticConstMacro( - Dimension, - unsigned int, - TInputImage::ImageDimension - ); - - typedef itk::Image< TScalar, Self::Dimension > TScalarImage; - typedef itk::ImageToImageFilter< TInputImage, TScalarImage > TCenterness; - - typedef fpa::Image::PolyLineParametricPath< Self::Dimension > TPath; - typedef fpa::Image::Dijkstra< TScalarImage, TScalarImage > TDijkstra; - - public: - itkNewMacro( Self ); - itkTypeMacro( fpa::Image::ExtractAxisFilter, fpa::Image::Dijkstra ); - - itkGetConstObjectMacro( Centerness, TCenterness ); - itkGetObjectMacro( Centerness, TCenterness ); - itkSetObjectMacro( Centerness, TCenterness ); - - itkGetConstMacro( StartIndex, TIndex ); - itkSetMacro( StartIndex, TIndex ); - - itkGetConstMacro( EndIndex, TIndex ); - itkSetMacro( EndIndex, TIndex ); - - public: - virtual itk::ModifiedTimeType GetMTime( ) const override; - - virtual void AddSeed( const TIndex& seed ); - virtual void AddSeed( const TPoint& seed ); - virtual void ClearSeeds( ); - - void SetInput( TInputImage* input ); - TInputImage* GetInput( ); - const TInputImage* GetInput( ) const; - - TPath* GetOutput( ); - const TPath* GetOutput( ) const; - - protected: - ExtractAxisFilter( ); - virtual ~ExtractAxisFilter( ); - - virtual void GenerateData( ) override; - - private: - // Purposely not implemented. - ExtractAxisFilter( const Self& other ); - Self& operator=( const Self& other ); - - protected: - typename TCenterness::Pointer m_Centerness; - typename TDijkstra::Pointer m_Dijkstra; - - TIndex m_StartIndex; - TIndex m_EndIndex; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__ExtractAxisFilter__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/ExtractAxisFilter.hxx b/lib/fpa/Image/ExtractAxisFilter.hxx deleted file mode 100644 index 9d14fe4..0000000 --- a/lib/fpa/Image/ExtractAxisFilter.hxx +++ /dev/null @@ -1,152 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__ExtractAxisFilter__hxx__ -#define __fpa__Image__ExtractAxisFilter__hxx__ - -#include -#include - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TScalar > -itk::ModifiedTimeType -fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -GetMTime( ) const -{ - itk::ModifiedTimeType a = this->Superclass::GetMTime( ); - itk::ModifiedTimeType b = this->m_Centerness->GetMTime( ); - itk::ModifiedTimeType c = this->m_Dijkstra->GetMTime( ); - a = ( a < b )? a: b; - return( ( a < c )? a: c ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TScalar > -void fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -AddSeed( const TIndex& seed ) -{ - this->m_Dijkstra->AddSeed( seed ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TScalar > -void fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -AddSeed( const TPoint& seed ) -{ - this->m_Dijkstra->AddSeed( seed ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TScalar > -void fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -ClearSeeds( ) -{ - this->m_Dijkstra->ClearSeeds( ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TScalar > -void fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -SetInput( TInputImage* input ) -{ - this->Superclass::SetNthInput( 0, input ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TScalar > -typename fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -TInputImage* fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -GetInput( ) -{ - return( dynamic_cast< TInputImage* >( this->Superclass::GetInput( 0 ) ) ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TScalar > -const typename fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -TInputImage* fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -GetInput( ) const -{ - return( - dynamic_cast< const TInputImage* >( this->Superclass::GetInput( 0 ) ) - ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TScalar > -typename fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -TPath* fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -GetOutput( ) -{ - return( dynamic_cast< TPath* >( this->Superclass::GetOutput( 0 ) ) ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TScalar > -const typename fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -TPath* fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -GetOutput( ) const -{ - return( dynamic_cast< const TPath* >( this->Superclass::GetOutput( 0 ) ) ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TScalar > -fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -ExtractAxisFilter( ) - : Superclass( ) -{ - // I/O configuration - this->SetNumberOfRequiredInputs( 1 ); - this->SetNumberOfRequiredOutputs( 1 ); - this->SetNthOutput( 0, TPath::New( ) ); - - // Prepare weight function - typedef fpa::Image::Functors::Dijkstra::Invert< TScalarImage, TScalar > _TWeight; - typename _TWeight::Pointer weight = _TWeight::New( ); - weight->SetAlpha( 1 ); - weight->SetBeta( 1 ); - - // Filters - typedef itk::SignedMaurerDistanceMapImageFilter< TInputImage, TScalarImage > _TDefaultCenterness; - typename _TDefaultCenterness::Pointer dc = _TDefaultCenterness::New( ); - dc->InsideIsPositiveOn( ); - dc->SquaredDistanceOn( ); - dc->UseImageSpacingOn( ); - this->m_Centerness = dc; - - // Axis extractor - this->m_Dijkstra = TDijkstra::New( ); - this->m_Dijkstra->SetWeightFunction( weight ); - this->m_Dijkstra->StopAtOneFront( ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TScalar > -fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -~ExtractAxisFilter( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TScalar > -void fpa::Image::ExtractAxisFilter< _TInputImage, _TScalar >:: -GenerateData( ) -{ - // Execute minipipeline - this->m_Centerness->SetInput( this->GetInput( ) ); - this->m_Dijkstra->SetInput( this->m_Centerness->GetOutput( ) ); - this->m_Dijkstra->Update( ); - - // Extract axis - typename TPath::Pointer out = this->GetOutput( ); - this->m_Dijkstra->GetMinimumSpanningTree( )->GetPolyLineParametricPath( - out, this->m_StartIndex, this->m_EndIndex - ); -} - -#endif // __fpa__Image__ExtractAxisFilter__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/Functors/Dijkstra/Function.h b/lib/fpa/Image/Functors/Dijkstra/Function.h deleted file mode 100644 index e9fa0b2..0000000 --- a/lib/fpa/Image/Functors/Dijkstra/Function.h +++ /dev/null @@ -1,69 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__Functors__Dijkstra__Function__h__ -#define __fpa__Image__Functors__Dijkstra__Function__h__ - -#include - -namespace fpa -{ - namespace Image - { - namespace Functors - { - namespace Dijkstra - { - /** - */ - template< class _TInputImage, class _TOutputValue > - class Function - : public fpa::Base::Functors::Dijkstra::Function< typename _TInputImage::IndexType, _TOutputValue > - { - public: - typedef typename _TInputImage::IndexType TVertex; - typedef Function Self; - typedef fpa::Base::Functors::Dijkstra::Function< TVertex, _TOutputValue > Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - public: - itkTypeMacro( - fpa::Image::Functors::Dijkstra::Function, - fpa::Base::Functors::Dijkstra::Function - ); - - itkGetConstObjectMacro( Image, _TInputImage ); - itkSetConstObjectMacro( Image, _TInputImage ); - - protected: - Function( ) - : Superclass( ) - { - } - virtual ~Function( ) - { - } - - private: - // Purposely not implemented - Function( const Self& other ); - Self& operator=( const Self& other ); - - protected: - typename _TInputImage::ConstPointer m_Image; - }; - - } // ecapseman - - } // ecapseman - - } // ecapseman - -} // ecapseman - -#endif // __fpa__Image__Functors__Dijkstra__Function__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/Functors/Dijkstra/Gaussian.h b/lib/fpa/Image/Functors/Dijkstra/Gaussian.h deleted file mode 100644 index d06d84d..0000000 --- a/lib/fpa/Image/Functors/Dijkstra/Gaussian.h +++ /dev/null @@ -1,91 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__Functors__Dijkstra__Gaussian__h__ -#define __fpa__Image__Functors__Dijkstra__Gaussian__h__ - -#include -#include - -namespace fpa -{ - namespace Image - { - namespace Functors - { - namespace Dijkstra - { - /** - * w_{i,j}=\left(\exp\left(\left(\frac{w_{i}-w_{j}}{\beta}\right)^{2}\right)-1\right)^{\alpha} - */ - template< class _TInputImage, class _TOutputValue > - class Gaussian - : public fpa::Image::Functors::Dijkstra::Function< _TInputImage, _TOutputValue > - { - public: - typedef Gaussian Self; - typedef fpa::Image::Functors::Dijkstra::Function< _TInputImage, _TOutputValue > Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef typename Superclass::TVertex TVertex; - - public: - itkNewMacro( Self ); - itkTypeMacro( - fpa::Image::Functors::Dijkstra::Gaussian, - fpa::Image::Functors::Dijkstra::Function - ); - - itkGetConstMacro( Alpha, double ); - itkSetMacro( Alpha, double ); - - itkGetConstMacro( Beta, double ); - itkSetMacro( Beta, double ); - - public: - virtual _TOutputValue Evaluate( - const TVertex& v, const TVertex& p - ) const override - { - double d = double( this->m_Image->GetPixel( v ) ); - d -= double( this->m_Image->GetPixel( p ) ); - d /= this->m_Beta; - d = std::exp( d * d ) - double( 1 ); - return( _TOutputValue( std::pow( d, this->m_Alpha ) ) ); - } - - protected: - Gaussian( ) - : Superclass( ), - m_Alpha( double( 1 ) ), - m_Beta( double( 1 ) ) - { - } - virtual ~Gaussian( ) - { - } - - private: - // Purposely not implemented - Gaussian( const Self& other ); - Self& operator=( const Self& other ); - - protected: - double m_Alpha; - double m_Beta; - }; - - } // ecapseman - - } // ecapseman - - } // ecapseman - -} // ecapseman - -#endif // __fpa__Image__Functors__Dijkstra__Gaussian__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/Functors/Dijkstra/Identity.h b/lib/fpa/Image/Functors/Dijkstra/Identity.h deleted file mode 100644 index 3a0b370..0000000 --- a/lib/fpa/Image/Functors/Dijkstra/Identity.h +++ /dev/null @@ -1,73 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__Functors__Dijkstra__Identity__h__ -#define __fpa__Image__Functors__Dijkstra__Identity__h__ - -#include - -namespace fpa -{ - namespace Image - { - namespace Functors - { - namespace Dijkstra - { - /** - */ - template< class _TInputImage, class _TOutputValue > - class Identity - : public fpa::Image::Functors::Dijkstra::Function< _TInputImage, _TOutputValue > - { - public: - typedef Identity Self; - typedef fpa::Image::Functors::Dijkstra::Function< _TInputImage, _TOutputValue > Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef typename Superclass::TVertex TVertex; - - public: - itkNewMacro( Self ); - itkTypeMacro( - fpa::Image::Functors::Dijkstra::Identity, - fpa::Image::Functors::Dijkstra::Function - ); - - public: - virtual _TOutputValue Evaluate( - const TVertex& v, const TVertex& p - ) const override - { - return( _TOutputValue( this->m_Image->GetPixel( v ) ) ); - } - - protected: - Identity( ) - : Superclass( ) - { - } - virtual ~Identity( ) - { - } - - private: - // Purposely not implemented - Identity( const Self& other ); - Self& operator=( const Self& other ); - }; - - } // ecapseman - - } // ecapseman - - } // ecapseman - -} // ecapseman - -#endif // __fpa__Image__Functors__Dijkstra__Identity__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/Functors/Dijkstra/Invert.h b/lib/fpa/Image/Functors/Dijkstra/Invert.h deleted file mode 100644 index 8341f2e..0000000 --- a/lib/fpa/Image/Functors/Dijkstra/Invert.h +++ /dev/null @@ -1,94 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__Functors__Dijkstra__Invert__h__ -#define __fpa__Image__Functors__Dijkstra__Invert__h__ - -#include -#include - -namespace fpa -{ - namespace Image - { - namespace Functors - { - namespace Dijkstra - { - /** - */ - template< class _TInputImage, class _TOutputValue > - class Invert - : public fpa::Image::Functors::Dijkstra::Function< _TInputImage, _TOutputValue > - { - public: - typedef Invert Self; - typedef fpa::Image::Functors::Dijkstra::Function< _TInputImage, _TOutputValue > Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef typename Superclass::TVertex TVertex; - - public: - itkNewMacro( Self ); - itkTypeMacro( - fpa::Image::Functors::Dijkstra::Invert, - fpa::Image::Functors::Dijkstra::Function - ); - - itkGetConstMacro( Alpha, double ); - itkGetConstMacro( Beta, double ); - - itkSetMacro( Alpha, double ); - itkSetMacro( Beta, double ); - - public: - virtual _TOutputValue Evaluate( - const TVertex& v, const TVertex& p - ) const override - { - double a = double( this->m_Image->GetPixel( v ) ); - double d = this->m_Alpha; - d += std::pow( double( a ), this->m_Beta ); - double x = -1; - if( std::fabs( d ) > double( 0 ) ) - x = - double( 1 ) / - ( this->m_Alpha + std::pow( double( a ), this->m_Beta ) ); - return( _TOutputValue( x ) ); - } - - protected: - Invert( ) - : Superclass( ), - m_Alpha( double( 1 ) ), - m_Beta( double( 1 ) ) - { - } - virtual ~Invert( ) - { - } - - private: - // Purposely not implemented - Invert( const Self& other ); - Self& operator=( const Self& other ); - - protected: - double m_Alpha; - double m_Beta; - }; - - } // ecapseman - - } // ecapseman - - } // ecapseman - -} // ecapseman - -#endif // __fpa__Image__Functors__Dijkstra__Invert__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/LabelledSeedsInterface.h b/lib/fpa/Image/LabelledSeedsInterface.h deleted file mode 100644 index 74ec756..0000000 --- a/lib/fpa/Image/LabelledSeedsInterface.h +++ /dev/null @@ -1,64 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__LabelledSeedsInterface__h__ -#define __fpa__Image__LabelledSeedsInterface__h__ - -#include - -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare = std::greater< _TVertex > > - class LabelledSeedsInterface - : public fpa::Base::SeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare > - { - public: - typedef _TVertex TVertex; - typedef _TPoint TPoint; - typedef _TInputValue TInputValue; - typedef _TOutputValue TOutputValue; - typedef _TFrontId TFrontId; - typedef _TCompare TCompare; - typedef LabelledSeedsInterface Self; - typedef fpa::Base::SeedsInterface< TVertex, TPoint, TInputValue, TOutputValue, TFrontId, TCompare > Superclass; - - typedef typename Superclass::TNode TNode; - typedef typename Superclass::TNodeCompare TNodeCompare; - typedef typename Superclass::TSeeds TSeeds; - - typedef itk::Image< TFrontId, TVertex::Dimension > TLabelImage; - - public: - virtual void AddSeed( const TVertex& seed ) override; - virtual void AddSeed( const TPoint& seed ) override; - - const TLabelImage* GetLabels( ) const; - void SetLabels( const TLabelImage* image ); - - protected: - LabelledSeedsInterface( itk::ProcessObject* filter ); - virtual ~LabelledSeedsInterface( ); - - protected: - typename TLabelImage::ConstPointer m_LabelImage; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__LabelledSeedsInterface__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/LabelledSeedsInterface.hxx b/lib/fpa/Image/LabelledSeedsInterface.hxx deleted file mode 100644 index 98cc334..0000000 --- a/lib/fpa/Image/LabelledSeedsInterface.hxx +++ /dev/null @@ -1,80 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__LabelledSeedsInterface__hxx__ -#define __fpa__Image__LabelledSeedsInterface__hxx__ - -#include -#include - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -void -fpa::Image::LabelledSeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -AddSeed( const TVertex& seed ) -{ - std::ostringstream msg; - msg << "itk::ERROR: fpa::Image::LabelledSeedsInterface (" << this - << "): \"AddSeed( const TVertex& seed )\" is not valid for this class. " - << "Use \"SetLabels( TLabelImage* labels )\" instead."; - ::itk::ExceptionObject e( - __FILE__, __LINE__, msg.str( ).c_str( ), ITK_LOCATION - ); - throw e; -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -void -fpa::Image::LabelledSeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -AddSeed( const TPoint& seed ) -{ - std::ostringstream msg; - msg << "itk::ERROR: fpa::Image::LabelledSeedsInterface (" << this - << "): \"AddSeed( const TPoint& seed )\" is not valid for this class. " - << "Use \"SetLabels( TLabelImage* labels )\" instead."; - ::itk::ExceptionObject e( - __FILE__, __LINE__, msg.str( ).c_str( ), ITK_LOCATION - ); - throw e; -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -const typename -fpa::Image::LabelledSeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -TLabelImage* -fpa::Image::LabelledSeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -GetLabels( ) const -{ - return( this->m_LabelImage ); -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -void fpa::Image::LabelledSeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -SetLabels( const TLabelImage* image ) -{ - this->m_LabelImage = image; -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -fpa::Image::LabelledSeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -LabelledSeedsInterface( itk::ProcessObject* filter ) - : Superclass( filter ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TVertex, class _TPoint, class _TInputValue, class _TOutputValue, class _TFrontId, class _TCompare > -fpa::Image::LabelledSeedsInterface< _TVertex, _TPoint, _TInputValue, _TOutputValue, _TFrontId, _TCompare >:: -~LabelledSeedsInterface( ) -{ -} - -#endif // __fpa__Image__LabelledSeedsInterface__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/MinimumSpanningTree.h b/lib/fpa/Image/MinimumSpanningTree.h deleted file mode 100644 index 22f7904..0000000 --- a/lib/fpa/Image/MinimumSpanningTree.h +++ /dev/null @@ -1,78 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__MinimumSpanningTree__h__ -#define __fpa__Image__MinimumSpanningTree__h__ - -#include -#include -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< unsigned int _VDim > - class MinimumSpanningTree - : public fpa::Base::MinimumSpanningTree< itk::Index< _VDim >, itk::Image< itk::Offset< _VDim >, _VDim > > - { - public: - typedef itk::Index< _VDim > TVertex; - typedef itk::Image< itk::Offset< _VDim >, _VDim > TBaseImage; - - typedef MinimumSpanningTree Self; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - typedef fpa::Base::MinimumSpanningTree< TVertex, TBaseImage > Superclass; - - typedef typename Superclass::TCollision TCollision; - typedef typename Superclass::TCollisionsRow TCollisionsRow; - typedef typename Superclass::TCollisions TCollisions; - typedef typename Superclass::TVertices TVertices; - - typedef fpa::Image::PolyLineParametricPath< _VDim > TPolyLineParametricPath; - - public: - itkNewMacro( Self ); - itkTypeMacro( - fpa::Image::MinimumSpanningTree, - fpa::Base::MinimumSpanningTree - ); - - public: - virtual TVertex GetParent( const TVertex& v ) const override; - virtual void SetParent( const TVertex& v, const TVertex& p ) override; - - void GetPolyLineParametricPath( - typename TPolyLineParametricPath::Pointer& path, - const TVertex& a - ) const; - void GetPolyLineParametricPath( - typename TPolyLineParametricPath::Pointer& path, - const TVertex& a, const TVertex& b - ) const; - - protected: - MinimumSpanningTree( ); - virtual ~MinimumSpanningTree( ); - - private: - MinimumSpanningTree( const Self& other ); - Self& operator=( const Self& other ); - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__MinimumSpanningTree__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/MinimumSpanningTree.hxx b/lib/fpa/Image/MinimumSpanningTree.hxx deleted file mode 100644 index 9bd7083..0000000 --- a/lib/fpa/Image/MinimumSpanningTree.hxx +++ /dev/null @@ -1,77 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__MinimumSpanningTree__hxx__ -#define __fpa__Image__MinimumSpanningTree__hxx__ - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -typename fpa::Image::MinimumSpanningTree< _VDim >:: -TVertex fpa::Image::MinimumSpanningTree< _VDim >:: -GetParent( const TVertex& v ) const -{ - return( v + this->GetPixel( v ) ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -void fpa::Image::MinimumSpanningTree< _VDim >:: -SetParent( const TVertex& v, const TVertex& p ) -{ - this->SetPixel( v, p - v ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -void fpa::Image::MinimumSpanningTree< _VDim >:: -GetPolyLineParametricPath( - typename TPolyLineParametricPath::Pointer& path, - const TVertex& a - ) const -{ - TVertices v = this->GetPath( a ); - if( path.IsNull( ) ) - path = TPolyLineParametricPath::New( ); - path->SetReferenceImage( this ); - typename TVertices::const_iterator vIt = v.begin( ); - for( ; vIt != v.end( ); ++vIt ) - path->AddVertex( *vIt ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -void fpa::Image::MinimumSpanningTree< _VDim >:: -GetPolyLineParametricPath( - typename TPolyLineParametricPath::Pointer& path, - const TVertex& a, const TVertex& b - ) const -{ - TVertices v = this->GetPath( a, b ); - if( path.IsNull( ) ) - path = TPolyLineParametricPath::New( ); - path->SetReferenceImage( this ); - typename TVertices::const_iterator vIt = v.begin( ); - for( ; vIt != v.end( ); ++vIt ) - path->AddVertex( *vIt ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -fpa::Image::MinimumSpanningTree< _VDim >:: -MinimumSpanningTree( ) - : Superclass( ) -{ -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -fpa::Image::MinimumSpanningTree< _VDim >:: -~MinimumSpanningTree( ) -{ -} - -#endif // __fpa__Image__MinimumSpanningTree__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/Mori.h b/lib/fpa/Image/Mori.h deleted file mode 100644 index 7e6b0e0..0000000 --- a/lib/fpa/Image/Mori.h +++ /dev/null @@ -1,108 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__Mori__h__ -#define __fpa__Image__Mori__h__ - -#include -#include -#include -#include -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TInputImage, class _TOutputImage > - class MoriTraits - : public fpa::Image::DefaultTraits< _TInputImage, _TOutputImage, typename _TOutputImage::PixelType > - { - public: - typedef MoriTraits Self; - typedef _TInputImage TInputImage; - typedef _TOutputImage TOutputImage; - typedef typename TOutputImage::PixelType TFrontId; - typedef fpa::Image::DefaultTraits< TInputImage, TOutputImage, TFrontId > Superclass; - - typedef typename Superclass::TVertex TVertex; - typedef typename Superclass::TInputValue TInputValue; - typedef typename Superclass::TPoint TPoint; - typedef typename Superclass::TOutputValue TOutputValue; - typedef typename Superclass::TCompare TCompare; - typedef typename Superclass::TNeighborhood TNeighborhood; - typedef typename Superclass::TFilter TFilter; - - typedef fpa::Base::SingleSeedInterface< TVertex, TPoint, TInputValue, TOutputValue, TFrontId, TCompare > TSeedsInterface; - typedef fpa::Base::MarksInterface< TVertex > TMarksInterface; - - typedef typename TSeedsInterface::TNode TNode; - typedef typename TSeedsInterface::TNodes TNodes; - typedef typename TSeedsInterface::TSeed TSeed; - typedef typename TSeedsInterface::TSeeds TSeeds; - - private: - // Purposely not implemented. - MoriTraits( ); - MoriTraits( const Self& other ); - virtual ~MoriTraits( ); - Self& operator=( const Self& other ); - }; - - /** - */ - template< class _TInputImage, class _TOutputImage > - class Mori - : public fpa::Base::Mori< fpa::Image::Algorithm< fpa::Image::MoriTraits< _TInputImage, _TOutputImage > > > - { - public: - typedef _TInputImage TInputImage; - typedef _TOutputImage TOutputImage; - typedef fpa::Image::MoriTraits< TInputImage, TOutputImage > TTraits; - typedef fpa::Image::Algorithm< TTraits > TAlgorithm; - - typedef Mori Self; - typedef fpa::Base::Mori< TAlgorithm > Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef typename TAlgorithm::TMarks TMarks; - - public: - itkNewMacro( Self ); - itkTypeMacro( fpa::Image::Mori, fpa::Base::Mori ); - - public: - TOutputImage* GetThresholdedOutput( ); - const TOutputImage* GetThresholdedOutput( ) const; - - protected: - Mori( ); - virtual ~Mori( ); - - virtual void _AfterGenerateData( ) override; - - private: - // Purposely not implemented. - Mori( const Self& other ); - Self& operator=( const Self& other ); - - protected: - unsigned long m_ThresholdedOutputIdx; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__Mori__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/Mori.hxx b/lib/fpa/Image/Mori.hxx deleted file mode 100644 index d33e5ec..0000000 --- a/lib/fpa/Image/Mori.hxx +++ /dev/null @@ -1,78 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__Mori__hxx__ -#define __fpa__Image__Mori__hxx__ - -#include - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TOutputImage > -typename fpa::Image::Mori< _TInputImage, _TOutputImage >:: -TOutputImage* fpa::Image::Mori< _TInputImage, _TOutputImage >:: -GetThresholdedOutput( ) -{ - return( - dynamic_cast< TOutputImage* >( - this->itk::ProcessObject::GetOutput( this->m_ThresholdedOutputIdx ) - ) - ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TOutputImage > -const typename fpa::Image::Mori< _TInputImage, _TOutputImage >:: -TOutputImage* fpa::Image::Mori< _TInputImage, _TOutputImage >:: -GetThresholdedOutput( ) const -{ - return( - dynamic_cast< const TOutputImage* >( - this->itk::ProcessObject::GetOutput( this->m_ThresholdedOutputIdx ) - ) - ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TOutputImage > -fpa::Image::Mori< _TInputImage, _TOutputImage >:: -Mori( ) - : Superclass( ) -{ - this->m_ThresholdedOutputIdx = this->GetNumberOfRequiredOutputs( ); - this->itk::ProcessObject::SetNumberOfRequiredOutputs( - this->m_ThresholdedOutputIdx + 1 - ); - this->SetNthOutput( this->m_ThresholdedOutputIdx, TOutputImage::New( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TOutputImage > -fpa::Image::Mori< _TInputImage, _TOutputImage >:: -~Mori( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TOutputImage > -void fpa::Image::Mori< _TInputImage, _TOutputImage >:: -_AfterGenerateData( ) -{ - typedef itk::BinaryThresholdImageFilter< TMarks, TOutputImage > _TFilter; - - this->Superclass::_AfterGenerateData( ); - - typename _TFilter::Pointer filter = _TFilter::New( ); - filter->SetInput( this->GetMarks( ) ); - filter->SetInsideValue( this->GetInsideValue( ) ); - filter->SetOutsideValue( this->GetOutsideValue( ) ); - filter->SetLowerThreshold( 1 ); - filter->SetUpperThreshold( this->GetNumberOfEvaluatedThresholds( ) - 1 ); - filter->Update( ); - this->GetThresholdedOutput( )->Graft( filter->GetOutput( ) ); -} - -#endif // __fpa__Image__Mori__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/PathsToImageFilter.h b/lib/fpa/Image/PathsToImageFilter.h deleted file mode 100644 index dd467cd..0000000 --- a/lib/fpa/Image/PathsToImageFilter.h +++ /dev/null @@ -1,84 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__PathsToImageFilter__h__ -#define __fpa__Image__PathsToImageFilter__h__ - -#include -#include -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TMST, class _TOutputPixelValue > - class PathsToImageFilter - : public itk::ImageToImageFilter< _TMST, itk::Image< itk::RGBAPixel< _TOutputPixelValue >, _TMST::ImageDimension > > - { - public: - typedef _TMST TMST; - typedef _TOutputPixelValue TOutputPixelValue; - typedef itk::RGBAPixel< TOutputPixelValue > TOutputPixel; - typedef itk::Image< TOutputPixel, TMST::ImageDimension > TOutputImage; - - typedef PathsToImageFilter Self; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - typedef itk::ImageToImageFilter< TMST, TOutputImage > Superclass; - - typedef typename TMST::IndexType TIndex; - struct TPathData - { - TIndex Start; - TIndex End; - TOutputPixelValue Red; - TOutputPixelValue Green; - TOutputPixelValue Blue; - }; - typedef std::vector< TPathData > TPaths; - - public: - itkNewMacro( Self ); - itkTypeMacro( - fpa::Image::PathsToImageFilter, - itk::ImageToImageFilter - ); - - public: - void AddPath( - const TIndex& start, const TIndex& end, - const TOutputPixelValue& r = TOutputPixelValue( 1 ), - const TOutputPixelValue& g = TOutputPixelValue( 0 ), - const TOutputPixelValue& b = TOutputPixelValue( 0 ) - ); - - protected: - PathsToImageFilter( ); - virtual ~PathsToImageFilter( ); - - virtual void GenerateData( ) override; - - private: - PathsToImageFilter( const Self& other ); - Self& operator=( const Self& other ); - - protected: - TPaths m_Paths; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__PathsToImageFilter__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/PathsToImageFilter.hxx b/lib/fpa/Image/PathsToImageFilter.hxx deleted file mode 100644 index 487b9c8..0000000 --- a/lib/fpa/Image/PathsToImageFilter.hxx +++ /dev/null @@ -1,79 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__PathsToImageFilter__hxx__ -#define __fpa__Image__PathsToImageFilter__hxx__ - -// ------------------------------------------------------------------------- -template< class _TMST, class _TOutputPixelValue > -void fpa::Image::PathsToImageFilter< _TMST, _TOutputPixelValue >:: -AddPath( - const TIndex& start, const TIndex& end, - const TOutputPixelValue& r, - const TOutputPixelValue& g, - const TOutputPixelValue& b - ) -{ - if( start != end ) - { - TPathData d; - d.Start = start; - d.End = end; - d.Red = r; - d.Green = g; - d.Blue = b; - this->m_Paths.push_back( d ); - this->Modified( ); - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TMST, class _TOutputPixelValue > -fpa::Image::PathsToImageFilter< _TMST, _TOutputPixelValue >:: -PathsToImageFilter( ) - : Superclass( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TMST, class _TOutputPixelValue > -fpa::Image::PathsToImageFilter< _TMST, _TOutputPixelValue >:: -~PathsToImageFilter( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TMST, class _TOutputPixelValue > -void fpa::Image::PathsToImageFilter< _TMST, _TOutputPixelValue >:: -GenerateData( ) -{ - TOutputPixel color; - color.Fill( 0 ); - - const TMST* mst = this->GetInput( ); - TOutputImage* output = this->GetOutput( ); - output->SetBufferedRegion( mst->GetBufferedRegion( ) ); - output->Allocate( ); - output->FillBuffer( color ); - - typename TPaths::const_iterator d = this->m_Paths.begin( ); - for( ; d != this->m_Paths.end( ); ++d ) - { - typename TMST::TVertices path = mst->GetPath( d->Start, d->End ); - color[ 0 ] = d->Red; - color[ 1 ] = d->Green; - color[ 2 ] = d->Blue; - color[ 3 ] = std::numeric_limits< TOutputPixelValue >::max( ); - typename TMST::TVertices::const_iterator i = path.begin( ); - for( ; i != path.end( ); ++i ) - output->SetPixel( *i, color ); - - } // rof -} - -#endif // __fpa__Image__PathsToImageFilter__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/PolyLineParametricPath.h b/lib/fpa/Image/PolyLineParametricPath.h deleted file mode 100644 index 83a6c05..0000000 --- a/lib/fpa/Image/PolyLineParametricPath.h +++ /dev/null @@ -1,99 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__PolyLineParametricPath__h__ -#define __fpa__Image__PolyLineParametricPath__h__ - -#include -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< unsigned int _VDim > - class PolyLineParametricPath - : public itk::PolyLineParametricPath< _VDim > - { - public: - typedef PolyLineParametricPath Self; - typedef itk::PolyLineParametricPath< _VDim > Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef itk::ImageBase< _VDim > TImageBase; - typedef typename TImageBase::SpacingType TSpacing; - typedef typename TImageBase::PointType TPoint; - typedef typename TImageBase::DirectionType TDirection; - typedef typename Superclass::ContinuousIndexType TContinuousIndex; - typedef typename TContinuousIndex::IndexType TIndex; - - public: - itkNewMacro( Self ); - itkTypeMacro( PolyLineParametricPath, itk::PolyLineParametricPath ); - - itkGetConstReferenceMacro( Spacing, TSpacing ); - itkGetConstReferenceMacro( Origin, TPoint ); - itkGetConstReferenceMacro( Direction, TDirection ); - itkGetConstReferenceMacro( InverseDirection, TDirection ); - - itkSetMacro( Origin, TPoint ); - - public: - unsigned long GetSize( ) const; - TContinuousIndex GetContinuousVertex( unsigned long i ) const; - TIndex GetVertex( unsigned long i ) const; - TPoint GetPoint( unsigned long i ) const; - - virtual void SetSpacing( const TSpacing& spac ); - virtual void SetSpacing( const double spac[ _VDim ] ); - virtual void SetSpacing( const float spac[ _VDim ] ); - virtual void SetOrigin( const double ori[ _VDim ] ); - virtual void SetOrigin( const float ori[ _VDim ] ); - virtual void SetDirection( const TDirection& dir ); - - template< class _TRefImage > - inline void SetReferenceImage( const _TRefImage* image ) - { - this->SetSpacing( image->GetSpacing( ) ); - this->SetOrigin( image->GetOrigin( ) ); - this->SetDirection( image->GetDirection( ) ); - } - - virtual void Graft( itk::DataObject* o ); - - protected: - PolyLineParametricPath( ); - virtual ~PolyLineParametricPath( ); - - virtual void _ComputeIndexToPhysicalPointMatrices( ); - - private: - // Purposely not implemented - PolyLineParametricPath( const Self& other ); - Self& operator=( const Self& other ); - - protected: - TSpacing m_Spacing; - TPoint m_Origin; - TDirection m_Direction; - TDirection m_InverseDirection; - TDirection m_IndexToPhysicalPoint; - TDirection m_PhysicalPointToIndex; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__PolyLineParametricPath__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/PolyLineParametricPath.hxx b/lib/fpa/Image/PolyLineParametricPath.hxx deleted file mode 100644 index 3093a99..0000000 --- a/lib/fpa/Image/PolyLineParametricPath.hxx +++ /dev/null @@ -1,217 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__PolyLineParametricPath__hxx__ -#define __fpa__Image__PolyLineParametricPath__hxx__ - -#include -#include - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -unsigned long fpa::Image::PolyLineParametricPath< _VDim >:: -GetSize( ) const -{ - return( this->GetVertexList( )->Size( ) ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -typename fpa::Image::PolyLineParametricPath< _VDim >:: -TContinuousIndex -fpa::Image::PolyLineParametricPath< _VDim >:: -GetContinuousVertex( unsigned long i ) const -{ - return( this->GetVertexList( )->GetElement( i ) ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -typename fpa::Image::PolyLineParametricPath< _VDim >:: -TIndex fpa::Image::PolyLineParametricPath< _VDim >:: -GetVertex( unsigned long i ) const -{ - TContinuousIndex cidx = this->GetContinuousVertex( i ); - TIndex idx; - for( unsigned int d = 0; d < _VDim; ++d ) - idx[ d ] = cidx[ d ]; - return( idx ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -typename fpa::Image::PolyLineParametricPath< _VDim >:: -TPoint fpa::Image::PolyLineParametricPath< _VDim >:: -GetPoint( unsigned long i ) const -{ - typedef typename TPoint::CoordRepType _TCoordRep; - TPoint pnt; - TContinuousIndex idx = this->GetVertex( i ); - for( unsigned int r = 0; r < _VDim; ++r ) - { - _TCoordRep sum = itk::NumericTraits< _TCoordRep >::ZeroValue( ); - for( unsigned int c = 0; c < _VDim; ++c ) - sum += this->m_IndexToPhysicalPoint( r, c ) * idx[ c ]; - pnt[ r ] = sum + this->m_Origin[ r ]; - - } // rof - return( pnt ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -void fpa::Image::PolyLineParametricPath< _VDim >:: -SetSpacing( const TSpacing& spac ) -{ - if( this->m_Spacing != spac ) - { - this->m_Spacing = spac; - this->_ComputeIndexToPhysicalPointMatrices( ); - this->Modified( ); - - } // fi -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -void fpa::Image::PolyLineParametricPath< _VDim >:: -SetSpacing( const double spac[ _VDim ] ) -{ - this->SetSpacing( TSpacing( spac ) ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -void fpa::Image::PolyLineParametricPath< _VDim >:: -SetSpacing( const float spac[ _VDim ] ) -{ - TSpacing s; - for( unsigned int d = 0; d < _VDim; ++d ) - s[ d ] = spac[ d ]; - this->SetSpacing( s ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -void fpa::Image::PolyLineParametricPath< _VDim >:: -SetOrigin( const double ori[ _VDim ] ) -{ - this->SetOrigin( TPoint( ori ) ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -void fpa::Image::PolyLineParametricPath< _VDim >:: -SetOrigin( const float ori[ _VDim ] ) -{ - this->SetOrigin( TPoint( ori ) ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -void fpa::Image::PolyLineParametricPath< _VDim >:: -SetDirection( const TDirection& dir ) -{ - bool modified = false; - for( unsigned int r = 0; r < _VDim; r++ ) - { - for( unsigned int c = 0; c < _VDim; c++ ) - { - if( - itk::Math::NotExactlyEquals( - this->m_Direction[ r ][ c ], dir[ r ][ c ] - ) - ) - { - this->m_Direction[ r ][ c ] = dir[ r ][ c ]; - modified = true; - } // fi - - } // rof - - } // rof - if( modified ) - { - this->_ComputeIndexToPhysicalPointMatrices( ); - this->m_InverseDirection = this->m_Direction.GetInverse( ); - this->Modified( ); - - } // fi -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -void fpa::Image::PolyLineParametricPath< _VDim >:: -Graft( itk::DataObject* o ) -{ - this->Superclass::Graft( o ); - Self* other = dynamic_cast< Self* >( o ); - if( other != NULL ) - { - this->m_DefaultInputStepSize = other->m_DefaultInputStepSize; - this->Initialize( ); - for( unsigned long i = 0; i < other->GetSize( ); ++i ) - this->AddVertex( other->GetContinuousVertex( i ) ); - this->m_Spacing = other->m_Spacing; - this->m_Origin = other->m_Origin; - this->m_Direction = other->m_Direction; - this->m_InverseDirection = other->m_InverseDirection; - this->m_IndexToPhysicalPoint = other->m_IndexToPhysicalPoint; - this->m_PhysicalPointToIndex = other->m_PhysicalPointToIndex; - - } // fi -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -fpa::Image::PolyLineParametricPath< _VDim >:: -PolyLineParametricPath( ) - : Superclass( ) -{ - this->m_Spacing.Fill( 1.0 ); - this->m_Origin.Fill( 0.0 ); - this->m_Direction.SetIdentity( ); - this->m_InverseDirection.SetIdentity( ); - this->m_IndexToPhysicalPoint.SetIdentity( ); - this->m_PhysicalPointToIndex.SetIdentity( ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -fpa::Image::PolyLineParametricPath< _VDim >:: -~PolyLineParametricPath( ) -{ -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -void fpa::Image::PolyLineParametricPath< _VDim >:: -_ComputeIndexToPhysicalPointMatrices( ) -{ - TDirection scale; - scale.Fill( 0.0 ); - for( unsigned int i = 0; i < _VDim; i++ ) - { - if( this->m_Spacing[ i ] == 0.0 ) - itkExceptionMacro( - "A spacing of 0 is not allowed: Spacing is " << this->m_Spacing - ); - scale[ i ][ i ] = this->m_Spacing[ i ]; - - } // rof - - if( vnl_determinant( this->m_Direction.GetVnlMatrix( ) ) == 0.0 ) - itkExceptionMacro( - << "Bad direction, determinant is 0. Direction is " - << this->m_Direction - ); - this->m_IndexToPhysicalPoint = this->m_Direction * scale; - this->m_PhysicalPointToIndex = this->m_IndexToPhysicalPoint.GetInverse( ); - this->Modified( ); -} - -#endif // __fpa__Image__PolyLineParametricPath__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/PolyLineParametricPathToPolyDataFilter.h b/lib/fpa/Image/PolyLineParametricPathToPolyDataFilter.h deleted file mode 100644 index 4c6318a..0000000 --- a/lib/fpa/Image/PolyLineParametricPathToPolyDataFilter.h +++ /dev/null @@ -1,81 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__PolyLineParametricPathToPolyDataFilter__h__ -#define __fpa__Image__PolyLineParametricPathToPolyDataFilter__h__ - -#include - -#ifdef USE_VTK -# include -#endif // USE_VTK - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TPolyLineParametricPath > - class PolyLineParametricPathToPolyDataFilter -#ifdef USE_VTK - : public vtkPolyDataAlgorithm -#endif // USE_VTK - { - public: - typedef PolyLineParametricPathToPolyDataFilter Self; - typedef _TPolyLineParametricPath TPolyLineParametricPath; - - public: -#ifdef USE_VTK - vtkTypeMacro( - PolyLineParametricPathToPolyDataFilter, - vtkPolyDataAlgorithm - ); -#endif // USE_VTK - - public: - static Self* New( ); - - const TPolyLineParametricPath* GetInput( ) const; - void SetInput( const TPolyLineParametricPath* path ); - - protected: - PolyLineParametricPathToPolyDataFilter( ); - virtual ~PolyLineParametricPathToPolyDataFilter( ); - -#ifdef USE_VTK - int RequestData( - vtkInformation* information, - vtkInformationVector** input, - vtkInformationVector* output - ); - int RequestInformation( - vtkInformation* information, - vtkInformationVector** input, - vtkInformationVector* output - ); -#endif // USE_VTK - - private: - // Purposely not implemented - PolyLineParametricPathToPolyDataFilter( const Self& ); - void operator=( const Self& ); - - protected: - const TPolyLineParametricPath* m_PolyLineParametricPath; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__PolyLineParametricPathToPolyDataFilter__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/PolyLineParametricPathToPolyDataFilter.hxx b/lib/fpa/Image/PolyLineParametricPathToPolyDataFilter.hxx deleted file mode 100644 index 7dd4cb1..0000000 --- a/lib/fpa/Image/PolyLineParametricPathToPolyDataFilter.hxx +++ /dev/null @@ -1,145 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__PolyLineParametricPathToPolyDataFilter__hxx__ -#define __fpa__Image__PolyLineParametricPathToPolyDataFilter__hxx__ - -#ifdef USE_VTK -# include -# include -# include -# include -# include -# include -#endif // USE_VTK - -// ------------------------------------------------------------------------- -template< class _TPolyLineParametricPath > -typename fpa::Image::PolyLineParametricPathToPolyDataFilter< _TPolyLineParametricPath >:: -Self* fpa::Image::PolyLineParametricPathToPolyDataFilter< _TPolyLineParametricPath >:: -New( ) -{ - return( new Self( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TPolyLineParametricPath > -const typename -fpa::Image::PolyLineParametricPathToPolyDataFilter< _TPolyLineParametricPath >:: -TPolyLineParametricPath* fpa::Image::PolyLineParametricPathToPolyDataFilter< _TPolyLineParametricPath >:: -GetInput( ) const -{ - return( this->m_PolyLineParametricPath ); -} - -// ------------------------------------------------------------------------- -template< class _TPolyLineParametricPath > -void fpa::Image::PolyLineParametricPathToPolyDataFilter< _TPolyLineParametricPath >:: -SetInput( const TPolyLineParametricPath* path ) -{ - if( this->m_PolyLineParametricPath != path ) - { - this->m_PolyLineParametricPath = path; -#ifdef USE_VTK - this->Modified( ); -#endif // USE_VTK - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TPolyLineParametricPath > -fpa::Image::PolyLineParametricPathToPolyDataFilter< _TPolyLineParametricPath >:: -PolyLineParametricPathToPolyDataFilter( ) -#ifdef USE_VTK - : vtkPolyDataAlgorithm( ), - m_PolyLineParametricPath( NULL ) -#endif // USE_VTK -{ -#ifdef USE_VTK - this->SetNumberOfInputPorts( 0 ); -#endif // USE_VTK -} - -// ------------------------------------------------------------------------- -template< class _TPolyLineParametricPath > -fpa::Image::PolyLineParametricPathToPolyDataFilter< _TPolyLineParametricPath >:: -~PolyLineParametricPathToPolyDataFilter( ) -{ -} - -#ifdef USE_VTK -// ------------------------------------------------------------------------- -template< class _TPolyLineParametricPath > -int fpa::Image::PolyLineParametricPathToPolyDataFilter< _TPolyLineParametricPath >:: -RequestData( - vtkInformation* information, - vtkInformationVector** input, - vtkInformationVector* output - ) -{ - static const unsigned int dim = TPolyLineParametricPath::PathDimension; - if( this->m_PolyLineParametricPath == NULL ) - return( 0 ); - - // Get output - vtkInformation* info = output->GetInformationObject( 0 ); - vtkPolyData* out = vtkPolyData::SafeDownCast( - info->Get( vtkDataObject::DATA_OBJECT( ) ) - ); - - // Prepare data - out->SetPoints( vtkSmartPointer< vtkPoints >::New( ) ); - out->SetVerts( vtkSmartPointer< vtkCellArray >::New( ) ); - out->SetLines( vtkSmartPointer< vtkCellArray >::New( ) ); - out->SetPolys( vtkSmartPointer< vtkCellArray >::New( ) ); - out->SetStrips( vtkSmartPointer< vtkCellArray >::New( ) ); - vtkSmartPointer< vtkUnsignedIntArray > darray = - vtkSmartPointer< vtkUnsignedIntArray >::New( ); - darray->SetNumberOfComponents( 1 ); - out->GetPointData( )->SetScalars( darray ); - vtkPoints* points = out->GetPoints( ); - vtkCellArray* lines = out->GetLines( ); - - // Assign all data - const TPolyLineParametricPath* path = this->GetInput( ); - for( unsigned long i = 0; i < path->GetSize( ); ++i ) - { - auto pnt = path->GetPoint( i ); - if( dim == 1 ) - points->InsertNextPoint( pnt[ 0 ], 0, 0 ); - else if( dim == 2 ) - points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], 0 ); - else - points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] ); - darray->InsertNextTuple1( double( i ) ); - if( i > 0 ) - { - lines->InsertNextCell( 2 ); - lines->InsertCellPoint( points->GetNumberOfPoints( ) - 2 ); - lines->InsertCellPoint( points->GetNumberOfPoints( ) - 1 ); - - } // fi - - } // rof - return( 1 ); -} - -// ------------------------------------------------------------------------- -template< class _TPolyLineParametricPath > -int fpa::Image::PolyLineParametricPathToPolyDataFilter< _TPolyLineParametricPath >:: -RequestInformation( - vtkInformation* information, - vtkInformationVector** input, - vtkInformationVector* output - ) -{ - return( 1 ); -} -#endif // USE_VTK - -#endif // __fpa__Image__PolyLineParametricPathToPolyDataFilterFilter__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/RandomWalker.h b/lib/fpa/Image/RandomWalker.h deleted file mode 100644 index 98b9492..0000000 --- a/lib/fpa/Image/RandomWalker.h +++ /dev/null @@ -1,121 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__RandomWalker__h__ -#define __fpa__Image__RandomWalker__h__ - -#include -#include -#include -#include -#include -#include -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TInputImage, class _TLabelImage, class _TScalar > - class RandomWalkerTraits - : public fpa::Image::DefaultTraits< _TInputImage, itk::Image< _TScalar, _TInputImage::ImageDimension >, typename _TLabelImage::PixelType > - { - public: - typedef RandomWalkerTraits Self; - typedef _TInputImage TInputImage; - typedef _TLabelImage TLabelImage; - typedef _TScalar TScalar; - typedef typename _TLabelImage::PixelType TFrontId; - typedef itk::Image< TScalar, _TInputImage::ImageDimension > TOutputImage; - typedef fpa::Image::DefaultTraits< TInputImage, TOutputImage, TFrontId > Superclass; - - typedef typename Superclass::TVertex TVertex; - typedef typename Superclass::TInputValue TInputValue; - typedef typename Superclass::TPoint TPoint; - typedef typename Superclass::TOutputValue TOutputValue; - typedef typename Superclass::TCompare TCompare; - typedef typename Superclass::TNeighborhood TNeighborhood; - typedef typename Superclass::TFilter TFilter; - - typedef fpa::Image::LabelledSeedsInterface< TVertex, TPoint, TInputValue, TOutputValue, TFrontId, TCompare > TSeedsInterface; - typedef fpa::Base::MarksInterface< TVertex > TMarksInterface; - - typedef typename TSeedsInterface::TNode TNode; - typedef typename TSeedsInterface::TNodes TNodes; - typedef typename TSeedsInterface::TSeed TSeed; - typedef typename TSeedsInterface::TSeeds TSeeds; - - public: - itkConceptMacro( - Check_SameDimension, - ( itk::Concept::SameDimension< TInputImage::ImageDimension, TLabelImage::ImageDimension > ) - ); - - private: - // Purposely not implemented. - RandomWalkerTraits( ); - RandomWalkerTraits( const Self& other ); - virtual ~RandomWalkerTraits( ); - Self& operator=( const Self& other ); - }; - - /** - */ - template< class _TInputImage, class _TLabelImage, class _TScalar > - class RandomWalker - : public fpa::Base::DijkstraBase< fpa::Image::Algorithm< fpa::Image::RandomWalkerTraits< _TInputImage, _TLabelImage, _TScalar > > > - { - public: - typedef _TInputImage TInputImage; - typedef _TLabelImage TLabelImage; - typedef _TScalar TScalar; - - typedef fpa::Image::RandomWalkerTraits< TInputImage, TLabelImage, TScalar > TTraits; - typedef fpa::Image::Algorithm< TTraits > TAlgorithm; - typedef fpa::Base::DijkstraBase< TAlgorithm > Superclass; - typedef RandomWalker Self; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef typename TTraits::TNode TNode; - typedef typename TTraits::TNodes TNodes; - typedef typename TTraits::TSeed TSeed; - typedef typename TTraits::TVertex TVertex; - - typedef fpa::Image::Functors::Dijkstra::Function< TInputImage, TScalar > TWeightFunction; - - public: - itkNewMacro( Self ); - itkTypeMacro( fpa::Image::RandomWalker, fpa::Base::RandomWalker ); - - public: - virtual itk::ModifiedTimeType GetMTime( ) const override; - - protected: - RandomWalker( ); - virtual ~RandomWalker( ); - - virtual void _BeforeGenerateData( ) override; - virtual TNodes _UnifySeeds( ) override; - - private: - // Purposely not implemented. - RandomWalker( const Self& other ); - Self& operator=( const Self& other ); - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__RandomWalker__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/RandomWalker.hxx b/lib/fpa/Image/RandomWalker.hxx deleted file mode 100644 index 6935abf..0000000 --- a/lib/fpa/Image/RandomWalker.hxx +++ /dev/null @@ -1,133 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__RandomWalker__hxx__ -#define __fpa__Image__RandomWalker__hxx__ - -#include - -#include -#include - -#include - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TLabelImage, class _TScalar > -itk::ModifiedTimeType -fpa::Image::RandomWalker< _TInputImage, _TLabelImage, _TScalar >:: -GetMTime( ) const -{ - const TLabelImage* labels = this->GetLabels( ); - itk::ModifiedTimeType t = this->Superclass::GetMTime( ); - if( labels != NULL ) - { - itk::ModifiedTimeType q = labels->GetMTime( ); - t = ( q < t )? q: t; - - } // fi - return( t ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TLabelImage, class _TScalar > -fpa::Image::RandomWalker< _TInputImage, _TLabelImage, _TScalar >:: -RandomWalker( ) - : Superclass( ) -{ - typedef fpa::Image::Functors::Dijkstra::Gaussian< TInputImage, TScalar > _TDefaultFunction; - this->SetWeightFunction( _TDefaultFunction::New( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TLabelImage, class _TScalar > -fpa::Image::RandomWalker< _TInputImage, _TLabelImage, _TScalar >:: -~RandomWalker( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TLabelImage, class _TScalar > -void fpa::Image::RandomWalker< _TInputImage, _TLabelImage, _TScalar >:: -_BeforeGenerateData( ) -{ - this->Superclass::_BeforeGenerateData( ); - TWeightFunction* wf = - dynamic_cast< TWeightFunction* >( this->GetWeightFunction( ) ); - if( wf != NULL ) - wf->SetImage( this->GetInput( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TLabelImage, class _TScalar > -typename fpa::Image::RandomWalker< _TInputImage, _TLabelImage, _TScalar >:: -TNodes fpa::Image::RandomWalker< _TInputImage, _TLabelImage, _TScalar >:: -_UnifySeeds( ) -{ - this->m_Seeds.clear( ); - const TLabelImage* lbl = this->GetLabels( ); - if( lbl == NULL ) - { - std::ostringstream msg; - msg << "itk::ERROR: fpa::Image::RandomWalker (" << this - << "): Labelled image not defined."; - ::itk::ExceptionObject e( - __FILE__, __LINE__, msg.str( ).c_str( ), ITK_LOCATION - ); - throw e; - - } // fi - - // Iterate over labels - typename TLabelImage::RegionType reg = lbl->GetRequestedRegion( ); - itk::ImageRegionConstIteratorWithIndex< TLabelImage > lIt( lbl, reg ); - for( lIt.GoToBegin( ); !lIt.IsAtEnd( ); ++lIt ) - { - if( lIt.Get( ) > 0 ) - { - bool is_seed = false; - for( unsigned int d = 0; d < TLabelImage::ImageDimension; ++d ) - { - for( int s = -1; s <= 1; s += 2 ) - { - TVertex neigh = lIt.GetIndex( ); - neigh[ d ] += s; - if( reg.IsInside( neigh ) ) - is_seed |= ( lbl->GetPixel( neigh ) == 0 ); - - } // rof - - } // rof - - if( !is_seed ) - { - TNode node; - node.Vertex = lIt.GetIndex( ); - node.Parent = lIt.GetIndex( ); - node.FrontId = lIt.Get( ); - node.Value = TScalar( 0 ); - this->_Mark( node.Vertex, node.FrontId ); - this->_UpdateOutputValue( node ); - } - else - { - TSeed seed; - seed.Vertex = lIt.GetIndex( ); - seed.IsPoint = false; - seed.FrontId = lIt.Get( ); - this->m_Seeds.push_back( seed ); - - } // fi - - } // fi - - } // rof - - // Ok, finish initialization - return( this->Superclass::_UnifySeeds( ) ); -} - -#endif // __fpa__Image__RandomWalker__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/RegionGrow.h b/lib/fpa/Image/RegionGrow.h deleted file mode 100644 index 4d190dc..0000000 --- a/lib/fpa/Image/RegionGrow.h +++ /dev/null @@ -1,55 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__RegionGrow__h__ -#define __fpa__Image__RegionGrow__h__ - -#include -#include -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TInputImage, class _TOutputImage, class _TFrontId = unsigned char > - class RegionGrow - : public fpa::Base::RegionGrow< fpa::Image::Algorithm< fpa::Image::DefaultTraits< _TInputImage, _TOutputImage, _TFrontId > > > - { - public: - typedef _TInputImage TInputImage; - typedef _TOutputImage TOutputImage; - typedef _TFrontId TFrontId; - - typedef fpa::Image::DefaultTraits< TInputImage, TOutputImage, TFrontId > TTraits; - typedef fpa::Image::Algorithm< TTraits > TAlgorithm; - typedef fpa::Base::RegionGrow< TAlgorithm > Superclass; - typedef RegionGrow Self; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - public: - itkNewMacro( Self ); - itkTypeMacro( fpa::Image::RegionGrow, fpa::Base::RegionGrow ); - - protected: - RegionGrow( ) : Superclass( ) { } - virtual ~RegionGrow( ) { } - - private: - // Purposely not implemented. - RegionGrow( const Self& other ); - Self& operator=( const Self& other ); - }; - - } // ecapseman - -} // ecapseman - -#endif // __fpa__Image__RegionGrow__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/Skeleton.h b/lib/fpa/Image/Skeleton.h deleted file mode 100644 index 4942702..0000000 --- a/lib/fpa/Image/Skeleton.h +++ /dev/null @@ -1,67 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__Skeleton__h__ -#define __fpa__Image__Skeleton__h__ - -#include -#include -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< unsigned int _VDim > - class Skeleton - : public fpa::Base::Graph< typename fpa::Image::PolyLineParametricPath< _VDim >::TIndex, typename fpa::Image::PolyLineParametricPath< _VDim >::Pointer, typename fpa::Image::PolyLineParametricPath< _VDim >::TIndex, typename fpa::Image::PolyLineParametricPath< _VDim >::TIndex::LexicographicCompare > - { - public: - typedef fpa::Image::PolyLineParametricPath< _VDim > TPath; - typedef typename TPath::TIndex TIndex; - typedef typename TIndex::LexicographicCompare TIndexCompare; - typedef typename TPath::Pointer TPathPointer; - - itkStaticConstMacro( Dimension, unsigned int, _VDim ); - - typedef fpa::Base::Graph< TIndex, TPathPointer, TIndex, TIndexCompare > Superclass; - typedef Skeleton Self; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - public: - itkNewMacro( Self ); - itkTypeMacro( Skeleton, fpa::Image::Graph ); - - public: - void AddBranch( TPath* path ); - const TPath* GetBranch( const TIndex& a, const TIndex& b ) const; - - std::vector< TIndex > GetEndPoints( ) const; - std::vector< TIndex > GetBifurcations( ) const; - - protected: - Skeleton( ); - virtual ~Skeleton( ); - - private: - // Purposely not implemented - Skeleton( const Self& other ); - Self& operator=( const Self& other ); - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__Skeleton__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/Skeleton.hxx b/lib/fpa/Image/Skeleton.hxx deleted file mode 100644 index 57a4184..0000000 --- a/lib/fpa/Image/Skeleton.hxx +++ /dev/null @@ -1,99 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__Skeleton__hxx__ -#define __fpa__Image__Skeleton__hxx__ - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -void fpa::Image::Skeleton< _VDim >:: -AddBranch( TPath* path ) -{ - // Check inputs - if( path == NULL ) - return; - unsigned long size = path->GetSize( ); - if( size == 0 ) - return; - TIndex a = path->GetVertex( 0 ); - TIndex b = path->GetVertex( size - 1 ); - if( this->HasEdge( a, b ) ) - return; - - // Add path - this->SetVertex( a, a ); - this->SetVertex( b, b ); - this->AddEdge( a, b, path ); - this->AddEdge( b, a, path ); - this->Modified( ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -const typename fpa::Image::Skeleton< _VDim >:: -TPath* fpa::Image::Skeleton< _VDim >:: -GetBranch( const TIndex& a, const TIndex& b ) const -{ - static const TPath* null_path = NULL; - if( this->HasEdge( a, b ) ) - return( this->GetEdges( a, b ).front( ) ); - else - return( null_path ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -std::vector< typename fpa::Image::Skeleton< _VDim >::TIndex > -fpa::Image::Skeleton< _VDim >:: -GetEndPoints( ) const -{ - std::vector< TIndex > res; - typename Superclass::TMatrix::const_iterator mIt = this->BeginEdgesRows( ); - for( ; mIt != this->EndEdgesRows( ); ++mIt ) - { - unsigned long count = mIt->second.size( ); - if( count == 1 ) - res.push_back( mIt->first ); - - } // rof - return( res ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -std::vector< typename fpa::Image::Skeleton< _VDim >::TIndex > -fpa::Image::Skeleton< _VDim >:: -GetBifurcations( ) const -{ - std::vector< TIndex > res; - typename Superclass::TMatrix::const_iterator mIt = this->BeginEdgesRows( ); - for( ; mIt != this->EndEdgesRows( ); ++mIt ) - { - unsigned long count = mIt->second.size( ); - if( count > 1 ) - res.push_back( mIt->first ); - - } // rof - return( res ); -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -fpa::Image::Skeleton< _VDim >:: -Skeleton( ) - : Superclass( ) -{ -} - -// ------------------------------------------------------------------------- -template< unsigned int _VDim > -fpa::Image::Skeleton< _VDim >:: -~Skeleton( ) -{ -} - -#endif // __fpa__Image__Skeleton__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/SkeletonFilter.h b/lib/fpa/Image/SkeletonFilter.h deleted file mode 100644 index 91ba5b8..0000000 --- a/lib/fpa/Image/SkeletonFilter.h +++ /dev/null @@ -1,152 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__SkeletonFilter__h__ -#define __fpa__Image__SkeletonFilter__h__ - -#include - -#include -#include - -#include -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TInputImage, class _TDistanceMap = itk::SignedMaurerDistanceMapImageFilter< _TInputImage, itk::Image< double, _TInputImage::ImageDimension > > > - class SkeletonFilter - : public itk::ProcessObject - { - public: - typedef SkeletonFilter Self; - typedef itk::ProcessObject Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef _TInputImage TInputImage; - typedef _TDistanceMap TDistanceMap; - itkStaticConstMacro( - Dimension, - unsigned int, - TInputImage::ImageDimension - ); - - typedef typename TDistanceMap::OutputImageType TOutputImage; - typedef typename TInputImage::IndexType TIndex; - typedef typename TOutputImage::PixelType TScalar; - - typedef fpa::Image::Skeleton< Self::Dimension > TSkeleton; - - protected: - typedef std::multimap< TScalar, TIndex > _TSkeletonQueue; - - /** - */ - class _TDijkstra - : public fpa::Image::Dijkstra< TOutputImage, TOutputImage > - { - public: - typedef _TDijkstra Self; - typedef fpa::Image::Dijkstra< TOutputImage, TOutputImage > Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef typename Superclass::TNode TNode; - typedef typename Superclass::TMST TMST; - - public: - itkNewMacro( Self ); - itkTypeMacro( _TDijkstra, fpa::Image::Dijkstra ); - - itkGetConstReferenceMacro( SkeletonQueue, _TSkeletonQueue ); - - protected: - _TDijkstra( ); - virtual ~_TDijkstra( ); - - virtual void _BeforeGenerateData( ) override; - virtual void _UpdateOutputValue( TNode& n ) override; - - private: - // Purposely not implemented - _TDijkstra( const Self& other ); - Self& operator=( const Self& other ); - - protected: - _TSkeletonQueue m_SkeletonQueue; - }; - typedef typename _TDijkstra::TMST _TMST; - - public: - itkNewMacro( Self ); - itkTypeMacro( fpa::Image::SkeletonFilter, fpa::Image::Dijkstra ); - - itkBooleanMacro( SeedFromMaximumDistance ); - itkGetConstMacro( SeedFromMaximumDistance, bool ); - itkSetMacro( SeedFromMaximumDistance, bool ); - - itkGetConstObjectMacro( DistanceMap, TDistanceMap ); - itkGetObjectMacro( DistanceMap, TDistanceMap ); - - itkGetConstMacro( Seed, TIndex ); - itkSetMacro( Seed, TIndex ); - - public: - virtual itk::ModifiedTimeType GetMTime( ) const override; - - void SetInput( TInputImage* input ); - TInputImage* GetInput( ); - const TInputImage* GetInput( ) const; - - TSkeleton* GetOutput( ); - const TSkeleton* GetOutput( ) const; - - protected: - SkeletonFilter( ); - virtual ~SkeletonFilter( ); - - virtual void GenerateData( ) override; - - template< class _TMarksPointer > - void _MarkSphere( - _TMarksPointer& marks, - const TOutputImage* dmap, - const TIndex& center - ); - - void _EndPoints( - std::vector< TIndex >& end_points, - const TOutputImage* dmap, - const _TMST* mst, - const _TSkeletonQueue& queue - ); - - private: - // Purposely not implemented. - SkeletonFilter( const Self& other ); - Self& operator=( const Self& other ); - - protected: - typename TDistanceMap::Pointer m_DistanceMap; - bool m_SeedFromMaximumDistance; - TIndex m_Seed; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__SkeletonFilter__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/SkeletonFilter.hxx b/lib/fpa/Image/SkeletonFilter.hxx deleted file mode 100644 index aa02e59..0000000 --- a/lib/fpa/Image/SkeletonFilter.hxx +++ /dev/null @@ -1,354 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__SkeletonFilter__hxx__ -#define __fpa__Image__SkeletonFilter__hxx__ - -#include -#include -#include -#include - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::_TDijkstra:: -_TDijkstra( ) - : Superclass( ) -{ - // Prepare weight function - typedef fpa::Image::Functors::Dijkstra::Invert< TOutputImage, TScalar > _TWeight; - typename _TWeight::Pointer weight = _TWeight::New( ); - weight->SetAlpha( 1 ); - weight->SetBeta( 1 ); - this->SetWeightFunction( weight ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::_TDijkstra:: -~_TDijkstra( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -void fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::_TDijkstra:: -_BeforeGenerateData( ) -{ - this->Superclass::_BeforeGenerateData( ); - this->m_SkeletonQueue.clear( ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -void fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >::_TDijkstra:: -_UpdateOutputValue( TNode& n ) -{ - typedef typename _TSkeletonQueue::value_type _TSkeletonQueueValue; - - this->Superclass::_UpdateOutputValue( n ); - double d = double( this->GetInput( )->GetPixel( n.Vertex ) ); - if( d >= double( 0 ) ) - { - // Update skeleton candidates - d += double( 1e-5 ); - double v = double( n.Value ) / ( d * d ); - this->m_SkeletonQueue.insert( _TSkeletonQueueValue( v, n.Vertex ) ); - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -itk::ModifiedTimeType -fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -GetMTime( ) const -{ - itk::ModifiedTimeType t = this->Superclass::GetMTime( ); - itk::ModifiedTimeType q = this->m_DistanceMap->GetMTime( ); - return( ( q < t )? q: t ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -void fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -SetInput( TInputImage* input ) -{ - this->Superclass::SetNthInput( 0, input ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -typename fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -TInputImage* fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -GetInput( ) -{ - return( dynamic_cast< TInputImage* >( this->Superclass::GetInput( 0 ) ) ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -const typename fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -TInputImage* fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -GetInput( ) const -{ - return( - dynamic_cast< const TInputImage* >( this->Superclass::GetInput( 0 ) ) - ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -typename fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -TSkeleton* fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -GetOutput( ) -{ - return( dynamic_cast< TSkeleton* >( this->Superclass::GetOutput( 0 ) ) ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -const typename fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -TSkeleton* fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -GetOutput( ) const -{ - return( - dynamic_cast< const TSkeleton* >( this->Superclass::GetOutput( 0 ) ) - ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -SkeletonFilter( ) - : Superclass( ), - m_SeedFromMaximumDistance( false ) -{ - this->SetNumberOfRequiredInputs( 1 ); - this->SetNumberOfRequiredOutputs( 1 ); - this->SetNthOutput( 0, TSkeleton::New( ) ); - - this->m_DistanceMap = TDistanceMap::New( ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -~SkeletonFilter( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -void fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -GenerateData( ) -{ - // Update distance map - this->m_DistanceMap->SetInput( this->GetInput( ) ); - this->m_DistanceMap->Update( ); - - // Correct seed - if( this->m_SeedFromMaximumDistance ) - { - typedef itk::MinimumMaximumImageCalculator< TOutputImage > _TMinMax; - typename _TMinMax::Pointer minmax = _TMinMax::New( ); - minmax->SetImage( this->m_DistanceMap->GetOutput( ) ); - minmax->Compute( ); - this->m_Seed = minmax->GetIndexOfMaximum( ); - - } // fi - - // Compute MST - typename _TDijkstra::Pointer dijkstra = _TDijkstra::New( ); - dijkstra->SetInput( this->m_DistanceMap->GetOutput( ) ); - dijkstra->AddSeed( this->m_Seed ); - dijkstra->Update( ); - - // Compute end-points - const _TMST* mst = dijkstra->GetMinimumSpanningTree( ); - std::vector< TIndex > end_points; - this->_EndPoints( - end_points, this->m_DistanceMap->GetOutput( ), - mst, dijkstra->GetSkeletonQueue( ) - ); - - // Compute symbolic branches - typedef std::map< TIndex, TIndex, typename TIndex::LexicographicCompare > _TTags; - _TTags tags, branches; - typename std::vector< TIndex >::const_iterator eIt = end_points.begin( ); - for( ; eIt != end_points.end( ); ++eIt ) - { - // Tag path - TIndex it = *eIt; - TIndex p = mst->GetParent( it ); - typename _TTags::iterator bIt = tags.end( ); - while( it != p && bIt == tags.end( ) ) - { - typename _TTags::iterator tIt = tags.find( it ); - if( tIt != tags.end( ) ) - { - // Ok, a bifurcation point has been found - // branch1: tIt->second <-> it (ok) - branches[ tIt->second ] = it; - - // branch2: *eit <-> it (ok) - branches[ *eIt ] = it; - - // branch3: it <-> until next bifurcation - bIt = tIt; - } - else - tags[ it ] = *eIt; - it = p; - p = mst->GetParent( it ); - - } // elihw - if( bIt != tags.end( ) ) - { - TIndex pTag = bIt->second; - TIndex nTag = bIt->first; - it = bIt->first; - p = it; - while( tags[ it ] == pTag ) - { - tags[ it ] = nTag; - p = it; - it = mst->GetParent( it ); - - } // elihw - tags[ it ] = nTag; - branches[ bIt->first ] = p; - } - else - { - tags[ it ] = *eIt; - branches[ *eIt ] = it; - - } // fi - - } // rof - - // Fill full branches - typedef typename _TMST::TVertices _TVertices; - typedef typename TSkeleton::TPath _TPath; - - TSkeleton* sk = this->GetOutput( ); - typename _TTags::const_iterator bIt = branches.begin( ); - for( ; bIt != branches.end( ); ++bIt ) - { - _TVertices v = mst->GetPath( bIt->first, bIt->second ); - typename _TPath::Pointer path = _TPath::New( ); - path->SetReferenceImage( this->GetInput( ) ); - typename _TVertices::const_reverse_iterator vIt = v.rbegin( ); - for( ; vIt != v.rend( ); ++vIt ) - path->AddVertex( *vIt ); - sk->AddBranch( path ); - - } // rof -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -template< class _TMarksPointer > -void fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -_MarkSphere( - _TMarksPointer& marks, const TOutputImage* dmap, const TIndex& center - ) -{ - typedef typename _TMarksPointer::ObjectType _TMarks; - typedef itk::ImageRegionIteratorWithIndex< _TMarks > _TMarksIt; - - static const double _eps = std::sqrt( double( Self::Dimension + 1 ) ); - typename _TMarks::SpacingType spac = dmap->GetSpacing( ); - typename _TMarks::RegionType region = dmap->GetRequestedRegion( ); - - typename _TMarks::PointType cnt; - dmap->TransformIndexToPhysicalPoint( center, cnt ); - double r = double( dmap->GetPixel( center ) ) * _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 ] = center[ d ] - off; - i1[ d ] = center[ 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 _TMarks::SizeType size; - for( unsigned int d = 0; d < Self::Dimension; ++d ) - size[ d ] = i1[ d ] - i0[ d ] + 1; - - typename _TMarks::RegionType neighRegion; - neighRegion.SetIndex( i0 ); - neighRegion.SetSize( size ); - - _TMarksIt mIt( marks, neighRegion ); - for( mIt.GoToBegin( ); !mIt.IsAtEnd( ); ++mIt ) - mIt.Set( true ); -} - -// ------------------------------------------------------------------------- -template< class _TInputImage, class _TDistanceMap > -void fpa::Image::SkeletonFilter< _TInputImage, _TDistanceMap >:: -_EndPoints( - std::vector< TIndex >& end_points, - const TOutputImage* dmap, - const _TMST* mst, - const _TSkeletonQueue& queue - ) -{ - typedef typename _TSkeletonQueue::value_type _TSkeletonQueueValue; - - // Some values - typedef itk::Image< bool, Self::Dimension > _TMarks; - typename _TMarks::Pointer marks = _TMarks::New( ); - 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( false ); - - // Get candidates in maximum to minimum iteration - typename _TSkeletonQueue::const_reverse_iterator nIt = queue.rbegin( ); - for( ; nIt != queue.rend( ); ++nIt ) - { - // Mark it and update end-points - if( !( marks->GetPixel( nIt->second ) ) ) - { - marks->SetPixel( nIt->second, true ); - end_points.push_back( nIt->second ); - - // Mark path - TIndex it = nIt->second; - TIndex p = mst->GetParent( it ); - while( it != p ) - { - this->_MarkSphere( marks, dmap, it ); - it = p; - p = mst->GetParent( it ); - - } // elihw - this->_MarkSphere( marks, dmap, it ); - - } // fi - - } // rof -} - -#endif // __fpa__Image__SkeletonFilter__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/SkeletonReader.h b/lib/fpa/Image/SkeletonReader.h deleted file mode 100644 index 2afce07..0000000 --- a/lib/fpa/Image/SkeletonReader.h +++ /dev/null @@ -1,83 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__SkeletonReader__h__ -#define __fpa__Image__SkeletonReader__h__ - -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TSkeleton > - class SkeletonReader - : public itk::ProcessObject - { - public: - // Basic types - typedef SkeletonReader Self; - typedef itk::ProcessObject Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef _TSkeleton TSkeleton; - - public: - itkNewMacro( Self ); - itkTypeMacro( SkeletonReader, itk::ProcessObject ); - - itkGetConstMacro( FileName, std::string ); - itkSetMacro( FileName, std::string ); - - public: - TSkeleton* GetOutput( ); - TSkeleton* GetOutput( unsigned int i ); - - virtual void GraftOutput( itk::DataObject* out ); - virtual void GraftOutput( - const typename Superclass::DataObjectIdentifierType& key, - itk::DataObject* out - ); - virtual void GraftNthOutput( unsigned int i, itk::DataObject* out ); - virtual itk::DataObject::Pointer MakeOutput( - itk::ProcessObject::DataObjectPointerArraySizeType i - ) override; - - virtual void Update( ) override - { this->GenerateData( ); } - - protected: - SkeletonReader( ); - virtual ~SkeletonReader( ); - - virtual void GenerateData( ) override; - - // Do nothing - virtual void GenerateOutputInformation( ) override - { } - - private: - // Purposely not implemented - SkeletonReader( const Self& ); - void operator=( const Self& ); - - protected: - std::string m_FileName; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__SkeletonReader__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/SkeletonReader.hxx b/lib/fpa/Image/SkeletonReader.hxx deleted file mode 100644 index 95e93fb..0000000 --- a/lib/fpa/Image/SkeletonReader.hxx +++ /dev/null @@ -1,209 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__SkeletonReader__hxx__ -#define __fpa__Image__SkeletonReader__hxx__ - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -_TSkeleton* fpa::Image::SkeletonReader< _TSkeleton >:: -GetOutput( ) -{ - return( - itkDynamicCastInDebugMode< TSkeleton* >( this->GetPrimaryOutput( ) ) - ); -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -_TSkeleton* fpa::Image::SkeletonReader< _TSkeleton >:: -GetOutput( unsigned int i ) -{ - return( - itkDynamicCastInDebugMode< TSkeleton* >( - this->itk::ProcessObject::GetOutput( i ) - ) - ); -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -void fpa::Image::SkeletonReader< _TSkeleton >:: -GraftOutput( itk::DataObject* out ) -{ - this->GraftNthOutput( 0, out ); -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -void fpa::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::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::Image::SkeletonReader< _TSkeleton >:: -MakeOutput( itk::ProcessObject::DataObjectPointerArraySizeType i ) -{ - return( TSkeleton::New( ).GetPointer( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -fpa::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::Image::SkeletonReader< _TSkeleton >:: -~SkeletonReader( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -void fpa::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__Image__SkeletonReader__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/SkeletonToPolyDataFilter.h b/lib/fpa/Image/SkeletonToPolyDataFilter.h deleted file mode 100644 index 9c2b941..0000000 --- a/lib/fpa/Image/SkeletonToPolyDataFilter.h +++ /dev/null @@ -1,78 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__SkeletonToPolyDataFilter__h__ -#define __fpa__Image__SkeletonToPolyDataFilter__h__ - -#include - -#ifdef USE_VTK -# include -#endif // USE_VTK - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TSkeleton > - class SkeletonToPolyDataFilter -#ifdef USE_VTK - : public vtkPolyDataAlgorithm -#endif // USE_VTK - { - public: - typedef SkeletonToPolyDataFilter Self; - typedef _TSkeleton TSkeleton; - - public: -#ifdef USE_VTK - vtkTypeMacro( SkeletonToPolyDataFilter, vtkPolyDataAlgorithm ); -#endif // USE_VTK - - public: - static Self* New( ); - - const TSkeleton* GetInput( ) const; - void SetInput( const TSkeleton* sk ); - - protected: - SkeletonToPolyDataFilter( ); - virtual ~SkeletonToPolyDataFilter( ); - -#ifdef USE_VTK - int RequestData( - vtkInformation* information, - vtkInformationVector** input, - vtkInformationVector* output - ); - int RequestInformation( - vtkInformation* information, - vtkInformationVector** input, - vtkInformationVector* output - ); -#endif // USE_VTK - - private: - // Purposely not implemented - SkeletonToPolyDataFilter( const Self& ); - void operator=( const Self& ); - - protected: - const TSkeleton* m_Skeleton; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__SkeletonToPolyDataFilter__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/SkeletonToPolyDataFilter.hxx b/lib/fpa/Image/SkeletonToPolyDataFilter.hxx deleted file mode 100644 index c9d1136..0000000 --- a/lib/fpa/Image/SkeletonToPolyDataFilter.hxx +++ /dev/null @@ -1,166 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__SkeletonToPolyDataFilter__hxx__ -#define __fpa__Image__SkeletonToPolyDataFilter__hxx__ - -#ifdef USE_VTK -# include -# include -# include -# include -# include -# include -#endif // USE_VTK - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -typename fpa::Image::SkeletonToPolyDataFilter< _TSkeleton >:: -Self* fpa::Image::SkeletonToPolyDataFilter< _TSkeleton >:: -New( ) -{ - return( new Self( ) ); -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -const typename -fpa::Image::SkeletonToPolyDataFilter< _TSkeleton >:: -TSkeleton* fpa::Image::SkeletonToPolyDataFilter< _TSkeleton >:: -GetInput( ) const -{ - return( this->m_Skeleton ); -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -void fpa::Image::SkeletonToPolyDataFilter< _TSkeleton >:: -SetInput( const TSkeleton* sk ) -{ - if( this->m_Skeleton != sk ) - { - this->m_Skeleton = sk; -#ifdef USE_VTK - this->Modified( ); -#endif // USE_VTK - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -fpa::Image::SkeletonToPolyDataFilter< _TSkeleton >:: -SkeletonToPolyDataFilter( ) -#ifdef USE_VTK - : vtkPolyDataAlgorithm( ), - m_Skeleton( NULL ) -#endif // USE_VTK -{ -#ifdef USE_VTK - this->SetNumberOfInputPorts( 0 ); -#endif // USE_VTK -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -fpa::Image::SkeletonToPolyDataFilter< _TSkeleton >:: -~SkeletonToPolyDataFilter( ) -{ -} - -#ifdef USE_VTK -// ------------------------------------------------------------------------- -template< class _TSkeleton > -int fpa::Image::SkeletonToPolyDataFilter< _TSkeleton >:: -RequestData( - vtkInformation* information, - vtkInformationVector** input, - vtkInformationVector* output - ) -{ - typedef typename _TSkeleton::TPath _TPath; - static const unsigned int dim = _TPath::PathDimension; - - if( this->m_Skeleton == NULL ) - return( 0 ); - - // Get output - vtkInformation* info = output->GetInformationObject( 0 ); - vtkPolyData* out = vtkPolyData::SafeDownCast( - info->Get( vtkDataObject::DATA_OBJECT( ) ) - ); - - // Prepare data - out->SetPoints( vtkSmartPointer< vtkPoints >::New( ) ); - out->SetVerts( vtkSmartPointer< vtkCellArray >::New( ) ); - out->SetLines( vtkSmartPointer< vtkCellArray >::New( ) ); - out->SetPolys( vtkSmartPointer< vtkCellArray >::New( ) ); - out->SetStrips( vtkSmartPointer< vtkCellArray >::New( ) ); - vtkSmartPointer< vtkUnsignedIntArray > darray = - vtkSmartPointer< vtkUnsignedIntArray >::New( ); - darray->SetNumberOfComponents( 1 ); - out->GetPointData( )->SetScalars( darray ); - vtkPoints* points = out->GetPoints( ); - vtkCellArray* lines = out->GetLines( ); - - // Assign all data - unsigned int dcount = 0; - typename TSkeleton::TMatrix::const_iterator mIt = this->m_Skeleton->BeginEdgesRows( ); - for( ; mIt != this->m_Skeleton->EndEdgesRows( ); ++mIt ) - { - // TODO: mIt->first; --> this is the row index. <-- - typename TSkeleton::TMatrixRow::const_iterator rIt = mIt->second.begin( ); - for( ; rIt != mIt->second.end( ); ++rIt ) - { - // TODO: rIt->first; --> this is the column index. - typename TSkeleton::TEdges::const_iterator eIt = rIt->second.begin( ); - for( ; eIt != rIt->second.end( ); ++eIt ) - { - _TPath* path = *eIt; - for( unsigned long i = 0; i < path->GetSize( ); ++i ) - { - auto pnt = path->GetPoint( i ); - if( dim == 1 ) - points->InsertNextPoint( pnt[ 0 ], 0, 0 ); - else if( dim == 2 ) - points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], 0 ); - else - points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] ); - darray->InsertNextTuple1( double( dcount ) ); - if( i > 0 ) - { - lines->InsertNextCell( 2 ); - lines->InsertCellPoint( points->GetNumberOfPoints( ) - 2 ); - lines->InsertCellPoint( points->GetNumberOfPoints( ) - 1 ); - - } // fi - - } // rof - dcount++; - - } // rof - - } // rof - - } // rof - return( 1 ); -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -int fpa::Image::SkeletonToPolyDataFilter< _TSkeleton >:: -RequestInformation( - vtkInformation* information, - vtkInformationVector** input, - vtkInformationVector* output - ) -{ - return( 1 ); -} -#endif // USE_VTK - -#endif // __fpa__Image__SkeletonToPolyDataFilterFilter__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/SkeletonWriter.h b/lib/fpa/Image/SkeletonWriter.h deleted file mode 100644 index 400d6ac..0000000 --- a/lib/fpa/Image/SkeletonWriter.h +++ /dev/null @@ -1,72 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__SkeletonWriter__h__ -#define __fpa__Image__SkeletonWriter__h__ - -#include - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TSkeleton > - class SkeletonWriter - : public itk::ProcessObject - { - public: - // Basic types - typedef SkeletonWriter Self; - typedef itk::ProcessObject Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef _TSkeleton TSkeleton; - typedef typename TSkeleton::TEdges TEdges; - typedef typename TSkeleton::TMatrix TMatrix; - typedef typename TSkeleton::TMatrixRow TMatrixRow; - typedef typename TSkeleton::TPath TPath; - typedef typename TSkeleton::TVertex TVertex; - - public: - itkNewMacro( Self ); - itkTypeMacro( SkeletonWriter, itk::ProcessObject ); - - itkGetConstMacro( FileName, std::string ); - itkSetMacro( FileName, std::string ); - - public: - const TSkeleton* GetInput( ) const; - void SetInput( const TSkeleton* skeleton ); - virtual void Update( ) override; - - protected: - SkeletonWriter( ); - virtual ~SkeletonWriter( ); - - virtual void GenerateData( ) override; - - private: - // Purposely not implemented - SkeletonWriter( const Self& ); - void operator=( const Self& ); - - protected: - std::string m_FileName; - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__SkeletonWriter__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/SkeletonWriter.hxx b/lib/fpa/Image/SkeletonWriter.hxx deleted file mode 100644 index c277dac..0000000 --- a/lib/fpa/Image/SkeletonWriter.hxx +++ /dev/null @@ -1,162 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__SkeletonWriter__hxx__ -#define __fpa__Image__SkeletonWriter__hxx__ - -#include - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -const _TSkeleton* fpa::Image::SkeletonWriter< _TSkeleton >:: -GetInput( ) const -{ - return( - dynamic_cast< const TSkeleton* >( - this->itk::ProcessObject::GetInput( 0 ) - ) - ); -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -void fpa::Image::SkeletonWriter< _TSkeleton >:: -SetInput( const _TSkeleton* skeleton ) -{ - this->itk::ProcessObject::SetNthInput( - 0, const_cast< TSkeleton* >( skeleton ) - ); -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -void fpa::Image::SkeletonWriter< _TSkeleton >:: -Update( ) -{ - TSkeleton* input = const_cast< TSkeleton* >( this->GetInput( ) ); - if( input != NULL ) - { - input->UpdateOutputInformation( ); - input->UpdateOutputData( ); - this->GenerateData( ); - this->ReleaseInputs( ); - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -fpa::Image::SkeletonWriter< _TSkeleton >:: -SkeletonWriter( ) - : Superclass( ), - m_FileName( "" ) -{ - this->SetNumberOfRequiredInputs( 1 ); -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -fpa::Image::SkeletonWriter< _TSkeleton >:: -~SkeletonWriter( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TSkeleton > -void fpa::Image::SkeletonWriter< _TSkeleton >:: -GenerateData( ) -{ - const TSkeleton* sk = this->GetInput( ); - typename TMatrix::const_iterator mIt = sk->BeginEdgesRows( ); - typename TMatrixRow::const_iterator rIt = mIt->second.begin( ); - typename TEdges::const_iterator eIt = rIt->second.begin( ); - const TPath* path = *eIt; - - // Write base information - std::stringstream out1, out2; - out1 << TSkeleton::Dimension << std::endl; - typename TPath::TSpacing spa = path->GetSpacing( ); - for( unsigned int d = 0; d < TSkeleton::Dimension; ++d ) - out1 << spa[ d ] << " "; - out1 << std::endl; - typename TPath::TDirection dir = path->GetDirection( ); - for( unsigned int d = 0; d < TSkeleton::Dimension; ++d ) - for( unsigned int e = 0; e < TSkeleton::Dimension; ++e ) - out1 << dir[ d ][ e ] << " "; - out1 << std::endl; - typename TPath::TPoint ori = path->GetOrigin( ); - for( unsigned int d = 0; d < TSkeleton::Dimension; ++d ) - out1 << ori[ d ] << " "; - out1 << std::endl; - - // End points - std::vector< TVertex > end_points = sk->GetEndPoints( ); - out1 << end_points.size( ) << std::endl; - typename std::vector< TVertex >::const_iterator epIt = end_points.begin( ); - for( ; epIt != end_points.end( ); ++epIt ) - { - for( unsigned int d = 0; d < TSkeleton::Dimension; ++d ) - out1 << ( *epIt )[ d ] << " "; - out1 << std::endl; - - } // rof - - // Bifurcations - std::vector< TVertex > bifurcations = sk->GetBifurcations( ); - out1 << bifurcations.size( ) << std::endl; - typename std::vector< TVertex >::const_iterator bIt = bifurcations.begin( ); - for( ; bIt != bifurcations.end( ); ++bIt ) - { - for( unsigned int d = 0; d < TSkeleton::Dimension; ++d ) - out1 << ( *bIt )[ d ] << " "; - out1 << std::endl; - - } // rof - - // Write paths - unsigned long pathCount = 0; - mIt = sk->BeginEdgesRows( ); - for( ; mIt != sk->EndEdgesRows( ); ++mIt ) - { - typename TMatrixRow::const_iterator rIt = mIt->second.begin( ); - for( ; rIt != mIt->second.end( ); ++rIt ) - { - typename TEdges::const_iterator eIt = rIt->second.begin( ); - for( ; eIt != rIt->second.end( ); ++eIt ) - { - TPath* path = *eIt; - pathCount++; - unsigned int size = path->GetSize( ); - out2 << size << std::endl; - for( unsigned int i = 0; i < path->GetSize( ); ++i ) - { - TVertex v = path->GetVertex( i ); - for( unsigned int d = 0; d < TSkeleton::Dimension; ++d ) - out2 << v[ d ] << " "; - - } // rof - out2 << std::endl; - - } // rof - - } // rof - - } // rof - out1 << pathCount << std::endl << out2.str( ); - - // Real write - std::ofstream file_stream( this->m_FileName.c_str( ), std::ofstream::binary ); - if( !file_stream ) - itkExceptionMacro( - << "Unable to write skeleton to \"" - << this->m_FileName - << "\"" - ); - file_stream.write( out1.str( ).c_str( ), out1.str( ).size( ) ); -} - -#endif // __fpa__Image__SkeletonWriter__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/VisualDebugger.h b/lib/fpa/Image/VisualDebugger.h deleted file mode 100644 index 90e94e1..0000000 --- a/lib/fpa/Image/VisualDebugger.h +++ /dev/null @@ -1,98 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__VisualDebugger__h__ -#define __fpa__Image__VisualDebugger__h__ - -#include - -#include - -#include -#include -#include - -#ifdef USE_ivq -#include -#endif // USE_ivq - -class vtkRenderer; -class vtkRenderWindowInteractor; - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TFilter > - class VisualDebugger - : public itk::Command - { - public: - typedef VisualDebugger Self; - typedef itk::Command Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef _TFilter TFilter; - typedef typename TFilter::TInputImage TImage; - - typedef itk::RGBAPixel< unsigned char > TLabel; - typedef itk::Image< TLabel, TImage::ImageDimension > TLabels; -#ifdef USE_ivq - typedef itk::ImageToVTKImageFilter< TLabels > TVTKLabels; -#endif // USE_ivq - - public: - itkTypeMacro( fpa::Image::VisualDebugger, itk::Command ); - - itkGetConstObjectMacro( Labels, TLabels ); - - public: - void SetVisualization( - vtkRenderer* renderer, vtkRenderWindowInteractor* iren - ); - virtual void Execute( - itk::Object* caller, const itk::EventObject& event - ) override; - virtual void Execute( - const itk::Object* caller, const itk::EventObject& event - ) override; - - virtual void Render( ) = 0; - virtual void StartVisualization( ) = 0; - virtual void EndVisualization( ) = 0; - - protected: - VisualDebugger( ); - virtual ~VisualDebugger( ); - - private: - // Purposely not implemented. - VisualDebugger( const Self& other ); - Self& operator=( const Self& other ); - - protected: - std::vector< TLabel > m_Colors; - typename TLabels::Pointer m_Labels; -#ifdef USE_ivq - vtkRenderer* m_Renderer; - vtkRenderWindowInteractor* m_Interactor; - typename TVTKLabels::Pointer m_VTKLabels; -#endif // USE_ivq - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__VisualDebugger__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/VisualDebugger.hxx b/lib/fpa/Image/VisualDebugger.hxx deleted file mode 100644 index d45a803..0000000 --- a/lib/fpa/Image/VisualDebugger.hxx +++ /dev/null @@ -1,134 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__VisualDebugger__hxx__ -#define __fpa__Image__VisualDebugger__hxx__ - -// ------------------------------------------------------------------------- -template< class _TFilter > -void fpa::Image::VisualDebugger< _TFilter >:: -SetVisualization( vtkRenderer* renderer, vtkRenderWindowInteractor* iren ) -{ -#ifdef USE_ivq - this->m_Renderer = renderer; - this->m_Interactor = iren; - this->Modified( ); -#endif // USE_ivq -} - -// ------------------------------------------------------------------------- -template< class _TFilter > -void fpa::Image::VisualDebugger< _TFilter >:: -Execute( itk::Object* caller, const itk::EventObject& event ) -{ - this->Execute( const_cast< const itk::Object* >( caller ), event ); -} - -// ------------------------------------------------------------------------- -template< class _TFilter > -void fpa::Image::VisualDebugger< _TFilter >:: -Execute( const itk::Object* caller, const itk::EventObject& event ) -{ - typedef itk::StartEvent _TStart; - typedef itk::EndEvent _TEnd; - typedef typename _TFilter::TEvent _TEvent; - - // Check validity - const TFilter* filter = dynamic_cast< const TFilter* >( caller ); - if( filter == NULL ) - return; - - // Get correct event type - const _TEvent* ev_fpa = dynamic_cast< const _TEvent* >( &event ); - const _TStart* ev_start = dynamic_cast< const _TStart* >( &event ); - const _TEnd* ev_end = dynamic_cast< const _TEnd* >( &event ); - if( ev_fpa != NULL ) - { - if( this->m_Labels.IsNotNull( ) ) - { - TLabel new_color; - if( ev_fpa->IntoQueue ) - new_color = this->m_Colors[ this->m_Colors.size( ) - 2 ]; - else - new_color = - this->m_Colors[ - ( ev_fpa->FrontId - 1 ) % ( this->m_Colors.size( ) - 2 ) - ]; - TLabel old_color = this->m_Labels->GetPixel( ev_fpa->Vertex ); - if( !( new_color == old_color ) ) - { - this->m_Labels->SetPixel( ev_fpa->Vertex, new_color ); - this->m_VTKLabels->Modified( ); - this->Render( ); - - } // fi - - } // fi - } - else if( ev_start != NULL ) - { - const TImage* image = filter->GetInput( ); - this->m_Labels = TLabels::New( ); - this->m_Labels-> - SetLargestPossibleRegion( image->GetLargestPossibleRegion( ) ); - this->m_Labels->SetRequestedRegion( image->GetRequestedRegion( ) ); - this->m_Labels->SetBufferedRegion( image->GetBufferedRegion( ) ); - this->m_Labels->SetOrigin( image->GetOrigin( ) ); - this->m_Labels->SetSpacing( image->GetSpacing( ) ); - this->m_Labels->SetDirection( image->GetDirection( ) ); - this->m_Labels->Allocate( ); - this->m_Labels->FillBuffer( this->m_Colors.back( ) ); -#ifdef USE_ivq - this->m_VTKLabels = TVTKLabels::New( ); - this->m_VTKLabels->SetInput( this->m_Labels ); - this->m_VTKLabels->Update( ); - this->StartVisualization( ); -#endif // USE_ivq - } - else if( ev_end != NULL ) - { - this->EndVisualization( ); - this->m_Labels = NULL; - this->m_VTKLabels = NULL; - - } // fi -} - -// ------------------------------------------------------------------------- -template< class _TFilter > -fpa::Image::VisualDebugger< _TFilter >:: -VisualDebugger( ) - : Superclass( ) -{ - unsigned char colors[ 8 ][ 4 ] = - { - { 255, 0, 0, 128 }, - { 0, 255, 0, 128 }, - { 0, 0, 255, 128 }, - { 0, 255, 255, 128 }, - { 255, 0, 255, 128 }, - { 255, 255, 0, 128 }, - { 255, 128, 64, 255 }, - { 0, 0, 0, 0 } - }; - for( unsigned int i = 0; i < 8; ++i ) - this->m_Colors.push_back( TLabel( colors[ i ] ) ); - -#ifdef USE_ivq - this->m_Renderer = NULL; - this->m_Interactor = NULL; -#endif // USE_ivq -} - -// ------------------------------------------------------------------------- -template< class _TFilter > -fpa::Image::VisualDebugger< _TFilter >:: -~VisualDebugger( ) -{ -} - -#endif // __fpa__Image__VisualDebugger__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/VisualDebugger2D.h b/lib/fpa/Image/VisualDebugger2D.h deleted file mode 100644 index 21346d9..0000000 --- a/lib/fpa/Image/VisualDebugger2D.h +++ /dev/null @@ -1,76 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__VisualDebugger2D__h__ -#define __fpa__Image__VisualDebugger2D__h__ - -#include -#ifdef USE_ivq -#include -#include -#endif // USE_ivq - -namespace fpa -{ - namespace Image - { - /** - */ - template< class _TFilter > - class VisualDebugger2D - : public fpa::Image::VisualDebugger< _TFilter > - { - public: - typedef VisualDebugger2D Self; - typedef fpa::Image::VisualDebugger< _TFilter > Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - typedef typename Superclass::TFilter TFilter; - typedef typename Superclass::TImage TImage; - typedef typename Superclass::TLabel TLabel; - typedef typename Superclass::TLabels TLabels; -#ifdef USE_ivq - typedef typename Superclass::TVTKLabels TVTKLabels; - typedef ivq::VTK::ImageActor TImageActor; -#endif // USE_ivq - - public: - itkNewMacro( Self ); - itkTypeMacro( fpa::Image::VisualDebugger2D, fpa::Image::VisualDebugger ); - - public: - virtual void Render( ) override; - virtual void StartVisualization( ) override; - virtual void EndVisualization( ) override; - - protected: - VisualDebugger2D( ); - virtual ~VisualDebugger2D( ); - - private: - // Purposely not implemented. - VisualDebugger2D( const Self& other ); - Self& operator=( const Self& other ); - - protected: -#ifdef USE_ivq - vtkSmartPointer< TImageActor > m_Actor; - unsigned long m_NumberOfPixels; - unsigned long m_RenderCount; -#endif // USE_ivq - }; - - } // ecapseman - -} // ecapseman - -#ifndef ITK_MANUAL_INSTANTIATION -# include -#endif // ITK_MANUAL_INSTANTIATION - -#endif // __fpa__Image__VisualDebugger2D__h__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Image/VisualDebugger2D.hxx b/lib/fpa/Image/VisualDebugger2D.hxx deleted file mode 100644 index 91eff97..0000000 --- a/lib/fpa/Image/VisualDebugger2D.hxx +++ /dev/null @@ -1,74 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__Image__VisualDebugger2D__hxx__ -#define __fpa__Image__VisualDebugger2D__hxx__ - -#include -#include - -// ------------------------------------------------------------------------- -template< class _TFilter > -void fpa::Image::VisualDebugger2D< _TFilter >:: -Render( ) -{ -#ifdef USE_ivq - if( this->m_Renderer == NULL || this->m_Interactor == NULL ) - return; - this->m_Actor->Modified( ); - this->m_RenderCount = ( this->m_RenderCount + 1 ) % this->m_NumberOfPixels; - if( this->m_RenderCount == 0 ) - this->m_Interactor->Render( ); -#endif // USE_ivq -} - -// ------------------------------------------------------------------------- -template< class _TFilter > -void fpa::Image::VisualDebugger2D< _TFilter >:: -StartVisualization( ) -{ -#ifdef USE_ivq - if( this->m_Renderer == NULL || this->m_Interactor == NULL ) - return; - this->m_Actor = vtkSmartPointer< TImageActor >::New( ); - this->m_Actor->SetInputData( this->m_VTKLabels->GetOutput( ) ); - this->m_Actor->Update( ); - this->m_Renderer->AddViewProp( this->m_Actor ); - - this->m_NumberOfPixels = - double( - this->m_VTKLabels->GetInput( )-> - GetRequestedRegion( ).GetNumberOfPixels( ) - ) * 0.005; - this->m_RenderCount = 0; - -#endif // USE_ivq -} - -// ------------------------------------------------------------------------- -template< class _TFilter > -void fpa::Image::VisualDebugger2D< _TFilter >:: -EndVisualization( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TFilter > -fpa::Image::VisualDebugger2D< _TFilter >:: -VisualDebugger2D( ) - : Superclass( ) -{ -} - -// ------------------------------------------------------------------------- -template< class _TFilter > -fpa::Image::VisualDebugger2D< _TFilter >:: -~VisualDebugger2D( ) -{ -} - -#endif // __fpa__Image__VisualDebugger2D__hxx__ - -// eof - $RCSfile$ diff --git a/lib/fpa/Version.cxx.in b/lib/fpa/Version.cxx.in deleted file mode 100644 index 445f314..0000000 --- a/lib/fpa/Version.cxx.in +++ /dev/null @@ -1,7 +0,0 @@ - -#include -#include - -std::string FPA_EXPORT version( ) { return( "@prj_VER@" ); } - -// eof - $RCSfile$ diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt deleted file mode 100644 index 7a3c48b..0000000 --- a/tests/CMakeLists.txt +++ /dev/null @@ -1,10 +0,0 @@ -option(fpa_BUILD_TESTS "Build command line tests." OFF) -if(fpa_BUILD_TESTS) - include_directories( - ${PROJECT_SOURCE_DIR}/lib - ${PROJECT_BINARY_DIR}/lib - ) - subdirs(image) -endif(fpa_BUILD_TESTS) - -## eof - $RCSfile$ diff --git a/tests/image/BaseFunctions.h b/tests/image/BaseFunctions.h deleted file mode 100644 index fc76be7..0000000 --- a/tests/image/BaseFunctions.h +++ /dev/null @@ -1,248 +0,0 @@ -// ========================================================================= -// @author Leonardo Florez Valencia -// @email florez-l@javeriana.edu.co -// ========================================================================= - -#ifndef __fpa__tests__image__BaseFunctions__h__ -#define __fpa__tests__image__BaseFunctions__h__ - -#include -#include - -#include -#include - -#include -/* TODO - #ifdef USE_ivq - # include - # include - # include - # include - # include - # include - # include - # include - #endif // USE_ivq -*/ - -namespace fpa -{ - namespace tests - { - namespace image - { - // ------------------------------------------------------------------- - template< class _TPointer > - void CreateImage( - _TPointer& img, - const typename _TPointer::ObjectType::PixelType& zero, - ... - ) - { - typedef typename _TPointer::ObjectType _TImage; - - va_list vl; - va_start( vl, zero ); - - typename _TImage::SizeType size; - for( unsigned int d = 0; d < _TImage::ImageDimension; ++d ) - size[ d ] = va_arg( vl, int ); - - typename _TImage::SpacingType spac; - for( unsigned int d = 0; d < _TImage::ImageDimension; ++d ) - spac[ d ] = va_arg( vl, double ); - - img = _TImage::New( ); - img->SetRegions( size ); - img->SetSpacing( spac ); - img->Allocate( ); - img->FillBuffer( zero ); - - va_end( vl ); - } - - // ------------------------------------------------------------------- - template< class _TPointer > - std::string Read( _TPointer& img, const std::string& fname ) - { - typedef typename _TPointer::ObjectType _TImage; - typedef itk::ImageFileReader< _TImage > _TReader; - - typename _TReader::Pointer reader = _TReader::New( ); - reader->SetFileName( fname ); - try - { - reader->Update( ); - } - catch( std::exception& err ) - { - return( err.what( ) ); - - } // ytr - img = reader->GetOutput( ); - img->DisconnectPipeline( ); - return( "" ); - } - - // ------------------------------------------------------------------- - template< class _TImage > - std::string Write( const _TImage* img, const std::string& fname ) - { - typedef itk::ImageFileWriter< _TImage > _TWriter; - - typename _TWriter::Pointer writer = _TWriter::New( ); - writer->SetInput( img ); - writer->SetFileName( fname ); - try - { - writer->Update( ); - } - catch( std::exception& err ) - { - return( err.what( ) ); - - } // ytr - return( "" ); - } - - // ------------------------------------------------------------------- - /* TODO - #ifdef USE_ivq - template< class _TFilter > - class Viewer - { - public: - typedef _TFilter TFilter; - typedef typename _TFilter::TInputImage TInputImage; - - public: - Viewer( const TInputImage* image ) - { - this->m_VTKInputImage = TVTKInputImage::New( ); - this->m_VTKInputImage->SetInput( image ); - this->m_VTKInputImage->Update( ); - - this->m_Viewer = vtkSmartPointer< ivq::VTK::ImageViewer >::New( ); - this->m_Viewer->SetInputData( this->m_VTKInputImage->GetOutput( ) ); - } - - virtual ~Viewer( ) - { - } - - void ActivateSeedWidget( ) - { - this->m_SeedWidget = - vtkSmartPointer< ivq::VTK::SeedWidgetOverImageActor >::New( ); - this->m_SeedWidget->SetActor( this->m_Viewer->GetImageActor( ) ); - this->m_SeedWidget->SetInteractor( - this->m_Viewer->GetRenderWindow( )->GetInteractor( ) - ); - } - - void ActivateBrushWidget( ) - { - this->m_BrushWidget = - vtkSmartPointer< ivq::VTK::BrushWidget >::New( ); - this->m_BrushWidget->SetImageActor( this->m_Viewer->GetImageActor( ) ); - this->m_BrushWidget->SetInteractor( - this->m_Viewer->GetRenderWindow( )->GetInteractor( ) - ); - } - - void Show( ) - { - this->m_Viewer->Render( ); - this->m_Viewer->ResetCamera( ); - this->m_Viewer->Initialize( ); - this->m_Viewer->Render( ); - if( this->m_SeedWidget.GetPointer( ) != NULL ) - this->m_SeedWidget->EnabledOn( ); - if( this->m_BrushWidget.GetPointer( ) != NULL ) - this->m_BrushWidget->EnabledOn( ); - this->m_Viewer->Start( ); - if( this->m_SeedWidget.GetPointer( ) != NULL ) - this->m_SeedWidget->EnabledOff( ); - if( this->m_BrushWidget.GetPointer( ) != NULL ) - this->m_BrushWidget->EnabledOff( ); - } - - void AssociateSeedsTo( TFilter* filter ) - { - if( this->m_SeedWidget.GetPointer( ) != NULL ) - { - const ivq::VTK::SeedWidgetOverImageActor::TSeeds& wdg_seeds = - this->m_SeedWidget->GetSeeds( ); - ivq::VTK::SeedWidgetOverImageActor::TSeeds::const_iterator wsIt; - for( wsIt = wdg_seeds.begin( ); wsIt != wdg_seeds.end( ); ++wsIt ) - { - typename TInputImage::PointType pnt; - for( unsigned int i = 0; i < wsIt->second.size( ); i += 3 ) - { - pnt[ 0 ] = wsIt->second[ i ]; - pnt[ 1 ] = wsIt->second[ i + 1 ]; - - typename TInputImage::IndexType idx; - filter->GetInput( )->TransformPhysicalPointToIndex( pnt, idx ); - filter->AddSeed( idx ); - - } // rof - - } // rof - - } // fi - } - - void AssociateLabelsTo( TFilter* filter ) - { - if( this->m_BrushWidget.GetPointer( ) != NULL ) - { - typedef typename TFilter::TLabelImage _TLabelImage; - typedef itk::VTKImageToImageFilter< _TLabelImage > TITKImage; - typename TITKImage::Pointer itk_image = TITKImage::New( ); - itk_image->SetInput( this->m_BrushWidget->GetCanvas( ) ); - itk_image->Update( ); - filter->SetLabels( itk_image->GetOutput( ) ); - - } // fi - } - - void ObserveFilter( TFilter* filter ) - { - typedef fpa::Image::VisualDebugger2D< TFilter > _TDeb; - typedef typename TFilter::TEvent _TEvent; - typename _TDeb::Pointer deb = _TDeb::New( ); - deb->SetVisualization( - this->m_Viewer->GetRenderer( ), - this->m_Viewer->GetRenderWindow( )->GetInteractor( ) - ); - this->m_Observer1 = filter->AddObserver( itk::StartEvent( ), deb ); - this->m_Observer2 = filter->AddObserver( itk::EndEvent( ), deb ); - this->m_Observer3 = filter->AddObserver( _TEvent( ), deb ); - filter->VisualDebugOn( ); - } - - protected: - typedef itk::ImageToVTKImageFilter< TInputImage > TVTKInputImage; - typename TVTKInputImage::Pointer m_VTKInputImage; - vtkSmartPointer< ivq::VTK::ImageViewer > m_Viewer; - vtkSmartPointer< ivq::VTK::SeedWidgetOverImageActor > m_SeedWidget; - vtkSmartPointer< ivq::VTK::BrushWidget > m_BrushWidget; - unsigned long m_Observer1; - unsigned long m_Observer2; - unsigned long m_Observer3; - }; - #endif // USE_ivq - */ - - } // ecapseman - - } // ecapseman - -} // ecapseman - - -#endif // __fpa__tests__image__BaseFunctions__h__ - -// eof - $RCSfile$ diff --git a/tests/image/CMakeLists.txt b/tests/image/CMakeLists.txt deleted file mode 100644 index fa58c65..0000000 --- a/tests/image/CMakeLists.txt +++ /dev/null @@ -1,18 +0,0 @@ -set(_pfx test_fpa_image_) -set( - _examples - RegionGrow_Tautology - RegionGrow_BinaryThreshold - MoriSegmentation - Dijkstra_Identity - Dijkstra_Gaussian - RandomWalker - SkeletonFilter - SkeletonToPolyData - ) -foreach(_e ${_examples}) - add_executable(${_pfx}${_e} ${_e}.cxx) - target_link_libraries(${_pfx}${_e} ivq::ivq fpa) -endforeach(_e) - -## eof - $RCSfile$ diff --git a/tests/image/Dijkstra_Gaussian.cxx b/tests/image/Dijkstra_Gaussian.cxx deleted file mode 100644 index 5622e7f..0000000 --- a/tests/image/Dijkstra_Gaussian.cxx +++ /dev/null @@ -1,87 +0,0 @@ -#include "BaseFunctions.h" -#include -#include -#include - -// ------------------------------------------------------------------------- -const unsigned int Dim = 3; -typedef short TPixel; -typedef float TScalar; - -typedef itk::Image< TPixel, Dim > TInputImage; -typedef itk::Image< TScalar, Dim > TScalarImage; -typedef fpa::Image::Dijkstra< TInputImage, TScalarImage > TFilter; -typedef fpa::Image::Functors::Dijkstra::Gaussian< TInputImage, TScalar > TWeight; - -// ------------------------------------------------------------------------- -int main( int argc, char* argv[] ) -{ - // Get arguments - if( argc < 7 ) - { - std::cerr - << "Usage: " << argv[ 0 ] - << " input_image output_image output_marks alpha beta" - << " stop_at_one_front ..." - << std::endl; - return( 1 ); - - } // fi - std::string input_image_filename = argv[ 1 ]; - std::string output_image_filename = argv[ 2 ]; - std::string output_marks_filename = argv[ 3 ]; - double alpha = std::atoi( argv[ 4 ] ); - double beta = std::atoi( argv[ 5 ] ); - bool stop_at_one_front = ( argv[ 6 ][ 0 ] == '1' ); - - // Create image - TInputImage::Pointer image; - std::string err0 = fpa::tests::image::Read( image, input_image_filename ); - if( err0 != "" ) - { - std::cerr << "Error caught: " << err0 << std::endl; - return( 1 ); - - } // fi - - // Prepare weight - TWeight::Pointer weight = TWeight::New( ); - weight->SetAlpha( alpha ); - weight->SetBeta( beta ); - - // Prepare filter - TFilter::Pointer filter = TFilter::New( ); - filter->SetInput( image ); - filter->SetWeightFunction( weight ); - filter->SetStopAtOneFront( stop_at_one_front ); - - // Get all seeds - for( int i = 7; i < argc; i += 3 ) - { - if( i + 1 < argc ) - { - TInputImage::IndexType seed; - seed[ 0 ] = std::atoi( argv[ i ] ); - seed[ 1 ] = std::atoi( argv[ i + 1 ] ); - seed[ 2 ] = std::atoi( argv[ i + 2 ] ); - filter->AddSeed( seed ); - - } // fi - - } // rof - - // Execute filter - filter->Update( ); - - // Save results - std::string err1 = - fpa::tests::image::Write( filter->GetOutput( ), output_image_filename ); - std::string err2 = - fpa::tests::image::Write( filter->GetMarks( ), output_marks_filename ); - if( err1 != "" ) std::cerr << "Error caught: " << err1 << std::endl; - if( err2 != "" ) std::cerr << "Error caught: " << err2 << std::endl; - - return( 0 ); -} - -// eof - $RCSfile$ diff --git a/tests/image/Dijkstra_Identity.cxx b/tests/image/Dijkstra_Identity.cxx deleted file mode 100644 index 54d1511..0000000 --- a/tests/image/Dijkstra_Identity.cxx +++ /dev/null @@ -1,74 +0,0 @@ -#include "BaseFunctions.h" -#include -#include -#include - -// ------------------------------------------------------------------------- -const unsigned int Dim = 2; -typedef unsigned char TPixel; -typedef float TScalar; - -typedef itk::Image< TPixel, Dim > TInputImage; -typedef itk::Image< TScalar, Dim > TScalarImage; -typedef fpa::Image::Dijkstra< TInputImage, TScalarImage > TFilter; -typedef fpa::Image::Functors::Dijkstra::Identity< TInputImage, TScalar > TWeight; - -// ------------------------------------------------------------------------- -int main( int argc, char* argv[] ) -{ - // Get arguments - if( argc < 5 ) - { - std::cerr - << "Usage: " << argv[ 0 ] - << " output_image output_marks width height ..." - << std::endl; - return( 1 ); - - } // fi - std::string output_image_filename = argv[ 1 ]; - std::string output_marks_filename = argv[ 2 ]; - int width = std::atoi( argv[ 3 ] ); - int height = std::atoi( argv[ 4 ] ); - - // Create image - TInputImage::Pointer image; - fpa::tests::image::CreateImage( image, 1, width, height, 1.0, 1.0 ); - - // Prepare weight - TWeight::Pointer weight = TWeight::New( ); - - // Prepare filter - TFilter::Pointer filter = TFilter::New( ); - filter->SetInput( image ); - filter->SetWeightFunction( weight ); - - // Get all seeds - for( int i = 5; i < argc; i += 2 ) - { - if( i + 1 < argc ) - { - TInputImage::IndexType seed; - seed[ 0 ] = std::atoi( argv[ i ] ); - seed[ 1 ] = std::atoi( argv[ i + 1 ] ); - filter->AddSeed( seed ); - - } // fi - - } // rof - - // Execute filter - filter->Update( ); - - // Save results - std::string err1 = - fpa::tests::image::Write( filter->GetOutput( ), output_image_filename ); - std::string err2 = - fpa::tests::image::Write( filter->GetMarks( ), output_marks_filename ); - if( err1 != "" ) std::cerr << err1 << std::endl; - if( err2 != "" ) std::cerr << err2 << std::endl; - - return( 0 ); -} - -// eof - $RCSfile$ diff --git a/tests/image/MoriSegmentation.cxx b/tests/image/MoriSegmentation.cxx deleted file mode 100644 index 5a5a472..0000000 --- a/tests/image/MoriSegmentation.cxx +++ /dev/null @@ -1,108 +0,0 @@ -#include "BaseFunctions.h" -#include -#include -#include - -// ------------------------------------------------------------------------- -const unsigned int Dim = 3; -typedef short TPixel; -typedef unsigned short TLabel; - -typedef itk::Image< TPixel, Dim > TInputImage; -typedef itk::Image< TLabel, Dim > TLabelImage; -typedef fpa::Image::Mori< TInputImage, TLabelImage > TFilter; - -// ------------------------------------------------------------------------- -int main( int argc, char* argv[] ) -{ - // Get arguments - if( argc < 9 + Dim ) - { - std::cerr - << "Usage: " << argv[ 0 ] - << " input_image output_image output_marks output_signal" - << " init_threshold end_threshold delta [index/point] seed" - << std::endl; - return( 1 ); - - } // fi - std::string input_image_filename = argv[ 1 ]; - std::string output_image_filename = argv[ 2 ]; - std::string output_marks_filename = argv[ 3 ]; - std::string output_signal_filename = argv[ 4 ]; - TPixel init_threshold = std::atoi( argv[ 5 ] ); - TPixel end_threshold = std::atoi( argv[ 6 ] ); - TPixel delta = std::atoi( argv[ 7 ] ); - std::string seed_type = argv[ 8 ]; - - TInputImage::IndexType iseed; - TInputImage::PointType pseed; - for( unsigned int i = 0; i < Dim; ++i ) - { - if( seed_type == "index" ) - iseed[ i ] = std::atoi( argv[ 9 + i ] ); - else - pseed[ i ] = std::atof( argv[ 9 + i ] ); - - } // rof - - // Create image - TInputImage::Pointer input_image; - std::string err0 = - fpa::tests::image::Read( input_image, input_image_filename ); - if( err0 != "" ) std::cerr << err0 << std::endl; - - // Prepare filter - TFilter::Pointer filter = TFilter::New( ); - filter->SetInput( input_image ); - if( seed_type == "index" ) - filter->SetSeed( iseed ); - else - filter->SetSeed( pseed ); - filter->SetThresholds( init_threshold, end_threshold, delta ); - filter->SetInsideValue( 255 ); - filter->SetOutsideValue( 0 ); - filter->SetSignalKernelSize( 20 ); - filter->SetSignalThreshold( 500 ); - filter->SetSignalInfluence( 0.5 ); - filter->SetMinimumThreshold( -850 ); - - // Execute filter - std::chrono::time_point< std::chrono::high_resolution_clock > tstart, tend; - tstart = std::chrono::high_resolution_clock::now( ); - filter->Update( ); - tend = std::chrono::high_resolution_clock::now( ); - std::chrono::duration< double > telapsed = tend - tstart; - - // Save results - std::string err1 = - fpa::tests::image::Write( filter->GetThresholdedOutput( ), output_image_filename ); - std::string err2 = - fpa::tests::image::Write( filter->GetMarks( ), output_marks_filename ); - if( err1 != "" ) std::cerr << err1 << std::endl; - if( err2 != "" ) std::cerr << err2 << std::endl; - - std::ofstream osignal( output_signal_filename.c_str( ) ); - unsigned long nThr = filter->GetNumberOfEvaluatedThresholds( ); - for( unsigned long i = 0; i < nThr; ++i ) - { - double x, y; - TFilter::TPeak p; - filter->GetSignalValues( i, x, y, p ); - osignal << x << " " << y << std::endl; - - } // rof - osignal.close( ); - - std::cout - << "------------------------------------------------------" << std::endl - << "Elapsed time: " << telapsed.count( ) << " s" << std::endl - << "Optimum threshold: " << filter->GetOptimumThreshold( ) << std::endl - << "Number of evaluated thresholds: " << nThr << std::endl - << "------------------------------------------------------" - << std::endl; - - return( 0 ); -} - -// eof - $RCSfile$ diff --git a/tests/image/RandomWalker.cxx b/tests/image/RandomWalker.cxx deleted file mode 100644 index 6bdca1c..0000000 --- a/tests/image/RandomWalker.cxx +++ /dev/null @@ -1,90 +0,0 @@ -#include "BaseFunctions.h" -#include -#include -#include - -// ------------------------------------------------------------------------- -const unsigned int Dim = 2; -typedef short TPixel; -typedef unsigned char TLabel; -typedef float TScalar; - -typedef itk::Image< TPixel, Dim > TInputImage; -typedef itk::Image< TLabel, Dim > TLabelImage; -typedef fpa::Image::RandomWalker< TInputImage, TLabelImage, TScalar > TFilter; -typedef fpa::Image::Functors::Dijkstra::Gaussian< TInputImage, TScalar > TWeight; - -// ------------------------------------------------------------------------- -int main( int argc, char* argv[] ) -{ - // Get arguments - if( argc < 6 ) - { - std::cerr - << "Usage: " << argv[ 0 ] - << " input_image labels_image output_image output_costs" - << " beta" - << std::endl; - return( 1 ); - - } // fi - std::string input_image_filename = argv[ 1 ]; - std::string labels_image_filename = argv[ 2 ]; - std::string output_image_filename = argv[ 3 ]; - std::string output_costs_filename = argv[ 4 ]; - double beta = std::atof( argv[ 5 ] ); - - // Read image - TInputImage::Pointer image; - std::string err0 = fpa::tests::image::Read( image, input_image_filename ); - if( err0 != "" ) - { - std::cerr << "Error caught: " << err0 << std::endl; - return( 1 ); - - } // fi - - // Read label - TLabelImage::Pointer labels; - std::string err1 = fpa::tests::image::Read( labels, labels_image_filename ); - if( err1 != "" ) - { - std::cerr << "Error caught: " << err1 << std::endl; - return( 1 ); - - } // fi - - // Prepare weight - TWeight::Pointer weight = TWeight::New( ); - weight->SetBeta( beta ); - - // Prepare filter - TFilter::Pointer filter = TFilter::New( ); - filter->SetInput( image ); - filter->SetWeightFunction( weight ); - filter->SetLabels( labels ); - - // Execute filter - try - { - filter->Update( ); - } - catch( std::exception& err ) - { - std::cerr << "Error caught: " << err.what( ) << std::endl; - return( 1 ); - - } // yrt - - // Save results - std::string err2 = - fpa::tests::image::Write( filter->GetMarks( ), output_image_filename ); - std::string err3 = - fpa::tests::image::Write( filter->GetOutput( ), output_costs_filename ); - if( err2 != "" ) std::cerr << "Error caught: " << err2 << std::endl; - if( err3 != "" ) std::cerr << "Error caught: " << err3 << std::endl; - - return( 0 ); -} - -// eof - $RCSfile$ diff --git a/tests/image/RegionGrow_BinaryThreshold.cxx b/tests/image/RegionGrow_BinaryThreshold.cxx deleted file mode 100644 index b40f25a..0000000 --- a/tests/image/RegionGrow_BinaryThreshold.cxx +++ /dev/null @@ -1,91 +0,0 @@ -#include "BaseFunctions.h" -#include -#include -#include - -// ------------------------------------------------------------------------- -const unsigned int Dim = 3; -typedef short TInputPixel; -typedef unsigned char TOutputPixel; - -typedef itk::Image< TInputPixel, Dim > TInputImage; -typedef itk::Image< TOutputPixel, Dim > TOutputImage; -typedef fpa::Image::RegionGrow< TInputImage, TOutputImage > TFilter; -typedef fpa::Base::Functors::RegionGrow::BinaryThreshold< TInputPixel > TPredicate; - -// ------------------------------------------------------------------------- -int main( int argc, char* argv[] ) -{ - // Get arguments - if( argc < 8 + Dim ) - { - std::cerr - << "Usage: " << argv[ 0 ] - << " input_image output_image output_marks" - << " lower upper strict [index/point] ..." - << std::endl; - return( 1 ); - - } // fi - std::string input_image_filename = argv[ 1 ]; - std::string output_image_filename = argv[ 2 ]; - std::string output_marks_filename = argv[ 3 ]; - TInputPixel lower = TInputPixel( std::atof( argv[ 4 ] ) ); - TInputPixel upper = TInputPixel( std::atof( argv[ 5 ] ) ); - bool strict = ( argv[ 6 ][ 0 ] == '1' ); - std::string seeds_type = argv[ 7 ]; - - // Create image - TInputImage::Pointer input_image; - std::string err0 = - fpa::tests::image::Read( input_image, input_image_filename ); - if( err0 != "" ) std::cerr << err0 << std::endl; - - // Prepare predicate - TPredicate::Pointer predicate = TPredicate::New( ); - predicate->SetLower( lower ); - predicate->SetUpper( upper ); - predicate->SetStrict( strict ); - - // Prepare filter - TFilter::Pointer filter = TFilter::New( ); - filter->SetInput( input_image ); - filter->SetPredicate( predicate ); - filter->SetInsideValue( 255 ); - filter->SetOutsideValue( 0 ); - - // Get all seeds - for( int i = 8; i < argc; i += Dim ) - { - if( seeds_type == "index" ) - { - TInputImage::IndexType seed; - for( unsigned int d = 0; d < Dim; ++d ) - seed[ d ] = std::atoi( argv[ i + d ] ); - filter->AddSeed( seed ); - } - else - { - TInputImage::PointType seed; - for( unsigned int d = 0; d < Dim; ++d ) - seed[ d ] = std::atof( argv[ i + d ] ); - filter->AddSeed( seed ); - - } // fi - } // rof - - // Execute filter - filter->Update( ); - - // Save results - std::string err1 = - fpa::tests::image::Write( filter->GetOutput( ), output_image_filename ); - std::string err2 = - fpa::tests::image::Write( filter->GetMarks( ), output_marks_filename ); - if( err1 != "" ) std::cerr << err1 << std::endl; - if( err2 != "" ) std::cerr << err2 << std::endl; - - return( 0 ); -} - -// eof - $RCSfile$ diff --git a/tests/image/RegionGrow_Tautology.cxx b/tests/image/RegionGrow_Tautology.cxx deleted file mode 100644 index db60d0a..0000000 --- a/tests/image/RegionGrow_Tautology.cxx +++ /dev/null @@ -1,74 +0,0 @@ -#include "BaseFunctions.h" -#include -#include -#include - -// ------------------------------------------------------------------------- -const unsigned int Dim = 2; -typedef unsigned char TPixel; - -typedef itk::Image< TPixel, Dim > TImage; -typedef fpa::Image::RegionGrow< TImage, TImage > TFilter; -typedef fpa::Base::Functors::RegionGrow::Tautology< TPixel > TPredicate; - -// ------------------------------------------------------------------------- -int main( int argc, char* argv[] ) -{ - // Get arguments - if( argc < 5 ) - { - std::cerr - << "Usage: " << argv[ 0 ] - << " output_image output_marks width height ..." - << std::endl; - return( 1 ); - - } // fi - std::string output_image_filename = argv[ 1 ]; - std::string output_marks_filename = argv[ 2 ]; - int width = std::atoi( argv[ 3 ] ); - int height = std::atoi( argv[ 4 ] ); - - // Create image - TImage::Pointer image; - fpa::tests::image::CreateImage( image, 0, width, height, 1.0, 1.0 ); - - // Prepare predicate - TPredicate::Pointer predicate = TPredicate::New( ); - - // Prepare filter - TFilter::Pointer filter = TFilter::New( ); - filter->SetInput( image ); - filter->SetPredicate( predicate ); - filter->SetInsideValue( 255 ); - filter->SetOutsideValue( 0 ); - - // Get all seeds - for( int i = 5; i < argc; i += 2 ) - { - if( i + 1 < argc ) - { - TImage::IndexType seed; - seed[ 0 ] = std::atoi( argv[ i ] ); - seed[ 1 ] = std::atoi( argv[ i + 1 ] ); - filter->AddSeed( seed ); - - } // fi - - } // rof - - // Execute filter - filter->Update( ); - - // Save results - std::string err1 = - fpa::tests::image::Write( filter->GetOutput( ), output_image_filename ); - std::string err2 = - fpa::tests::image::Write( filter->GetMarks( ), output_marks_filename ); - if( err1 != "" ) std::cerr << err1 << std::endl; - if( err2 != "" ) std::cerr << err2 << std::endl; - - return( 0 ); -} - -// eof - $RCSfile$ diff --git a/tests/image/SkeletonFilter.cxx b/tests/image/SkeletonFilter.cxx deleted file mode 100644 index 5cff164..0000000 --- a/tests/image/SkeletonFilter.cxx +++ /dev/null @@ -1,86 +0,0 @@ -#include "BaseFunctions.h" -#include -#include -#include - -// ------------------------------------------------------------------------- -const unsigned int Dim = 3; -typedef short TPixel; - -typedef itk::Image< TPixel, Dim > TInputImage; -typedef fpa::Image::SkeletonFilter< TInputImage > TFilter; - -// ------------------------------------------------------------------------- -int main( int argc, char* argv[] ) -{ - // Get arguments - if( argc < 3 ) - { - std::cerr - << "Usage: " << argv[ 0 ] - << " input_image output_skeleton ..." - << std::endl; - return( 1 ); - - } // fi - std::string input_image_filename = argv[ 1 ]; - std::string output_skeleton_filename = argv[ 2 ]; - - // Read image - TInputImage::Pointer image; - std::string err1 = fpa::tests::image::Read( image, input_image_filename ); - if( err1 != "" ) - { - std::cerr << "Error caught: " << err1 << std::endl; - return( 1 ); - - } // fi - - // Prepare filter - TFilter::Pointer filter = TFilter::New( ); - filter->SetInput( image ); - - // Configure seed - if( argc == 6 ) - { - TInputImage::PointType pnt; - pnt[ 0 ] = std::atof( argv[ 3 ] ); - pnt[ 1 ] = std::atof( argv[ 4 ] ); - pnt[ 2 ] = std::atof( argv[ 5 ] ); - - TInputImage::IndexType seed; - image->TransformPhysicalPointToIndex( pnt, seed ); - - filter->SeedFromMaximumDistanceOff( ); - filter->SetSeed( seed ); - } - else - filter->SeedFromMaximumDistanceOn( ); - - // Configure distance map - filter->GetDistanceMap( )->InsideIsPositiveOn( ); - filter->GetDistanceMap( )->SquaredDistanceOff( ); - filter->GetDistanceMap( )->UseImageSpacingOn( ); - - // Update - filter->Update( ); - - // Save results - fpa::Image::SkeletonWriter< TFilter::TSkeleton >::Pointer writer = - fpa::Image::SkeletonWriter< TFilter::TSkeleton >::New( ); - writer->SetInput( filter->GetOutput( ) ); - writer->SetFileName( output_skeleton_filename ); - try - { - writer->Update( ); - } - catch( std::exception& err ) - { - std::cerr << "Error caught: " << err.what( ) << std::endl; - return( 1 ); - - } // yrt - return( 0 ); -} - -// eof - $RCSfile$ diff --git a/tests/image/SkeletonToPolyData.cxx b/tests/image/SkeletonToPolyData.cxx deleted file mode 100644 index 6ee6fd8..0000000 --- a/tests/image/SkeletonToPolyData.cxx +++ /dev/null @@ -1,63 +0,0 @@ - -#include -#include - -#include -#include -#include - -// ------------------------------------------------------------------------- -const unsigned int Dim = 3; -typedef fpa::Image::Skeleton< Dim > TSkeleton; -typedef fpa::Image::SkeletonToPolyDataFilter< TSkeleton > TFilter; - -// ------------------------------------------------------------------------- -int main( int argc, char* argv[] ) -{ -#ifdef USE_VTK - // Get arguments - if( argc < 3 ) - { - std::cerr - << "Usage: " << argv[ 0 ] - << " input_skeleton output_polydata" - << std::endl; - return( 1 ); - - } // fi - std::string input_skeleton_filename = argv[ 1 ]; - std::string output_polydata_filename = argv[ 2 ]; - - fpa::Image::SkeletonReader< TSkeleton >::Pointer reader = - fpa::Image::SkeletonReader< TSkeleton >::New( ); - reader->SetFileName( input_skeleton_filename ); - try - { - reader->Update( ); - } - catch( std::exception& err ) - { - std::cerr << "Error caught: " << err.what( ) << std::endl; - return( 1 ); - - } // yrt - - vtkSmartPointer< TFilter > filter = vtkSmartPointer< TFilter >::New( ); - filter->SetInput( reader->GetOutput( ) ); - - vtkSmartPointer< vtkPolyDataWriter > writer = - vtkSmartPointer< vtkPolyDataWriter >::New( ); - writer->SetInputConnection( filter->GetOutputPort( ) ); - writer->SetFileName( output_polydata_filename.c_str( ) ); - writer->Update( ); - - return( 0 ); -#else // USE_VTK - std::cerr - << "Error: FrontAlgorithms was compiled without VTK support." - << std::endl; - return( 1 ); -#endif // USE_VTK -} - -// eof - $RCSfile$