Extracts the voxel-wise main directions of the input fiber bundle. More...

#include <itkTractsToVectorImageFilter.h>

Inheritance diagram for itk::TractsToVectorImageFilter< PixelType >:

Collaboration diagram for itk::TractsToVectorImageFilter< PixelType >:

Public Types
typedef TractsToVectorImageFilter	Self

typedef ProcessObject	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef itk::Vector< float, 3 >	OutputVectorType

typedef itk::Image< OutputVectorType, 3 >	OutputImageType

typedef std::vector< OutputImageType::Pointer >	OutputImageContainerType

typedef vnl_vector_fixed< double, 3 >	DirectionType

typedef VectorContainer< unsigned int, DirectionType >	DirectionContainerType

typedef VectorContainer< unsigned int, DirectionContainerType::Pointer >	ContainerType

typedef Image< Vector< float, 3 >, 3 >	ItkDirectionImageType

typedef VectorContainer< unsigned int, ItkDirectionImageType::Pointer >	DirectionImageContainerType

typedef itk::Image< unsigned char, 3 >	ItkUcharImgType

typedef itk::Image< double, 3 >	ItkDoubleImgType

Public Types inherited from mitk::ImageSource< VectorImage< float, 3 > >
typedef ImageSource	Self

typedef BaseDataSource	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef mitk::Image	OutputImageType
	Some convenient typedefs. More...

typedef OutputImageType	OutputType

typedef OutputImageType::Pointer	OutputImagePointer

typedef SlicedData::RegionType	OutputImageRegionType

Public Member Functions
Pointer	Clone () const

virtual const char *	GetClassName () const

virtual void	SetSizeThreshold (float _arg)

virtual float	GetSizeThreshold ()

virtual void	SetAngularThreshold (float _arg)
	cluster directions that are closer together than the specified threshold More...

virtual float	GetAngularThreshold ()
	cluster directions that are closer together than the specified threshold More...

virtual void	SetNormalizeVectors (bool _arg)
	Normalize vectors to length 1. More...

virtual bool	GetNormalizeVectors ()
	Normalize vectors to length 1. More...

virtual void	SetUseWorkingCopy (bool _arg)
	Do not modify input fiber bundle. Use a copy. More...

virtual bool	GetUseWorkingCopy ()
	Do not modify input fiber bundle. Use a copy. More...

virtual void	SetMaxNumDirections (unsigned long _arg)
	If more directions are extracted, only the largest are kept. More...

virtual unsigned long	GetMaxNumDirections ()
	If more directions are extracted, only the largest are kept. More...

virtual void	SetMaskImage (ItkUcharImgType::Pointer _arg)
	only process voxels inside mask More...

virtual void	SetFiberBundle (FiberBundle::Pointer _arg)
	input fiber bundle More...

virtual ContainerType::Pointer	GetClusteredDirectionsContainer ()
	output directions More...

virtual ItkUcharImgType::Pointer	GetNumDirectionsImage ()
	number of directions per voxel More...

virtual FiberBundle::Pointer	GetOutputFiberBundle ()
	vector field for visualization purposes More...

virtual DirectionImageContainerType::Pointer	GetDirectionImageContainer ()
	output directions More...

virtual void	SetCreateDirectionImages (bool _arg)

void	GenerateData () override
	A version of GenerateData() specific for image processing filters. More...

Public Member Functions inherited from mitk::ImageSource< VectorImage< float, 3 > >
virtual std::vector< std::string >	GetClassHierarchy () const override

Pointer	Clone () const

OutputType *	GetOutput ()
	Get the output data of this image source object. More...

const OutputType *	GetOutput () const

OutputType *	GetOutput (DataObjectPointerArraySizeType idx)

const OutputType *	GetOutput (DataObjectPointerArraySizeType idx) const

virtual itk::DataObject::Pointer	MakeOutput (DataObjectPointerArraySizeType idx) override
	Make a DataObject of the correct type to used as the specified output. More...

virtual itk::DataObject::Pointer	MakeOutput (const DataObjectIdentifierType &name) override

virtual vtkImageData *	GetVtkImageData ()

virtual const vtkImageData *	GetVtkImageData () const

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from mitk::ImageSource< VectorImage< float, 3 > >
static const char *	GetStaticNameOfClass ()

static Pointer	New ()
	Method for creation through the object factory. More...

Protected Member Functions
DirectionContainerType::Pointer	FastClustering (DirectionContainerType::Pointer inDirs, std::vector< double > lengths)
	cluster fiber directions More...

vnl_vector_fixed< double, 3 >	GetVnlVector (double point[3])

itk::Point< double, 3 >	GetItkPoint (double point[3])

	TractsToVectorImageFilter ()

virtual	~TractsToVectorImageFilter ()

Protected Member Functions inherited from mitk::ImageSource< VectorImage< float, 3 > >
	ImageSource ()

virtual	~ImageSource ()

virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, itk::ThreadIdType threadId)
	If an imaging filter can be implemented as a multithreaded algorithm, the filter will provide an implementation of ThreadedGenerateData(). More...

virtual void	PrepareOutputs () override
	This method is intentionally left blank. More...

virtual void	AllocateOutputs ()
	The GenerateData method normally allocates the buffers for all of the outputs of a filter. More...

virtual void	BeforeThreadedGenerateData ()
	If an imaging filter needs to perform processing after the buffer has been allocated but before threads are spawned, the filter can can provide an implementation for BeforeThreadedGenerateData(). More...

virtual void	AfterThreadedGenerateData ()
	If an imaging filter needs to perform processing after all processing threads have completed, the filter can can provide an implementation for AfterThreadedGenerateData(). More...

virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int num, OutputImageRegionType &splitRegion)
	Split the output's RequestedRegion into "num" pieces, returning region "i" as "splitRegion". More...

Protected Attributes
FiberBundle::Pointer	m_FiberBundle
	input fiber bundle More...

float	m_AngularThreshold
	cluster directions that are closer together than the specified threshold More...

float	m_Epsilon
	epsilon for vector equality check More...

ItkUcharImgType::Pointer	m_MaskImage
	only voxels inside the binary mask are processed More...

bool	m_NormalizeVectors
	normalize vectors to length 1 More...

itk::Vector< float >	m_OutImageSpacing
	spacing of output image More...

ContainerType::Pointer	m_DirectionsContainer
	container for fiber directions More...

bool	m_UseWorkingCopy
	do not modify input fiber bundle but work on copy More...

unsigned long	m_MaxNumDirections
	if more directions per voxel are extracted, only the largest are kept More...

float	m_SizeThreshold

bool	m_CreateDirectionImages

ContainerType::Pointer	m_ClusteredDirectionsContainer
	contains direction vectors for each voxel More...

ItkUcharImgType::Pointer	m_NumDirectionsImage
	shows number of fibers per voxel More...

DirectionImageContainerType::Pointer	m_DirectionImageContainer
	contains images that contain the output directions More...

FiberBundle::Pointer	m_OutputFiberBundle
	vector field for visualization purposes More...

Additional Inherited Members
Static Protected Member Functions inherited from mitk::ImageSource< VectorImage< float, 3 > >
static ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)
	Static function used as a "callback" by the MultiThreader. More...

Detailed Description

template<class PixelType>
class itk::TractsToVectorImageFilter< PixelType >

Extracts the voxel-wise main directions of the input fiber bundle.

Definition at line 26 of file itkTractsToVectorImageFilter.h.

Member Typedef Documentation

template<class PixelType>

typedef SmartPointer< const Self > itk::TractsToVectorImageFilter< PixelType >::ConstPointer

Definition at line 33 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

typedef VectorContainer< unsigned int, DirectionContainerType::Pointer > itk::TractsToVectorImageFilter< PixelType >::ContainerType

Definition at line 41 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

typedef VectorContainer< unsigned int, DirectionType > itk::TractsToVectorImageFilter< PixelType >::DirectionContainerType

Definition at line 40 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

typedef VectorContainer< unsigned int, ItkDirectionImageType::Pointer > itk::TractsToVectorImageFilter< PixelType >::DirectionImageContainerType

Definition at line 43 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

typedef vnl_vector_fixed< double, 3 > itk::TractsToVectorImageFilter< PixelType >::DirectionType

Definition at line 39 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

typedef Image< Vector< float, 3 >, 3> itk::TractsToVectorImageFilter< PixelType >::ItkDirectionImageType

Definition at line 42 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

typedef itk::Image<double, 3> itk::TractsToVectorImageFilter< PixelType >::ItkDoubleImgType

Definition at line 45 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

typedef itk::Image<unsigned char, 3> itk::TractsToVectorImageFilter< PixelType >::ItkUcharImgType

Definition at line 44 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

typedef std::vector< OutputImageType::Pointer > itk::TractsToVectorImageFilter< PixelType >::OutputImageContainerType

Definition at line 37 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

typedef itk::Image<OutputVectorType, 3> itk::TractsToVectorImageFilter< PixelType >::OutputImageType

Definition at line 36 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

typedef itk::Vector<float,3> itk::TractsToVectorImageFilter< PixelType >::OutputVectorType

Definition at line 35 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

typedef SmartPointer< Self > itk::TractsToVectorImageFilter< PixelType >::Pointer

Definition at line 32 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

typedef TractsToVectorImageFilter itk::TractsToVectorImageFilter< PixelType >::Self

Definition at line 30 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

typedef ProcessObject itk::TractsToVectorImageFilter< PixelType >::Superclass

Definition at line 31 of file itkTractsToVectorImageFilter.h.

Constructor & Destructor Documentation

template<class PixelType >

itk::TractsToVectorImageFilter< PixelType >::TractsToVectorImageFilter ( )

protected

Definition at line 26 of file itkTractsToVectorImageFilter.cpp.

template<class PixelType >

itk::TractsToVectorImageFilter< PixelType >::~TractsToVectorImageFilter ( )

protectedvirtual

Definition at line 42 of file itkTractsToVectorImageFilter.cpp.

Member Function Documentation

template<class PixelType>

Pointer itk::TractsToVectorImageFilter< PixelType >::Clone ( ) const

template<class PixelType >

TractsToVectorImageFilter< PixelType >::DirectionContainerType::Pointer itk::TractsToVectorImageFilter< PixelType >::FastClustering	(	DirectionContainerType::Pointer	inDirs,
		std::vector< double >	lengths
	)

protected

cluster fiber directions

Definition at line 320 of file itkTractsToVectorImageFilter.cpp.

References max(), and mitk::New().

template<class PixelType >

void itk::TractsToVectorImageFilter< PixelType >::GenerateData ( )

overridevirtual

A version of GenerateData() specific for image processing filters.

This implementation will split the processing across multiple threads. The buffer is allocated by this method. Then the BeforeThreadedGenerateData() method is called (if provided). Then, a series of threads are spawned each calling ThreadedGenerateData(). After all the threads have completed processing, the AfterThreadedGenerateData() method is called (if provided). If an image processing filter cannot be threaded, the filter should provide an implementation of GenerateData(). That implementation is responsible for allocating the output buffer. If a filter an be threaded, it should NOT provide a GenerateData() method but should provide a ThreadedGenerateData() instead.

See also: ThreadedGenerateData()

Reimplemented from mitk::ImageSource< VectorImage< float, 3 > >.

Definition at line 69 of file itkTractsToVectorImageFilter.cpp.

References itk::CompareVectorLengths(), MITK_INFO, and mitk::New().

template<class PixelType>

virtual float itk::TractsToVectorImageFilter< PixelType >::GetAngularThreshold ( )

virtual

cluster directions that are closer together than the specified threshold

template<class PixelType>

virtual const char* itk::TractsToVectorImageFilter< PixelType >::GetClassName ( ) const

virtual

Reimplemented from mitk::ImageSource< VectorImage< float, 3 > >.

template<class PixelType>

virtual ContainerType::Pointer itk::TractsToVectorImageFilter< PixelType >::GetClusteredDirectionsContainer ( )

virtual

output directions

template<class PixelType>

virtual DirectionImageContainerType::Pointer itk::TractsToVectorImageFilter< PixelType >::GetDirectionImageContainer ( )

virtual

output directions

template<class PixelType>

itk::Point< double, 3 > itk::TractsToVectorImageFilter< PixelType >::GetItkPoint ( double point[3] )

protected

Definition at line 59 of file itkTractsToVectorImageFilter.cpp.

template<class PixelType>

virtual unsigned long itk::TractsToVectorImageFilter< PixelType >::GetMaxNumDirections ( )

virtual

If more directions are extracted, only the largest are kept.

template<class PixelType>

virtual bool itk::TractsToVectorImageFilter< PixelType >::GetNormalizeVectors ( )

virtual

Normalize vectors to length 1.

template<class PixelType>

virtual ItkUcharImgType::Pointer itk::TractsToVectorImageFilter< PixelType >::GetNumDirectionsImage ( )

virtual

number of directions per voxel

template<class PixelType>

virtual FiberBundle::Pointer itk::TractsToVectorImageFilter< PixelType >::GetOutputFiberBundle ( )

virtual

vector field for visualization purposes

template<class PixelType>

virtual float itk::TractsToVectorImageFilter< PixelType >::GetSizeThreshold ( )

virtual

template<class PixelType>

virtual bool itk::TractsToVectorImageFilter< PixelType >::GetUseWorkingCopy ( )

virtual

Do not modify input fiber bundle. Use a copy.

template<class PixelType>

vnl_vector_fixed< double, 3 > itk::TractsToVectorImageFilter< PixelType >::GetVnlVector ( double point[3] )

protected

Definition at line 48 of file itkTractsToVectorImageFilter.cpp.

template<class PixelType>

static Pointer itk::TractsToVectorImageFilter< PixelType >::New ( )

static

Referenced by main().

template<class PixelType>

virtual void itk::TractsToVectorImageFilter< PixelType >::SetAngularThreshold ( float _arg )

virtual

cluster directions that are closer together than the specified threshold

template<class PixelType>

virtual void itk::TractsToVectorImageFilter< PixelType >::SetCreateDirectionImages ( bool _arg )

virtual

template<class PixelType>

virtual void itk::TractsToVectorImageFilter< PixelType >::SetFiberBundle ( FiberBundle::Pointer _arg )

virtual

input fiber bundle

template<class PixelType>

virtual void itk::TractsToVectorImageFilter< PixelType >::SetMaskImage ( ItkUcharImgType::Pointer _arg )

virtual

only process voxels inside mask

template<class PixelType>

virtual void itk::TractsToVectorImageFilter< PixelType >::SetMaxNumDirections ( unsigned long _arg )

virtual

If more directions are extracted, only the largest are kept.

template<class PixelType>

virtual void itk::TractsToVectorImageFilter< PixelType >::SetNormalizeVectors ( bool _arg )

virtual

Normalize vectors to length 1.

template<class PixelType>

virtual void itk::TractsToVectorImageFilter< PixelType >::SetSizeThreshold ( float _arg )

virtual

template<class PixelType>

virtual void itk::TractsToVectorImageFilter< PixelType >::SetUseWorkingCopy ( bool _arg )

virtual

Do not modify input fiber bundle. Use a copy.

Member Data Documentation

template<class PixelType>

float itk::TractsToVectorImageFilter< PixelType >::m_AngularThreshold

protected

cluster directions that are closer together than the specified threshold

Definition at line 86 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

ContainerType::Pointer itk::TractsToVectorImageFilter< PixelType >::m_ClusteredDirectionsContainer

protected

contains direction vectors for each voxel

Definition at line 98 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

bool itk::TractsToVectorImageFilter< PixelType >::m_CreateDirectionImages

protected

Definition at line 95 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

DirectionImageContainerType::Pointer itk::TractsToVectorImageFilter< PixelType >::m_DirectionImageContainer

protected

contains images that contain the output directions

Definition at line 100 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

ContainerType::Pointer itk::TractsToVectorImageFilter< PixelType >::m_DirectionsContainer

protected

container for fiber directions

Definition at line 91 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

float itk::TractsToVectorImageFilter< PixelType >::m_Epsilon

protected

epsilon for vector equality check

Definition at line 87 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

FiberBundle::Pointer itk::TractsToVectorImageFilter< PixelType >::m_FiberBundle

protected

input fiber bundle

Definition at line 85 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

ItkUcharImgType::Pointer itk::TractsToVectorImageFilter< PixelType >::m_MaskImage

protected

only voxels inside the binary mask are processed

Definition at line 88 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

unsigned long itk::TractsToVectorImageFilter< PixelType >::m_MaxNumDirections

protected

if more directions per voxel are extracted, only the largest are kept

Definition at line 93 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

bool itk::TractsToVectorImageFilter< PixelType >::m_NormalizeVectors

protected

normalize vectors to length 1

Definition at line 89 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

ItkUcharImgType::Pointer itk::TractsToVectorImageFilter< PixelType >::m_NumDirectionsImage

protected

shows number of fibers per voxel

Definition at line 99 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

itk::Vector<float> itk::TractsToVectorImageFilter< PixelType >::m_OutImageSpacing

protected

spacing of output image

Definition at line 90 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

FiberBundle::Pointer itk::TractsToVectorImageFilter< PixelType >::m_OutputFiberBundle

protected

vector field for visualization purposes

Definition at line 101 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

float itk::TractsToVectorImageFilter< PixelType >::m_SizeThreshold

protected

Definition at line 94 of file itkTractsToVectorImageFilter.h.

template<class PixelType>

bool itk::TractsToVectorImageFilter< PixelType >::m_UseWorkingCopy

protected

do not modify input fiber bundle but work on copy

Definition at line 92 of file itkTractsToVectorImageFilter.h.

The documentation for this class was generated from the following files:

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

template<class PixelType> class itk::TractsToVectorImageFilter< PixelType >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<class PixelType>
class itk::TractsToVectorImageFilter< PixelType >