#include <itkMorphologicalContourInterpolator.h>

Inheritance diagram for itk::MorphologicalContourInterpolator< TImage >:

Collaboration diagram for itk::MorphologicalContourInterpolator< TImage >:

Detailed Description

template<typename TImage>
class itk::MorphologicalContourInterpolator< TImage >

Interpolates contours between slices. Based on a paper by Albu et al.

Inputs and Outputs: This is an image-to-image filter. The dimensionality is 3D or higher. Input contains an image with some slices segmented, usually manually. The output has all in-between slices also segmented.

Parameters: Slices are detected at positions where a pixel exists with same labeled neighbors in slice and only clear (0) neighbors perpendicular to the slice. If default behaviour is unwanted, contour indices can be set by enabling UseCustomSlicePositions and calling SetLabeledSliceIndices.

Filter can be restricted to run along only one axis, and/or to interpolate just one label.

Since optimal alignment between slices would require exhaustive search, the default is to use heuristic (breadth first search starting from centroid).

There is also an alternative algorithm based on distance transform approach. It is slightly faster, but it can jump across a twisty shape (not geodesic).

Reference: Albu AB, Beugeling T, Laurendeau D. "A morphology-based approach for interslice interpolation of anatomical slices from volumetric images." IEEE Trans Biomed Eng. 2008 Aug;55(8):2022-38. DOI:10.1109/TBME.2008.921158

Acknowledgement: This work is supported by NIH grant R01 EB014346, "Continued development and maintenance of the ITK-SNAP 3D image segmentation software."

Definition at line 65 of file itkMorphologicalContourInterpolator.h.

Public Types
typedef itksys::hash_map < typename TImage::PixelType, SliceSetType >	LabeledSlicesType

typedef SmartPointer< Self >	Pointer

typedef MorphologicalContourInterpolator	Self

typedef std::vector < LabeledSlicesType >	SliceIndicesType

typedef std::set< typename TImage::IndexValueType >	SliceSetType

typedef Image< typename TImage::PixelType, TImage::ImageDimension-1 >	SliceType

typedef ImageToImageFilter < TImage, TImage >	Superclass

Public Types inherited from itk::ImageToImageFilter< TImage, TImage >
typedef SmartPointer< const Self >	ConstPointer

typedef InputImageType::ConstPointer	InputImageConstPointer

typedef InputImageType::PixelType	InputImagePixelType

typedef InputImageType::Pointer	InputImagePointer

typedef InputImageType::RegionType	InputImageRegionType

typedef TImage	InputImageType

typedef Superclass::OutputImagePixelType	OutputImagePixelType

typedef Superclass::OutputImageRegionType	OutputImageRegionType

typedef SmartPointer< Self >	Pointer

typedef ImageToImageFilter	Self

typedef ImageSource< TImage >	Superclass

Public Types inherited from itk::ImageSource< TImage >
typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::DataObjectIdentifierType	DataObjectIdentifierType

typedef DataObject::Pointer	DataObjectPointer

typedef Superclass::DataObjectPointerArraySizeType	DataObjectPointerArraySizeType

typedef OutputImageType::PixelType	OutputImagePixelType

typedef OutputImageType::Pointer	OutputImagePointer

typedef OutputImageType::RegionType	OutputImageRegionType

typedef TImage	OutputImageType

typedef SmartPointer< Self >	Pointer

typedef ImageSource	Self

typedef ProcessObject	Superclass

Public Types inherited from itk::ProcessObject
typedef SmartPointer< const Self >	ConstPointer

typedef DataObject::DataObjectIdentifierType	DataObjectIdentifierType

typedef DataObject::Pointer	DataObjectPointer

typedef std::vector < DataObjectPointer >	DataObjectPointerArray

typedef DataObjectPointerArray::size_type	DataObjectPointerArraySizeType

typedef MultiThreader	MultiThreaderType

typedef std::vector < DataObjectIdentifierType >	NameArray

typedef SmartPointer< Self >	Pointer

typedef ProcessObject	Self

typedef Object	Superclass

Public Types inherited from itk::Object
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef Object	Self

typedef LightObject	Superclass

Public Types inherited from itk::LightObject
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef LightObject	Self

Public Member Functions
virtual ::itk::LightObject::Pointer	CreateAnother () const

void	DetermineSliceOrientations ()

virtual int	GetAxis ()

virtual int	GetAxis () const

virtual bool	GetHeuristicAlignment ()

virtual bool	GetHeuristicAlignment () const

virtual TImage::PixelType	GetLabel ()

virtual TImage::PixelType	GetLabel () const

SliceSetType	GetLabeledSliceIndices (unsigned int axis, typename TImage::PixelType label)

SliceIndicesType	GetLabeledSliceIndices ()

virtual const char *	GetNameOfClass () const

virtual bool	GetUseBallStructuringElement ()

virtual bool	GetUseBallStructuringElement () const

virtual bool	GetUseCustomSlicePositions ()

virtual bool	GetUseCustomSlicePositions () const

virtual bool	GetUseDistanceTransform ()

virtual bool	GetUseDistanceTransform () const

virtual void	SetAxis (int _arg)

virtual void	SetHeuristicAlignment (bool _arg)

virtual void	SetLabel (typename TImage::PixelType _arg)

virtual void	SetUseCustomSlicePositions (bool _arg)

virtual void	SetUseDistanceTransform (bool _arg)


void	SetUseBallStructuringElement (bool useBall)


void	ClearLabeledSliceIndices ()


void	SetLabeledSliceIndices (unsigned int axis, typename TImage::PixelType label, const std::vector< typename TImage::IndexValueType > &indices)


void	SetLabeledSliceIndices (unsigned int axis, typename TImage::PixelType label, const SliceSetType &indices)

Public Member Functions inherited from itk::ImageToImageFilter< TImage, TImage >
const InputImageType *	GetInput () const

const InputImageType *	GetInput (unsigned int idx) const

virtual void	PopBackInput () override

virtual void	PopFrontInput () override

virtual void	PushBackInput (const InputImageType *image)

virtual void	PushFrontInput (const InputImageType *image)

virtual void	SetInput (const InputImageType *image)

virtual void	SetInput (unsigned int, const TImage *image)

virtual void	SetCoordinateTolerance (double _arg)

virtual double	GetCoordinateTolerance () const

virtual void	SetDirectionTolerance (double _arg)

virtual double	GetDirectionTolerance () const

Public Member Functions inherited from itk::ImageSource< TImage >
OutputImageType *	GetOutput (unsigned int idx)

virtual void	GraftNthOutput (unsigned int idx, DataObject *output)

virtual void	GraftOutput (const DataObjectIdentifierType &key, DataObject *output)

OutputImageType *	GetOutput ()

const OutputImageType *	GetOutput () const

virtual void	GraftOutput (DataObject *output)

virtual ProcessObject::DataObjectPointer	MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx) override

virtual ProcessObject::DataObjectPointer	MakeOutput (const ProcessObject::DataObjectIdentifierType &) override

Public Member Functions inherited from itk::ProcessObject
virtual void	AbortGenerateDataOff ()

virtual void	AbortGenerateDataOn ()

virtual void	EnlargeOutputRequestedRegion (DataObject *)

virtual const bool &	GetAbortGenerateData () const

DataObjectPointerArray	GetIndexedInputs ()

DataObjectPointerArray	GetIndexedOutputs ()

NameArray	GetInputNames () const

DataObjectPointerArray	GetInputs ()

MultiThreaderType *	GetMultiThreader () const

DataObjectPointerArraySizeType	GetNumberOfIndexedInputs () const

DataObjectPointerArraySizeType	GetNumberOfIndexedOutputs () const

DataObjectPointerArraySizeType	GetNumberOfInputs () const

DataObjectPointerArraySizeType	GetNumberOfOutputs () const

virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const

NameArray	GetOutputNames () const

DataObjectPointerArray	GetOutputs ()

virtual const float &	GetProgress () const

NameArray	GetRequiredInputNames () const

bool	HasInput (const DataObjectIdentifierType &key) const

bool	HasOutput (const DataObjectIdentifierType &key) const

virtual void	PrepareOutputs ()

virtual void	PropagateRequestedRegion (DataObject *output)

virtual void	ResetPipeline ()

virtual void	SetAbortGenerateData (bool _arg)

virtual void	Update ()

virtual void	UpdateLargestPossibleRegion ()

virtual void	UpdateOutputData (DataObject *output)

virtual void	UpdateOutputInformation ()

void	UpdateProgress (float progress)

void	SetProgress (float progress)

virtual void	SetReleaseDataFlag (bool flag)

virtual bool	GetReleaseDataFlag () const

void	ReleaseDataFlagOn ()

void	ReleaseDataFlagOff ()

virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)

virtual const bool &	GetReleaseDataBeforeUpdateFlag () const

virtual void	ReleaseDataBeforeUpdateFlagOn ()

virtual void	ReleaseDataBeforeUpdateFlagOff ()

virtual void	SetNumberOfThreads (ThreadIdType _arg)

virtual const ThreadIdType &	GetNumberOfThreads () const

Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *)

unsigned long	AddObserver (const EventObject &event, Command *) const

virtual void	DebugOff () const

virtual void	DebugOn () const

Command *	GetCommand (unsigned long tag)

bool	GetDebug () const

MetaDataDictionary &	GetMetaDataDictionary ()

const MetaDataDictionary &	GetMetaDataDictionary () const

virtual ModifiedTimeType	GetMTime () const

virtual const TimeStamp &	GetTimeStamp () const

bool	HasObserver (const EventObject &event) const

void	InvokeEvent (const EventObject &)

void	InvokeEvent (const EventObject &) const

virtual void	Modified () const

virtual void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

virtual void	SetReferenceCount (int) override

virtual void	UnRegister () const noexceptoverride

virtual void	SetObjectName (std::string _arg)

virtual const std::string &	GetObjectName () const

Public Member Functions inherited from itk::LightObject
virtual void	Delete ()

virtual int	GetReferenceCount () const

	itkCloneMacro (Self)

void	Print (std::ostream &os, Indent indent=0) const

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from itk::Object
static bool	GetGlobalWarningDisplay ()

static void	GlobalWarningDisplayOff ()

static void	GlobalWarningDisplayOn ()

static Pointer	New ()

static void	SetGlobalWarningDisplay (bool flag)

Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()

static Pointer	New ()

Protected Types
typedef BinaryThresholdImageFilter < SliceType, BoolSliceType >	BinarizerType

typedef Image< bool, TImage::ImageDimension >	BoolImageType

typedef Image< bool, TImage::ImageDimension-1 >	BoolSliceType

typedef itksys::hash_map < typename TImage::PixelType, typename TImage::RegionType >	BoundingBoxesType

typedef ConnectedComponentImageFilter < BoolSliceType, SliceType >	ConnectedComponentsType

typedef Image< float, TImage::ImageDimension-1 >	FloatSliceType

typedef std::vector< typename TImage::PixelType >	PixelList

typedef ExtractImageFilter < TImage, SliceType >	RoiType

Protected Types inherited from itk::ImageToImageFilter< TImage, TImage >
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(OutputImageDimension), itkGetStaticConstMacro(InputImageDimension) >	InputToOutputRegionCopierType

typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(InputImageDimension), itkGetStaticConstMacro(OutputImageDimension) >	OutputToInputRegionCopierType

Protected Member Functions
SliceType::IndexType	Align (typename SliceType::Pointer &iConn, typename TImage::PixelType iRegionId, typename SliceType::Pointer &jConn, const PixelList &jRegionIds)

virtual void	AllocateOutputs () override

SliceType::RegionType	BoundingBox (itk::SmartPointer< SliceType > image)

IdentifierType	CardSymDifference (typename BoolSliceType::Pointer &shape1, typename BoolSliceType::Pointer &shape2)

SliceType::IndexType	Centroid (typename SliceType::Pointer &conn, const PixelList &regionIds)

BoolSliceType::Pointer	Dilate1 (typename BoolSliceType::Pointer &seed, typename BoolSliceType::Pointer &mask, ThreadIdType threadId)

template<typename T2 >
void	ExpandRegion (typename T2::RegionType &region, const typename T2::IndexType &index)

void	Extrapolate (int axis, TImage *out, typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, typename SliceType::Pointer &iConn, typename TImage::PixelType iRegionId, ThreadIdType threadId)

BoolSliceType::Pointer	FindMedianImageDilations (typename BoolSliceType::Pointer &intersection, typename BoolSliceType::Pointer &iMask, typename BoolSliceType::Pointer &jMask, ThreadIdType threadId)

BoolSliceType::Pointer	FindMedianImageDistances (typename BoolSliceType::Pointer &intersection, typename BoolSliceType::Pointer &iMask, typename BoolSliceType::Pointer &jMask, ThreadIdType threadId)

virtual void	GenerateData () override

std::vector< typename BoolSliceType::Pointer >	GenerateDilationSequence (typename BoolSliceType::Pointer &begin, typename BoolSliceType::Pointer &end, ThreadIdType threadId)

bool	ImagesEqual (typename BoolSliceType::Pointer &a, typename BoolSliceType::Pointer &b)

void	Interpolate1to1 (int axis, TImage *out, typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, typename SliceType::Pointer &iConn, typename TImage::PixelType iRegionId, typename SliceType::Pointer &jConn, typename TImage::PixelType jRegionId, const typename SliceType::IndexType &translation, bool recursive, ThreadIdType threadId)

void	Interpolate1toN (int axis, TImage *out, typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, typename SliceType::Pointer &iConn, typename TImage::PixelType iRegionId, typename SliceType::Pointer &jConn, const PixelList &jRegionIds, const typename SliceType::IndexType &translation, ThreadIdType threadId)

void	InterpolateAlong (int axis, TImage *out)

void	InterpolateBetweenTwo (int axis, TImage *out, typename TImage::PixelType label, typename TImage::IndexValueType i, typename TImage::IndexValueType j, typename SliceType::Pointer &iconn, typename SliceType::Pointer &jconn, ThreadIdType threadId)

IdentifierType	Intersection (typename SliceType::Pointer &iConn, typename TImage::PixelType iRegionId, typename SliceType::Pointer &jConn, const PixelList &jRegionIds, const typename SliceType::IndexType &translation)

void	IntersectionRegions (const typename SliceType::IndexType &translation, typename SliceType::RegionType &iRegion, typename SliceType::RegionType &jRegion)

FloatSliceType::Pointer	MaurerDM (typename BoolSliceType::Pointer &inImage, ThreadIdType threadId)

	MorphologicalContourInterpolator ()

SliceType::Pointer	RegionedConnectedComponents (const typename TImage::RegionType &region, typename TImage::PixelType label, IdentifierType &objectCount)

SliceType::Pointer	TranslateImage (typename SliceType::Pointer &image, const typename SliceType::IndexType &translation, typename SliceType::RegionType newRegion)

	~MorphologicalContourInterpolator ()

Protected Member Functions inherited from itk::ImageToImageFilter< TImage, TImage >
virtual void	CallCopyInputRegionToOutputRegion (OutputImageRegionType &destRegion, const InputImageRegionType &srcRegion)

virtual void	CallCopyOutputRegionToInputRegion (InputImageRegionType &destRegion, const OutputImageRegionType &srcRegion)

virtual void	GenerateInputRequestedRegion () override

	ImageToImageFilter ()

virtual void	PrintSelf (std::ostream &os, Indent indent) const override

virtual void	VerifyInputInformation () override

	~ImageToImageFilter () override

void	PushBackInput (const DataObject *input) override

void	PushFrontInput (const DataObject *input) override

Protected Member Functions inherited from itk::ImageSource< TImage >
virtual void	AfterThreadedGenerateData ()

virtual void	BeforeThreadedGenerateData ()

virtual const ImageRegionSplitterBase *	GetImageRegionSplitter () const

	ImageSource ()

virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int pieces, OutputImageRegionType &splitRegion)

virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId)

virtual	~ImageSource () override

Protected Member Functions inherited from itk::ProcessObject
virtual void	AddInput (DataObject *input)

void	AddOptionalInputName (const DataObjectIdentifierType &)

void	AddOptionalInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)

virtual void	AddOutput (DataObject *output)

bool	AddRequiredInputName (const DataObjectIdentifierType &)

bool	AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)

virtual void	CacheInputReleaseDataFlags ()

virtual void	GenerateOutputInformation ()

virtual void	GenerateOutputRequestedRegion (DataObject *output)

DataObject *	GetInput (const DataObjectIdentifierType &key)

const DataObject *	GetInput (const DataObjectIdentifierType &key) const

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs () const

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs () const

bool	IsIndexedInputName (const DataObjectIdentifierType &) const

bool	IsIndexedOutputName (const DataObjectIdentifierType &) const

bool	IsRequiredInputName (const DataObjectIdentifierType &) const

	itkLegacyMacro (virtual void RemoveOutput(DataObject *output))

	itkLegacyMacro (void SetNumberOfOutputs(DataObjectPointerArraySizeType num))

	itkLegacyMacro (virtual void RemoveInput(DataObject *input))

	itkLegacyMacro (void SetNumberOfInputs(DataObjectPointerArraySizeType num))

DataObjectPointerArraySizeType	MakeIndexFromInputName (const DataObjectIdentifierType &name) const

DataObjectPointerArraySizeType	MakeIndexFromOutputName (const DataObjectIdentifierType &name) const

DataObjectIdentifierType	MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const

DataObjectIdentifierType	MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) const

	ProcessObject ()

virtual void	PropagateResetPipeline ()

virtual void	ReleaseInputs ()

virtual void	RemoveInput (const DataObjectIdentifierType &key)

virtual void	RemoveInput (DataObjectPointerArraySizeType)

virtual void	RemoveOutput (const DataObjectIdentifierType &key)

virtual void	RemoveOutput (DataObjectPointerArraySizeType idx)

bool	RemoveRequiredInputName (const DataObjectIdentifierType &)

virtual void	RestoreInputReleaseDataFlags ()

virtual void	SetInput (const DataObjectIdentifierType &key, DataObject *input)

virtual void	SetNthInput (DataObjectPointerArraySizeType num, DataObject *input)

virtual void	SetNthOutput (DataObjectPointerArraySizeType num, DataObject *output)

void	SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)

void	SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)

virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)

virtual void	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)

virtual void	SetOutput (const DataObjectIdentifierType &key, DataObject *output)

virtual void	SetPrimaryInput (DataObject *input)

virtual void	SetPrimaryOutput (DataObject *output)

void	SetRequiredInputNames (const NameArray &)

virtual void	VerifyPreconditions ()

	~ProcessObject () override

DataObject *	GetInput (DataObjectPointerArraySizeType idx)

const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryInput ()

const DataObject *	GetPrimaryInput () const

virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryInputName (void) const

DataObject *	GetOutput (const DataObjectIdentifierType &key)

const DataObject *	GetOutput (const DataObjectIdentifierType &key) const

virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryOutputName (void) const

DataObject *	GetOutput (DataObjectPointerArraySizeType idx)

const DataObject *	GetOutput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryOutput ()

const DataObject *	GetPrimaryOutput () const

Protected Member Functions inherited from itk::Object
	Object ()

bool	PrintObservers (std::ostream &os, Indent indent) const

virtual void	SetTimeStamp (const TimeStamp &time)

virtual	~Object () override

Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer	InternalClone () const

	LightObject ()

virtual void	PrintHeader (std::ostream &os, Indent indent) const

virtual void	PrintTrailer (std::ostream &os, Indent indent) const

virtual	~LightObject ()

Protected Attributes
int	m_Axis

BinarizerType::Pointer	m_Binarizer

BoundingBoxesType	m_BoundingBoxes

ConnectedComponentsType::Pointer	m_ConnectedComponents

bool	m_HeuristicAlignment

TImage::PixelType	m_Label

SliceIndicesType	m_LabeledSlices

IdentifierType	m_MaxAlignIters

IdentifierType	m_MinAlignIters

RoiType::Pointer	m_RoI

IdentifierType	m_ThreadCount

bool	m_UseBallStructuringElement

bool	m_UseCustomSlicePositions

bool	m_UseDistanceTransform

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime

bool	m_Updating

Protected Attributes inherited from itk::LightObject
AtomicInt< int >	m_ReferenceCount

Private Member Functions
	MorphologicalContourInterpolator (const Self &) ITK_DELETE_FUNCTION

void	operator= (const Self &) ITK_DELETE_FUNCTION

Friends
template<typename T >
class	MorphologicalContourInterpolatorParallelInvoker

Additional Inherited Members
Static Public Attributes inherited from itk::ImageToImageFilter< TImage, TImage >
static const unsigned int	InputImageDimension

static const unsigned int	OutputImageDimension

Static Public Attributes inherited from itk::ImageSource< TImage >
static const unsigned int	OutputImageDimension

Static Protected Member Functions inherited from itk::ImageSource< TImage >
static const ImageRegionSplitterBase *	GetGlobalDefaultSplitter ()

static ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)

Member Typedef Documentation

template<typename TImage >

typedef BinaryThresholdImageFilter< SliceType, BoolSliceType > itk::MorphologicalContourInterpolator< TImage >::BinarizerType

protected

Definition at line 403 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

typedef Image< bool, TImage::ImageDimension > itk::MorphologicalContourInterpolator< TImage >::BoolImageType

protected

Derived image typedefs.

Definition at line 237 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

typedef Image< bool, TImage::ImageDimension - 1 > itk::MorphologicalContourInterpolator< TImage >::BoolSliceType

protected

Definition at line 239 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

typedef itksys::hash_map< typename TImage::PixelType, typename TImage::RegionType > itk::MorphologicalContourInterpolator< TImage >::BoundingBoxesType

protected

Definition at line 376 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

typedef ConnectedComponentImageFilter< BoolSliceType, SliceType > itk::MorphologicalContourInterpolator< TImage >::ConnectedComponentsType

protected

Definition at line 406 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

typedef Image< float, TImage::ImageDimension - 1 > itk::MorphologicalContourInterpolator< TImage >::FloatSliceType

protected

Definition at line 238 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

typedef itksys::hash_map< typename TImage::PixelType, SliceSetType > itk::MorphologicalContourInterpolator< TImage >::LabeledSlicesType

Definition at line 212 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

typedef std::vector< typename TImage::PixelType > itk::MorphologicalContourInterpolator< TImage >::PixelList

protected

Definition at line 319 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

typedef SmartPointer< Self > itk::MorphologicalContourInterpolator< TImage >::Pointer

Definition at line 75 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

typedef ExtractImageFilter< TImage, SliceType > itk::MorphologicalContourInterpolator< TImage >::RoiType

protected

Definition at line 400 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

typedef MorphologicalContourInterpolator itk::MorphologicalContourInterpolator< TImage >::Self

Standard class typedefs.

Definition at line 73 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

typedef std::vector< LabeledSlicesType > itk::MorphologicalContourInterpolator< TImage >::SliceIndicesType

Definition at line 213 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

typedef std::set< typename TImage::IndexValueType > itk::MorphologicalContourInterpolator< TImage >::SliceSetType

An std::set of slice indices which need to be interpolated.

Definition at line 168 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

typedef Image< typename TImage::PixelType, TImage::ImageDimension - 1 > itk::MorphologicalContourInterpolator< TImage >::SliceType

Definition at line 76 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

typedef ImageToImageFilter< TImage, TImage > itk::MorphologicalContourInterpolator< TImage >::Superclass

Definition at line 74 of file itkMorphologicalContourInterpolator.h.

Constructor & Destructor Documentation

template<typename TImage >

itk::MorphologicalContourInterpolator< TImage >::MorphologicalContourInterpolator ( )

protected

template<typename TImage >

itk::MorphologicalContourInterpolator< TImage >::~MorphologicalContourInterpolator ( )

inlineprotected

Definition at line 224 of file itkMorphologicalContourInterpolator.h.

template<typename TImage >

itk::MorphologicalContourInterpolator< TImage >::MorphologicalContourInterpolator ( const Self & )

private

Member Function Documentation

template<typename TImage >

SliceType::IndexType itk::MorphologicalContourInterpolator< TImage >::Align	(	typename SliceType::Pointer &	iConn,
		typename TImage::PixelType	iRegionId,
		typename SliceType::Pointer &	jConn,
		const PixelList &	jRegionIds
	)

protected

How much j needs to be translated to best align with i

template<typename TImage >

virtual void itk::MorphologicalContourInterpolator< TImage >::AllocateOutputs ( )

overrideprotectedvirtual

Copied from ImageSource and changed to allocate a cleared buffer.

Reimplemented from itk::ImageSource< TImage >.

template<typename TImage >

SliceType::RegionType itk::MorphologicalContourInterpolator< TImage >::BoundingBox ( itk::SmartPointer< SliceType > image )

protected

Calculates a bounding box of non-zero pixels.

template<typename TImage >

IdentifierType itk::MorphologicalContourInterpolator< TImage >::CardSymDifference	(	typename BoolSliceType::Pointer &	shape1,
		typename BoolSliceType::Pointer &	shape2
	)

protected

The returns cardingal of the symmetric distance between images. The images must cover the same region

template<typename TImage >

SliceType::IndexType itk::MorphologicalContourInterpolator< TImage >::Centroid	(	typename SliceType::Pointer &	conn,
		const PixelList &	regionIds
	)

protected

Returns the centroid of given regions

template<typename TImage >

void itk::MorphologicalContourInterpolator< TImage >::ClearLabeledSliceIndices ( )

inline

Clears all custom slice positions.

Definition at line 172 of file itkMorphologicalContourInterpolator.h.

References itk::MorphologicalContourInterpolator< TImage >::m_LabeledSlices, and itk::Object::Modified().

template<typename TImage >

virtual::itk::LightObject::Pointer itk::MorphologicalContourInterpolator< TImage >::CreateAnother ( ) const

virtual

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::Object.

template<typename TImage >

void itk::MorphologicalContourInterpolator< TImage >::DetermineSliceOrientations ( )

If there is a pixel whose all 4-way neighbors belong the the same label except along one axis, and along that axis its neighbors are 0 (background), then that axis should be interpolated along. Interpolation is possible along more than one axis. Updates LabeledSliceIndices.

template<typename TImage >

BoolSliceType::Pointer itk::MorphologicalContourInterpolator< TImage >::Dilate1	(	typename BoolSliceType::Pointer &	seed,
		typename BoolSliceType::Pointer &	mask,
		ThreadIdType	threadId
	)

protected

Seed and mask must cover the same region (size and index the same).

template<typename TImage >

template<typename T2 >

void itk::MorphologicalContourInterpolator< TImage >::ExpandRegion	(	typename T2::RegionType &	region,
		const typename T2::IndexType &	index
	)

protected

Expands a region to incorporate the provided index. Assumes both a valid region and a valid index. It can be invoked with 2D or 3D region, hence the additional template parameter.

template<typename TImage >

void itk::MorphologicalContourInterpolator< TImage >::Extrapolate	(	int	axis,
		TImage *	out,
		typename TImage::PixelType	label,
		typename TImage::IndexValueType	i,
		typename TImage::IndexValueType	j,
		typename SliceType::Pointer &	iConn,
		typename TImage::PixelType	iRegionId,
		ThreadIdType	threadId
	)

protected

Slice i has a region, slice j does not

template<typename TImage >

BoolSliceType::Pointer itk::MorphologicalContourInterpolator< TImage >::FindMedianImageDilations	(	typename BoolSliceType::Pointer &	intersection,
		typename BoolSliceType::Pointer &	iMask,
		typename BoolSliceType::Pointer &	jMask,
		ThreadIdType	threadId
	)

protected

Finds an interpolating mask for these two aligned masks

template<typename TImage >

BoolSliceType::Pointer itk::MorphologicalContourInterpolator< TImage >::FindMedianImageDistances	(	typename BoolSliceType::Pointer &	intersection,
		typename BoolSliceType::Pointer &	iMask,
		typename BoolSliceType::Pointer &	jMask,
		ThreadIdType	threadId
	)

protected

Finds an interpolating mask for these two aligned masks

template<typename TImage >

virtual void itk::MorphologicalContourInterpolator< TImage >::GenerateData ( )

overrideprotectedvirtual

Does the real work.

Reimplemented from itk::ImageSource< TImage >.

template<typename TImage >

std::vector< typename BoolSliceType::Pointer > itk::MorphologicalContourInterpolator< TImage >::GenerateDilationSequence	(	typename BoolSliceType::Pointer &	begin,
		typename BoolSliceType::Pointer &	end,
		ThreadIdType	threadId
	)

protected

A sequence of conditional dilations starting with begin and reaching end. begin and end must cover the same region (size and index the same)

template<typename TImage >

virtual int itk::MorphologicalContourInterpolator< TImage >::GetAxis ( )

virtual

Axis of interpolation. -1 means interpolation along all axes (default).

template<typename TImage >

virtual int itk::MorphologicalContourInterpolator< TImage >::GetAxis ( ) const

virtual

Axis of interpolation. -1 means interpolation along all axes (default).

template<typename TImage >

virtual bool itk::MorphologicalContourInterpolator< TImage >::GetHeuristicAlignment ( )

virtual

Heuristic alignment of regions for interpolation is faster than optimal alignment. Default is heuristic.

template<typename TImage >

virtual bool itk::MorphologicalContourInterpolator< TImage >::GetHeuristicAlignment ( ) const

virtual

Heuristic alignment of regions for interpolation is faster than optimal alignment. Default is heuristic.

template<typename TImage >

virtual TImage::PixelType itk::MorphologicalContourInterpolator< TImage >::GetLabel ( )

virtual

Which label is interpolated. 0 means all labels (default).

template<typename TImage >

virtual TImage::PixelType itk::MorphologicalContourInterpolator< TImage >::GetLabel ( ) const

virtual

Which label is interpolated. 0 means all labels (default).

template<typename TImage >

SliceSetType itk::MorphologicalContourInterpolator< TImage >::GetLabeledSliceIndices	(	unsigned int	axis,
		typename TImage::PixelType	label
	)

inline

Slice indices between which interpolation is done.

Definition at line 206 of file itkMorphologicalContourInterpolator.h.

References itk::MorphologicalContourInterpolator< TImage >::m_LabeledSlices.

template<typename TImage >

SliceIndicesType itk::MorphologicalContourInterpolator< TImage >::GetLabeledSliceIndices ( )

inline

Slice indices between which interpolation is done.

Definition at line 217 of file itkMorphologicalContourInterpolator.h.

References itk::MorphologicalContourInterpolator< TImage >::m_LabeledSlices.

template<typename TImage >

virtual const char* itk::MorphologicalContourInterpolator< TImage >::GetNameOfClass ( ) const

virtual

Run-time type information (and related methods).

Reimplemented from itk::ImageToImageFilter< TImage, TImage >.

template<typename TImage >

virtual bool itk::MorphologicalContourInterpolator< TImage >::GetUseBallStructuringElement ( )

virtual

Use ball instead of default cross structuring element for repeated dilations.

template<typename TImage >

virtual bool itk::MorphologicalContourInterpolator< TImage >::GetUseBallStructuringElement ( ) const

virtual

Use ball instead of default cross structuring element for repeated dilations.

template<typename TImage >

virtual bool itk::MorphologicalContourInterpolator< TImage >::GetUseCustomSlicePositions ( )

virtual

Use custom slice positions (not slice auto-detection). SetLabeledSliceIndices has to be called prior to Update().

template<typename TImage >

virtual bool itk::MorphologicalContourInterpolator< TImage >::GetUseCustomSlicePositions ( ) const

virtual

Use custom slice positions (not slice auto-detection). SetLabeledSliceIndices has to be called prior to Update().

template<typename TImage >

virtual bool itk::MorphologicalContourInterpolator< TImage >::GetUseDistanceTransform ( )

virtual

Using distance transform instead of repeated dilations to calculate the median contour is slightly faster, but produces lower quality interpolations. Default is OFF (that is, use repeated dilations).

template<typename TImage >

virtual bool itk::MorphologicalContourInterpolator< TImage >::GetUseDistanceTransform ( ) const

virtual

Using distance transform instead of repeated dilations to calculate the median contour is slightly faster, but produces lower quality interpolations. Default is OFF (that is, use repeated dilations).

template<typename TImage >

bool itk::MorphologicalContourInterpolator< TImage >::ImagesEqual	(	typename BoolSliceType::Pointer &	a,
		typename BoolSliceType::Pointer &	b
	)

protected

Are these two slices equal?

template<typename TImage >

void itk::MorphologicalContourInterpolator< TImage >::Interpolate1to1	(	int	axis,
		TImage *	out,
		typename TImage::PixelType	label,
		typename TImage::IndexValueType	i,
		typename TImage::IndexValueType	j,
		typename SliceType::Pointer &	iConn,
		typename TImage::PixelType	iRegionId,
		typename SliceType::Pointer &	jConn,
		typename TImage::PixelType	jRegionId,
		const typename SliceType::IndexType &	translation,
		bool	recursive,
		ThreadIdType	threadId
	)

protected

Build transition sequence and pick the median

template<typename TImage >

void itk::MorphologicalContourInterpolator< TImage >::Interpolate1toN	(	int	axis,
		TImage *	out,
		typename TImage::PixelType	label,
		typename TImage::IndexValueType	i,
		typename TImage::IndexValueType	j,
		typename SliceType::Pointer &	iConn,
		typename TImage::PixelType	iRegionId,
		typename SliceType::Pointer &	jConn,
		const PixelList &	jRegionIds,
		const typename SliceType::IndexType &	translation,
		ThreadIdType	threadId
	)

protected

Splits the bigger region and does N 1-to-1 interpolations

template<typename TImage >

void itk::MorphologicalContourInterpolator< TImage >::InterpolateAlong	(	int	axis,
		TImage *	out
	)

protected

If interpolation is done along more than one axis, the interpolations are merged using a modified "or" rule: -if all interpolated images have 0 for a given pixel, the output is 0 -if just one image has a non-zero label, then that label is chosen -if more than one image has a non-zero label, last written label is chosen

template<typename TImage >

void itk::MorphologicalContourInterpolator< TImage >::InterpolateBetweenTwo	(	int	axis,
		TImage *	out,
		typename TImage::PixelType	label,
		typename TImage::IndexValueType	i,
		typename TImage::IndexValueType	j,
		typename SliceType::Pointer &	iconn,
		typename SliceType::Pointer &	jconn,
		ThreadIdType	threadId
	)

protected

Determines correspondances between two slices and calls apropriate methods.

template<typename TImage >

IdentifierType itk::MorphologicalContourInterpolator< TImage >::Intersection	(	typename SliceType::Pointer &	iConn,
		typename TImage::PixelType	iRegionId,
		typename SliceType::Pointer &	jConn,
		const PixelList &	jRegionIds,
		const typename SliceType::IndexType &	translation
	)

protected

Returns number of intersecting pixels

template<typename TImage >

void itk::MorphologicalContourInterpolator< TImage >::IntersectionRegions	(	const typename SliceType::IndexType &	translation,
		typename SliceType::RegionType &	iRegion,
		typename SliceType::RegionType &	jRegion
	)

protected

Calculates maximum intersection region for both slices given a translation. Both inputs are modified so that jRegion is a translated version of iRegion.

template<typename TImage >

FloatSliceType::Pointer itk::MorphologicalContourInterpolator< TImage >::MaurerDM	(	typename BoolSliceType::Pointer &	inImage,
		ThreadIdType	threadId
	)

protected

Creates a signed distance field image.

template<typename TImage >

static Pointer itk::MorphologicalContourInterpolator< TImage >::New ( )

static

Method for creation through the object factory.

template<typename TImage >

void itk::MorphologicalContourInterpolator< TImage >::operator= ( const Self & )

private

template<typename TImage >

SliceType::Pointer itk::MorphologicalContourInterpolator< TImage >::RegionedConnectedComponents	(	const typename TImage::RegionType &	region,
		typename TImage::PixelType	label,
		IdentifierType &	objectCount
	)

protected

Connected components of a specified region.

template<typename TImage >

virtual void itk::MorphologicalContourInterpolator< TImage >::SetAxis ( int _arg )

virtual

Interpolate only along this axis. Interpolates along all axes if set to -1 (default).

template<typename TImage >

virtual void itk::MorphologicalContourInterpolator< TImage >::SetHeuristicAlignment ( bool _arg )

virtual

Heuristic alignment of regions for interpolation is faster than optimal alignment. Default is heuristic.

template<typename TImage >

virtual void itk::MorphologicalContourInterpolator< TImage >::SetLabel ( typename TImage::PixelType _arg )

virtual

Interpolate only this label. Interpolates all labels if set to 0 (default).

template<typename TImage >

void itk::MorphologicalContourInterpolator< TImage >::SetLabeledSliceIndices	(	unsigned int	axis,
		typename TImage::PixelType	label,
		const std::vector< typename TImage::IndexValueType > &	indices
	)

inline

If default slice detection is not wanted, slice indices between which interpolation is done can be set using this method.

Definition at line 183 of file itkMorphologicalContourInterpolator.h.

References itk::MorphologicalContourInterpolator< TImage >::m_LabeledSlices, and itk::Object::Modified().

template<typename TImage >

void itk::MorphologicalContourInterpolator< TImage >::SetLabeledSliceIndices	(	unsigned int	axis,
		typename TImage::PixelType	label,
		const SliceSetType &	indices
	)

inline

If default slice detection is not wanted, slice indices between which interpolation is done can be set using this method.

Definition at line 197 of file itkMorphologicalContourInterpolator.h.

References itk::MorphologicalContourInterpolator< TImage >::m_LabeledSlices, and itk::Object::Modified().

template<typename TImage >

void itk::MorphologicalContourInterpolator< TImage >::SetUseBallStructuringElement ( bool useBall )

inline

Use ball instead of default cross structuring element for repeated dilations.

Definition at line 143 of file itkMorphologicalContourInterpolator.h.

References itk::MorphologicalContourInterpolator< TImage >::m_ConnectedComponents, itk::MorphologicalContourInterpolator< TImage >::m_UseBallStructuringElement, and itk::Object::Modified().

template<typename TImage >

virtual void itk::MorphologicalContourInterpolator< TImage >::SetUseCustomSlicePositions ( bool _arg )

virtual

Use custom slice positions (not slice auto-detection). SetLabeledSliceIndices has to be called prior to Update().

template<typename TImage >

virtual void itk::MorphologicalContourInterpolator< TImage >::SetUseDistanceTransform ( bool _arg )

virtual

Using distance transform instead of repeated dilations to calculate the median contour is slightly faster, but produces lower quality interpolations. Default is OFF (that is, use repeated dilations).

template<typename TImage >

SliceType::Pointer itk::MorphologicalContourInterpolator< TImage >::TranslateImage	(	typename SliceType::Pointer &	image,
		const typename SliceType::IndexType &	translation,
		typename SliceType::RegionType	newRegion
	)