#include <itkBinaryMask3DMeshSource.h>

Inheritance diagram for itk::BinaryMask3DMeshSource< TInputImage, TOutputMesh >:

Collaboration diagram for itk::BinaryMask3DMeshSource< TInputImage, TOutputMesh >:

Detailed Description

template<typename TInputImage, typename TOutputMesh>
class itk::BinaryMask3DMeshSource< TInputImage, TOutputMesh >

: This class tries to construct a 3D mesh surface based on a binary mask. It can be used to integrate a region-based segmentation method and a deformable model into one hybrid framework.

: To construct a mesh, we need to construct elements in a voxel and combine those elements later to form the final mesh. Before go through every voxel in the 3D volume, we first construct 2 look up tables. The index of these 2 tables are the on-off combination of the 8 nodes that form the voxel. So both of these tables has the size of $2^8$ bytes. According to previous work, all those $2^8$ combination of the nodes can be grouped into 16 final combinations. In the first table, we record the final combination that can be transformed from the current combination. The entries of the second table are made up of the transforming sequence that is necessary for the current combination transform to one of the final combinations.

: We then go through the 3D volume voxel by voxel, using those two tables we have defined to construct elements within each voxel. We then merge all these mesh elements into one 3D mesh.

PARAMETERS: The ObjectValue parameter is used to identify the object. In most applications, pixels in the object region are assigned to "1", so the default value of ObjectValue is set to "1"

REFERENCE: W. Lorensen and H. Cline, "Marching Cubes: A High Resolution 3D Surface Construction Algorithm", Computer Graphics 21, pp. 163-169, 1987.

INPUT: The input should be a 3D binary image.

Examples:: Examples/Filtering/SurfaceExtraction.cxx, and SphinxExamples/src/Core/Mesh/ExtractIsoSurface/Code.cxx.

Definition at line 71 of file itkBinaryMask3DMeshSource.h.

Public Types
using	CellsContainer = typename OutputMeshType::CellsContainer

using	CellsContainerPointer = typename OutputMeshType::CellsContainerPointer

using	CellTraits = typename OutputMeshType::CellTraits

using	ConstPointer = SmartPointer< const Self >

using	doubleVector = CovariantVector< double, 2 >

using	IdentifierType = itk::IdentifierType

using	InputImageConstPointer = typename InputImageType::ConstPointer

using	InputImageIndexType = typename InputImageType::IndexType

using	InputImageIterator = ImageRegionConstIterator< InputImageType >

using	InputImagePointer = typename InputImageType::Pointer

using	InputImageType = TInputImage

using	InputPixelType = typename InputImageType::PixelType

using	intVector = CovariantVector< int, 2 >

using	OMeshTraits = typename OutputMeshType::MeshTraits

using	OPixelType = typename OMeshTraits::PixelType

using	OPointType = typename OutputMeshType::PointType

using	OriginType = typename InputImageType::PointType

using	OutputMeshPointer = typename OutputMeshType::Pointer

using	OutputMeshType = TOutputMesh

using	Pointer = SmartPointer< Self >

using	PointsContainer = typename OutputMeshType::PointsContainer

using	PointsContainerPointer = typename OutputMeshType::PointsContainerPointer

using	RegionType = typename InputImageType::RegionType

using	Self = BinaryMask3DMeshSource

using	SizeType = typename InputImageType::SizeType

using	SizeValueType = itk::SizeValueType

using	SpacingType = typename InputImageType::SpacingType

using	Superclass = ImageToMeshFilter< TInputImage, TOutputMesh >

using	TCellInterface = CellInterface< OPixelType, CellTraits >

using	TriCell = TriangleCell< TCellInterface >

using	TriCellAutoPointer = typename TriCell::SelfAutoPointer

Public Types inherited from itk::ImageToMeshFilter< TInputImage, TOutputMesh >
using	ConstPointer = SmartPointer< const Self >

using	DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType

using	InputImageConstPointer = typename InputImageType::ConstPointer

using	InputImagePixelType = typename InputImageType::PixelType

using	InputImagePointer = typename InputImageType::Pointer

using	InputImageRegionType = typename InputImageType::RegionType

using	InputImageType = TInputImage

using	OutputMeshPointer = typename OutputMeshType::Pointer

using	OutputMeshType = TOutputMesh

using	Pointer = SmartPointer< Self >

using	Self = ImageToMeshFilter

using	Superclass = MeshSource< TOutputMesh >

Public Types inherited from itk::MeshSource< TOutputMesh >
using	ConstPointer = SmartPointer< const Self >

using	DataObjectIdentifierType = Superclass::DataObjectIdentifierType

using	DataObjectPointer = DataObject::Pointer

using	OutputMeshPointer = typename OutputMeshType::Pointer

using	OutputMeshType = TOutputMesh

using	Pointer = SmartPointer< Self >

using	Self = MeshSource

using	Superclass = ProcessObject

using	DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType

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

using	DataObjectIdentifierType = DataObject::DataObjectIdentifierType

using	DataObjectPointer = DataObject::Pointer

using	DataObjectPointerArray = std::vector< DataObjectPointer >

using	DataObjectPointerArraySizeType = DataObjectPointerArray::size_type

using	MultiThreaderType = MultiThreaderBase

using	NameArray = std::vector< DataObjectIdentifierType >

using	Pointer = SmartPointer< Self >

using	Self = ProcessObject

using	Superclass = Object

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

using	Pointer = SmartPointer< Self >

using	Self = Object

using	Superclass = LightObject

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

using	Pointer = SmartPointer< Self >

using	Self = LightObject

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

virtual const char *	GetNameOfClass () const

virtual SizeValueType	GetNumberOfCells () const

virtual SizeValueType	GetNumberOfNodes () const

virtual const RegionType &	GetRegionOfInterest () const

virtual void	SetInput (const InputImageType *inputImage)

virtual void	SetObjectValue (InputPixelType _arg)

void	SetRegionOfInterest (const RegionType &iRegion)

Public Member Functions inherited from itk::ImageToMeshFilter< TInputImage, TOutputMesh >
void	GenerateOutputInformation () override

OutputMeshType *	GetOutput ()

DataObject::Pointer	MakeOutput (DataObjectPointerArraySizeType idx) override

void	SetInput (unsigned int idx, const InputImageType *input)

void	SetInput (const InputImageType *input)

const InputImageType *	GetInput (unsigned int idx)

const InputImageType *	GetInput ()

Public Member Functions inherited from itk::MeshSource< TOutputMesh >
virtual ::itk::LightObject::Pointer	CreateAnother () const

OutputMeshType *	GetOutput ()

OutputMeshType *	GetOutput (unsigned int idx)

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

virtual void	GraftOutput (DataObject *output)

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

void	SetOutput (TOutputMesh *output)

DataObjectPointer	MakeOutput (DataObjectPointerArraySizeType idx) 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 DataObjectPointer	MakeOutput (const DataObjectIdentifierType &)

virtual void	PrepareOutputs ()

virtual void	PropagateRequestedRegion (DataObject *output)

virtual void	ResetPipeline ()

virtual void	SetAbortGenerateData (bool _arg)

void	SetMultiThreader (MultiThreaderType *threader)

virtual void	Update ()

virtual void	UpdateLargestPossibleRegion ()

virtual void	UpdateOutputData (DataObject *output)

virtual void	UpdateOutputInformation ()

void	UpdateProgress (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	SetNumberOfWorkUnits (ThreadIdType _arg)

virtual const ThreadIdType &	GetNumberOfWorkUnits () 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

void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetReferenceCount (int) override

void	UnRegister () const noexceptoverride

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

void	SetMetaDataDictionary (MetaDataDictionary &&rrhs)

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::MeshSource< TOutputMesh >
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 Member Functions
	BinaryMask3DMeshSource ()

void	GenerateData () override

void	GenerateOutputInformation () override

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

	~BinaryMask3DMeshSource () override

Protected Member Functions inherited from itk::ImageToMeshFilter< TInputImage, TOutputMesh >
	ImageToMeshFilter ()

	~ImageToMeshFilter () override=default

Protected Member Functions inherited from itk::MeshSource< TOutputMesh >
void	GenerateInputRequestedRegion () override

	MeshSource ()

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

	~MeshSource () override=default

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	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

DataObjectPointerArraySizeType	MakeIndexFromInputName (const DataObjectIdentifierType &name) const

DataObjectPointerArraySizeType	MakeIndexFromOutputName (const DataObjectIdentifierType &name) const

DataObjectIdentifierType	MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const

DataObjectIdentifierType	MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) const

virtual void	PopBackInput ()

virtual void	PopFrontInput ()

	ProcessObject ()

virtual void	PropagateResetPipeline ()

virtual void	PushBackInput (const DataObject *input)

virtual void	PushFrontInput (const DataObject *input)

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	VerifyInputInformation () ITKv5_CONST

virtual void	VerifyPreconditions () ITKv5_CONST

	~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 () const

DataObject *	GetOutput (const DataObjectIdentifierType &key)

const DataObject *	GetOutput (const DataObjectIdentifierType &key) const

virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryOutputName () 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)

	~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
RegionType	m_RegionOfInterest

bool	m_RegionOfInterestProvidedByUser {false}

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime

bool	m_Updating

Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount

Private Types
using	InputImageSizeType = typename InputImageType::SizeType

Private Member Functions
void	AddCells (unsigned char celltype, unsigned char celltran, int index)

void	AddNodes (int index, unsigned char nodesid, IdentifierType globalnodesid, IdentifierType currentrowtmp, IdentifierType currentframetmp)

void	CellTransfer (unsigned char *nodesid, unsigned char celltran)

void	CreateMesh ()

void	InitializeLUT ()

void	inverse (unsigned char *tp)

IdentifierType	SearchThroughLastFrame (int index, int start, int end)

IdentifierType	SearchThroughLastRow (int index, int start, int end)

void	XFlip (unsigned char *tp)

void	XRotation (unsigned char *tp)

void	YFlip (unsigned char *tp)

void	YRotation (unsigned char *tp)

void	ZFlip (unsigned char *tp)

void	ZRotation (unsigned char *tp)

Private Attributes
unsigned char	m_AvailableNodes [14]

int	m_CellLimit {4000}

int	m_ColFlag {0}

IdentifierType **	m_CurrentFrame {nullptr}

unsigned short	m_CurrentFrameIndex {0}

unsigned short	m_CurrentFrameNum {2000}

IdentifierType **	m_CurrentRow {nullptr}

unsigned short	m_CurrentRowIndex {0}

unsigned short	m_CurrentRowNum {200}

IdentifierType	m_CurrentVoxel [14]

int	m_FrameFlag {0}

int	m_ImageDepth {0}

int	m_ImageHeight {0}

int	m_ImageWidth {0}

const InputImageType *	m_InputImage

IdentifierType **	m_LastFrame {nullptr}

int	m_LastFrameIndex {0}

unsigned short	m_LastFrameNum {0}

IdentifierType **	m_LastRow {nullptr}

int	m_LastRowIndex {0}

unsigned short	m_LastRowNum {0}

IdentifierType	m_LastVoxel [14]

int	m_LastVoxelIndex {0}

double	m_LocationOffset [14][3]

unsigned char	m_LUT [256][2]

int	m_NodeLimit {2000}

SizeValueType	m_NumberOfCells {0}

SizeValueType	m_NumberOfNodes {0}

InputPixelType	m_ObjectValue

OutputMeshType *	m_OutputMesh

unsigned char	m_PointFound {0}

int	m_RowFlag {0}