ANIMA  4.0
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | List of all members
anima::NLinksFilter< TInput, TOutput > Class Template Reference

Class creating a 3D graph in a graph cut framework. More...

#include <animaNLinksFilter.h>

+ Inheritance diagram for anima::NLinksFilter< TInput, TOutput >:
+ Collaboration diagram for anima::NLinksFilter< TInput, TOutput >:

Public Types

typedef itk::SmartPointer< const SelfConstPointer
 
typedef itk::VariableSizeMatrix< NumericTypedoubleVariableSizeMatrixType
 
typedef Graph< double, double, double > GraphType
 
typedef itk::ImageRegionIterator< ImageTypeIntImageIteratorTypeInt
 
typedef itk::ImageRegionIterator< TSeedProbaImageIteratorTypeProba
 
typedef TSeedProba::Pointer ImagePointerProba
 
typedef itk::Image< PixelTypeInt, 3 > ImageTypeInt
 
typedef TInput::ConstPointer InputImageConstPointer
 
typedef TInput::Pointer InputImagePointer
 
typedef TInput::PixelType InputPixelType
 
typedef itk::ImageRegionConstIterator< TInput > InRegionConstIteratorType
 
typedef itk::ImageRegionConstIterator< TMaskMaskRegionConstIteratorType
 
typedef itk::ImageRegionIterator< TMaskMaskRegionIteratorType
 
typedef double NumericType
 
typedef TOutput::Pointer OutputImagePointer
 
typedef Superclass::OutputImageRegionType OutputImageRegionType
 
typedef itk::ImageRegionIterator< TOutput > OutputIteratorType
 
typedef TOutput::PixelType OutputPixelType
 
typedef ImageTypeInt::IndexType pixelIndexInt
 
typedef double PixelTypeD
 
typedef int PixelTypeInt
 
typedef unsigned char PixelTypeUC
 
typedef itk::SmartPointer< SelfPointer
 
typedef TSeedProba::PixelType SeedProbaPixelType
 
typedef NLinksFilter Self
 
typedef itk::ImageToImageFilter< TInput, TOutput > Superclass
 
typedef itk::Image< PixelTypeUC, 3 > TMask
 
typedef TMask::Pointer TMaskPointer
 
typedef itk::Image< PixelTypeD, 3 > TSeedProba
 

Public Member Functions

virtual ::itk::LightObject::Pointer CreateAnother (void) const
 
virtual const char * GetNameOfClass () const
 
virtual unsigned int GetNbModalities ()
 
OutputImagePointer GetOutput ()
 
OutputImagePointer GetOutputBackground ()
 
virtual double GetSigma ()
 
virtual bool GetUseSpectralGradient ()
 
virtual bool GetVerbose ()
 
void SetInputImage1 (const TInput *image)
 
void SetInputImage2 (const TInput *image)
 
void SetInputImage3 (const TInput *image)
 
void SetInputImage4 (const TInput *image)
 
void SetInputImage5 (const TInput *image)
 
void SetInputSeedProbaSinks (const TSeedProba *mask)
 
void SetInputSeedProbaSources (const TSeedProba *mask)
 
void SetMask (const TMask *mask)
 
void SetMatFilename (std::string mat)
 
void SetMatrix (doubleVariableSizeMatrixType mat)
 
virtual void SetNbModalities (unsigned int _arg)
 
virtual void SetSigma (double _arg)
 
void SetTol (const double tol)
 
virtual void SetUseSpectralGradient (bool _arg)
 
virtual void SetVerbose (bool _arg)
 

Static Public Member Functions

static Pointer New ()
 

Protected Member Functions

void CheckSpectralGradient (void)
 
double computeNLink (int i1, int j1, int k1, int i2, int j2, int k2)
 
void CreateGraph ()
 
void GenerateData () ITK_OVERRIDE
 
TInput::ConstPointer GetInputImage1 ()
 
TInput::ConstPointer GetInputImage2 ()
 
TInput::ConstPointer GetInputImage3 ()
 
TInput::ConstPointer GetInputImage4 ()
 
TInput::ConstPointer GetInputImage5 ()
 
TInput::ConstPointer GetInputImage6 ()
 
TSeedProba::ConstPointer GetInputSeedProbaSinks ()
 
TSeedProba::ConstPointer GetInputSeedProbaSources ()
 
TMask::ConstPointer GetMask ()
 
std::string GetMatFilename (void)
 
doubleVariableSizeMatrixType GetMatrix (void)
 
bool isInside (unsigned int x, unsigned int y, unsigned int z) const
 
itk::DataObject::Pointer MakeOutput (unsigned int idx)
 
 NLinksFilter ()
 
bool readMatrixFile ()
 
void SetGraph ()
 
virtual ~NLinksFilter ()
 

Detailed Description

template<typename TInput, typename TOutput>
class anima::NLinksFilter< TInput, TOutput >

Class creating a 3D graph in a graph cut framework.

The nodes correspond to the voxels of the image to segment. Two additional nodes represent the object (SOURCE) and the background (SINK). N-links represent edges between neighboring nodes/voxels. T-links that bind each classical node to both the SOURCE and the SINK represent the probability for the corresponding voxel to belong respectively to the object and to the background.

Definition at line 23 of file animaNLinksFilter.h.

Member Typedef Documentation

◆ ConstPointer

template<typename TInput , typename TOutput >
typedef itk::SmartPointer<const Self> anima::NLinksFilter< TInput, TOutput >::ConstPointer

Definition at line 31 of file animaNLinksFilter.h.

◆ doubleVariableSizeMatrixType

template<typename TInput , typename TOutput >
typedef itk::VariableSizeMatrix<NumericType> anima::NLinksFilter< TInput, TOutput >::doubleVariableSizeMatrixType

Definition at line 69 of file animaNLinksFilter.h.

◆ GraphType

template<typename TInput , typename TOutput >
typedef Graph<double,double,double> anima::NLinksFilter< TInput, TOutput >::GraphType

Definition at line 66 of file animaNLinksFilter.h.

◆ ImageIteratorTypeInt

template<typename TInput , typename TOutput >
typedef itk::ImageRegionIterator<ImageTypeInt> anima::NLinksFilter< TInput, TOutput >::ImageIteratorTypeInt

Definition at line 58 of file animaNLinksFilter.h.

◆ ImageIteratorTypeProba

template<typename TInput , typename TOutput >
typedef itk::ImageRegionIterator<TSeedProba> anima::NLinksFilter< TInput, TOutput >::ImageIteratorTypeProba

Definition at line 52 of file animaNLinksFilter.h.

◆ ImagePointerProba

template<typename TInput , typename TOutput >
typedef TSeedProba::Pointer anima::NLinksFilter< TInput, TOutput >::ImagePointerProba

Definition at line 51 of file animaNLinksFilter.h.

◆ ImageTypeInt

template<typename TInput , typename TOutput >
typedef itk::Image<PixelTypeInt,3> anima::NLinksFilter< TInput, TOutput >::ImageTypeInt

Definition at line 56 of file animaNLinksFilter.h.

◆ InputImageConstPointer

template<typename TInput , typename TOutput >
typedef TInput::ConstPointer anima::NLinksFilter< TInput, TOutput >::InputImageConstPointer

Definition at line 41 of file animaNLinksFilter.h.

◆ InputImagePointer

template<typename TInput , typename TOutput >
typedef TInput::Pointer anima::NLinksFilter< TInput, TOutput >::InputImagePointer

Image typedef support

Definition at line 40 of file animaNLinksFilter.h.

◆ InputPixelType

template<typename TInput , typename TOutput >
typedef TInput::PixelType anima::NLinksFilter< TInput, TOutput >::InputPixelType

Definition at line 43 of file animaNLinksFilter.h.

◆ InRegionConstIteratorType

template<typename TInput , typename TOutput >
typedef itk::ImageRegionConstIterator< TInput > anima::NLinksFilter< TInput, TOutput >::InRegionConstIteratorType

Definition at line 42 of file animaNLinksFilter.h.

◆ MaskRegionConstIteratorType

template<typename TInput , typename TOutput >
typedef itk::ImageRegionConstIterator< TMask > anima::NLinksFilter< TInput, TOutput >::MaskRegionConstIteratorType

Definition at line 64 of file animaNLinksFilter.h.

◆ MaskRegionIteratorType

template<typename TInput , typename TOutput >
typedef itk::ImageRegionIterator< TMask > anima::NLinksFilter< TInput, TOutput >::MaskRegionIteratorType

Definition at line 63 of file animaNLinksFilter.h.

◆ NumericType

template<typename TInput , typename TOutput >
typedef double anima::NLinksFilter< TInput, TOutput >::NumericType

Definition at line 68 of file animaNLinksFilter.h.

◆ OutputImagePointer

template<typename TInput , typename TOutput >
typedef TOutput::Pointer anima::NLinksFilter< TInput, TOutput >::OutputImagePointer

Definition at line 45 of file animaNLinksFilter.h.

◆ OutputImageRegionType

template<typename TInput , typename TOutput >
typedef Superclass::OutputImageRegionType anima::NLinksFilter< TInput, TOutput >::OutputImageRegionType

Superclass typedefs.

Definition at line 94 of file animaNLinksFilter.h.

◆ OutputIteratorType

template<typename TInput , typename TOutput >
typedef itk::ImageRegionIterator< TOutput > anima::NLinksFilter< TInput, TOutput >::OutputIteratorType

Definition at line 47 of file animaNLinksFilter.h.

◆ OutputPixelType

template<typename TInput , typename TOutput >
typedef TOutput::PixelType anima::NLinksFilter< TInput, TOutput >::OutputPixelType

Definition at line 46 of file animaNLinksFilter.h.

◆ pixelIndexInt

template<typename TInput , typename TOutput >
typedef ImageTypeInt::IndexType anima::NLinksFilter< TInput, TOutput >::pixelIndexInt

Definition at line 57 of file animaNLinksFilter.h.

◆ PixelTypeD

template<typename TInput , typename TOutput >
typedef double anima::NLinksFilter< TInput, TOutput >::PixelTypeD

Definition at line 49 of file animaNLinksFilter.h.

◆ PixelTypeInt

template<typename TInput , typename TOutput >
typedef int anima::NLinksFilter< TInput, TOutput >::PixelTypeInt

Definition at line 55 of file animaNLinksFilter.h.

◆ PixelTypeUC

template<typename TInput , typename TOutput >
typedef unsigned char anima::NLinksFilter< TInput, TOutput >::PixelTypeUC

Definition at line 60 of file animaNLinksFilter.h.

◆ Pointer

template<typename TInput , typename TOutput >
typedef itk::SmartPointer<Self> anima::NLinksFilter< TInput, TOutput >::Pointer

Definition at line 30 of file animaNLinksFilter.h.

◆ SeedProbaPixelType

template<typename TInput , typename TOutput >
typedef TSeedProba::PixelType anima::NLinksFilter< TInput, TOutput >::SeedProbaPixelType

Definition at line 53 of file animaNLinksFilter.h.

◆ Self

template<typename TInput , typename TOutput >
typedef NLinksFilter anima::NLinksFilter< TInput, TOutput >::Self

Standard class typedefs.

Definition at line 28 of file animaNLinksFilter.h.

◆ Superclass

template<typename TInput , typename TOutput >
typedef itk::ImageToImageFilter< TInput , TOutput> anima::NLinksFilter< TInput, TOutput >::Superclass

Definition at line 29 of file animaNLinksFilter.h.

◆ TMask

template<typename TInput , typename TOutput >
typedef itk::Image<PixelTypeUC,3> anima::NLinksFilter< TInput, TOutput >::TMask

Definition at line 61 of file animaNLinksFilter.h.

◆ TMaskPointer

template<typename TInput , typename TOutput >
typedef TMask::Pointer anima::NLinksFilter< TInput, TOutput >::TMaskPointer

Definition at line 62 of file animaNLinksFilter.h.

◆ TSeedProba

template<typename TInput , typename TOutput >
typedef itk::Image<PixelTypeD,3> anima::NLinksFilter< TInput, TOutput >::TSeedProba

Definition at line 50 of file animaNLinksFilter.h.

Constructor & Destructor Documentation

◆ NLinksFilter()

template<typename TInput , typename TOutput >
anima::NLinksFilter< TInput, TOutput >::NLinksFilter ( )
inlineprotected

◆ ~NLinksFilter()

template<typename TInput , typename TOutput >
virtual anima::NLinksFilter< TInput, TOutput >::~NLinksFilter ( )
inlineprotectedvirtual

Member Function Documentation

◆ CheckSpectralGradient()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::CheckSpectralGradient ( void  )
protected

◆ computeNLink()

template<typename TInput , typename TOutput >
double anima::NLinksFilter< TInput, TOutput >::computeNLink ( int  i1,
int  j1,
int  k1,
int  i2,
int  j2,
int  k2 
)
protected

◆ CreateAnother()

template<typename TInput , typename TOutput >
virtual::itk::LightObject::Pointer anima::NLinksFilter< TInput, TOutput >::CreateAnother ( void  ) const

◆ CreateGraph()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::CreateGraph ( )
protected

◆ GenerateData()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::GenerateData ( )
protected

◆ GetInputImage1()

template<typename TInput , typename TOutput >
TInput::ConstPointer anima::NLinksFilter< TInput, TOutput >::GetInputImage1 ( )
protected

◆ GetInputImage2()

template<typename TInput , typename TOutput >
TInput::ConstPointer anima::NLinksFilter< TInput, TOutput >::GetInputImage2 ( )
protected

◆ GetInputImage3()

template<typename TInput , typename TOutput >
TInput::ConstPointer anima::NLinksFilter< TInput, TOutput >::GetInputImage3 ( )
protected

◆ GetInputImage4()

template<typename TInput , typename TOutput >
TInput::ConstPointer anima::NLinksFilter< TInput, TOutput >::GetInputImage4 ( )
protected

◆ GetInputImage5()

template<typename TInput , typename TOutput >
TInput::ConstPointer anima::NLinksFilter< TInput, TOutput >::GetInputImage5 ( )
protected

◆ GetInputImage6()

template<typename TInput , typename TOutput >
TInput::ConstPointer anima::NLinksFilter< TInput, TOutput >::GetInputImage6 ( )
protected

◆ GetInputSeedProbaSinks()

template<typename TInput , typename TOutput >
itk::Image< double, 3 >::ConstPointer anima::NLinksFilter< TInput, TOutput >::GetInputSeedProbaSinks ( )
protected

◆ GetInputSeedProbaSources()

template<typename TInput , typename TOutput >
itk::Image< double, 3 >::ConstPointer anima::NLinksFilter< TInput, TOutput >::GetInputSeedProbaSources ( )
protected

◆ GetMask()

template<typename TInput , typename TOutput >
itk::Image< unsigned char, 3 >::ConstPointer anima::NLinksFilter< TInput, TOutput >::GetMask ( )
protected

◆ GetMatFilename()

template<typename TInput , typename TOutput >
std::string anima::NLinksFilter< TInput, TOutput >::GetMatFilename ( void  )
inlineprotected

◆ GetMatrix()

template<typename TInput , typename TOutput >
doubleVariableSizeMatrixType anima::NLinksFilter< TInput, TOutput >::GetMatrix ( void  )
inlineprotected

Definition at line 154 of file animaNLinksFilter.h.

◆ GetNameOfClass()

template<typename TInput , typename TOutput >
virtual const char* anima::NLinksFilter< TInput, TOutput >::GetNameOfClass ( ) const
virtual

Run-time type information (and related methods)

◆ GetNbModalities()

template<typename TInput , typename TOutput >
virtual unsigned int anima::NLinksFilter< TInput, TOutput >::GetNbModalities ( )
virtual

◆ GetOutput()

template<typename TInputImage , typename TOutput >
TOutput::Pointer anima::NLinksFilter< TInputImage, TOutput >::GetOutput ( )

◆ GetOutputBackground()

template<typename TInputImage , typename TOutput >
TOutput::Pointer anima::NLinksFilter< TInputImage, TOutput >::GetOutputBackground ( )

◆ GetSigma()

template<typename TInput , typename TOutput >
virtual double anima::NLinksFilter< TInput, TOutput >::GetSigma ( )
virtual

◆ GetUseSpectralGradient()

template<typename TInput , typename TOutput >
virtual bool anima::NLinksFilter< TInput, TOutput >::GetUseSpectralGradient ( )
virtual

◆ GetVerbose()

template<typename TInput , typename TOutput >
virtual bool anima::NLinksFilter< TInput, TOutput >::GetVerbose ( )
virtual

◆ isInside()

template<typename TInput , typename TOutput >
bool anima::NLinksFilter< TInput, TOutput >::isInside ( unsigned int  x,
unsigned int  y,
unsigned int  z 
) const
protected

◆ MakeOutput()

template<typename TInputImage , typename TOutput >
itk::DataObject::Pointer anima::NLinksFilter< TInputImage, TOutput >::MakeOutput ( unsigned int  idx)
protected

◆ New()

template<typename TInput , typename TOutput >
static Pointer anima::NLinksFilter< TInput, TOutput >::New ( )
static

Method for creation through the object factory.

Referenced by anima::Graph3DFilter< TInput, TOutput >::Graph3DFilter().

◆ readMatrixFile()

template<typename TInput , typename TOutput >
bool anima::NLinksFilter< TInput, TOutput >::readMatrixFile ( )
protected

◆ SetGraph()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::SetGraph ( )
protected

◆ SetInputImage1()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::SetInputImage1 ( const TInput *  image)

The mri images.

Definition at line 9 of file animaNLinksFilter.hxx.

◆ SetInputImage2()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::SetInputImage2 ( const TInput *  image)

Definition at line 35 of file animaNLinksFilter.hxx.

◆ SetInputImage3()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::SetInputImage3 ( const TInput *  image)

Definition at line 45 of file animaNLinksFilter.hxx.

◆ SetInputImage4()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::SetInputImage4 ( const TInput *  image)

Definition at line 55 of file animaNLinksFilter.hxx.

◆ SetInputImage5()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::SetInputImage5 ( const TInput *  image)

Definition at line 65 of file animaNLinksFilter.hxx.

◆ SetInputSeedProbaSinks()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::SetInputSeedProbaSinks ( const TSeedProba mask)

Definition at line 23 of file animaNLinksFilter.hxx.

◆ SetInputSeedProbaSources()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::SetInputSeedProbaSources ( const TSeedProba mask)

probabilities of the object and the background, respectively

Definition at line 17 of file animaNLinksFilter.hxx.

◆ SetMask()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::SetMask ( const TMask mask)

mask in which the segmentation will be performed

Definition at line 29 of file animaNLinksFilter.hxx.

◆ SetMatFilename()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::SetMatFilename ( std::string  mat)
inline

Definition at line 87 of file animaNLinksFilter.h.

◆ SetMatrix()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::SetMatrix ( doubleVariableSizeMatrixType  mat)
inline

◆ SetNbModalities()

template<typename TInput , typename TOutput >
virtual void anima::NLinksFilter< TInput, TOutput >::SetNbModalities ( unsigned int  _arg)
virtual

◆ SetSigma()

template<typename TInput , typename TOutput >
virtual void anima::NLinksFilter< TInput, TOutput >::SetSigma ( double  _arg)
virtual

◆ SetTol()

template<typename TInput , typename TOutput >
void anima::NLinksFilter< TInput, TOutput >::SetTol ( const double  tol)
inline

Definition at line 96 of file animaNLinksFilter.h.

◆ SetUseSpectralGradient()

template<typename TInput , typename TOutput >
virtual void anima::NLinksFilter< TInput, TOutput >::SetUseSpectralGradient ( bool  _arg)
virtual

◆ SetVerbose()

template<typename TInput , typename TOutput >
virtual void anima::NLinksFilter< TInput, TOutput >::SetVerbose ( bool  _arg)
virtual

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