anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput > Class Template Reference

Class selecting the connected components touching a given mask border. In MRI, external CSF may contain artifacts due to fluid flow. These effects can cause voxels in the cortex or external CSF to have intensities similar to MS lesions. In order to reduce the number of false positives due to these effects, we remove all candidate lesions that are contiguous to the brain mask border. More...

#include <animaRemoveTouchingBorderFilter.h>

Inheritance diagram for anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >:

Collaboration diagram for anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >:

Public Types
typedef itk::ConnectedComponentImageFilter< InputImageType, ImageTypeInt >	ConnectedComponentImageFilterType
typedef itk::ConnectedComponentImageFilter< TMask, ImageTypeInt >	ConnectedComponentImageFilterType2
typedef itk::SmartPointer< const Self >	ConstPointer
typedef itk::ImageRegionIterator< ImageTypeInt >	ImageIteratorTypeInt
typedef itk::Image< PixelTypeInt, 3 >	ImageTypeInt
typedef itk::ImageRegionConstIterator< InputImageType >	InputConstIteratorType
typedef InputImageType::Pointer	InputImagePointer
typedef TInput	InputImageType
typedef itk::ImageRegionIterator< InputImageType >	InputIteratorType
typedef itk::LabelContourImageFilter< ImageTypeInt, ImageTypeInt >	LabelContourImageFilterType
typedef itk::LabelImageToLabelMapFilter< ImageTypeInt >	LabelImageToLabelMapFilterType
typedef itk::LabelImageToLabelMapFilter< TInput, TOutputMap >	LabelImageToLabelMapFilterType2
typedef itk::LabelMapToLabelImageFilter< TOutputMap, ImageTypeInt >	LabelMapToLabelImageFilterType
typedef itk::ImageRegionConstIterator< MaskImageType >	MaskConstIteratorType
typedef MaskImageType::Pointer	MaskImagePointer
typedef TMask	MaskImageType
typedef itk::ImageRegionIterator< MaskImageType >	MaskIteratorType
typedef OutputImageType::Pointer	OutputImagePointer
typedef Superclass::OutputImageRegionType	OutputImageRegionType
typedef TOutput	OutputImageType
typedef itk::ImageRegionIterator< OutputImageType >	OutputIteratorType
typedef unsigned int	PixelTypeInt
typedef itk::SmartPointer< Self >	Pointer
typedef RemoveTouchingBorderFilter	Self
typedef itk::ImageToImageFilter< TInput, TOutput >	Superclass
typedef LabelImageToLabelMapFilterType::OutputImageType	TOutputMap

Public Member Functions
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
virtual bool	GetLabeledImage ()
virtual const char *	GetNameOfClass () const
virtual bool	GetNoContour ()
TOutput *	GetOutputNonTouchingBorder ()
TOutput *	GetOutputTouchingBorder ()
virtual bool	GetVerbose ()
void	SetInputImageSeg (const TInput *image)
virtual void	SetLabeledImage (bool _arg)
void	SetMask (const TMask *mask)
virtual void	SetNoContour (bool _arg)
void	SetOutputNonTouchingBorderFilename (std::string fn)
void	SetOutputTouchingBorderFilename (std::string fn)
void	SetTol (const double tol)
virtual void	SetVerbose (bool _arg)
void	WriteOutputs ()

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
virtual void	GenerateData () ITK_OVERRIDE
TInput::ConstPointer	GetInputImageSeg ()
TMask::ConstPointer	GetMask ()
itk::DataObject::Pointer	MakeOutput (unsigned int idx)
	RemoveTouchingBorderFilter ()
virtual	~RemoveTouchingBorderFilter ()

Detailed Description

template<typename TInput, typename TMask, typename TOutput>
class anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >

Class selecting the connected components touching a given mask border. In MRI, external CSF may contain artifacts due to fluid flow. These effects can cause voxels in the cortex or external CSF to have intensities similar to MS lesions. In order to reduce the number of false positives due to these effects, we remove all candidate lesions that are contiguous to the brain mask border.

Definition at line 22 of file animaRemoveTouchingBorderFilter.h.

Member Typedef Documentation

ConnectedComponentImageFilterType

template<typename TInput , typename TMask , typename TOutput >

typedef itk::ConnectedComponentImageFilter<InputImageType,ImageTypeInt> anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::ConnectedComponentImageFilterType

Definition at line 67 of file animaRemoveTouchingBorderFilter.h.

ConnectedComponentImageFilterType2

template<typename TInput , typename TMask , typename TOutput >

typedef itk::ConnectedComponentImageFilter<TMask, ImageTypeInt > anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::ConnectedComponentImageFilterType2

Definition at line 68 of file animaRemoveTouchingBorderFilter.h.

ConstPointer

template<typename TInput , typename TMask , typename TOutput >

typedef itk::SmartPointer<const Self> anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::ConstPointer

Definition at line 30 of file animaRemoveTouchingBorderFilter.h.

ImageIteratorTypeInt

template<typename TInput , typename TMask , typename TOutput >

typedef itk::ImageRegionIterator< ImageTypeInt > anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::ImageIteratorTypeInt

Definition at line 59 of file animaRemoveTouchingBorderFilter.h.

ImageTypeInt

template<typename TInput , typename TMask , typename TOutput >

typedef itk::Image<PixelTypeInt,3> anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::ImageTypeInt

Definition at line 58 of file animaRemoveTouchingBorderFilter.h.

InputConstIteratorType

template<typename TInput , typename TMask , typename TOutput >

typedef itk::ImageRegionConstIterator< InputImageType > anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::InputConstIteratorType

Definition at line 44 of file animaRemoveTouchingBorderFilter.h.

InputImagePointer

template<typename TInput , typename TMask , typename TOutput >

typedef InputImageType::Pointer anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::InputImagePointer

Definition at line 42 of file animaRemoveTouchingBorderFilter.h.

InputImageType

template<typename TInput , typename TMask , typename TOutput >

typedef TInput anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::InputImageType

Image typedef support Type of the input image.

Definition at line 41 of file animaRemoveTouchingBorderFilter.h.

InputIteratorType

template<typename TInput , typename TMask , typename TOutput >

typedef itk::ImageRegionIterator< InputImageType > anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::InputIteratorType

Definition at line 43 of file animaRemoveTouchingBorderFilter.h.

LabelContourImageFilterType

template<typename TInput , typename TMask , typename TOutput >

typedef itk::LabelContourImageFilter<ImageTypeInt, ImageTypeInt> anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::LabelContourImageFilterType

Definition at line 70 of file animaRemoveTouchingBorderFilter.h.

LabelImageToLabelMapFilterType

template<typename TInput , typename TMask , typename TOutput >

typedef itk::LabelImageToLabelMapFilter<ImageTypeInt> anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::LabelImageToLabelMapFilterType

Definition at line 61 of file animaRemoveTouchingBorderFilter.h.

LabelImageToLabelMapFilterType2

template<typename TInput , typename TMask , typename TOutput >

typedef itk::LabelImageToLabelMapFilter<TInput,TOutputMap> anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::LabelImageToLabelMapFilterType2

Definition at line 63 of file animaRemoveTouchingBorderFilter.h.

LabelMapToLabelImageFilterType

template<typename TInput , typename TMask , typename TOutput >

typedef itk::LabelMapToLabelImageFilter<TOutputMap, ImageTypeInt> anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::LabelMapToLabelImageFilterType

Definition at line 65 of file animaRemoveTouchingBorderFilter.h.

MaskConstIteratorType

template<typename TInput , typename TMask , typename TOutput >

typedef itk::ImageRegionConstIterator< MaskImageType > anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::MaskConstIteratorType

Definition at line 50 of file animaRemoveTouchingBorderFilter.h.

MaskImagePointer

template<typename TInput , typename TMask , typename TOutput >

typedef MaskImageType::Pointer anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::MaskImagePointer

Definition at line 48 of file animaRemoveTouchingBorderFilter.h.

MaskImageType

template<typename TInput , typename TMask , typename TOutput >

typedef TMask anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::MaskImageType

Type of the mask image.

Definition at line 47 of file animaRemoveTouchingBorderFilter.h.

MaskIteratorType

template<typename TInput , typename TMask , typename TOutput >

typedef itk::ImageRegionIterator< MaskImageType > anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::MaskIteratorType

Definition at line 49 of file animaRemoveTouchingBorderFilter.h.

OutputImagePointer

template<typename TInput , typename TMask , typename TOutput >

typedef OutputImageType::Pointer anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::OutputImagePointer

Definition at line 54 of file animaRemoveTouchingBorderFilter.h.

OutputImageRegionType

template<typename TInput , typename TMask , typename TOutput >

typedef Superclass::OutputImageRegionType anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::OutputImageRegionType

Superclass typedefs.

Definition at line 94 of file animaRemoveTouchingBorderFilter.h.

OutputImageType

template<typename TInput , typename TMask , typename TOutput >

typedef TOutput anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::OutputImageType

Type of the output image.

Definition at line 53 of file animaRemoveTouchingBorderFilter.h.

OutputIteratorType

template<typename TInput , typename TMask , typename TOutput >

typedef itk::ImageRegionIterator< OutputImageType > anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::OutputIteratorType

Definition at line 55 of file animaRemoveTouchingBorderFilter.h.

PixelTypeInt

template<typename TInput , typename TMask , typename TOutput >

typedef unsigned int anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::PixelTypeInt

Definition at line 57 of file animaRemoveTouchingBorderFilter.h.

Pointer

template<typename TInput , typename TMask , typename TOutput >

typedef itk::SmartPointer<Self> anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::Pointer

Definition at line 29 of file animaRemoveTouchingBorderFilter.h.

Self

template<typename TInput , typename TMask , typename TOutput >

typedef RemoveTouchingBorderFilter anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::Self

Standard class typedefs.

Definition at line 27 of file animaRemoveTouchingBorderFilter.h.

Superclass

template<typename TInput , typename TMask , typename TOutput >

typedef itk::ImageToImageFilter< TInput , TOutput > anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::Superclass

Definition at line 28 of file animaRemoveTouchingBorderFilter.h.

TOutputMap

template<typename TInput , typename TMask , typename TOutput >

typedef LabelImageToLabelMapFilterType::OutputImageType anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::TOutputMap

Definition at line 62 of file animaRemoveTouchingBorderFilter.h.

Constructor & Destructor Documentation

RemoveTouchingBorderFilter()

template<typename TInput , typename TMask , typename TOutput >

anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::RemoveTouchingBorderFilter ( )

inlineprotected

Definition at line 106 of file animaRemoveTouchingBorderFilter.h.

References anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::MakeOutput().

~RemoveTouchingBorderFilter()

template<typename TInput , typename TMask , typename TOutput >

virtual anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::~RemoveTouchingBorderFilter ( )

inlineprotectedvirtual

Definition at line 121 of file animaRemoveTouchingBorderFilter.h.

References anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GenerateData(), anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GetInputImageSeg(), anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GetMask(), and anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::MakeOutput().

Member Function Documentation

CreateAnother()

template<typename TInput , typename TMask , typename TOutput >

virtual::itk::LightObject::Pointer anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::CreateAnother

(

void

)

const

GenerateData()

template<typename TInput , typename TMask , typename TOutput >

void anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GenerateData ( )

protectedvirtual

Does the real work.

Definition at line 89 of file animaRemoveTouchingBorderFilter.hxx.

Referenced by anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::WriteOutputs(), and anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::~RemoveTouchingBorderFilter().

GetInputImageSeg()

template<typename TInput , typename TMask , typename TOutput >

TInput::ConstPointer anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GetInputImageSeg ( )

protected

Definition at line 22 of file animaRemoveTouchingBorderFilter.hxx.

Referenced by anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::~RemoveTouchingBorderFilter().

GetLabeledImage()

template<typename TInput , typename TMask , typename TOutput >

virtual bool anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GetLabeledImage ( )

virtual

GetMask()

template<typename TInput , typename TMask , typename TOutput >

TMask::ConstPointer anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GetMask ( )

protected

Definition at line 28 of file animaRemoveTouchingBorderFilter.hxx.

Referenced by anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::~RemoveTouchingBorderFilter().

GetNameOfClass()

template<typename TInput , typename TMask , typename TOutput >

virtual const char* anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GetNameOfClass ( ) const

virtual

Run-time type information (and related methods)

GetNoContour()

template<typename TInput , typename TMask , typename TOutput >

virtual bool anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GetNoContour ( )

virtual

GetOutputNonTouchingBorder()

template<typename TInput , typename TMask , typename TOutput >

TOutput * anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GetOutputNonTouchingBorder

(

)

Definition at line 57 of file animaRemoveTouchingBorderFilter.hxx.

Referenced by anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::SetOutputTouchingBorderFilename().

GetOutputTouchingBorder()

template<typename TInput , typename TMask , typename TOutput >

TOutput * anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GetOutputTouchingBorder

(

)

Definition at line 63 of file animaRemoveTouchingBorderFilter.hxx.

References anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::WriteOutputs().

Referenced by anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::SetOutputTouchingBorderFilename().

GetVerbose()

template<typename TInput , typename TMask , typename TOutput >

virtual bool anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GetVerbose ( )

virtual

MakeOutput()

template<typename TInput , typename TMask , typename TOutput >

itk::DataObject::Pointer anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::MakeOutput ( unsigned int  idx )

protected

Create the Output

Definition at line 36 of file animaRemoveTouchingBorderFilter.hxx.

Referenced by anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::RemoveTouchingBorderFilter(), and anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::~RemoveTouchingBorderFilter().

New()

template<typename TInput , typename TMask , typename TOutput >

static Pointer anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::New ( )

static

Method for creation through the object factory.

SetInputImageSeg()

template<typename TInput , typename TMask , typename TOutput >

void anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::SetInputImageSeg

(

const TInput *

image

)

The mri images.

Definition at line 9 of file animaRemoveTouchingBorderFilter.hxx.

SetLabeledImage()

template<typename TInput , typename TMask , typename TOutput >

virtual void anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::SetLabeledImage ( bool  _arg )

virtual

SetMask()

template<typename TInput , typename TMask , typename TOutput >

void anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::SetMask

(

const TMask *

mask

)

mask in which the segmentation will be performed

Definition at line 15 of file animaRemoveTouchingBorderFilter.hxx.

Referenced by anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::SetOutputTouchingBorderFilename().

SetNoContour()

template<typename TInput , typename TMask , typename TOutput >

virtual void anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::SetNoContour ( bool  _arg )

virtual

SetOutputNonTouchingBorderFilename()

template<typename TInput , typename TMask , typename TOutput >

void anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::SetOutputNonTouchingBorderFilename ( std::string  fn )

inline

Definition at line 75 of file animaRemoveTouchingBorderFilter.h.

SetOutputTouchingBorderFilename()

template<typename TInput , typename TMask , typename TOutput >

void anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::SetOutputTouchingBorderFilename ( std::string  fn )

inline

Definition at line 76 of file animaRemoveTouchingBorderFilter.h.

References anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GetOutputNonTouchingBorder(), anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GetOutputTouchingBorder(), anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::SetMask(), and anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::WriteOutputs().

SetTol()

template<typename TInput , typename TMask , typename TOutput >

void anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::SetTol ( const double  tol )

inline

Definition at line 86 of file animaRemoveTouchingBorderFilter.h.

SetVerbose()

template<typename TInput , typename TMask , typename TOutput >

virtual void anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::SetVerbose ( bool  _arg )

virtual

WriteOutputs()

template<typename TInput , typename TMask , typename TOutput >

void anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::WriteOutputs

(

)

Definition at line 71 of file animaRemoveTouchingBorderFilter.hxx.

References anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GenerateData().

Referenced by anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::GetOutputTouchingBorder(), and anima::RemoveTouchingBorderFilter< TInput, TMask, TOutput >::SetOutputTouchingBorderFilename().

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

• animaRemoveTouchingBorderFilter.h
• animaRemoveTouchingBorderFilter.hxx