anima::PatientToGroupComparisonImageFilter< PixelScalarType > Class Template Reference

Implements patient to group comparison as in http://dx.doi.org/10.1007/978-3-540-85988-8_116. More...

#include <animaPatientToGroupComparisonImageFilter.h>

Inheritance diagram for anima::PatientToGroupComparisonImageFilter< PixelScalarType >:

Collaboration diagram for anima::PatientToGroupComparisonImageFilter< PixelScalarType >:

Public Types
typedef itk::SmartPointer< const Self >	ConstPointer
typedef vnl_matrix< double >	CovMatrixType
typedef InputImageType::IndexType	InputImageIndexType
typedef InputImageType::Pointer	InputImagePointer
typedef itk::VectorImage< PixelScalarType, 3 >	InputImageType
typedef Superclass::MaskImageType	MaskImageType
typedef OutputImageType::Pointer	OutputImagePointer
typedef Superclass::OutputImageRegionType	OutputImageRegionType
typedef itk::Image< PixelScalarType, 3 >	OutputImageType
typedef itk::SmartPointer< Self >	Pointer
typedef PatientToGroupComparisonImageFilter< PixelScalarType >	Self
typedef anima::MaskedImageToImageFilter< InputImageType, OutputImageType >	Superclass
enum	TestType {   CHI_SQUARE = 0,   FISHER }
typedef InputImageType::PixelType	VectorType
Public Types inherited from anima::MaskedImageToImageFilter< itk::VectorImage< PixelScalarType, 3 >, itk::Image< PixelScalarType, 3 > >
typedef itk::SmartPointer< const Self >	ConstPointer
typedef Superclass::InputImageRegionType	InputImageRegionType
typedef MaskImageType::Pointer	MaskImagePointer
typedef itk::Image< unsigned char, itk::VectorImage< PixelScalarType, 3 > ::ImageDimension >	MaskImageType
typedef MaskImageType::IndexType	MaskIndexType
typedef MaskImageType::RegionType	MaskRegionType
typedef MaskImageType::SizeType	MaskSizeType
typedef Superclass::OutputImageRegionType	OutputImageRegionType
typedef itk::SmartPointer< Self >	Pointer
typedef MaskedImageToImageFilter	Self
typedef anima::NumberedThreadImageToImageFilter< itk::VectorImage< PixelScalarType, 3 >, itk::Image< PixelScalarType, 3 > >	Superclass
typedef itk::ImageSource< itk::Image< PixelScalarType, 3 > >::ThreadStruct	ThreadStruct
Public Types inherited from anima::NumberedThreadImageToImageFilter< itk::VectorImage< PixelScalarType, 3 >, itk::Image< PixelScalarType, 3 > >
typedef itk::SmartPointer< const Self >	ConstPointer
typedef Superclass::OutputImageRegionType	OutputImageRegionType
typedef itk::SmartPointer< Self >	Pointer
typedef NumberedThreadImageToImageFilter	Self
typedef itk::ImageToImageFilter< itk::VectorImage< PixelScalarType, 3 >, itk::Image< PixelScalarType, 3 > >	Superclass
typedef itk::ImageSource< itk::Image< PixelScalarType, 3 > >::ThreadStruct	ThreadStruct

Public Member Functions
void	AddDatabaseInput (InputImageType *tmpIm)
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
virtual const char *	GetNameOfClass () const
virtual void	SetExplainedRatio (double _arg)
virtual void	SetNumEigenValuesPCA (unsigned int _arg)
virtual void	SetStatisticalTestType (TestType _arg)
Public Member Functions inherited from anima::MaskedImageToImageFilter< itk::VectorImage< PixelScalarType, 3 >, itk::Image< PixelScalarType, 3 > >
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
virtual MaskImageType *	GetComputationMask ()
virtual void	SetComputationMask (MaskImagePointer _arg)
Public Member Functions inherited from anima::NumberedThreadImageToImageFilter< itk::VectorImage< PixelScalarType, 3 >, itk::Image< PixelScalarType, 3 > >
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
virtual OutputImageRegionType	GetComputationRegion ()
virtual void	SetComputationRegion (OutputImageRegionType _arg)
virtual void	SetNumberOfPointsToProcess (unsigned int _arg)

Static Public Member Functions
static Pointer	New ()
Static Public Member Functions inherited from anima::MaskedImageToImageFilter< itk::VectorImage< PixelScalarType, 3 >, itk::Image< PixelScalarType, 3 > >
static Pointer	New ()
Static Public Member Functions inherited from anima::NumberedThreadImageToImageFilter< itk::VectorImage< PixelScalarType, 3 >, itk::Image< PixelScalarType, 3 > >
static Pointer	New ()

Protected Member Functions
virtual void	BeforeThreadedGenerateData () ITK_OVERRIDE
void	DynamicThreadedGenerateData (const OutputImageRegionType &outputRegionForThread) ITK_OVERRIDE
	PatientToGroupComparisonImageFilter ()
virtual unsigned int	SampleFromDiffusionModels (std::vector< VectorType > &databaseValues, VectorType &patientVectorValue)
virtual	~PatientToGroupComparisonImageFilter ()
Protected Member Functions inherited from anima::MaskedImageToImageFilter< itk::VectorImage< PixelScalarType, 3 >, itk::Image< PixelScalarType, 3 > >
virtual void	CheckComputationMask ()
void	InitializeComputationRegionFromMask ()
	MaskedImageToImageFilter ()
virtual	~MaskedImageToImageFilter ()
Protected Member Functions inherited from anima::NumberedThreadImageToImageFilter< itk::VectorImage< PixelScalarType, 3 >, itk::Image< PixelScalarType, 3 > >
virtual void	GenerateData () ITK_OVERRIDE
unsigned int	GetSafeThreadId ()
void	IncrementNumberOfProcessedPoints ()
void	InitializeZeroPixel (itk::Image< PixelScalarType, 3 > *image, itk::VariableLengthVector< ScalarRealType > &zeroPixel)
	Utility function to initialize output images pixel to zero for vector images. More...
void	InitializeZeroPixel (itk::Image< PixelScalarType, 3 > *, PixelType &zeroPixel)
	Utility function to initialize output images pixel to zero for all images except vector images. More...
	NumberedThreadImageToImageFilter ()
void	SafeReleaseThreadId (unsigned int threadId)
virtual void	ThreadProcessSlices ()
virtual	~NumberedThreadImageToImageFilter ()

Additional Inherited Members
Static Public Attributes inherited from anima::NumberedThreadImageToImageFilter< itk::VectorImage< PixelScalarType, 3 >, itk::Image< PixelScalarType, 3 > >
static constexpr unsigned int	OutputImageDimension
Static Protected Member Functions inherited from anima::NumberedThreadImageToImageFilter< itk::VectorImage< PixelScalarType, 3 >, itk::Image< PixelScalarType, 3 > >
static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION	ThreaderMultiSplitCallback (void *arg)

Detailed Description

template<class PixelScalarType>
class anima::PatientToGroupComparisonImageFilter< PixelScalarType >

Implements patient to group comparison as in http://dx.doi.org/10.1007/978-3-540-85988-8_116.

Provides an ITK implementation of z-score and p-value computation telling how much different a single vector image is from a database of controls. It can virtually process any type of input, however for tensor images, be warned that they should be expressed as log-vectors.

Definition at line 22 of file animaPatientToGroupComparisonImageFilter.h.

Member Typedef Documentation

ConstPointer

template<class PixelScalarType>

typedef itk::SmartPointer<const Self> anima::PatientToGroupComparisonImageFilter< PixelScalarType >::ConstPointer

Definition at line 29 of file animaPatientToGroupComparisonImageFilter.h.

CovMatrixType

template<class PixelScalarType>

typedef vnl_matrix<double> anima::PatientToGroupComparisonImageFilter< PixelScalarType >::CovMatrixType

Definition at line 58 of file animaPatientToGroupComparisonImageFilter.h.

InputImageIndexType

template<class PixelScalarType>

typedef InputImageType::IndexType anima::PatientToGroupComparisonImageFilter< PixelScalarType >::InputImageIndexType

Definition at line 51 of file animaPatientToGroupComparisonImageFilter.h.

InputImagePointer

template<class PixelScalarType>

typedef InputImageType::Pointer anima::PatientToGroupComparisonImageFilter< PixelScalarType >::InputImagePointer

Definition at line 50 of file animaPatientToGroupComparisonImageFilter.h.

InputImageType

template<class PixelScalarType>

typedef itk::VectorImage<PixelScalarType, 3> anima::PatientToGroupComparisonImageFilter< PixelScalarType >::InputImageType

Image typedef support

Definition at line 35 of file animaPatientToGroupComparisonImageFilter.h.

MaskImageType

template<class PixelScalarType>

typedef Superclass::MaskImageType anima::PatientToGroupComparisonImageFilter< PixelScalarType >::MaskImageType

Superclass typedefs.

Definition at line 55 of file animaPatientToGroupComparisonImageFilter.h.

OutputImagePointer

template<class PixelScalarType>

typedef OutputImageType::Pointer anima::PatientToGroupComparisonImageFilter< PixelScalarType >::OutputImagePointer

Definition at line 52 of file animaPatientToGroupComparisonImageFilter.h.

OutputImageRegionType

template<class PixelScalarType>

typedef Superclass::OutputImageRegionType anima::PatientToGroupComparisonImageFilter< PixelScalarType >::OutputImageRegionType

Definition at line 56 of file animaPatientToGroupComparisonImageFilter.h.

OutputImageType

template<class PixelScalarType>

typedef itk::Image<PixelScalarType, 3> anima::PatientToGroupComparisonImageFilter< PixelScalarType >::OutputImageType

Definition at line 39 of file animaPatientToGroupComparisonImageFilter.h.

Pointer

template<class PixelScalarType>

typedef itk::SmartPointer<Self> anima::PatientToGroupComparisonImageFilter< PixelScalarType >::Pointer

Definition at line 28 of file animaPatientToGroupComparisonImageFilter.h.

Self

template<class PixelScalarType>

typedef PatientToGroupComparisonImageFilter<PixelScalarType> anima::PatientToGroupComparisonImageFilter< PixelScalarType >::Self

Standard class typedefs.

Definition at line 27 of file animaPatientToGroupComparisonImageFilter.h.

Superclass

template<class PixelScalarType>

typedef anima::MaskedImageToImageFilter< InputImageType, OutputImageType > anima::PatientToGroupComparisonImageFilter< PixelScalarType >::Superclass

Definition at line 49 of file animaPatientToGroupComparisonImageFilter.h.

VectorType

template<class PixelScalarType>

typedef InputImageType::PixelType anima::PatientToGroupComparisonImageFilter< PixelScalarType >::VectorType

Definition at line 41 of file animaPatientToGroupComparisonImageFilter.h.

Member Enumeration Documentation

TestType

template<class PixelScalarType>

enum anima::PatientToGroupComparisonImageFilter::TestType

Enumerator
CHI_SQUARE
FISHER

Definition at line 43 of file animaPatientToGroupComparisonImageFilter.h.

Constructor & Destructor Documentation

PatientToGroupComparisonImageFilter()

template<class PixelScalarType>

anima::PatientToGroupComparisonImageFilter< PixelScalarType >::PatientToGroupComparisonImageFilter ( )

inlineprotected

Definition at line 71 of file animaPatientToGroupComparisonImageFilter.h.

References anima::PatientToGroupComparisonImageFilter< PixelScalarType >::FISHER.

~PatientToGroupComparisonImageFilter()

template<class PixelScalarType>

virtual anima::PatientToGroupComparisonImageFilter< PixelScalarType >::~PatientToGroupComparisonImageFilter ( )

inlineprotectedvirtual

Definition at line 85 of file animaPatientToGroupComparisonImageFilter.h.

References anima::PatientToGroupComparisonImageFilter< PixelScalarType >::BeforeThreadedGenerateData(), and anima::PatientToGroupComparisonImageFilter< PixelScalarType >::DynamicThreadedGenerateData().

Member Function Documentation

AddDatabaseInput()

template<class PixelScalarType>

void anima::PatientToGroupComparisonImageFilter< PixelScalarType >::AddDatabaseInput ( InputImageType *  tmpIm )

inline

Definition at line 60 of file animaPatientToGroupComparisonImageFilter.h.

BeforeThreadedGenerateData()

template<class PixelScalarType >

void anima::PatientToGroupComparisonImageFilter< PixelScalarType >::BeforeThreadedGenerateData ( )

protectedvirtual

Reimplemented from anima::MaskedImageToImageFilter< itk::VectorImage< PixelScalarType, 3 >, itk::Image< PixelScalarType, 3 > >.

Reimplemented in anima::PatientToGroupODFComparisonImageFilter< PixelScalarType >.

Definition at line 21 of file animaPatientToGroupComparisonImageFilter.hxx.

References anima::PatientToGroupComparisonImageFilter< PixelScalarType >::DynamicThreadedGenerateData().

Referenced by anima::PatientToGroupComparisonImageFilter< PixelScalarType >::~PatientToGroupComparisonImageFilter().

CreateAnother()

template<class PixelScalarType>

virtual::itk::LightObject::Pointer anima::PatientToGroupComparisonImageFilter< PixelScalarType >::CreateAnother

(

void

)

const

DynamicThreadedGenerateData()

template<class PixelScalarType >

void anima::PatientToGroupComparisonImageFilter< PixelScalarType >::DynamicThreadedGenerateData ( const OutputImageRegionType &  outputRegionForThread )

protected

Definition at line 43 of file animaPatientToGroupComparisonImageFilter.hxx.

Referenced by anima::PatientToGroupComparisonImageFilter< PixelScalarType >::BeforeThreadedGenerateData(), and anima::PatientToGroupComparisonImageFilter< PixelScalarType >::~PatientToGroupComparisonImageFilter().

GetNameOfClass()

template<class PixelScalarType>

virtual const char* anima::PatientToGroupComparisonImageFilter< PixelScalarType >::GetNameOfClass ( ) const

virtual

Run-time type information (and related methods)

Reimplemented from anima::MaskedImageToImageFilter< itk::VectorImage< PixelScalarType, 3 >, itk::Image< PixelScalarType, 3 > >.

Reimplemented in anima::PatientToGroupODFComparisonImageFilter< PixelScalarType >.

New()

template<class PixelScalarType>

static Pointer anima::PatientToGroupComparisonImageFilter< PixelScalarType >::New ( )

static

Method for creation through the object factory.

Referenced by anima::LowMemoryPatientToGroupComparisonBridge::Update().

SampleFromDiffusionModels()

template<class PixelScalarType>

virtual unsigned int anima::PatientToGroupComparisonImageFilter< PixelScalarType >::SampleFromDiffusionModels ( std::vector< VectorType > &  databaseValues, VectorType &  patientVectorValue  )

inlineprotectedvirtual

Reimplemented in anima::PatientToGroupODFComparisonImageFilter< PixelScalarType >.

Definition at line 90 of file animaPatientToGroupComparisonImageFilter.h.

SetExplainedRatio()

template<class PixelScalarType>

virtual void anima::PatientToGroupComparisonImageFilter< PixelScalarType >::SetExplainedRatio ( double  _arg )

virtual

SetNumEigenValuesPCA()

template<class PixelScalarType>

virtual void anima::PatientToGroupComparisonImageFilter< PixelScalarType >::SetNumEigenValuesPCA ( unsigned int  _arg )

virtual

SetStatisticalTestType()

template<class PixelScalarType>

virtual void anima::PatientToGroupComparisonImageFilter< PixelScalarType >::SetStatisticalTestType ( TestType  _arg )

virtual

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

• animaPatientToGroupComparisonImageFilter.h
• animaPatientToGroupComparisonImageFilter.hxx