Normalizes MR images using linear scaling based on statistical measures within a mask region. More...

#include <mitkMRNormLinearStatisticBasedFilter.h>

Inheritance diagram for mitk::MRNormLinearStatisticBasedFilter:

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Collaboration diagram for mitk::MRNormLinearStatisticBasedFilter:

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Public Types
enum	NormalizationBase { MEAN , MODE , MEDIAN }
	Enumeration for the statistical measure used as normalization center. More...

Public Types inherited from mitk::ImageToImageFilter
typedef Superclass::OutputImageRegionType	OutputImageRegionType
	Superclass typedefs. More...

typedef mitk::Image	InputImageType
	Some convenient typedefs. More...

typedef InputImageType::Pointer	InputImagePointer

typedef InputImageType::ConstPointer	InputImageConstPointer

typedef SlicedData::RegionType	InputImageRegionType

Public Types inherited from mitk::ImageSource
typedef mitk::Image	OutputImageType
	Some convenient typedefs. More...

typedef OutputImageType	OutputType

typedef OutputImageType::Pointer	OutputImagePointer

typedef SlicedData::RegionType	OutputImageRegionType

Public Types inherited from mitk::BaseDataSource
typedef BaseData	OutputType
	Output data type. More...

typedef itk::DataObject::DataObjectIdentifierType	DataObjectIdentifierType
	Identifier type for named data objects. More...

Public Member Functions
	mitkClassMacro (MRNormLinearStatisticBasedFilter, ImageToImageFilter)

Pointer	Clone () const

void	SetMask (const mitk::Image *mask)
	Set the mask image defining the region used for computing statistics. More...

const mitk::Image *	GetMask () const
	Get the mask image used for computing statistics. More...

virtual NormalizationBase	GetCenterMode () const

virtual void	SetCenterMode (NormalizationBase _arg)

virtual bool	GetIgnoreOutlier () const

virtual void	SetIgnoreOutlier (bool _arg)

virtual double	GetTargetValue () const

virtual void	SetTargetValue (double _arg)

virtual double	GetTargetWidth () const

virtual void	SetTargetWidth (double _arg)

Public Member Functions inherited from mitk::ImageToImageFilter
	mitkClassMacro (ImageToImageFilter, ImageSource)

Pointer	Clone () const

virtual void	SetInput (const InputImageType *image)
	Set the image input of this process object. More...

virtual void	SetInput (unsigned int idx, const InputImageType *image)
	Set the image input at the specified index. More...

InputImageType *	GetInput (void)
	Get the input image (non-const). More...

InputImageType *	GetInput (unsigned int idx)
	Get the input image at the specified index (non-const). More...

const InputImageType *	GetInput (void) const
	Get the input image (const). More...

const InputImageType *	GetInput (unsigned int idx) const
	Get the input image at the specified index (const). More...

Public Member Functions inherited from mitk::ImageSource
	mitkClassMacro (ImageSource, BaseDataSource)

Pointer	Clone () const

mitkBaseDataSourceGetOutputDeclarations itk::DataObject::Pointer	MakeOutput (DataObjectPointerArraySizeType idx) override
	Get the output data of this image source object. More...

itk::DataObject::Pointer	MakeOutput (const DataObjectIdentifierType &name) override

virtual vtkImageData *	GetVtkImageData ()
	Get the output as VTK image data (non-const version). More...

virtual const vtkImageData *	GetVtkImageData () const
	Get the output as VTK image data (const version). More...

Public Member Functions inherited from mitk::BaseDataSource
	mitkClassMacroItkParent (BaseDataSource, itk::ProcessObject)

OutputType *	GetOutput ()

const OutputType *	GetOutput () const

OutputType *	GetOutput (DataObjectPointerArraySizeType idx)

const OutputType *	GetOutput (DataObjectPointerArraySizeType idx) const

virtual void	GraftOutput (OutputType *output)
	Graft the specified BaseData onto this BaseDataSource's output. More...

virtual void	GraftOutput (const DataObjectIdentifierType &key, OutputType *output)
	Graft the specified base data object onto a named output. More...

virtual void	GraftNthOutput (unsigned int idx, OutputType *output)
	Graft the specified base data object onto this BaseDataSource's idx'th output. More...

bool	Updating () const
	Check whether the pipeline is currently executing. More...

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from mitk::ImageToImageFilter
static Pointer	New ()
	Method for creation through the object factory. More...

Static Public Member Functions inherited from mitk::ImageSource
static Pointer	New ()
	Method for creation through the object factory. More...

Protected Member Functions
	MRNormLinearStatisticBasedFilter ()

	~MRNormLinearStatisticBasedFilter () override

void	GenerateInputRequestedRegion () override

void	GenerateOutputInformation () override

void	GenerateData () override

template<typename TPixel , unsigned int VImageDimension>
void	InternalComputeMask (itk::Image< TPixel, VImageDimension > *itkImage)
	Internal templated implementation that computes statistics and normalizes the image. More...

Protected Member Functions inherited from mitk::ImageToImageFilter
	ImageToImageFilter ()

	~ImageToImageFilter () override

void	PrintSelf (std::ostream &os, itk::Indent indent) const override
	Print self information to the given stream. More...

void	GenerateInputRequestedRegion () override
	Determine the input requested region to produce the output requested region. More...

Protected Member Functions inherited from mitk::ImageSource
	ImageSource ()

	~ImageSource () override

void	GenerateData () override
	A version of GenerateData() specific for image processing filters. More...

virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, itk::ThreadIdType threadId)
	If an imaging filter can be implemented as a multithreaded algorithm, the filter will provide an implementation of ThreadedGenerateData(). More...

void	PrepareOutputs () override
	This method is intentionally left blank. More...

virtual void	AllocateOutputs ()
	The GenerateData method normally allocates the buffers for all of the outputs of a filter. More...

virtual void	BeforeThreadedGenerateData ()
	If an imaging filter needs to perform processing after the buffer has been allocated but before threads are spawned, the filter can provide an implementation for BeforeThreadedGenerateData(). More...

virtual void	AfterThreadedGenerateData ()
	If an imaging filter needs to perform processing after all processing threads have completed, the filter can provide an implementation for AfterThreadedGenerateData(). More...

virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int num, OutputImageRegionType &splitRegion)
	Split the output's RequestedRegion into "num" pieces, returning region "i" as "splitRegion". More...

Protected Member Functions inherited from mitk::BaseDataSource
	BaseDataSource ()
	Constructor. More...

	~BaseDataSource () override
	Destructor. More...

Protected Attributes
NormalizationBase	m_CenterMode

bool	m_IgnoreOutlier

Additional Inherited Members
Static Protected Member Functions inherited from mitk::ImageSource
static itk::ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)
	Static function used as a "callback" by the MultiThreader. More...

Static Protected Member Functions inherited from mitk::BaseDataSource
static Pointer	New ()

Detailed Description

Normalizes MR images using linear scaling based on statistical measures within a mask region.

This filter computes a statistical center (mean, median, or mode) and the standard deviation within a masked region of the input image, then applies a linear transformation to normalize the image: output = (input - (center + TargetValue)) / (stddev * TargetWidth). Optionally, outlier voxels (below 2nd or above 98th percentile) can be clamped.

Definition at line 34 of file mitkMRNormLinearStatisticBasedFilter.h.

Member Enumeration Documentation

◆ NormalizationBase

enum mitk::MRNormLinearStatisticBasedFilter::NormalizationBase

Enumeration for the statistical measure used as normalization center.

Enumerator
MEAN	Use the arithmetic mean as center.
MODE	Use the histogram mode as center.
MEDIAN	Use the median as center.

Definition at line 55 of file mitkMRNormLinearStatisticBasedFilter.h.

Constructor & Destructor Documentation

◆ MRNormLinearStatisticBasedFilter()

mitk::MRNormLinearStatisticBasedFilter::MRNormLinearStatisticBasedFilter ( )

protected

◆ ~MRNormLinearStatisticBasedFilter()

mitk::MRNormLinearStatisticBasedFilter::~MRNormLinearStatisticBasedFilter ( )

overrideprotected

Member Function Documentation

◆ Clone()

Pointer mitk::MRNormLinearStatisticBasedFilter::Clone ( ) const

◆ GenerateData()

void mitk::MRNormLinearStatisticBasedFilter::GenerateData ( )

overrideprotected

◆ GenerateInputRequestedRegion()

void mitk::MRNormLinearStatisticBasedFilter::GenerateInputRequestedRegion ( )

overrideprotected

◆ GenerateOutputInformation()

void mitk::MRNormLinearStatisticBasedFilter::GenerateOutputInformation ( )

overrideprotected

◆ GetCenterMode()

virtual NormalizationBase mitk::MRNormLinearStatisticBasedFilter::GetCenterMode ( ) const

virtual

◆ GetIgnoreOutlier()

virtual bool mitk::MRNormLinearStatisticBasedFilter::GetIgnoreOutlier ( ) const

virtual

◆ GetMask()

const mitk::Image* mitk::MRNormLinearStatisticBasedFilter::GetMask ( ) const

Get the mask image used for computing statistics.

Returns: Pointer to the mask image, or nullptr if not set.

◆ GetTargetValue()

virtual double mitk::MRNormLinearStatisticBasedFilter::GetTargetValue ( ) const

virtual

◆ GetTargetWidth()

virtual double mitk::MRNormLinearStatisticBasedFilter::GetTargetWidth ( ) const

virtual

◆ InternalComputeMask()

template<typename TPixel , unsigned int VImageDimension>

void mitk::MRNormLinearStatisticBasedFilter::InternalComputeMask ( itk::Image< TPixel, VImageDimension > * itkImage )

protected

Internal templated implementation that computes statistics and normalizes the image.

◆ mitkClassMacro()

mitk::MRNormLinearStatisticBasedFilter::mitkClassMacro	(	MRNormLinearStatisticBasedFilter	,
		ImageToImageFilter
	)

◆ New()

static Pointer mitk::MRNormLinearStatisticBasedFilter::New ( )

static

◆ SetCenterMode()

virtual void mitk::MRNormLinearStatisticBasedFilter::SetCenterMode ( NormalizationBase _arg )

virtual

◆ SetIgnoreOutlier()

virtual void mitk::MRNormLinearStatisticBasedFilter::SetIgnoreOutlier ( bool _arg )

virtual

◆ SetMask()

void mitk::MRNormLinearStatisticBasedFilter::SetMask ( const mitk::Image * mask )

Set the mask image defining the region used for computing statistics.

Parameters

mask	The mask image. Voxels with label 1 are included.

◆ SetTargetValue()

virtual void mitk::MRNormLinearStatisticBasedFilter::SetTargetValue ( double _arg )

virtual

◆ SetTargetWidth()

virtual void mitk::MRNormLinearStatisticBasedFilter::SetTargetWidth ( double _arg )

virtual

Member Data Documentation

◆ m_CenterMode

NormalizationBase mitk::MRNormLinearStatisticBasedFilter::m_CenterMode

protected

Definition at line 89 of file mitkMRNormLinearStatisticBasedFilter.h.

◆ m_IgnoreOutlier

bool mitk::MRNormLinearStatisticBasedFilter::m_IgnoreOutlier

protected

Definition at line 90 of file mitkMRNormLinearStatisticBasedFilter.h.

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

mitkMRNormLinearStatisticBasedFilter.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ NormalizationBase

Constructor & Destructor Documentation

◆ MRNormLinearStatisticBasedFilter()

◆ ~MRNormLinearStatisticBasedFilter()

Member Function Documentation

◆ Clone()

◆ GenerateData()

◆ GenerateInputRequestedRegion()

◆ GenerateOutputInformation()

◆ GetCenterMode()

◆ GetIgnoreOutlier()

◆ GetMask()

◆ GetTargetValue()

◆ GetTargetWidth()

◆ InternalComputeMask()

◆ mitkClassMacro()

◆ New()

◆ SetCenterMode()

◆ SetIgnoreOutlier()

◆ SetMask()

◆ SetTargetValue()

◆ SetTargetWidth()

Member Data Documentation

◆ m_CenterMode

◆ m_IgnoreOutlier