mitk::GIFNeighbourhoodGreyToneDifferenceFeatures Class Reference

Calculates the Neighbourhood Grey Tone Difference Features. More...

#include <mitkGIFNeighbourhoodGreyToneDifferenceFeatures.h>

Inheritance diagram for mitk::GIFNeighbourhoodGreyToneDifferenceFeatures:

Collaboration diagram for mitk::GIFNeighbourhoodGreyToneDifferenceFeatures:

Public Member Functions
	mitkClassMacro (GIFNeighbourhoodGreyToneDifferenceFeatures, AbstractGlobalImageFeature)
Pointer	Clone () const
	GIFNeighbourhoodGreyToneDifferenceFeatures ()
virtual void	SetRange (int _arg)
virtual int	GetRange () const
FeatureListType	CalculateFeatures (const Image *image, const Image *mask, const Image *maskNoNAN) override
void	AddArguments (mitkCommandLineParser &parser) const override
Public Member Functions inherited from mitk::AbstractGlobalImageFeature
	mitkClassMacro (AbstractGlobalImageFeature, BaseData)
FeatureListType	CalculateFeatures (const Image *image, const Image *mask)
	Calculates the feature of this abstract interface. Does not necessarily considers the parameter settings. More...
FeatureListType	CalculateFeaturesSlicewise (const Image::Pointer &image, const Image::Pointer &mask, int sliceID)
	Calculates the given feature Slice-wise. Might not be available for an individual filter! More...
virtual void	CalculateAndAppendFeaturesSliceWise (const Image::Pointer &image, const Image::Pointer &mask, int sliceID, FeatureListType &featureList, bool checkParameterActivation=true)
	Calculates the feature of this abstract interface. Does not necessarily considers the parameter settings. More...
void	CalculateAndAppendFeatures (const Image *image, const Image *mask, const Image *maskNoNaN, FeatureListType &featureList, bool checkParameterActivation=true)
	Calculates the feature of this abstract interface. Does not necessarily considers the parameter settings. More...
virtual void	SetPrefix (std::string _arg)
virtual void	SetShortName (std::string _arg)
virtual void	SetLongName (std::string _arg)
virtual void	SetFeatureClassName (std::string _arg)
virtual void	SetDirection (int _arg)
void	SetParameters (ParametersType param)
virtual std::string	GetPrefix () const
virtual std::string	GetShortName () const
virtual std::string	GetLongName () const
virtual std::string	GetFeatureClassName () const
virtual ParametersType	GetParameters () const
virtual IntensityQuantifier::Pointer	GetQuantifier ()
virtual int	GetDirection () const
virtual void	SetMinimumIntensity (double _arg)
virtual void	SetUseMinimumIntensity (bool _arg)
virtual void	SetMaximumIntensity (double _arg)
virtual void	SetUseMaximumIntensity (bool _arg)
virtual double	GetMinimumIntensity () const
virtual bool	GetUseMinimumIntensity () const
virtual double	GetMaximumIntensity () const
virtual bool	GetUseMaximumIntensity () const
virtual void	SetBinsize (double _arg)
virtual void	SetUseBinsize (bool _arg)
virtual double	GetBinsize () const
virtual bool	GetUseBinsize () const
virtual void	SetMorphMask (mitk::Image::Pointer _arg)
virtual mitk::Image::Pointer	GetMorphMask () const
virtual void	SetBins (int _arg)
virtual void	SetUseBins (bool _arg)
virtual bool	GetUseBins () const
virtual int	GetBins () const
virtual void	SetIgnoreMask (bool _arg)
virtual bool	GetIgnoreMask () const
virtual void	SetEncodeParametersInFeaturePrefix (bool _arg)
virtual bool	GetEncodeParametersInFeaturePrefix () const
virtual void	EncodeParametersInFeaturePrefixOn ()
virtual void	EncodeParametersInFeaturePrefixOff ()
std::string	GetOptionPrefix () const
void	SetRequestedRegionToLargestPossibleRegion () override
	Set the RequestedRegion to the LargestPossibleRegion. More...
bool	RequestedRegionIsOutsideOfTheBufferedRegion () override
	Determine whether the RequestedRegion is outside of the BufferedRegion. More...
bool	VerifyRequestedRegion () override
	Verify that the RequestedRegion is within the LargestPossibleRegion. More...
void	SetRequestedRegion (const itk::DataObject *) override
	Set the requested region from this data object to match the requested region of the data object passed in as a parameter. More...
bool	IsEmpty () const override
	Check whether object contains data (at least at one point in time), e.g., a set of points may be empty. More...
Public Member Functions inherited from mitk::BaseData
virtual std::vector< std::string >	GetClassHierarchy () const
virtual const char *	GetClassName () const
BaseProperty::ConstPointer	GetConstProperty (const std::string &propertyKey, const std::string &contextName="", bool fallBackOnDefaultContext=true) const override
	Get property by its key. More...
std::vector< std::string >	GetPropertyKeys (const std::string &contextName="", bool includeDefaultContext=false) const override
	Query keys of existing properties. More...
std::vector< std::string >	GetPropertyContextNames () const override
	Query names of existing contexts. More...
BaseProperty *	GetNonConstProperty (const std::string &propertyKey, const std::string &contextName="", bool fallBackOnDefaultContext=true) override
	Get property by its key. More...
void	SetProperty (const std::string &propertyKey, BaseProperty *property, const std::string &contextName="", bool fallBackOnDefaultContext=false) override
	Add new or change existent property. More...
void	RemoveProperty (const std::string &propertyKey, const std::string &contextName="", bool fallBackOnDefaultContext=false) override
	Removes a property. If the property does not exist, nothing will be done. More...
const mitk::TimeGeometry *	GetTimeGeometry () const
	Return the TimeGeometry of the data as const pointer. More...
mitk::TimeGeometry *	GetTimeGeometry ()
	Return the TimeGeometry of the data as pointer. More...
const mitk::TimeGeometry *	GetUpdatedTimeGeometry ()
	Return the TimeGeometry of the data. More...
virtual void	Expand (unsigned int timeSteps)
	Expands the TimeGeometry to a number of TimeSteps. More...
const mitk::BaseGeometry *	GetUpdatedGeometry (int t=0)
	Return the BaseGeometry of the data at time t. More...
mitk::BaseGeometry *	GetGeometry (int t=0) const
	Return the geometry, which is a TimeGeometry, of the data as non-const pointer. More...
void	UpdateOutputInformation () override
	Update the information for this BaseData (the geometry in particular) so that it can be used as an output of a BaseProcess. More...
void	CopyInformation (const itk::DataObject *data) override
	Copy information from the specified data set. More...
virtual bool	IsInitialized () const
	Check whether the data has been initialized, i.e., at least the Geometry and other header data has been set. More...
virtual void	Clear ()
	Calls ClearData() and InitializeEmpty();. More...
virtual bool	IsEmptyTimeStep (unsigned int t) const
	Check whether object contains data (at a specified time), e.g., a set of points may be empty. More...
void	ExecuteOperation (Operation *operation) override
	overwrite if the Data can be called by an Interactor (StateMachine). More...
virtual void	SetGeometry (BaseGeometry *aGeometry3D)
	Set the BaseGeometry of the data, which will be referenced (not copied!). Assumes the data object has only 1 time step ( is a 3D object ) and creates a new TimeGeometry which saves the given BaseGeometry. If an TimeGeometry has already been set for the object, it will be replaced after calling this function. More...
virtual void	SetTimeGeometry (TimeGeometry *geometry)
	Set the TimeGeometry of the data, which will be referenced (not copied!). More...
virtual void	SetClonedGeometry (const BaseGeometry *aGeometry3D)
	Set a clone of the provided Geometry as Geometry of the data. Assumes the data object has only 1 time step ( is a 3D object ) and creates a new TimeGeometry. If an TimeGeometry has already been set for the object, it will be replaced after calling this function. More...
virtual void	SetClonedTimeGeometry (const TimeGeometry *geometry)
	Set a clone of the provided TimeGeometry as TimeGeometry of the data. More...
virtual void	SetClonedGeometry (const BaseGeometry *aGeometry3D, unsigned int time)
	Set a clone of the provided geometry as BaseGeometry of a given time step. More...
mitk::PropertyList::Pointer	GetPropertyList () const
	Get the data's property list. More...
void	SetPropertyList (PropertyList *propertyList)
	Set the data's property list. More...
mitk::BaseProperty::Pointer	GetProperty (const char *propertyKey) const
	Get the property (instance of BaseProperty) with key propertyKey from the PropertyList, and set it to this, respectively;. More...
void	SetProperty (const char *propertyKey, BaseProperty *property)
virtual void	SetOrigin (const Point3D &origin)
	Convenience method for setting the origin of the BaseGeometry instances of all time steps. More...
itk::SmartPointer< mitk::BaseDataSource >	GetSource () const
	Get the process object that generated this data object. More...
unsigned int	GetTimeSteps () const
	Get the number of time steps from the TimeGeometry As the base data has not a data vector given by itself, the number of time steps is defined over the time sliced geometry. In sub classes, a better implementation could be over the length of the data vector. More...
itk::ModifiedTimeType	GetMTime () const override
	Get the modified time of the last change of the contents this data object or its geometry. More...
void	Graft (const DataObject *) override
Public Member Functions inherited from mitk::OperationActor
	itkTypeMacroNoParent (OperationActor) virtual ~OperationActor()
Public Member Functions inherited from mitk::Identifiable
	Identifiable ()
	Identifiable (const UIDType &uid)
	Identifiable (const Identifiable &)=delete
	Identifiable (Identifiable &&) noexcept
virtual	~Identifiable ()
Identifiable &	operator= (const Identifiable &)=delete
Identifiable &	operator= (Identifiable &&other) noexcept
virtual UIDType	GetUID () const
	Get unique ID of an object. More...
Public Member Functions inherited from mitk::IPropertyOwner
	~IPropertyOwner () override
Public Member Functions inherited from mitk::IPropertyProvider
virtual	~IPropertyProvider ()

Static Public Member Functions
static Pointer	New ()
Static Public Member Functions inherited from mitk::AbstractGlobalImageFeature
static std::string	GenerateLegacyFeatureNameWOEncoding (const FeatureID &id)
Static Public Member Functions inherited from mitk::BaseData
static const char *	GetStaticNameOfClass ()

Protected Member Functions
std::string	GenerateLegacyFeatureEncoding (const FeatureID &id) const override
FeatureListType	DoCalculateFeatures (const Image *image, const Image *mask) override
void	ConfigureSettingsByParameters (const ParametersType &parameters) override
Protected Member Functions inherited from mitk::AbstractGlobalImageFeature
std::vector< double >	SplitDouble (std::string str, char delimiter)
void	AddQuantifierArguments (mitkCommandLineParser &parser) const
void	ConfigureQuantifierSettingsByParameters ()
void	InitializeQuantifier (const Image *image, const Image *mask, unsigned int defaultBins=256)
std::string	QuantifierParameterString () const
FeatureID	CreateTemplateFeatureID (std::string settingsSuffix="", FeatureID::ParametersType additionalParams={})
virtual std::string	GenerateLegacyFeatureName (const FeatureID &id) const
virtual std::string	GenerateLegacyFeatureNamePart (const FeatureID &id) const
Protected Member Functions inherited from mitk::BaseData
	BaseData ()
	BaseData (const BaseData &other)
	~BaseData () override
virtual void	InitializeTimeGeometry (unsigned int timeSteps=1)
	Initialize the TimeGeometry for a number of time steps. The TimeGeometry is initialized empty and evenly timed. In many cases it will be necessary to overwrite this in sub-classes. More...
virtual void	ClearData ()
	reset to non-initialized state, release memory More...
virtual void	InitializeEmpty ()
	Pure virtual; Must be used in subclasses to get a data object to a valid state. Should at least create one empty object and call Superclass::InitializeTimeGeometry() to ensure an existing valid geometry. More...
void	PrintSelf (std::ostream &os, itk::Indent indent) const override
Protected Member Functions inherited from mitk::Identifiable
virtual void	SetUID (const UIDType &uid)

Additional Inherited Members
Public Types inherited from mitk::AbstractGlobalImageFeature
typedef std::vector< std::pair< FeatureID, double > >	FeatureListType
using	ParametersType = FeatureID::ParametersType
Public Types inherited from mitk::BaseData
typedef BaseData	Self
typedef itk::DataObject	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer< const Self >	ConstPointer
Public Types inherited from mitk::Identifiable
using	UIDType = std::string
Protected Attributes inherited from mitk::BaseData
bool	m_LastRequestedRegionWasOutsideOfTheBufferedRegion
unsigned int	m_SourceOutputIndexDuplicate
bool	m_Initialized

Detailed Description

Calculates the Neighbourhood Grey Tone Difference Features.

This class can be used to calculate Neighbourhood Grey Tone Difference Features which have been introduced in Amadasun and King: Textural features corresponding to textural properties. IEEE Transactions on Systems, Man and Cybernetricy, 1989.

The Neighbourhood Grey Tone Difference (NGTD) is based on a table and is calculated using a defined neighbourhood for each voxel. Within this neighbourhood, the mean intensity of the neighbouring voxel is calculated \(A_i\), i.e. the mean intensity of the neighbourhood excluding the center voxel. Based on this a table with four columns is calculated. The first column represents the voxel value, or in our implementation, the histogram bin index \(i\). The second column represents the number of voxel with this intensity value \(n_i\). The proability for each intensity value \(p_i\), which is equal to the bin probability. And the sum of the absolute differences of the intensity of all voxels with this intensity and the mean intensity of their neighbourhood:

\[s_i = \sum \left \| i- A_i \right \| \]

. Additional \( N_v\) is the number of voxels, \( N_g \) the number of bins, and \(N_{g,p}\) the number of bins with a non-zero probability.

This feature calculator is activated by the option -neighbourhood-grey-tone-difference or -ngtd.

The range that is used to calculate the local intensity can be set using the function SetRange. To set it with parameters set the option ngtd::range which expects an int value n that is interpreted as voxel count. The neighbourhood includes symmetrical n voxels additional to the center voxel in each directions. The default value for this parameter is 1.

The features are calculated based on a mask. It is assumed that the mask is of the type of an unsigned short image and all voxels with an value of greater than zero are treated as masked.

For the definition of the features we use the sum, this is always the sum over the bins of the histogram. If the denominator of a feature evaluates to zero, the feature is defined as zero. The resulting features are:

• Neighbourhood Grey Tone Difference::Coarsness: The coarsness is defined as :

  \[ \textup{Coarsness}= \frac{1}{\sum p_i s_i} \]

• Neighbourhood Grey Tone Difference::Contrast: The contrast is defined as :

  \[ \textup{contrast}= \left( \frac{1}{N_{g,p} ( N_{g,p} - 1) } \sum_i \sum_j p_i p_j (i-j)^2 \right) \left( \frac{1}{N_v} \sum s_i \right) \]

• Neighbourhood Grey Tone Difference::Busyness: for all bins with a non-zero probability

  \[ \textup{busyness} = \frac{\sum p_i s_i}{\sum_i \sum_j \left \| i p_i - j p_j \right \| } \]

• Neighbourhood Grey Tone Difference::Complexity: for all bins with a non-zero probability

  \[ \textup{complexity} = \frac{1}{N_v} \sum_i \sum_j \left \| i - j \right \| \frac{p_i s_i + p_j s_j}{p_i + p_j} \]

• Neighbourhood Grey Tone Difference::Strength: for all bins with a non-zero probability

  \[ \textup{strength} = \frac{\sum_i \sum_j (p_i + p_j) (i + j)^2}{\sum_i s_i } \]

Definition at line 64 of file mitkGIFNeighbourhoodGreyToneDifferenceFeatures.h.

Constructor & Destructor Documentation

GIFNeighbourhoodGreyToneDifferenceFeatures()

mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::GIFNeighbourhoodGreyToneDifferenceFeatures

(

)

Member Function Documentation

AddArguments()

void mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::AddArguments ( mitkCommandLineParser &  parser ) const

overridevirtual

Can be called to add all relevant argument for configuring the feature instance to the passed parser instance. Must be implemented be derived classes. For adding the quantifier arguments use AddQuantifierArguments(...) as helper function.

Implements mitk::AbstractGlobalImageFeature.

CalculateFeatures()

FeatureListType mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::CalculateFeatures ( const Image *  image, const Image *  mask, const Image *  maskNoNAN  )

overridevirtual

Implements mitk::AbstractGlobalImageFeature.

Clone()

Pointer mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::Clone

(

)

const

ConfigureSettingsByParameters()

void mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::ConfigureSettingsByParameters ( const ParametersType &  parameters )

overrideprotectedvirtual

Ensures that the instance is configured according to the information given in the passed parameters. This method will be called by SetParameters(...) after ConfigureQuantifierSettingsByParameters() was called.

Reimplemented from mitk::AbstractGlobalImageFeature.

DoCalculateFeatures()

FeatureListType mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::DoCalculateFeatures ( const Image *  image, const Image *  mask  )

overrideprotectedvirtual

Implements mitk::AbstractGlobalImageFeature.

GenerateLegacyFeatureEncoding()

std::string mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::GenerateLegacyFeatureEncoding ( const FeatureID &  id ) const

overrideprotectedvirtual

Reimplemented from mitk::AbstractGlobalImageFeature.

GetRange()

virtual int mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::GetRange ( ) const

virtual

mitkClassMacro()

mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::mitkClassMacro	(	GIFNeighbourhoodGreyToneDifferenceFeatures	,
		AbstractGlobalImageFeature
	)

New()

static Pointer mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::New ( )

static

SetRange()

virtual void mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::SetRange ( int  _arg )

virtual

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

• mitkGIFNeighbourhoodGreyToneDifferenceFeatures.h