mitk::GIFGreyLevelRunLength Class Reference

Calculates the Run Length based features. More...

#include <mitkGIFGreyLevelRunLength.h>

Inheritance diagram for mitk::GIFGreyLevelRunLength:

Collaboration diagram for mitk::GIFGreyLevelRunLength:

Public Member Functions
	mitkClassMacro (GIFGreyLevelRunLength, AbstractGlobalImageFeature)
Pointer	Clone () const
	GIFGreyLevelRunLength ()
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 abstact 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 availble 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 abstact 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 abstact 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
FeatureListType	DoCalculateFeatures (const Image *image, const Image *mask) override
Protected Member Functions inherited from mitk::AbstractGlobalImageFeature
std::vector< double >	SplitDouble (std::string str, char delimiter)
void	AddQuantifierArguments (mitkCommandLineParser &parser) const
void	ConfigureQuantifierSettingsByParameters ()
virtual void	ConfigureSettingsByParameters (const ParametersType &parameters)
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
virtual std::string	GenerateLegacyFeatureEncoding (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 Run Length based features.

Grey Level Run Length based features are calcualted using the Run-Length-Matrix and were originally defined by Galloway (1975). The basic idea behind this feature is to measure the length of lines with similar intensity in an image. This allows to asses line-based structures in an image. For this, the Run-Length-Matrix created that gives the number of lines \( m_{x,l} \) with the intensity \( x \) and the length of \( l \) with the given intensity.

The image is quantified prior to the calculation of the features. This reduces the number of available intensity values. Instead of using the pure intensity value, the features are calculated using the number of the bins as intensity value \( x_i \). The parameter of the quantification of the image can be controlled using the general binning parameters as defined in AbstractGlobalImageFeature.

By default, the calculation is based on a 26 neighourhood for 3D and a 8 neighbourhood in 2D. It is further possible to exclude directions from the calculation, e.g. calculating the feature in 2D, even if a 3D image is passed. This is controlled by determine the dimensionality of the neighbourhood using direction-related commands as described in AbstractGlobalImageFeature. No other options are possible beside these two options.

This feature calculator is activated by the option -run-length or -rl.

The features are calculated based on a mask. It is assumed that the mask is of the same type as the input image. All voxels with a value greater 0.5 are treated as masked.

Several values are definied for the definition of the features. \( N_v \) is the number of masked voxels, \(N_s \) is the number of different lines, \( m_{x,\cdot} = \sum_l m{x,l} \) is the number of all lines with a given intensity value, and likewise \( m_{\cdot, l} = \sum_x m{x,l} \) is the number of all lines with a given length. There are two options how to make this feature orientation-invariant. Either calculating a single matrix for all directions and then extracting the features or by calculating a matrix per direction, calculating all features and then reporting the mean and standard deviation for each feature. The result of the first option is given with the extension "Comb.", the results for the second with "Std." and "Means". All three options are always calculated, although we state only one in the following list:

• Run Length::Short run emphasis Comb.:

  \[ \textup{Short run emphasis}= \frac{1}{N_s} \sum_l { \frac{m_{\cdot, l}}{l^2} } \]

• Run Length::Long run emphasis Comb.:

  \[ \textup{Long run emphasis}= \frac{1}{N_s} \sum_l { m_{\cdot, l} l^2} \]

• Run Length::Low grey level run emphasis Comb.:

  \[ \textup{Low grey level run emphasis}= \frac{1}{N_s} \sum_x { \frac{m_{x,\cdot}}{x^2} } \]

• Run Length::High grey level run emphasis Comb.:

  \[ \textup{High grey level run emphasis}= \frac{1}{N_s} \sum_x { m_{x,\cdot} x^2} \]

• Run Length::Short run low grey level emphasis Comb.:

  \[ \textup{Short run low grey level emphasis}= \frac{1}{N_s} \sum_x \sum_l { \frac{m_{x,l}}{x^2 l^2} } \]

• Run Length::Short run high grey level emphasis Comb.:

  \[ \textup{Short run high grey level emphasis}= \frac{1}{N_s} \sum_x \sum_l { \frac{x^2 m_{x,s}}{l^2} } \]

• Run Length::Long run low grey level emphasis Comb.:

  \[ \textup{Long run low grey level emphasis}= \frac{1}{N_s} \sum_x \sum_l { \frac{l^2 m_{x,l}}{x^2} } \]

• Run Length::Long run high grey level emphasis Comb.:

  \[ \textup{Long run high grey level emphasis}= \frac{1}{N_s} \sum_x \sum_l { x^2 l^2 m_{x,l} } \]

• Run Length::Grey level nonuniformity Comb.:

  \[ \textup{Grey level nonuniformity}= \frac{1}{N_s} \sum_x m_{x,\cdot}^2 \]

• Run Length::Grey level nonuniformity normalized Comb.:

  \[ \textup{Grey level nonuniformity normalized}= \frac{1}{N_s^2} \sum_x m_{x,\cdot}^2 \]

• Run Length::Run length nonuniformity:

  \[ \textup{Run length nonuniformity}= \frac{1}{N_s} \sum_l m_{\cdot, l}^2 \]

• Run Length::Run length nonuniformity normalized:

  \[ \textup{Run length nonuniformity normalized}= \frac{1}{N_s^2} \sum_l m_{\cdot, l}^2 \]

• Run Length::Run percentage: The ratio of realized runs to the theoretical limit of zones:

  \[ \textup{Run percentage}= \frac{N_s}{N_v} \]

• Run Length::Grey level variance:

  \[ \textup{Grey level variance} = \frac{1}{N_s} \sum_x (x -mu_x)^2 m_{x, \cdot} \]

• Run Length::Run length variance:

  \[ \textup{Run length variance} = \frac{1}{N_s} \sum_l (l -mu_l)^2 m_{\cdot, l} \]

• Run Length::Run length entropy: This feature would be equivalent with the Grey Level Entropy, which is therefore not included. It is based on the likelihood for a given intensity- size combination \( p_{x,s} = \frac{m_{x,s}}{N_s} \). :

  \[ \textup{Run length entropy} = \sum_x \sum_s p_{x,s} \textup{log}_2 \left( p{_x,s} \right) \]

• Run Length::Number of runs: The overall number of realized runs:

  \[ \textup{Number of runs} = \sum m_{x, l} \]

Definition at line 93 of file mitkGIFGreyLevelRunLength.h.

Constructor & Destructor Documentation

GIFGreyLevelRunLength()

mitk::GIFGreyLevelRunLength::GIFGreyLevelRunLength

(

)

Member Function Documentation

AddArguments()

void mitk::GIFGreyLevelRunLength::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::GIFGreyLevelRunLength::CalculateFeatures ( const Image *  image, const Image *  mask, const Image *  maskNoNAN  )

overridevirtual

Implements mitk::AbstractGlobalImageFeature.

Clone()

Pointer mitk::GIFGreyLevelRunLength::Clone

(

)

const

DoCalculateFeatures()

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

overrideprotectedvirtual

Implements mitk::AbstractGlobalImageFeature.

mitkClassMacro()

mitk::GIFGreyLevelRunLength::mitkClassMacro	(	GIFGreyLevelRunLength	,
		AbstractGlobalImageFeature
	)

New()

static Pointer mitk::GIFGreyLevelRunLength::New ( )

static

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

• mitkGIFGreyLevelRunLength.h