mitk::GIFFirstOrderHistogramStatistics Class Reference

Calculates first order features based on a histogram. More...

#include <mitkGIFFirstOrderHistogramStatistics.h>

Inheritance diagram for mitk::GIFFirstOrderHistogramStatistics:

Collaboration diagram for mitk::GIFFirstOrderHistogramStatistics:

Public Member Functions
	mitkClassMacro (GIFFirstOrderHistogramStatistics, AbstractGlobalImageFeature)
Pointer	Clone () const
	GIFFirstOrderHistogramStatistics ()
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
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 first order features based on a histogram.

This class can be used to calculate first order features based on a histogram. For each feature, two variations are given, once the value of the feature that is obtained if the mean intensity of the histogram bins is used and the histogram bin that corresponds to the feature value. See AbstractGlobalImageFeature for more information on the histogram initialization. The histogram gives a probability \(p_i\) for the intensity \(x_i\) that is linked to the bin \(i\). The histogram bins start at index 1.

This feature calculator is activated by the option "<b>-first-order-histogram</b>" or "<b>-foh</b>". Beside the options for the histogram definitions, which are given in the description of AbstractGlobalImageFeature , no additional parameters are available.

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 1 are treated as masked.

The resulting features are:

• First Order Histogram::Mean Value: The mean intensity of all voxels, calculated by \( \mu_x = \sum p_i x_i\).
• First Order Histogram::Variance Value The variance intensity is calculated as : \( \sigma^2 = \sum p_i (x_i - \mu_x)^2\).
• First Order Histogram::Skewness Value:

  \[ skewness = \frac{\sum p_i (x_i - \mu_x)^3}{\sigma^3} \]

• First Order Histogram::Excess Kurtosis Value:

  \[ skewness = \frac{\sum p_i (x_i - \mu_x)^4}{\sigma^4} - 3 \]

• First Order Histogram::Median Value: The median intensity value based on the histogram values.
• First Order Histogram::Minimum Value: The minimum observed intensity value.
• First Order Histogram::Percentile 10 Value: The intensity that is equal or greater than 10% of all observed intensities.
• First Order Histogram::Percentile 90 Value: The intensity that is equal or greater than 90% of all observed intensities.
• First Order Histogram::Maximum Value: The maximum observerd intensity value.
• First Order Histogram::Mode Value: The most common intensity value, i.e. the value of the bin with the highest probability.
• First Order Histogram::Interquantile Range Value: The intensity difference between Percentile 75% ( \( P75\)) and Percentile 25% ( \( P25\)).
• First Order Histogram::Range Value: The difference between the observed maximum and minimum intensity.
• First Order Histogram::Mean Absolute Deviation Value:

  \[ \textup{mean absolute deviation} = \sum p_i \left \| (x_i - \mu_x) \right \| \]

• First Order Histogram::Robust Mean Value: The mean of all intensities between the 10% and 90% quantile.
• First Order Histogram::Robust Mean Absolute Deviation Value: The Mean absolute deviation for all values between the 10% and 90% quantile. It is based on the robust mean value.
• First Order Histogram::Median Absolute Deviation Value:

  \[ \textup{mean absolute deviation} = \sum p_i \left \| (x_i - \textup{median}) \right \| \]

• First Order Histogram::Coefficient of Variation Value:

  \[ \frac{\sigma_x}{\mu_x} \]

• First Order Histogram::Quantile coefficient of Dispersion Value:

  \[ \textup{Quantile coefficient of Dispersion} = \frac{P75 - P25}{P75 + P25} \]

• First Order Histogram::Entropy Value: The entropy is only based on histogram bins with a probability greater than 0.0000001:

  \[ \textup{entropy} = - \sum p_i \textup{log}_2 p_i \]

• First Order Histogram::Uniformity Value: \( \sum p_i^2 \)
• First Order Histogram::Mean Index: The mean index of all voxels, calculated by \( \mu_i = \sum p_i i\).
• First Order Histogram::Variance Index: The variance index is calculated as : \( \sigma_i^2 = \sum p_i (i - \mu_i)^2\).
• First Order Histogram::Skewness Index:

  \[ skewness = \frac{\sum p_i (i - \mu_i)^3}{\sigma_i^3} \]

• First Order Histogram::Excess Kurtosis Index:

  \[ skewness = \frac{\sum p_i (i - \mu_i)^4}{\sigma_i^4} - 3 \]

• First Order Histogram::Median Index: The median index value based on the histogram values.
• First Order Histogram::Minimum Index: The index of the minimum observed intensity value.
• First Order Histogram::Percentile 10 Index: The index oft the intensity that is equal or greater than 10% of all observed intensities.
• First Order Histogram::Percentile 90 Index: The index of the intensity that is equal or greater than 90% of all observed intensities.
• First Order Histogram::Maximum Index: The index of the maximum observerd intensity value.
• First Order Histogram::Mode Index: The index of the most common intensity value, i.e. the index of the bin with the highest probability.
• First Order Histogram::Interquantile Range Index: The index difference between Percentile 75% ( \( P75\)) and Percentile 25% ( \( P25\)).
• First Order Histogram::Range Index: The index difference between the index of the observed maximum and minimum intensity.
• First Order Histogram::Mean Absolute Deviation Index:

  \[ \textup{mean absolute deviation} = \sum p_i \left \| (i - \mu_i) \right \| \]

• First Order Histogram::Robust Mean Absolute Deviation Index: The Mean absolute deviation for all values between the 10% and 90% quantile. It is based on the robust mean value.
• First Order Histogram::Median Absolute Deviation Index:

  \[ \textup{mean absolute deviation} = \sum p_i \left \| (i - \textup{median}) \right \| \]

• First Order Histogram::Coefficient of Variation Index:

  \[ \frac{\sigma_i}{\mu_i} \]

• First Order Histogram::Quantile coefficient of Dispersion Index:

  \[ \textup{Quantile coefficient of Dispersion} = \frac{P75 - P25}{P75 + P25} \]

• First Order Histogram::Entropy Index: The entropy is only based on histogram bins with a probability greater than 0.0000001: \( \textup{entropy} = - \sum p_i \textup{log}_2 p_i \). Note that this is the same as the entropy value.
• First Order Histogram::Uniformity Index: \( \sum p_i^2 \). Note that this is the same as the uniformity value.
• First Order Histogram::Maximum Gradient: The maximum difference between the probability of three neighbouring bins. For bins at the edge of the histogram, only two bins are used for the calculation.
• First Order Histogram::Maximum Gradient Index: The index of the bin that belongs to the maximum gradient.
• First Order Histogram::Minimum Gradient: The minimum difference between the probability of three neighbouring bins. For bins at the edge of the histogram, only two bins are used for the calculation.
• First Order Histogram::Minimum Gradient Index:The index of the bin that belongs to the minimum gradient.
• First Order Histogram::Robust Mean Index: The mean index of all intensities between the 10% and 90% quantile.
• First Order Histogram::Number of Bins: The number of bins in the histogram. This is rather for control, as this parameter is likely to be determined by the configuration rather than the image.
• First Order Histogram::Bin Size: The binsize of the bins from the histogram. This is rather for control, as this parameter is likely to be determined by the configuration rather than the image.

Definition at line 88 of file mitkGIFFirstOrderHistogramStatistics.h.

Constructor & Destructor Documentation

GIFFirstOrderHistogramStatistics()

mitk::GIFFirstOrderHistogramStatistics::GIFFirstOrderHistogramStatistics

(

)

Member Function Documentation

AddArguments()

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

overridevirtual

Implements mitk::AbstractGlobalImageFeature.

Clone()

Pointer mitk::GIFFirstOrderHistogramStatistics::Clone

(

)

const

DoCalculateFeatures()

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

overrideprotectedvirtual

Implements mitk::AbstractGlobalImageFeature.

mitkClassMacro()

mitk::GIFFirstOrderHistogramStatistics::mitkClassMacro	(	GIFFirstOrderHistogramStatistics	,
		AbstractGlobalImageFeature
	)

New()

static Pointer mitk::GIFFirstOrderHistogramStatistics::New ( )

static

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

• mitkGIFFirstOrderHistogramStatistics.h