mitk::GIFFirstOrderStatistics Class Reference

#include <mitkGIFFirstOrderStatistics.h>

Inheritance diagram for mitk::GIFFirstOrderStatistics:

Collaboration diagram for mitk::GIFFirstOrderStatistics:

Public Member Functions
	mitkClassMacro (GIFFirstOrderStatistics, AbstractGlobalImageFeature)
	Calculates first order statistics of the given image. More...
Pointer	Clone () const
	GIFFirstOrderStatistics ()
FeatureListType	CalculateFeatures (const Image *image, const Image *mask, const Image *maskNoNAN) override
	Calculate first-order statistics features for the given image and mask. More...
void	AddArguments (mitkCommandLineParser &parser) const override
	Add command line arguments for configuring this feature class. More...
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)
	Set the prefix prepended to command line option names. More...
virtual void	SetShortName (std::string _arg)
	Set the short name used in option keys and feature names. More...
virtual void	SetLongName (std::string _arg)
	Set the long (human-readable) name of this feature class. More...
virtual void	SetFeatureClassName (std::string _arg)
	Set the feature class name used in FeatureID. More...
virtual void	SetDirection (int _arg)
	Set the direction index for directional feature computation. More...
void	SetParameters (ParametersType param)
	Set the parameter map and reconfigure the instance accordingly. More...
virtual std::string	GetPrefix () const
	Get the command line option prefix. More...
virtual std::string	GetShortName () const
	Get the short name of this feature class. More...
virtual std::string	GetLongName () const
	Get the long name of this feature class. More...
virtual std::string	GetFeatureClassName () const
	Get the feature class name. More...
virtual ParametersType	GetParameters () const
	Get the current parameter map. More...
virtual IntensityQuantifier::Pointer	GetQuantifier ()
	Get the IntensityQuantifier used for histogram-based feature computation. More...
virtual int	GetDirection () const
	Get the direction index. More...
virtual void	SetMinimumIntensity (double _arg)
	Set the minimum intensity for histogram initialization. More...
virtual void	SetUseMinimumIntensity (bool _arg)
	Set whether to use the explicit minimum intensity. More...
virtual void	SetMaximumIntensity (double _arg)
	Set the maximum intensity for histogram initialization. More...
virtual void	SetUseMaximumIntensity (bool _arg)
	Set whether to use the explicit maximum intensity. More...
virtual double	GetMinimumIntensity () const
	Get the minimum intensity for histogram initialization. More...
virtual bool	GetUseMinimumIntensity () const
	Get whether the explicit minimum intensity is used. More...
virtual double	GetMaximumIntensity () const
	Get the maximum intensity for histogram initialization. More...
virtual bool	GetUseMaximumIntensity () const
	Get whether the explicit maximum intensity is used. More...
virtual void	SetBinsize (double _arg)
	Set the histogram bin size. More...
virtual void	SetUseBinsize (bool _arg)
	Set whether to use the explicit bin size for histogram initialization. More...
virtual double	GetBinsize () const
	Get the histogram bin size. More...
virtual bool	GetUseBinsize () const
	Get whether the explicit bin size is used. More...
virtual void	SetMorphMask (mitk::Image::Pointer _arg)
	Set the morphological mask image used by some feature classes. More...
virtual mitk::Image::Pointer	GetMorphMask () const
	Get the morphological mask image. More...
virtual void	SetBins (int _arg)
	Set the number of histogram bins. More...
virtual void	SetUseBins (bool _arg)
	Set whether to use the explicit bin count for histogram initialization. More...
virtual bool	GetUseBins () const
	Get whether the explicit bin count is used. More...
virtual int	GetBins () const
	Get the number of histogram bins. More...
virtual void	SetIgnoreMask (bool _arg)
	Set whether to ignore the mask when computing histogram ranges. More...
virtual bool	GetIgnoreMask () const
	Get whether the mask is ignored for histogram range computation. More...
virtual void	SetEncodeParametersInFeaturePrefix (bool _arg)
	Set whether to encode parameter values in the feature name prefix. More...
virtual bool	GetEncodeParametersInFeaturePrefix () const
	Get whether parameter values are encoded in the feature name prefix. More...
virtual void	EncodeParametersInFeaturePrefixOn ()
	Toggle encoding of parameter values in the feature name prefix. More...
virtual void	EncodeParametersInFeaturePrefixOff ()
std::string	GetOptionPrefix () const
	Build the full option prefix string for command line parameters. More...
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 the object contains data at any time step. More...
Public Member Functions inherited from mitk::BaseData
	mitkClassMacroItkParent (BaseData, itk::DataObject)
BaseProperty::ConstPointer	GetConstProperty (const std::string &propertyKey, const std::string &contextName="", bool fallBackOnDefaultContext=true) const override
	Get a const property by its key. More...
std::vector< std::string >	GetPropertyKeys (const std::string &contextName="", bool includeDefaultContext=false) const override
	Get all property keys stored in the property list. More...
std::vector< std::string >	GetPropertyContextNames () const override
	Get the names of all property contexts. More...
BaseProperty *	GetNonConstProperty (const std::string &propertyKey, const std::string &contextName="", bool fallBackOnDefaultContext=true) override
	Get a non-const property by its key. More...
void	SetProperty (const std::string &propertyKey, BaseProperty *property, const std::string &contextName="", bool fallBackOnDefaultContext=false) override
	Set a property in the property list. More...
void	RemoveProperty (const std::string &propertyKey, const std::string &contextName="", bool fallBackOnDefaultContext=false) override
	Remove a property from the property list. 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 non-const pointer. More...
const mitk::TimeGeometry *	GetUpdatedTimeGeometry ()
	Return the TimeGeometry of the data after ensuring it is up-to-date. More...
virtual void	Expand (unsigned int timeSteps)
	Expand the TimeGeometry to a number of time steps. More...
const mitk::BaseGeometry *	GetUpdatedGeometry (int t=0)
	Return the BaseGeometry of the data at time step t after ensuring it is up-to-date. More...
mitk::BaseGeometry *	GetGeometry (int t=0) const
	Return the BaseGeometry of the data at time step t as a non-const pointer. More...
void	UpdateOutputInformation () override
	Update the information for this BaseData 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. More...
virtual void	Clear ()
	Reset the data object by calling ClearData() and InitializeEmpty(). More...
virtual bool	IsEmptyTimeStep (unsigned int t) const
	Check whether the object contains data at the specified time step. More...
void	ExecuteOperation (Operation *operation) override
	Execute an operation on this data object. More...
virtual void	SetGeometry (BaseGeometry *aGeometry3D)
	Set the BaseGeometry of the data, which will be referenced (not copied!). 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 the BaseGeometry of the data. More...
virtual void	SetClonedTimeGeometry (const TimeGeometry *geometry)
	Set a clone of the provided TimeGeometry as the TimeGeometry of the data. More...
virtual void	SetClonedGeometry (const BaseGeometry *aGeometry3D, unsigned int time)
	Set a clone of the provided geometry as the 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, replacing the existing one. More...
mitk::BaseProperty::Pointer	GetProperty (const char *propertyKey) const
	Get a property by its key from the PropertyList. More...
void	SetProperty (const char *propertyKey, BaseProperty *property)
	Set a property in the PropertyList. More...
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. More...
itk::ModifiedTimeType	GetMTime () const override
	Get the modification time of this data object or its geometry, whichever was modified most recently. More...
void	Graft (const DataObject *) override
	Graft data and information from another data object. More...
Public Member Functions inherited from mitk::OperationActor
	itkTypeMacroNoParent (OperationActor) virtual ~OperationActor()
Public Member Functions inherited from mitk::Identifiable
	Identifiable ()
	Default constructor. Generates a new random UID. More...
	Identifiable (const UIDType &uid)
	Construct with a pre-existing UID. More...
	Identifiable (const Identifiable &)=delete
	Copy construction is deleted to prevent UID duplication. More...
	Identifiable (Identifiable &&) noexcept
	Move constructor. Transfers ownership of the UID. More...
virtual	~Identifiable ()
	Virtual destructor. More...
Identifiable &	operator= (const Identifiable &)=delete
	Copy assignment is deleted to prevent UID duplication. More...
Identifiable &	operator= (Identifiable &&other) noexcept
	Move assignment operator. Transfers ownership of the UID. More...
virtual UIDType	GetUID () const
	Get the unique identifier of this object. More...
UIDType	GetRuntimeUID () const noexcept
	Get a runtime-unique ID for this object instance. More...
Public Member Functions inherited from mitk::IPropertyOwner
	~IPropertyOwner () override
virtual bool	PropertyIsOwned (const std::string &propertyKey, const std::string &contextName="", bool fallBackOnDefaultContext=true) const
	Checks if a certain property exists. More...
Public Member Functions inherited from mitk::IPropertyProvider
virtual	~IPropertyProvider ()
	Virtual destructor. More...

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

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::Identifiable
using	UIDType = std::string
	Type alias for unique identifiers. More...
Protected Attributes inherited from mitk::BaseData
bool	m_LastRequestedRegionWasOutsideOfTheBufferedRegion
unsigned int	m_SourceOutputIndexDuplicate
bool	m_Initialized

Detailed Description

Definition at line 22 of file mitkGIFFirstOrderStatistics.h.

Constructor & Destructor Documentation

GIFFirstOrderStatistics()

mitk::GIFFirstOrderStatistics::GIFFirstOrderStatistics

(

)

Member Function Documentation

AddArguments()

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

overridevirtual

Add command line arguments for configuring this feature class.

Parameters

[in,out]

parser

The command line parser to add arguments to.

Implements mitk::AbstractGlobalImageFeature.

CalculateFeatures()

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

overridevirtual

Calculate first-order statistics features for the given image and mask.

Parameters

[in]	image	The input intensity image.
[in]	mask	The binary mask defining the region of interest.
[in]	maskNoNAN	The mask with NaN voxels excluded.

Returns

A list of computed feature name-value pairs.

Implements mitk::AbstractGlobalImageFeature.

Clone()

Pointer mitk::GIFFirstOrderStatistics::Clone

(

)

const

DoCalculateFeatures()

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

overrideprotectedvirtual

Implements mitk::AbstractGlobalImageFeature.

mitkClassMacro()

mitk::GIFFirstOrderStatistics::mitkClassMacro	(	GIFFirstOrderStatistics	,
		AbstractGlobalImageFeature
	)

Calculates first order statistics of the given image.

The first order statistics for the intensity distribution within a given Region of Interest (ROI) is calculated. The ROI is defined using a mask.

The features are calculated on a quantified image. If the bin-size is too big, the obtained values can be erroneous and misleading. It is therefore important to use enough bins. The binned approach is used in order to avoid floating-point related errors.

This feature calculator is activated by the option -first-order or -fo.

The connected areas are based on the binned image, the binning parameters can be set via the default parameters as described in AbstractGlobalImageFeature. It is also possible to determine the dimensionality of the neighbourhood using direction-related commands as described in AbstractGlobalImageFeature. No other options are possible beside these two options.

The features are calculated based on a mask. It is assumed that the mask is of the type of an unsigned short image. All voxels with the value 1 are treated as masked.

The following features are then defined using the (binned) voxel intensity \( x_i \) of each voxel, the probability an intensity \( p_x \), and the overall number of voxels within the mask \( N_v \):

• First Order::Mean: The mean intensity within the ROI

  \[ \textup{Mean}= \mu = \frac{1}{N_v} \sum x_i \]

• First Order::Unbiased Variance: An unbiased estimation of the variance:

  \[ \textup{Unbiased Variance} = \frac{1}{N_v - 1} \sum \left( x_i - \mu \right)^2 \]

• First Order::Biased Variance: An biased estimation of the variance. If not specified otherwise, this is used as the variance:

  \[ \textup{Biased Variance} = \sigma^2 = \frac{1}{N_v} \sum \left( x_i - \mu \right)^2 \]

• First Order::Unbiased Standard Deviation: Estimation of diversity within the intensity values

  \[ \textup{Unbiased Standard Deviation} = \sqrt{\frac{1}{N_v-1} \sum \left( x_i - \mu \right)^2} \]

• First Order::Biased Standard Deviation: Estimation of diversity within the intensity values

  \[ \textup{Biased Standard Deviation} = \sigma = \sqrt{\frac{1}{N_v} \sum \left( x_i - \mu \right)^2} \]

• First Order::Skewness:

  \[ \textup{Skewness} = \frac{\frac{1}{N_v} \sum \left( x_i - \mu \right)^3}{\sigma^3} \]

• First Order::Kurtosis: The kurtosis is a measurement of the peakness of the given distribution:

  \[ \textup{Kurtosis} = \frac{\frac{1}{N_v} \sum \left( x_i - \mu \right)^4}{\sigma^4} \]

• First Order::Excess Kurtosis: The kurtosis is a measurement of the peakness of the given distribution. The excess kurtosis is similar to the kurtosis, but is corrected by a fisher correction, ensuring that a gaussian distribution has an excess kurtosis of 0.

  \[ \textup{Excess Kurtosis} = \frac{\frac{1}{N_v} \sum \left( x_i - \mu \right)^4}{\sigma^4} - 3 \]

• First Order::Median: The median is defined as the median of the all intensities in the ROI.
• First Order::Minimum: The minimum is defined as the minimum of the all intensities in the ROI.
• First Order::05th Percentile: \( P_{5\%} \) The 5% percentile. 5% of all voxel do have this or a lower intensity.
• First Order::10th Percentile: \( P_{10\%} \) The 10% percentile. 10% of all voxel do have this or a lower intensity.
• First Order::15th Percentile: \( P_{15\%} \) The 15% percentile. 15% of all voxel do have this or a lower intensity.
• First Order::20th Percentile: \( P_{20\%} \) The 20% percentile. 20% of all voxel do have this or a lower intensity.
• First Order::25th Percentile: \( P_{25\%} \) The 25% percentile. 25% of all voxel do have this or a lower intensity.
• First Order::30th Percentile: \( P_{30\%} \) The 30% percentile. 30% of all voxel do have this or a lower intensity.
• First Order::35th Percentile: \( P_{35\%} \) The 35% percentile. 35% of all voxel do have this or a lower intensity.
• First Order::40th Percentile: \( P_{40\%} \) The 40% percentile. 40% of all voxel do have this or a lower intensity.
• First Order::45th Percentile: \( P_{45\%} \) The 45% percentile. 45% of all voxel do have this or a lower intensity.
• First Order::50th Percentile: \( P_{50\%} \) The 50% percentile. 50% of all voxel do have this or a lower intensity.
• First Order::55th Percentile: \( P_{55\%} \) The 55% percentile. 55% of all voxel do have this or a lower intensity.
• First Order::60th Percentile: \( P_{60\%} \) The 60% percentile. 60% of all voxel do have this or a lower intensity.
• First Order::65th Percentile: \( P_{65\%} \) The 65% percentile. 65% of all voxel do have this or a lower intensity.
• First Order::70th Percentile: \( P_{70\%} \) The 70% percentile. 70% of all voxel do have this or a lower intensity.
• First Order::75th Percentile: \( P_{75\%} \) The 75% percentile. 75% of all voxel do have this or a lower intensity.
• First Order::80th Percentile: \( P_{80\%} \) The 80% percentile. 80% of all voxel do have this or a lower intensity.
• First Order::85th Percentile: \( P_{85\%} \) The 85% percentile. 85% of all voxel do have this or a lower intensity.
• First Order::90th Percentile: \( P_{90\%} \) The 90% percentile. 90% of all voxel do have this or a lower intensity.
• First Order::95th Percentile: \( P_{95\%} \) The 95% percentile. 95% of all voxel do have this or a lower intensity.
• First Order::Maximum: The maximum is defined as the minimum of the all intensities in the ROI.
• First Order::Range: The range of intensity values is defined as the difference between the maximum and minimum intensity in the ROI.
• First Order::Interquartile Range: The difference between the 75% and 25% quantile.
• First Order::Mean Absolute Deviation: The mean absolute deviation gives the mean distance of each voxel intensity to the overall mean intensity and is a measure of the dispersion of the intensity form the mean value:

  \[ \textup{Mean Absolute Deviation} = \frac{1}{N_v} \sum \left \| x_i - \mu \right \| \]

• First Order::Robust Mean: The mean intensity within the ROI for all voxels between the 10% and 90% quantile:

  \[ \textup{Robust Mean}= \mu_R = \frac{1}{N_{vr}} \sum x_i \]

• First Order::Robust Mean Absolute Deviation: The absolute deviation of all intensities within the ROI for all voxels between the 10% and 90% quantilefrom the robust mean intensity:

  \[ \textup{Robust Mean Absolute Deviation}= \mu_R = \frac{1}{N_{vr}} \sum \left \| x_i - \mu_R \right \| \]

• First Order::Median Absolute Deviation: Similar to the mean absolute deviation, but uses the median instead of the mean to measure the center of the distribution.
• First Order::Coefficient Of Variation: Measures the dispersion of the intensity distribution:

  \[ \textup{Coefficient Of Variation} = \frac{sigma}{\mu} \]

• First Order::Quantile Coefficient Of Dispersion: A robust alternative to the coefficient of variance:

  \[ \textup{Quantile Coefficient Of Dispersion} = \frac{P_{75\%} - P_{25\%} }{P_{75\%} + P_{25\%}} \]

• First Order::Energy: The intensity energy:

  \[ \textup{Energy} = \sum x_i ^2 \]

• First Order::Root Mean Square: Root mean square is an important measure for the error.

  \[ \textup{Root Mean Square} = \sqrt{\frac{\sum x_i ^2}{N_v}} \]

• First Order::Uniformity:

  \[ \textup{Uniformity} = \sum p_x^2 \]

• First Order::Entropy:

  \[ \textup{Entropy} = - \sum p_x \textup{log}_2(p_x) \]

• First Order::Entropy:

  \[ \textup{Entropy} = - \sum p_x \textup{log}_2(p_x) \]

• First Order::Covered Image Intensity Range: Percentage of the image intensity range (maximum - minimum in whole image) that is covered by the ROI.
• First Order::Sum: The sum of all intensities. It is correlated to the mean intensity.

  \[ \textup{Sum} = \sum x_i \]

• First Order::Mode: The most common intensity.
• First Order::Mode Probability: The likelihood of the most common intensity.
• First Order::Number Of Voxels: \( N_v \) the number of voxels covered by the ROI.
• First Order::Image Dimension: The dimensionality of the image (e.g. 2D, 3D, etc.).
• First Order::Number Of Voxels: The product of all spacing along all dimensions. In 3D, this is equal to the volume.
• First Order::Number Of Voxels: The volume of a single voxel. If the dimensionality is only 2D, this is the surface of an voxel.

New()

static Pointer mitk::GIFFirstOrderStatistics::New ( )

static

---

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

• mitkGIFFirstOrderStatistics.h