mitk::GIFVolumetricDensityStatistics Class Reference

Calculates Volumetric Density Features. More...

#include <mitkGIFVolumetricDensityStatistics.h>

Inheritance diagram for mitk::GIFVolumetricDensityStatistics:

Collaboration diagram for mitk::GIFVolumetricDensityStatistics:

Public Member Functions
	mitkClassMacro (GIFVolumetricDensityStatistics, AbstractGlobalImageFeature)
Pointer	Clone () const
	GIFVolumetricDensityStatistics ()
FeatureListType	CalculateFeatures (const Image::Pointer &image, const Image::Pointer &feature) override
	Calculates the Cooccurence-Matrix based features for this class. More...
FeatureNameListType	GetFeatureNames () override
	Returns a list of the names of all features that are calculated from this class. More...
void	CalculateFeaturesUsingParameters (const Image::Pointer &feature, const Image::Pointer &mask, const Image::Pointer &maskNoNAN, FeatureListType &featureList) override
	Calculates the feature of this abstact interface. Does not necessarily considers the parameter settings. More...
void	AddArguments (mitkCommandLineParser &parser) override
Public Member Functions inherited from mitk::AbstractGlobalImageFeature
	mitkClassMacro (AbstractGlobalImageFeature, BaseData)
FeatureListType	CalculateFeaturesSlicewise (const Image::Pointer &feature, const Image::Pointer &mask, int sliceID)
	Calculates the given feature Slice-wise. Might not be availble for an individual filter! More...
virtual void	CalculateFeaturesSliceWiseUsingParameters (const Image::Pointer &feature, const Image::Pointer &mask, int sliceID, FeatureListType &featureList)
	Calculates the feature of this abstact interface. Does not necessarily considers the parameter settings. More...
virtual std::string	GetCurrentFeatureEncoding ()
	Adds an additional Separator to the name of the feature, which encodes the used parameters. More...
std::string	FeatureDescriptionPrefix ()
	Returns a string that encodes the feature class name. 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	SetParameter (ParameterTypes param)
virtual std::string	GetPrefix () const
virtual std::string	GetShortName () const
virtual std::string	GetLongName () const
virtual std::string	GetFeatureClassName () const
virtual ParameterTypes	GetParameter () const
virtual void	SetUseQuantifier (bool _arg)
virtual bool	GetUseQuantifier () const
virtual void	SetQuantifier (IntensityQuantifier::Pointer _arg)
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	SetEncodeParameters (bool _arg)
virtual bool	GetEncodeParameters () const
std::string	GetOptionPrefix () const
std::vector< double >	SplitDouble (std::string str, char delimiter)
void	AddQuantifierArguments (mitkCommandLineParser &parser)
void	InitializeQuantifierFromParameters (const Image::Pointer &feature, const Image::Pointer &mask, unsigned int defaultBins=256)
void	InitializeQuantifier (const Image::Pointer &feature, const Image::Pointer &mask, unsigned int defaultBins=256)
std::string	QuantifierParameterString ()
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...
const mitk::TimeGeometry *	GetTimeSlicedGeometry () 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...
const mitk::TimeGeometry *	GetUpdatedTimeSliceGeometry ()
	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...
unsigned long	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
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::BaseData
static const char *	GetStaticNameOfClass ()

Additional Inherited Members
Public Types inherited from mitk::AbstractGlobalImageFeature
typedef std::vector< std::pair< std::string, double > >	FeatureListType
typedef std::vector< std::string >	FeatureNameListType
typedef std::map< std::string, us::Any >	ParameterTypes
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 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	InitializeTimeSlicedGeometry (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 Attributes inherited from mitk::BaseData
bool	m_LastRequestedRegionWasOutsideOfTheBufferedRegion
unsigned int	m_SourceOutputIndexDuplicate
bool	m_Initialized

Detailed Description

Calculates Volumetric Density Features.

These features characterize the compactness of the volume and shape by comparing the volumes of different volume and shape estimation methods.

This feature calculator is activated by the option -volume-density or -volden.

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 equal or greater than 1 are treated as masked.

The volume and surface are compared to the volume \( V \) and surface \( A \) that is calculated directly from the mask. The following features are then defined:

• Morphological Density::Volume density axis-aligned bounding box: The axis-aligned bounding box is defined as the minimum axis aligned box in 3D space that encloses all masked voxels. It is calculated by using the maximum spacial extension of the mask. Based on the volume of the bounding box, \( V_{aabb} \), the feature is defined as:

  \[ \textup{Volume density axis-aligned bounding box}= \frac{V}{V_{aabb}} \]

• Morphological Density::Surface density axis-aligned bounding box: As for the previous feature, the axis-aligned bounding box is compared to the mask, this time using the surface of the bounding box \( A_{aabb} \):

  \[ \textup{Surface density axis-aligned bounding box}= \frac{A}{A_{aabb}} \]

• Morphological Density::Volume density oriented minimum bounding box: A three-dimensional bounding box is defined using the box with the minimum volume. We do not use an estimation for this feature, which makes the calculation of this feature slow. Based on the volume of the bounding box, \( V_{ombb} \), the feature is defined as:

  \[ \textup{Volume density oriented minimum bounding box}= \frac{V}{V_{ombb}} \]

• Morphological Density::Surface density axis-aligned bounding box: As for the previous feature, theminimum oriented bounding box is compared to the mask, this time using the surface of the bounding box \( A_{ombb} \):

  \[ \textup{Surface density axis-aligned bounding box}= \frac{A}{A_{ombb}} \]

• Morphological Density::Volume density approx. enclosing ellipsoid: Using a Principal Component Analysis (PCA) of the spacial coordinates gives the three main axis of the mask. They correspond to the length of a eclipse enclosing the mask. The length of the axis of the eclipse are given by the eigenvalues of the decomposition: \( a = 2 \sqrt{\lambda_1} \), \( b = 2 \sqrt{\lambda_2} \), and \( c = 2 \sqrt{\lambda_3} \) with \(\lambda_x\) being the sorted eigenvalues (higher number indicates larger values). The volume of the enclosing eclipse can be estimated by \( V_{aee} = 4 \pi a b c \):

  \[ \textup{Volume density approx. enclosing ellipsoid}= \frac{V}{V_{aee}} \]

• Morphological Density::Surface density approx. enclosing ellipsoid: As for the previous feature, the surface of the enclosing ellipsoid is used. To simplify the calulation of it, an approximation (20 iterations) for the surface is used ( \( \alpha = \sqrt{1-\frac{b^2}{a^2}} \), \( \beta = \sqrt{1-\frac{c^2}{a^2}} \)):

  \[ A_{aee} = 2 \pi a b \frac{\alpha^2 + \beta^2}{\alpha \beta} \sum_v^\infty \frac{(a \beta)^v}{1-a v^2} \]

  \[ \textup{Surface density approx. enclosing ellipsoid}= \frac{A}{A_{aee}} \]

• Morphological Density::Volume density approx. minimum volume enclosing ellipsoid: The volume is compared to the volume of the minimum enclosing ellipsoid. While this ellipsoid can be found by brute-force calculation, this is quite time-consuming. It is therefore estimated using Khachiyan's Algorithm (Khachiyan, Rounding of Polytopes in the Real Number Model of Computation. Mathematics of Operations Research 1996) The so-found ellipsoid is described by the lengths \(a, b, c \) of its axis. The volume is then defined as \( V_{mvee} = 4 \pi a b c \) and the feature given by:

  \[ \textup{Volume density approx. minimum volume enclosing ellipsoid}= \frac{V}{V_{mvee}} \]

• Morphological Density::Surface density approx. minimum volume enclosing ellipsoid: As for the previous feature, the surface of the minimum volume enclosing ellipsoid is used. To simplify the calulation of it, an approximation with 20 iterations instead of infinite iterations is used for the calculation of the the surface ( \( \alpha = \sqrt{1-\frac{b^2}{a^2}} \), \( \beta = \sqrt{1-\frac{c^2}{a^2}} \)):

  \[ A_{mvee} = 2 \pi a b \frac{\alpha^2 + \beta^2}{\alpha \beta} \sum_v^\infty \frac{(a \beta)^v}{1-a v^2} \]

  \[ \textup{Surface density approx. minimum volume enclosing ellipsoid}= \frac{A}{A_{mvee}} \]

• Morphological Density::Volume density convex hull: The volume of the density hull is calculated using a convex mesh and then calculating the volume of this mesh \(V_{convex} \). The feature is then calculated using:

  \[ \textup{Volume density convex hull}= \frac{V}{V_{convex}} \]

• Morphological Density::Surface density convex hull: The surface of the density hull is calculated using a convex mesh and then calculating the surface of this mesh \(A_{convex} \). The feature is then calculated using:

  \[ \textup{Volume density convex hull}= \frac{A}{A_{convex}} \]

• Morphological Density::Volume integrated intensity: Integrated intensity is the average intensity times the volume. It is often used in conjunction with PET-images, where this feature is also called "total legion glycolysis". It is defined using the volume \(V \), the number of masked voxels \( N_v \) and the intensity of each voxel \( x_i \):

  \[ \textup{Volume integrated intensity}= V \frac{1}{N_v} \sum x_i \]

• Morphological Density::Volume Moran's I index: Moran's I index is an measure for the spacial autocorrelation. It is defined using the inverse spacial distance between two voxels \(i, j \) \(w_{ij} \), the number of masked voxels \( N_v \), the intensity of each voxel \( x_i \), and the mean intensity of all masked voxels \( \mu = \frac{1}{N_v} sum x_i \):

  \[ \textup{Volume Moran's I index}= \frac{N_v}{\sum_i \sum_j w_{ij}} \frac{\sum_i \sum_j (x_i - \mu) (x_j -\mu)}{\sum_i (x_i - \mu)^2 } \enspace \enspace {; i \neq j} \]

• Morphological Density::Volume Geary's C measure: Geary's C meansure is similar to Moran's I index. However, it is more sensitive to grey level differences and spacial autocorrelation: the spacial autocorrelation. It is defined using the inverse spacial distance between two voxels \(i, j \) \(w_{ij} \), the number of masked voxels \( N_v \), the intensity of each voxel \( x_i \), and the mean intensity of all masked voxels \( \mu = \frac{1}{N_v} sum x_i \):

  \[ \textup{Volume Geary's C measure}= \frac{N_v - 1}{2 \sum_i \sum_j w_{ij}} \frac{ \sum_i \sum_j w_{ij} (x_i - x_j)^2 }{\sum_i (x_i - \mu)^2 } \enspace \enspace {; i \neq j} \]

Definition at line 103 of file mitkGIFVolumetricDensityStatistics.h.

Constructor & Destructor Documentation

GIFVolumetricDensityStatistics()

mitk::GIFVolumetricDensityStatistics::GIFVolumetricDensityStatistics

(

)

Definition at line 494 of file mitkGIFVolumetricDensityStatistics.cpp.

Member Function Documentation

AddArguments()

void mitk::GIFVolumetricDensityStatistics::AddArguments ( mitkCommandLineParser &  parser )

overridevirtual

Implements mitk::AbstractGlobalImageFeature.

Definition at line 508 of file mitkGIFVolumetricDensityStatistics.cpp.

References mitkCommandLineParser::addArgument(), and mitkCommandLineParser::Bool.

CalculateFeatures()

mitk::GIFVolumetricDensityStatistics::FeatureListType mitk::GIFVolumetricDensityStatistics::CalculateFeatures ( const Image::Pointer &  image, const Image::Pointer &  feature  )

overridevirtual

Calculates the Cooccurence-Matrix based features for this class.

Implements mitk::AbstractGlobalImageFeature.

Definition at line 291 of file mitkGIFVolumetricDensityStatistics.cpp.

References AccessByItk_3, calculateMEE(), calculateMOBB(), CalculateVolumeDensityStatistic(), mitk::FastSinglePixelAccess(), image, mask, and mitkPixelTypeMultiplex5.

CalculateFeaturesUsingParameters()

void mitk::GIFVolumetricDensityStatistics::CalculateFeaturesUsingParameters ( const Image::Pointer &  feature, const Image::Pointer &  mask, const Image::Pointer &  maskNoNAN, FeatureListType &  featureList  )

overridevirtual

Calculates the feature of this abstact interface. Does not necessarily considers the parameter settings.

Implements mitk::AbstractGlobalImageFeature.

Definition at line 516 of file mitkGIFVolumetricDensityStatistics.cpp.

References CalculateFeatures(), and MITK_INFO.

Clone()

Pointer mitk::GIFVolumetricDensityStatistics::Clone

(

)

const

GetFeatureNames()

mitk::GIFVolumetricDensityStatistics::FeatureNameListType mitk::GIFVolumetricDensityStatistics::GetFeatureNames ( )

overridevirtual

Returns a list of the names of all features that are calculated from this class.

Implements mitk::AbstractGlobalImageFeature.

Definition at line 501 of file mitkGIFVolumetricDensityStatistics.cpp.

mitkClassMacro()

mitk::GIFVolumetricDensityStatistics::mitkClassMacro	(	GIFVolumetricDensityStatistics	,
		AbstractGlobalImageFeature
	)

New()

static Pointer mitk::GIFVolumetricDensityStatistics::New ( )

static

Referenced by main().

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

• mitkGIFVolumetricDensityStatistics.h
• mitkGIFVolumetricDensityStatistics.cpp