mitk::GIFVolumetricStatistics Class Reference

Calculates simpel shape-related features. More...

#include <mitkGIFVolumetricStatistics.h>

Inheritance diagram for mitk::GIFVolumetricStatistics:

Collaboration diagram for mitk::GIFVolumetricStatistics:

Public Member Functions
	mitkClassMacro (GIFVolumetricStatistics, AbstractGlobalImageFeature)
Pointer	Clone () const
	GIFVolumetricStatistics ()
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 simpel shape-related features.

This class can be used to calculate simple, shape-related features describing a given segmentation. There are no parameters that can be externally set.

This feature calculator is activated by the option "<b>-volume</b>" or "<b>-vol</b>"

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 larger or equal to one are treated as masked. (Standard MITK mask)

Some of the features are calculated twice using different methods. For voxel- based approaches, the corresponding parameter is calculated using the voxel, for example the volume is then calculated by multiplying the volume of a single volume with the number of voxels in the mask. In the second method, the mesh based approach, a mesh is created prior to the feature calculation which is then done using the features.

Another difference between two features might be the evaluation of invalid values within the image. There are two possibilities: By default, only those voxels are used with an valid intensity value, i.e. where the value is not infinite or NaN. The second possibility is not correcting for these voxels and only looking at the mask. Features that use these method are marked as "(uncorrected)"

The resulting features are:

• Volumetric Features:: Voxel Volume: \( V_{single\_voxel} \) , the volume of an single volume, calculated as the multiplication of the voxel spacing in all directions.
• Volumetric Features:: Volume (voxel based): \( V_{voxel} \), the volume of the masked area. Calculated by multiplying the number of voxels with the Voxel Volume.
• Volumetric Features:: Volume (mesh based): \( V_{shape} \), The volume based on the mesh-representation of the mask.
• Volumetric Features:: Surface (voxel based): \( A_{voxel} \), the surface of the given mask. It is calculated by summing the surfaces between a masked and an unmasked voxel.
• Volumetric Features:: Surface (mesh based): \( A_{mesh} \), the surface of the given mask calculated using the mask representation
• Volumetric Features:: Surface to volume ration (voxel based): The ratio between voxel based surface and voxel based volume given as:

  \[ F_{av\_voxel}=\frac{A_{voxel}}{V_{voxel}} \]

• Volumetric Features:: Surface to volume ration (mesh based): The ratio between voxel based surface and voxel based volume given as:

  \[ F_{av\_mesh}=\frac{A_{mesh}}{V_{mesh}} \]

• Volumetric Features:: Compactness 1 (voxel based):
• Volumetric Features:: Compactness 1 (mesh based): The compatness is a measure how spheric a shape is given. Compactness 1 is defined as:

  \[ F_{compactness\_1} = \frac{V}{\pi^{1/2} A^{3/2}}\]

• Volumetric Features:: Compactness 1 old (voxel based):
• Volumetric Features:: Compactness 1 old (mesh based): Some implementations use a slightly different definition of compactness 1. Although this is most likely an error and leads to an non-dimensionless feature, this definition is still calculated as:

  \[ F_{compactness\_1\_old} = \frac{V}{\pi^{1/2} A^{2/3}}\]

• Volumetric Features:: Compactness 2 (voxel based):
• Volumetric Features:: Compactness 2 (mesh based): The compatness is a measure how spheric a shape is given. Compactness 2 is defined as:

  \[ F_{compactness\_1} = 36 \pi \frac{V^2}{A^3}\]

• Volumetric Features::Sphericity (voxel based):
• Volumetric Features::Sphericity (mesh based): Sphericity is measure of how sphere-like a shape is:

  \[ F_{sphericity} = \frac{(36 \pi V^2)^{1/3}}{A} \]

• Volumetric Features::Asphericity (voxel based):
• Volumetric Features::Asphericity (mesh based): Sphericity is measure of how sphere-like a shape is:

  \[ F_{asphericity} = \left(\frac{1}{36 \pi }\frac{(A^3}{V^2}\right)^{1/3} - 1 \]

• Volumetric Features::Spherical disproportion (voxel based):
• Volumetric Features::Spherical disproportion (mesh based): Sphericity is measure of how sphere-like a shape is:

  \[ F_{spherical\_disproportion} = \frac{A}{4\pi R^2}= \frac{A}{\left(36\pi V^2\right)^{1/3}} \]

• Volumetric Features:: Maximum 3D diameter: This is the largest distance between the centers of two voxels that are masked.
• Volumetric Features::Bounding box volume: The bounding box volume is the volume of the smallest axis-aligned box that encapuslates all voxel centres.
• Volumetric Features::Centre of mass shift:
• Volumetric Features::Centre of mass shift (uncorrected): This is the distance between two centres of mass, namely the geometric centre and the weighted centre. The geometric centre is the mean position of all masked voxels, and the weighted centre is the mean position if the position of each voxel is weighted according to its intensity.
• Volumetric Features::PCA Major Axis length:
• Volumetric Features::PCA Major Axis length (uncorrected): A Principal component analysis (PCA) of the masekd voxel positions will give the main orientation and elongation of the masked area. The resulting eigenvectors of the PCA are sorted so that \( \lambda_{major}\geq \lambda_{minor} \geq \lambda_{least}\). The major axis length is defined as:

  \[ F_{pca\_major} = 4 \sqrt{\lambda_{major}} \]

• Volumetric Features::PCA Minor axis length:
• Volumetric Features::PCA Minor axis length: The Minor axis length is defined as:

  \[ F_{pca\_minor} = 4 \sqrt{\lambda_{minor}} \]

• Volumetric Features::PCA Least axis length:
• Volumetric Features::PCA Least axis length: The Minor axis length is defined as:

  \[ F_{pca\_Least} = 4 \sqrt{\lambda_{Least}} \]

Definition at line 108 of file mitkGIFVolumetricStatistics.h.

Constructor & Destructor Documentation

GIFVolumetricStatistics()

mitk::GIFVolumetricStatistics::GIFVolumetricStatistics

(

)

Member Function Documentation

AddArguments()

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

overridevirtual

Implements mitk::AbstractGlobalImageFeature.

Clone()

Pointer mitk::GIFVolumetricStatistics::Clone

(

)

const

DoCalculateFeatures()

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

overrideprotectedvirtual

Implements mitk::AbstractGlobalImageFeature.

mitkClassMacro()

mitk::GIFVolumetricStatistics::mitkClassMacro	(	GIFVolumetricStatistics	,
		AbstractGlobalImageFeature
	)

New()

static Pointer mitk::GIFVolumetricStatistics::New ( )

static

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

• mitkGIFVolumetricStatistics.h