mitk::GIFVolumetricStatistics Class Reference

Calulates 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::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

Calulates 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 externaly 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 calcualted 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 appraoch, 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. Calulated by multiplying the numer 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 calulated 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 defition 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

(

)

Definition at line 219 of file mitkGIFVolumetricStatistics.cpp.

References mitk::AbstractGlobalImageFeature::SetFeatureClassName(), mitk::AbstractGlobalImageFeature::SetLongName(), and mitk::AbstractGlobalImageFeature::SetShortName().

Member Function Documentation

AddArguments()

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

overridevirtual

Implements mitk::AbstractGlobalImageFeature.

Definition at line 447 of file mitkGIFVolumetricStatistics.cpp.

References mitkCommandLineParser::addArgument(), mitkCommandLineParser::Bool, mitk::AbstractGlobalImageFeature::GetLongName(), and mitk::AbstractGlobalImageFeature::GetOptionPrefix().

CalculateFeatures()

mitk::GIFVolumetricStatistics::FeatureListType mitk::GIFVolumetricStatistics::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 226 of file mitkGIFVolumetricStatistics.cpp.

References AccessByItk_3, CalculateLargestDiameter(), CalculateVolumeStatistic(), mitk::FastSinglePixelAccess(), mitk::AbstractGlobalImageFeature::FeatureDescriptionPrefix(), image, mask, MITK_INFO, and mitkPixelTypeMultiplex5.

Referenced by CalculateFeaturesUsingParameters().

CalculateFeaturesUsingParameters()

void mitk::GIFVolumetricStatistics::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 455 of file mitkGIFVolumetricStatistics.cpp.

References CalculateFeatures(), mitk::AbstractGlobalImageFeature::GetLongName(), mitk::AbstractGlobalImageFeature::GetParameter(), and MITK_INFO.

Clone()

Pointer mitk::GIFVolumetricStatistics::Clone

(

)

const

GetFeatureNames()

mitk::GIFVolumetricStatistics::FeatureNameListType mitk::GIFVolumetricStatistics::GetFeatureNames ( )

overridevirtual

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

Implements mitk::AbstractGlobalImageFeature.

Definition at line 440 of file mitkGIFVolumetricStatistics.cpp.

mitkClassMacro()

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

New()

static Pointer mitk::GIFVolumetricStatistics::New ( )

static

Referenced by main().

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

• mitkGIFVolumetricStatistics.h
• mitkGIFVolumetricStatistics.cpp