Medical Imaging Interaction Toolkit  2021.02.99-4e0dbe47
Medical Imaging Interaction Toolkit
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 *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 abstact 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 availble 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 abstact 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 abstact 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...
 
BasePropertyGetNonConstProperty (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::TimeGeometryGetTimeGeometry () const
 Return the TimeGeometry of the data as const pointer. More...
 
const mitk::TimeGeometryGetTimeSlicedGeometry () const
 Return the TimeGeometry of the data as const pointer. More...
 
mitk::TimeGeometryGetTimeGeometry ()
 Return the TimeGeometry of the data as pointer. More...
 
const mitk::TimeGeometryGetUpdatedTimeGeometry ()
 Return the TimeGeometry of the data. More...
 
const mitk::TimeGeometryGetUpdatedTimeSliceGeometry ()
 Return the TimeGeometry of the data. More...
 
virtual void Expand (unsigned int timeSteps)
 Expands the TimeGeometry to a number of TimeSteps. More...
 
const mitk::BaseGeometryGetUpdatedGeometry (int t=0)
 Return the BaseGeometry of the data at time t. More...
 
mitk::BaseGeometryGetGeometry (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::BaseDataSourceGetSource () 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 ()
 
Identifiableoperator= (const Identifiable &)=delete
 
Identifiableoperator= (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 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 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< SelfPointer
 
typedef itk::SmartPointer< const SelfConstPointer
 
- 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 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 ( )

Member Function Documentation

◆ AddArguments()

void mitk::GIFVolumetricDensityStatistics::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::GIFVolumetricDensityStatistics::CalculateFeatures ( const Image image,
const Image mask,
const Image maskNoNAN 
)
overridevirtual

◆ Clone()

Pointer mitk::GIFVolumetricDensityStatistics::Clone ( ) const

◆ DoCalculateFeatures()

FeatureListType mitk::GIFVolumetricDensityStatistics::DoCalculateFeatures ( const Image image,
const Image mask 
)
overrideprotectedvirtual

◆ mitkClassMacro()

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

◆ New()

static Pointer mitk::GIFVolumetricDensityStatistics::New ( )
static

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