Medical Imaging Interaction Toolkit  2024.06.00
Medical Imaging Interaction Toolkit
mitk::GIFGreyLevelDistanceZone Class Reference

#include <mitkGIFGreyLevelDistanceZone.h>

Inheritance diagram for mitk::GIFGreyLevelDistanceZone:
Collaboration diagram for mitk::GIFGreyLevelDistanceZone:

Public Member Functions

 mitkClassMacro (GIFGreyLevelDistanceZone, AbstractGlobalImageFeature)
 Calculates the Grey Level Distance Zone. More...
 
Pointer Clone () const
 
 GIFGreyLevelDistanceZone ()
 
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...
 
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...
 
mitk::TimeGeometryGetTimeGeometry ()
 Return the TimeGeometry of the data as pointer. More...
 
const mitk::TimeGeometryGetUpdatedTimeGeometry ()
 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...
 
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 ()
 
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 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

Definition at line 70 of file mitkGIFGreyLevelDistanceZone.h.

Constructor & Destructor Documentation

◆ GIFGreyLevelDistanceZone()

mitk::GIFGreyLevelDistanceZone::GIFGreyLevelDistanceZone ( )

Member Function Documentation

◆ AddArguments()

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

◆ Clone()

Pointer mitk::GIFGreyLevelDistanceZone::Clone ( ) const

◆ DoCalculateFeatures()

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

◆ mitkClassMacro()

mitk::GIFGreyLevelDistanceZone::mitkClassMacro ( GIFGreyLevelDistanceZone  ,
AbstractGlobalImageFeature   
)

Calculates the Grey Level Distance Zone.

This class can be used to calculate Grey Level Distance Zone as presented in Thibault et al. 2014.

The basic idea behind the Grey Level Distance Zone based features is to count the connected areas with a given intensity value \(x_i\) and a given distance to the border of each segmentation \(d_i\). Several features are then calculated based on a matrix, that gives the number of occurrence for each combination of \(x_i\) and \( d_i \) as \(m_{x,d}\).

This feature calculator is activated by the option -grey-level-distance-zone or -gldz.

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. It is expected that the image contains only voxels with value 0 and 1, of which all voxels with an value equal to one are treated as masked.

The features depend on the distance to the border of the segmentation ROI. In some cases, the border definition might be different from the definition of the masked area, for example, if small openings in the mask should not influence the distance. Due to that, it is possible to submit a second mask, named Morphological Mask to the features that is then used to calculate the distance of each voxel to border of the segmented area. The morpological mask can be either set by the function call SetMorphMask() or by the corresponding global option. (Not parsed by the filter itself, but by the command line tool).

Beside the complete matrix, which is represented by its individual elements \(m_{x,d}\), som eadditional values are used for the definition. \(N_g\) is the number of discrete grey levels, \( N_d\) the number (or maximum value) of possible distances, and \(N_s\) the total number of zones. \(m_{x,d}\) gives the number of connected areas with the discrete grey level x and distance to the boarder of d. Corresponding, \(p_{x,d} = \frac{m_{x,d}}{N_s} gives the relativ probability of this matrix cell. \) \(N_v\) is the number of voxels. In addition, the marginal sums \(m_{x,\cdot} = m_x = \sum_d m_{x,d} \) , representing the sum of all zones with a given intensity, and sums \(m_{\cdot, d} = m_d = \sum_x m_{x,d} \) , representing the sum of all zones with a given distance, are used. The distance are given as the number of voxels to the border and the voxel intensity is given as the bin number of the binned image, starting with 1.

The following features are then defined:

  • Grey Level Distance Zone::Small Distance Emphasis:

    \[ \textup{Small Distance Emphasis}= \frac{1}{N_s} \sum_d \frac{m_d}{d^2} \]

  • Grey Level Distance Zone::Large Distance Emphasis:

    \[ \textup{Large Distance Emphasis}= \frac{1}{N_s} \sum_d d^2 m_d \]

  • Grey Level Distance Zone::Low Grey Level Emphasis:

    \[ \textup{Low Grey Level Emphasis}= \frac{1}{N_s} \sum_x \frac{m_x}{x^2} \]

  • Grey Level Distance Zone::High Grey Level Emphasis:

    \[ \textup{High Grey Level Emphasis}= \frac{1}{N_s} \sum_x x^2 m_x \]

  • Grey Level Distance Zone::Small Distance Low Grey Level Emphasis:

    \[ \textup{Small Distance Low Grey Level Emphasis}= \frac{1}{N_s} \sum_x \sum_d \frac{ m_{x,d}}{x^2 d^2}\]

  • Grey Level Distance Zone::Small Distance High Grey Level Emphasis:

    \[ \textup{Small Distance High Grey Level Emphasis}= \frac{1}{N_s} \sum_x \sum_d \frac{x^2 m_{x,d}}{d^2}\]

  • Grey Level Distance Zone::Large Distance Low Grey Level Emphasis:

    \[ \textup{Large Distance Low Grey Level Emphasis}= \frac{1}{N_s} \sum_x \sum_d \frac{d^2 m_{x,d}}{x^2}\]

  • Grey Level Distance Zone::Large Distance High Grey Level Emphasis:

    \[ \textup{Large Distance High Grey Level Emphasis}= \frac{1}{N_s} \sum_x \sum_d \x^2 d^2 m_{x,d} \]

  • Grey Level Distance Zone::Grey Level Non-Uniformity:

    \[ \textup{Grey Level Non-Uniformity}= \frac{1}{N_s} \sum_x m_x^2 \]

  • Grey Level Distance Zone::Grey Level Non-Uniformity Normalized:

    \[ \textup{Grey Level Non-Uniformity Normalized}= \frac{1}{N_s^2} \sum_x m_x^2 \]

  • Grey Level Distance Zone::Zone Distance Non-Uniformity:

    \[ \textup{Grey Level Non-Uniformity}= \frac{1}{N_s} \sum_d m_d^2 \]

  • Grey Level Distance Zone::Zone Distance Non-Uniformity Normalized:

    \[ \textup{Grey Level Non-Uniformity Normalized}= \frac{1}{N_s^2} \sum_d m_d^2 \]

  • Grey Level Distance Zone::Zone Percentage: The ratio of zones to the possible zones:

    \[ \textup{Zone Percentage}= \frac{N_s}{N_v} \]

  • Grey Level Distance Zone::Grey Level Mean:

    \[ \textup{Grey Level Mean}= \mu_x = \sum_x \sum_d x p_{x,d} \]

  • Grey Level Distance Zone::Grey Level Variance:

    \[ \textup{Grey Level Variance} = \sum_x \sum_d \left(x - \mu_x \right)^2 p_{x,d} \]

  • Grey Level Distance Zone::Zone Distance Mean:

    \[ \textup{Zone Distance Mean}= \mu_d = \sum_x \sum_d d p_{x,d} \]

  • Grey Level Distance Zone::Zone Distance Variance:

    \[ \textup{Zone Distance Variance} = \sum_x \sum_d \left(d - \mu_d \right)^2 p_{x,d} \]

  • Grey Level Distance Zone::Zone Distance Entropy :

    \[ \textup{Zone Distance Entropy} = - \sum_x \sum_d p_{x,d} \textup{log}_2 ( p_{x,d} ) \]

  • Grey Level Distance Zone::Grey Level Entropy :

    \[ \textup{Grey Level Entropy} = - \sum_x \sum_d p_{x,d} \textup{log}_2 ( p_{x,d} ) \]

◆ New()

static Pointer mitk::GIFGreyLevelDistanceZone::New ( )
static

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