Calculates the Neighbouring Grey Level Dependence Features. More...
#include <mitkGIFNeighbouringGreyLevelDependenceFeatures.h>
Public Member Functions | |
| mitkClassMacro (GIFNeighbouringGreyLevelDependenceFeature, AbstractGlobalImageFeature) | |
| Pointer | Clone () const |
| GIFNeighbouringGreyLevelDependenceFeature () | |
| FeatureListType | CalculateFeatures (const Image *image, const Image *mask, const Image *maskNoNAN) override |
| virtual std::vector< double > | GetRanges () const |
| void | SetRanges (std::vector< double > ranges) |
| void | SetRange (double range) |
| virtual int | GetAlpha () const |
| virtual void | SetAlpha (int _arg) |
| 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 | |
| std::string | GenerateLegacyFeatureEncoding (const FeatureID &id) const override |
| FeatureListType | DoCalculateFeatures (const Image *image, const Image *mask) override |
| void | ConfigureSettingsByParameters (const ParametersType ¶meters) override |
| Protected Member Functions inherited from mitk::AbstractGlobalImageFeature | |
| std::vector< double > | SplitDouble (std::string str, char delimiter) |
| void | AddQuantifierArguments (mitkCommandLineParser &parser) const |
| void | ConfigureQuantifierSettingsByParameters () |
| 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 |
| 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 the Neighbouring Grey Level Dependence Features.
The Neighbouring Grey Level Dependence Features were proposed by Sun and Wee (1983) and capture the coarsness of the image texture. They are rotational invariant.
The features are calculated on a matrix \( m \). To obtain the matrix, a neighbourhood around each feature is calculated and the number of voxels within the neighbourhood that are greater than the center voxel plus \( \alpha \) is counted. This is called the number of dependence voxels. The matrix gives the number of voxels with an intensity \( x \) and \( d \) dependence neighbourhood voxels.
The image is quantified prior to the calculation of the features. This reduces the number of available intensity values. Instead of using the pure intensity value, the features are calculated using the number of the bins as intensity value \( x_i \). The parameter of the quantification of the image can be controlled using the general binning parameters as defined in AbstractGlobalImageFeature.
By default, the calculation is based on a 26 neighbourhood for 3D and a 8 neighbourhood in 2D. It is further possible to exclude directions from the calculation, e.g. calculating the feature in 2D, even if a 3D image is passed. This is controlled by determine the dimensionality of the neighbourhood using direction-related commands as described in AbstractGlobalImageFeature.
In addition to this, the size of the neighbourhood can be controlled by setting the parameter ngld::range. By default it is one. To pass more than one range, separate the ranges with a semicolon. E.g. 1;2;3 would calculate the features for the ranges 1, 2, and 3.
This feature calculator is activated by the option -neighbouring-grey-level-dependence or -ngld.
The features are calculated based on a mask. It is assumed that the mask is a unsigned short image. All voxels with a value greater 0 are treated as masked.
Several values are defined for the definition of the features. \( N_v \) is the number of masked voxels, \(N_s \) is the number of neighbourhoods, \( m_{x,\cdot} = \sum_d m{x,d} \) is the number of neighbourhoods with a given intensity value, and likewise \( m_{\cdot, d} = \sum_x m{x,d} \) is the number of neighbourhoods with a given number of dependence features:
- Neighbouring Grey Level Dependence::Low Dependence Emphasis:
\[ \textup{Low dependence emphasis}= \frac{1}{N_s} \sum_d { \frac{m_{\cdot, d}}{d^2} } \]
- Neighbouring Grey Level Dependence::High Dependence Emphasis:
\[ \textup{High dependence emphasis}= \frac{1}{N_s} \sum_d { m_{\cdot, d} d^2} \]
- Neighbouring Grey Level Dependence::Low Grey Level Count Emphasis:
\[ \textup{Low grey level count emphasis}= \frac{1}{N_s} \sum_x { \frac{m_{x,\cdot}}{x^2} } \]
- Neighbouring Grey Level Dependence::High Grey Level Count Emphasis:
\[ \textup{High grey level count emphasis}= \frac{1}{N_s} \sum_x { m_{x,\cdot} x^2} \]
- Neighbouring Grey Level Dependence::Low Dependence Low Grey Level Emphasis:
\[ \textup{Low Dependence Low Grey Level Emphasis}= \frac{1}{N_s} \sum_x \sum_d { \frac{m_{x,d}}{x^2 d^2} } \]
- Neighbouring Grey Level Dependence::Low Dependence High Grey Level Emphasis:
\[ \textup{Low dependence high grey level emphasis}= \frac{1}{N_s} \sum_x \sum_d { \frac{x^2 m_{x,d}}{d^2} } \]
- Neighbouring Grey Level Dependence::High Dependence Low Grey Level Emphasis:
\[ \textup{High Dependence Low Grey Level Emphasis}= \frac{1}{N_s} \sum_x \sum_d { \frac{d^2 m_{x,d}}{x^2} } \]
- Neighbouring Grey Level Dependence::High Dependence High Grey Level Emphasis:
\[ \textup{High dependence high grey level emphasis}= \frac{1}{N_s} \sum_x \sum_d { x^2 d^2 m_{x,d} } \]
- Neighbouring Grey Level Dependence::Grey level nonuniformity:
\[ \textup{Grey level nonuniformity}= \frac{1}{N_s} \sum_x m_{x,\cdot}^2 \]
- Neighbouring Grey Level Dependence::Grey level nonuniformity normalized:
\[ \textup{Grey level nonuniformity normalized}= \frac{1}{N_s^2} \sum_x m_{x,\cdot}^2 \]
- Neighbouring Grey Level Dependence::Dependence Count Nonuniformity:
\[ \textup{Dependence count nonuniformity}= \frac{1}{N_s} \sum_d m_{\cdot, d}^2 \]
- Neighbouring Grey Level Dependence::Dependence Count Nonuniformity Normalized:
\[ \textup{Dependence count nonuniformity normalized}= \frac{1}{N_s^2} \sum_d m_{\cdot, d}^2 \]
- Neighbouring Grey Level Dependence::DEpendence Count Percentage THe number of realized neighbourhoods relativ to the theoretical maximum of realized neighbourhoods. This feature is always one for this implementation as partial neighbourhoods are still considered.
- Neighbouring Grey Level Dependence::Grey Level Mean: The mean value of all grey level.
\[ \textup{Grey Level Mean} = \mu_x = \frac{1}{N_s} \sum_x x m_{x,\cdot} \]
- Neighbouring Grey Level Dependence::Grey Level Variance:
\[ \textup{Grey level variance} = \frac{1}{N_s} \sum_x (x -mu_x)^2 m_{x, \cdot} \]
- Neighbouring Grey Level Dependence::Dependence Count Mean: The mean value of all dependence counts.
\[ \textup{Dependence count mean} = \mu_d = \frac{1}{N_s} \sum_d d m_{\cdot,d} \]
- Neighbouring Grey Level Dependence::Dependence Count Variance:
\[ \textup{Dependence count variance} = \frac{1}{N_s} \sum_d (d -mu_d)^2 m_{\cdot, d} \]
- Neighbouring Grey Level Dependence::Dependence Count Entropy: This feature would be equivalent with the Grey Level Entropy, which is therefore not included. It is based on the likelihood for a given intensity- size combination \( p_{x,d} = \frac{m_{x,d}}{N_s} \). :
\[ \textup{Dependence count entropy} = \sum_x \sum_d p_{x,d} \textup{log}_2 \left( p_{x,d} \right) \]
- Neighbouring Grey Level Dependence::Dependence Count Energy: This feature would be equivalent with the Grey Level Energy, which is therefore not included. It is based on the likelihood for a given intensity- size combination \( p_{x,d} = \frac{m_{x,d}}{N_s} \). :
\[ \textup{Dependence count energy} = \sum_x \sum_d p_{x,d}^2 \]
- Neighbouring Grey Level Dependence::Expected Neighbourhood Size: The expected size of a full neighbourhood. It depends on the dimension of the area that is looked at.
- Neighbouring Grey Level Dependence::Average Neighbourhood Size: The feature calculation allows to consider partially masked neighbourhoods. Due to that, some neighbourhoods might be smaller. This feature gives not the theoretical neighbourhood size but the average realized neighbourhood sizes.
- Neighbouring Grey Level Dependence::Average Incomplete Neighbourhood Size: Gives the average size of all neighbourhoods that are not complete.
- Neighbouring Grey Level Dependence::Percentage of complete Neighbourhoods: Gives the percentage of all complete neighbourhoods from all realized neighbourhoods.
- Neighbouring Grey Level Dependence::Percentage of Dependence Neighbour Voxels: Gives the percentage of voxels in all neighbourhoods compared to the expected number of voxels.
Definition at line 116 of file mitkGIFNeighbouringGreyLevelDependenceFeatures.h.
Constructor & Destructor Documentation
◆ GIFNeighbouringGreyLevelDependenceFeature()
| mitk::GIFNeighbouringGreyLevelDependenceFeature::GIFNeighbouringGreyLevelDependenceFeature | ( | ) |
Member Function Documentation
◆ AddArguments()
|
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()
|
overridevirtual |
Implements mitk::AbstractGlobalImageFeature.
◆ Clone()
| Pointer mitk::GIFNeighbouringGreyLevelDependenceFeature::Clone | ( | ) | const |
◆ ConfigureSettingsByParameters()
|
overrideprotectedvirtual |
Ensures that the instance is configured according to the information given in the passed parameters. This method will be called by SetParameters(...) after ConfigureQuantifierSettingsByParameters() was called.
Reimplemented from mitk::AbstractGlobalImageFeature.
◆ DoCalculateFeatures()
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overrideprotectedvirtual |
Implements mitk::AbstractGlobalImageFeature.
◆ GenerateLegacyFeatureEncoding()
|
overrideprotectedvirtual |
Reimplemented from mitk::AbstractGlobalImageFeature.
◆ GetAlpha()
|
virtual |
◆ GetRanges()
|
virtual |
◆ mitkClassMacro()
| mitk::GIFNeighbouringGreyLevelDependenceFeature::mitkClassMacro | ( | GIFNeighbouringGreyLevelDependenceFeature | , |
| AbstractGlobalImageFeature | |||
| ) |
◆ New()
|
static |
◆ SetAlpha()
|
virtual |
◆ SetRange()
| void mitk::GIFNeighbouringGreyLevelDependenceFeature::SetRange | ( | double | range | ) |
◆ SetRanges()
| void mitk::GIFNeighbouringGreyLevelDependenceFeature::SetRanges | ( | std::vector< double > | ranges | ) |
The documentation for this class was generated from the following file:
