Calculates the Neighbourhood Grey Tone Difference Features. More...
#include <mitkGIFNeighbourhoodGreyToneDifferenceFeatures.h>
Public Member Functions | |
| mitkClassMacro (GIFNeighbourhoodGreyToneDifferenceFeatures, AbstractGlobalImageFeature) | |
| Pointer | Clone () const |
| GIFNeighbourhoodGreyToneDifferenceFeatures () | |
| 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... | |
| std::string | GetCurrentFeatureEncoding () override |
| Adds an additional Separator to the name of the feature, which encodes the used parameters. 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 |
| virtual void | SetRange (int _arg) |
| virtual int | GetRange () const |
 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... | |
| 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
Calculates the Neighbourhood Grey Tone Difference Features.
This class can be used to calculate Neighbourhood Grey Tone Difference Features which have been introduced in Amadasun and King: Textural features corresponding to textural properties. IEEE Transactions on Systems, Man and Cybernetricy, 1989.
The Neighbourhood Grey Tone Difference (NGTD) is based on a table and is calcualted using a defined neighbourhood for each voxel. Within this neighbourhood, the mean intensity of the neighbouring voxel is calculated \(A_i\), i.e. the mean intensity of the neighbourhood excluding the center voxel. Based on this a table with four columns is calculated. The first column represents the voxel value, or in our implementation, the histogram bin index \(i\). The second column represents the number of voxel with this intensity value \(n_i\). The proability for each intensity value \(p_i\), which is equal to the bin probability. And the sum of the absolut differences of the intensity of all voxels with this intensity and the mean intensity of their neighbourhood:
\[s_i = \sum \left \| i- A_i \right \| \]
. Additional \( N_v\) is the number of voxels, \( N_g \) the number of bins, and \(N_{g,p}\) the number of bins with a non-zero probability.
This feature calculator is activated by the option -neighbourhood-grey-tone-difference or -ngtd.
The range that is used to calculate the local intensity can be set using the function SetRange. To set it with parameters set the option ngtd::range which expects an int value n that is interpreted as voxel count. The neighbourhood includes symetrical n voxels additional to the center voxel in each directions. The default value for this parameter is 1.
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 of greater than zero are treated as masked.
For the definition of the features we use the sum, this is always the sum over the bins of the histogram. If the denominator of a feature evaluates to zero, the feature is defined as zero. The resulting features are:
- Neighbourhood Grey Tone Difference::Coarsness: The coarsness is defined as :
\[ \textup{Coarsness}= \frac{1}{\sum p_i s_i} \]
- Neighbourhood Grey Tone Difference::Contrast: The contrast is defined as :
\[ \textup{contrast}= \left( \frac{1}{N_{g,p} ( N_{g,p} - 1) } \sum_i \sum_j p_i p_j (i-j)^2 \right) \left( \frac{1}{N_v} \sum s_i \right) \]
- Neighbourhood Grey Tone Difference::Busyness: for all bins with a non-zero probability
\[ \textup{busyness} = \frac{\sum p_i s_i}{\sum_i \sum_j \left \| i p_i - j p_j \right \| } \]
- Neighbourhood Grey Tone Difference::Complexity: for all bins with a non-zero probability
\[ \textup{complexity} = \frac{1}{N_v} \sum_i \sum_j \left \| i - j \right \| \frac{p_i s_i + p_j s_j}{p_i + p_j} \]
- Neighbourhood Grey Tone Difference::Strength: for all bins with a non-zero probability
\[ \textup{strength} = \frac{\sum_i \sum_j (p_i + p_j) (i + j)^2}{\sum_i s_i } \]
Definition at line 64 of file mitkGIFNeighbourhoodGreyToneDifferenceFeatures.h.
Constructor & Destructor Documentation
◆ GIFNeighbourhoodGreyToneDifferenceFeatures()
| mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::GIFNeighbourhoodGreyToneDifferenceFeatures | ( | ) |
Member Function Documentation
◆ AddArguments()
|
overridevirtual |
Implements mitk::AbstractGlobalImageFeature.
Definition at line 177 of file mitkGIFNeighbourhoodGreyToneDifferenceFeatures.cpp.
References mitkCommandLineParser::addArgument(), mitk::AbstractGlobalImageFeature::AddQuantifierArguments(), mitkCommandLineParser::Bool, mitk::AbstractGlobalImageFeature::GetLongName(), mitk::AbstractGlobalImageFeature::GetOptionPrefix(), and mitkCommandLineParser::Int.
◆ CalculateFeatures()
|
overridevirtual |
Calculates the Cooccurence-Matrix based features for this class.
Implements mitk::AbstractGlobalImageFeature.
Definition at line 155 of file mitkGIFNeighbourhoodGreyToneDifferenceFeatures.cpp.
References AccessByItk_3, CalculateIntensityPeak(), mitk::AbstractGlobalImageFeature::FeatureDescriptionPrefix(), mitk::AbstractGlobalImageFeature::GetQuantifier(), GetRange(), and mitk::AbstractGlobalImageFeature::InitializeQuantifierFromParameters().
Referenced by CalculateFeaturesUsingParameters().
◆ CalculateFeaturesUsingParameters()
|
overridevirtual |
Calculates the feature of this abstact interface. Does not necessarily considers the parameter settings.
Implements mitk::AbstractGlobalImageFeature.
Definition at line 188 of file mitkGIFNeighbourhoodGreyToneDifferenceFeatures.cpp.
References us::any_cast(), CalculateFeatures(), mitk::AbstractGlobalImageFeature::GetLongName(), mitk::AbstractGlobalImageFeature::GetOptionPrefix(), mitk::AbstractGlobalImageFeature::GetParameter(), mitk::AbstractGlobalImageFeature::InitializeQuantifierFromParameters(), MITK_INFO, and SetRange().
◆ Clone()
| Pointer mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::Clone | ( | ) | const |
◆ GetCurrentFeatureEncoding()
|
overridevirtual |
Adds an additional Separator to the name of the feature, which encodes the used parameters.
Reimplemented from mitk::AbstractGlobalImageFeature.
Definition at line 208 of file mitkGIFNeighbourhoodGreyToneDifferenceFeatures.cpp.
References mitk::AbstractGlobalImageFeature::QuantifierParameterString().
◆ GetFeatureNames()
|
overridevirtual |
Returns a list of the names of all features that are calculated from this class.
Implements mitk::AbstractGlobalImageFeature.
Definition at line 170 of file mitkGIFNeighbourhoodGreyToneDifferenceFeatures.cpp.
◆ GetRange()
|
virtual |
Referenced by CalculateFeatures().
◆ mitkClassMacro()
| mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::mitkClassMacro | ( | GIFNeighbourhoodGreyToneDifferenceFeatures | , |
| AbstractGlobalImageFeature | |||
| ) |
◆ New()
|
static |
Referenced by main().
◆ SetRange()
|
virtual |
Referenced by CalculateFeaturesUsingParameters().
The documentation for this class was generated from the following files:
