Public Member Functions |
Static Public Member Functions |
Protected Member Functions |
List of all members
mitk::GIFIntensityVolumeHistogramFeatures Class Reference
Calculates the Intensity Volume Histogram features. More...
#include <mitkGIFIntensityVolumeHistogramFeatures.h>
Inheritance diagram for mitk::GIFIntensityVolumeHistogramFeatures:
Collaboration diagram for mitk::GIFIntensityVolumeHistogramFeatures:
Public Member Functions | |
| mitkClassMacro (GIFIntensityVolumeHistogramFeatures, AbstractGlobalImageFeature) | |
| Pointer | Clone () const |
| GIFIntensityVolumeHistogramFeatures () | |
| 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... | |
| 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 | |
| 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 ¶meters) |
| 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< 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 Intensity Volume Histogram features.
This class can be used to calculate the volume histogram and features that are calculated from it. It is based on the intensity-volume histogram (IVH) which describes the relation between the grey level index i (and the corresponding intensity \(x_i\)) and the volume fraction \(f\) that with an intensity that is equal or greater than \(x_i\). This feature is original proposed in El Naqa et al. Exploring feature-based approaches in PET images for prediciting cancer treatment outcomes. Pattern recognition 2009.
This feature calculator is activated by the option "<b>-intensity-volume-histogram</b>" or "<b>-ivoh</b>". Beside the configuration of the histogram, which follows the description given in AbstractGlobalImageFeature there are no additional parameters to configure this feature. Remark that, different from other features, the number of bins is 1000 by default and not 256.
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.
The resulting features are:
- Intensity Volume Histogram::Volume fraction at 0.10 intensity: The volume fraction with an intensity of greater or equal to 10% of the maximum intensity.
- Intensity Volume Histogram::Volume fraction at 0.90 intensity: The volume fraction with an intensity of greater or equal to 90% of the maximum intensity.
- Intensity Volume Histogram::Intensity at 0.10 volume: The highest intensity so that at least 10% of the masked image area has the same or higher intensity.
- Intensity Volume Histogram::Intensity at 0.90 volume: The highest intensity so that at least 10% of the masked image area has the same or higher intensity.
- Intensity Volume Histogram::Difference volume fraction at 0.10 and 0.90 intensity: The difference between the volume fraction at 10% intensity and 90% intensity.
- Intensity Volume Histogram::Difference intensity at 0.10 and 0.90 volume: The intensity difference between the intenstiy of 90% of the volume and 10% volume.
- Intensity Volume Histogram::Area under IVH curve: If the IVH is interpreted as curve, this value represents the area under the curve. It is calculated using the bin indexes rather than the intensity values.
Definition at line 57 of file mitkGIFIntensityVolumeHistogramFeatures.h.
Constructor & Destructor Documentation
◆ GIFIntensityVolumeHistogramFeatures()
| mitk::GIFIntensityVolumeHistogramFeatures::GIFIntensityVolumeHistogramFeatures | ( | ) |
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::GIFIntensityVolumeHistogramFeatures::Clone | ( | ) | const |
◆ DoCalculateFeatures()
|
overrideprotectedvirtual |
Implements mitk::AbstractGlobalImageFeature.
◆ mitkClassMacro()
| mitk::GIFIntensityVolumeHistogramFeatures::mitkClassMacro | ( | GIFIntensityVolumeHistogramFeatures | , |
| AbstractGlobalImageFeature | |||
| ) |
◆ New()
|
static |
The documentation for this class was generated from the following file:
