Medical Imaging Interaction Toolkit  2018.4.99-a3d2e8fb
Medical Imaging Interaction Toolkit
mitk::GIFVolumetricStatistics Class Reference

Calulates simpel shape-related features. More...

#include <mitkGIFVolumetricStatistics.h>

Inheritance diagram for mitk::GIFVolumetricStatistics:
Collaboration diagram for mitk::GIFVolumetricStatistics:

Public Member Functions

 mitkClassMacro (GIFVolumetricStatistics, AbstractGlobalImageFeature)
 
Pointer Clone () const
 
 GIFVolumetricStatistics ()
 
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...
 
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
 
- 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...
 
virtual std::string GetCurrentFeatureEncoding ()
 Adds an additional Separator to the name of the feature, which encodes the used parameters. 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...
 
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
 
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::AnyParameterTypes
 
- 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 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

Calulates simpel shape-related features.

This class can be used to calculate simple, shape-related features describing a given segmentation. There are no parameters that can be externaly set.

This feature calculator is activated by the option "<b>-volume</b>" or "<b>-vol</b>"

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 larger or equal to one are treated as masked. (Standard MITK mask)

Some of the features are calculated twice using different methods. For voxel- based approaches, the corresponding parameter is calcualted using the voxel, for example the volume is then calculated by multiplying the volume of a single volume with the number of voxels in the mask. In the second method, the mesh based appraoch, a mesh is created prior to the feature calculation which is then done using the features.

Another difference between two features might be the evaluation of invalid values within the image. There are two possibilities: By default, only those voxels are used with an valid intensity value, i.e. where the value is not infinite or NaN. The second possibility is not correcting for these voxels and only looking at the mask. Features that use these method are marked as "(uncorrected)"

The resulting features are:

  • Volumetric Features:: Voxel Volume: \( V_{single\_voxel} \) , the volume of an single volume, calculated as the multiplication of the voxel spacing in all directions.
  • Volumetric Features:: Volume (voxel based): \( V_{voxel} \), the volume of the masked area. Calulated by multiplying the numer of voxels with the Voxel Volume.
  • Volumetric Features:: Volume (mesh based): \( V_{shape} \), The volume based on the mesh-representation of the mask.
  • Volumetric Features:: Surface (voxel based): \( A_{voxel} \), the surface of the given mask. It is calulated by summing the surfaces between a masked and an unmasked voxel.
  • Volumetric Features:: Surface (mesh based): \( A_{mesh} \), the surface of the given mask calculated using the mask representation
  • Volumetric Features:: Surface to volume ration (voxel based): The ratio between voxel based surface and voxel based volume given as:

    \[ F_{av\_voxel}=\frac{A_{voxel}}{V_{voxel}} \]

  • Volumetric Features:: Surface to volume ration (mesh based): The ratio between voxel based surface and voxel based volume given as:

    \[ F_{av\_mesh}=\frac{A_{mesh}}{V_{mesh}} \]

  • Volumetric Features:: Compactness 1 (voxel based):
  • Volumetric Features:: Compactness 1 (mesh based): The compatness is a measure how spheric a shape is given. Compactness 1 is defined as:

    \[ F_{compactness\_1} = \frac{V}{\pi^{1/2} A^{3/2}}\]

  • Volumetric Features:: Compactness 1 old (voxel based):
  • Volumetric Features:: Compactness 1 old (mesh based): Some implementations use a slightly different definition of compactness 1. Although this is most likely an error and leads to an non-dimensionless feature, this defition is still calculated as:

    \[ F_{compactness\_1\_old} = \frac{V}{\pi^{1/2} A^{2/3}}\]

  • Volumetric Features:: Compactness 2 (voxel based):
  • Volumetric Features:: Compactness 2 (mesh based): The compatness is a measure how spheric a shape is given. Compactness 2 is defined as:

    \[ F_{compactness\_1} = 36 \pi \frac{V^2}{A^3}\]

  • Volumetric Features::Sphericity (voxel based):
  • Volumetric Features::Sphericity (mesh based): Sphericity is measure of how sphere-like a shape is:

    \[ F_{sphericity} = \frac{(36 \pi V^2)^{1/3}}{A} \]

  • Volumetric Features::Asphericity (voxel based):
  • Volumetric Features::Asphericity (mesh based): Sphericity is measure of how sphere-like a shape is:

    \[ F_{asphericity} = \left(\frac{1}{36 \pi }\frac{(A^3}{V^2}\right)^{1/3} - 1 \]

  • Volumetric Features::Spherical disproportion (voxel based):
  • Volumetric Features::Spherical disproportion (mesh based): Sphericity is measure of how sphere-like a shape is:

    \[ F_{spherical\_disproportion} = \frac{A}{4\pi R^2}= \frac{A}{\left(36\pi V^2\right)^{1/3}} \]

  • Volumetric Features:: Maximum 3D diameter: This is the largest distance between the centers of two voxels that are masked.
  • Volumetric Features::Bounding box volume: The bounding box volume is the volume of the smallest axis-aligned box that encapuslates all voxel centres.
  • Volumetric Features::Centre of mass shift:
  • Volumetric Features::Centre of mass shift (uncorrected): This is the distance between two centres of mass, namely the geometric centre and the weighted centre. The geometric centre is the mean position of all masked voxels, and the weighted centre is the mean position if the position of each voxel is weighted according to its intensity.
  • Volumetric Features::PCA Major Axis length:
  • Volumetric Features::PCA Major Axis length (uncorrected): A Principal component analysis (PCA) of the masekd voxel positions will give the main orientation and elongation of the masked area. The resulting eigenvectors of the PCA are sorted so that \( \lambda_{major}\geq \lambda_{minor} \geq \lambda_{least}\). The major axis length is defined as:

    \[ F_{pca\_major} = 4 \sqrt{\lambda_{major}} \]

  • Volumetric Features::PCA Minor axis length:
  • Volumetric Features::PCA Minor axis length: The Minor axis length is defined as:

    \[ F_{pca\_minor} = 4 \sqrt{\lambda_{minor}} \]

  • Volumetric Features::PCA Least axis length:
  • Volumetric Features::PCA Least axis length: The Minor axis length is defined as:

    \[ F_{pca\_Least} = 4 \sqrt{\lambda_{Least}} \]

Definition at line 108 of file mitkGIFVolumetricStatistics.h.

Constructor & Destructor Documentation

◆ GIFVolumetricStatistics()

Member Function Documentation

◆ AddArguments()

◆ CalculateFeatures()

mitk::GIFVolumetricStatistics::FeatureListType mitk::GIFVolumetricStatistics::CalculateFeatures ( const Image::Pointer image,
const Image::Pointer feature 
)
overridevirtual

◆ CalculateFeaturesUsingParameters()

void mitk::GIFVolumetricStatistics::CalculateFeaturesUsingParameters ( const Image::Pointer feature,
const Image::Pointer mask,
const Image::Pointer maskNoNAN,
FeatureListType featureList 
)
overridevirtual

Calculates the feature of this abstact interface. Does not necessarily considers the parameter settings.

Implements mitk::AbstractGlobalImageFeature.

Definition at line 455 of file mitkGIFVolumetricStatistics.cpp.

References CalculateFeatures(), mitk::AbstractGlobalImageFeature::GetLongName(), mitk::AbstractGlobalImageFeature::GetParameter(), and MITK_INFO.

◆ Clone()

Pointer mitk::GIFVolumetricStatistics::Clone ( ) const

◆ GetFeatureNames()

mitk::GIFVolumetricStatistics::FeatureNameListType mitk::GIFVolumetricStatistics::GetFeatureNames ( )
overridevirtual

Returns a list of the names of all features that are calculated from this class.

Implements mitk::AbstractGlobalImageFeature.

Definition at line 440 of file mitkGIFVolumetricStatistics.cpp.

◆ mitkClassMacro()

mitk::GIFVolumetricStatistics::mitkClassMacro ( GIFVolumetricStatistics  ,
AbstractGlobalImageFeature   
)

◆ New()

static Pointer mitk::GIFVolumetricStatistics::New ( )
static

Referenced by main().


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