Medical Imaging Interaction Toolkit  2021.02.99-00f000b3
Medical Imaging Interaction Toolkit
mitk::AbstractClassifier Class Referenceabstract

#include <mitkAbstractClassifier.h>

Inheritance diagram for mitk::AbstractClassifier:
Collaboration diagram for mitk::AbstractClassifier:

Public Member Functions

 mitkClassMacro (AbstractClassifier, BaseData)
 
virtual void Train (const Eigen::MatrixXd &X, const Eigen::MatrixXi &Y)=0
 Build a forest of trees from the training set (X, y). More...
 
virtual Eigen::MatrixXi Predict (const Eigen::MatrixXd &X)=0
 Predict class for X. More...
 
Eigen::MatrixXi & GetLabels ()
 GetPointWiseWeightCopy. More...
 
virtual bool SupportsPointWiseWeight ()=0
 SupportsPointWiseWeight. More...
 
virtual Eigen::MatrixXd & GetPointWiseWeight ()
 GetPointWiseWeightCopy. More...
 
virtual void SetPointWiseWeight (const Eigen::MatrixXd &W)
 SetPointWiseWeight. More...
 
virtual void UsePointWiseWeight (bool value)
 UsePointWiseWeight. More...
 
virtual bool IsUsingPointWiseWeight ()
 IsUsingPointWiseWeight. More...
 
virtual bool SupportsPointWiseProbability ()=0
 SupportsPointWiseProbability. More...
 
virtual Eigen::MatrixXd & GetPointWiseProbabilities ()
 GetPointWiseWeightCopy. More...
 
virtual void UsePointWiseProbability (bool value)
 UsePointWiseProbabilities. More...
 
virtual bool IsUsingPointWiseProbability ()
 IsUsingPointWiseProbabilities. More...
 
void SetNthItems (const char *val, unsigned int idx)
 
std::string GetNthItems (unsigned int idx) const
 
void SetItemList (std::vector< std::string >)
 
std::vector< std::string > GetItemList () 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...
 
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
 
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 ()
 

Protected Attributes

Eigen::MatrixXi m_OutLabel
 
Eigen::MatrixXd m_PointWiseWeight
 
bool m_IsUsingPointWiseWeight
 
Eigen::MatrixXd m_OutProbability
 
bool m_IsUsingPointWiseProbability
 
- Protected Attributes inherited from mitk::BaseData
bool m_LastRequestedRegionWasOutsideOfTheBufferedRegion
 
unsigned int m_SourceOutputIndexDuplicate
 
bool m_Initialized
 

Additional Inherited Members

- 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
 
- Static Public Member Functions inherited from mitk::BaseData
static const char * GetStaticNameOfClass ()
 
- 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)
 

Detailed Description

Definition at line 32 of file mitkAbstractClassifier.h.

Member Function Documentation

◆ GetItemList()

std::vector<std::string> mitk::AbstractClassifier::GetItemList ( ) const

◆ GetLabels()

Eigen::MatrixXi& mitk::AbstractClassifier::GetLabels ( )
inline

GetPointWiseWeightCopy.

Returns
return label matrix of shape = [n_samples , 1]

Definition at line 56 of file mitkAbstractClassifier.h.

◆ GetNthItems()

std::string mitk::AbstractClassifier::GetNthItems ( unsigned int  idx) const

◆ GetPointWiseProbabilities()

virtual Eigen::MatrixXd& mitk::AbstractClassifier::GetPointWiseProbabilities ( )
inlinevirtual

GetPointWiseWeightCopy.

Returns
return probability matrix

Definition at line 131 of file mitkAbstractClassifier.h.

◆ GetPointWiseWeight()

virtual Eigen::MatrixXd& mitk::AbstractClassifier::GetPointWiseWeight ( )
inlinevirtual

GetPointWiseWeightCopy.

Returns
Create and return a copy of W

Definition at line 80 of file mitkAbstractClassifier.h.

◆ IsEmpty()

bool mitk::AbstractClassifier::IsEmpty ( ) const
inlineoverridevirtual

Check whether object contains data (at least at one point in time), e.g., a set of points may be empty.

Warning
Returns IsInitialized()==false by default for compatibility reasons. Override in sub-classes that support distinction between empty/non-empty state.

Reimplemented from mitk::BaseData.

Definition at line 180 of file mitkAbstractClassifier.h.

◆ IsUsingPointWiseProbability()

virtual bool mitk::AbstractClassifier::IsUsingPointWiseProbability ( )
inlinevirtual

IsUsingPointWiseProbabilities.

Returns

Definition at line 149 of file mitkAbstractClassifier.h.

◆ IsUsingPointWiseWeight()

virtual bool mitk::AbstractClassifier::IsUsingPointWiseWeight ( )
inlinevirtual

IsUsingPointWiseWeight.

Returns
true if pointewise weighting is enabled.

Definition at line 107 of file mitkAbstractClassifier.h.

◆ mitkClassMacro()

mitk::AbstractClassifier::mitkClassMacro ( AbstractClassifier  ,
BaseData   
)

◆ Predict()

virtual Eigen::MatrixXi mitk::AbstractClassifier::Predict ( const Eigen::MatrixXd &  X)
pure virtual

Predict class for X.

Parameters
XThe input samples.
Returns
The predicted classes. Y matrix of shape = [n_samples, 1]

Implemented in mitk::PURFClassifier, mitk::VigraRandomForestClassifier, and mitk::LibSVMClassifier.

◆ RequestedRegionIsOutsideOfTheBufferedRegion()

bool mitk::AbstractClassifier::RequestedRegionIsOutsideOfTheBufferedRegion ( )
inlineoverridevirtual

Determine whether the RequestedRegion is outside of the BufferedRegion.

This method returns true if the RequestedRegion is outside the BufferedRegion (true if at least one pixel is outside). This is used by the pipeline mechanism to determine whether a filter needs to re-execute in order to satisfy the current request. If the current RequestedRegion is already inside the BufferedRegion from the previous execution (and the current filter is up to date), then a given filter does not need to re-execute

Implements mitk::BaseData.

Definition at line 173 of file mitkAbstractClassifier.h.

◆ SetItemList()

void mitk::AbstractClassifier::SetItemList ( std::vector< std::string >  )

◆ SetNthItems()

void mitk::AbstractClassifier::SetNthItems ( const char *  val,
unsigned int  idx 
)

◆ SetPointWiseWeight()

virtual void mitk::AbstractClassifier::SetPointWiseWeight ( const Eigen::MatrixXd &  W)
inlinevirtual

SetPointWiseWeight.

Parameters
WThe pointwise weights. W matrix of shape = [n_samples, 1]

Definition at line 89 of file mitkAbstractClassifier.h.

◆ SetRequestedRegion()

void mitk::AbstractClassifier::SetRequestedRegion ( const itk::DataObject *  data)
inlineoverridevirtual

Set the requested region from this data object to match the requested region of the data object passed in as a parameter.

This method is implemented in the concrete subclasses of BaseData.

Implements mitk::BaseData.

Definition at line 176 of file mitkAbstractClassifier.h.

◆ SetRequestedRegionToLargestPossibleRegion()

void mitk::AbstractClassifier::SetRequestedRegionToLargestPossibleRegion ( )
inlineoverridevirtual

Set the RequestedRegion to the LargestPossibleRegion.

This forces a filter to produce all of the output in one execution (i.e. not streaming) on the next call to Update().

Implements mitk::BaseData.

Definition at line 172 of file mitkAbstractClassifier.h.

◆ SupportsPointWiseProbability()

virtual bool mitk::AbstractClassifier::SupportsPointWiseProbability ( )
pure virtual

SupportsPointWiseProbability.

Returns
True if the classifier supports pointwise class probability calculation else false

Implemented in mitk::PURFClassifier, mitk::VigraRandomForestClassifier, and mitk::LibSVMClassifier.

◆ SupportsPointWiseWeight()

virtual bool mitk::AbstractClassifier::SupportsPointWiseWeight ( )
pure virtual

SupportsPointWiseWeight.

Returns
True if the classifier supports pointwise weighting else false

Implemented in mitk::PURFClassifier, mitk::VigraRandomForestClassifier, and mitk::LibSVMClassifier.

◆ Train()

virtual void mitk::AbstractClassifier::Train ( const Eigen::MatrixXd &  X,
const Eigen::MatrixXi &  Y 
)
pure virtual

Build a forest of trees from the training set (X, y).

Parameters
XThe training input samples. Matrix of shape = [n_samples, n_features]
YThe target values (class labels in classification, real numbers in regression). Matrix of shape = [n_samples, 1]

Implemented in mitk::LibSVMClassifier, mitk::PURFClassifier, and mitk::VigraRandomForestClassifier.

◆ UsePointWiseProbability()

virtual void mitk::AbstractClassifier::UsePointWiseProbability ( bool  value)
inlinevirtual

UsePointWiseProbabilities.

Parameters
value

Definition at line 140 of file mitkAbstractClassifier.h.

◆ UsePointWiseWeight()

virtual void mitk::AbstractClassifier::UsePointWiseWeight ( bool  value)
inlinevirtual

UsePointWiseWeight.

Parameters
valueweighting on/off

Reimplemented in mitk::PURFClassifier, and mitk::VigraRandomForestClassifier.

Definition at line 98 of file mitkAbstractClassifier.h.

◆ VerifyRequestedRegion()

bool mitk::AbstractClassifier::VerifyRequestedRegion ( )
inlineoverridevirtual

Verify that the RequestedRegion is within the LargestPossibleRegion.

If the RequestedRegion is not within the LargestPossibleRegion, then the filter cannot possibly satisfy the request. This method returns true if the request can be satisfied (even if it will be necessary to process the entire LargestPossibleRegion) and returns false otherwise. This method is used by PropagateRequestedRegion(). PropagateRequestedRegion() throws a InvalidRequestedRegionError exception if the requested region is not within the LargestPossibleRegion.

Implements mitk::BaseData.

Definition at line 174 of file mitkAbstractClassifier.h.

Member Data Documentation

◆ m_IsUsingPointWiseProbability

bool mitk::AbstractClassifier::m_IsUsingPointWiseProbability
protected

Definition at line 156 of file mitkAbstractClassifier.h.

◆ m_IsUsingPointWiseWeight

bool mitk::AbstractClassifier::m_IsUsingPointWiseWeight
protected

Definition at line 114 of file mitkAbstractClassifier.h.

◆ m_OutLabel

Eigen::MatrixXi mitk::AbstractClassifier::m_OutLabel
protected

Definition at line 62 of file mitkAbstractClassifier.h.

◆ m_OutProbability

Eigen::MatrixXd mitk::AbstractClassifier::m_OutProbability
protected

Definition at line 155 of file mitkAbstractClassifier.h.

◆ m_PointWiseWeight

Eigen::MatrixXd mitk::AbstractClassifier::m_PointWiseWeight
protected

Definition at line 113 of file mitkAbstractClassifier.h.


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