#include <mitkVigraRandomForestClassifier.h>

Inheritance diagram for mitk::VigraRandomForestClassifier:

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Collaboration diagram for mitk::VigraRandomForestClassifier:

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Public Member Functions
	mitkClassMacro (VigraRandomForestClassifier, AbstractClassifier)

Pointer	Clone () const

	VigraRandomForestClassifier ()

	~VigraRandomForestClassifier () override

void	Train (const Eigen::MatrixXd &X, const Eigen::MatrixXi &Y) override
	Build a forest of trees from the training set (X, y). More...

void	OnlineTrain (const Eigen::MatrixXd &X, const Eigen::MatrixXi &Y)

Eigen::MatrixXi	Predict (const Eigen::MatrixXd &X) override
	Predict class for X. More...

Eigen::MatrixXi	PredictWeighted (const Eigen::MatrixXd &X)

bool	SupportsPointWiseWeight () override
	SupportsPointWiseWeight. More...

bool	SupportsPointWiseProbability () override
	SupportsPointWiseProbability. More...

void	ConvertParameter ()

void	SetRandomForest (const vigra::RandomForest< int > &rf)

const vigra::RandomForest< int > &	GetRandomForest () const

void	UsePointWiseWeight (bool) override
	UsePointWiseWeight. More...

void	SetMaximumTreeDepth (int)

void	SetMinimumSplitNodeSize (int)

void	SetPrecision (double)

void	SetSamplesPerTree (double)

void	UseSampleWithReplacement (bool)

void	SetTreeCount (int)

void	SetWeightLambda (double)

void	SetTreeWeights (Eigen::MatrixXd weights)

void	SetTreeWeight (int treeId, double weight)

Eigen::MatrixXd	GetTreeWeights () const

void	PrintParameter (std::ostream &str=std::cout)

Public Member Functions inherited from mitk::AbstractClassifier
	mitkClassMacro (AbstractClassifier, BaseData)

Eigen::MatrixXi &	GetLabels ()
	GetPointWiseWeightCopy. More...

virtual Eigen::MatrixXd &	GetPointWiseWeight ()
	GetPointWiseWeightCopy. More...

virtual void	SetPointWiseWeight (const Eigen::MatrixXd &W)
	SetPointWiseWeight. More...

virtual bool	IsUsingPointWiseWeight ()
	IsUsingPointWiseWeight. 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...

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::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::AbstractClassifier
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

Detailed Description

Definition at line 26 of file mitkVigraRandomForestClassifier.h.

Constructor & Destructor Documentation

◆ VigraRandomForestClassifier()

mitk::VigraRandomForestClassifier::VigraRandomForestClassifier ( )

Definition at line 96 of file mitkVigraRandomForestClassifier.cpp.

References ConvertParameter(), and mitk::BaseData::GetPropertyList().

◆ ~VigraRandomForestClassifier()

mitk::VigraRandomForestClassifier::~VigraRandomForestClassifier ( )

override

Definition at line 104 of file mitkVigraRandomForestClassifier.cpp.

Member Function Documentation

◆ Clone()

Pointer mitk::VigraRandomForestClassifier::Clone ( ) const

◆ ConvertParameter()

void mitk::VigraRandomForestClassifier::ConvertParameter ( )

Definition at line 450 of file mitkVigraRandomForestClassifier.cpp.

References mitk::eps, mitk::BaseData::GetPropertyList(), and MITK_INFO.

Referenced by PrintParameter(), Train(), and VigraRandomForestClassifier().

◆ GetRandomForest()

const vigra::RandomForest< int > & mitk::VigraRandomForestClassifier::GetRandomForest ( ) const

Definition at line 586 of file mitkVigraRandomForestClassifier.cpp.

◆ GetTreeWeights()

Eigen::MatrixXd mitk::VigraRandomForestClassifier::GetTreeWeights ( ) const

Definition at line 243 of file mitkVigraRandomForestClassifier.cpp.

References k(), mitk::ThresholdSplit< TColumnDecisionFunctor, TFeatureCalculator, TTag >::SetMaximumTreeDepth(), mitk::ThresholdSplit< TColumnDecisionFunctor, TFeatureCalculator, TTag >::SetPrecision(), mitk::ThresholdSplit< TColumnDecisionFunctor, TFeatureCalculator, TTag >::SetWeights(), mitk::ThresholdSplit< TColumnDecisionFunctor, TFeatureCalculator, TTag >::UsePointBasedWeights(), and mitk::ThresholdSplit< TColumnDecisionFunctor, TFeatureCalculator, TTag >::UseRandomSplit().

◆ mitkClassMacro()

mitk::VigraRandomForestClassifier::mitkClassMacro	(	VigraRandomForestClassifier	,
		AbstractClassifier
	)

◆ New()

static Pointer mitk::VigraRandomForestClassifier::New ( )

static

Referenced by main(), and mitk::RandomForestFileIO::Read().

◆ OnlineTrain()

void mitk::VigraRandomForestClassifier::OnlineTrain	(	const Eigen::MatrixXd &	X,
		const Eigen::MatrixXi &	Y
	)

Definition at line 118 of file mitkVigraRandomForestClassifier.cpp.

◆ Predict()

Eigen::MatrixXi mitk::VigraRandomForestClassifier::Predict ( const Eigen::MatrixXd & X )

overridevirtual

Predict class for X.

Parameters

X,The input samples.

Returns: The predicted classes. Y matrix of shape = [n_samples, 1]

Implements mitk::AbstractClassifier.

Definition at line 173 of file mitkVigraRandomForestClassifier.cpp.

References mitk::AbstractClassifier::m_OutLabel, and mitk::AbstractClassifier::m_OutProbability.

◆ PredictWeighted()

Eigen::MatrixXi mitk::VigraRandomForestClassifier::PredictWeighted ( const Eigen::MatrixXd & X )

Definition at line 205 of file mitkVigraRandomForestClassifier.cpp.

References mitk::AbstractClassifier::m_OutLabel, and mitk::AbstractClassifier::m_OutProbability.

◆ PrintParameter()

void mitk::VigraRandomForestClassifier::PrintParameter ( std::ostream & str = std::cout )

Definition at line 470 of file mitkVigraRandomForestClassifier.cpp.

References ConvertParameter(), mitk::BaseData::GetPropertyList(), and MITK_WARN.

◆ SetMaximumTreeDepth()

void mitk::VigraRandomForestClassifier::SetMaximumTreeDepth ( int val )

Definition at line 536 of file mitkVigraRandomForestClassifier.cpp.

References mitk::BaseData::GetPropertyList().

Referenced by SetRandomForest().

◆ SetMinimumSplitNodeSize()

void mitk::VigraRandomForestClassifier::SetMinimumSplitNodeSize ( int val )

Definition at line 541 of file mitkVigraRandomForestClassifier.cpp.

References mitk::BaseData::GetPropertyList().

Referenced by SetRandomForest().

◆ SetPrecision()

void mitk::VigraRandomForestClassifier::SetPrecision ( double val )

Definition at line 546 of file mitkVigraRandomForestClassifier.cpp.

References mitk::BaseData::GetPropertyList().

◆ SetRandomForest()

void mitk::VigraRandomForestClassifier::SetRandomForest ( const vigra::RandomForest< int > & rf )

Definition at line 576 of file mitkVigraRandomForestClassifier.cpp.

References SetMaximumTreeDepth(), SetMinimumSplitNodeSize(), SetSamplesPerTree(), SetTreeCount(), and UseSampleWithReplacement().

◆ SetSamplesPerTree()

void mitk::VigraRandomForestClassifier::SetSamplesPerTree ( double val )

Definition at line 551 of file mitkVigraRandomForestClassifier.cpp.

References mitk::BaseData::GetPropertyList().

Referenced by SetRandomForest().

◆ SetTreeCount()

void mitk::VigraRandomForestClassifier::SetTreeCount ( int val )

Definition at line 561 of file mitkVigraRandomForestClassifier.cpp.

References mitk::BaseData::GetPropertyList().

Referenced by SetRandomForest().

◆ SetTreeWeight()

void mitk::VigraRandomForestClassifier::SetTreeWeight	(	int	treeId,
		double	weight
	)

Definition at line 571 of file mitkVigraRandomForestClassifier.cpp.

◆ SetTreeWeights()

void mitk::VigraRandomForestClassifier::SetTreeWeights ( Eigen::MatrixXd weights )

Definition at line 238 of file mitkVigraRandomForestClassifier.cpp.

◆ SetWeightLambda()

void mitk::VigraRandomForestClassifier::SetWeightLambda ( double val )

Definition at line 566 of file mitkVigraRandomForestClassifier.cpp.

References mitk::BaseData::GetPropertyList().

◆ SupportsPointWiseProbability()

bool mitk::VigraRandomForestClassifier::SupportsPointWiseProbability ( )

overridevirtual

SupportsPointWiseProbability.

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

Implements mitk::AbstractClassifier.

Definition at line 113 of file mitkVigraRandomForestClassifier.cpp.

◆ SupportsPointWiseWeight()

bool mitk::VigraRandomForestClassifier::SupportsPointWiseWeight ( )

overridevirtual

SupportsPointWiseWeight.

Returns: True if the classifier supports pointwise weighting else false

Implements mitk::AbstractClassifier.

Definition at line 108 of file mitkVigraRandomForestClassifier.cpp.

◆ Train()

void mitk::VigraRandomForestClassifier::Train	(	const Eigen::MatrixXd &	X,
		const Eigen::MatrixXi &	Y
	)

overridevirtual

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

Parameters

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

Implements mitk::AbstractClassifier.

Definition at line 125 of file mitkVigraRandomForestClassifier.cpp.

References ConvertParameter(), mitk::AbstractClassifier::m_PointWiseWeight, mitk::ThresholdSplit< TColumnDecisionFunctor, TFeatureCalculator, TTag >::SetMaximumTreeDepth(), mitk::ThresholdSplit< TColumnDecisionFunctor, TFeatureCalculator, TTag >::SetPrecision(), mitk::ThresholdSplit< TColumnDecisionFunctor, TFeatureCalculator, TTag >::SetWeights(), mitk::ThresholdSplit< TColumnDecisionFunctor, TFeatureCalculator, TTag >::UsePointBasedWeights(), and mitk::ThresholdSplit< TColumnDecisionFunctor, TFeatureCalculator, TTag >::UseRandomSplit().