Medical Imaging Interaction Toolkit  2018.4.99-3e3f1a6e
Medical Imaging Interaction Toolkit
mitk::VigraRandomForestClassifier Class Reference

#include <mitkVigraRandomForestClassifier.h>

Inheritance diagram for mitk::VigraRandomForestClassifier:
Collaboration diagram for mitk::VigraRandomForestClassifier:

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...
 
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::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::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 ( )

◆ ~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 ( )

◆ GetRandomForest()

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

Definition at line 586 of file mitkVigraRandomForestClassifier.cpp.

◆ GetTreeWeights()

◆ mitkClassMacro()

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

◆ New()

static Pointer mitk::VigraRandomForestClassifier::New ( )
static

◆ 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,Theinput 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)

◆ PrintParameter()

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

◆ 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)

◆ SetRandomForest()

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

◆ 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)

◆ 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

◆ UsePointWiseWeight()

void mitk::VigraRandomForestClassifier::UsePointWiseWeight ( bool  value)
overridevirtual

UsePointWiseWeight.

Parameters
toggleweighting on/off

Reimplemented from mitk::AbstractClassifier.

Definition at line 530 of file mitkVigraRandomForestClassifier.cpp.

References mitk::BaseData::GetPropertyList(), and mitk::AbstractClassifier::UsePointWiseWeight().

◆ UseSampleWithReplacement()

void mitk::VigraRandomForestClassifier::UseSampleWithReplacement ( bool  val)

Definition at line 556 of file mitkVigraRandomForestClassifier.cpp.

References mitk::BaseData::GetPropertyList().

Referenced by SetRandomForest().


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