A class for multivariate principal component analysis. More...

#include <vtkPCAStatistics.h>

Inheritance diagram for vtkPCAStatistics:

Collaboration diagram for vtkPCAStatistics:

Public Types
enum	NormalizationType { NONE , TRIANGLE_SPECIFIED , DIAGONAL_SPECIFIED , DIAGONAL_VARIANCE , NUM_NORMALIZATION_SCHEMES }
	Methods by which the covariance matrix may be normalized. More...

enum	ProjectionType { FULL_BASIS , FIXED_BASIS_SIZE , FIXED_BASIS_ENERGY , NUM_BASIS_SCHEMES }
	These are the enumeration values that SetBasisScheme() accepts and GetBasisScheme returns. More...

typedef vtkMultiCorrelativeStatistics	Superclass

Public Types inherited from vtkMultiCorrelativeStatistics
typedef vtkStatisticsAlgorithm	Superclass

Public Types inherited from vtkStatisticsAlgorithm
enum	InputPorts { INPUT_DATA = 0 , LEARN_PARAMETERS = 1 , INPUT_MODEL = 2 }
	enumeration values to specify input port types More...

enum	OutputIndices { OUTPUT_DATA = 0 , OUTPUT_MODEL = 1 , OUTPUT_TEST = 2 }
	enumeration values to specify output port types More...

typedef vtkTableAlgorithm	Superclass

Public Types inherited from vtkTableAlgorithm
typedef vtkAlgorithm	Superclass

Public Types inherited from vtkAlgorithm
enum	DesiredOutputPrecision { SINGLE_PRECISION , DOUBLE_PRECISION , DEFAULT_PRECISION }
	Values used for setting the desired output precision for various algorithms. More...

typedef vtkObject	Superclass

Public Member Functions
virtual vtkTypeBool	IsA (const char *type)
	Return 1 if this class is the same type of (or a subclass of) the named class.

vtkPCAStatistics *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

bool	SetParameter (const char *parameter, int index, vtkVariant value) override
	A convenience method (in particular for access from other applications) to set parameter values.


virtual void	SetNormalizationScheme (int)
	This determines how (or if) the covariance matrix cov is normalized before PCA.

virtual int	GetNormalizationScheme ()
	This determines how (or if) the covariance matrix cov is normalized before PCA.

virtual void	SetNormalizationSchemeByName (const char *schemeName)
	This determines how (or if) the covariance matrix cov is normalized before PCA.

virtual const char *	GetNormalizationSchemeName (int scheme)
	This determines how (or if) the covariance matrix cov is normalized before PCA.


virtual vtkTable *	GetSpecifiedNormalization ()
	These methods allow you to set/get values used to normalize the covariance matrix before PCA.

virtual void	SetSpecifiedNormalization (vtkTable *)
	These methods allow you to set/get values used to normalize the covariance matrix before PCA.


void	GetEigenvalues (int request, vtkDoubleArray *)
	Get the eigenvalues.

void	GetEigenvalues (vtkDoubleArray *)
	Get the eigenvalues.

double	GetEigenvalue (int request, int i)
	Get the eigenvalues.

double	GetEigenvalue (int i)
	Get the eigenvalues.


void	GetEigenvectors (int request, vtkDoubleArray *eigenvectors)
	Get the eigenvectors.

void	GetEigenvectors (vtkDoubleArray *eigenvectors)
	Get the eigenvectors.

void	GetEigenvector (int i, vtkDoubleArray *eigenvector)
	Get the eigenvectors.

void	GetEigenvector (int request, int i, vtkDoubleArray *eigenvector)
	Get the eigenvectors.


virtual void	SetBasisScheme (int)
	This variable controls the dimensionality of output tuples in Assess operation.

virtual int	GetBasisScheme ()
	This variable controls the dimensionality of output tuples in Assess operation.

virtual const char *	GetBasisSchemeName (int schemeIndex)
	This variable controls the dimensionality of output tuples in Assess operation.

virtual void	SetBasisSchemeByName (const char *schemeName)
	This variable controls the dimensionality of output tuples in Assess operation.


virtual void	SetFixedBasisSize (int)
	The number of basis vectors to use.

virtual int	GetFixedBasisSize ()
	The number of basis vectors to use.


virtual void	SetFixedBasisEnergy (double)
	The minimum energy the new basis should use, as a fraction.

virtual double	GetFixedBasisEnergy ()
	The minimum energy the new basis should use, as a fraction.

Public Member Functions inherited from vtkMultiCorrelativeStatistics
virtual vtkTypeBool	IsA (const char *type)
	Return 1 if this class is the same type of (or a subclass of) the named class.

vtkMultiCorrelativeStatistics *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

void	Aggregate (vtkDataObjectCollection , vtkMultiBlockDataSet ) override
	Given a collection of models, calculate aggregate model.

virtual void	SetMedianAbsoluteDeviation (bool)
	If set to true, the covariance matrix is replaced by the Median Absolute Deviation matrix.

virtual bool	GetMedianAbsoluteDeviation ()
	If set to true, the covariance matrix is replaced by the Median Absolute Deviation matrix.

virtual void	MedianAbsoluteDeviationOn ()
	If set to true, the covariance matrix is replaced by the Median Absolute Deviation matrix.

virtual void	MedianAbsoluteDeviationOff ()
	If set to true, the covariance matrix is replaced by the Median Absolute Deviation matrix.

virtual void	SetGhostsToSkip (unsigned char)
	If there is a ghost array in the input, then ghosts matching `GhostsToSkip` mask will be skipped.

virtual unsigned char	GetGhostsToSkip ()
	If there is a ghost array in the input, then ghosts matching `GhostsToSkip` mask will be skipped.

Public Member Functions inherited from vtkStatisticsAlgorithm
virtual vtkTypeBool	IsA (const char *type)
	Return 1 if this class is the same type of (or a subclass of) the named class.

vtkStatisticsAlgorithm *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

virtual void	SetLearnOptionParameterConnection (vtkAlgorithmOutput *params)
	A convenience method for setting learn input parameters (if one is expected or allowed).

virtual void	SetLearnOptionParameters (vtkDataObject *params)
	A convenience method for setting learn input parameters (if one is expected or allowed).

virtual void	SetInputModelConnection (vtkAlgorithmOutput *model)
	A convenience method for setting the input model connection (if one is expected or allowed).

virtual void	SetInputModel (vtkDataObject *model)
	A convenience method for setting the input model (if one is expected or allowed).

virtual void	SetColumnStatus (const char *namCol, int status)
	Add or remove a column from the current analysis request.

virtual void	ResetAllColumnStates ()
	Set the status of each and every column in the current request to OFF (0).

virtual int	RequestSelectedColumns ()
	Use the current column status values to produce a new request for statistics to be produced when RequestData() is called.

virtual void	ResetRequests ()
	Empty the list of current requests.

virtual vtkIdType	GetNumberOfRequests ()
	Return the number of requests.

virtual vtkIdType	GetNumberOfColumnsForRequest (vtkIdType request)
	Return the number of columns for a given request.

virtual const char *	GetColumnForRequest (vtkIdType r, vtkIdType c)
	Provide the name of the c-th column for the r-th request.

virtual int	GetColumnForRequest (vtkIdType r, vtkIdType c, vtkStdString &columnName)

void	AddColumn (const char *namCol)
	Convenience method to create a request with a single column name `namCol` in a single call; this is the preferred method to select columns, ensuring selection consistency (a single column per request).

void	AddColumnPair (const char namColX, const char namColY)
	Convenience method to create a request with a single column name pair (`namColX`, `namColY`) in a single call; this is the preferred method to select columns pairs, ensuring selection consistency (a pair of columns per request).

virtual bool	SetParameter (const char *parameter, int index, vtkVariant value)
	A convenience method (in particular for access from other applications) to set parameter values of Learn mode.

virtual void	Aggregate (vtkDataObjectCollection , vtkMultiBlockDataSet )=0
	Given a collection of models, calculate aggregate model.

virtual void	SetLearnOption (bool)
	Set/Get the Learn operation.

virtual bool	GetLearnOption ()
	Set/Get the Learn operation.

virtual void	SetDeriveOption (bool)
	Set/Get the Derive operation.

virtual bool	GetDeriveOption ()
	Set/Get the Derive operation.

virtual void	SetAssessOption (bool)
	Set/Get the Assess operation.

virtual bool	GetAssessOption ()
	Set/Get the Assess operation.

virtual void	SetTestOption (bool)
	Set/Get the Test operation.

virtual bool	GetTestOption ()
	Set/Get the Test operation.

virtual void	SetNumberOfPrimaryTables (vtkIdType)
	Set/Get the number of tables in the primary model.

virtual vtkIdType	GetNumberOfPrimaryTables ()
	Set/Get the number of tables in the primary model.

virtual void	SetAssessNames (vtkStringArray *)
	Set/get assessment names.

virtual vtkStringArray *	GetAssessNames ()
	Set/get assessment names.

Public Member Functions inherited from vtkTableAlgorithm
virtual vtkTypeBool	IsA (const char *type)
	Return 1 if this class is the same type of (or a subclass of) the named class.

vtkTableAlgorithm *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

vtkTypeBool	ProcessRequest (vtkInformation , vtkInformationVector , vtkInformationVector ) override
	see vtkAlgorithm for details

vtkTable *	GetOutput ()
	Get the output data object for a port on this algorithm.

vtkTable *	GetOutput (int index)

void	SetInputData (vtkDataObject *obj)
	Assign a data object as input.

void	SetInputData (int index, vtkDataObject *obj)

Public Member Functions inherited from vtkAlgorithm
virtual vtkTypeBool	IsA (const char *type)
	Return 1 if this class is the same type of (or a subclass of) the named class.

vtkAlgorithm *	NewInstance () const

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

vtkTypeBool	HasExecutive ()
	Check whether this algorithm has an assigned executive.

vtkExecutive *	GetExecutive ()
	Get this algorithm's executive.

virtual void	SetExecutive (vtkExecutive *executive)
	Set this algorithm's executive.

virtual vtkTypeBool	ProcessRequest (vtkInformation request, vtkInformationVector inInfo, vtkInformationVector outInfo)
	Upstream/Downstream requests form the generalized interface through which executives invoke a algorithm's functionality.

vtkTypeBool	ProcessRequest (vtkInformation request, vtkCollection inInfo, vtkInformationVector *outInfo)
	Version of ProcessRequest() that is wrapped.

virtual int	ComputePipelineMTime (vtkInformation request, vtkInformationVector inInfoVec, vtkInformationVector outInfoVec, int requestFromOutputPort, vtkMTimeType *mtime)
	A special version of ProcessRequest meant specifically for the pipeline modified time request.

virtual int	ModifyRequest (vtkInformation *request, int when)
	This method gives the algorithm a chance to modify the contents of a request before or after (specified in the when argument) it is forwarded.

vtkInformation *	GetInputPortInformation (int port)
	Get the information object associated with an input port.

vtkInformation *	GetOutputPortInformation (int port)
	Get the information object associated with an output port.

int	GetNumberOfInputPorts ()
	Get the number of input ports used by the algorithm.

int	GetNumberOfOutputPorts ()
	Get the number of output ports provided by the algorithm.

void	SetAbortExecuteAndUpdateTime ()
	Set AbortExecute Flag and update LastAbortTime.

void	UpdateProgress (double amount)
	Update the progress of the process object.

bool	CheckAbort ()
	Checks to see if this filter should abort.

vtkInformation *	GetInputArrayInformation (int idx)
	Get the info object for the specified input array to this algorithm.

void	RemoveAllInputs ()
	Remove all the input data.

vtkDataObject *	GetOutputDataObject (int port)
	Get the data object that will contain the algorithm output for the given port.

vtkDataObject *	GetInputDataObject (int port, int connection)
	Get the data object that will contain the algorithm input for the given port and given connection.

virtual void	RemoveInputConnection (int port, vtkAlgorithmOutput *input)
	Remove a connection from the given input port index.

virtual void	RemoveInputConnection (int port, int idx)
	Remove a connection given by index idx.

virtual void	RemoveAllInputConnections (int port)
	Removes all input connections.

virtual void	SetInputDataObject (int port, vtkDataObject *data)
	Sets the data-object as an input on the given port index.

virtual void	SetInputDataObject (vtkDataObject *data)

virtual void	AddInputDataObject (int port, vtkDataObject *data)
	Add the data-object as an input to this given port.

virtual void	AddInputDataObject (vtkDataObject *data)

vtkAlgorithmOutput *	GetOutputPort (int index)
	Get a proxy object corresponding to the given output port of this algorithm.

vtkAlgorithmOutput *	GetOutputPort ()

int	GetNumberOfInputConnections (int port)
	Get the number of inputs currently connected to a port.

int	GetTotalNumberOfInputConnections ()
	Get the total number of inputs for this algorithm.

vtkAlgorithmOutput *	GetInputConnection (int port, int index)
	Get the algorithm output port connected to an input port.

vtkAlgorithm *	GetInputAlgorithm (int port, int index, int &algPort)
	Returns the algorithm and the output port index of that algorithm connected to a port-index pair.

vtkAlgorithm *	GetInputAlgorithm (int port, int index)
	Returns the algorithm connected to a port-index pair.

vtkAlgorithm *	GetInputAlgorithm ()
	Equivalent to GetInputAlgorithm(0, 0).

vtkExecutive *	GetInputExecutive (int port, int index)
	Returns the executive associated with a particular input connection.

vtkExecutive *	GetInputExecutive ()
	Equivalent to GetInputExecutive(0, 0)

vtkInformation *	GetInputInformation (int port, int index)
	Return the information object that is associated with a particular input connection.

vtkInformation *	GetInputInformation ()
	Equivalent to GetInputInformation(0, 0)

vtkInformation *	GetOutputInformation (int port)
	Return the information object that is associated with a particular output port.

virtual vtkTypeBool	Update (int port, vtkInformationVector *requests)
	This method enables the passing of data requests to the algorithm to be used during execution (in addition to bringing a particular port up-to-date).

virtual vtkTypeBool	Update (vtkInformation *requests)
	Convenience method to update an algorithm after passing requests to its first output port.

virtual int	UpdatePiece (int piece, int numPieces, int ghostLevels, const int extents[6]=nullptr)
	Convenience method to update an algorithm after passing requests to its first output port.

virtual VTK_UNBLOCKTHREADS int	UpdateExtent (const int extents[6])
	Convenience method to update an algorithm after passing requests to its first output port.

virtual VTK_UNBLOCKTHREADS int	UpdateTimeStep (double time, int piece=-1, int numPieces=1, int ghostLevels=0, const int extents[6]=nullptr)
	Convenience method to update an algorithm after passing requests to its first output port.

virtual VTK_UNBLOCKTHREADS void	UpdateInformation ()
	Bring the algorithm's information up-to-date.

virtual void	UpdateDataObject ()
	Create output object(s).

virtual void	PropagateUpdateExtent ()
	Propagate meta-data upstream.

virtual VTK_UNBLOCKTHREADS void	UpdateWholeExtent ()
	Bring this algorithm's outputs up-to-date.

void	ConvertTotalInputToPortConnection (int ind, int &port, int &conn)
	Convenience routine to convert from a linear ordering of input connections to a port/connection pair.

void	RemoveNoPriorTemporalAccessInformationKey ()
	Removes any information key `vtkStreamingDemandDrivenPipeline::NO_PRIOR_TEMPORAL_ACCESS()` to all output ports of this `vtkAlgorithm`.

virtual vtkInformation *	GetInformation ()
	Set/Get the information object associated with this algorithm.

virtual void	SetInformation (vtkInformation *)
	Set/Get the information object associated with this algorithm.

bool	UsesGarbageCollector () const override
	Participate in garbage collection.

virtual void	SetAbortExecute (vtkTypeBool)
	Set/Get the AbortExecute flag for the process object.

virtual vtkTypeBool	GetAbortExecute ()
	Set/Get the AbortExecute flag for the process object.

virtual void	AbortExecuteOn ()
	Set/Get the AbortExecute flag for the process object.

virtual void	AbortExecuteOff ()
	Set/Get the AbortExecute flag for the process object.

virtual double	GetProgress ()
	Get the execution progress of a process object.

void	SetContainerAlgorithm (vtkAlgorithm *containerAlg)
	Set/get a Container algorithm for this algorithm.

vtkAlgorithm *	GetContainerAlgorithm ()
	Set/get a Container algorithm for this algorithm.

virtual void	SetAbortOutput (bool)
	Set/Get an internal variable used to communicate between the algorithm and executive.

virtual bool	GetAbortOutput ()
	Set/Get an internal variable used to communicate between the algorithm and executive.

void	SetProgressShiftScale (double shift, double scale)
	Specify the shift and scale values to use to apply to the progress amount when `UpdateProgress` is called.

virtual double	GetProgressShift ()
	Specify the shift and scale values to use to apply to the progress amount when `UpdateProgress` is called.

virtual double	GetProgressScale ()
	Specify the shift and scale values to use to apply to the progress amount when `UpdateProgress` is called.

void	SetProgressText (const char *ptext)
	Set the current text message associated with the progress state.

virtual char *	GetProgressText ()
	Set the current text message associated with the progress state.

virtual unsigned long	GetErrorCode ()
	The error code contains a possible error that occurred while reading or writing the file.

void	SetInputArrayToProcess (const char *name, int fieldAssociation)
	Set the input data arrays that this algorithm will process.

virtual void	SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, const char *name)
	Set the input data arrays that this algorithm will process.

virtual void	SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, int fieldAttributeType)
	Set the input data arrays that this algorithm will process.

virtual void	SetInputArrayToProcess (int idx, vtkInformation *info)
	Set the input data arrays that this algorithm will process.

virtual void	SetInputArrayToProcess (int idx, int port, int connection, const char fieldAssociation, const char attributeTypeorName)
	Set the input data arrays that this algorithm will process.

virtual void	SetInputConnection (int port, vtkAlgorithmOutput *input)
	Set the connection for the given input port index.

virtual void	SetInputConnection (vtkAlgorithmOutput *input)
	Set the connection for the given input port index.

virtual void	AddInputConnection (int port, vtkAlgorithmOutput *input)
	Add a connection to the given input port index.

virtual void	AddInputConnection (vtkAlgorithmOutput *input)
	Add a connection to the given input port index.

virtual VTK_UNBLOCKTHREADS void	Update (int port)
	Bring this algorithm's outputs up-to-date.

virtual VTK_UNBLOCKTHREADS void	Update ()
	Bring this algorithm's outputs up-to-date.

virtual void	SetReleaseDataFlag (vtkTypeBool)
	Turn release data flag on or off for all output ports.

virtual vtkTypeBool	GetReleaseDataFlag ()
	Turn release data flag on or off for all output ports.

void	ReleaseDataFlagOn ()
	Turn release data flag on or off for all output ports.

void	ReleaseDataFlagOff ()
	Turn release data flag on or off for all output ports.

int	UpdateExtentIsEmpty (vtkInformation pinfo, vtkDataObject output)
	This detects when the UpdateExtent will generate no data This condition is satisfied when the UpdateExtent has zero volume (0,-1,...) or the UpdateNumberOfPieces is 0.

int	UpdateExtentIsEmpty (vtkInformation *pinfo, int extentType)
	This detects when the UpdateExtent will generate no data This condition is satisfied when the UpdateExtent has zero volume (0,-1,...) or the UpdateNumberOfPieces is 0.

int *	GetUpdateExtent ()
	These functions return the update extent for output ports that use 3D extents.

int *	GetUpdateExtent (int port)
	These functions return the update extent for output ports that use 3D extents.

void	GetUpdateExtent (int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)
	These functions return the update extent for output ports that use 3D extents.

void	GetUpdateExtent (int port, int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)
	These functions return the update extent for output ports that use 3D extents.

void	GetUpdateExtent (int extent[6])
	These functions return the update extent for output ports that use 3D extents.

void	GetUpdateExtent (int port, int extent[6])
	These functions return the update extent for output ports that use 3D extents.

int	GetUpdatePiece ()
	These functions return the update extent for output ports that use piece extents.

int	GetUpdatePiece (int port)
	These functions return the update extent for output ports that use piece extents.

int	GetUpdateNumberOfPieces ()
	These functions return the update extent for output ports that use piece extents.

int	GetUpdateNumberOfPieces (int port)
	These functions return the update extent for output ports that use piece extents.

int	GetUpdateGhostLevel ()
	These functions return the update extent for output ports that use piece extents.

int	GetUpdateGhostLevel (int port)
	These functions return the update extent for output ports that use piece extents.

void	SetProgressObserver (vtkProgressObserver *)
	If an ProgressObserver is set, the algorithm will report progress through it rather than directly.

virtual vtkProgressObserver *	GetProgressObserver ()
	If an ProgressObserver is set, the algorithm will report progress through it rather than directly.

void	SetNoPriorTemporalAccessInformationKey (int key)
	Set to all output ports of this algorithm the information key `vtkStreamingDemandDrivenPipeline::NO_PRIOR_TEMPORAL_ACCESS()`.

void	SetNoPriorTemporalAccessInformationKey ()
	Set to all output ports of this algorithm the information key `vtkStreamingDemandDrivenPipeline::NO_PRIOR_TEMPORAL_ACCESS()`.

Public Member Functions inherited from vtkObject
	vtkBaseTypeMacro (vtkObject, vtkObjectBase)

virtual void	DebugOn ()
	Turn debugging output on.

virtual void	DebugOff ()
	Turn debugging output off.

bool	GetDebug ()
	Get the value of the debug flag.

void	SetDebug (bool debugFlag)
	Set the value of the debug flag.

virtual void	Modified ()
	Update the modification time for this object.

virtual vtkMTimeType	GetMTime ()
	Return this object's modified time.

void	PrintSelf (ostream &os, vtkIndent indent) override
	Methods invoked by print to print information about the object including superclasses.

void	RemoveObserver (unsigned long tag)

void	RemoveObservers (unsigned long event)

void	RemoveObservers (const char *event)

void	RemoveAllObservers ()

vtkTypeBool	HasObserver (unsigned long event)

vtkTypeBool	HasObserver (const char *event)

vtkTypeBool	InvokeEvent (unsigned long event)

vtkTypeBool	InvokeEvent (const char *event)

std::string	GetObjectDescription () const override
	The object description printed in messages and PrintSelf output.

unsigned long	AddObserver (unsigned long event, vtkCommand *, float priority=0.0f)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

unsigned long	AddObserver (const char event, vtkCommand , float priority=0.0f)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

vtkCommand *	GetCommand (unsigned long tag)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

void	RemoveObserver (vtkCommand *)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

void	RemoveObservers (unsigned long event, vtkCommand *)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

void	RemoveObservers (const char event, vtkCommand )
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

vtkTypeBool	HasObserver (unsigned long event, vtkCommand *)
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

vtkTypeBool	HasObserver (const char event, vtkCommand )
	Allow people to add/remove/invoke observers (callbacks) to any VTK object.

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, void(T::*callback)(), float priority=0.0f)
	Overloads to AddObserver that allow developers to add class member functions as callbacks for events.

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, void(T::callback)(vtkObject , unsigned long, void *), float priority=0.0f)
	Overloads to AddObserver that allow developers to add class member functions as callbacks for events.

template<class U , class T >
unsigned long	AddObserver (unsigned long event, U observer, bool(T::callback)(vtkObject , unsigned long, void *), float priority=0.0f)
	Allow user to set the AbortFlagOn() with the return value of the callback method.

vtkTypeBool	InvokeEvent (unsigned long event, void *callData)
	This method invokes an event and return whether the event was aborted or not.

vtkTypeBool	InvokeEvent (const char event, void callData)
	This method invokes an event and return whether the event was aborted or not.

virtual void	SetObjectName (const std::string &objectName)
	Set/get the name of this object for reporting purposes.

virtual std::string	GetObjectName () const
	Set/get the name of this object for reporting purposes.

Public Member Functions inherited from vtkObjectBase
const char *	GetClassName () const
	Return the class name as a string.

virtual std::string	GetObjectDescription () const
	The object description printed in messages and PrintSelf output.

virtual vtkTypeBool	IsA (const char *name)
	Return 1 if this class is the same type of (or a subclass of) the named class.

virtual vtkIdType	GetNumberOfGenerationsFromBase (const char *name)
	Given the name of a base class of this class type, return the distance of inheritance between this class type and the named class (how many generations of inheritance are there between this class and the named class).

virtual void	Delete ()
	Delete a VTK object.

virtual void	FastDelete ()
	Delete a reference to this object.

void	InitializeObjectBase ()

void	Print (ostream &os)
	Print an object to an ostream.

void	Register (vtkObjectBase *o)
	Increase the reference count (mark as used by another object).

virtual void	UnRegister (vtkObjectBase *o)
	Decrease the reference count (release by another object).

int	GetReferenceCount ()
	Return the current reference count of this object.

void	SetReferenceCount (int)
	Sets the reference count.

bool	GetIsInMemkind () const
	A local state flag that remembers whether this object lives in the normal or extended memory space.

virtual void	PrintHeader (ostream &os, vtkIndent indent)
	Methods invoked by print to print information about the object including superclasses.

virtual void	PrintTrailer (ostream &os, vtkIndent indent)
	Methods invoked by print to print information about the object including superclasses.

Static Public Member Functions
static vtkTypeBool	IsTypeOf (const char *type)

static vtkPCAStatistics *	SafeDownCast (vtkObjectBase *o)

static vtkPCAStatistics *	New ()

Static Public Member Functions inherited from vtkMultiCorrelativeStatistics
static vtkTypeBool	IsTypeOf (const char *type)

static vtkMultiCorrelativeStatistics *	SafeDownCast (vtkObjectBase *o)

static vtkMultiCorrelativeStatistics *	New ()

Static Public Member Functions inherited from vtkStatisticsAlgorithm
static vtkTypeBool	IsTypeOf (const char *type)

static vtkStatisticsAlgorithm *	SafeDownCast (vtkObjectBase *o)

Static Public Member Functions inherited from vtkTableAlgorithm
static vtkTableAlgorithm *	New ()

static vtkTypeBool	IsTypeOf (const char *type)

static vtkTableAlgorithm *	SafeDownCast (vtkObjectBase *o)

Static Public Member Functions inherited from vtkAlgorithm
static vtkAlgorithm *	New ()

static vtkTypeBool	IsTypeOf (const char *type)

static vtkAlgorithm *	SafeDownCast (vtkObjectBase *o)

static vtkInformationIntegerKey *	INPUT_IS_OPTIONAL ()
	Keys used to specify input port requirements.

static vtkInformationIntegerKey *	INPUT_IS_REPEATABLE ()

static vtkInformationInformationVectorKey *	INPUT_REQUIRED_FIELDS ()

static vtkInformationStringVectorKey *	INPUT_REQUIRED_DATA_TYPE ()

static vtkInformationInformationVectorKey *	INPUT_ARRAYS_TO_PROCESS ()

static vtkInformationIntegerKey *	INPUT_PORT ()

static vtkInformationIntegerKey *	INPUT_CONNECTION ()

static vtkInformationIntegerKey *	CAN_PRODUCE_SUB_EXTENT ()
	This key tells the executive that a particular output port is capable of producing an arbitrary subextent of the whole extent.

static vtkInformationIntegerKey *	CAN_HANDLE_PIECE_REQUEST ()
	Key that tells the pipeline that a particular algorithm can or cannot handle piece request.

static vtkInformationIntegerKey *	ABORTED ()

static void	SetDefaultExecutivePrototype (vtkExecutive *proto)
	If the DefaultExecutivePrototype is set, a copy of it is created in CreateDefaultExecutive() using NewInstance().

Static Public Member Functions inherited from vtkObject
static vtkObject *	New ()
	Create an object with Debug turned off, modified time initialized to zero, and reference counting on.

static void	BreakOnError ()
	This method is called when vtkErrorMacro executes.

static void	SetGlobalWarningDisplay (vtkTypeBool val)
	This is a global flag that controls whether any debug, warning or error messages are displayed.

static void	GlobalWarningDisplayOn ()
	This is a global flag that controls whether any debug, warning or error messages are displayed.

static void	GlobalWarningDisplayOff ()
	This is a global flag that controls whether any debug, warning or error messages are displayed.

static vtkTypeBool	GetGlobalWarningDisplay ()
	This is a global flag that controls whether any debug, warning or error messages are displayed.

Static Public Member Functions inherited from vtkObjectBase
static vtkTypeBool	IsTypeOf (const char *name)
	Return 1 if this class type is the same type of (or a subclass of) the named class.

static vtkIdType	GetNumberOfGenerationsFromBaseType (const char *name)
	Given a the name of a base class of this class type, return the distance of inheritance between this class type and the named class (how many generations of inheritance are there between this class and the named class).

static vtkObjectBase *	New ()
	Create an object with Debug turned off, modified time initialized to zero, and reference counting on.

static void	SetMemkindDirectory (const char *directoryname)
	The name of a directory, ideally mounted -o dax, to memory map an extended memory space within.

static bool	GetUsingMemkind ()
	A global state flag that controls whether vtkObjects are constructed in the usual way (the default) or within the extended memory space.

Protected Member Functions
virtual vtkObjectBase *	NewInstanceInternal () const

	vtkPCAStatistics ()

	~vtkPCAStatistics () override

int	FillInputPortInformation (int port, vtkInformation *info) override
	This algorithm accepts a vtkTable containing normalization values for its fourth input (port 3).

void	Derive (vtkMultiBlockDataSet *) override
	Execute the calculations required by the Derive option.

void	Test (vtkTable , vtkMultiBlockDataSet , vtkTable *) override
	Execute the calculations required by the Test option.

void	Assess (vtkTable , vtkMultiBlockDataSet , vtkTable *) override
	Execute the calculations required by the Assess option.

virtual vtkDoubleArray *	CalculatePValues (vtkIdTypeArray , vtkDoubleArray )
	Calculate p-value.

void	SelectAssessFunctor (vtkTable inData, vtkDataObject inMeta, vtkStringArray rowNames, AssessFunctor &dfunc) override
	Provide the appropriate assessment functor.

Protected Member Functions inherited from vtkMultiCorrelativeStatistics
virtual vtkObjectBase *	NewInstanceInternal () const

	vtkMultiCorrelativeStatistics ()

	~vtkMultiCorrelativeStatistics () override

int	RequestData (vtkInformation , vtkInformationVector , vtkInformationVector ) override
	This is called by the superclass.

void	Learn (vtkTable , vtkTable , vtkMultiBlockDataSet *) override
	Execute the calculations required by the Learn option.

void	Derive (vtkMultiBlockDataSet *) override
	Execute the calculations required by the Derive option.

void	Assess (vtkTable , vtkMultiBlockDataSet , vtkTable *) override
	Execute the calculations required by the Assess option.

void	Test (vtkTable , vtkMultiBlockDataSet , vtkTable *) override
	Execute the calculations required by the Test option.

void	SelectAssessFunctor (vtkTable inData, vtkDataObject inMeta, vtkStringArray rowNames, AssessFunctor &dfunc) override
	Provide the appropriate assessment functor.

virtual void	ComputeMedian (vtkTable inData, vtkTable outData)
	Computes the median of inData with vtkOrderStatistics.

virtual vtkOrderStatistics *	CreateOrderStatisticsInstance ()
	Return a new vtkOrderStatistics instance.

Protected Member Functions inherited from vtkStatisticsAlgorithm
virtual vtkObjectBase *	NewInstanceInternal () const

	vtkStatisticsAlgorithm ()

	~vtkStatisticsAlgorithm () override

int	FillInputPortInformation (int port, vtkInformation *info) override
	Fill the input port information objects for this algorithm.

int	FillOutputPortInformation (int port, vtkInformation *info) override
	Fill the output port information objects for this algorithm.

int	RequestData (vtkInformation , vtkInformationVector , vtkInformationVector ) override
	This is called by the superclass.

virtual void	Learn (vtkTable , vtkTable , vtkMultiBlockDataSet *)=0
	Execute the calculations required by the Learn option, given some input Data.

virtual void	Derive (vtkMultiBlockDataSet *)=0
	Execute the calculations required by the Derive option.

virtual void	Assess (vtkTable , vtkMultiBlockDataSet , vtkTable *)=0
	Execute the calculations required by the Assess option.

void	Assess (vtkTable , vtkMultiBlockDataSet , vtkTable *, int)
	A convenience implementation for generic assessment with variable number of variables.

virtual void	Test (vtkTable , vtkMultiBlockDataSet , vtkTable *)=0
	Execute the calculations required by the Test option.

virtual void	SelectAssessFunctor (vtkTable outData, vtkDataObject inMeta, vtkStringArray rowNames, AssessFunctor &dfunc)=0
	A pure virtual method to select the appropriate assessment functor.

Protected Member Functions inherited from vtkTableAlgorithm
virtual vtkObjectBase *	NewInstanceInternal () const

	vtkTableAlgorithm ()

	~vtkTableAlgorithm () override

virtual int	RequestInformation (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)

virtual int	RequestData (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector)
	This is called by the superclass.

virtual int	RequestUpdateExtent (vtkInformation , vtkInformationVector , vtkInformationVector )
	This is called by the superclass.

virtual int	RequestUpdateTime (vtkInformation , vtkInformationVector , vtkInformationVector )

int	FillOutputPortInformation (int port, vtkInformation *info) override
	Fill the output port information objects for this algorithm.

int	FillInputPortInformation (int port, vtkInformation *info) override
	Fill the input port information objects for this algorithm.

Protected Member Functions inherited from vtkAlgorithm
virtual vtkObjectBase *	NewInstanceInternal () const

	vtkAlgorithm ()

	~vtkAlgorithm () override

bool	CheckUpstreamAbort ()
	Checks to see if an upstream filter has been aborted.

virtual int	FillInputPortInformation (int port, vtkInformation *info)
	Fill the input port information objects for this algorithm.

virtual int	FillOutputPortInformation (int port, vtkInformation *info)
	Fill the output port information objects for this algorithm.

virtual void	SetNumberOfInputPorts (int n)
	Set the number of input ports used by the algorithm.

virtual void	SetNumberOfOutputPorts (int n)
	Set the number of output ports provided by the algorithm.

int	InputPortIndexInRange (int index, const char *action)

int	OutputPortIndexInRange (int index, const char *action)

int	GetInputArrayAssociation (int idx, vtkInformationVector **inputVector)
	Get the association of the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass.

vtkInformation *	GetInputArrayFieldInformation (int idx, vtkInformationVector **inputVector)
	This method takes in an index (as specified in SetInputArrayToProcess) and a pipeline information vector.

virtual vtkExecutive *	CreateDefaultExecutive ()
	Create a default executive.

void	ReportReferences (vtkGarbageCollector *) override

virtual void	SetNthInputConnection (int port, int index, vtkAlgorithmOutput *input)
	Replace the Nth connection on the given input port.

virtual void	SetNumberOfInputConnections (int port, int n)
	Set the number of input connections on the given input port.

void	SetInputDataInternal (int port, vtkDataObject *input)
	These methods are used by subclasses to implement methods to set data objects directly as input.

void	AddInputDataInternal (int port, vtkDataObject *input)

int	GetInputArrayAssociation (int idx, int connection, vtkInformationVector **inputVector)
	Filters that have multiple connections on one port can use this signature.

int	GetInputArrayAssociation (int idx, vtkDataObject *input)
	Filters that have multiple connections on one port can use this signature.

vtkDataArray *	GetInputArrayToProcess (int idx, vtkInformationVector **inputVector)
	Get the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass.

vtkDataArray *	GetInputArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
	Get the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass.

vtkDataArray *	GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
	Filters that have multiple connections on one port can use this signature.

vtkDataArray *	GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
	Filters that have multiple connections on one port can use this signature.

vtkDataArray *	GetInputArrayToProcess (int idx, vtkDataObject *input)
	Filters that have multiple connections on one port can use this signature.

vtkDataArray *	GetInputArrayToProcess (int idx, vtkDataObject *input, int &association)
	Filters that have multiple connections on one port can use this signature.

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector)
	Get the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass.

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
	Get the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass.

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
	Filters that have multiple connections on one port can use this signature.

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
	Filters that have multiple connections on one port can use this signature.

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkDataObject *input)
	Filters that have multiple connections on one port can use this signature.

vtkAbstractArray *	GetInputAbstractArrayToProcess (int idx, vtkDataObject *input, int &association)
	Filters that have multiple connections on one port can use this signature.

virtual void	SetErrorCode (unsigned long)
	The error code contains a possible error that occurred while reading or writing the file.

Protected Member Functions inherited from vtkObject
	vtkObject ()

	~vtkObject () override

void	RegisterInternal (vtkObjectBase *, vtkTypeBool check) override

void	UnRegisterInternal (vtkObjectBase *, vtkTypeBool check) override

void	InternalGrabFocus (vtkCommand mouseEvents, vtkCommand keypressEvents=nullptr)
	These methods allow a command to exclusively grab all events.

void	InternalReleaseFocus ()
	These methods allow a command to exclusively grab all events.

Protected Member Functions inherited from vtkObjectBase
	vtkObjectBase ()

virtual	~vtkObjectBase ()

virtual void	RegisterInternal (vtkObjectBase *, vtkTypeBool check)

virtual void	UnRegisterInternal (vtkObjectBase *, vtkTypeBool check)

virtual void	ReportReferences (vtkGarbageCollector *)

virtual void	ObjectFinalize ()

	vtkObjectBase (const vtkObjectBase &)

void	operator= (const vtkObjectBase &)

Protected Attributes
int	NormalizationScheme

int	BasisScheme

int	FixedBasisSize

double	FixedBasisEnergy

Protected Attributes inherited from vtkMultiCorrelativeStatistics
bool	MedianAbsoluteDeviation

vtkIdType	NumberOfGhosts
	Storing the number of ghosts in the input to avoid computing this value multiple times.

unsigned char	GhostsToSkip

Protected Attributes inherited from vtkStatisticsAlgorithm
vtkIdType	NumberOfPrimaryTables

bool	LearnOption

bool	DeriveOption

bool	AssessOption

bool	TestOption

vtkStringArray *	AssessNames

vtkStatisticsAlgorithmPrivate *	Internals

Protected Attributes inherited from vtkAlgorithm
vtkTimeStamp	LastAbortCheckTime

vtkInformation *	Information

double	Progress

char *	ProgressText

vtkProgressObserver *	ProgressObserver

unsigned long	ErrorCode
	The error code contains a possible error that occurred while reading or writing the file.

Protected Attributes inherited from vtkObject
bool	Debug

vtkTimeStamp	MTime

vtkSubjectHelper *	SubjectHelper

std::string	ObjectName

Protected Attributes inherited from vtkObjectBase
std::atomic< int32_t >	ReferenceCount

vtkWeakPointerBase **	WeakPointers

Static Protected Attributes
static const char *	BasisSchemeEnumNames [NUM_BASIS_SCHEMES+1]

static const char *	NormalizationSchemeEnumNames [NUM_NORMALIZATION_SCHEMES+1]

Static Protected Attributes inherited from vtkAlgorithm
static vtkTimeStamp	LastAbortTime

static vtkExecutive *	DefaultExecutivePrototype

Additional Inherited Members
Public Attributes inherited from vtkAlgorithm
std::atomic< vtkTypeBool >	AbortExecute

Static Protected Member Functions inherited from vtkAlgorithm
static vtkInformationIntegerKey *	PORT_REQUIREMENTS_FILLED ()

Static Protected Member Functions inherited from vtkObjectBase
static vtkMallocingFunction	GetCurrentMallocFunction ()

static vtkReallocingFunction	GetCurrentReallocFunction ()

static vtkFreeingFunction	GetCurrentFreeFunction ()

static vtkFreeingFunction	GetAlternateFreeFunction ()

Detailed Description

A class for multivariate principal component analysis.

This class derives from the multi-correlative statistics algorithm and uses the covariance matrix and Cholesky decomposition computed by it. However, when it finalizes the statistics in learn operation, the PCA class computes the SVD of the covariance matrix in order to obtain its eigenvectors.

In the assess operation, the input data are

projected into the basis defined by the eigenvectors,
the energy associated with each datum is computed,
or some combination thereof. Additionally, the user may specify some threshold energy or eigenvector entry below which the basis is truncated. This allows projection into a lower-dimensional state while minimizing (in a least squares sense) the projection error.

In the test operation, a Jarque-Bera-Srivastava test of n-d normality is performed.

The Robust PCA can be computed by using the median instead of the mean, and the MAD matrix (Median Absolute Deviation) instead of the covariance matrix. This can be done by activating the MedianAbsoluteDeviation boolean (declared in the superclass).

Thanks:: Thanks to David Thompson, Philippe Pebay and Jackson Mayo from Sandia National Laboratories for implementing this class. Updated by Philippe Pebay, Kitware SAS 2012 Updated by Tristan Coulange and Joachim Pouderoux, Kitware SAS 2013

Online Examples:

PCADemo

PCAStatistics

Tests:: vtkPCAStatistics (Tests)

Definition at line 79 of file vtkPCAStatistics.h.

Member Typedef Documentation

◆ Superclass

typedef vtkMultiCorrelativeStatistics vtkPCAStatistics::Superclass

Definition at line 82 of file vtkPCAStatistics.h.

Member Enumeration Documentation

◆ NormalizationType

enum vtkPCAStatistics::NormalizationType

Methods by which the covariance matrix may be normalized.

Enumerator
NONE	The covariance matrix should be used as computed.
TRIANGLE_SPECIFIED	Normalize cov(i,j) by V(i,j) where V is supplied by the user.
DIAGONAL_SPECIFIED	Normalize cov(i,j) by sqrt(V(i)*V(j)) where V is supplied by the user.
DIAGONAL_VARIANCE	Normalize cov(i,j) by sqrt(cov(i,i)*cov(j,j)).
NUM_NORMALIZATION_SCHEMES	The number of normalization schemes.

Definition at line 89 of file vtkPCAStatistics.h.

◆ ProjectionType

enum vtkPCAStatistics::ProjectionType

These are the enumeration values that SetBasisScheme() accepts and GetBasisScheme returns.

Enumerator
FULL_BASIS	Use all entries in the basis matrix.
FIXED_BASIS_SIZE	Use the first N entries in the basis matrix.
FIXED_BASIS_ENERGY	Use consecutive basis matrix entries whose energies sum to at least T.
NUM_BASIS_SCHEMES	The number of schemes (not a valid scheme).

Definition at line 101 of file vtkPCAStatistics.h.

Constructor & Destructor Documentation

◆ vtkPCAStatistics()

vtkPCAStatistics::vtkPCAStatistics ( )

protected

◆ ~vtkPCAStatistics()

vtkPCAStatistics::~vtkPCAStatistics ( )

overrideprotected

Member Function Documentation

◆ IsTypeOf()

static vtkTypeBool vtkPCAStatistics::IsTypeOf ( const char * type )

static

◆ IsA()

virtual vtkTypeBool vtkPCAStatistics::IsA ( const char * name )

virtual

Return 1 if this class is the same type of (or a subclass of) the named class.

Returns 0 otherwise. This method works in combination with vtkTypeMacro found in vtkSetGet.h.

Reimplemented from vtkMultiCorrelativeStatistics.

Reimplemented in vtkPPCAStatistics.

◆ SafeDownCast()

static vtkPCAStatistics * vtkPCAStatistics::SafeDownCast ( vtkObjectBase * o )

static

◆ NewInstanceInternal()

virtual vtkObjectBase * vtkPCAStatistics::NewInstanceInternal ( ) const

protectedvirtual

Reimplemented from vtkMultiCorrelativeStatistics.

Reimplemented in vtkPPCAStatistics.

◆ NewInstance()

vtkPCAStatistics * vtkPCAStatistics::NewInstance ( ) const

◆ PrintSelf()

void vtkPCAStatistics::PrintSelf	(	ostream &	os,
		vtkIndent	indent
	)

overridevirtual

Methods invoked by print to print information about the object including superclasses.

Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from vtkMultiCorrelativeStatistics.

Reimplemented in vtkPPCAStatistics.

◆ New()

static vtkPCAStatistics * vtkPCAStatistics::New ( )

static

◆ SetNormalizationScheme()

virtual void vtkPCAStatistics::SetNormalizationScheme ( int )

virtual

This determines how (or if) the covariance matrix cov is normalized before PCA.

When set to NONE, no normalization is performed. This is the default.

When set to TRIANGLE_SPECIFIED, each entry cov(i,j) is divided by V(i,j). The list V of normalization factors must be set using the SetNormalization method before the filter is executed.

When set to DIAGONAL_SPECIFIED, each entry cov(i,j) is divided by sqrt(V(i)*V(j)). The list V of normalization factors must be set using the SetNormalization method before the filter is executed.

When set to DIAGONAL_VARIANCE, each entry cov(i,j) is divided by sqrt(cov(i,i)*cov(j,j)). Warning: Although this is accepted practice in some fields, some people think you should not turn this option on unless there is a good physically-based reason for doing so. Much better instead to determine how component magnitudes should be compared using physical reasoning and use DIAGONAL_SPECIFIED, TRIANGLE_SPECIFIED, or perform some pre-processing to shift and scale input data columns appropriately than to expect magical results from a shady normalization hack.

◆ GetNormalizationScheme()

virtual int vtkPCAStatistics::GetNormalizationScheme ( )

virtual

This determines how (or if) the covariance matrix cov is normalized before PCA.

When set to NONE, no normalization is performed. This is the default.

When set to TRIANGLE_SPECIFIED, each entry cov(i,j) is divided by V(i,j). The list V of normalization factors must be set using the SetNormalization method before the filter is executed.

When set to DIAGONAL_SPECIFIED, each entry cov(i,j) is divided by sqrt(V(i)*V(j)). The list V of normalization factors must be set using the SetNormalization method before the filter is executed.

When set to DIAGONAL_VARIANCE, each entry cov(i,j) is divided by sqrt(cov(i,i)*cov(j,j)). Warning: Although this is accepted practice in some fields, some people think you should not turn this option on unless there is a good physically-based reason for doing so. Much better instead to determine how component magnitudes should be compared using physical reasoning and use DIAGONAL_SPECIFIED, TRIANGLE_SPECIFIED, or perform some pre-processing to shift and scale input data columns appropriately than to expect magical results from a shady normalization hack.

◆ SetNormalizationSchemeByName()

virtual void vtkPCAStatistics::SetNormalizationSchemeByName ( const char * schemeName )

virtual

This determines how (or if) the covariance matrix cov is normalized before PCA.

When set to NONE, no normalization is performed. This is the default.

When set to TRIANGLE_SPECIFIED, each entry cov(i,j) is divided by V(i,j). The list V of normalization factors must be set using the SetNormalization method before the filter is executed.

When set to DIAGONAL_SPECIFIED, each entry cov(i,j) is divided by sqrt(V(i)*V(j)). The list V of normalization factors must be set using the SetNormalization method before the filter is executed.

When set to DIAGONAL_VARIANCE, each entry cov(i,j) is divided by sqrt(cov(i,i)*cov(j,j)). Warning: Although this is accepted practice in some fields, some people think you should not turn this option on unless there is a good physically-based reason for doing so. Much better instead to determine how component magnitudes should be compared using physical reasoning and use DIAGONAL_SPECIFIED, TRIANGLE_SPECIFIED, or perform some pre-processing to shift and scale input data columns appropriately than to expect magical results from a shady normalization hack.

◆ GetNormalizationSchemeName()

virtual const char * vtkPCAStatistics::GetNormalizationSchemeName ( int scheme )

virtual

This determines how (or if) the covariance matrix cov is normalized before PCA.

When set to NONE, no normalization is performed. This is the default.

When set to TRIANGLE_SPECIFIED, each entry cov(i,j) is divided by V(i,j). The list V of normalization factors must be set using the SetNormalization method before the filter is executed.

When set to DIAGONAL_SPECIFIED, each entry cov(i,j) is divided by sqrt(V(i)*V(j)). The list V of normalization factors must be set using the SetNormalization method before the filter is executed.

When set to DIAGONAL_VARIANCE, each entry cov(i,j) is divided by sqrt(cov(i,i)*cov(j,j)). Warning: Although this is accepted practice in some fields, some people think you should not turn this option on unless there is a good physically-based reason for doing so. Much better instead to determine how component magnitudes should be compared using physical reasoning and use DIAGONAL_SPECIFIED, TRIANGLE_SPECIFIED, or perform some pre-processing to shift and scale input data columns appropriately than to expect magical results from a shady normalization hack.

◆ GetSpecifiedNormalization()

virtual vtkTable * vtkPCAStatistics::GetSpecifiedNormalization ( )

virtual

These methods allow you to set/get values used to normalize the covariance matrix before PCA.

The normalization values apply to all requests, so you do not specify a single vector but a 3-column table.

The first two columns contain the names of columns from input 0 and the third column contains the value to normalize the corresponding entry in the covariance matrix. The table must always have 3 columns even when the NormalizationScheme is DIAGONAL_SPECIFIED. When only diagonal entries are to be used, only table rows where the first two columns are identical to one another will be employed. If there are multiple rows specifying different values for the same pair of columns, the entry nearest the bottom of the table takes precedence.

These functions are actually convenience methods that set/get the third input of the filter. Because the table is the third input, you may use other filters to produce a table of normalizations and have the pipeline take care of updates.

Any missing entries will be set to 1.0 and a warning issued. An error will occur if the third input to the filter is not set and the NormalizationScheme is DIAGONAL_SPECIFIED or TRIANGLE_SPECIFIED.

NOTE: SetSpecifiedNormalization( table ) is equivalent to SetInputData(3, table) and therefore does not make a pipeline connection.

◆ SetSpecifiedNormalization()

virtual void vtkPCAStatistics::SetSpecifiedNormalization ( vtkTable * )

virtual

These methods allow you to set/get values used to normalize the covariance matrix before PCA.

The normalization values apply to all requests, so you do not specify a single vector but a 3-column table.

The first two columns contain the names of columns from input 0 and the third column contains the value to normalize the corresponding entry in the covariance matrix. The table must always have 3 columns even when the NormalizationScheme is DIAGONAL_SPECIFIED. When only diagonal entries are to be used, only table rows where the first two columns are identical to one another will be employed. If there are multiple rows specifying different values for the same pair of columns, the entry nearest the bottom of the table takes precedence.

These functions are actually convenience methods that set/get the third input of the filter. Because the table is the third input, you may use other filters to produce a table of normalizations and have the pipeline take care of updates.

Any missing entries will be set to 1.0 and a warning issued. An error will occur if the third input to the filter is not set and the NormalizationScheme is DIAGONAL_SPECIFIED or TRIANGLE_SPECIFIED.

NOTE: SetSpecifiedNormalization( table ) is equivalent to SetInputData(3, table) and therefore does not make a pipeline connection.

◆ GetEigenvalues() [1/2]

void vtkPCAStatistics::GetEigenvalues	(	int	request,
		vtkDoubleArray *
	)

Get the eigenvalues.

The eigenvalues are ordered according from largest to smallest. This function: void GetEigenvalues(int request, int i, vtkDoubleArray*); does all of the work. The other functions simply call this function with the appropriate parameters. These functions are not valid unless Update() has been called and the Derive option is turned on.

◆ GetEigenvalues() [2/2]

void vtkPCAStatistics::GetEigenvalues ( vtkDoubleArray * )

Get the eigenvalues.

The eigenvalues are ordered according from largest to smallest. This function: void GetEigenvalues(int request, int i, vtkDoubleArray*); does all of the work. The other functions simply call this function with the appropriate parameters. These functions are not valid unless Update() has been called and the Derive option is turned on.

◆ GetEigenvalue() [1/2]

double vtkPCAStatistics::GetEigenvalue	(	int	request,
		int	i
	)

Get the eigenvalues.

The eigenvalues are ordered according from largest to smallest. This function: void GetEigenvalues(int request, int i, vtkDoubleArray*); does all of the work. The other functions simply call this function with the appropriate parameters. These functions are not valid unless Update() has been called and the Derive option is turned on.

◆ GetEigenvalue() [2/2]

double vtkPCAStatistics::GetEigenvalue ( int i )

Get the eigenvalues.

The eigenvalues are ordered according from largest to smallest. This function: void GetEigenvalues(int request, int i, vtkDoubleArray*); does all of the work. The other functions simply call this function with the appropriate parameters. These functions are not valid unless Update() has been called and the Derive option is turned on.

◆ GetEigenvectors() [1/2]

void vtkPCAStatistics::GetEigenvectors	(	int	request,
		vtkDoubleArray *	eigenvectors
	)

Get the eigenvectors.

The eigenvectors are ordered according to the magnitude of their associated eigenvalues, sorted from largest to smallest. That is, eigenvector 0 corresponds to the largest eigenvalue. This function: void GetEigenvectors(int request, vtkDoubleArray* eigenvectors) does all of the work. The other functions are convenience functions that call this function with default arguments. These functions are not valid unless Update() has been called and the Derive option is turned on.

◆ GetEigenvectors() [2/2]

void vtkPCAStatistics::GetEigenvectors ( vtkDoubleArray * eigenvectors )

Get the eigenvectors.

The eigenvectors are ordered according to the magnitude of their associated eigenvalues, sorted from largest to smallest. That is, eigenvector 0 corresponds to the largest eigenvalue. This function: void GetEigenvectors(int request, vtkDoubleArray* eigenvectors) does all of the work. The other functions are convenience functions that call this function with default arguments. These functions are not valid unless Update() has been called and the Derive option is turned on.

◆ GetEigenvector() [1/2]

void vtkPCAStatistics::GetEigenvector	(	int	i,
		vtkDoubleArray *	eigenvector
	)

Get the eigenvectors.

The eigenvectors are ordered according to the magnitude of their associated eigenvalues, sorted from largest to smallest. That is, eigenvector 0 corresponds to the largest eigenvalue. This function: void GetEigenvectors(int request, vtkDoubleArray* eigenvectors) does all of the work. The other functions are convenience functions that call this function with default arguments. These functions are not valid unless Update() has been called and the Derive option is turned on.

◆ GetEigenvector() [2/2]

void vtkPCAStatistics::GetEigenvector	(	int	request,
		int	i,
		vtkDoubleArray *	eigenvector
	)

Get the eigenvectors.

The eigenvectors are ordered according to the magnitude of their associated eigenvalues, sorted from largest to smallest. That is, eigenvector 0 corresponds to the largest eigenvalue. This function: void GetEigenvectors(int request, vtkDoubleArray* eigenvectors) does all of the work. The other functions are convenience functions that call this function with default arguments. These functions are not valid unless Update() has been called and the Derive option is turned on.

◆ SetBasisScheme()

virtual void vtkPCAStatistics::SetBasisScheme ( int )

virtual

This variable controls the dimensionality of output tuples in Assess operation.

Consider the case where you have requested a PCA on D columns.

When set to vtkPCAStatistics::FULL_BASIS, the entire set of basis vectors is used to derive new coordinates for each tuple being assessed. In this mode, you are guaranteed to have output tuples of the same dimension as the input tuples. (That dimension is D, so there will be D additional columns added to the table for the request.)

When set to vtkPCAStatistics::FIXED_BASIS_SIZE, only the first N basis vectors are used to derive new coordinates for each tuple being assessed. In this mode, you are guaranteed to have output tuples of dimension min(N,D). You must set N prior to assessing data using the SetFixedBasisSize() method. When N < D, this turns the PCA into a projection (instead of change of basis).

When set to vtkPCAStatistics::FIXED_BASIS_ENERGY, the number of basis vectors used to derive new coordinates for each tuple will be the minimum number of columns N that satisfy

\[ \frac{\sum_{i=1}^{N} \lambda_i}{\sum_{i=1}^{D} \lambda_i} < T \]

You must set T prior to assessing data using the SetFixedBasisEnergy() method. When T < 1, this turns the PCA into a projection (instead of change of basis).

By default BasisScheme is set to vtkPCAStatistics::FULL_BASIS.

◆ GetBasisScheme()

virtual int vtkPCAStatistics::GetBasisScheme ( )

virtual

This variable controls the dimensionality of output tuples in Assess operation.

Consider the case where you have requested a PCA on D columns.

When set to vtkPCAStatistics::FULL_BASIS, the entire set of basis vectors is used to derive new coordinates for each tuple being assessed. In this mode, you are guaranteed to have output tuples of the same dimension as the input tuples. (That dimension is D, so there will be D additional columns added to the table for the request.)

When set to vtkPCAStatistics::FIXED_BASIS_SIZE, only the first N basis vectors are used to derive new coordinates for each tuple being assessed. In this mode, you are guaranteed to have output tuples of dimension min(N,D). You must set N prior to assessing data using the SetFixedBasisSize() method. When N < D, this turns the PCA into a projection (instead of change of basis).

When set to vtkPCAStatistics::FIXED_BASIS_ENERGY, the number of basis vectors used to derive new coordinates for each tuple will be the minimum number of columns N that satisfy

\[ \frac{\sum_{i=1}^{N} \lambda_i}{\sum_{i=1}^{D} \lambda_i} < T \]

You must set T prior to assessing data using the SetFixedBasisEnergy() method. When T < 1, this turns the PCA into a projection (instead of change of basis).

By default BasisScheme is set to vtkPCAStatistics::FULL_BASIS.

◆ GetBasisSchemeName()

virtual const char * vtkPCAStatistics::GetBasisSchemeName ( int schemeIndex )

virtual

This variable controls the dimensionality of output tuples in Assess operation.

Consider the case where you have requested a PCA on D columns.

When set to vtkPCAStatistics::FULL_BASIS, the entire set of basis vectors is used to derive new coordinates for each tuple being assessed. In this mode, you are guaranteed to have output tuples of the same dimension as the input tuples. (That dimension is D, so there will be D additional columns added to the table for the request.)

When set to vtkPCAStatistics::FIXED_BASIS_SIZE, only the first N basis vectors are used to derive new coordinates for each tuple being assessed. In this mode, you are guaranteed to have output tuples of dimension min(N,D). You must set N prior to assessing data using the SetFixedBasisSize() method. When N < D, this turns the PCA into a projection (instead of change of basis).

When set to vtkPCAStatistics::FIXED_BASIS_ENERGY, the number of basis vectors used to derive new coordinates for each tuple will be the minimum number of columns N that satisfy

\[ \frac{\sum_{i=1}^{N} \lambda_i}{\sum_{i=1}^{D} \lambda_i} < T \]

You must set T prior to assessing data using the SetFixedBasisEnergy() method. When T < 1, this turns the PCA into a projection (instead of change of basis).

By default BasisScheme is set to vtkPCAStatistics::FULL_BASIS.

◆ SetBasisSchemeByName()

virtual void vtkPCAStatistics::SetBasisSchemeByName ( const char * schemeName )

virtual

This variable controls the dimensionality of output tuples in Assess operation.

Consider the case where you have requested a PCA on D columns.

When set to vtkPCAStatistics::FULL_BASIS, the entire set of basis vectors is used to derive new coordinates for each tuple being assessed. In this mode, you are guaranteed to have output tuples of the same dimension as the input tuples. (That dimension is D, so there will be D additional columns added to the table for the request.)

When set to vtkPCAStatistics::FIXED_BASIS_SIZE, only the first N basis vectors are used to derive new coordinates for each tuple being assessed. In this mode, you are guaranteed to have output tuples of dimension min(N,D). You must set N prior to assessing data using the SetFixedBasisSize() method. When N < D, this turns the PCA into a projection (instead of change of basis).

When set to vtkPCAStatistics::FIXED_BASIS_ENERGY, the number of basis vectors used to derive new coordinates for each tuple will be the minimum number of columns N that satisfy

\[ \frac{\sum_{i=1}^{N} \lambda_i}{\sum_{i=1}^{D} \lambda_i} < T \]

You must set T prior to assessing data using the SetFixedBasisEnergy() method. When T < 1, this turns the PCA into a projection (instead of change of basis).

By default BasisScheme is set to vtkPCAStatistics::FULL_BASIS.

◆ SetFixedBasisSize()

virtual void vtkPCAStatistics::SetFixedBasisSize ( int )

virtual

The number of basis vectors to use.

See SetBasisScheme() for more information. When FixedBasisSize <= 0 (the default), the fixed basis size scheme is equivalent to the full basis scheme.

◆ GetFixedBasisSize()

virtual int vtkPCAStatistics::GetFixedBasisSize ( )

virtual

The number of basis vectors to use.

See SetBasisScheme() for more information. When FixedBasisSize <= 0 (the default), the fixed basis size scheme is equivalent to the full basis scheme.

◆ SetFixedBasisEnergy()

virtual void vtkPCAStatistics::SetFixedBasisEnergy ( double )

virtual

The minimum energy the new basis should use, as a fraction.

See SetBasisScheme() for more information. When FixedBasisEnergy >= 1 (the default), the fixed basis energy scheme is equivalent to the full basis scheme.

◆ GetFixedBasisEnergy()

virtual double vtkPCAStatistics::GetFixedBasisEnergy ( )

virtual

The minimum energy the new basis should use, as a fraction.

See SetBasisScheme() for more information. When FixedBasisEnergy >= 1 (the default), the fixed basis energy scheme is equivalent to the full basis scheme.

◆ SetParameter()

bool vtkPCAStatistics::SetParameter	(	const char *	parameter,
		int	index,
		vtkVariant	value
	)

overridevirtual

A convenience method (in particular for access from other applications) to set parameter values.

Return true if setting of requested parameter name was executed, false otherwise.

Reimplemented from vtkStatisticsAlgorithm.

◆ FillInputPortInformation()

int vtkPCAStatistics::FillInputPortInformation	(	int	port,
		vtkInformation *	info
	)

overrideprotectedvirtual

This algorithm accepts a vtkTable containing normalization values for its fourth input (port 3).

We override FillInputPortInformation to indicate this.

Reimplemented from vtkAlgorithm.

◆ Derive()

void vtkPCAStatistics::Derive ( vtkMultiBlockDataSet * )

overrideprotectedvirtual

Execute the calculations required by the Derive option.

Reimplemented from vtkMultiCorrelativeStatistics.

◆ Test()

void vtkPCAStatistics::Test	(	vtkTable *	,
		vtkMultiBlockDataSet *	,
		vtkTable *
	)

overrideprotectedvirtual

Execute the calculations required by the Test option.

Reimplemented from vtkMultiCorrelativeStatistics.

Reimplemented in vtkPPCAStatistics.

◆ Assess()

void vtkPCAStatistics::Assess	(	vtkTable *	,
		vtkMultiBlockDataSet *	,
		vtkTable *
	)

overrideprotectedvirtual

Execute the calculations required by the Assess option.

Reimplemented from vtkMultiCorrelativeStatistics.

◆ CalculatePValues()

virtual vtkDoubleArray * vtkPCAStatistics::CalculatePValues	(	vtkIdTypeArray *	,
		vtkDoubleArray *
	)

protectedvirtual

Calculate p-value.

This will be overridden using the object factory with an R implementation if R is present.

◆ SelectAssessFunctor()

void vtkPCAStatistics::SelectAssessFunctor	(	vtkTable *	inData,
		vtkDataObject *	inMeta,
		vtkStringArray *	rowNames,
		AssessFunctor *&	dfunc
	)

overrideprotectedvirtual

Provide the appropriate assessment functor.

Reimplemented from vtkMultiCorrelativeStatistics.

Member Data Documentation

◆ NormalizationScheme

int vtkPCAStatistics::NormalizationScheme

protected

Definition at line 298 of file vtkPCAStatistics.h.

◆ BasisScheme

int vtkPCAStatistics::BasisScheme

protected

Definition at line 299 of file vtkPCAStatistics.h.

◆ FixedBasisSize

int vtkPCAStatistics::FixedBasisSize

protected

Definition at line 300 of file vtkPCAStatistics.h.

◆ FixedBasisEnergy

double vtkPCAStatistics::FixedBasisEnergy

protected

Definition at line 301 of file vtkPCAStatistics.h.

◆ BasisSchemeEnumNames

const char* vtkPCAStatistics::BasisSchemeEnumNames[NUM_BASIS_SCHEMES+1]

staticprotected

Definition at line 303 of file vtkPCAStatistics.h.

◆ NormalizationSchemeEnumNames

const char* vtkPCAStatistics::NormalizationSchemeEnumNames[NUM_NORMALIZATION_SCHEMES+1]

staticprotected

Definition at line 304 of file vtkPCAStatistics.h.

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

Filters/Statistics/vtkPCAStatistics.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Superclass

Member Enumeration Documentation

◆ NormalizationType

◆ ProjectionType

Constructor & Destructor Documentation

◆ vtkPCAStatistics()

◆ ~vtkPCAStatistics()

Member Function Documentation

◆ IsTypeOf()

◆ IsA()

◆ SafeDownCast()

◆ NewInstanceInternal()

◆ NewInstance()

◆ PrintSelf()

◆ New()

◆ SetNormalizationScheme()

◆ GetNormalizationScheme()

◆ SetNormalizationSchemeByName()

◆ GetNormalizationSchemeName()

◆ GetSpecifiedNormalization()

◆ SetSpecifiedNormalization()

◆ GetEigenvalues() [1/2]

◆ GetEigenvalues() [2/2]

◆ GetEigenvalue() [1/2]

◆ GetEigenvalue() [2/2]

◆ GetEigenvectors() [1/2]

◆ GetEigenvectors() [2/2]

◆ GetEigenvector() [1/2]

◆ GetEigenvector() [2/2]

◆ SetBasisScheme()

◆ GetBasisScheme()

◆ GetBasisSchemeName()

◆ SetBasisSchemeByName()

◆ SetFixedBasisSize()

◆ GetFixedBasisSize()

◆ SetFixedBasisEnergy()

◆ GetFixedBasisEnergy()

◆ SetParameter()

◆ FillInputPortInformation()

◆ Derive()

◆ Test()

◆ Assess()

◆ CalculatePValues()

◆ SelectAssessFunctor()

Member Data Documentation

◆ NormalizationScheme

◆ BasisScheme

◆ FixedBasisSize

◆ FixedBasisEnergy

◆ BasisSchemeEnumNames

◆ NormalizationSchemeEnumNames