VTK  9.0.20201128
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | Static Protected Attributes | List of all members
vtkPCAStatistics Class Reference

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

#include <vtkPCAStatistics.h>

Inheritance diagram for vtkPCAStatistics:
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Collaboration diagram for vtkPCAStatistics:
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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. More...
 
vtkPCAStatisticsNewInstance () const
 
void PrintSelf (ostream &os, vtkIndent indent) override
 Methods invoked by print to print information about the object including superclasses. More...
 
virtual void SetNormalizationScheme (int)
 This determines how (or if) the covariance matrix cov is normalized before PCA. More...
 
virtual int GetNormalizationScheme ()
 
virtual void SetNormalizationSchemeByName (const char *schemeName)
 
virtual const char * GetNormalizationSchemeName (int scheme)
 
virtual vtkTableGetSpecifiedNormalization ()
 These methods allow you to set/get values used to normalize the covariance matrix before PCA. More...
 
virtual void SetSpecifiedNormalization (vtkTable *)
 
void GetEigenvalues (int request, vtkDoubleArray *)
 Get the eigenvalues. More...
 
void GetEigenvalues (vtkDoubleArray *)
 
double GetEigenvalue (int request, int i)
 
double GetEigenvalue (int i)
 
void GetEigenvectors (int request, vtkDoubleArray *eigenvectors)
 Get the eigenvectors. More...
 
void GetEigenvectors (vtkDoubleArray *eigenvectors)
 
void GetEigenvector (int i, vtkDoubleArray *eigenvector)
 
void GetEigenvector (int request, int i, vtkDoubleArray *eigenvector)
 
virtual void SetBasisScheme (int)
 This variable controls the dimensionality of output tuples in Assess operation. More...
 
virtual int GetBasisScheme ()
 
virtual const char * GetBasisSchemeName (int schemeIndex)
 
virtual void SetBasisSchemeByName (const char *schemeName)
 
virtual void SetFixedBasisSize (int)
 The number of basis vectors to use. More...
 
virtual int GetFixedBasisSize ()
 
virtual void SetFixedBasisEnergy (double)
 The minimum energy the new basis should use, as a fraction. More...
 
virtual double GetFixedBasisEnergy ()
 
bool SetParameter (const char *parameter, int index, vtkVariant value) override
 A convenience method (in particular for access from other applications) to set parameter values. More...
 
- Public Member Functions inherited from vtkMultiCorrelativeStatistics
vtkMultiCorrelativeStatisticsNewInstance () const
 
void Aggregate (vtkDataObjectCollection *, vtkMultiBlockDataSet *) override
 Given a collection of models, calculate aggregate model. More...
 
virtual void SetMedianAbsoluteDeviation (bool)
 If set to true, the covariance matrix is replaced by the Median Absolute Deviation matrix. More...
 
virtual bool GetMedianAbsoluteDeviation ()
 
virtual void MedianAbsoluteDeviationOn ()
 
virtual void MedianAbsoluteDeviationOff ()
 
- Public Member Functions inherited from vtkStatisticsAlgorithm
vtkStatisticsAlgorithmNewInstance () const
 
void PrintSelf (ostream &os, vtkIndent indent) override
 Methods invoked by print to print information about the object including superclasses. More...
 
virtual void SetLearnOptionParameterConnection (vtkAlgorithmOutput *params)
 A convenience method for setting learn input parameters (if one is expected or allowed). More...
 
virtual void SetLearnOptionParameters (vtkDataObject *params)
 A convenience method for setting learn input parameters (if one is expected or allowed). More...
 
virtual void SetInputModelConnection (vtkAlgorithmOutput *model)
 A convenience method for setting the input model connection (if one is expected or allowed). More...
 
virtual void SetInputModel (vtkDataObject *model)
 A convenience method for setting the input model (if one is expected or allowed). More...
 
virtual void SetLearnOption (bool)
 Set/Get the Learn operation. More...
 
virtual bool GetLearnOption ()
 
virtual void SetDeriveOption (bool)
 Set/Get the Derive operation. More...
 
virtual bool GetDeriveOption ()
 
virtual void SetAssessOption (bool)
 Set/Get the Assess operation. More...
 
virtual bool GetAssessOption ()
 
virtual void SetTestOption (bool)
 Set/Get the Test operation. More...
 
virtual bool GetTestOption ()
 
virtual void SetNumberOfPrimaryTables (vtkIdType)
 Set/Get the number of tables in the primary model. More...
 
virtual vtkIdType GetNumberOfPrimaryTables ()
 
virtual void SetAssessNames (vtkStringArray *)
 Set/get assessment names. More...
 
virtual vtkStringArrayGetAssessNames ()
 
virtual void SetColumnStatus (const char *namCol, int status)
 Add or remove a column from the current analysis request. More...
 
virtual void ResetAllColumnStates ()
 Set the status of each and every column in the current request to OFF (0). More...
 
virtual int RequestSelectedColumns ()
 Use the current column status values to produce a new request for statistics to be produced when RequestData() is called. More...
 
virtual void ResetRequests ()
 Empty the list of current requests. More...
 
virtual vtkIdType GetNumberOfRequests ()
 Return the number of requests. More...
 
virtual vtkIdType GetNumberOfColumnsForRequest (vtkIdType request)
 Return the number of columns for a given request. More...
 
virtual const char * GetColumnForRequest (vtkIdType r, vtkIdType c)
 Provide the name of the c-th column for the r-th request. More...
 
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). More...
 
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). More...
 
- Public Member Functions inherited from vtkTableAlgorithm
vtkTableAlgorithmNewInstance () const
 
vtkTypeBool ProcessRequest (vtkInformation *, vtkInformationVector **, vtkInformationVector *) override
 see vtkAlgorithm for details More...
 
vtkTableGetOutput ()
 Get the output data object for a port on this algorithm. More...
 
vtkTableGetOutput (int index)
 
void SetInputData (vtkDataObject *obj)
 Assign a data object as input. More...
 
void SetInputData (int index, vtkDataObject *obj)
 
- Public Member Functions inherited from vtkAlgorithm
vtkAlgorithmNewInstance () const
 
int HasExecutive ()
 Check whether this algorithm has an assigned executive. More...
 
vtkExecutiveGetExecutive ()
 Get this algorithm's executive. More...
 
virtual void SetExecutive (vtkExecutive *executive)
 Set this algorithm's executive. More...
 
vtkTypeBool ProcessRequest (vtkInformation *request, vtkCollection *inInfo, vtkInformationVector *outInfo)
 Version of ProcessRequest() that is wrapped. More...
 
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. More...
 
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. More...
 
vtkInformationGetInputPortInformation (int port)
 Get the information object associated with an input port. More...
 
vtkInformationGetOutputPortInformation (int port)
 Get the information object associated with an output port. More...
 
virtual vtkInformationGetInformation ()
 Set/Get the information object associated with this algorithm. More...
 
virtual void SetInformation (vtkInformation *)
 
int GetNumberOfInputPorts ()
 Get the number of input ports used by the algorithm. More...
 
int GetNumberOfOutputPorts ()
 Get the number of output ports provided by the algorithm. More...
 
void Register (vtkObjectBase *o) override
 Participate in garbage collection. More...
 
void UnRegister (vtkObjectBase *o) override
 Decrease the reference count (release by another object). More...
 
virtual void SetAbortExecute (vtkTypeBool)
 Set/Get the AbortExecute flag for the process object. More...
 
virtual vtkTypeBool GetAbortExecute ()
 
virtual void AbortExecuteOn ()
 
virtual void AbortExecuteOff ()
 
virtual double GetProgress ()
 Get the execution progress of a process object. More...
 
void SetProgress (double)
 SetProgress is deprecated. More...
 
void UpdateProgress (double amount)
 Update the progress of the process object. More...
 
void SetProgressShiftScale (double shift, double scale)
 Specify the shift and scale values to use to apply to the progress amount when UpdateProgress is called. More...
 
virtual double GetProgressShift ()
 
virtual double GetProgressScale ()
 
void SetProgressText (const char *ptext)
 Set the current text message associated with the progress state. More...
 
virtual char * GetProgressText ()
 
virtual unsigned long GetErrorCode ()
 The error code contains a possible error that occurred while reading or writing the file. More...
 
virtual void SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, const char *name)
 Set the input data arrays that this algorithm will process. More...
 
virtual void SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, int fieldAttributeType)
 
virtual void SetInputArrayToProcess (int idx, vtkInformation *info)
 
virtual void SetInputArrayToProcess (int idx, int port, int connection, const char *fieldAssociation, const char *attributeTypeorName)
 String based versions of SetInputArrayToProcess(). More...
 
vtkInformationGetInputArrayInformation (int idx)
 Get the info object for the specified input array to this algorithm. More...
 
void RemoveAllInputs ()
 Remove all the input data. More...
 
vtkDataObjectGetOutputDataObject (int port)
 Get the data object that will contain the algorithm output for the given port. More...
 
vtkDataObjectGetInputDataObject (int port, int connection)
 Get the data object that will contain the algorithm input for the given port and given connection. More...
 
virtual void SetInputConnection (int port, vtkAlgorithmOutput *input)
 Set the connection for the given input port index. More...
 
virtual void SetInputConnection (vtkAlgorithmOutput *input)
 
virtual void AddInputConnection (int port, vtkAlgorithmOutput *input)
 Add a connection to the given input port index. More...
 
virtual void AddInputConnection (vtkAlgorithmOutput *input)
 
virtual void RemoveInputConnection (int port, vtkAlgorithmOutput *input)
 Remove a connection from the given input port index. More...
 
virtual void RemoveInputConnection (int port, int idx)
 Remove a connection given by index idx. More...
 
virtual void RemoveAllInputConnections (int port)
 Removes all input connections. More...
 
virtual void SetInputDataObject (int port, vtkDataObject *data)
 Sets the data-object as an input on the given port index. More...
 
virtual void SetInputDataObject (vtkDataObject *data)
 
virtual void AddInputDataObject (int port, vtkDataObject *data)
 Add the data-object as an input to this given port. More...
 
virtual void AddInputDataObject (vtkDataObject *data)
 
vtkAlgorithmOutputGetOutputPort (int index)
 Get a proxy object corresponding to the given output port of this algorithm. More...
 
vtkAlgorithmOutputGetOutputPort ()
 
int GetNumberOfInputConnections (int port)
 Get the number of inputs currently connected to a port. More...
 
int GetTotalNumberOfInputConnections ()
 Get the total number of inputs for this algorithm. More...
 
vtkAlgorithmOutputGetInputConnection (int port, int index)
 Get the algorithm output port connected to an input port. More...
 
vtkAlgorithmGetInputAlgorithm (int port, int index, int &algPort)
 Returns the algorithm and the output port index of that algorithm connected to a port-index pair. More...
 
vtkAlgorithmGetInputAlgorithm (int port, int index)
 Returns the algorithm connected to a port-index pair. More...
 
vtkAlgorithmGetInputAlgorithm ()
 Equivalent to GetInputAlgorithm(0, 0). More...
 
vtkExecutiveGetInputExecutive (int port, int index)
 Returns the executive associated with a particular input connection. More...
 
vtkExecutiveGetInputExecutive ()
 Equivalent to GetInputExecutive(0, 0) More...
 
vtkInformationGetInputInformation (int port, int index)
 Return the information object that is associated with a particular input connection. More...
 
vtkInformationGetInputInformation ()
 Equivalent to GetInputInformation(0, 0) More...
 
vtkInformationGetOutputInformation (int port)
 Return the information object that is associated with a particular output port. More...
 
virtual void Update (int port)
 Bring this algorithm's outputs up-to-date. More...
 
virtual void Update ()
 
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). More...
 
virtual vtkTypeBool Update (vtkInformation *requests)
 Convenience method to update an algorithm after passing requests to its first output port. More...
 
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. More...
 
virtual int UpdateExtent (const int extents[6])
 Convenience method to update an algorithm after passing requests to its first output port. More...
 
virtual 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. More...
 
virtual void UpdateInformation ()
 Bring the algorithm's information up-to-date. More...
 
virtual void UpdateDataObject ()
 Create output object(s). More...
 
virtual void PropagateUpdateExtent ()
 Propagate meta-data upstream. More...
 
virtual void UpdateWholeExtent ()
 Bring this algorithm's outputs up-to-date. More...
 
void ConvertTotalInputToPortConnection (int ind, int &port, int &conn)
 Convenience routine to convert from a linear ordering of input connections to a port/connection pair. More...
 
virtual void SetReleaseDataFlag (int)
 Turn release data flag on or off for all output ports. More...
 
virtual int GetReleaseDataFlag ()
 
void ReleaseDataFlagOn ()
 
void ReleaseDataFlagOff ()
 
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. More...
 
int UpdateExtentIsEmpty (vtkInformation *pinfo, int extentType)
 
int * GetUpdateExtent ()
 These functions return the update extent for output ports that use 3D extents. More...
 
int * GetUpdateExtent (int port)
 
void GetUpdateExtent (int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)
 
void GetUpdateExtent (int port, int &x0, int &x1, int &y0, int &y1, int &z0, int &z1)
 
void GetUpdateExtent (int extent[6])
 
void GetUpdateExtent (int port, int extent[6])
 
int GetUpdatePiece ()
 These functions return the update extent for output ports that use piece extents. More...
 
int GetUpdatePiece (int port)
 
int GetUpdateNumberOfPieces ()
 
int GetUpdateNumberOfPieces (int port)
 
int GetUpdateGhostLevel ()
 
int GetUpdateGhostLevel (int port)
 
void SetProgressObserver (vtkProgressObserver *)
 If an ProgressObserver is set, the algorithm will report progress through it rather than directly. More...
 
virtual vtkProgressObserverGetProgressObserver ()
 
- Public Member Functions inherited from vtkObject
 vtkBaseTypeMacro (vtkObject, vtkObjectBase)
 
virtual void DebugOn ()
 Turn debugging output on. More...
 
virtual void DebugOff ()
 Turn debugging output off. More...
 
bool GetDebug ()
 Get the value of the debug flag. More...
 
void SetDebug (bool debugFlag)
 Set the value of the debug flag. More...
 
virtual void Modified ()
 Update the modification time for this object. More...
 
virtual vtkMTimeType GetMTime ()
 Return this object's modified time. More...
 
unsigned long AddObserver (unsigned long event, vtkCommand *, float priority=0.0f)
 Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...
 
unsigned long AddObserver (const char *event, vtkCommand *, float priority=0.0f)
 
vtkCommandGetCommand (unsigned long tag)
 
void RemoveObserver (vtkCommand *)
 
void RemoveObservers (unsigned long event, vtkCommand *)
 
void RemoveObservers (const char *event, vtkCommand *)
 
vtkTypeBool HasObserver (unsigned long event, vtkCommand *)
 
vtkTypeBool HasObserver (const char *event, vtkCommand *)
 
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)
 
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. More...
 
template<class U , class T >
unsigned long AddObserver (unsigned long event, U observer, void(T::*callback)(vtkObject *, unsigned long, void *), float priority=0.0f)
 
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. More...
 
int InvokeEvent (unsigned long event, void *callData)
 This method invokes an event and return whether the event was aborted or not. More...
 
int InvokeEvent (const char *event, void *callData)
 
int InvokeEvent (unsigned long event)
 
int InvokeEvent (const char *event)
 
- Public Member Functions inherited from vtkObjectBase
const char * GetClassName () const
 Return the class name as a string. More...
 
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). More...
 
virtual void Delete ()
 Delete a VTK object. More...
 
virtual void FastDelete ()
 Delete a reference to this object. More...
 
void InitializeObjectBase ()
 
void Print (ostream &os)
 Print an object to an ostream. More...
 
virtual void PrintHeader (ostream &os, vtkIndent indent)
 
virtual void PrintTrailer (ostream &os, vtkIndent indent)
 
int GetReferenceCount ()
 Return the current reference count of this object. More...
 
void SetReferenceCount (int)
 Sets the reference count. More...
 
bool GetIsInMemkind () const
 A local state flag that remembers whether this object lives in the normal or extended memory space. More...
 

Static Public Member Functions

static vtkTypeBool IsTypeOf (const char *type)
 
static vtkPCAStatisticsSafeDownCast (vtkObjectBase *o)
 
static vtkPCAStatisticsNew ()
 
- Static Public Member Functions inherited from vtkMultiCorrelativeStatistics
static vtkTypeBool IsTypeOf (const char *type)
 
static vtkMultiCorrelativeStatisticsSafeDownCast (vtkObjectBase *o)
 
static vtkMultiCorrelativeStatisticsNew ()
 
- Static Public Member Functions inherited from vtkStatisticsAlgorithm
static vtkTypeBool IsTypeOf (const char *type)
 
static vtkStatisticsAlgorithmSafeDownCast (vtkObjectBase *o)
 
- Static Public Member Functions inherited from vtkTableAlgorithm
static vtkTableAlgorithmNew ()
 
static vtkTypeBool IsTypeOf (const char *type)
 
static vtkTableAlgorithmSafeDownCast (vtkObjectBase *o)
 
- Static Public Member Functions inherited from vtkAlgorithm
static vtkAlgorithmNew ()
 
static vtkTypeBool IsTypeOf (const char *type)
 
static vtkAlgorithmSafeDownCast (vtkObjectBase *o)
 
static vtkInformationIntegerKeyINPUT_IS_OPTIONAL ()
 Keys used to specify input port requirements. More...
 
static vtkInformationIntegerKeyINPUT_IS_REPEATABLE ()
 
static vtkInformationInformationVectorKeyINPUT_REQUIRED_FIELDS ()
 
static vtkInformationStringVectorKeyINPUT_REQUIRED_DATA_TYPE ()
 
static vtkInformationInformationVectorKeyINPUT_ARRAYS_TO_PROCESS ()
 
static vtkInformationIntegerKeyINPUT_PORT ()
 
static vtkInformationIntegerKeyINPUT_CONNECTION ()
 
static vtkInformationIntegerKeyCAN_PRODUCE_SUB_EXTENT ()
 This key tells the executive that a particular output port is capable of producing an arbitrary subextent of the whole extent. More...
 
static vtkInformationIntegerKeyCAN_HANDLE_PIECE_REQUEST ()
 Key that tells the pipeline that a particular algorithm can or cannot handle piece request. More...
 
static void SetDefaultExecutivePrototype (vtkExecutive *proto)
 If the DefaultExecutivePrototype is set, a copy of it is created in CreateDefaultExecutive() using NewInstance(). More...
 
- Static Public Member Functions inherited from vtkObject
static vtkObjectNew ()
 Create an object with Debug turned off, modified time initialized to zero, and reference counting on. More...
 
static void BreakOnError ()
 This method is called when vtkErrorMacro executes. More...
 
static void SetGlobalWarningDisplay (int val)
 This is a global flag that controls whether any debug, warning or error messages are displayed. More...
 
static void GlobalWarningDisplayOn ()
 
static void GlobalWarningDisplayOff ()
 
static int GetGlobalWarningDisplay ()
 
- 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. More...
 
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). More...
 
static vtkObjectBaseNew ()
 Create an object with Debug turned off, modified time initialized to zero, and reference counting on. More...
 
static void SetMemkindDirectory (const char *directoryname)
 The name of a directory, ideally mounted -o dax, to memory map an extended memory space within. More...
 
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. More...
 

Protected Member Functions

virtual vtkObjectBaseNewInstanceInternal () 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). More...
 
void Derive (vtkMultiBlockDataSet *) override
 Execute the calculations required by the Derive option. More...
 
void Test (vtkTable *, vtkMultiBlockDataSet *, vtkTable *) override
 Execute the calculations required by the Test option. More...
 
void Assess (vtkTable *, vtkMultiBlockDataSet *, vtkTable *) override
 Execute the calculations required by the Assess option. More...
 
virtual vtkDoubleArrayCalculatePValues (vtkIdTypeArray *, vtkDoubleArray *)
 Calculate p-value. More...
 
void SelectAssessFunctor (vtkTable *inData, vtkDataObject *inMeta, vtkStringArray *rowNames, AssessFunctor *&dfunc) override
 Provide the appropriate assessment functor. More...
 
- Protected Member Functions inherited from vtkMultiCorrelativeStatistics
 vtkMultiCorrelativeStatistics ()
 
 ~vtkMultiCorrelativeStatistics () override
 
void Learn (vtkTable *, vtkTable *, vtkMultiBlockDataSet *) override
 Execute the calculations required by the Learn option. More...
 
virtual void ComputeMedian (vtkTable *inData, vtkTable *outData)
 Computes the median of inData with vtkOrderStatistics. More...
 
virtual vtkOrderStatisticsCreateOrderStatisticsInstance ()
 Return a new vtkOrderStatistics instance. More...
 
- Protected Member Functions inherited from vtkStatisticsAlgorithm
 vtkStatisticsAlgorithm ()
 
 ~vtkStatisticsAlgorithm () override
 
int FillInputPortInformation (int port, vtkInformation *info) override
 Fill the input port information objects for this algorithm. More...
 
int FillOutputPortInformation (int port, vtkInformation *info) override
 Fill the output port information objects for this algorithm. More...
 
int RequestData (vtkInformation *, vtkInformationVector **, vtkInformationVector *) override
 This is called by the superclass. More...
 
void Assess (vtkTable *, vtkMultiBlockDataSet *, vtkTable *, int)
 A convenience implementation for generic assessment with variable number of variables. More...
 
- Protected Member Functions inherited from vtkTableAlgorithm
 vtkTableAlgorithm ()
 
 ~vtkTableAlgorithm () override
 
virtual int RequestInformation (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector)
 
virtual int RequestUpdateExtent (vtkInformation *, vtkInformationVector **, vtkInformationVector *)
 This is called by the superclass. More...
 
- Protected Member Functions inherited from vtkAlgorithm
 vtkAlgorithm ()
 
 ~vtkAlgorithm () override
 
virtual void SetNumberOfInputPorts (int n)
 Set the number of input ports used by the algorithm. More...
 
virtual void SetNumberOfOutputPorts (int n)
 Set the number of output ports provided by the algorithm. More...
 
int InputPortIndexInRange (int index, const char *action)
 
int OutputPortIndexInRange (int index, const char *action)
 
int GetInputArrayAssociation (int idx, vtkInformationVector **inputVector)
 Get the assocition of the actual data array for the input array specified by idx, this is only reasonable during the REQUEST_DATA pass. More...
 
int GetInputArrayAssociation (int idx, int connection, vtkInformationVector **inputVector)
 Filters that have multiple connections on one port can use this signature. More...
 
int GetInputArrayAssociation (int idx, vtkDataObject *input)
 
vtkDataArrayGetInputArrayToProcess (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. More...
 
vtkDataArrayGetInputArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
 
vtkDataArrayGetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
 Filters that have multiple connections on one port can use this signature. More...
 
vtkDataArrayGetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
 
vtkDataArrayGetInputArrayToProcess (int idx, vtkDataObject *input)
 
vtkDataArrayGetInputArrayToProcess (int idx, vtkDataObject *input, int &association)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (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. More...
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector, int &association)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector)
 Filters that have multiple connections on one port can use this signature. More...
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, vtkDataObject *input)
 
vtkAbstractArrayGetInputAbstractArrayToProcess (int idx, vtkDataObject *input, int &association)
 
vtkInformationGetInputArrayFieldInformation (int idx, vtkInformationVector **inputVector)
 This method takes in an index (as specified in SetInputArrayToProcess) and a pipeline information vector. More...
 
virtual vtkExecutiveCreateDefaultExecutive ()
 Create a default executive. More...
 
virtual void SetErrorCode (unsigned long)
 The error code contains a possible error that occurred while reading or writing the file. More...
 
void ReportReferences (vtkGarbageCollector *) override
 
virtual void SetNthInputConnection (int port, int index, vtkAlgorithmOutput *input)
 Replace the Nth connection on the given input port. More...
 
virtual void SetNumberOfInputConnections (int port, int n)
 Set the number of input connections on the given input port. More...
 
void SetInputDataInternal (int port, vtkDataObject *input)
 These methods are used by subclasses to implement methods to set data objects directly as input. More...
 
void AddInputDataInternal (int port, vtkDataObject *input)
 
- 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. More...
 
void InternalReleaseFocus ()
 
- Protected Member Functions inherited from vtkObjectBase
 vtkObjectBase ()
 
virtual ~vtkObjectBase ()
 
 vtkObjectBase (const vtkObjectBase &)
 
void operator= (const vtkObjectBase &)
 

Protected Attributes

int NormalizationScheme
 
int BasisScheme
 
int FixedBasisSize
 
double FixedBasisEnergy
 
- Protected Attributes inherited from vtkMultiCorrelativeStatistics
bool MedianAbsoluteDeviation
 
- Protected Attributes inherited from vtkStatisticsAlgorithm
vtkIdType NumberOfPrimaryTables
 
bool LearnOption
 
bool DeriveOption
 
bool AssessOption
 
bool TestOption
 
vtkStringArrayAssessNames
 
vtkStatisticsAlgorithmPrivateInternals
 
- Protected Attributes inherited from vtkAlgorithm
vtkInformationInformation
 
unsigned long ErrorCode
 
double Progress
 
char * ProgressText
 
vtkProgressObserverProgressObserver
 
- Protected Attributes inherited from vtkObject
bool Debug
 
vtkTimeStamp MTime
 
vtkSubjectHelper * SubjectHelper
 
- 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 vtkExecutiveDefaultExecutivePrototype
 

Additional Inherited Members

- Public Attributes inherited from vtkAlgorithm
vtkTypeBool AbortExecute
 
- Static Protected Member Functions inherited from vtkAlgorithm
static vtkInformationIntegerKeyPORT_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

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

Definition at line 62 of file vtkPCAStatistics.h.

Member Typedef Documentation

◆ Superclass

Definition at line 65 of file vtkPCAStatistics.h.

Member Enumeration Documentation

◆ 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 72 of file vtkPCAStatistics.h.

◆ 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 84 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.

◆ 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

◆ SetNormalizationSchemeByName()

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

◆ GetNormalizationSchemeName()

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

◆ 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

◆ 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 )

◆ GetEigenvalue() [1/2]

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

◆ GetEigenvalue() [2/2]

double vtkPCAStatistics::GetEigenvalue ( int  i)

◆ 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)

◆ GetEigenvector() [1/2]

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

◆ GetEigenvector() [2/2]

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

◆ 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

◆ GetBasisSchemeName()

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

◆ SetBasisSchemeByName()

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

◆ 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

◆ 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

◆ 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 vtkTableAlgorithm.

◆ 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.

◆ 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 281 of file vtkPCAStatistics.h.

◆ BasisScheme

int vtkPCAStatistics::BasisScheme
protected

Definition at line 282 of file vtkPCAStatistics.h.

◆ FixedBasisSize

int vtkPCAStatistics::FixedBasisSize
protected

Definition at line 283 of file vtkPCAStatistics.h.

◆ FixedBasisEnergy

double vtkPCAStatistics::FixedBasisEnergy
protected

Definition at line 284 of file vtkPCAStatistics.h.

◆ BasisSchemeEnumNames

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

Definition at line 286 of file vtkPCAStatistics.h.

◆ NormalizationSchemeEnumNames

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

Definition at line 287 of file vtkPCAStatistics.h.


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