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virtual vtkTypeBool | IsA (const char *type) |
| Return 1 if this class is the same type of (or a subclass of) the named class. More...
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vtkPConnectivityFilter * | NewInstance () const |
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void | PrintSelf (ostream &os, vtkIndent indent) override |
| Methods invoked by print to print information about the object including superclasses. More...
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vtkConnectivityFilter * | NewInstance () const |
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virtual void | SetScalarConnectivity (vtkTypeBool) |
| Turn on/off connectivity based on scalar value. More...
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virtual vtkTypeBool | GetScalarConnectivity () |
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virtual void | ScalarConnectivityOn () |
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virtual void | ScalarConnectivityOff () |
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virtual void | SetScalarRange (double, double) |
| Set the scalar range to use to extract cells based on scalar connectivity. More...
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void | SetScalarRange (double[2]) |
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virtual double * | GetScalarRange () |
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virtual void | GetScalarRange (double &, double &) |
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virtual void | GetScalarRange (double[2]) |
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virtual void | SetExtractionMode (int) |
| Control the extraction of connected surfaces. More...
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virtual int | GetExtractionMode () |
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void | SetExtractionModeToPointSeededRegions () |
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void | SetExtractionModeToCellSeededRegions () |
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void | SetExtractionModeToLargestRegion () |
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void | SetExtractionModeToSpecifiedRegions () |
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void | SetExtractionModeToClosestPointRegion () |
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void | SetExtractionModeToAllRegions () |
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const char * | GetExtractionModeAsString () |
| Return the method of extraction as a string. More...
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void | InitializeSeedList () |
| Initialize list of point ids/cell ids used to seed regions. More...
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void | AddSeed (vtkIdType id) |
| Add a seed id (point or cell id). More...
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void | DeleteSeed (vtkIdType id) |
| Delete a seed id (point or cell id). More...
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void | InitializeSpecifiedRegionList () |
| Initialize list of region ids to extract. More...
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void | AddSpecifiedRegion (int id) |
| Add a region id to extract. More...
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void | DeleteSpecifiedRegion (int id) |
| Delete a region id to extract. More...
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virtual void | SetClosestPoint (double, double, double) |
| Use to specify x-y-z point coordinates when extracting the region closest to a specified point. More...
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virtual void | SetClosestPoint (double[3]) |
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virtual double * | GetClosestPoint () |
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virtual void | GetClosestPoint (double data[3]) |
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int | GetNumberOfExtractedRegions () |
| Obtain the number of connected regions. More...
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virtual void | SetColorRegions (vtkTypeBool) |
| Turn on/off the coloring of connected regions. More...
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virtual vtkTypeBool | GetColorRegions () |
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virtual void | ColorRegionsOn () |
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virtual void | ColorRegionsOff () |
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virtual void | SetRegionIdAssignmentMode (int) |
| Set/get mode controlling how RegionIds are assigned. More...
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virtual int | GetRegionIdAssignmentMode () |
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virtual void | SetOutputPointsPrecision (int) |
| Set/get the desired precision for the output types. More...
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virtual int | GetOutputPointsPrecision () |
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int | ProcessRequest (vtkInformation *, vtkInformationVector **, vtkInformationVector *) override |
| see vtkAlgorithm for details More...
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vtkPointSetAlgorithm * | NewInstance () const |
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vtkPointSet * | GetOutput () |
| Get the output data object for a port on this algorithm. More...
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vtkPointSet * | GetOutput (int) |
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vtkPolyData * | GetPolyDataOutput () |
| Get the output as vtkPolyData. More...
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vtkStructuredGrid * | GetStructuredGridOutput () |
| Get the output as vtkStructuredGrid. More...
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vtkUnstructuredGrid * | GetUnstructuredGridOutput () |
| Get the output as vtkUnstructuredGrid. More...
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void | SetInputData (vtkDataObject *) |
| Assign a data object as input. More...
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void | SetInputData (int, vtkDataObject *) |
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void | SetInputData (vtkPointSet *) |
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void | SetInputData (int, vtkPointSet *) |
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void | AddInputData (vtkDataObject *) |
| Assign a data object as input. More...
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void | AddInputData (vtkPointSet *) |
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void | AddInputData (int, vtkPointSet *) |
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void | AddInputData (int, vtkDataObject *) |
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vtkDataObject * | GetInput () |
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vtkAlgorithm * | NewInstance () const |
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int | HasExecutive () |
| Check whether this algorithm has an assigned executive. More...
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vtkExecutive * | GetExecutive () |
| Get this algorithm's executive. More...
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virtual void | SetExecutive (vtkExecutive *executive) |
| Set this algorithm's executive. More...
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int | ProcessRequest (vtkInformation *request, vtkCollection *inInfo, vtkInformationVector *outInfo) |
| Version of ProcessRequest() that is wrapped. More...
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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...
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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...
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vtkInformation * | GetInputPortInformation (int port) |
| Get the information object associated with an input port. More...
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vtkInformation * | GetOutputPortInformation (int port) |
| Get the information object associated with an output port. More...
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virtual vtkInformation * | GetInformation () |
| Set/Get the information object associated with this algorithm. More...
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virtual void | SetInformation (vtkInformation *) |
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int | GetNumberOfInputPorts () |
| Get the number of input ports used by the algorithm. More...
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int | GetNumberOfOutputPorts () |
| Get the number of output ports provided by the algorithm. More...
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void | Register (vtkObjectBase *o) override |
| Participate in garbage collection. More...
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void | UnRegister (vtkObjectBase *o) override |
| Decrease the reference count (release by another object). More...
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virtual void | SetAbortExecute (vtkTypeBool) |
| Set/Get the AbortExecute flag for the process object. More...
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virtual vtkTypeBool | GetAbortExecute () |
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virtual void | AbortExecuteOn () |
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virtual void | AbortExecuteOff () |
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virtual void | SetProgress (double) |
| Set/Get the execution progress of a process object. More...
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virtual double | GetProgress () |
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void | UpdateProgress (double amount) |
| Update the progress of the process object. More...
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void | SetProgressText (const char *ptext) |
| Set the current text message associated with the progress state. More...
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virtual char * | GetProgressText () |
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virtual unsigned long | GetErrorCode () |
| The error code contains a possible error that occurred while reading or writing the file. More...
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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...
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virtual void | SetInputArrayToProcess (int idx, int port, int connection, int fieldAssociation, int fieldAttributeType) |
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virtual void | SetInputArrayToProcess (int idx, vtkInformation *info) |
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virtual void | SetInputArrayToProcess (int idx, int port, int connection, const char *fieldAssociation, const char *attributeTypeorName) |
| String based versions of SetInputArrayToProcess(). More...
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vtkInformation * | GetInputArrayInformation (int idx) |
| Get the info object for the specified input array to this algorithm. More...
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void | RemoveAllInputs () |
| Remove all the input data. More...
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vtkDataObject * | GetOutputDataObject (int port) |
| Get the data object that will contain the algorithm output for the given port. More...
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vtkDataObject * | GetInputDataObject (int port, int connection) |
| Get the data object that will contain the algorithm input for the given port and given connection. More...
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virtual void | SetInputConnection (int port, vtkAlgorithmOutput *input) |
| Set the connection for the given input port index. More...
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virtual void | SetInputConnection (vtkAlgorithmOutput *input) |
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virtual void | AddInputConnection (int port, vtkAlgorithmOutput *input) |
| Add a connection to the given input port index. More...
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virtual void | AddInputConnection (vtkAlgorithmOutput *input) |
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virtual void | RemoveInputConnection (int port, vtkAlgorithmOutput *input) |
| Remove a connection from the given input port index. More...
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virtual void | RemoveInputConnection (int port, int idx) |
| Remove a connection given by index idx. More...
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virtual void | RemoveAllInputConnections (int port) |
| Removes all input connections. More...
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virtual void | SetInputDataObject (int port, vtkDataObject *data) |
| Sets the data-object as an input on the given port index. More...
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virtual void | SetInputDataObject (vtkDataObject *data) |
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virtual void | AddInputDataObject (int port, vtkDataObject *data) |
| Add the data-object as an input to this given port. More...
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virtual void | AddInputDataObject (vtkDataObject *data) |
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vtkAlgorithmOutput * | GetOutputPort (int index) |
| Get a proxy object corresponding to the given output port of this algorithm. More...
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vtkAlgorithmOutput * | GetOutputPort () |
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int | GetNumberOfInputConnections (int port) |
| Get the number of inputs currently connected to a port. More...
|
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int | GetTotalNumberOfInputConnections () |
| Get the total number of inputs for this algorithm. More...
|
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vtkAlgorithmOutput * | GetInputConnection (int port, int index) |
| Get the algorithm output port connected to an input port. More...
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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. More...
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vtkAlgorithm * | GetInputAlgorithm (int port, int index) |
| Returns the algorithm connected to a port-index pair. More...
|
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vtkAlgorithm * | GetInputAlgorithm () |
| Equivalent to GetInputAlgorithm(0, 0). More...
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vtkExecutive * | GetInputExecutive (int port, int index) |
| Returns the executive associated with a particular input connection. More...
|
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vtkExecutive * | GetInputExecutive () |
| Equivalent to GetInputExecutive(0, 0) More...
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vtkInformation * | GetInputInformation (int port, int index) |
| Return the information object that is associated with a particular input connection. More...
|
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vtkInformation * | GetInputInformation () |
| Equivalent to GetInputInformation(0, 0) More...
|
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vtkInformation * | GetOutputInformation (int port) |
| Return the information object that is associated with a particular output port. More...
|
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virtual void | Update (int port) |
| Bring this algorithm's outputs up-to-date. More...
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virtual void | Update () |
|
virtual int | 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...
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|
virtual int | Update (vtkInformation *requests) |
| Convenience method to update an algorithm after passing requests to its first output port. More...
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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...
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virtual int | UpdateExtent (const int extents[6]) |
| Convenience method to update an algorithm after passing requests to its first output port. More...
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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...
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virtual void | UpdateInformation () |
| Bring the algorithm's information up-to-date. More...
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virtual void | UpdateDataObject () |
| Create output object(s). More...
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virtual void | PropagateUpdateExtent () |
| Propagate meta-data upstream. More...
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virtual void | UpdateWholeExtent () |
| Bring this algorithm's outputs up-to-date. More...
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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...
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virtual void | SetReleaseDataFlag (int) |
| Turn release data flag on or off for all output ports. More...
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virtual int | GetReleaseDataFlag () |
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void | ReleaseDataFlagOn () |
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void | ReleaseDataFlagOff () |
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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...
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int | UpdateExtentIsEmpty (vtkInformation *pinfo, int extentType) |
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int * | GetUpdateExtent () |
| These functions return the update extent for output ports that use 3D extents. More...
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int * | GetUpdateExtent (int port) |
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void | GetUpdateExtent (int &x0, int &x1, int &y0, int &y1, int &z0, int &z1) |
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void | GetUpdateExtent (int port, int &x0, int &x1, int &y0, int &y1, int &z0, int &z1) |
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void | GetUpdateExtent (int extent[6]) |
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void | GetUpdateExtent (int port, int extent[6]) |
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int | GetUpdatePiece () |
| These functions return the update extent for output ports that use piece extents. More...
|
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int | GetUpdatePiece (int port) |
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int | GetUpdateNumberOfPieces () |
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int | GetUpdateNumberOfPieces (int port) |
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int | GetUpdateGhostLevel () |
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int | GetUpdateGhostLevel (int port) |
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void | SetProgressObserver (vtkProgressObserver *) |
| If an ProgressObserver is set, the algorithm will report progress through it rather than directly. More...
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virtual vtkProgressObserver * | GetProgressObserver () |
|
| vtkBaseTypeMacro (vtkObject, vtkObjectBase) |
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virtual void | DebugOn () |
| Turn debugging output on. More...
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virtual void | DebugOff () |
| Turn debugging output off. More...
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bool | GetDebug () |
| Get the value of the debug flag. More...
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void | SetDebug (bool debugFlag) |
| Set the value of the debug flag. More...
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virtual void | Modified () |
| Update the modification time for this object. More...
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virtual vtkMTimeType | GetMTime () |
| Return this object's modified time. More...
|
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unsigned long | AddObserver (unsigned long event, vtkCommand *, float priority=0.0f) |
| Allow people to add/remove/invoke observers (callbacks) to any VTK object. More...
|
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unsigned long | AddObserver (const char *event, vtkCommand *, float priority=0.0f) |
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vtkCommand * | GetCommand (unsigned long tag) |
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void | RemoveObserver (vtkCommand *) |
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void | RemoveObservers (unsigned long event, vtkCommand *) |
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void | RemoveObservers (const char *event, vtkCommand *) |
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vtkTypeBool | HasObserver (unsigned long event, vtkCommand *) |
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vtkTypeBool | HasObserver (const char *event, vtkCommand *) |
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void | RemoveObserver (unsigned long tag) |
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void | RemoveObservers (unsigned long event) |
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void | RemoveObservers (const char *event) |
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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...
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|
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...
|
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int | InvokeEvent (unsigned long event, void *callData) |
| This method invokes an event and return whether the event was aborted or not. More...
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int | InvokeEvent (const char *event, void *callData) |
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int | InvokeEvent (unsigned long event) |
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int | InvokeEvent (const char *event) |
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const char * | GetClassName () const |
| Return the class name as a string. More...
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virtual void | Delete () |
| Delete a VTK object. More...
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virtual void | FastDelete () |
| Delete a reference to this object. More...
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void | InitializeObjectBase () |
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void | Print (ostream &os) |
| Print an object to an ostream. More...
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virtual void | PrintHeader (ostream &os, vtkIndent indent) |
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virtual void | PrintTrailer (ostream &os, vtkIndent indent) |
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int | GetReferenceCount () |
| Return the current reference count of this object. More...
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void | SetReferenceCount (int) |
| Sets the reference count. More...
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void | PrintRevisions (ostream &) |
| Legacy. More...
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virtual vtkObjectBase * | NewInstanceInternal () const |
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| vtkPConnectivityFilter () |
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| ~vtkPConnectivityFilter () override |
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int | RequestData (vtkInformation *, vtkInformationVector **, vtkInformationVector *) override |
| This is called by the superclass. More...
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| vtkConnectivityFilter () |
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| ~vtkConnectivityFilter () override |
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int | RequestDataObject (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector) override |
| This is called by the superclass. More...
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int | FillInputPortInformation (int port, vtkInformation *info) override |
| Fill the input port information objects for this algorithm. More...
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int | FillOutputPortInformation (int vtkNotUsed(port), vtkInformation *info) override |
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void | TraverseAndMark (vtkDataSet *input) |
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void | OrderRegionIds (vtkIdTypeArray *pointRegionIds, vtkIdTypeArray *cellRegionIds) |
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| vtkPointSetAlgorithm () |
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| ~vtkPointSetAlgorithm () override |
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virtual int | ExecuteInformation (vtkInformation *, vtkInformationVector **, vtkInformationVector *) |
| This is called by the superclass. More...
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virtual int | ComputeInputUpdateExtent (vtkInformation *, vtkInformationVector **, vtkInformationVector *) |
| This is called by the superclass. More...
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int | FillOutputPortInformation (int port, vtkInformation *info) override |
| Fill the output port information objects for this algorithm. More...
|
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| vtkAlgorithm () |
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| ~vtkAlgorithm () override |
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virtual void | SetNumberOfInputPorts (int n) |
| Set the number of input ports used by the algorithm. More...
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virtual void | SetNumberOfOutputPorts (int n) |
| Set the number of output ports provided by the algorithm. More...
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int | InputPortIndexInRange (int index, const char *action) |
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int | OutputPortIndexInRange (int index, const char *action) |
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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...
|
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int | GetInputArrayAssociation (int idx, int connection, vtkInformationVector **inputVector) |
| Filters that have multiple connections on one port can use this signature. More...
|
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int | GetInputArrayAssociation (int idx, vtkDataObject *input) |
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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. More...
|
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vtkDataArray * | GetInputArrayToProcess (int idx, vtkInformationVector **inputVector, int &association) |
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vtkDataArray * | GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector) |
| Filters that have multiple connections on one port can use this signature. More...
|
|
vtkDataArray * | GetInputArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association) |
|
vtkDataArray * | GetInputArrayToProcess (int idx, vtkDataObject *input) |
|
vtkDataArray * | GetInputArrayToProcess (int idx, vtkDataObject *input, int &association) |
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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. More...
|
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vtkAbstractArray * | GetInputAbstractArrayToProcess (int idx, vtkInformationVector **inputVector, int &association) |
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vtkAbstractArray * | GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector) |
| Filters that have multiple connections on one port can use this signature. More...
|
|
vtkAbstractArray * | GetInputAbstractArrayToProcess (int idx, int connection, vtkInformationVector **inputVector, int &association) |
|
vtkAbstractArray * | GetInputAbstractArrayToProcess (int idx, vtkDataObject *input) |
|
vtkAbstractArray * | GetInputAbstractArrayToProcess (int idx, vtkDataObject *input, int &association) |
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vtkInformation * | GetInputArrayFieldInformation (int idx, vtkInformationVector **inputVector) |
| This method takes in an index (as specified in SetInputArrayToProcess) and a pipeline information vector. More...
|
|
virtual vtkExecutive * | CreateDefaultExecutive () |
| 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 |
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virtual void | SetNthInputConnection (int port, int index, vtkAlgorithmOutput *input) |
| Replace the Nth connection on the given input port. More...
|
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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) |
|
| vtkObject () |
|
| ~vtkObject () override |
|
void | RegisterInternal (vtkObjectBase *, vtkTypeBool check) override |
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void | UnRegisterInternal (vtkObjectBase *, vtkTypeBool check) override |
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void | InternalGrabFocus (vtkCommand *mouseEvents, vtkCommand *keypressEvents=nullptr) |
| These methods allow a command to exclusively grab all events. More...
|
|
void | InternalReleaseFocus () |
|
| vtkObjectBase () |
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virtual | ~vtkObjectBase () |
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virtual void | CollectRevisions (ostream &) |
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| vtkObjectBase (const vtkObjectBase &) |
|
void | operator= (const vtkObjectBase &) |
|
Parallel version of vtkConnectivityFilter.
This class computes connectivity of a distributed data set in parallel.
Problem
Datasets are distributed among ranks in a distributed process (Figure 1). vtkConnectivityFilter already runs in parallel on each piece in a typical VTK application run with MPI, but it does not produce correct results. As Figure 2 shows, distributed pieces of each connected component may end up with different labels.
Figure 1: Pieces in a distributed data set colored by processor rank.
Figure 2: Left). Incorrect parallel labeling. Right). Correct labeling.
The part missing from a fully parallel connectivity filter implementation is the identification of which pieces on different ranks are actually connected. This parallel filter provides that missing piece.
Approach
Run vtkConnectivityFilter on each rank’s piece and resolve the connected pieces afterwards. The implementation uses vtkMPIProcessController to communicate among processes.
Steps in the vtkPConnectivityFilter
High-level steps
- Run local connectivity algorithm.
- Identify region connections across ranks and create a graph of these links.
- Run a connected components algorithm on the graph created in the previous step to unify the regions across ranks.
- Relabel cells and points with their “global” RegionIds.
Low-level steps
- In GenerateData(), invoke the superclass’s GenerateData() method. Make temporary changes to extract all connected regions - we’ll handle the different extraction modes at the end. Example results on 3 ranks are shown in Figure 3 where color indicates RegionId computed by vtkConnectivityFilter.
- Check for errors in superclass GenerateData() on any rank and exit the algorithm if any encountered an error-indicating return code.
Figure 3: Results after vtkConnectivityFilter superclass is called on each piece.
- AllGatherv the number of connected RegionIds from each rank and AllGatherv the RegionIds themselves.
- Gather all axis-aligned bounding boxes from all other ranks. This is used to compute potential neighbors with which each rank should exchange points and RegionIds.
Figure 4: Point and associated RegionId exchange.
- Each rank gathers up points potentially coincident with points on neighboring ranks and sends them to their neighbors as well as the RegionId assigned to each point.
- Each rank runs through the received points and determines which points it owns using a locator object. If a point is found on the local rank, add the RegionId from the remote point to a set associated with the local RegionId. This signifies that the local RegionId is connected to the remote RegionId associated with the point.
- Each rank gathers the local-RegionId-to-remote-RegionId links from all other ranks.
- From these links, each rank generates a graph structure of the global links. The graph structure is identical on all ranks. (Optimization opportunity: To reduce communication, this link exchange could be avoided and the graph could be made distributed. This is just more complicated to program, however).
Figure 5: Connected region graph depicted by black line segments.
- Run a connected components algorithm that relabels the RegionIds, yielding the full connectivity graph across ranks. Figure 6 shows an example result.
- Relabel the remaining RegionIds by a contiguous set of RegionIds (e.g., go from [0, 5, 8, 9] to [0, 1, 2, 3]).
Figure 6: Connected components of graph linking RegionIds across ranks.
- From the RegionId graph, relabel points and cells in the output. The result is shown in Figure 7.
Figure 7: Dataset relabeled with global connected RegionIds.
- Handle ScalarConnectivy option and ExtractionMode after full region connectivity is determined by identifying the correct RegionId and extracting it by thresholding.
Caveats
This parallel implementation does not support a number of features that the vtkConnectivityFilter class supports, including:
- ScalarConnectivity
- VTK_EXTRACT_POINT_SEEDED_REGIONS extraction mode
- VTK_EXTRACT_CELL_SEEDED_REGIONS extraction mode
- VTK_EXTRACT_SPECIFIED_REGIONS extraction mode
Definition at line 136 of file vtkPConnectivityFilter.h.