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/*=========================================================================
Program: Visualization Toolkit
Module: vtkPKMeansStatistics.cxx
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notice for more information.
=========================================================================*/
/*-------------------------------------------------------------------------
Copyright 2011 Sandia Corporation.
Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
the U.S. Government retains certain rights in this software.
-------------------------------------------------------------------------*/
#include "vtkToolkits.h"
#include "vtkPKMeansStatistics.h"
#include "vtkKMeansStatistics.h"
#include "vtkKMeansDistanceFunctor.h"
#include "vtkIntArray.h"
#include "vtkDoubleArray.h"
#include "vtkVariantArray.h"
#include "vtkIdTypeArray.h"
#include "vtkCommunicator.h"
#include "vtkObjectFactory.h"
#include "vtkMultiProcessController.h"
#include "vtkTable.h"
vtkStandardNewMacro(vtkPKMeansStatistics);
vtkCxxSetObjectMacro(vtkPKMeansStatistics, Controller, vtkMultiProcessController);
//-----------------------------------------------------------------------------
vtkPKMeansStatistics::vtkPKMeansStatistics()
{
this->Controller = 0;
this->SetController( vtkMultiProcessController::GetGlobalController() );
}
//-----------------------------------------------------------------------------
vtkPKMeansStatistics::~vtkPKMeansStatistics()
{
this->SetController( 0 );
}
//-----------------------------------------------------------------------------
void vtkPKMeansStatistics::PrintSelf(ostream& os, vtkIndent indent)
{
this->Superclass::PrintSelf(os, indent);
os << indent << "Controller: " << this->Controller << endl;
}
// ----------------------------------------------------------------------
vtkIdType vtkPKMeansStatistics::GetTotalNumberOfObservations( vtkIdType numObservations )
{
int np = this->Controller->GetNumberOfProcesses();
if( np < 2 )
{
return numObservations;
}
// Now get ready for parallel calculations
vtkCommunicator* com = this->Controller->GetCommunicator();
if ( ! com )
{
vtkGenericWarningMacro("No parallel communicator.");
return numObservations;
}
vtkIdType totalNumObservations;
com->AllReduce( &numObservations, &totalNumObservations, 1, vtkCommunicator::SUM_OP );
return totalNumObservations;
}
// ----------------------------------------------------------------------
void vtkPKMeansStatistics::UpdateClusterCenters( vtkTable* newClusterElements,
vtkTable* curClusterElements,
vtkIdTypeArray* numMembershipChanges,
vtkIdTypeArray* numDataElementsInCluster,
vtkDoubleArray* error,
vtkIdTypeArray* startRunID,
vtkIdTypeArray* endRunID,
vtkIntArray* computeRun )
{
int np = this->Controller->GetNumberOfProcesses();
if( np < 2 )
{
this->Superclass::UpdateClusterCenters( newClusterElements, curClusterElements, numMembershipChanges,
numDataElementsInCluster, error, startRunID, endRunID, computeRun );
return;
}
// Now get ready for parallel calculations
vtkCommunicator* com = this->Controller->GetCommunicator();
if ( ! com )
{
vtkGenericWarningMacro("No parallel communicator.");
this->Superclass::UpdateClusterCenters( newClusterElements, curClusterElements, numMembershipChanges,
numDataElementsInCluster, error, startRunID, endRunID, computeRun );
return;
}
// (All) gather numMembershipChanges
vtkIdType nm = numMembershipChanges->GetNumberOfTuples();
vtkIdType nd = numDataElementsInCluster->GetNumberOfTuples();
vtkIdType totalIntElements = nm+nd ;
vtkIdType* localIntElements = new vtkIdType[totalIntElements];
vtkIdType* globalIntElements = new vtkIdType[totalIntElements * np];
vtkIdType* nmPtr = numMembershipChanges->GetPointer( 0 );
vtkIdType* ndPtr = numDataElementsInCluster->GetPointer( 0 );
memcpy( localIntElements, nmPtr, nm*sizeof( vtkIdType ) );
memcpy( localIntElements + nm, ndPtr, nd*sizeof( vtkIdType ) );
com->AllGather( localIntElements, globalIntElements, totalIntElements );
for( vtkIdType runID = 0; runID < nm; runID++ )
{
if ( computeRun->GetValue( runID ) )
{
vtkIdType numChanges = 0;
for( int j = 0; j < np; j++ )
{
numChanges += globalIntElements[j*totalIntElements+runID];
}
numMembershipChanges->SetValue( runID, numChanges );
}
}
vtkIdType numCols = newClusterElements->GetNumberOfColumns();
vtkIdType numRows = newClusterElements->GetNumberOfRows();
vtkIdType numElements = numCols*numRows;
vtkDoubleArray *totalError = vtkDoubleArray::New();
totalError->SetNumberOfTuples( numRows );
totalError->SetNumberOfComponents( 1 );
com->AllReduce( error, totalError, vtkCommunicator::SUM_OP );
for( vtkIdType runID = 0; runID < startRunID->GetNumberOfTuples(); runID++ )
{
if( computeRun->GetValue(runID) )
{
for( vtkIdType i = startRunID->GetValue(runID); i < endRunID->GetValue(runID); i++ )
{
error->SetValue( i, totalError->GetValue( i ) );
}
}
}
totalError->Delete();
vtkTable* allNewClusterElements = vtkTable::New();
void* localElements = this->DistanceFunctor->AllocateElementArray( numElements );
void* globalElements = this->DistanceFunctor->AllocateElementArray( numElements*np );
this->DistanceFunctor->PackElements( newClusterElements, localElements );
com->AllGatherVoidArray( localElements, globalElements, numElements, this->DistanceFunctor->GetDataType() );
this->DistanceFunctor->UnPackElements( newClusterElements, allNewClusterElements, localElements, globalElements, np );
for( vtkIdType runID = 0; runID < startRunID->GetNumberOfTuples(); runID++ )
{
if( computeRun->GetValue(runID) )
{
for( vtkIdType i = startRunID->GetValue(runID); i < endRunID->GetValue(runID); i++ )
{
newClusterElements->SetRow(i, this->DistanceFunctor->GetEmptyTuple( numCols ) );
vtkIdType numClusterElements = 0;
for( int j = 0; j < np; j++ )
{
numClusterElements += globalIntElements[j*totalIntElements + nm + i];
this->DistanceFunctor->PairwiseUpdate( newClusterElements, i, allNewClusterElements->GetRow( j*numRows + i ),
globalIntElements[j*totalIntElements + nm + i], numClusterElements );
}
numDataElementsInCluster->SetValue( i, numClusterElements );
// check to see if need to perturb
if( numDataElementsInCluster->GetValue( i ) == 0 )
{
vtkWarningMacro("cluster center " << i-startRunID->GetValue(runID)
<< " in run " << runID
<< " is degenerate. Attempting to perturb");
this->DistanceFunctor->PerturbElement(newClusterElements,
curClusterElements,
i,
startRunID->GetValue(runID),
endRunID->GetValue(runID),
0.8 ) ;
}
}
}
}
delete [] localIntElements;
delete [] globalIntElements;
allNewClusterElements->Delete();
}
// ----------------------------------------------------------------------
void vtkPKMeansStatistics::CreateInitialClusterCenters(vtkIdType numToAllocate,
vtkIdTypeArray* numberOfClusters,
vtkTable* inData,
vtkTable* curClusterElements,
vtkTable* newClusterElements)
{
int np = this->Controller->GetNumberOfProcesses();
if( np < 2 )
{
this->Superclass::CreateInitialClusterCenters( numToAllocate, numberOfClusters,
inData, curClusterElements, newClusterElements );
return;
}
// Now get ready for parallel calculations
vtkCommunicator* com = this->Controller->GetCommunicator();
if ( ! com )
{
vtkGenericWarningMacro("No parallel communicator.");
this->Superclass::CreateInitialClusterCenters( numToAllocate, numberOfClusters,
inData, curClusterElements, newClusterElements );
return;
}
vtkIdType myRank = com->GetLocalProcessId();
// use node 0 to broadcast
vtkIdType broadcastNode = 0;
// generate data on one node only
if( myRank == broadcastNode )
{
this->Superclass::CreateInitialClusterCenters( numToAllocate, numberOfClusters,
inData, curClusterElements, newClusterElements );
}
int numElements = numToAllocate * curClusterElements->GetNumberOfColumns() ;
void* localElements = this->DistanceFunctor->AllocateElementArray( numElements );
this->DistanceFunctor->PackElements( curClusterElements, localElements );
if( !com->BroadcastVoidArray( localElements, numElements, this->DistanceFunctor->GetDataType(), broadcastNode ) )
{
vtkErrorMacro("Could not broadcast initial cluster coordinates");
return;
}
if( myRank != broadcastNode )
{
vtkIdType numCols = curClusterElements->GetNumberOfColumns() ;
this->DistanceFunctor->UnPackElements( curClusterElements, localElements, numToAllocate, numCols );
this->DistanceFunctor->UnPackElements( newClusterElements, localElements, numToAllocate, numCols );
for ( vtkIdType i = 0; i < numToAllocate; i++ )
{
numberOfClusters->InsertNextValue( numToAllocate );
}
}
this->DistanceFunctor->DeallocateElementArray( localElements ) ;
}
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