KMeansClustering
VTKExamples/Cxx/InfoVis/KMeansClustering
Description
This example clusters 3D points using the KMeans algorithm. The points are assigned to a cluster by creating an array with each point's cluster id.
Code
KMeansClustering.cxx
#include <vtkVersion.h>
#include <vtkSmartPointer.h>
#include <vtkProperty.h>
#include <vtkPointData.h>
#include <vtkPolyData.h>
#include <vtkXMLPolyDataWriter.h>
#include <vtkIntArray.h>
#include <vtkMultiBlockDataSet.h>
#include <vtkPoints.h>
#include <vtkTable.h>
#include <vtkDoubleArray.h>
#include <vtkKMeansStatistics.h>
#include <vtkPolyDataMapper.h>
#include <vtkActor.h>
#include <vtkRenderWindow.h>
#include <vtkRenderer.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkVertexGlyphFilter.h>
#include <vtkInteractorStyleTrackballCamera.h>
#include <sstream>
int main(int, char*[])
{
// Create 2 clusters, one near (0,0,0) and the other near (3,3,3)
vtkSmartPointer<vtkPoints> points =
vtkSmartPointer<vtkPoints>::New();
points->InsertNextPoint ( 0.0, 0.0, 0.0 );
points->InsertNextPoint ( 3.0, 3.0, 3.0 );
points->InsertNextPoint ( 0.1, 0.1, 0.1 );
points->InsertNextPoint ( 3.1, 3.1, 3.1 );
points->InsertNextPoint ( 0.2, 0.2, 0.2 );
points->InsertNextPoint ( 3.2, 3.2, 3.2 );
// Get the points into the format needed for KMeans
vtkSmartPointer<vtkTable> inputData =
vtkSmartPointer<vtkTable>::New();
for( int c = 0; c < 3; ++c )
{
std::stringstream colName;
colName << "coord " << c;
vtkSmartPointer<vtkDoubleArray> doubleArray =
vtkSmartPointer<vtkDoubleArray>::New();
doubleArray->SetNumberOfComponents(1);
doubleArray->SetName( colName.str().c_str() );
doubleArray->SetNumberOfTuples(points->GetNumberOfPoints());
for( int r = 0; r < points->GetNumberOfPoints(); ++ r )
{
double p[3];
points->GetPoint(r, p);
doubleArray->SetValue( r, p[c] );
}
inputData->AddColumn( doubleArray );
}
vtkSmartPointer<vtkKMeansStatistics> kMeansStatistics =
vtkSmartPointer<vtkKMeansStatistics>::New();
#if VTK_MAJOR_VERSION <= 5
kMeansStatistics->SetInput( vtkStatisticsAlgorithm::INPUT_DATA, inputData );
#else
kMeansStatistics->SetInputData( vtkStatisticsAlgorithm::INPUT_DATA, inputData );
#endif
kMeansStatistics->SetColumnStatus( inputData->GetColumnName( 0 ) , 1 );
kMeansStatistics->SetColumnStatus( inputData->GetColumnName( 1 ) , 1 );
kMeansStatistics->SetColumnStatus( inputData->GetColumnName( 2 ) , 1 );
//kMeansStatistics->SetColumnStatus( "Testing", 1 );
kMeansStatistics->RequestSelectedColumns();
kMeansStatistics->SetAssessOption( true );
kMeansStatistics->SetDefaultNumberOfClusters( 2 );
kMeansStatistics->Update() ;
// Display the results
kMeansStatistics->GetOutput()->Dump();
vtkSmartPointer<vtkIntArray> clusterArray =
vtkSmartPointer<vtkIntArray>::New();
clusterArray->SetNumberOfComponents(1);
clusterArray->SetName( "ClusterId" );
for(int r = 0; r < kMeansStatistics->GetOutput()->GetNumberOfRows(); r++)
{
vtkVariant v = kMeansStatistics->GetOutput()->GetValue(r,kMeansStatistics->GetOutput()->GetNumberOfColumns() - 1);
std::cout << "Point " << r << " is in cluster " << v.ToInt() << std::endl;
clusterArray->InsertNextValue(v.ToInt());
}
/*
// Output the cluster centers
vtkMultiBlockDataSet* outputMetaDS = vtkMultiBlockDataSet::SafeDownCast( kMeansStatistics->GetOutputDataObject( vtkStatisticsAlgorithm::OUTPUT_MODEL ) );
vtkSmartPointer<vtkTable> outputMeta = vtkTable::SafeDownCast( outputMetaDS->GetBlock( 0 ) );
//vtkSmartPointer<vtkTable> outputMeta = vtkTable::SafeDownCast( outputMetaDS->GetBlock( 1 ) );
vtkDoubleArray* coord0 = vtkDoubleArray::SafeDownCast(outputMeta->GetColumnByName("coord 0"));
vtkDoubleArray* coord1 = vtkDoubleArray::SafeDownCast(outputMeta->GetColumnByName("coord 1"));
vtkDoubleArray* coord2 = vtkDoubleArray::SafeDownCast(outputMeta->GetColumnByName("coord 2"));
for(unsigned int i = 0; i < coord0->GetNumberOfTuples(); ++i)
{
std::cout << coord0->GetValue(i) << " " << coord1->GetValue(i) << " " << coord2->GetValue(i) << std::endl;
}
*/
vtkSmartPointer<vtkPolyData> polydata =
vtkSmartPointer<vtkPolyData>::New();
polydata->SetPoints(points);
//polydata->GetPointData()->AddArray(clusterArray);
polydata->GetPointData()->SetScalars(clusterArray);
vtkSmartPointer<vtkXMLPolyDataWriter> writer =
vtkSmartPointer<vtkXMLPolyDataWriter>::New();
writer->SetFileName("output.vtp");
#if VTK_MAJOR_VERSION <= 5
writer->SetInputConnection(polydata->GetProducerPort());
#else
writer->SetInputData(polydata);
#endif
writer->Write();
// Display
vtkSmartPointer<vtkVertexGlyphFilter> glyphFilter =
vtkSmartPointer<vtkVertexGlyphFilter>::New();
#if VTK_MAJOR_VERSION <= 5
glyphFilter->SetInputConnection(polydata->GetProducerPort());
#else
glyphFilter->SetInputData(polydata);
#endif
glyphFilter->Update();
// Create a mapper and actor
vtkSmartPointer<vtkPolyDataMapper> mapper =
vtkSmartPointer<vtkPolyDataMapper>::New();
mapper->SetInputConnection(glyphFilter->GetOutputPort());
vtkSmartPointer<vtkActor> actor =
vtkSmartPointer<vtkActor>::New();
actor->SetMapper(mapper);
actor->GetProperty()->SetPointSize(3);
// Create a renderer, render window, and interactor
vtkSmartPointer<vtkRenderer> renderer =
vtkSmartPointer<vtkRenderer>::New();
vtkSmartPointer<vtkRenderWindow> renderWindow =
vtkSmartPointer<vtkRenderWindow>::New();
renderWindow->AddRenderer(renderer);
vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
vtkSmartPointer<vtkRenderWindowInteractor>::New();
renderWindowInteractor->SetRenderWindow(renderWindow);
// Add the actor to the scene
renderer->AddActor(actor);
//renderer->SetBackground(.3, .6, .3); // Background color green
vtkSmartPointer<vtkInteractorStyleTrackballCamera> style =
vtkSmartPointer<vtkInteractorStyleTrackballCamera>::New();
renderWindowInteractor->SetInteractorStyle( style );
// Render and interact
renderWindow->Render();
renderWindowInteractor->Start();
return EXIT_SUCCESS;
}
CMakeLists.txt
cmake_minimum_required(VERSION 2.8)
PROJECT(KMeansClustering)
find_package(VTK REQUIRED)
include(${VTK_USE_FILE})
add_executable(KMeansClustering MACOSX_BUNDLE KMeansClustering.cxx)
target_link_libraries(KMeansClustering ${VTK_LIBRARIES})
Download and Build KMeansClustering
Click here to download KMeansClustering and its CMakeLists.txt file. Once the tarball KMeansClustering.tar has been downloaded and extracted,
cd KMeansClustering/build
If VTK is installed:
cmake ..
If VTK is not installed but compiled on your system, you will need to specify the path to your VTK build:
cmake -DVTK_DIR:PATH=/home/me/vtk_build ..
Build the project:
make
and run it:
./KMeansClustering
WINDOWS USERS PLEASE NOTE: Be sure to add the VTK bin directory to your path. This will resolve the VTK dll's at run time.