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¶
Danger
The generation of tar files has not been ported to the new VTKExamples. Some tarballs may be missing or out-of-date.
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.