ITK/Examples/Statistics/KdTreeBasedKmeansEstimator3D: Difference between revisions
Daviddoria (talk | contribs) m (moved ITK/Examples/Statistics/KdTreeBasedKMeansClustering 3D to ITK/Examples/Statistics/KdTreeBasedKmeansEstimator 3D: Match class name.) |
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vtkSmartPointer<vtkVertexGlyphFilter> glyphFilter1 = | vtkSmartPointer<vtkVertexGlyphFilter> glyphFilter1 = | ||
vtkSmartPointer<vtkVertexGlyphFilter>::New(); | vtkSmartPointer<vtkVertexGlyphFilter>::New(); | ||
#if VTK_MAJOR_VERSION <= 5 | |||
glyphFilter1->SetInputConnection(polyData1->GetProducerPort()); | glyphFilter1->SetInputConnection(polyData1->GetProducerPort()); | ||
#else | |||
glyphFilter1->SetInputData(polyData1); | |||
#endif | |||
glyphFilter1->Update(); | glyphFilter1->Update(); | ||
vtkSmartPointer<vtkPolyDataMapper> mapper1 = | vtkSmartPointer<vtkPolyDataMapper> mapper1 = | ||
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vtkSmartPointer<vtkVertexGlyphFilter> glyphFilter2 = | vtkSmartPointer<vtkVertexGlyphFilter> glyphFilter2 = | ||
vtkSmartPointer<vtkVertexGlyphFilter>::New(); | vtkSmartPointer<vtkVertexGlyphFilter>::New(); | ||
#if VTK_MAJOR_VERSION <= 5 | |||
glyphFilter2->SetInputConnection(polyData2->GetProducerPort()); | glyphFilter2->SetInputConnection(polyData2->GetProducerPort()); | ||
#else | |||
glyphFilter2->SetInputData(polyData2); | |||
#endif | |||
glyphFilter2->Update(); | glyphFilter2->Update(); | ||
vtkSmartPointer<vtkPolyDataMapper> mapper2 = | vtkSmartPointer<vtkPolyDataMapper> mapper2 = |
Revision as of 23:25, 7 March 2012
Description
Cluster a collection of measurements using the KMeans algorithm. The name "KdTreeBased" indicates that this is an efficient implementation which uses a KdTree.
ITK Classes Demonstrated
Output
The input is shown on the left. It consists of a single collection of 3D points that lend themselves to easy clustering into 2 clusters. The output clusters are shown on the right. Points belonging to the same cluster as shown in the same color.
KdTreeBasedKMeansClustering_3D.cxx
<source lang="cpp">
- include "itkDecisionRule.h"
- include "itkVector.h"
- include "itkListSample.h"
- include "itkKdTree.h"
- include "itkWeightedCentroidKdTreeGenerator.h"
- include "itkKdTreeBasedKmeansEstimator.h"
- if ITK_VERSION_MAJOR < 4
- include "itkMinimumDecisionRule2.h"
- else
- include "itkMinimumDecisionRule.h"
- endif
- include "itkEuclideanDistanceMetric.h"
- include "itkDistanceToCentroidMembershipFunction.h"
- include "itkSampleClassifierFilter.h"
- include "itkNormalVariateGenerator.h"
- include "vtkActor.h"
- include "vtkInteractorStyleTrackballCamera.h"
- include "vtkPolyData.h"
- include "vtkPolyDataMapper.h"
- include "vtkProperty.h"
- include "vtkRenderer.h"
- include "vtkRenderWindow.h"
- include "vtkRenderWindowInteractor.h"
- include "vtkSmartPointer.h"
- include "vtkVertexGlyphFilter.h"
int main(int, char *[]) {
typedef itk::Vector< double, 3 > MeasurementVectorType; typedef itk::Statistics::ListSample< MeasurementVectorType > SampleType; SampleType::Pointer sample = SampleType::New();
typedef itk::Statistics::NormalVariateGenerator NormalGeneratorType; NormalGeneratorType::Pointer normalGenerator = NormalGeneratorType::New();
normalGenerator->Initialize( 101 );
MeasurementVectorType mv; double mean = 100; double standardDeviation = 30; for ( unsigned int i = 0 ; i < 100 ; ++i ) { mv[0] = ( normalGenerator->GetVariate() * standardDeviation ) + mean; mv[1] = ( normalGenerator->GetVariate() * standardDeviation ) + mean; mv[2] = ( normalGenerator->GetVariate() * standardDeviation ) + mean; sample->PushBack( mv ); }
normalGenerator->Initialize( 3024 ); mean = 200; standardDeviation = 30; for ( unsigned int i = 0 ; i < 100 ; ++i ) { mv[0] = ( normalGenerator->GetVariate() * standardDeviation ) + mean; mv[1] = ( normalGenerator->GetVariate() * standardDeviation ) + mean; mv[2] = ( normalGenerator->GetVariate() * standardDeviation ) + mean; sample->PushBack( mv ); }
typedef itk::Statistics::WeightedCentroidKdTreeGenerator< SampleType > TreeGeneratorType; TreeGeneratorType::Pointer treeGenerator = TreeGeneratorType::New();
treeGenerator->SetSample( sample ); treeGenerator->SetBucketSize( 16 ); treeGenerator->Update();
typedef TreeGeneratorType::KdTreeType TreeType; typedef itk::Statistics::KdTreeBasedKmeansEstimator<TreeType> EstimatorType; EstimatorType::Pointer estimator = EstimatorType::New();
EstimatorType::ParametersType initialMeans(6); initialMeans[0] = 0.0; // Cluster 1, mean[0] initialMeans[1] = 0.0; // Cluster 1, mean[1] initialMeans[2] = 0.0; // Cluster 1, mean[2] initialMeans[3] = 5.0; // Cluster 2, mean[0] initialMeans[4] = 5.0; // Cluster 2, mean[1] initialMeans[5] = 5.0; // Cluster 2, mean[2]
estimator->SetParameters( initialMeans ); estimator->SetKdTree( treeGenerator->GetOutput() ); estimator->SetMaximumIteration( 200 ); estimator->SetCentroidPositionChangesThreshold(0.0); estimator->StartOptimization();
EstimatorType::ParametersType estimatedMeans = estimator->GetParameters();
for ( unsigned int i = 0 ; i < 6 ; i+=2 ) { std::cout << "cluster[" << i << "] " << std::endl; std::cout << " estimated mean : " << estimatedMeans[i] << " , " << estimatedMeans[i+1] << std::endl; }
typedef itk::Statistics::DistanceToCentroidMembershipFunction< MeasurementVectorType > MembershipFunctionType; typedef MembershipFunctionType::Pointer MembershipFunctionPointer;
- if ITK_VERSION_MAJOR < 4
typedef itk::Statistics::MinimumDecisionRule2 DecisionRuleType;
- else
typedef itk::Statistics::MinimumDecisionRule DecisionRuleType;
- endif
DecisionRuleType::Pointer decisionRule = DecisionRuleType::New();
typedef itk::Statistics::SampleClassifierFilter< SampleType > ClassifierType; ClassifierType::Pointer classifier = ClassifierType::New();
classifier->SetDecisionRule(decisionRule); classifier->SetInput( sample ); classifier->SetNumberOfClasses( 2 );
typedef ClassifierType::ClassLabelVectorObjectType ClassLabelVectorObjectType; typedef ClassifierType::ClassLabelVectorType ClassLabelVectorType; typedef ClassifierType::MembershipFunctionVectorObjectType MembershipFunctionVectorObjectType; typedef ClassifierType::MembershipFunctionVectorType MembershipFunctionVectorType;
ClassLabelVectorObjectType::Pointer classLabelsObject = ClassLabelVectorObjectType::New(); classifier->SetClassLabels( classLabelsObject );
ClassLabelVectorType & classLabelsVector = classLabelsObject->Get(); classLabelsVector.push_back( 100 ); classLabelsVector.push_back( 200 );
MembershipFunctionVectorObjectType::Pointer membershipFunctionsObject = MembershipFunctionVectorObjectType::New(); classifier->SetMembershipFunctions( membershipFunctionsObject );
MembershipFunctionVectorType & membershipFunctionsVector = membershipFunctionsObject->Get();
MembershipFunctionType::CentroidType origin( sample->GetMeasurementVectorSize() ); int index = 0; for ( unsigned int i = 0 ; i < 2 ; i++ ) { MembershipFunctionPointer membershipFunction = MembershipFunctionType::New(); for ( unsigned int j = 0 ; j < sample->GetMeasurementVectorSize(); j++ ) { origin[j] = estimatedMeans[index++]; } membershipFunction->SetCentroid( origin ); membershipFunctionsVector.push_back( membershipFunction.GetPointer() ); }
classifier->Update();
const ClassifierType::MembershipSampleType* membershipSample = classifier->GetOutput(); ClassifierType::MembershipSampleType::ConstIterator iter = membershipSample->Begin();
while ( iter != membershipSample->End() ) { std::cout << "measurement vector = " << iter.GetMeasurementVector() << "class label = " << iter.GetClassLabel() << std::endl; ++iter; }
// Visualize vtkSmartPointer<vtkPoints> points1 = vtkSmartPointer<vtkPoints>::New(); vtkSmartPointer<vtkPoints> points2 = vtkSmartPointer<vtkPoints>::New();
iter = membershipSample->Begin(); while ( iter != membershipSample->End() ) { if(iter.GetClassLabel() == 100) { points1->InsertNextPoint( iter.GetMeasurementVector()[0], iter.GetMeasurementVector()[1], iter.GetMeasurementVector()[2]); } else { points2->InsertNextPoint( iter.GetMeasurementVector()[0], iter.GetMeasurementVector()[1], iter.GetMeasurementVector()[2]); } ++iter; }
vtkSmartPointer<vtkPolyData> polyData1 = vtkSmartPointer<vtkPolyData>::New(); polyData1->SetPoints(points1); vtkSmartPointer<vtkVertexGlyphFilter> glyphFilter1 = vtkSmartPointer<vtkVertexGlyphFilter>::New();
- if VTK_MAJOR_VERSION <= 5
glyphFilter1->SetInputConnection(polyData1->GetProducerPort());
- else
glyphFilter1->SetInputData(polyData1);
- endif
glyphFilter1->Update(); vtkSmartPointer<vtkPolyDataMapper> mapper1 = vtkSmartPointer<vtkPolyDataMapper>::New(); mapper1->SetInputConnection(glyphFilter1->GetOutputPort()); vtkSmartPointer<vtkActor> actor1 = vtkSmartPointer<vtkActor>::New(); actor1->GetProperty()->SetColor(0,1,0); actor1->GetProperty()->SetPointSize(3); actor1->SetMapper(mapper1);
vtkSmartPointer<vtkPolyData> polyData2 = vtkSmartPointer<vtkPolyData>::New(); polyData2->SetPoints(points2); vtkSmartPointer<vtkVertexGlyphFilter> glyphFilter2 = vtkSmartPointer<vtkVertexGlyphFilter>::New();
- if VTK_MAJOR_VERSION <= 5
glyphFilter2->SetInputConnection(polyData2->GetProducerPort());
- else
glyphFilter2->SetInputData(polyData2);
- endif
glyphFilter2->Update(); vtkSmartPointer<vtkPolyDataMapper> mapper2 = vtkSmartPointer<vtkPolyDataMapper>::New(); mapper2->SetInputConnection(glyphFilter2->GetOutputPort()); vtkSmartPointer<vtkActor> actor2 = vtkSmartPointer<vtkActor>::New(); actor2->GetProperty()->SetColor(1,0,0); actor2->GetProperty()->SetPointSize(3); actor2->SetMapper(mapper2);
vtkSmartPointer<vtkRenderWindow> renderWindow = vtkSmartPointer<vtkRenderWindow>::New(); renderWindow->SetSize(300,300);
vtkSmartPointer<vtkRenderer> renderer = vtkSmartPointer<vtkRenderer>::New(); renderWindow->AddRenderer(renderer);
renderer->AddActor(actor1); renderer->AddActor(actor2); renderer->ResetCamera(); renderer->Render();
vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor = vtkSmartPointer<vtkRenderWindowInteractor>::New(); vtkSmartPointer<vtkInteractorStyleTrackballCamera> style = vtkSmartPointer<vtkInteractorStyleTrackballCamera>::New();
renderWindowInteractor->SetInteractorStyle(style);
renderWindowInteractor->SetRenderWindow(renderWindow); renderWindowInteractor->Initialize();
renderWindowInteractor->Start();
return EXIT_SUCCESS;
} </source>
CMakeLists.txt
<syntaxhighlight lang="cmake"> cmake_minimum_required(VERSION 3.9.5)
project(KdTreeBasedKMeansClustering_3D)
find_package(ITK REQUIRED) include(${ITK_USE_FILE}) if (ITKVtkGlue_LOADED)
find_package(VTK REQUIRED) include(${VTK_USE_FILE})
else()
find_package(ItkVtkGlue REQUIRED) include(${ItkVtkGlue_USE_FILE}) set(Glue ItkVtkGlue)
endif()
add_executable(KdTreeBasedKMeansClustering_3D MACOSX_BUNDLE KdTreeBasedKMeansClustering_3D.cxx) target_link_libraries(KdTreeBasedKMeansClustering_3D
${Glue} ${VTK_LIBRARIES} ${ITK_LIBRARIES})
</syntaxhighlight>
Download and Build KdTreeBasedKMeansClustering_3D
Click here to download KdTreeBasedKMeansClustering_3D. and its CMakeLists.txt file. Once the tarball KdTreeBasedKMeansClustering_3D.tar has been downloaded and extracted,
cd KdTreeBasedKMeansClustering_3D/build
- If ITK is installed:
cmake ..
- If ITK is not installed but compiled on your system, you will need to specify the path to your ITK build:
cmake -DITK_DIR:PATH=/home/me/itk_build ..
Build the project,
make
and run it:
./KdTreeBasedKMeansClustering_3D
WINDOWS USERS PLEASE NOTE: Be sure to add the VTK and ITK bin directories to your path. This will resolve the VTK and ITK dll's at run time.
Building All of the Examples
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ItkVtkGlue
ITK >= 4
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ITK < 4
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