Examples/Statistics/KdTreeBasedKMeansClustering.cxx

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// Software Guide : BeginLatex
//
// \index{Statistics!k-means clustering (using k-d tree)}
//
// \index{itk::Statistics::KdTree\-Based\-Kmeans\-Estimator}
//
// K-means clustering is a popular clustering algorithm because it is simple
// and usually converges to a reasonable solution. The k-means algorithm
// works as follows:
//
// \begin{enumerate}
//   \item{Obtains the initial k means input from the user.}
//   \item{Assigns each measurement vector in a sample container to its
// closest mean among the k number of means (i.e., update the membership of
// each measurement vectors to the nearest of the k clusters).}
//   \item{Calculates each cluster's mean from the newly assigned
// measurement vectors (updates the centroid (mean) of k clusters).}
//   \item{Repeats step 2 and step 3 until it meets the termination
// criteria.}
// \end{enumerate}
//
// The most common termination criterion is that if there is no
// measurement vector that changes its cluster membership from the
// previous iteration, then the algorithm stops.
//
// The \subdoxygen{Statistics}{KdTreeBasedKmeansEstimator} is a variation of
// this logic. The k-means clustering algorithm is computationally very
// expensive because it has to recalculate the mean at each iteration. To
// update the mean values, we have to calculate the distance between k means
// and each and every measurement vector. To reduce the computational burden,
// the KdTreeBasedKmeansEstimator uses a special data structure: the
// k-d tree (\subdoxygen{Statistics}{KdTree}) with additional
// information. The additional information includes the number and the vector
// sum of measurement vectors under each node under the tree architecture.
//
// With such additional information and the k-d tree data structure,
// we can reduce the computational cost of the distance calculation
// and means. Instead of calculating each measurement vector and k
// means, we can simply compare each node of the k-d tree and the k
// means. This idea of utilizing a k-d tree can be found in multiple
// articles \cite{Alsabti1998} \cite{Pelleg1999}
// \cite{Kanungo2000}. Our implementation of this scheme follows the
// article by the Kanungo et al \cite{Kanungo2000}.
//
// We use the \subdoxygen{Statistics}{ListSample} as the input sample, the
// \doxygen{Vector} as the measurement vector. The following code
// snippet includes their header files.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkVector.h"
#include "itkListSample.h"
// Software Guide : EndCodeSnippet

// Software Guide : BeginLatex
//
// Since our k-means algorithm requires a \subdoxygen{Statistics}{KdTree}
// object as an input, we include the KdTree class header file. As mentioned
// above, we need a k-d tree with the vector sum and the number of
// measurement vectors. Therefore we use the
// \subdoxygen{Statistics}{WeightedCentroidKdTreeGenerator} instead of the
// \subdoxygen{Statistics}{KdTreeGenerator} that generate a k-d tree without
// such additional information.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkKdTree.h"
#include "itkWeightedCentroidKdTreeGenerator.h"
// Software Guide : EndCodeSnippet

// Software Guide : BeginLatex
//
// The KdTreeBasedKmeansEstimator class is the implementation of the
// k-means algorithm. It does not create k clusters. Instead, it
// returns the mean estimates for the k clusters.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkKdTreeBasedKmeansEstimator.h"
// Software Guide : EndCodeSnippet

// Software Guide : BeginLatex
//
// To generate the clusters, we must create k instances of\newline
// \subdoxygen{Statistics}{DistanceToCentroidMembershipFunction} function as
// the membership functions for each cluster and plug
// that---along with a sample---into an
// \subdoxygen{Statistics}{SampleClassifierFilter} object to get a
// \subdoxygen{Statistics}{MembershipSample} that stores pairs of measurement
// vectors and their associated class labels (k labels).
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkMinimumDecisionRule.h"
#include "itkSampleClassifierFilter.h"
// Software Guide : EndCodeSnippet

// Software Guide : BeginLatex
//
// We will fill the sample with random variables from two normal
// distribution using the \subdoxygen{Statistics}{NormalVariateGenerator}.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkNormalVariateGenerator.h"
// Software Guide : EndCodeSnippet

int main()
{
  // Software Guide : BeginLatex
  //
  // Since the \code{NormalVariateGenerator} class only supports 1-D, we
  // define our measurement vector type as one component vector. We
  // then, create a \code{ListSample} object for data inputs. Each
  // measurement vector is of length 1. We set this using the
  // \code{SetMeasurementVectorSize()} method.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using MeasurementVectorType = itk::Vector< double, 1 >;
  using SampleType = itk::Statistics::ListSample< MeasurementVectorType >;
  SampleType::Pointer sample = SampleType::New();
  sample->SetMeasurementVectorSize( 1 );
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // The following code snippet creates a NormalVariateGenerator
  // object. Since the random variable generator returns values
  // according to the standard normal distribution (The mean is zero,
  // and the standard deviation is one), before pushing random values
  // into the \code{sample}, we change the mean and standard
  // deviation. We want two normal (Gaussian) distribution data. We have
  // two for loops. Each for loop uses different mean and standard
  // deviation. Before we fill the \code{sample} with the second
  // distribution data, we call \code{Initialize(random seed)} method,
  // to recreate the pool of random variables in the
  // \code{normalGenerator}.
  //
  // To see the probability density plots from the two distribution,
  // refer to the Figure~\ref{fig:TwoNormalDensityFunctionPlot}.
  //
  // \begin{figure}
  //   \center
  //   \includegraphics[width=0.8\textwidth]{TwoNormalDensityFunctionPlot}
  //   \itkcaption[Two normal distributions plot]{Two normal distributions' probability density plot
  // (The means are 100 and 200, and the standard deviation is 30 )}
  //  \protect\label{fig:TwoNormalDensityFunctionPlot}
  // \end{figure}
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using NormalGeneratorType = itk::Statistics::NormalVariateGenerator;
  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;
    sample->PushBack( mv );
    }

  normalGenerator->Initialize( 3024 );
  mean = 200;
  standardDeviation = 30;
  for (unsigned int i = 0; i < 100; ++i)
    {
    mv[0] = ( normalGenerator->GetVariate() * standardDeviation ) + mean;
    sample->PushBack( mv );
    }
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // We create a k-d tree. To see the details on the k-d tree generation, see
  // the Section~\ref{sec:KdTree}.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using TreeGeneratorType =
    itk::Statistics::WeightedCentroidKdTreeGenerator<SampleType>;
  TreeGeneratorType::Pointer treeGenerator = TreeGeneratorType::New();

  treeGenerator->SetSample( sample );
  treeGenerator->SetBucketSize( 16 );
  treeGenerator->Update();
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // Once we have the k-d tree, it is a simple procedure to produce k
  // mean estimates.
  //
  // We create the KdTreeBasedKmeansEstimator. Then, we provide the initial
  // mean values using the \code{SetParameters()}. Since we are dealing with
  // two normal distribution in a 1-D space, the size of the mean value array
  // is two. The first element is the first mean value, and the second is the
  // second mean value. If we used two normal distributions in a 2-D space,
  // the size of array would be four, and the first two elements would be the
  // two components of the first normal distribution's mean vector. We
  // plug-in the k-d tree using the \code{SetKdTree()}.
  //
  // The remaining two methods specify the termination condition. The
  // estimation process stops when the number of iterations reaches the
  // maximum iteration value set by the \code{SetMaximumIteration()}, or the
  // distances between the newly calculated mean (centroid) values and
  // previous ones are within the threshold set by the
  // \code{SetCentroidPositionChangesThreshold()}. The final step is
  // to call the \code{StartOptimization()} method.
  //
  // The for loop will print out the mean estimates from the estimation
  // process.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using TreeType = TreeGeneratorType::KdTreeType;
  using EstimatorType = itk::Statistics::KdTreeBasedKmeansEstimator<TreeType>;
  EstimatorType::Pointer estimator = EstimatorType::New();

  EstimatorType::ParametersType initialMeans(2);
  initialMeans[0] = 0.0;
  initialMeans[1] = 0.0;

  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 < 2; ++i)
    {
    std::cout << "cluster[" << i << "] " << std::endl;
    std::cout << "    estimated mean : " << estimatedMeans[i] << std::endl;
    }
  // Software Guide : EndCodeSnippet


  // Software Guide : BeginLatex
  //
  // If we are only interested in finding the mean estimates, we might
  // stop. However, to illustrate how a classifier can be formed using
  // the statistical classification framework. We go a little bit
  // further in this example.
  //
  // Since the k-means algorithm is an minimum distance classifier using
  // the estimated k means and the measurement vectors. We use the
  // DistanceToCentroidMembershipFunction class as membership functions.
  // Our choice for the decision rule is the
  // \subdoxygen{Statistics}{MinimumDecisionRule} that returns the
  // index of the membership functions that have the smallest value for
  // a measurement vector.
  //
  // After creating a SampleClassifier filter object and a
  // MinimumDecisionRule object, we plug-in the \code{decisionRule} and
  // the \code{sample} to the classifier filter. Then, we must specify
  // the number of classes that will be considered using the
  // \code{SetNumberOfClasses()} method.
  //
  // The remainder of the following code snippet shows how to use
  // user-specified class labels. The classification result will be stored
  // in a MembershipSample object, and for each measurement vector, its
  // class label will be one of the two class labels, 100 and 200
  // (\code{unsigned int}).
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using MembershipFunctionType =
    itk::Statistics::DistanceToCentroidMembershipFunction
      <MeasurementVectorType>;
  using DecisionRuleType = itk::Statistics::MinimumDecisionRule;
  DecisionRuleType::Pointer decisionRule = DecisionRuleType::New();

  using ClassifierType = itk::Statistics::SampleClassifierFilter< SampleType >;
  ClassifierType::Pointer classifier = ClassifierType::New();

  classifier->SetDecisionRule( decisionRule );
  classifier->SetInput( sample );
  classifier->SetNumberOfClasses( 2 );

  using ClassLabelVectorObjectType =
    ClassifierType::ClassLabelVectorObjectType;
  using ClassLabelVectorType =
    ClassifierType::ClassLabelVectorType;
  using ClassLabelType =
    ClassifierType::ClassLabelType;

  ClassLabelVectorObjectType::Pointer classLabelsObject =
    ClassLabelVectorObjectType::New();
  ClassLabelVectorType& classLabelsVector = classLabelsObject->Get();

  ClassLabelType class1 = 200;
  classLabelsVector.push_back( class1 );
  ClassLabelType class2 = 100;
  classLabelsVector.push_back( class2 );

  classifier->SetClassLabels( classLabelsObject );
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // The \code{classifier} is almost ready to do the classification
  // process except that it needs two membership functions that
  // represents two clusters respectively.
  //
  // In this example, the two clusters are modeled by two Euclidean distance
  // functions. The distance function (model) has only one parameter, its mean
  // (centroid) set by the \code{SetCentroid()} method. To plug-in two distance
  // functions, we create a MembershipFunctionVectorObject that contains a
  // MembershipFunctionVector with two components and add it using the
  // \code{SetMembershipFunctions} method. Then invocation of the
  // \code{Update()} method will perform the classification.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet

  using MembershipFunctionVectorObjectType =
    ClassifierType::MembershipFunctionVectorObjectType;
  using MembershipFunctionVectorType =
    ClassifierType::MembershipFunctionVectorType;

  MembershipFunctionVectorObjectType::Pointer membershipFunctionVectorObject =
    MembershipFunctionVectorObjectType::New();
  MembershipFunctionVectorType& membershipFunctionVector =
    membershipFunctionVectorObject->Get();

  int index = 0;
  for (unsigned int i = 0; i < 2; i++)
    {
    MembershipFunctionType::Pointer membershipFunction
                                               = MembershipFunctionType::New();
    MembershipFunctionType::CentroidType centroid(
                                          sample->GetMeasurementVectorSize() );
    for ( unsigned int j = 0; j < sample->GetMeasurementVectorSize(); j++ )
      {
      centroid[j] = estimatedMeans[index++];
      }
    membershipFunction->SetCentroid( centroid );
    membershipFunctionVector.push_back( membershipFunction );
    }
  classifier->SetMembershipFunctions( membershipFunctionVectorObject );

  classifier->Update();
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // The following code snippet prints out the measurement vectors and
  // their class labels in the \code{sample}.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  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;
    }
  // Software Guide : EndCodeSnippet
  return EXIT_SUCCESS;
}