GenerateData Class Reference

#include <dimred_tools.h>

Collaboration diagram for GenerateData:

Public Member Functions
void	generateNewDataset (const DatasetType &type, int N=1000, double noise=0.05)

Public Attributes
Matrix2D< double >	X
Matrix2D< double >	t
Matrix1D< unsigned char >	label

Detailed Description

Definition at line 43 of file dimred_tools.h.

Member Function Documentation

generateNewDataset()

void GenerateData::generateNewDataset	(	const DatasetType &	type,
		int	N = 1000,
		double	noise = 0.05
	)

Generate data with a given number of points and a given method. Generates an artificial dataset. Possible datasets are: 'swiss' for the Swiss roll dataset, 'helix' for the helix dataset, 'twinpeaks' for the twinpeaks dataset, '3d_clusters' for the 3D clusters dataset, and 'intersect' for the intersecting dataset. The variable n indicates the number of datapoints to generate. The variable noise indicates the amount of noise that is added to the data. The function generates the high-dimensional dataset in X, and corresponding labels in labels. In addition, the function keeps the coordinates of the datapoints on the underlying manifold in t.

Definition at line 31 of file dimred_tools.cpp.

{
    label.resizeNoCopy(N);
    X.resizeNoCopy(N,3);
    t.resizeNoCopy(N,2);

    auto g = std::mt19937();
    if (0 == noise) {
        g.seed(42);
    } else {
        std::random_device rd;
        g.seed(rd());
    }

    auto distUniform = std::uniform_real_distribution<>(0.0, 1.0);
    auto distGauss = std::normal_distribution<>(0.0, 1.0);
    switch (type) {
    case DatasetType::SWISS:
    {
        for (int i=0; i<N; ++i)
        {
            // Generate t
            MAT_ELEM(t,i,0)=(3 * PI / 2) * (1 + 2 * distUniform(g)); // t
            MAT_ELEM(t,i,1) = 30 * distUniform(g); // height
            double localT=MAT_ELEM(t,i,0);
            double localHeight=MAT_ELEM(t,i,1);

            // Generate X
            double s,c;
            //sincos(localT,&s,&c);
            s = sin(localT);
            c = cos(localT);
            MAT_ELEM(X,i,0)=localT * c + noise * distGauss(g);
            MAT_ELEM(X,i,1)=localHeight + noise * distGauss(g);
            MAT_ELEM(X,i,2)=localT * s + noise * distGauss(g);

            // Generate label
            VEC_ELEM(label,i)=(unsigned char)(round(localT/2)+round(localHeight/12))%2;
        }
        break;
    }
    case DatasetType::HELIX:
    {
        double iN=1.0/N;
        for (int i=0; i<N; ++i)
        {
            // Generate t
            MAT_ELEM(t,i,0)=2 * PI * i*iN;
            MAT_ELEM(t,i,1)=30 * distUniform(g); // height
            double localT=MAT_ELEM(t,i,0);

            // Generate X
            double s,c;
            //sincos(localT,&s,&c);
            s = sin(localT);
            c = cos(localT);
            double s8,c8;
            //sincos(8*localT,&s8,&c8);
            s8 = sin(8*localT);
            c8 = cos(8*localT);
            MAT_ELEM(X,i,0)=(2 + c8)*c+noise*distGauss(g);
            MAT_ELEM(X,i,1)=(2 + c8)*s+noise*distGauss(g);
            MAT_ELEM(X,i,2)=s8+noise*distGauss(g);

            // Generate label
            VEC_ELEM(label,i)=(unsigned char)(round(localT * 1.5))%2;
        }
        break;
    }
    case DatasetType::TWINPEAKS:
    {
        int actualN=round(sqrt(N));
        X.resizeNoCopy(actualN*actualN,3);
        t.resizeNoCopy(actualN*actualN,2);
        label.resizeNoCopy(actualN*actualN);
        for (int ii=0; ii<actualN; ii++)
        {
            for (int jj=0; jj<actualN; jj++)
            {
                int i=ii*actualN+jj;

                // Generate t
                double x = 1 - 2 * distUniform(g);
                double y = 1 - 2 * distUniform(g);
                MAT_ELEM(t,i,0)=x;
                MAT_ELEM(t,i,1)=y;

                // Generate X
                MAT_ELEM(X,i,0)=x+noise*distGauss(g);
                MAT_ELEM(X,i,1)=y+noise*distGauss(g);
                double z=10*sin(PI * x) * tanh(3 * y);
                MAT_ELEM(X,i,2)=z+noise*distGauss(g);

                // Generate label
                VEC_ELEM(label,i)=(unsigned char)(round(0.1*(x+y+z-3)))%2;
            }
        }
        break;
    }
    case DatasetType::CLUSTER3D:
    {
        // Create centers
        std::vector<Matrix1D<double> > centers;
        Matrix1D<double> center(3);
        const int Nclusters=5;
        for (int i=0; i<Nclusters; i++)
        {
            FOR_ALL_ELEMENTS_IN_MATRIX1D(center)
                VEC_ELEM(center,i)=10*distUniform(g);
            centers.push_back(center);
        }

        // Measure the minimum distance between centers
        Matrix1D<double> diff;
        double minDistance=1e38;
        for (int i=0; i<Nclusters-1; ++i)
            for (int j=i+1; j<Nclusters; ++j)
            {
                diff=centers[i]-centers[j];
                double distance=diff.module();
                minDistance=std::min(minDistance,distance);
            }

        // Create clusters
        t.initZeros();
        double sigma=minDistance/sqrt(12);
        for (int n=0; n<N; ++n)
        {
            int i=(Nclusters*n)/N;
            const Matrix1D<double> &center=centers[i];
            MAT_ELEM(X,n,0)=XX(center)+(distUniform(g)-0.5)*sigma+noise*distGauss(g);
            MAT_ELEM(X,n,1)=YY(center)+(distUniform(g)-0.5)*sigma+noise*distGauss(g);
            MAT_ELEM(X,n,2)=ZZ(center)+(distUniform(g)-0.5)*sigma+noise*distGauss(g);
        }
        break;
    }
    case DatasetType::INTERSECT:
    {
        double iN=1.0/N;
        for (int i=0; i<N; ++i)
        {
            // Generate t
            MAT_ELEM(t,i,0)=2 * PI * i*iN;
            MAT_ELEM(t,i,1)=5*distUniform(g);
            double localT=MAT_ELEM(t,i,0);
            double height=MAT_ELEM(t,i,1);

            // Generate X
            double s,c;
            //sincos(localT,&s,&c);
            s = sin(localT);
            c = cos(localT);
            MAT_ELEM(X,i,0)=c+noise*distGauss(g);
            MAT_ELEM(X,i,1)=c*s+noise*distGauss(g);
            MAT_ELEM(X,i,2)=height+noise*distGauss(g);

            // Generate label
            VEC_ELEM(label,i)=(unsigned char)(round(localT *0.5)+round(height*0.5))%2;
        }
        break;
    }
    default:
        REPORT_ERROR(ERR_ARG_INCORRECT,"Incorrect method passed to generate data");
    }
}

Member Data Documentation

label

Matrix1D<unsigned char> GenerateData::label

Vector of labels for the observations

Definition at line 56 of file dimred_tools.h.

t

Matrix2D<double> GenerateData::t

Underlying manifold coordinates. Eeach row of the matrix corresponds to the manifold coordinates of the observation in X.

Definition at line 53 of file dimred_tools.h.

X

Matrix2D<double> GenerateData::X

Generated data. Each row of the matrix is an individual observation

Definition at line 48 of file dimred_tools.h.

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The documentation for this class was generated from the following files:

• xmipp/libraries/dimred/dimred_tools.h
• xmipp/libraries/dimred/dimred_tools.cpp