Sample code for t-SNE visualization with T-SNE-Java or Deeplearning4j

TSnePlot.java

import java.io.File;
import java.util.Arrays;

import javax.swing.JFrame;

import org.math.plot.FrameView;
import org.math.plot.Plot2DPanel;
import org.math.plot.PlotPanel;
import org.math.plot.plots.ColoredScatterPlot;
import org.math.plot.plots.ScatterPlot;

import com.jujutsu.tsne.barneshut.BHTSne;
import com.jujutsu.tsne.barneshut.BarnesHutTSne;
import com.jujutsu.tsne.barneshut.ParallelBHTsne;
import com.jujutsu.utils.MatrixOps;
import com.jujutsu.utils.MatrixUtils;

import org.deeplearning4j.plot.BarnesHutTsne;
import org.nd4j.linalg.factory.Nd4j;

public class TSnePlot {
    public static void main(String [] args) throws Exception {
        int initial_dims = -1;
        double perplexity = 20.0;
        int iterations = 100;
        double theta = 0.500000;

        // Some random data
        String [] labels = new String[50000];
        double [][] X = new double[50000][100];
        for (int i = 0; i < 50000; i++) {
            for (int j = 0; j < 100; j++) {
                X[i][j] = Math.random();
            }
        }

if (false) {
        System.out.println(MatrixOps.doubleArrayToPrintString(X, ", ", 50,10));
        BarnesHutTSne tsne;
        boolean parallel = true;
        if(parallel) {          
            tsne = new ParallelBHTsne();
        } else {
            tsne = new BHTSne();
        }
        double [][] Y = tsne.tsne(X, 2, initial_dims, perplexity, iterations, false, theta);   

        // Plot Y or save Y to file and plot with some other tool such as for instance R
        Plot2DPanel plot = new Plot2DPanel();
        if(labels != null) {
            ColoredScatterPlot setosaPlot = new ColoredScatterPlot("TSne Result", Y, labels);
            plot.plotCanvas.addPlot(setosaPlot);
        } else {
            ScatterPlot dataPlot = new ScatterPlot("Data", PlotPanel.COLORLIST[0], Y);
            plot.plotCanvas.addPlot(dataPlot);

        }
        plot.plotCanvas.setNotable(true);
        plot.plotCanvas.setNoteCoords(true);

        FrameView plotframe = new FrameView(plot);
        plotframe.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        plotframe.setVisible(true);

} else {
        BarnesHutTsne tsne = new BarnesHutTsne.Builder()
                .setMaxIter(iterations)
                .perplexity(perplexity)
                .theta(theta)
                .normalize(false)
//                .usePca(false)
                .build();
        tsne.plot(Nd4j.create(X), 2, Arrays.asList(labels), "plot.csv");
}

    }
}