JavaFX version with support for coloring labels

tsne-core/src/main/java/com/jujutsu/utils/MatrixUtils.java

@@ -22,7 +22,7 @@ public static double[][] simpleRead2DMatrix(File file, String columnDelimiter) {
                 String[] cols = line.trim().split(columnDelimiter);
                 double [] row = new double[cols.length];
                 for (int j = 0; j < cols.length; j++) {
-                	if(!(cols[j].length()==0)) {
+                	if (cols[j].length() != 0) {
                 		row[j] = Double.parseDouble(cols[j].trim());
                     }
                 }

tsne-demos/pom.xml

@@ -144,8 +144,8 @@
 				<artifactId>maven-compiler-plugin</artifactId>
 				<version>3.1</version>
 				<configuration>
-					<source>1.7</source>
-					<target>1.7</target>
+					<source>1.8</source>
+					<target>1.8</target>
 				</configuration>
 			</plugin>
 		</plugins>

tsne-demos/src/main/java/com/jujutsu/tsne/demos/TSneFX.java

@@ -0,0 +1,199 @@
+package com.jujutsu.tsne.demos;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Map;
+
+import com.jujutsu.tsne.FastTSne;
+import com.jujutsu.tsne.TSne;
+import com.jujutsu.utils.MatrixUtils;
+
+import javafx.application.Application;
+import javafx.collections.ObservableList;
+import javafx.geometry.Bounds;
+import javafx.geometry.Point2D;
+import javafx.scene.Scene;
+import javafx.scene.chart.Axis;
+import javafx.scene.chart.NumberAxis;
+import javafx.scene.chart.ScatterChart;
+import javafx.scene.chart.XYChart;
+import javafx.scene.chart.XYChart.Series;
+import javafx.scene.paint.Color;
+import javafx.scene.text.Font;
+import javafx.scene.text.Text;
+import javafx.stage.Stage;
+
+public class TSneFX extends Application {
+
+	static double perplexity = 20.0;
+	private static int initial_dims = 50;
+
+	public static void saveFile(File file, String text) {
+		saveFile(file,text,false);
+	}
+
+	public static void saveFile(File file, String text, boolean append) {
+        try (FileWriter fw = new FileWriter(file, append);
+            BufferedWriter bw = new BufferedWriter(fw)) {
+            bw.write(text);
+            bw.close();
+        } catch (IOException e) {
+            throw new IllegalArgumentException(e);
+        }
+    }
+
+	static Color[] palette = {
+			Color.BLUE,
+			Color.RED,
+			Color.GREEN,
+			Color.GRAY,
+			Color.BLUEVIOLET,
+			Color.ORANGE,
+			Color.AQUAMARINE,
+			Color.INDIGO,
+			Color.DARKGOLDENROD
+	};
+
+	double zoomx, zoomy;
+	double x0, x1, y0, y1;
+    NumberAxis xaxis = new NumberAxis(), yaxis = new NumberAxis();
+    ScatterChart<Number, Number> chart;
+
+    public void fast_tsne(Stage stage) {
+    	TSne tsne = new FastTSne();
+    	int iters = 2000;
+    	System.out.println("Running " + iters + " iterations of TSne on " + filename);
+    	System.out.println("Reading data");
+        double [][] X = MatrixUtils.simpleRead2DMatrix(new File(filename), ",");
+        String[] labels;
+        Map<Integer, Integer> colors = new HashMap<>();
+        if (labelfilename != null) {
+        	System.out.println("Reading labels");
+        	labels = MatrixUtils.simpleReadLines(new File(labelfilename));
+        	for (int i = 0; i < labels.length; i++) {
+        		labels[i] = labels[i].trim();
+        		if (labels[i].contains(",")) {
+        			int comma = labels[i].indexOf(',');
+        			colors.put(i,  Integer.parseInt(labels[i].substring(comma+1)));
+        			labels[i] = labels[i].substring(0, comma);
+        		}
+        	}
+        } else {
+        	labels = new String[X.length];
+        	for (int i = 0; i < X.length; i++) {
+        		labels[i] = Integer.toString(i);
+        	}
+        }
+        System.out.println("Shape is: " + X.length + " x " + X[0].length);
+        System.out.println("Starting TSNE: " + new Date());
+        double [][] Y = tsne.tsne(X, 2, initial_dims, perplexity, iters);
+        System.out.println("Finished TSNE: " + new Date());
+        System.out.println("Result is = " + Y.length + " x " + Y[0].length);
+
+        xaxis.setAutoRanging(true);
+        yaxis.setAutoRanging(true);
+        chart = new ScatterChart<>(xaxis, yaxis);
+
+        Series<Number, Number> series = new XYChart.Series<>();
+        ObservableList<XYChart.Data<Number, Number>> data = series.getData();
+        for (int i = 0; i < Y.length; i++) {
+        	XYChart.Data<Number, Number> datum = new XYChart.Data<>(Y[i][0], Y[i][1]);
+        	datum.setExtraValue(labels[i]);
+        	Text t = new Text(labels[i]);
+        	t.setFont(new Font("Helvetica", 200/Math.sqrt(Y.length)));
+        	if (colors.get(i) != null) {
+        		int ci = Math.abs(colors.get(i) % palette.length);
+        		t.setFill(palette[ci]);
+        	}
+
+        	datum.setNode(t);
+        	data.add(datum);
+        }
+        final Scene sc = new Scene(chart);
+        chart.getData().add(series);
+        chart.setOnZoomStarted(ze -> {
+
+        	Point2D p = xaxis.sceneToLocal(ze.getSceneX(), ze.getSceneY());
+
+        	x0 = xaxis.getLowerBound();
+        	x1 = xaxis.getUpperBound();
+        	y0 = yaxis.getLowerBound();
+        	y1 = yaxis.getUpperBound();
+
+        	Bounds b = chart.getLayoutBounds();
+
+        	zoomx = x0 + p.getX() / b.getWidth() * (x1 - x0);
+        	zoomy = y0 - p.getY() / b.getHeight() * (y1 - y0);
+
+        	System.out.println("" + x0 + " " + x1 + " " + y0 + " " + y1 + "p=" + p);
+
+        	System.out.println("zoom started at " + zoomx + " " + zoomy + " point " + p);
+        	System.out.println("chart size = " + chart.getLayoutBounds());
+        });
+        chart.setOnZoom(ze -> {
+        	double z = 1/ze.getZoomFactor();
+        	System.out.println("zoom = " + z);
+        	System.out.println(" range was " + x0 + "-" + x1 + ", " + y0 + "-" + y1);
+            double xm = zoomx;
+            double ym = zoomy;
+            double x0n = xm * (1-z) + x0 * z, x1n = xm * (1 - z) + x1 * z;
+            double y0n = ym * (1-z) + y0 * z, y1n = ym * (1 - z) + y1 * z;
+            double ticks = 1.0;
+            while ((x1n-x0n)/ticks > 100) ticks *= 10.0;
+            if ((x1n-x0n)/ticks > 20) ticks *= 5.0;
+            else if ((x1n - x0n)/ticks > 5) ticks *= 2.0;
+//            x0n = ticks * Math.ceil(x0n/ticks);
+//            x1n = ticks * Math.floor(x1n/ticks);
+//            y0n = ticks * Math.ceil(y0n/ticks);
+//            y1n = ticks * Math.floor(y1n/ticks);
+            x0 = x0n; x1 = x1n; y0 = y0n; y1 = y1n;
+            System.out.println("updating range to " + x0 + "-" + x1 + ", " + y0 + "-" + y1);
+            xaxis = new NumberAxis(x0, x1, ticks);
+            yaxis = new NumberAxis(y0, y1, ticks);
+            ScatterChart<Number, Number> chart2 = new ScatterChart<>(xaxis, yaxis);
+            chart2.getData().add(series);
+            sc.setRoot(chart2);
+            chart2.setOnZoom(chart.getOnZoom());
+            chart2.setOnZoomStarted(chart.getOnZoomStarted());
+            chart2.setOnZoomFinished(chart.getOnZoomFinished());
+            chart = chart2;
+        });
+        chart.setOnZoomFinished(ze -> { System.out.println("Zoom finished"); });
+
+        stage.setScene(sc);
+        stage.show();
+    }
+
+
+    String filename;
+    String labelfilename; // null if no labels
+
+    public static void main(String [] args) {
+        System.out.println("TSneFX: Runs t-SNE on various datasets.");
+        if (args.length<1 || args.length>2) {
+        	System.out.println("usage: For the data format TSneFX accepts, look at the file 'src/main/resources/datasets/mnist2500_X.txt' file and accompaning label file 'src/main/resources/datasets/mnist2500_labels.txt'.");
+        	System.out.println("       The label file must have as meny rows as the input matrix");
+        	System.out.println("usage: Example using the data and label file in: tsne-demos/src/main/resources/datasets/");
+        	System.out.println("usage: java -cp target/tsne-demos-X.X.X.jar com.jujutsu.tsne.demos.TSneFX minst2500_X.txt mnist2500_labels.txt");
+        	System.out.println("usage: Example using only data file in: tsne-demos/src/main/resources/datasets/");
+        	System.out.println("usage: java -cp target/tsne-demos-X.X.X.jar com.jujutsu.tsne.demos.TSneFX minst2500_X.txt");
+        	System.exit(0);
+        }
+        Application.launch(args);
+    }
+
+	@Override
+	public void start(Stage stage) throws Exception {
+		Application.Parameters params = getParameters();
+		filename = params.getUnnamed().get(0);
+		if (params.getUnnamed().size() > 1) {
+			labelfilename = params.getUnnamed().get(1);
+		}
+		fast_tsne(stage);
+	}
+
+}