prepare for v1.0 release

Kohonen.java

@@ -50,6 +50,7 @@ public class Kohonen extends JFrame
 	private JTextField xDim = new JTextField(3);
 	private JTextField yDim = new JTextField(3);
 	private JTextField epochs = new JTextField(4);
+	private JComboBox<String> colorBox = new JComboBox<String>(new String[]{"Red", "Green", "Blue"});
 
 	/**
 	 * Read in the input csv data
@@ -155,27 +156,102 @@ public void readFile(File input)
 			xVal = Integer.parseInt(xDim.getText());
 			yVal = Integer.parseInt(yDim.getText());
 			epochVal = Integer.parseInt(epochs.getText());
+			if(xVal <= 0 || yVal <= 0 || epochVal <= 0)
+			{
+				throw new NumberFormatException();
+			}
 		}
 		catch(NumberFormatException nfe)
 		{
 			JOptionPane.showMessageDialog(null, "The grid dimensions and training epochs must be positive integers.");
 			return;
 		}
 		// Create the SOM object
+		long startTime = System.nanoTime();
+		//JFrame status = new JFrame("Training the Kohonen network...");
+		//status.setVisible(true);
+		//status.setSize(100, 100);
+		JOptionPane.showMessageDialog(null,"Training the Kohonen network. Please be patient.\nThis may take a while for large datasets, networks, and epochs.");
 		SOM training = new SOM(validData, xVal, yVal, epochVal);
-		// Prepare the object for training (i.e. weights and distances)
-		//training.init();
-		// Train the object and store the result
+		// Train the Kohonen network
 		training.train();
-
-
-
-		// Scale will fail if a column is all the same value
-		// Ensure non-zero variance of columns
-
-		// Now scale the grid
+		long endTime = System.nanoTime();
+		//System.out.println("" + (endTime - startTime / 1000000));
+		// Plot the network as a heatmap
+		//status.setVisible(false);
+		plot(xVal, yVal, training.getNodes());
 	}
 
+	/**
+	 * Plot the trained Kohonen network.
+	 * 
+	 * This method takes as inputs the x dimension
+	 * of the map, the y dimension of the map, and 
+	 * an array for the node labels of each observation
+	 * and produces a grid heatmap showing the count
+	 * of observations assigned to each node.
+	 * 
+	 * 
+	 * */
+	 public void plot(int xDim, int yDim, int [] nodes)
+	 {
+		 // Determine the number of observations assigned to each node
+		 int [] counts = new int[xDim * yDim];
+		 for(int i = 0; i < nodes.length; i++)
+		 {
+			 counts[nodes[i]] += 1;
+		 }
+		 // Determine the maximum and minimum counts for shading
+		 int maxCount = 0;
+		 int minCount = Integer.MAX_VALUE;
+		 for(int i = 0; i < counts.length; i++)
+		 {
+			if(counts[i] < minCount)
+			{
+				minCount = counts[i];
+			}
+			if(counts[i] > maxCount)
+			{
+				maxCount = counts[i];
+			}
+			//System.out.println("Node " + i + ": " + counts[i]);
+		 }
+		 // Create the window
+		 JFrame map = new JFrame ("Kohonen network");
+		 // Set the output resolution, don't let it exceed 1024x768
+		 //double aspectRatio = (double)xdim / yDim;
+		 String col = colorBox.getSelectedItem().toString();
+		 map.setSize(800, 600);
+		 map.setLayout (new GridLayout(xDim, yDim));
+
+		 // Plot the counts
+		 JButton [] jB = new JButton[counts.length];
+		 // Set the colors
+		 float r = 0;
+		 float g = 0;
+		 float b = 0;
+		 for(int i = 0; i < counts.length; i++)
+		 {
+			 if(col.equals("Red"))
+			 {
+				 r = (float)counts[i] / maxCount;
+			 }
+			 else if(col.equals("Green"))
+			 {
+				 g = (float)counts[i] / maxCount;
+			 }
+			 else
+			 {
+				 b = (float)counts[i] / maxCount;
+			 }
+			 jB[i] = new JButton("");
+			 jB[i].setBackground(new Color(r, g, b));
+			 jB[i].setOpaque(true);
+			 map.add(jB[i]);
+		 }
+		 map.setVisible(true); 
+	 }
+
 	class ButtonListener implements ActionListener 
 	{
 		/**
@@ -214,8 +290,7 @@ public Kohonen()
 		//Color
 		JLabel colorLabel = new JLabel("Shading");
 		window.add(colorLabel);
-		String [] colors = new String[]{"Red", "Green", "Blue"};
-		JComboBox<String> colorBox = new JComboBox<String>(colors);
+		//String [] colors = new String[]{"Red", "Green", "Blue"};
 		window.add(colorBox);
 
 		//Epochs