Working on new symbol options for deep learning and sud file options in SoundAcquisition GUI

src/Acquisition/FileInputSystem.java

@@ -180,7 +180,6 @@ public class FileInputSystem  extends DaqSystem implements ActionListener, PamSe
 
 		this.acquisitionDialog = acquisitionDialog;
 
-
 		return getDialogPanel();
 	}
 
@@ -197,7 +196,7 @@ public class FileInputSystem  extends DaqSystem implements ActionListener, PamSe
 
 	protected JPanel createDaqDialogPanel() {
 
-		JPanel p = new JPanel();
+		PamPanel p = new PamPanel();
 		p.setBorder(new TitledBorder("Select sound file"));
 		GridBagLayout layout = new GridBagLayout();
 		layout.columnWidths = new int[]{100, 100, 10};
@@ -252,6 +251,7 @@ public class FileInputSystem  extends DaqSystem implements ActionListener, PamSe
 		//		constraints.gridwidth = 2;
 		//		addComponent(p, fileDateText = new JTextField(), constraints);
 		//		fileDateText.setEnabled(false);
+
 		return p;
 
 	}

src/Acquisition/FolderInputSystem.java

@@ -32,6 +32,7 @@ import javafx.application.Platform;
 import pamguard.GlobalArguments;
 import Acquisition.pamAudio.PamAudioFileManager;
 import Acquisition.pamAudio.PamAudioFileFilter;
+import Acquisition.pamAudio.PamAudioFileLoader;
 import Acquisition.pamAudio.PamAudioSystem;
 import PamController.DataInputStore;
 import PamController.InputStoreInfo;
@@ -92,6 +93,12 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 	 * Text field for skipping initial few seconds of a file. 
 	 */
 	private JTextField skipSecondsField;
+	
+	/**
+	 * Panel which shows bespoke settings for certain audio loaders. Contains nothing
+	 * if the audio loader has no settings or no file is selected. 
+	 */
+	protected PamPanel audioLoaderHolder;
 
 	@Override
 	public boolean runFileAnalysis() {
@@ -170,6 +177,8 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 		}
 
 	}
+	
+	
 	@Override
 	protected JPanel createDaqDialogPanel() {
 		JPanel p = new JPanel();
@@ -228,6 +237,7 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 		constraints.gridwidth = 2;
 		constraints.fill = GridBagConstraints.NONE;
 		constraints.anchor = GridBagConstraints.WEST;
+
 		addComponent(p, mergeFiles = new JCheckBox("Merge contiguous files"), constraints);
 		if (PamController.getInstance().getRunMode() == PamController.RUN_PAMVIEW) {
 			constraints.gridx+=2;
@@ -236,18 +246,28 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 			checkFiles.addActionListener(new CheckFiles());
 		}
 
-//		if (SMRUEnable.isEnable()) {
+		//		if (SMRUEnable.isEnable()) {
 		// no reason to hide this option from users. 
-			constraints.gridy++;
+		constraints.gridy++;
-			constraints.gridx = 0;
+		constraints.gridx = 0;
-			constraints.gridwidth = 1;
+		constraints.gridwidth = 1;
-			addComponent(p,  new JLabel("Skip initial :"), constraints);
+		addComponent(p,  new JLabel("Skip initial :"), constraints);
-			constraints.gridx++;
+		constraints.gridx++;
-			addComponent(p, skipSecondsField = new JTextField(4), constraints);
+		addComponent(p, skipSecondsField = new JTextField(4), constraints);
-			constraints.gridx++;
+		constraints.gridx++;
-			addComponent(p,  new JLabel("seconds"), constraints);
+		addComponent(p,  new JLabel("seconds"), constraints);
-			constraints.anchor = GridBagConstraints.EAST;
+		constraints.anchor = GridBagConstraints.EAST;
-//		}
+		//		}
+
+
+		//panel to show bespoke settings for certain audio loaders. 
+		constraints.gridx = 0;
+		constraints.gridy++;
+		constraints.gridwidth = 3;
+		addComponent(p,  audioLoaderHolder = new PamPanel(), constraints);
+
+		GridBagLayout layout2 = new GridBagLayout();
+		audioLoaderHolder.setLayout(layout2);
 
 		return p;
 	}
@@ -525,10 +545,14 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 		List<WavFileType> asList = allFiles;
 		setSelectedFileTypes(acquisitionControl.soundFileTypes.getUsedTypes(allFiles));
 
+		//set the date of the first file. 
 		setFileDateText();
+		
+		//set any bespoke options for the files to be laoded. 
+		setFileOptionPanel();
+		
 		// also open up the first file and get the sample rate and number of channels from it
 		// and set these
-
 		File file = getCurrentFile();
 		if (file == null) return;
 		AudioInputStream audioStream;		
@@ -558,7 +582,7 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 		/****FX GUI stuff****/
 		if (folderInputPane!=null) {
 			Platform.runLater(()->{
-			folderInputPane.newFileList(fileListData); 
+				folderInputPane.newFileList(fileListData); 
 			});
 		}
 	}
@@ -572,7 +596,38 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 	protected int fudgeNumChannels(int nChannels) {
 		return nChannels;
 	}
+	
+	/**
+	 * Set bespoke options for certain file types. 
+	 */
+	public void setFileOptionPanel() {
+		getDialogPanel(); // make sure panel is created
 
+		audioLoaderHolder.removeAll();
+
+		if (allFiles.size() > 0) {
+			//Get all the audio file laoders that will be used for this list of files. Usually 
+			//just one but possible that there can be mixed files. 
+			ArrayList<PamAudioFileLoader> loaders = PamAudioFileManager.getInstance().getAudioFileLoaders(allFiles);
+
+			GridBagConstraints constraints = new GridBagConstraints();
+			constraints.gridx = 0;
+			constraints.gridy = 0;
+			for (PamAudioFileLoader loader : loaders) {
+				if (loader.getSettingsPane()!=null) {
+//					System.out.println("ADD AUDIO PANEL: " +loader.getSettingsPane().getAudioLoaderPanel());
+					//gridbag layout
+					addComponent(audioLoaderHolder, loader.getSettingsPane().getAudioLoaderPanel(), constraints);
+					constraints.gridy++;
+				}
+			}
+		}
+
+	}
+
+	/**
+	 * Show the date of the first file in the dialog. 
+	 */
 	public void setFileDateText() {
 		if (allFiles.size() > 0) {
 			long fileTime = getFileStartTime(getCurrentFile());

src/Acquisition/layoutFX/FolderInputPane.java

@@ -48,7 +48,7 @@ import pamViewFX.fxNodes.PamProgressBar;
 import pamViewFX.fxNodes.PamVBox;
 
 /**
- * Pane for the folder input of the sound acquisition. 
+ * JavaFX pane for the folder input of the sound acquisition. 
  * 
  * @author Jamie Macaulay 
  *

src/Acquisition/offlineFuncs/OfflineWavFileServer.java

@@ -178,7 +178,7 @@ public class OfflineWavFileServer extends OfflineFileServer<FileDataMapPoint> {
 			return false;
 		}
 		
-		PamAudioFileLoader audioFile = PamAudioFileManager.getInstance().getAudioLoader(mapPoint.getSoundFile()); 
+		PamAudioFileLoader audioFile = PamAudioFileManager.getInstance().getAudioFileLoader(mapPoint.getSoundFile()); 
 		
 		if (audioFile==null) {
 			System.err.println("OfflineWavFileServer: could not find audio loader for mapped sound file: " + mapPoint.getSoundFile()); 

src/Acquisition/pamAudio/FlacAudioFile.java

@@ -233,4 +233,10 @@ public class FlacAudioFile implements PamAudioFileLoader {
 		return (end.equals(".flac"));
 	}
 
+	@Override
+	public PamAudioSettingsPane getSettingsPane() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
 }

src/Acquisition/pamAudio/PamAudioFileLoader.java

@@ -48,5 +48,11 @@ public interface PamAudioFileLoader {
 	public boolean loadAudioData(OfflineFileServer offlineFileServer, PamDataBlock dataBlock,
 			OfflineDataLoadInfo offlineDataLoadInfo, ViewLoadObserver loadObserver); 
 	
+	/**
+	 * Get a settings pane for the audio loader
+	 * @return settings pane for audio loader - can be null. 
+	 */
+	public PamAudioSettingsPane getSettingsPane();
+	
 
 }

src/Acquisition/pamAudio/PamAudioFileManager.java

@@ -56,7 +56,7 @@ public class PamAudioFileManager {
 	 * @param soundFile - the sound file
 	 * @return the audio file loader.
 	 */
-	public PamAudioFileLoader getAudioLoader(File soundFile) {
+	public PamAudioFileLoader getAudioFileLoader(File soundFile) {
 		for (int i = 0; i < pamAudioFileTypes.size(); i++) {
 			if (isExtension(soundFile, pamAudioFileTypes.get(i))) {
 				return pamAudioFileTypes.get(i);
@@ -169,6 +169,23 @@ public class PamAudioFileManager {
 	public ArrayList<PamAudioFileLoader> getAudioFileLoaders() {
 		return this.pamAudioFileTypes;
 	}
+	
+	/**
+	 * Get the loaders which are needed to open a list of files
+	 * @param  files - the files to find audio loaders for. 
+	 * @return a list of the  audio loaders required for the file list
+	 */
+	public ArrayList<PamAudioFileLoader> getAudioFileLoaders(ArrayList<? extends File> files) {
+		ArrayList<PamAudioFileLoader> audioLoaders = new ArrayList<PamAudioFileLoader>(); 
+		PamAudioFileLoader loader;
+		for (int i=0; i<files.size(); i++) {
+			 loader =  getAudioFileLoader(files.get(i)); 
+			 if (!audioLoaders.contains(loader)) {
+				 audioLoaders.add(loader); 
+			 }
+		}
+		return audioLoaders;
+	}
 
 	/**
 	 * Get the default file loader for raw files. 

src/Acquisition/pamAudio/PamAudioSettingsPane.java

@@ -0,0 +1,21 @@
+package Acquisition.pamAudio;
+
+import PamView.panel.PamPanel;
+import javafx.scene.layout.Pane;
+
+public interface PamAudioSettingsPane {
+	
+	/**
+	 * Get the JavaFX pane for loading audio. 
+	 * @return
+	 */
+	public Pane getAudioLoaderPane();
+	
+	/**
+	 * Get the swing audio loader pane. 
+	 * @return
+	 */
+	public PamPanel getAudioLoaderPanel();
+
+
+}

src/Acquisition/pamAudio/SudAudioFile.java

@@ -12,6 +12,7 @@ import javax.swing.SwingUtilities;
 import org.pamguard.x3.sud.ChunkHeader;
 import org.pamguard.x3.sud.SudMapListener;
 
+import Acquisition.sud.SudAudioSettingsPane;
 import PamController.PamController;
 import PamUtils.worker.PamWorkProgressMessage;
 import PamUtils.worker.PamWorkWrapper;
@@ -37,6 +38,11 @@ public class SudAudioFile extends WavAudioFile {
 	private volatile PamWorker<AudioInputStream> worker;
 	private volatile SudMapWorker sudMapWorker;
 
+	/**
+	 * Settings pane to allow users to set some additional options.  
+	 */
+	private SudAudioSettingsPane sudAudioSettingsPane;
+
 	public SudAudioFile() {
 		super();
 		fileExtensions = new ArrayList<String>(Arrays.asList(new String[] { ".sud" }));
@@ -216,5 +222,13 @@ public class SudAudioFile extends WavAudioFile {
 		}
 
 	}
+	
+	@Override
+	public PamAudioSettingsPane getSettingsPane() {
+		if (sudAudioSettingsPane==null) {
+			sudAudioSettingsPane = new SudAudioSettingsPane(this); 
+		}
+		return sudAudioSettingsPane;
+	}
 
 }

src/Acquisition/pamAudio/WavAudioFile.java

@@ -296,5 +296,11 @@ public class WavAudioFile implements PamAudioFileLoader {
 		}
 	}
 
+	@Override
+	public PamAudioSettingsPane getSettingsPane() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
 
 }

src/Acquisition/sud/SudAudioSettingsPane.java

@@ -0,0 +1,41 @@
+package Acquisition.sud;
+
+import javax.swing.JLabel;
+
+import Acquisition.pamAudio.PamAudioSettingsPane;
+import Acquisition.pamAudio.SudAudioFile;
+import PamView.panel.PamPanel;
+import javafx.scene.layout.Pane;
+
+public class SudAudioSettingsPane implements PamAudioSettingsPane {
+	
+	private SudAudioFile sudAudioFile;
+	
+	private PamPanel sudAudioPanel;
+
+	public SudAudioSettingsPane(SudAudioFile sudAudioFile) {
+		this.sudAudioFile=sudAudioFile; 
+	}
+
+	@Override
+	public Pane getAudioLoaderPane() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public PamPanel getAudioLoaderPanel() {
+		if (sudAudioPanel==null) {
+			createSudAudioPanel(); 
+		}
+		return sudAudioPanel;
+	}
+
+	private void createSudAudioPanel() {
+		sudAudioPanel = new PamPanel(); 
+		
+		sudAudioPanel.add(new JLabel("Hello"));
+		
+	}
+
+}

src/PamUtils/PamArrayUtils.java

@@ -564,6 +564,55 @@ public class PamArrayUtils {
 		return index;
 	}
 	
+	/**
+	 * Get the index of the maximum value in an array 
+	 * @param arr  - the array to find the position of the maximum value. 
+	 * m value of. 
+	 * @return the index of the maximum value
+	 */
+	public static int maxPos(float[] arr) {
+		double max = Double.NEGATIVE_INFINITY;
+		int index = -1; 
+		
+		int count = 0; 
+		for(float cur: arr) {
+			if (cur>max) {
+				index = count; 
+				max=cur;
+			}
+			count++; 
+		}
+		
+
+		return index;
+	}
+	
+	/**
+	 * Get the index of the maximum value within a 2D matrix
+	 * @param arr  - the array to find the position of the maximum value. 
+	 * m value of. 
+	 * @return the index i and j of the maximum value 
+	 */
+	public static int[] maxPos(float[][] arr) {
+		float max = Float.NEGATIVE_INFINITY;
+		int[] index = new int[] {-1,-1};
+
+		//		int count = 0; 
+		float cur;
+		for(int i=0; i<arr.length; i++) {
+			for(int j=0; j<arr.length; j++) {
+				cur = arr[i][j];
+				if (cur>max) {
+					index[0]=i;
+					index[1]=j;
+					max=cur;
+				}
+				//			count++; 
+			}
+		}
+		return index;
+	}
+	
 	/**
 	 * Get the minimum index of an array
 	 * @param arr  - the array to find the position of the maximum value. 

src/pamViewFX/fxNodes/utilsFX/ColourArray.java

@@ -244,7 +244,6 @@ public class ColourArray implements Cloneable, Serializable{
 			colors[4]=Color.web("#0000ff");
 			colors[5]=Color.web("#ff00ff");
 			colors[6]=Color.web("#ff0000");
-
 			return colors; 
 		case PATRIOTIC:
 			colors=new Color[3];
@@ -254,22 +253,22 @@ public class ColourArray implements Cloneable, Serializable{
 			return colors; 
 		case MATLAB:
 			colors=new Color[7];
-			colors[0]= Color.color( 0,    0.4470,    0.7410);
+			colors[0]= Color.color(0,    	 0.4470,    0.7410);
-			colors[1]= Color.color(0.8500 ,   0.3250   , 0.0980);
+			colors[1]= Color.color(0.8500,   0.3250,	0.0980);
-			colors[2]=  Color.color(0.9290 ,   0.6940 ,   0.1250);
+			colors[2]=  Color.color(0.9290,  0.6940,   	0.1250);
-			colors[3]= Color.color( 0.4940 ,   0.1840 ,   0.5560);
+			colors[3]= Color.color(0.4940,   0.1840,   	0.5560);
-			colors[4]= Color.color(0.4660 ,   0.6740 ,   0.1880);
+			colors[4]= Color.color(0.4660,   0.6740,   	0.1880);
-			colors[5]= Color.color( 0.3010 ,   0.7450 ,   0.9330);
+			colors[5]= Color.color(0.3010,   0.7450,   	0.9330);
-			colors[6]= Color.color(   0.6350  ,  0.0780 ,   0.1840);
+			colors[6]= Color.color(0.6350,   0.0780,   	0.1840);
 			return colors; 
 		case PARULA:
 			colors=new Color[6];
-			colors[0]= Color.color(  0.24220,  0.150400,   0.66030);
+			colors[0]= Color.color(0.24220,  0.150400, 0.66030);
-			colors[1]= Color.color(  0.264700 ,0.403000  , 0.993500);
+			colors[1]= Color.color(0.264700, 0.403000, 0.993500);
-			colors[2]= Color.color(  0.108500,  0.66690 ,  0.873400);
+			colors[2]= Color.color(0.108500, 0.66690,  0.873400);
-			colors[3]= Color.color(  0.280900 , 0.796400,   0.526600);
+			colors[3]= Color.color(0.280900, 0.796400, 0.526600);
-			colors[4]= Color.color(  0.918400,  0.73080  , 0.18900);
+			colors[4]= Color.color(0.918400, 0.73080,  0.18900);
-			colors[5]= Color.color(  0.9769 , 0.98390   ,0.0805000);
+			colors[5]= Color.color(0.9769,   0.98390,  0.0805000);
 			return colors; 
 		case INFERNO:
 			return InfernoColorMap.getInfernoColourMap();

src/pamViewFX/fxNodes/utilsFX/PamUtilsFX.java

@@ -632,13 +632,37 @@ public class PamUtilsFX {
 	 * @param color - the color. 
 	 * @return the color. 
 	 */
-	 public static String toRGBCode( Color color )
+	public static String toRGBCode( Color color ){
-	    {
+		return String.format( "#%02X%02X%02X",
-	        return String.format( "#%02X%02X%02X",
+				(int)( color.getRed() * 255 ),
-	            (int)( color.getRed() * 255 ),
+				(int)( color.getGreen() * 255 ),
-	            (int)( color.getGreen() * 255 ),
+				(int)( color.getBlue() * 255 ) );
-	            (int)( color.getBlue() * 255 ) );
+	}
-	    }
+	 
+	 
+	 /**
+	  * Convert a colour to an int.
+	  * @param c - the colour to change.
+	  * @return the int representation of the colour
+	  */
+	 public static int colorToInt(Color c) {
+		    int r = (int) Math.round(c.getRed() * 255);
+		    int g = (int) Math.round(c.getGreen() * 255);
+		    int b = (int) Math.round(c.getBlue() * 255);
+		    return (r << 16) | (g << 8) | b;
+		}
+	 
+	 /**
+	  * Convert an int encoded with a colour to a Color object. 
+	  * @param value - the int to convert to colour
+	  * @return the Color object for the int
+	  */
+	 public static Color intToColor(int value) {
+		    int r = (value >>> 16) & 0xFF;
+		    int g = (value >>> 8) & 0xFF;
+		    int b = value & 0xFF;
+		    return Color.rgb(r,g,b);
+		}
 	
 
 }

src/rawDeepLearningClassifier/dataPlotFX/DLSymbolModifier.java

@@ -2,6 +2,7 @@ package rawDeepLearningClassifier.dataPlotFX;
 
 import java.awt.Color;
 
+import PamUtils.PamArrayUtils;
 import PamView.GeneralProjector;
 import PamView.PamSymbolType;
 import PamView.symbol.PamSymbolChooser;
@@ -20,7 +21,8 @@ import rawDeepLearningClassifier.logging.DLAnnotationType;
 
 
 /**
- * The DL symbol modifier. Colours symbols by prediction.
+ * The DL symbol modifier. Colours symbols by eother the vlaue of the prediction by a user selected class
+ * or by the class with the highest prediction value. 
  * 
  * @author Jamie Macaulay. 
  *
@@ -94,7 +96,70 @@ public class DLSymbolModifier extends SymbolModifier {
 			return null; 
 		}	
 		
-		//System.out.println("Class index: " + dlSymbolOptions.classIndex); 
+		
+		//modify the default symbol
+		if (dlSymbolOptions.colTypeSelection == DLSymbolModifierParams.PREDICITON_COL) {
+			getSymbolDataPred(annotation);
+		}
+		
+		else if (dlSymbolOptions.colTypeSelection == DLSymbolModifierParams.CLASS_COL) {
+			getSymbolDataClass(annotation);
+		}
+		
+		return symbolData;
+	}
+	
+	/**
+	 * Get symbol data for colouring by the species class with the maximum prediction
+	 * @param annotation - the annotation
+	 * @return symbol data for colouring by class maximum. 
+	 */
+	private SymbolData getSymbolDataClass(DLAnnotation annotation ) {
+
+		boolean passed = false; 
+		int colIndex = -1; 
+		
+		float[][] results = new float[ annotation.getModelResults().size()][]; 
+		
+		//A detection might have multiple prediction results, i.e. predictions are a matrix. Need 
+		//to iterate through all the predictions and then work out whihc is the maximum. That index is then then]
+		//class colour. 
+		int i=0;
+		for (PredictionResult modelResult: annotation.getModelResults()) {
+			if (modelResult.isBinaryClassification()) passed = true; 
+			results[i] = modelResult.getPrediction();
+			i++;
+		}
+		
+		int[] indexBest = PamArrayUtils.maxPos(results); 
+		
+		
+		if (passed || !dlSymbolOptions.showOnlyBinary) {
+			//work out the class colour...
+						
+			javafx.scene.paint.Color color = PamUtilsFX.intToColor(dlSymbolOptions.classColors[indexBest[1]]);
+			
+			Color colorAWT = PamUtilsFX.fxToAWTColor(color);
+			
+			symbolData.setFillColor(colorAWT);
+			symbolData.setLineColor(colorAWT);
+
+			return symbolData; 
+		}
+		else {
+			//has data but we have only show binary option selected. 
+			return null; 
+		}
+		
+	}
+	
+	
+	/**
+	 * Get symbol data for colouring by the prediction value for a selected species class. 
+	 * @param annotation - the annotation
+	 * @return symbol data for colouring by prediction value for a selected species class. 
+	 */
+	private SymbolData getSymbolDataPred(DLAnnotation annotation ) {
 		
 		if (dlSymbolOptions.classIndex<0) {
 			dlSymbolOptions.classIndex=0;

src/rawDeepLearningClassifier/dataPlotFX/DLSymbolModifierParams.java

@@ -1,7 +1,10 @@
 package rawDeepLearningClassifier.dataPlotFX;
 
+
 import PamView.symbol.modifier.SymbolModifierParams;
+import javafx.scene.paint.Color;
 import pamViewFX.fxNodes.utilsFX.ColourArray.ColourArrayType;
+import pamViewFX.fxNodes.utilsFX.PamUtilsFX;
 
 /**
  * Parameters for colouring symbols by deep learning probability. 
@@ -10,11 +13,28 @@ import pamViewFX.fxNodes.utilsFX.ColourArray.ColourArrayType;
  *
  */
 public class DLSymbolModifierParams extends SymbolModifierParams {
+	
+	public DLSymbolModifierParams() {
+		setDefaultClassColors(32);
+	}
 
 	/**
 	 * 
 	 */
-	private static final long serialVersionUID = 1L;
+	private static final long serialVersionUID = 3L;
+	
+	
+	public static final int PREDICITON_COL = 0;
+
+	public static final int CLASS_COL = 1;
+	
+	/**
+	 * The way to colour the predictions.
+	 */
+	public int colTypeSelection = PREDICITON_COL;
+	
+	
+	/****Prediction colours****/
 	
 	/**
 	 * The colour limits.
@@ -27,16 +47,72 @@ public class DLSymbolModifierParams extends SymbolModifierParams {
 	 */
 	public int classIndex = 0; 
 	
+	
+	/*******Class colours******/
+	
 	/**
-	 * Show only binary. 
+	 * The current colours for each 
 	 */
-	public boolean showOnlyBinary = false;
+	public int[] classColors = new int[32];
-
+	
+	/**
+	 * The currently selected class for colour picker- just so the user sees the same selection. 
+	 */
+	public int classIndex2 = 0;
+	
 	/**
 	 * The colour array to show. 
 	 */
 	public ColourArrayType colArray  = ColourArrayType.FIRE; 
 	
+	/***************************/
+	
+	
+	/**
+	 * Show only detections which have passed a decision threshold.
+	 */
+	public boolean showOnlyBinary = false;
+
+	/**
+	 * Set the default colours. 
+	 * @param num - the number of colours to set. 
+	 */
+	public void setDefaultClassColors(int num) {
+		if (classColors==null || classColors.length<num) {
+			classColors = new int[32];
+		}
+		
+		//run through default colours
+		for (int i=0; i<classColors.length; i++) {
+			switch (i%8) {
+			case 0:
+				classColors[i]=PamUtilsFX.colorToInt(Color.RED);
+				break;
+			case 1:
+				classColors[i]=PamUtilsFX.colorToInt(Color.GREEN);
+				break;
+			case 2:
+				classColors[i]=PamUtilsFX.colorToInt(Color.BLUE);
+				break;
+			case 3:
+				classColors[i]=PamUtilsFX.colorToInt(Color.CYAN);
+				break;
+			case 4:
+				classColors[i]=PamUtilsFX.colorToInt(Color.MAGENTA);
+				break;
+			case 5:
+				classColors[i]=PamUtilsFX.colorToInt(Color.YELLOW);
+				break;
+			case 6:
+				classColors[i]=PamUtilsFX.colorToInt(Color.ORANGE);
+				break;
+			case 7:
+				classColors[i]=PamUtilsFX.colorToInt(Color.PURPLE);
+				break;
+
+			}
+		}
+	}
 
 	@Override
 	protected DLSymbolModifierParams clone()  {

src/rawDeepLearningClassifier/dataPlotFX/DLSymbolOptionPane.java

@@ -1,20 +1,29 @@
 package rawDeepLearningClassifier.dataPlotFX;
 
+import org.controlsfx.control.SegmentedButton;
+
 import PamView.symbol.StandardSymbolOptions;
 import PamView.symbol.modifier.SymbolModifier;
-import PamView.symbol.modifier.SymbolModifierParams;
 import javafx.geometry.Insets;
 import javafx.geometry.Orientation;
 import javafx.geometry.Pos;
 import javafx.scene.control.CheckBox;
+import javafx.scene.control.ColorPicker;
 import javafx.scene.control.ComboBox;
 import javafx.scene.control.Label;
+import javafx.scene.control.ToggleButton;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.BorderPane;
+import javafx.scene.layout.HBox;
 import javafx.scene.layout.Pane;
+import javafx.scene.layout.Priority;
+import pamViewFX.fxNodes.PamBorderPane;
 import pamViewFX.fxNodes.PamHBox;
 import pamViewFX.fxNodes.PamVBox;
 import pamViewFX.fxNodes.comboBox.ColorComboBox;
 import pamViewFX.fxNodes.sliders.ColourRangeSlider;
 import pamViewFX.fxNodes.utilsFX.ColourArray;
+import pamViewFX.fxNodes.utilsFX.PamUtilsFX;
 import pamViewFX.symbol.StandardSymbolModifierPane;
 import rawDeepLearningClassifier.dlClassification.DLClassName;
 
@@ -25,6 +34,8 @@ import rawDeepLearningClassifier.dlClassification.DLClassName;
 public class DLSymbolOptionPane extends StandardSymbolModifierPane {
 	
 	
+	private static final double CLASS_NAME_BOX_WIDTH = 130;
+
 	/**
 	 * The colour range slider for colouring probabilities. 
 	 */
@@ -42,20 +53,138 @@ public class DLSymbolOptionPane extends StandardSymbolModifierPane {
 
 	
 	/**
-	 * Combo box which allows a user to select colour
+	 * Color picker which allows a user to select the gradient for colouring predictions
 	 */
 	private ColorComboBox colourBox;
 	
+	/**
+	 * Color picker which allows a user to select colour for each class. 
+	 */
+	private ColorPicker colourPicker;
+	
 	private boolean initialised=true;
 
-	private DLSymbolModifier dlSymbolModifier; 
+	private DLSymbolModifier dlSymbolModifier;
+	
+	private ComboBox<String> classNameBox2;
+
+	/**
+	 * Pane which holds controls for changing the colour based on prediciton value
+	 */
+	private Pane probPane;
+
+	/**
+	 * Pane which holds controls for changing the colour based on the highest prediction value
+	 */
+	private Pane classPane;
+
+	
+	private PamBorderPane holder;
+
+	/**
+	 * Button to select how to colour. 
+	 */
+	private ToggleButton b1, b2; 
 
 	public DLSymbolOptionPane(SymbolModifier symbolModifer) {
 		super(symbolModifer, Orientation.HORIZONTAL, true, 0);
-		this.setBottom(createProbPane());
+		
+		probPane = 	createProbPane();
+		classPane = 	createClassPane();
+		classPane.setPadding(new Insets(0,0,5,0));
+
+		b1 = new ToggleButton("Prediction");
+		b1.setPrefWidth(80);
+		b1.setStyle("-fx-border-radius: 5 0 0 5; -fx-background-radius: 5 0 0 5;");
+		
+		b2 = new ToggleButton("Class");
+		b2.setPrefWidth(80);
+		
+		b1.setOnAction((a)->{
+			setSettingsPane();
+			//change the colour of the colour range slider.     
+			notifySettingsListeners();
+		});
+		b2.setStyle("-fx-border-radius: 0 5 5 0;  -fx-background-radius: 0 5 5 0;");
+		
+		
+		b2.setOnAction((a)->{
+			setSettingsPane();
+			//change the colour of the colour range slider.     
+			notifySettingsListeners();
+		});
+		
+		SegmentedButton segmentedButton = new SegmentedButton();    
+		segmentedButton.getButtons().addAll(b1, b2);
+		segmentedButton.setPadding(new Insets(5,0,5,0));
+		
+		BorderPane.setAlignment(segmentedButton, Pos.CENTER);
+		b1.setSelected(true);
+		
+		showOnlyBinary = new CheckBox("Show only binary classificaiton"); 
+		showOnlyBinary.setOnAction((action)->{                
+			getParams();
+			//change the colour of the colour range slider.     
+			notifySettingsListeners();
+		});
+		showOnlyBinary.setTooltip(new Tooltip("Colour detections only if they passed decision threshold"));
+
+		holder = new PamBorderPane(); 
+
+		holder.setTop(segmentedButton);
+		holder.setCenter(probPane);
+		holder.setBottom(showOnlyBinary);
+
+		this.setBottom(holder);
+		
 		this.dlSymbolModifier = (DLSymbolModifier) symbolModifer; 
 		initialised=true; 
 	}
+	
+	private void setSettingsPane() {
+		if (b1.isSelected()) {
+			holder.setCenter(probPane);
+		}
+		if (b2.isSelected()) {
+			holder.setCenter(classPane);
+		}
+	}
+	
+	
+	private Pane createClassPane() {
+		
+		classNameBox2 = new ComboBox<String>(); 
+		classNameBox2.setOnAction((action)->{                
+			getParams();
+			//change the colour of the colour range slider.     
+			notifySettingsListeners();
+		});
+		classNameBox2.setMaxWidth(Double.MAX_VALUE);
+		
+		classNameBox2.setOnAction((action)->{                
+			colourPicker.setValue(PamUtilsFX.intToColor(dlSymbolModifier.getSymbolModifierParams().classColors[classNameBox2.getSelectionModel().getSelectedIndex()]));
+		});
+		
+		classNameBox2.setPrefWidth(CLASS_NAME_BOX_WIDTH);
+
+		colourPicker = new ColorPicker();
+		colourPicker.setPrefWidth(60);
+		colourPicker.setOnAction((action)->{                
+			getParams();
+			notifySettingsListeners();
+		});
+		
+		HBox.setHgrow(classNameBox, Priority.ALWAYS);
+
+		PamHBox classHolder = new PamHBox(); 
+		classHolder.setSpacing(5);
+		classHolder.setAlignment(Pos.CENTER_LEFT);
+		classHolder.getChildren().addAll(classNameBox2, colourPicker); 
+		
+		return classHolder; 
+
+	}
+
 
 	private Pane createProbPane() {
 				
@@ -82,6 +211,8 @@ public class DLSymbolOptionPane extends StandardSymbolModifierPane {
 			//change the colour of the colour range slider.     
 			notifySettingsListeners();
 		});
+		classNameBox.setPrefWidth(CLASS_NAME_BOX_WIDTH);
+
 
 		colourBox = new ColorComboBox(ColorComboBox.COLOUR_ARRAY_BOX); 
 		colourBox.setPrefWidth(50); 
@@ -92,17 +223,10 @@ public class DLSymbolOptionPane extends StandardSymbolModifierPane {
 			colourRangeSlider.setColourArrayType( dlSymbolModifier.getSymbolModifierParams().colArray);
 		});
 
-		showOnlyBinary = new CheckBox("Show only binary classificaiton"); 
-		showOnlyBinary.setOnAction((action)->{                
-			getParams();
-			//change the colour of the colour range slider.     
-			notifySettingsListeners();
-		});
-
 		PamHBox classHolder = new PamHBox(); 
 		classHolder.setSpacing(5);
 		classHolder.setAlignment(Pos.CENTER_LEFT);
-		classHolder.getChildren().addAll(new Label("Show Class"), classNameBox); 
+		classHolder.getChildren().addAll(new Label("Show class"), classNameBox); 
 		
 		PamHBox colorHolder = new PamHBox(); 
 		colorHolder.setSpacing(5);
@@ -112,7 +236,7 @@ public class DLSymbolOptionPane extends StandardSymbolModifierPane {
 		holder.getChildren().addAll(classHolder, new Label("Probability"), colorHolder); 
 		
 
-		holder.getChildren().add(showOnlyBinary); 
+//		holder.getChildren().add(showOnlyBinary); 
 		holder.setPadding(new Insets(5,0,5,0));
 
 		setParams = false; 
@@ -120,35 +244,68 @@ public class DLSymbolOptionPane extends StandardSymbolModifierPane {
 		return holder; 
 	}
 	
-	@Override
+	
-	public StandardSymbolOptions getParams(){
+	/**
-		StandardSymbolOptions standardSymbolOptions  = super.getParams(); 
+	 * get parameters for colouring by class. 
+	 * @param symbolOptions - the symbol options. 
+	 * @return
+	 */
+	public DLSymbolModifierParams getClassColParams(DLSymbolModifierParams symbolOptions ) {
+
+		int index = classNameBox2.getSelectionModel().getSelectedIndex()>=0 ? classNameBox2.getSelectionModel().getSelectedIndex():0;
 		
-
+		symbolOptions.classColors[index] = PamUtilsFX.colorToInt(colourPicker.getValue());
-		//bit messy but works / 
+		
-		DLSymbolModifierParams symbolOptions =  dlSymbolModifier.getSymbolModifierParams(); 
+		symbolOptions.classIndex2 = classNameBox2.getSelectionModel().getSelectedIndex(); 
+		
+		return symbolOptions; 
+	}
+	
+	/**
+	 * 
+	 * @param symbolOptions
+	 * @return
+	 */
+	public DLSymbolModifierParams getPredictionColParams(DLSymbolModifierParams symbolOptions ) {
 		
-		//need to chekc this here. 
-		//checkClassNamesBox(symbolOptions); 
-
-
 		symbolOptions.clims=new double[] {colourRangeSlider.getLowValue(), colourRangeSlider.getHighValue()};
 		
 		symbolOptions.colArray = ColourArray.getColorArrayType(this.colourBox.getSelectionModel().getSelectedItem()); 
 		
 		symbolOptions.classIndex = classNameBox.getSelectionModel().getSelectedIndex(); 
 		
+		return symbolOptions; 
+	}
+	
+	
+	@Override
+	public StandardSymbolOptions getParams(){
+		StandardSymbolOptions standardSymbolOptions  = super.getParams(); 
+		
+		//bit messy but works
+		DLSymbolModifierParams symbolOptions =  dlSymbolModifier.getSymbolModifierParams(); 
+		
+		//need to check this here. 
+		//checkClassNamesBox(symbolOptions); 
+		
+		if (b1.isSelected()) symbolOptions.colTypeSelection = DLSymbolModifierParams.PREDICITON_COL;
+		if (b2.isSelected()) symbolOptions.colTypeSelection = DLSymbolModifierParams.CLASS_COL;
+		
+		//get parameters for colouring 
+		symbolOptions = getClassColParams(symbolOptions);
+
+		//get parameters for colouring by prediction value
+		symbolOptions = getPredictionColParams(symbolOptions) ;
+		
 		symbolOptions.showOnlyBinary = showOnlyBinary.isSelected(); 
 		
 		dlSymbolModifier.checkColourArray(); 
 
-		//System.out.println("Get params: " ); 
-
 		return standardSymbolOptions; 
-
 	}
 	
-	private void checkClassNamesBox(DLSymbolModifierParams symbolOptions) {
+	
+	private int checkClassNamesBox(DLSymbolModifierParams symbolOptions, ComboBox<String> classNameBox) {
 		
 		DLClassName[] classNames = dlSymbolModifier.getDLAnnotType().getDlControl().getDLModel().getClassNames(); 
 		
@@ -167,8 +324,51 @@ public class DLSymbolOptionPane extends StandardSymbolModifierPane {
 				classNameBox.getItems().add("Class: " +  i);
 			}
 		}
+		
+		return nClass;
+	
+	}
+	
+	/**
+	 * Set parameters for controls to change the colour gradient based on prediction. 
+	 * @param symbolOptions - the symbol options
+	 */
+	private void setPredictionColParams(DLSymbolModifierParams symbolOptions) {
+				
+		//now set frequency parameters 
+		colourRangeSlider.setLowValue(symbolOptions.clims[0]);
+		colourRangeSlider.setHighValue(symbolOptions.clims[1]);
+		colourRangeSlider.setColourArrayType( symbolOptions.colArray);
+
+		
+		int nClass = checkClassNamesBox( symbolOptions, classNameBox); 
 		symbolOptions.classIndex = Math.min(symbolOptions.classIndex, nClass-1); 
 		classNameBox.getSelectionModel().select(Math.max(symbolOptions.classIndex, 0));
+		
+		//color box.
+		colourBox.setValue(symbolOptions.colArray);
+	}
+	
+	/**
+	 * Set parameters for controls to change the colour gradient based on prediction. 
+	 * @param symbolOptions - the symbol options
+	 */
+	private void setClassColParams(DLSymbolModifierParams symbolOptions) {
+		
+		int nClass = checkClassNamesBox( symbolOptions, classNameBox2); 
+		
+		symbolOptions.classIndex = Math.min(symbolOptions.classIndex, nClass-1); 
+		classNameBox2.getSelectionModel().select(Math.max(symbolOptions.classIndex2, 0));
+		
+		
+		int index = symbolOptions.classIndex2>=0? symbolOptions.classIndex2 : 0;
+		
+		if (symbolOptions.classColors==null) {
+			symbolOptions.setDefaultClassColors(nClass);
+		}
+		
+		//set the correct colour
+		colourPicker.setValue(PamUtilsFX.intToColor(symbolOptions.classColors[index]));
 	}
 
 	@Override
@@ -180,24 +380,27 @@ public class DLSymbolOptionPane extends StandardSymbolModifierPane {
 
 			setParams = true; 
 
-//			StandardSymbolOptions standardSymbolOptions = (StandardSymbolOptions) getSymbolModifier().getSymbolChooser().getSymbolOptions();
+			//get the symbool options
-			
 			DLSymbolModifierParams symbolOptions =  dlSymbolModifier.getSymbolModifierParams(); 
-			//now set frequency parameters 
-			colourRangeSlider.setLowValue(symbolOptions.clims[0]);
-			colourRangeSlider.setHighValue(symbolOptions.clims[1]);
-			colourRangeSlider.setColourArrayType( symbolOptions.colArray);
-
 			
-			//set the combo box class types. 
+//			b1.setSelected(false);
-			checkClassNamesBox( symbolOptions); 
+//			b2.setSelected(false);
+			if (symbolOptions.colTypeSelection == DLSymbolModifierParams.PREDICITON_COL) b1.setSelected(true);
+			if (symbolOptions.colTypeSelection == DLSymbolModifierParams.PREDICITON_COL) b2.setSelected(true);
 			
+			setSettingsPane();
 			
-			//color box.
+			symbolOptions.colTypeSelection = b1.isSelected() ? DLSymbolModifierParams.PREDICITON_COL : DLSymbolModifierParams.CLASS_COL;
-			colourBox.setValue(symbolOptions.colArray);
+			
+			//set the parameters for colouring by prediction
+			setPredictionColParams(symbolOptions);
+			
+			//set the class colour parameters
+			setClassColParams(symbolOptions);
 			
 			//set the selected. 
 			showOnlyBinary.setSelected(symbolOptions.showOnlyBinary);
+			
 
 			setParams = false; 
 	}