Merge branch 'main' of https://github.com/douggillespie/PAMGuard.git into main

.classpath

@@ -1,11 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry including="**/*.java" kind="src" output="target/classes" path="src">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
@@ -16,5 +10,11 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry including="**/*.java" kind="src" output="target/classes" path="src">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

.gitignore

@@ -21,6 +21,7 @@
 *.zip
 *.tar.gz
 *.rar
+*.dll
 
 # eclipse project file
 .project

.settings/org.eclipse.jdt.core.prefs

@@ -1,7 +1,12 @@
 eclipse.preferences.version=1
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
 org.eclipse.jdt.core.compiler.codegen.targetPlatform=11
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
 org.eclipse.jdt.core.compiler.compliance=11
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
 org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
 org.eclipse.jdt.core.compiler.problem.enumIdentifier=error

buildconfigurations/Build PAMGuard.launch

@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<launchConfiguration type="org.eclipse.m2e.Maven2LaunchConfigurationType">
-    <booleanAttribute key="M2_DEBUG_OUTPUT" value="false"/>
-    <stringAttribute key="M2_GOALS" value="package shade:shade"/>
-    <booleanAttribute key="M2_NON_RECURSIVE" value="false"/>
-    <booleanAttribute key="M2_OFFLINE" value="false"/>
-    <stringAttribute key="M2_PROFILES" value=""/>
-    <listAttribute key="M2_PROPERTIES"/>
-    <stringAttribute key="M2_RUNTIME" value="EMBEDDED"/>
-    <booleanAttribute key="M2_SKIP_TESTS" value="true"/>
-    <intAttribute key="M2_THREADS" value="1"/>
-    <booleanAttribute key="M2_UPDATE_SNAPSHOTS" value="false"/>
-    <stringAttribute key="M2_USER_SETTINGS" value=""/>
-    <booleanAttribute key="M2_WORKSPACE_RESOLUTION" value="false"/>
-    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_ATTR_USE_ARGFILE" value="false"/>
-    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_SHOW_CODEDETAILS_IN_EXCEPTION_MESSAGES" value="true"/>
-    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_CLASSPATH_ONLY_JAR" value="false"/>
-    <stringAttribute key="org.eclipse.jdt.launching.JRE_CONTAINER" value="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-13/"/>
-    <stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-mx6000m&#13;&#10;-Djava.library.path=lib64"/>
-    <stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${workspace_loc:/PamGuard Main}"/>
-</launchConfiguration>

dependency-reduced-pom.xml

@@ -4,7 +4,7 @@
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
   <name>Pamguard Java12+</name>
-  <version>2.02.03</version>
+  <version>2.02.04</version>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
   <url>www.pamguard.org</url>
   <organization>

pom.xml

@@ -4,7 +4,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
-  <version>2.02.03</version>
+  <version>2.02.04</version>
   <name>Pamguard Java12+</name>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
 	<url>www.pamguard.org</url>

src/Acquisition/layoutFX/CheckWavHeadersPane.java

@@ -7,6 +7,7 @@ import Acquisition.FolderInputSystem;
 import Acquisition.WavFileFuncs;
 import PamUtils.PamAudioFileFilter;
 import javafx.geometry.Insets;
+import javafx.application.Platform;
 import javafx.beans.property.SimpleDoubleProperty;
 import javafx.concurrent.Task;
 import javafx.geometry.Pos;
@@ -89,6 +90,8 @@ public class CheckWavHeadersPane extends PamBorderPane {
 	 */
 	private SimpleDoubleProperty progressProperty = new SimpleDoubleProperty(0);
 
+	private PamButton runButton;
+
 	/**
 	 * Constructor for the CheckWavHeadersPane
 	 * @param folderInputSystem - the folder input system. 
@@ -102,20 +105,19 @@ public class CheckWavHeadersPane extends PamBorderPane {
 		this.folderInputSystem=folderInputSystem;
 
 		folderName = new Label(" ");
-		PamGuiManagerFX.titleFont2style(folderName);
+		//PamGuiManagerFX.titleFont2style(folderName);
 		
 		textArea = new TextArea();
 		textArea.setEditable(false);
 		ScrollPane scrollPane = new ScrollPane(textArea);
 		scrollPane.setHbarPolicy(ScrollBarPolicy.NEVER);
 		//scrollPane.setPrefSize(322, 300);
-		this.setCenter(scrollPane);
 		
 		PamHBox pamHBox = new PamHBox();
 		pamHBox.setAlignment(Pos.CENTER_LEFT);
 		pamHBox.setSpacing(5);
 		
-		PamButton runButton = new PamButton();
+		runButton = new PamButton();
 		runButton.setGraphic(PamGlyphDude.createPamIcon("mdi2p-play"));
 		runButton.setOnAction((action)->{
 			checkFiles();
@@ -128,15 +130,15 @@ public class CheckWavHeadersPane extends PamBorderPane {
 		pamHBox.getChildren().addAll(runButton, progressBar);
 		progressBar.setMaxWidth(Double.MAX_VALUE);
 		
-		
 		mainPane.getChildren().addAll(folderName, textArea, pamHBox);
-	
-		this.setPadding(new Insets(5,0,5,15));
 		
+		this.setCenter(mainPane);
+
+		this.setPadding(new Insets(5,0,5,15));
 	}
 	
 	
-	private void setParams() {
+	void setParams() {
 		running = ran = false;
 		subFolders = folderInputSystem.getFolderInputParameters().subFolders;
 		if (subFolders) {
@@ -149,7 +151,7 @@ public class CheckWavHeadersPane extends PamBorderPane {
 		textArea.setText(" ");
 		allFiles.clear();
 		nFiles = countFiles(folder);
-		progressBar.setProgress(0);
+		progressProperty.setValue(0);
 		progressBar.progressProperty().bind(progressProperty);
 		//progressBar.setMaximum(Math.max(nFiles, 1));
 		enableControls();
@@ -213,6 +215,10 @@ public class CheckWavHeadersPane extends PamBorderPane {
 		nErrors = 0;
 		enableControls();
 		checkFilesWorker = new CheckFiles();
+
+        Thread th = new Thread(checkFilesWorker);
+        th.setDaemon(true);
+        th.start();
 	}
 	
 
@@ -245,10 +251,16 @@ public class CheckWavHeadersPane extends PamBorderPane {
 			 *  for each file, report on progress with it's name and 
 			 *  whether or not it had an error
 			 */
-			int error;
 			File aFile;
+			System.out.println("Analaysing files: Start: " + allFiles.size() );
 			for (int i = 0; i < allFiles.size(); i++) {
-				error = checkFile(aFile = allFiles.get(i));
+				System.out.println("Analaysing files: " + i);
+				final int error = checkFile(aFile = allFiles.get(i));
+				final File aFile1 = aFile;
+				Platform.runLater(()->{
+					textArea.appendText(String.format("\n File %s %s" , aFile1.getName() , 
+							error == AudioFileFuncs.FILE_OK ? "OK" : ("Error " + error)));
+				});
 				//progressBar.progressProperty().bind(null);
 				progressProperty.setValue(100*i/(double) allFiles.size());
 			}

src/Acquisition/layoutFX/FolderInputPane.java

@@ -304,6 +304,7 @@ public class FolderInputPane extends DAQSettingsPane<FolderInputParameters>{
 		wavFix.setOnAction((action)->{
 			acquisitionPaneFX.getAdvancedLabel().setText("Fix Wave Files");
 			acquisitionPaneFX.getAdvancedPane().setCenter(this.fixWavPane);
+			fixWavPane.setParams();
 			acquisitionPaneFX.getFlipPane().flipToBack();
 		});
 		

src/IshmaelLocator/IshLocProcess.java

@@ -380,6 +380,10 @@ abstract public class IshLocProcess extends PamProcess implements SpectrogramMar
 			} else {
 				newTime = oldTime*2;
 			}
+			/*
+			 * Above causes same error as in Rocca and needs fixing
+			 */
+			newTime = Math.min(newTime, 600000); // don't let this exceed 10 minutes. 
 //			System.out.println("Adjusting raw data natural lifetime from " + oldTime + " ms to " + newTime + " ms");
 			daqBlock.setNaturalLifetimeMillis(newTime); // increase the lifetime to try and prevent this from happening again
 			return;		

src/PamController/PamguardVersionInfo.java

@@ -31,12 +31,12 @@ public class PamguardVersionInfo {
 	 * Version number, major version.minorversion.sub-release.
 	 * Note: can't go higher than sub-release 'f'
 	 */
-	static public final String version = "2.02.03";
+	static public final String version = "2.02.04";
 	
 	/**
 	 * Release date
 	 */
-	static public final String date = "8 February 2022";
+	static public final String date = "11 June 2022";
 	
 //	/**
 //	 * Release type - Beta or Core

src/PamModel/PamDependency.java

@@ -20,12 +20,22 @@ public class PamDependency {
 	
 	private String dataBlockName;
 
+	/**
+	 * 
+	 * @param requiredDataType Class of Data unit
+	 * @param defaultProvider Class name of default provider.
+	 * @param dataBlockName Specific data block name
+	 */
 	public PamDependency(Class requiredDataType, String defaultProvider, String dataBlockName) {
 		this.requiredDataType = requiredDataType;
 		this.defaultProvider = defaultProvider;
 		this.dataBlockName = dataBlockName;
 	}
 
+	/**
+	 * @param requiredDataType Class of Data unit
+	 * @param defaultProvider Class name of default provider.
+	 */
 	public PamDependency(Class requiredDataType, String defaultProvider) {
 		this.requiredDataType = requiredDataType;
 		this.defaultProvider = defaultProvider;
@@ -41,12 +51,10 @@ public class PamDependency {
 	/**
 	 * @return Returns the requiredDataType.
 	 */
-//	public DataType getRequiredDataType() {
-//		return requiredDataType;
-//	}
 	public Class getRequiredDataType() {
 		return requiredDataType;
 	}
+	
 	/**
 	 * @return Returns the dataBlockName.
 	 */

src/PamModel/PamPluginInterface.java

@@ -67,6 +67,8 @@ public interface PamPluginInterface extends CommonPluginInterface {
 	 * A short description of the plug in module.  This text is used in various informational
 	 * windows displayed to the user.  The value returned here is typically the same as the text returned
 	 * from the {@link #getDefaultName() getDefaultName()} method (e.g. <em>Click Detector</em> or <em>FFT (Spectrogram) Engine</em>).
+	 * <br>This is the text used in the main 'Add Modules' menus and is used as the 
+	 * second argument to PamModuleInfo.registerControlledUnit
 	 * <p>
 	 * This field cannot be null.
 	 * @return String describing the plugin.  Cannot be null.

src/PamView/ColourArray.java

@@ -344,7 +344,7 @@ public class ColourArray implements Cloneable, Serializable, ManagedParameters {
 	 * @return a contrasting colour. 
 	 */
 	private Color createContrastingColour() {
-		Color[] tryCols = {Color.white, Color.red, Color.blue, Color.green, Color.black};
+		Color[] tryCols = {Color.white, Color.red, Color.CYAN, Color.blue, Color.green, Color.black};
 		if (colours == null) {
 			return tryCols[0];
 		}

src/PamView/ColourComboBox.java

@@ -81,6 +81,15 @@ public class ColourComboBox extends PamPanel {
     	
     }
     
+//    private void createImages() {
+//    	for (int i = 0; i < ColourArray.ColourArrayType.values().length; i++) {
+//    		intArray[i] = new Integer(i);
+//    		colourStrings[i]=ColourArray.getName(types[i]);
+//    		colourArray=ColourArray.createStandardColourArray(256, ColourArray.ColourArrayType.values()[i]);
+//    		images[i]=new ImageIcon(createColourMapImage(colourArray,  height,  width));
+//    	}
+//    }
+    
     public void addActionListener(ActionListener actionListener){
     	colourBox.addActionListener(actionListener);
     }
@@ -161,7 +170,7 @@ public class ColourComboBox extends PamPanel {
 			    for (int i = 0; i < ColourArray.ColourArrayType.values().length; i++) {
 			    	intArray[i] = new Integer(i);
 			    	colourStrings[i]=ColourArray.getName(types[i]);
-			    	colourArray=ColourArray.createStandardColourArray(256, ColourArray.ColourArrayType.values()[i]);
+			    	colourArray=ColourArray.createStandardColourArray(width, ColourArray.ColourArrayType.values()[i]);
 			    	images[i]=new ImageIcon(createColourMapImage(colourArray,  height,  width));
 			    }
 			}

src/PamView/GeneralProjector.java

@@ -85,7 +85,7 @@ public abstract class GeneralProjector<T extends PamCoordinate> {
 		TIME ("Time"), FREQUENCY ("Frequency"), AMPLITUDE ("Amplitude"), LATITUDE ("Latitude"), LONGITUDE ("Longitude") ,
 		BEARING ("Bearing"), RANGE ("Range"), SLANTANGLE ("Slant angle"), ICI ("Inter-click-interval"),
 		DEPTH ("Depth"), SLANTBEARING ("Slant bearing"), AMPLITUDE_STEM ("Amplitude (stem)"), AMPLITUDE_LIN ("Linear Amplitude"),
-		SPEED ("Speed"), PROBABILITY ("Probability"),  NCYCLES ("No. cycles"), BANDWIDTH("Bandwidth"), ISHDET("Detector Output");
+		SPEED ("Speed"), PROBABILITY ("Probability"),  NCYCLES ("No. cycles"), BANDWIDTH("Bandwidth"), ISHDET("Detector Output"), X("x coordinate"), Y("y coordinate");
 		
 		private String unit;
 

src/PamView/dialog/GenericSwingDialog.java

@@ -1,5 +1,8 @@
 package PamView.dialog;
 
+import java.awt.Dimension;
+import java.awt.Point;
+import java.awt.Toolkit;
 import java.awt.Window;
 
 import javax.swing.BoxLayout;
@@ -8,9 +11,9 @@ import javax.swing.JPanel;
 import javax.swing.border.EmptyBorder;
 
 public class GenericSwingDialog extends PamDialog {
-	
+
 	private boolean allOk;
-	
+
 	private PamDialogPanel[] dialogPanels;
 
 	private GenericSwingDialog(Window parentFrame, String title, PamDialogPanel ...dialogPanels) {
@@ -25,15 +28,48 @@ public class GenericSwingDialog extends PamDialog {
 			}
 			mainPanel.add(comp);
 		}
-		
+
 		setDialogComponent(mainPanel);
 	}
-	
-	public static boolean showDialog(Window parentFrame, String title, PamDialogPanel ...dialogPanels) {
 
+	public static boolean showDialog(Window parentFrame, String title, PamDialogPanel ...dialogPanels) {
+		return showDialog(parentFrame, title, null, dialogPanels);
+	}
+
+	/**
+	 * Show dialog at a specific location on the screen. 
+	 * @param parentFrame
+	 * @param title
+	 * @param screenPoint
+	 * @param dialogPanels
+	 * @return
+	 */
+	public static boolean showDialog(Window parentFrame, String title, Point screenPoint, PamDialogPanel ...dialogPanels) {
 		GenericSwingDialog swingDialog = new GenericSwingDialog(parentFrame, title, dialogPanels);
 		swingDialog.setParams();
 		swingDialog.pack();
+		if (screenPoint != null) {
+			try {
+				// check we're not going too far off the screen. 
+				Dimension sz = swingDialog.getPreferredSize();
+				Dimension screen = null;
+				if (parentFrame != null) {
+					screen = parentFrame.getSize();
+				}
+				else {
+					screen = Toolkit.getDefaultToolkit().getScreenSize();
+				}
+				screenPoint.y = Math.min(screenPoint.y, screen.height-sz.height-10);
+				screenPoint.y = Math.max(screenPoint.y, 0);
+				screenPoint.x = Math.min(screenPoint.x, screen.width-sz.width-10);
+				screenPoint.x = Math.max(screenPoint.x, 0);
+
+				swingDialog.setLocation(screenPoint);
+			}
+			catch (Exception e) {
+				// shouldn't happen, but if it does, it doesn't matter much
+			}
+		}
 		swingDialog.setVisible(true);
 		return swingDialog.allOk;
 	}

src/PamView/dialog/PamDialog.java

@@ -3,10 +3,14 @@ package PamView.dialog;
 import java.awt.BorderLayout;
 import java.awt.Component;
 import java.awt.Dialog;
+import java.awt.Dimension;
 import java.awt.FlowLayout;
 import java.awt.GridBagConstraints;
 import java.awt.GridBagLayout;
+import java.awt.MouseInfo;
+import java.awt.Point;
 import java.awt.Rectangle;
+import java.awt.Toolkit;
 import java.awt.Window;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -225,6 +229,9 @@ abstract public class PamDialog extends JDialog {
 			synchronized (this) {
 				PamColors.getInstance().notifyContianer(this.getContentPane());
 			}
+			if (getOwner() == null) {
+				moveToMouseLocation();
+			}
 		}
 		try{
 			super.setVisible(visible);
@@ -235,6 +242,35 @@ abstract public class PamDialog extends JDialog {
 		}
 	}
 
+	/**
+	 * put the dialog near the mouse location. 
+	 */
+	public void moveToMouseLocation() {
+		Point mouse = MouseInfo.getPointerInfo().getLocation();
+		moveToLocation(mouse);
+	}
+	
+	public void moveToLocation(Point point) {
+		if (point == null) {
+			return;
+		}
+		// check we're not going too far off the screen. 
+		Dimension sz = getPreferredSize();
+		Dimension screen = null;
+		if (getOwner() != null) {
+			screen = getOwner().getSize();
+		}
+		else {
+			screen = Toolkit.getDefaultToolkit().getScreenSize();
+		}
+		point.y = Math.min(point.y, screen.height-sz.height-10);
+		point.y = Math.max(point.y, 0);
+		point.x = Math.min(point.x, screen.width-sz.width-10);
+		point.x = Math.max(point.x, 0);
+
+		setLocation(point);
+	}
+
 	/**
 	 * Reschedule closing of the window to happen
 	 * on the AWT thread using SwingUtilities.invokeLater(...)

src/PamView/panel/CornerLayoutContraint.java

@@ -23,6 +23,24 @@ public class CornerLayoutContraint  implements Serializable, Cloneable {
 	
 	public int anchor = FIRST_LINE_START;
 
+	/**
+	 * Construct a corner layout constraint with the given anchor
+	 * @param anchor
+	 */
+	public CornerLayoutContraint(int anchor) {
+		super();
+		this.anchor = anchor;
+	}
+
+
+	/**
+	 * construct a corner layout constraint with the default anchor
+	 */
+	public CornerLayoutContraint() {
+		super();
+		this.anchor = anchor;
+	}
+
 	@Override
 	protected CornerLayoutContraint clone() {
 		try {

src/PamView/paneloverlay/OverlayDataManager.java

@@ -42,7 +42,6 @@ public abstract class OverlayDataManager<TOverlayInfoType extends OverlayDataInf
 	private ParameterType[] parameterTypes;
 
 	private ParameterUnits[] parameterUnits;
-	
 
 	/**
 	 * @param generalProjector

src/PamView/paneloverlay/overlaymark/ExtMouseAdapter.java

@@ -87,7 +87,8 @@ public class ExtMouseAdapter {
 	}
 
 	final public boolean mouseWheelMoved(MouseWheelEvent e) {
-		return mouseWheelMoved(fxScroll(e));
+//		return mouseWheelMoved(fxScroll(e));
+		return false;
 	}
 
 //	private MouseEvent swingMouse(javafx.scene.input.MouseEvent e) {

src/PamView/paneloverlay/overlaymark/OverlayMarker.java

@@ -610,8 +610,6 @@ abstract public class OverlayMarker extends ExtMouseAdapter implements MarkManag
 			}
 		}
 		
-//		Debug.out.printf("OverlayMarker: _ 2 In getSelectedMarkedDataUnits with %d available units\n", selectedData.size());
-
 		
 		return selectedData;
 	}

src/PamView/symbol/modifier/SuperDetSymbolWrapper.java

@@ -32,12 +32,13 @@ public class SuperDetSymbolWrapper extends SymbolModifier {
 
 	@Override
 	public SymbolData getSymbolData(GeneralProjector projector, PamDataUnit dataUnit) {
-		PamDataUnit superDet = dataUnit.getSuperDetection(superDetDataBlock);
+		PamDataUnit superDet = dataUnit.getSuperDetection(superDetDataBlock, true);
 		if (superDet == null) {
 			return null;
 		}
 		return superDetModifier.getSymbolData(getSymbolChooser().getProjector(), superDet);
 	}
+	
 
 	@Override
 	public String getToolTipText() {

src/PamguardMVC/PamDataBlock.java

@@ -986,7 +986,9 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
 	}
 
 	/**
-	 * Instruction from the viewer scroll manager to load new data.
+	 * Instruction from the viewer scroll manager to load new data. <p>This just calls through
+	 * to loadViewerData(OfflineDataLoadInfo ...) so this should not be overridden. Override
+	 * the other function instead. 
 	 * 
 	 * @param dataStart    data start time in millis
 	 * @param dataEnd      data end time in millis.

src/PamguardMVC/PamDataUnit.java

@@ -943,23 +943,27 @@ abstract public class PamDataUnit<T extends PamDataUnit, U extends PamDataUnit>
 			}
 		}
 
-		int nAttotations = getNumDataAnnotations();
-		for (int i = 0; i < nAttotations; i++) {
-			DataAnnotation an = getDataAnnotation(i);
-			DataAnnotationType ant = an.getDataAnnotationType();
-			String anName = ant.getAnnotationName();
-			String anString = an.toString();
-			if (anString == null) {
-				continue;
-			}
-			if (anString.contains("<html>")) {
-				anString = anString.replace("<html>", "");
-			}
-			if (anString.contains("</html>")) {
-				anString = anString.replace("</html>", "");
-			}
-			str += anName + ": " + anString + "<br>";
+		String annotString = getAnnotationsSummaryString();
+		if (annotString != null) {
+			str += annotString;
 		}
+//		int nAttotations = getNumDataAnnotations();
+//		for (int i = 0; i < nAttotations; i++) {
+//			DataAnnotation an = getDataAnnotation(i);
+//			DataAnnotationType ant = an.getDataAnnotationType();
+//			String anName = ant.getAnnotationName();
+//			String anString = an.toString();
+//			if (anString == null) {
+//				continue;
+//			}
+//			if (anString.contains("<html>")) {
+//				anString = anString.replace("<html>", "");
+//			}
+//			if (anString.contains("</html>")) {
+//				anString = anString.replace("</html>", "");
+//			}
+//			str += anName + ": " + anString + "<br>";
+//		}
 
 		
 		// add frequency and amplitude information
@@ -999,6 +1003,36 @@ abstract public class PamDataUnit<T extends PamDataUnit, U extends PamDataUnit>
 		return str;
 	}
 	
+	/**
+	 * Get string information for the annotations. Kept separate so 
+	 * it can be called in overridden version of getSummaryString()
+	 * @return
+	 */
+	public String getAnnotationsSummaryString() {
+		int nAnnotations = getNumDataAnnotations();
+		if (nAnnotations == 0) {
+			return null;
+		}
+		String str = "";
+		for (int i = 0; i < nAnnotations; i++) {
+			DataAnnotation an = getDataAnnotation(i);
+			DataAnnotationType ant = an.getDataAnnotationType();
+			String anName = ant.getAnnotationName();
+			String anString = an.toString();
+			if (anString == null) {
+				continue;
+			}
+			if (anString.contains("<html>")) {
+				anString = anString.replace("<html>", "");
+			}
+			if (anString.contains("</html>")) {
+				anString = anString.replace("</html>", "");
+			}
+			str += anName + ": " + anString + "<br>";
+		}
+		return str.length() > 0 ? str : null;
+	}
+	
 	/**
 	 * Some functions to do with data annotations
 	 */
@@ -1258,6 +1292,32 @@ abstract public class PamDataUnit<T extends PamDataUnit, U extends PamDataUnit>
 		return null;
 	}
 
+	/**
+	 * find a super detection form the parent data block of the super detection. 
+	 * @param superDataBlock data block of super detection
+	 * @param allowSuperSuper Allow iteration through mutilple super detection layers
+	 * @return data unit from that block, or null.
+	 */
+	public SuperDetection getSuperDetection(PamDataBlock superDataBlock, boolean allowSuperSuper) {
+		synchronized (superDetectionSyncronisation) {
+			if (superDetections == null) return null;
+			SuperDetection superDet;
+			for (int i = 0; i < superDetections.size(); i++) {
+				superDet = superDetections.get(i);
+				if (superDet.getParentDataBlock() == superDataBlock) {
+					return superDet;
+				}
+				if (allowSuperSuper) {
+					SuperDetection supersuper = superDet.getSuperDetection(superDataBlock, allowSuperSuper);
+					if (supersuper != null) {
+						return supersuper;
+					}
+				}
+			}
+		}		
+		return null;
+	}
+
 	public SuperDetection getSuperDetection(int ind) {
 		synchronized (superDetectionSyncronisation) {
 			if (superDetections == null || superDetections.size()<=ind) return null;

src/PamguardMVC/RawDataTransforms.java

@@ -99,35 +99,11 @@ public class RawDataTransforms {
 	 */
 	private int shortestFFTLength;
 
-	/**
-	 * Object for synchronization. Get thread lock if this isn't the same as
-	 * the object holding the data. 
-	 */
-	private Object synchObject;
 
 
-
-	/**
-	 * Raw Data Transforms for a RawDataHolder using the rawDataHolder as the synchronization 
-	 * object.
-	 * @param rawDataHolder RawDataHolder object (e.g. a click)
-	 */
 	public RawDataTransforms(@SuppressWarnings("rawtypes") PamDataUnit rawDataHolder) {
-		this(rawDataHolder, rawDataHolder);
-	}
-	
-	/**
-	 * Raw Data Transforms for a RawDataHolder. 
-	 * @param rawDataHolder RawDataHolder object (e.g. a click)
-	 * @param synchObject synchronization object, which is most likely the RawDataHolder object. 
-	 */
-	public RawDataTransforms(@SuppressWarnings("rawtypes") PamDataUnit rawDataHolder, Object synchObject) {
 		this.rawData=(RawDataHolder) rawDataHolder; 
 		this.dataUnit  = rawDataHolder; 
-		this.synchObject = synchObject;
-		if (this.synchObject == null) {
-			this.synchObject = this;
-		}
 	}
 
 
@@ -167,25 +143,23 @@ public class RawDataTransforms {
 	 * @param fftLength
 	 * @return Power spectrum
 	 */
-	public double[] getPowerSpectrum(int channel, int minBin, int maxBin, int fftLength) {
-		synchronized (synchObject) {
-			if (minBin==0 && maxBin>=this.getWaveData(0).length-1) {
-				return getPowerSpectrum(channel,  fftLength); 
-			}		
-			if (fftLength == 0) {
-				fftLength = getCurrentSpectrumLength();
-			}
-
-			double[] waveformTrim = new double[maxBin-minBin]; 
-
-			//		System.out.println("minBin: " +  minBin + " maxBin: " + maxBin + " raw waveform: " + this.getWaveData(channel).length); 
-
-			System.arraycopy(this.getWaveData(channel), minBin, waveformTrim, 0, Math.min(this.getWaveData(channel).length-minBin-1, waveformTrim.length));
-
-			ComplexArray cData =  getComplexSpectrumHann(waveformTrim, fftLength); 
-
-			return cData.magsq();
+	public synchronized double[] getPowerSpectrum(int channel, int minBin, int maxBin, int fftLength) {
+		if (minBin==0 && maxBin>=this.getWaveData(0).length-1) {
+			return getPowerSpectrum(channel,  fftLength); 
+		}		
+		if (fftLength == 0) {
+			fftLength = getCurrentSpectrumLength();
 		}
+		
+		double[] waveformTrim = new double[maxBin-minBin]; 
+		
+		//System.out.println("minBin: " +  minBin + " maxBin: " + maxBin + " raw waveform: " + this.getWaveData(channel).length); 
+		
+		System.arraycopy(this.getWaveData(channel), minBin, waveformTrim, 0, Math.min(this.getWaveData(channel).length-minBin-1, waveformTrim.length));
+
+		ComplexArray cData =  getComplexSpectrumHann(waveformTrim, fftLength); 
+
+		return cData.magsq();
 	}
 
 	/**
@@ -196,31 +170,29 @@ public class RawDataTransforms {
 	 * @param fftLength
 	 * @return Power spectrum
 	 */
-	public double[] getPowerSpectrum(int channel, int fftLength) {
-		synchronized (synchObject) {
-			if (powerSpectra == null) {
-				powerSpectra = new double[PamUtils.getNumChannels(dataUnit.getChannelBitmap())][];
-			}
-			if (fftLength == 0) {
-				fftLength = getCurrentSpectrumLength();
-			}
-
-			if (powerSpectra[channel] == null
-					|| powerSpectra[channel].length != fftLength / 2) {
-				ComplexArray cData = getComplexSpectrumHann(channel, fftLength);
-				currentSpecLen = fftLength;
-				powerSpectra[channel] = cData.magsq();
-				if (powerSpectra==null){
-					System.err.println("DLDetection: could not calculate power spectra");
-					return null;
-
-				}
-				if (powerSpectra[channel].length != fftLength/2) {
-					powerSpectra[channel] = Arrays.copyOf(powerSpectra[channel], fftLength/2);
-				}
-			}
-			return powerSpectra[channel];
+	public synchronized double[] getPowerSpectrum(int channel, int fftLength) {
+		if (powerSpectra == null) {
+			powerSpectra = new double[PamUtils.getNumChannels(dataUnit.getChannelBitmap())][];
 		}
+		if (fftLength == 0) {
+			fftLength = getCurrentSpectrumLength();
+		}
+
+		if (powerSpectra[channel] == null
+				|| powerSpectra[channel].length != fftLength / 2) {
+			ComplexArray cData = getComplexSpectrumHann(channel, fftLength);
+			currentSpecLen = fftLength;
+			powerSpectra[channel] = cData.magsq();
+			if (powerSpectra==null){
+				System.err.println("DLDetection: could not calculate power spectra");
+				return null;
+
+			}
+			if (powerSpectra[channel].length != fftLength/2) {
+				powerSpectra[channel] = Arrays.copyOf(powerSpectra[channel], fftLength/2);
+			}
+		}
+		return powerSpectra[channel];
 	}
 
 
@@ -230,27 +202,25 @@ public class RawDataTransforms {
 	 * @param fftLength
 	 * @return Sum of power spectra
 	 */
-	public double[] getTotalPowerSpectrum(int fftLength) {
-		synchronized (synchObject) {
-			if (fftLength == 0) {
-				fftLength = getCurrentSpectrumLength();
-			}
-			if (fftLength == 0) {
-				fftLength = PamUtils.getMinFftLength(getSampleDuration());
-			}
-			double[] ps;
-			if (totalPowerSpectrum == null
-					|| totalPowerSpectrum.length != fftLength / 2) {
-				totalPowerSpectrum = new double[fftLength / 2];
-				for (int c = 0; c < PamUtils.getNumChannels(this.dataUnit.getChannelBitmap()); c++) {
-					ps = getPowerSpectrum(c, fftLength);
-					for (int i = 0; i < fftLength / 2; i++) {
-						totalPowerSpectrum[i] += ps[i];
-					}
+	public synchronized double[] getTotalPowerSpectrum(int fftLength) {
+		if (fftLength == 0) {
+			fftLength = getCurrentSpectrumLength();
+		}
+		if (fftLength == 0) {
+			fftLength = PamUtils.getMinFftLength(getSampleDuration());
+		}
+		double[] ps;
+		if (totalPowerSpectrum == null
+				|| totalPowerSpectrum.length != fftLength / 2) {
+			totalPowerSpectrum = new double[fftLength / 2];
+			for (int c = 0; c < PamUtils.getNumChannels(this.dataUnit.getChannelBitmap()); c++) {
+				ps = getPowerSpectrum(c, fftLength);
+				for (int i = 0; i < fftLength / 2; i++) {
+					totalPowerSpectrum[i] += ps[i];
 				}
 			}
-			return totalPowerSpectrum;
 		}
+		return totalPowerSpectrum;
 	}
 
 
@@ -265,17 +235,15 @@ public class RawDataTransforms {
 	 * @param fftLength - the FFT length to use. 
 	 * @return the complex spectrum - the comnplex spectrum of the wave data from the specified channel. 
 	 */
-	public ComplexArray getComplexSpectrumHann(int channel, int fftLength) {
-		synchronized (synchObject) {
-			complexSpectrum = new ComplexArray[PamUtils.getNumChannels(dataUnit.getChannelBitmap())];
-			if (complexSpectrum[channel] == null
-					|| complexSpectrum.length != fftLength / 2) {
+	public synchronized ComplexArray getComplexSpectrumHann(int channel, int fftLength) {
+		complexSpectrum = new ComplexArray[PamUtils.getNumChannels(dataUnit.getChannelBitmap())];
+		if (complexSpectrum[channel] == null
+				|| complexSpectrum.length != fftLength / 2) {
 
-				complexSpectrum[channel] =  getComplexSpectrumHann(rawData.getWaveData()[channel], fftLength); 
-				currentSpecLen = fftLength;
-			}
-			return complexSpectrum[channel];
+			complexSpectrum[channel] =  getComplexSpectrumHann(rawData.getWaveData()[channel], fftLength); 
+			currentSpecLen = fftLength;
 		}
+		return complexSpectrum[channel];
 	}
 
 
@@ -314,12 +282,10 @@ public class RawDataTransforms {
 	 * @return the spectrogram length. 
 	 */
 	private int getCurrentSpectrumLength() {
-		synchronized (synchObject) {
-			if (currentSpecLen<=0) {
-				currentSpecLen = PamUtils.getMinFftLength(dataUnit.getSampleDuration());
-			}
-			return currentSpecLen; 
+		if (currentSpecLen<=0) {
+			currentSpecLen = PamUtils.getMinFftLength(dataUnit.getSampleDuration());
 		}
+		return currentSpecLen; 
 	}
 
 
@@ -405,31 +371,29 @@ public class RawDataTransforms {
 	 * @param fftLength
 	 * @return the complex spectrum
 	 */
-	public ComplexArray getComplexSpectrum(int channel, int fftLength) {
-		synchronized (synchObject) {
-			double[] paddedRawData;
-			double[] rawData;
-			int i, mn;
+	public synchronized ComplexArray getComplexSpectrum(int channel, int fftLength) {
+		double[] paddedRawData;
+		double[] rawData;
+		int i, mn;
 
-			if (complexSpectrum == null) {
-				complexSpectrum = new ComplexArray[getNChan()];
-			}
-			if (complexSpectrum[channel] == null
-					|| complexSpectrum.length != fftLength / 2) {
-				paddedRawData = new double[fftLength];
-				rawData = getWaveData(channel);
-				//double[] rotData = getRotationCorrection(channel);
-				mn = Math.min(fftLength, getSampleDuration().intValue());
-				for (i = 0; i < mn; i++) {
-					paddedRawData[i] = rawData[i];//-rotData[i];
-				}
-				for (i = mn; i < fftLength; i++) {
-					paddedRawData[i] = 0;
-				}
-				complexSpectrum[channel] = fastFFT.rfft(paddedRawData, fftLength);
-			}
-			return complexSpectrum[channel];
+		if (complexSpectrum == null) {
+			complexSpectrum = new ComplexArray[getNChan()];
 		}
+		if (complexSpectrum[channel] == null
+				|| complexSpectrum.length != fftLength / 2) {
+			paddedRawData = new double[fftLength];
+			rawData = getWaveData(channel);
+			//double[] rotData = getRotationCorrection(channel);
+			mn = Math.min(fftLength, getSampleDuration().intValue());
+			for (i = 0; i < mn; i++) {
+				paddedRawData[i] = rawData[i];//-rotData[i];
+			}
+			for (i = mn; i < fftLength; i++) {
+				paddedRawData[i] = 0;
+			}
+			complexSpectrum[channel] = fastFFT.rfft(paddedRawData, fftLength);
+		}
+		return complexSpectrum[channel];
 	}
 
 
@@ -438,16 +402,14 @@ public class RawDataTransforms {
 	 * @param iChan channel index
 	 * @return analytic waveform
 	 */
-	public double[] getAnalyticWaveform(int iChan) {
-		synchronized (synchObject) {
-			if (analyticWaveform == null) {
-				analyticWaveform = new double[getNChan()][];
-			}
-			//		if (analyticWaveform[iChan] == null) {
-			analyticWaveform[iChan] = hilbert.getHilbert(getWaveData(iChan));
-			//		}
-			return analyticWaveform[iChan];
+	public synchronized double[] getAnalyticWaveform(int iChan) {
+		if (analyticWaveform == null) {
+			analyticWaveform = new double[getNChan()][];
 		}
+		//		if (analyticWaveform[iChan] == null) {
+		analyticWaveform[iChan] = hilbert.getHilbert(getWaveData(iChan));
+		//		}
+		return analyticWaveform[iChan];
 	}
 
 	/**
@@ -459,14 +421,12 @@ public class RawDataTransforms {
 	 * @param fftFilterParams fft filter parameters. 
 	 * @return analystic waveform. 
 	 */
-	public double[] getAnalyticWaveform(int iChan, boolean filtered, FFTFilterParams fftFilterParams) {
-		synchronized (synchObject) {
-			if (filtered == false || fftFilterParams == null) {
-				return getAnalyticWaveform(iChan);
-			}
-			else {
-				return getFilteredAnalyticWaveform(fftFilterParams, iChan);
-			}
+	public synchronized double[] getAnalyticWaveform(int iChan, boolean filtered, FFTFilterParams fftFilterParams) {
+		if (filtered == false || fftFilterParams == null) {
+			return getAnalyticWaveform(iChan);
+		}
+		else {
+			return getFilteredAnalyticWaveform(fftFilterParams, iChan);
 		}
 	}
 
@@ -477,8 +437,7 @@ public class RawDataTransforms {
 	 * @param iChan channel number
 	 * @return envelope of the filtered data. 
 	 */
-	public double[] getFilteredAnalyticWaveform(FFTFilterParams fftFilterParams, int iChan) {
-		synchronized (synchObject) {
+	public synchronized double[] getFilteredAnalyticWaveform(FFTFilterParams fftFilterParams, int iChan) {
 		if (analyticWaveform == null) {
 			analyticWaveform = new double[getNChan()][];
 		}
@@ -487,7 +446,6 @@ public class RawDataTransforms {
 				getHilbert(getFilteredWaveData(fftFilterParams, iChan));
 		//		}
 		return analyticWaveform[iChan];
-		}
 	}
 
 	/**
@@ -497,21 +455,19 @@ public class RawDataTransforms {
 	 * @return analystic waveforms 
 	 */
 	public double[][] getFilteredAnalyticWaveform(FFTFilterParams fftFilterParams) {
-		synchronized (synchObject) { // new
-			if (analyticWaveform == null) {
-				analyticWaveform = new double[getNChan()][];
-			}
-			for (int iChan = 0; iChan < getNChan(); iChan++) {
-				if (fftFilterParams != null) {
-					analyticWaveform[iChan] = hilbert.
-							getHilbert(getFilteredWaveData(fftFilterParams, iChan));
-				}
-				else {
-					analyticWaveform[iChan] = getAnalyticWaveform(iChan);
-				}
-			}
-			return analyticWaveform;
+		if (analyticWaveform == null) {
+			analyticWaveform = new double[getNChan()][];
 		}
+		for (int iChan = 0; iChan < getNChan(); iChan++) {
+			if (fftFilterParams != null) {
+				analyticWaveform[iChan] = hilbert.
+						getHilbert(getFilteredWaveData(fftFilterParams, iChan));
+			}
+			else {
+				analyticWaveform[iChan] = getAnalyticWaveform(iChan);
+			}
+		}
+		return analyticWaveform;
 	}
 
 
@@ -522,7 +478,7 @@ public class RawDataTransforms {
 	 * @param channelIndex channel index
 	 * @return filtered waveform data
 	 */
-	public double[] getFilteredWaveData(FFTFilterParams filterParams, int channelIndex) {
+	public synchronized double[] getFilteredWaveData(FFTFilterParams filterParams, int channelIndex) {
 		filteredWaveData = getFilteredWaveData(filterParams);
 		return filteredWaveData[channelIndex];
 	}
@@ -533,14 +489,12 @@ public class RawDataTransforms {
 	 * @param filterParams filter parameters
 	 * @return array of filtered data
 	 */
-	public double[][] getFilteredWaveData(FFTFilterParams filterParams) {
-		synchronized (synchObject) {
+	public synchronized double[][] getFilteredWaveData(FFTFilterParams filterParams) {
 		//System.out.println("Make filterred wave data!: " + (filterParams != oldFFTFilterParams));
 		if (filteredWaveData == null || filterParams != oldFFTFilterParams) {
 			filteredWaveData = makeFilteredWaveData(filterParams);
 		}
 		return filteredWaveData;
-		}
 	}
 
 	private double[][] makeFilteredWaveData(FFTFilterParams filterParams) {
@@ -579,15 +533,13 @@ public class RawDataTransforms {
 	 * @return FFT filter object. 
 	 */
 	public FFTFilter getFFTFilter(FFTFilterParams fftFilterParams) {
-		synchronized (synchObject) {
-			if (fftFilter == null) {
-				fftFilter = new FFTFilter(fftFilterParams, this.dataUnit.getParentDataBlock().getSampleRate());
-			}
-			else {
-				fftFilter.setParams(fftFilterParams, this.dataUnit.getParentDataBlock().getSampleRate());
-			}
-			return fftFilter;
+		if (fftFilter == null) {
+			fftFilter = new FFTFilter(fftFilterParams, this.dataUnit.getParentDataBlock().getSampleRate());
 		}
+		else {
+			fftFilter.setParams(fftFilterParams, this.dataUnit.getParentDataBlock().getSampleRate());
+		}
+		return fftFilter;
 	}
 
 
@@ -654,9 +606,7 @@ public class RawDataTransforms {
 	 * @return
 	 */
 	private int getNChan() {
-		synchronized (synchObject) { // new
-			return this.rawData.getWaveData().length;
-		}
+		return this.rawData.getWaveData().length;
 	}
 
 	/**
@@ -689,11 +639,9 @@ public class RawDataTransforms {
 	 * Free eup some memory by deleting the filtered wave data, power spectra and analytic waveform. 
 	 */
 	public void freeMemory() {
-		synchronized (synchObject) {
-			filteredWaveData = null;
-			powerSpectra = null;
-			analyticWaveform = null;
-		}
+		filteredWaveData = null;
+		powerSpectra = null;
+		analyticWaveform = null;
 	}
 
 

src/PamguardMVC/dataSelector/DataSelectorSettings.java

@@ -32,7 +32,7 @@ public class DataSelectorSettings implements Serializable, ManagedParameters {
 	 * @return Params or null if they don't exist. 
 	 */
 	public DataSelectParams getParams(String name) {
-		if (selectorParams == null) {
+		if (selectorParams == null || name == null) {
 			return null;
 		}
 		return selectorParams.get(name);

src/PamguardMVC/superdet/SuperDetDataBlock.java

@@ -471,6 +471,7 @@ public class SuperDetDataBlock<Tunit extends SuperDetection, TSubDet extends Pam
 						PamDataUnit subDet = subDetectionFinder.findDataUnit(sdInfo);
 						sdInfo.setSubDetection(subDet);
 						if (subDet != null) {
+							aData.addSubDetection(subDet);
 							subDet.addSuperDetection(aData);
 						}
 					}

src/Resources/css/pamSettingsCSS.css

@@ -35,8 +35,8 @@
   -fx-font-color: -fx-text;
   -fx-font-family: "Ubuntu";
 
-   -fx-border-radius: 5 5 5 5;
-   -fx-background-radius: 5 5 5 5;
+  -fx-border-radius: 5 5 5 5;
+  -fx-background-radius: 5 5 5 5;
 
    -icons-color: -fx-icon_col;
 }
@@ -615,7 +615,7 @@
   -fx-background: -fx-darkbackground;
   -fx-background-color: -fx-darkbackground;
   -fx-border-radius: 0 0 0 0;
-  -fx-padding: 7 0 7 0;
+  -fx-padding: 5 0 5 0;
   -fx-border-color: transparent;
 }
 
@@ -623,9 +623,9 @@
   -fx-text-fill: white;
   -fx-background-color: -fx-darkbackground;
   -fx-border-color: -fx-border_col;
-  -fx-background-radius: 6 6 0 0;
-  -fx-border-radius: 6 6 0 0;
-  -fx-padding: 7 0 7 0;
+  -fx-background-radius: 5 5 0 0;
+  -fx-border-radius: 5 5 0 0;
+  -fx-padding: 5 0 5 0;
 }
 
 .spinner .increment-arrow {
@@ -635,16 +635,16 @@
 .spinner .increment-arrow-button:hover {
    -fx-background-color: -fx-highlight; 
    -fx-border-color: -fx-highlight_border;
-   -fx-background-radius: 6 6 0 0;
-   -fx-border-radius: 6 6 0 0;
+   -fx-background-radius: 5 5 0 0;
+   -fx-border-radius: 5 5 0 0;
 }
 
 .spinner .decrement-arrow-button {
   -fx-text-fill: white;
   -fx-background-color: -fx-darkbackground;
   -fx-border-color: -fx-border_col;
-  -fx-background-radius: 0 0 6 6;
-  -fx-border-radius: 0 0 6 6
+  -fx-background-radius: 0 0 5 5;
+  -fx-border-radius: 0 0 5 5
 }
 
 .spinner .decrement-arrow {
@@ -654,8 +654,8 @@
 .spinner .decrement-arrow-button:hover {
    -fx-background-color: -fx-highlight; 
    -fx-border-color: -fx-highlight_border;
-   -fx-background-radius: 0 0 6 6;
-   -fx-border-radius: 0 0 6 6;
+   -fx-background-radius: 0 0 5 5;
+   -fx-border-radius: 0 0 5 5;
 }
 
 /*Arrows are horizontal either side of text box*/
@@ -663,7 +663,7 @@
   -fx-text-fill: white;
   -fx-background-color: -fx-darkbackground;
   -fx-border-color: -fx-border_col;
-  -fx-border-radius: 0 6 6 0
+  -fx-border-radius: 0 5 5 0
 }
 
 
@@ -671,22 +671,22 @@
    -fx-text-fill: white;
   -fx-background-color: -fx-darkbackground;
   -fx-border-color: -fx-border_col;
-  -fx-border-radius: 6 0 0 6
+  -fx-border-radius: 5 0 0 5
  }
 
  .spinner.split-arrows-horizontal .increment-arrow-button:hover {
    -fx-background-color: -fx-highlight; 
    -fx-border-color: -fx-highlight_border;
-   -fx-background-radius: 0 6 6 0;
-   -fx-border-radius: 0 6 6 0;
+   -fx-background-radius: 0 5 5 0;
+   -fx-border-radius: 0 5 5 0;
 }
 
 
 .spinner.split-arrows-horizontal .decrement-arrow-button:hover {
    -fx-background-color: -fx-highlight; 
    -fx-border-color: -fx-highlight_border;
-   -fx-background-radius: 6 0 0 6;
-   -fx-border-radius: 6 0 0 6;
+   -fx-background-radius: 5 0 0 5;
+   -fx-border-radius: 5 0 0 5;
  }
 
 .spinner.split-arrows-horizontal .text-field {

src/annotation/handler/AnnotationChoiceHandler.java

@@ -146,6 +146,17 @@ public abstract class AnnotationChoiceHandler extends AnnotationHandler {
 	 * @param annotationType
 	 */
 	public boolean updateAnnotation(PamDataUnit pamDataUnit, DataAnnotationType annotationType) {
+		/* 
+		 * need to check this is actually the right data unit, which matches the datablock of 
+		 * this annotatoin handler. Gets very confused when dealing with superdetections 
+		 */
+		if (pamDataUnit.getParentDataBlock() != this.getPamDataBlock()) {
+			pamDataUnit = pamDataUnit.getSuperDetection(getPamDataBlock(), true);
+			if (pamDataUnit == null) {
+				return false;
+			}
+		}
+		
 		DataAnnotation existingAnnotation = pamDataUnit.findDataAnnotation(annotationType.getAnnotationClass(), annotationType.getAnnotationName());
 		boolean changed = false;
 		if (annotationType.canAutoAnnotate()) {

src/annotation/string/StringDialogPanel.java

@@ -10,6 +10,7 @@ import java.awt.event.WindowEvent;
 import javax.swing.JComponent;
 import javax.swing.SwingUtilities;
 
+import PamUtils.PamCalendar;
 import annotation.AnnotationDialogPanel;
 import PamView.DBTextArea;
 import PamView.dialog.PamDialogPanel;
@@ -51,13 +52,21 @@ public class StringDialogPanel implements AnnotationDialogPanel {
 			note = note.trim();
 		}
 		if (note != null && note.length() > 0) {
-			StringAnnotation an = (StringAnnotation) pamDataUnit.findDataAnnotation(StringAnnotation.class,
-					stringAnnotationType.getAnnotationName());
-			if (an == null) {
+			StringAnnotation an;
+			/*
+			 *  always add a new annotation rather than editing the old one since
+			 *  the old one will get removed to handle annotation types which really 
+			 *  do need to make a new one each time. 
+			 */
+			
+//			= (StringAnnotation) pamDataUnit.findDataAnnotation(StringAnnotation.class,
+//					stringAnnotationType.getAnnotationName());
+//			if (an == null) {
 				an = new StringAnnotation(stringAnnotationType);
 				pamDataUnit.addDataAnnotation(an);
-			}
+//			}
 			an.setString(textArea.getText());
+			pamDataUnit.setLastUpdateTime(PamCalendar.getTimeInMillis());
 		}
 		return true;
 	}

src/clickDetector/ClickBTDisplay.java

@@ -1572,6 +1572,9 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
 	}
 	private double clickAngleToY(ClickDetection click) {
 		AbstractLocalisation loc = click.getLocalisation();
+//		if (click.getUID() == 110006089) {
+//			System.out.println("Click 110006089 angle " + click.getAngle());
+//		}
 		if (loc == null) return 0;
 		double angle = 0;
 		GpsData oll;

src/clickDetector/ClickBinaryDataSource.java

@@ -210,8 +210,8 @@ public class ClickBinaryDataSource extends BinaryDataSource {
 //		long uid = binaryObjectData.getDataUnitBaseData().getUID();
 //		System.out.printf("Loading click with UID %d at %s\n", uid, 
 //				PamCalendar.formatDateTime(binaryObjectData.getTimeMilliseconds()));
-//		if (uid == lastUID) {
-//			System.out.println("Click repeat UID: " + lastUID);
+//		if (uid == 110006089) {
+//			System.out.println("Click  UID: " + 110006089);
 //		}
 //		else {
 //			lastUID = binaryObjectData.getDataUnitBaseData().getUID();

src/clickDetector/ClickDetection.java

@@ -1328,6 +1328,8 @@ public class ClickDetection extends PamDataUnit<PamDataUnit, PamDataUnit> implem
 
 	/**
 	 * Returns the angle in degrees for compatibilty with older version of click detector
+	 * This is really bad to use for anything apart from two element arrays and it would be
+	 * sensible to remove the function entirely. 
 	 * @return angle of the click detection in degrees
 	 */
 	public double getAngle() {

src/clickDetector/dataSelector/ClickSelectPaneFX.java

@@ -217,7 +217,8 @@ public class ClickSelectPaneFX extends DynamicSettingsPane<Boolean>  {
 		void setParams() {
 			ClickAlarmParameters clickAlarmParameters = clickDataSelector.getClickAlarmParameters();
 			speciesSelect.getChildren().clear();
-
+			
+			
 			//species pane setup
 			species = null;
 			weights = null;
@@ -350,6 +351,7 @@ public class ClickSelectPaneFX extends DynamicSettingsPane<Boolean>  {
 		}
 
 		boolean getParams() {
+			
 
 			ClickAlarmParameters clickAlarmParameters = clickDataSelector.getClickAlarmParameters().clone();
 			clickAlarmParameters.useEchoes = useEchoes.isSelected();
@@ -397,6 +399,7 @@ public class ClickSelectPaneFX extends DynamicSettingsPane<Boolean>  {
 
 			//			btDisplayParameters.showANDEvents = andEvents.isSelected();
 			//			btDisplayParameters.showEventsOnly = onlyEvents.isSelected();
+			
 			clickDataSelector.setClickAlarmParameters(clickAlarmParameters);
 			return true;
 		}

src/clickTrainDetector/classification/CTClassifierManager.java

@@ -1,9 +1,8 @@
 package clickTrainDetector.classification;
 
 import java.util.ArrayList;
+import java.util.UUID;
 
-import PamUtils.PamCalendar;
-import PamguardMVC.debug.Debug;
 import clickTrainDetector.CTDataUnit;
 import clickTrainDetector.ClickTrainControl;
 import clickTrainDetector.classification.bearingClassifier.BearingClassification;
@@ -158,10 +157,10 @@ public class CTClassifierManager {
 		//first check the pre-classifier
 		Chi2CTClassification classification = this.preClassifier.classifyClickTrain(ctDataUnit); 
 		
-		System.out.println("Pre classifier: " + PamCalendar.formatDateTime(ctDataUnit.getTimeMilliseconds()) + " N. " + ctDataUnit.getSubDetectionsCount() + "UID first: " + ctDataUnit.getSubDetection(0).getUID() ); 
+		//System.out.println("Pre classifier: " + PamCalendar.formatDateTime(ctDataUnit.getTimeMilliseconds()) + " N. " + ctDataUnit.getSubDetectionsCount() + "UID first: " + ctDataUnit.getSubDetection(0).getUID() ); 
 
 		if (classification.getSpeciesID()==CTClassifier.NOSPECIES) {
-			System.out.println("No SPECIES: chi^2" + ctDataUnit.getCTChi2()); 
+			//System.out.println("No SPECIES: chi^2" + ctDataUnit.getCTChi2()); 
 			ctDataUnit.setJunkTrain(true);
 			//no need to do any more classification- the click train has been flagged for deletion.
 			ctDataUnit.clearClassifiers();
@@ -189,17 +188,17 @@ public class CTClassifierManager {
 		ctDataUnit.clearClassifiers();
 		ctDataUnit.setClassificationIndex(-1);
 		
-		System.out.println("Classify species: Num classifier " +  this.cTClassifiers.size()); 
+		//System.out.println("Classify species: Num classifier " +  this.cTClassifiers.size()); 
 
 		for (int i=0; i<this.cTClassifiers.size(); i++) {
 			
 		
-			System.out.println("Classifier: " + i); 
+			//System.out.println("Classifier: " + i); 
 
 			//the first classifier 
 			ctclassification = this.cTClassifiers.get(i).classifyClickTrain(ctDataUnit);
 			
-			System.out.println("Classifier complete: SPECIES: " + ctclassification.getSpeciesID()); 
+			//System.out.println("Classifier complete: SPECIES: " + ctclassification.getSpeciesID()); 
 
 			
 //			Debug.out.println(i + " ClassifierManager: Classify a click train data unit: " + ctDataUnit  + " parent data block: " +
@@ -208,7 +207,7 @@ public class CTClassifierManager {
 			
 			//set the species flag but only if this is the first time the ct data unit has been classified. 
 			if (ctclassification.getSpeciesID()>CTClassifier.NOSPECIES && !hasBeenClssfd) {
-				System.out.println("Set classiifcation index: " + i); 
+				//System.out.println("Set classiifcation index: " + i); 
 				ctDataUnit.setClassificationIndex(i); //set the classification index. 
 				hasBeenClssfd = true; 
 			}
@@ -238,12 +237,26 @@ public class CTClassifierManager {
 				System.err.println("CTCLassifier manager: the classifier is null");
 				continue; 
 			}
+			
+			if (ctParams[i].uniqueID ==null) {
+				//old versions may not have a unique ID so needs to be added. 
+				ctParams[i].uniqueID = UUID.randomUUID().toString();
+			}
 			aClassifier.setParams(ctParams[i]); 
 			cTClassifiers.add(aClassifier); 
 		}
 
 	}
 
+	/**
+	 * Get the pre-classifer. This is an intial very broad classifier that is used to determine
+	 * whether a click train should be saved or dumped from memory. 
+	 * @return the pre-classifier. 
+	 */
+	public Chi2ThresholdClassifier getPreClassifier() {
+		return preClassifier;
+	}
+
 
 
 

src/clickTrainDetector/classification/CTClassifierParams.java

@@ -1,6 +1,7 @@
 package clickTrainDetector.classification;
 
 import java.io.Serializable;
+import java.util.UUID;
 
 import PamModel.parametermanager.ManagedParameters;
 import PamModel.parametermanager.PamParameterSet;
@@ -20,12 +21,23 @@ public class CTClassifierParams implements Cloneable, Serializable, ManagedParam
 	private static final long serialVersionUID = 1L;
 	
 	
+	public CTClassifierParams() {
+		this.uniqueID = UUID.randomUUID().toString();
+	}
+	
+	
 	/**
-	 * A very simple species flag to indicate what classifier was used. 0 means not classified. 
+	 * The name of the classifier. 
 	 */
 	public String classifierName = ""; 
 	
 	
+	/**
+	 * A unique ID for the classifier that never changes. This is important for accessing data selectors. 
+	 */
+	public String uniqueID; 
+	
+	
 	/**
 	 * A very simple species flag to indicate what classifier was used. 0 means not classified. 
 	 */

src/clickTrainDetector/classification/bearingClassifier/BearingClassifierParams.java

@@ -15,6 +15,7 @@ public class BearingClassifierParams extends CTClassifierParams implements Manag
 	
 	
 	public BearingClassifierParams(){
+		super();
 		type = CTClassifierType.BEARINGCLASSIFIER; 
 	}
 

src/clickTrainDetector/classification/idiClassifier/IDIClassifierParams.java

@@ -4,9 +4,15 @@ import java.io.Serializable;
 
 import PamModel.parametermanager.ManagedParameters;
 import clickTrainDetector.classification.CTClassifierParams;
+import clickTrainDetector.classification.CTClassifierType;
 
 public class IDIClassifierParams extends CTClassifierParams implements Serializable, Cloneable, ManagedParameters {
 	
+	public IDIClassifierParams(){
+		super();
+		type = CTClassifierType.IDICLASSIFIER; 
+	}
+	
 	/**
 	 * 
 	 */

src/clickTrainDetector/classification/simplechi2classifier/Chi2CTClassification.java

@@ -1,5 +1,7 @@
 package clickTrainDetector.classification.simplechi2classifier;
 
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.dataSelector.DataSelector;
 import clickTrainDetector.classification.CTClassification;
 import clickTrainDetector.classification.CTClassifierType;
 import clickTrainDetector.classification.ClassifierJSONLogging;
@@ -22,15 +24,14 @@ public class Chi2CTClassification implements CTClassification {
 	private int speciesCode = -1;
 	
 	
-	private SimpleClassifierJSONLogging simpleClassifierJSONLogging; 
+	private SimpleClassifierJSONLogging simpleClassifierJSONLogging;
 
 
-	
 	public Chi2CTClassification(int speciesCode) {
 		this.speciesCode = speciesCode; 
 		simpleClassifierJSONLogging=new SimpleClassifierJSONLogging(); 
 	}
-	
+
 
 	/**
 	 * Create the classification from a JSON string
@@ -62,5 +63,7 @@ public class Chi2CTClassification implements CTClassification {
 	public ClassifierJSONLogging getJSONLogging() {
 		return simpleClassifierJSONLogging;
 	}
+	
+	
 
 }

src/clickTrainDetector/classification/simplechi2classifier/Chi2ThresholdClassifier.java

@@ -1,6 +1,8 @@
 package clickTrainDetector.classification.simplechi2classifier;
 
 import PamUtils.PamCalendar;
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.dataSelector.DataSelector;
 import PamguardMVC.debug.Debug;
 import clickTrainDetector.CTDataUnit;
 import clickTrainDetector.ClickTrainControl;
@@ -32,10 +34,17 @@ public class Chi2ThresholdClassifier implements CTClassifier {
 	 */
 	private ClickTrainControl clickTrainControl;
 
+	
+	/**
+	 * Data selector for the chi2 threshold classifier. 
+	 */
+	private DataSelector dataSelector;
+
 
 	public Chi2ThresholdClassifier(ClickTrainControl clickTrainControl, int defaultSpeciesID) {
 		this.clickTrainControl=clickTrainControl; 
 		clssfrParams.speciesFlag=defaultSpeciesID; 
+		createDataSelector(clickTrainControl.getParentDataBlock());
 	}
 
 	
@@ -65,8 +74,62 @@ public class Chi2ThresholdClassifier implements CTClassifier {
 			return new Chi2CTClassification(CTClassifier.NOSPECIES); //no classification
 		}
 		
+		if (!isPercClicks(clickTrain)) {
+//			Debug.out.println("Failed on chi2Threshold"); 
+			return new Chi2CTClassification(CTClassifier.NOSPECIES); //no classification
+		}
+		
+		
 		return new Chi2CTClassification(clssfrParams.speciesFlag);
 	}
+	
+	
+	/**
+	 * Check the percentage of clicks which are correctly classified by the data selector. 
+	 * @param clickTrain - the click train
+	 * @return true if the percentage critera is passed
+	 * 
+	 */
+	private boolean isPercClicks(CTDataUnit clickTrain) {
+			
+		//no point iterating through click if we do not need to. 
+		if (clssfrParams.minPercentage==0) return true;
+				
+		double count = 0; 
+		for (int i=0; i<clickTrain.getSubDetectionsCount(); i++) {
+			if (this.getDataSelector().scoreData(clickTrain.getSubDetection(i))>0) {
+				count = count+1.; 
+			}
+		}
+		if (count/clickTrain.getSubDetectionsCount()>=clssfrParams.minPercentage) {
+			return true;	
+		}
+		else {
+			return false;
+		}
+	}
+
+
+	/**
+	 * Get the data selector. 
+	 * @param source - the source data block 
+	 * @return the data selector.
+	 */
+	public void createDataSelector(PamDataBlock<?> source) {
+		if (dataSelector==null || dataSelector.getPamDataBlock()!=source) {
+			//create the data selector
+			//System.out.println("Data selector: " + dataSelector); 
+			if (source!=null) {
+				dataSelector=source.getDataSelectCreator().getDataSelector(clickTrainControl.getUnitName() +  " " + clssfrParams.uniqueID
+						+ "_X2_threshold_classifier", false, null);
+				//System.out.println("Data selector: " + dataSelector); 
+			}
+			else {
+				dataSelector=null; 
+			}
+		}
+	}
+	
 
 	@Override
 	public String getName() {
@@ -122,7 +185,6 @@ public class Chi2ThresholdClassifier implements CTClassifier {
 	public void setParams(Chi2ThresholdParams clssfrParams) {
 		//System.out.println("HELLO CLASSIFIER PARAMS: " + clssfrParams.chi2Threahold );
 		this.clssfrParams=clssfrParams;
-
 	}
 
 	/**
@@ -145,4 +207,10 @@ public class Chi2ThresholdClassifier implements CTClassifier {
 	}
 
 
+	public DataSelector getDataSelector() {
+		createDataSelector(clickTrainControl.getParentDataBlock());
+		return dataSelector;
+	}
+
+
 }

src/clickTrainDetector/classification/simplechi2classifier/Chi2ThresholdParams.java

@@ -1,5 +1,8 @@
 package clickTrainDetector.classification.simplechi2classifier;
 
+import java.io.Serializable;
+import java.util.UUID;
+
 import PamModel.parametermanager.ManagedParameters;
 import PamModel.parametermanager.PamParameterSet;
 import clickTrainDetector.classification.CTClassifierParams;
@@ -12,9 +15,10 @@ import clickTrainDetector.classification.CTClassifierType;
  * @author Jamie Macaulay
  *
  */
-public class Chi2ThresholdParams extends CTClassifierParams implements ManagedParameters  {
+public class Chi2ThresholdParams extends CTClassifierParams implements ManagedParameters, Serializable, Cloneable  {
 	
 	public Chi2ThresholdParams(){
+		super();
 		super.type=CTClassifierType.CHI2THRESHOLD;
 	}
 	
@@ -25,7 +29,7 @@ public class Chi2ThresholdParams extends CTClassifierParams implements ManagedPa
 	
 	/**
 	 * The chi2 threshold to set. This is the chi2 value divided by the number of clicks in the train.
-	 * If zero then the classification always passes...A bit fo a hack for testing
+	 * If zero then the classification always passes...A bit of a hack for testing
 	 */
 	public double chi2Threshold = 1500.;
 
@@ -33,7 +37,13 @@ public class Chi2ThresholdParams extends CTClassifierParams implements ManagedPa
 	 * The minimum number of clicks. 
 	 */
 	public int minClicks = 5;
-
+	
+	/**
+	 * The minimum %percentage which must the parent data selector of clicks/
+	 *. values are 0-1. 
+	 */
+	public double minPercentage = 0;
+	
 	/**
 	 * The minimum time in seconds.
 	 */

src/clickTrainDetector/classification/standardClassifier/StandardClassifier.java

@@ -130,7 +130,7 @@ public class StandardClassifier implements CTClassifier {
 		
 		int speciesID = standardClssfrParams.speciesFlag; 
 		
-		System.out.println("Standard Classificiation: " ); 
+		//System.out.println("Standard Classificiation: " ); 
 	
 		//all classifiers have to pass.  
 		CTClassification[] ctClassification = new CTClassification[classifiers.size()]; 
@@ -138,8 +138,8 @@ public class StandardClassifier implements CTClassifier {
 			
 			ctClassification[i] = classifiers.get(i).classifyClickTrain(clickTrain); 
 			
-			System.out.println("Standard Classificiation: " + i + "  speciesID: " + ctClassification[i].getSpeciesID() 
-					+ "  sub species: "+ classifiers.get(i).getParams().speciesFlag + " standard species: " +speciesID + " use? : " + standardClssfrParams.enable[i]); 
+//			System.out.println("Standard Classificiation: " + i + "  speciesID: " + ctClassification[i].getSpeciesID() 
+//					+ "  sub species: "+ classifiers.get(i).getParams().speciesFlag + " standard species: " +speciesID + " use? : " + standardClssfrParams.enable[i]); 
 
 			if (standardClssfrParams.enable[i]) {
 				if (ctClassification[i].getSpeciesID() != SUB_CLASSIFIER_SPECIESID){
@@ -148,7 +148,7 @@ public class StandardClassifier implements CTClassifier {
 			}
 		}
 	
-		System.out.println("SPECIES ID: " + speciesID); 
+		//System.out.println("SPECIES ID: " + speciesID); 
 
 		//create the classification. 
 		StandardClassification classification = new StandardClassification(ctClassification, speciesID); 

src/clickTrainDetector/classification/standardClassifier/StandardClassifierParams.java

@@ -1,5 +1,7 @@
 package clickTrainDetector.classification.standardClassifier;
 
+import java.util.UUID;
+
 import clickTrainDetector.classification.CTClassifierParams;
 import clickTrainDetector.classification.CTClassifierType;
 
@@ -27,6 +29,7 @@ public class StandardClassifierParams extends CTClassifierParams {
 	
 	
 	public StandardClassifierParams(){
+		super();
 		///very important to set this or else the clasifier manager does not
 		//know which classifier to create. 
 		type = CTClassifierType.STANDARDCLASSIFIER; 

src/clickTrainDetector/classification/templateClassifier/TemplateClassifierParams.java

@@ -22,6 +22,7 @@ public class TemplateClassifierParams extends CTClassifierParams implements Mana
 	private static final long serialVersionUID = 10L;
 	
 	public TemplateClassifierParams(){
+		super();
 		super.type=CTClassifierType.TEMPLATECLASSIFIER;
 //		chi2ThresholdParams = new Chi2ThresholdParams();  
 //		template = DefualtSpectrumTemplates.getTemplate(SpectrumTemplateType.BEAKED_WHALE);

src/clickTrainDetector/clickTrainAlgorithms/mht/mhtvar/AmplitudeChi2.java

@@ -39,7 +39,10 @@ public class AmplitudeChi2 extends SimpleChi2VarDelta {
 	@Override
 	public double getDiffValue(PamDataUnit pamDataUnit0, PamDataUnit pamDataUnit1) {
 		//System.out.println("DB: " + pamDataUnit0.getAmplitudeDB());
-		return pamDataUnit0.getAmplitudeDB()-pamDataUnit1.getAmplitudeDB();
+		//made this abs so it can deal with increasing then decreasing click trains. i.e.
+		//the click trian is not penalised if it gradually increasing then starts to gradually decrease
+		//in amplitude. 
+		return Math.abs(pamDataUnit0.getAmplitudeDB()-pamDataUnit1.getAmplitudeDB());
 	}
 
 	@Override

src/clickTrainDetector/dataselector/CTDataSelector.java

@@ -1,9 +1,12 @@
 package clickTrainDetector.dataselector;
 
+import java.util.Arrays;
+
 import PamDetection.LocContents;
 import PamguardMVC.PamDataUnit;
 import PamguardMVC.dataSelector.DataSelectParams;
 import PamguardMVC.dataSelector.DataSelector;
+import clickTrainDetector.CTDataUnit;
 import clickTrainDetector.CTDetectionGroupDataUnit;
 import clickTrainDetector.ClickTrainControl;
 import clickTrainDetector.ClickTrainDataBlock;
@@ -43,6 +46,8 @@ public class CTDataSelector extends DataSelector {
 
 	private boolean allowScores;
 
+	private boolean[] useSpeciesList;
+
 	public CTDataSelector(ClickTrainControl clickTrainControl, ClickTrainDataBlock clickTrainDataBlock, 
 			String selectorName, boolean allowScores) {
 		super(clickTrainDataBlock, selectorName, allowScores);
@@ -83,6 +88,7 @@ public class CTDataSelector extends DataSelector {
 
 	@Override
 	public DataSelectParams getParams() {
+		getDialogPanel().getParams(ctSelectParams);
 		return ctSelectParams;
 	}
 	
@@ -99,6 +105,8 @@ public class CTDataSelector extends DataSelector {
 		CTDetectionGroupDataUnit ctDataUnit = (CTDetectionGroupDataUnit) pamDataUnit;
 		
 		if (ctDataUnit.getSubDetectionsCount()<ctSelectParams.minSubDetections) return 0; 
+		
+		if (!isClassified(ctDataUnit)) return 0; 
 	
 		if (ctSelectParams.needsLoc && pamDataUnit.getLocalisation()==null) return 0; 
 		
@@ -108,4 +116,31 @@ public class CTDataSelector extends DataSelector {
 		return 1;
 	}
 
+	/**
+	 * Check whether a click train passes the data selector classification criteria. 
+	 * @param ctDataUnit - the click train data unit to test.
+	 * @return true of the click train passes detection criterea. 
+	 */
+	private boolean isClassified(CTDetectionGroupDataUnit ctDataUnit) {
+
+		if (!ctSelectParams.needsClassification) return true; 
+
+		if (ctDataUnit instanceof CTDataUnit) {
+
+			CTDataUnit clickTrain = (CTDataUnit) ctDataUnit; 
+
+			if (clickTrain.ctClassifications==null) return false; 
+
+			//iterate through all the classifiers and allowed classification types. 
+			for (int i=0; i<ctSelectParams.classifier.length; i++) {
+				for (int j=0; j<clickTrain.ctClassifications.size(); j++) {
+					if (clickTrain.ctClassifications.get(j).getSpeciesID()==ctSelectParams.classifier[i]) {
+						return true; 
+					}
+				}
+			}
+		}
+		return false;
+	}
+
 }

src/clickTrainDetector/dataselector/CTSelectParams.java

@@ -33,6 +33,16 @@ public class CTSelectParams extends DataSelectParams implements Serializable, Cl
 	 * The minimum number of sub detections before a click train is plotted. 
 	 */
 	public int minSubDetections = 10; 
+	
+	/**
+	 * True of the click train detector needs a classifcation
+	 */
+	public boolean needsClassification = false; 
+	
+	/**
+	 * The classifier type(s) to select
+	 */
+	public int[] classifier = null; 
 
 
 	/**
@@ -56,6 +66,8 @@ public class CTSelectParams extends DataSelectParams implements Serializable, Cl
 	 */
 	public double maxAngleChange = Math.toRadians(5);
 	
+	
+	
 	@Override
 	public ClickTrainSelectParameters clone() {
 		try {

src/clickTrainDetector/layout/CTSwingGUI.java

@@ -73,7 +73,7 @@ public class CTSwingGUI extends PamControlledGUISwing {
 			settingsDialog = new PamDialogFX2AWT<ClickTrainParams>(parentFrame, setPane, false);
 		}
 		
-		if (classificationTab!=null) settingsPane.setTab(classificationTab ? 2 : 0); //set the tab to the classification tab
+		if (classificationTab!=null && classificationTab) settingsPane.setTab(2); //set the tab to the classification tab
 		
 		ClickTrainParams newParams = settingsDialog.showDialog(this.clickTrainControl.getClickTrainParams());
 		

src/clickTrainDetector/layout/ClickTrainAlgorithmPaneFX.java

@@ -324,7 +324,13 @@ public class ClickTrainAlgorithmPaneFX extends SettingsPane<ClickTrainParams> {
 
 		popOver.showingProperty().addListener((obs, old, newval)->{
 			if (newval) {
-			clickTrainControl.getDataSelector().getDialogPaneFX().setParams(true);
+				//the dialog has opened
+				clickTrainControl.getDataSelector().getDialogPaneFX().setParams(true);
+			}
+			else {
+				//the dialog has closed
+				clickTrainControl.getDataSelector().getDialogPaneFX().getParams(true);
+	
 			}
 		});
 

src/clickTrainDetector/layout/PreClassifierPane.java

@@ -34,7 +34,7 @@ public class PreClassifierPane extends PamBorderPane {
 
 	
 	private Pane createClassifierPane() {
-		simpleCTClassifierPane = new SimpleCTClassifierPane(null); 
+		simpleCTClassifierPane = new SimpleCTClassifierPane(clickTrainControl.getClassifierManager().getPreClassifier()); 
 		return (Pane) simpleCTClassifierPane.getContentNode();
 	}
 	

src/clickTrainDetector/layout/classification/simplechi2classifier/SimpleCTClassifierGraphics.java

@@ -35,14 +35,15 @@ public class SimpleCTClassifierGraphics implements CTClassifierGraphics {
 		if (simpleCTClassiferPane==null) {
 			simpleCTClassiferPane = new SimpleCTClassifierPane(simpleChi2Classifier);
 		}
-		//params are set here. 
-		simpleCTClassiferPane.setParams(simpleChi2Classifier.getParams());
+		//System.out.println("SimpleCTClassifierGraphics getCTClassifierPane: " + simpleChi2Classifier.getParams().chi2Threshold); 
+		//params are set here. <- do not do this because you may wish to store the classifier params somewhere else. 
+		//simpleCTClassiferPane.setParams(simpleChi2Classifier.getParams());
 		return (Pane) simpleCTClassiferPane.getContentNode();
 	}
 
 	@Override
 	public CTClassifierParams getParams() {
-		Chi2ThresholdParams clssfrParams = simpleCTClassiferPane.getParams(simpleChi2Classifier.getParams()); 
+		Chi2ThresholdParams clssfrParams = simpleCTClassiferPane.getParams(simpleChi2Classifier.getParams()).clone(); 
 		if (clssfrParams==null) {
 			System.err.print("Simple Chi2 Classifier returned null params");
 			return null;
@@ -51,13 +52,14 @@ public class SimpleCTClassifierGraphics implements CTClassifierGraphics {
 //			simpleChi2Classifier.setParams(clssfrParams); 
 //			return clssfrParams;
 //		}
+		//System.out.println("SimpleCTClassifierGraphics - getParams: " + clssfrParams.chi2Threshold);
 		return clssfrParams; 
 	}
 
 	@Override
 	public void setParams(CTClassifierParams params) {
 		simpleCTClassiferPane.setParams((Chi2ThresholdParams) params);
-		
+		//System.out.println("SimpleCTClassifierGraphics - setParams: " + ((Chi2ThresholdParams) params).chi2Threshold);
 	}
 
 }

src/clickTrainDetector/layout/classification/simplechi2classifier/SimpleCTClassifierPane.java

@@ -1,18 +1,32 @@
 package clickTrainDetector.layout.classification.simplechi2classifier;
 
+import java.text.DecimalFormat;
+
+import org.controlsfx.control.PopOver;
+
 import PamController.SettingsPane;
+import PamguardMVC.PamDataBlock;
 import clickTrainDetector.classification.simplechi2classifier.Chi2ThresholdClassifier;
 import clickTrainDetector.classification.simplechi2classifier.Chi2ThresholdParams;
 import javafx.geometry.Insets;
 import javafx.geometry.Orientation;
+import javafx.geometry.Pos;
 import javafx.scene.Node;
 import javafx.scene.control.CheckBox;
+import javafx.scene.control.Control;
 import javafx.scene.control.Spinner;
+import javafx.scene.control.SpinnerValueFactory;
 import javafx.scene.control.Tooltip;
 import javafx.scene.layout.Pane;
+import javafx.util.StringConverter;
+import pamViewFX.PamGuiManagerFX;
+import pamViewFX.fxGlyphs.PamGlyphDude;
+import pamViewFX.fxNodes.PamBorderPane;
+import pamViewFX.fxNodes.PamButton;
 import pamViewFX.fxNodes.PamHBox;
 import pamViewFX.fxNodes.PamSpinner;
 import pamViewFX.fxNodes.PamVBox;
+import pamViewFX.fxNodes.utilityPanes.PamToggleSwitch;
 import pamViewFX.fxNodes.utilsFX.ControlField;
 
 /**
@@ -51,6 +65,17 @@ public class SimpleCTClassifierPane extends SettingsPane<Chi2ThresholdParams>  {
 	 */
 	private ControlField<Double> minTime;
 
+	private PamToggleSwitch dataSelectorCheckBox;
+
+	private PamButton dataSelectorButton;
+
+	private PopOver popOver;
+
+	/**
+	 * The minimum percentage of clicks for a certain class. 
+	 */
+	private ControlField<Double> minPercClicks;
+
 	public SimpleCTClassifierPane(Chi2ThresholdClassifier simpleChi2Classifier) {
 		super(null);
 		this.simpleChi2Classifier=simpleChi2Classifier; 
@@ -96,17 +121,35 @@ public class SimpleCTClassifierPane extends SettingsPane<Chi2ThresholdParams>  {
 		chi2Threshold.getSpinner().getValueFactory().setConverter(PamSpinner.createStringConverter(0));		
 		chi2Threshold.setTooltip(new Tooltip(
 							"A click train has a X\u00b2 value which is based on the consistancy of inter detection interval \n"
-						+ 	"amplitude and other factors. The calculation of X\\\\u00b2 changes depending on the click train \n"
+						+ 	"amplitude and other factors. The calculation of X\u00b2 changes depending on the click train \n"
 						+ 	"detector is used."));
 		chi2Threshold.getLabel1().setPrefWidth(LABEL_WIDTH);
 
-		minClicks = new ControlField<Double>("Min. Clicks	", "", 0, Integer.MAX_VALUE, 5);
+		minClicks = new ControlField<Double>("Min. clicks	", "", 0, Integer.MAX_VALUE, 5);
 		minClicks.setTooltip(new Tooltip(
 				"The minimum number of detections."));
 		minClicks.getSpinner().setEditable(true);
 		minClicks.getLabel1().setPrefWidth(LABEL_WIDTH);
+		
+		
+		minPercClicks = new ControlField<Double>("Min. % clicks	", "", 0, 100., 1.);
+		minPercClicks.setTooltip(new Tooltip(
+				"The minimum number of detections."));
+		minPercClicks.getSpinner().setEditable(true);
+		SpinnerValueFactory<Double> valueFactory = new SpinnerValueFactory.DoubleSpinnerValueFactory(0, 100., 0., 1.);		
+		valueFactory.setConverter(doubleConverter);
+		minPercClicks.getSpinner().setValueFactory(valueFactory);
+		minPercClicks.getSpinner().setEditable(true);
+		///HACK to get the percentage sign to show?
+		minPercClicks.getSpinner().increment();
+		minPercClicks.getSpinner().decrement();
 
-		minTime = new ControlField<Double>("Min. Time		", "s", 0.0, Double.MAX_VALUE, 1.0);
+		minPercClicks.getLabel1().setPrefWidth(LABEL_WIDTH);
+		
+		minPercClicks.getChildren().add( createDataSelectorPane()); 
+		
+
+		minTime = new ControlField<Double>("Min. time		", "s", 0.0, Double.MAX_VALUE, 1.0);
 		minTime.getSpinner().getValueFactory().setConverter(PamSpinner.createStringConverter(2));		
 		minTime.setTooltip(new Tooltip(
 				"The minimum time for a click train."));
@@ -115,29 +158,83 @@ public class SimpleCTClassifierPane extends SettingsPane<Chi2ThresholdParams>  {
 
 		chi2Threshold.getSpinner().setEditable(true);
 		
-		vBox.getChildren().addAll(chi2Threshold, minClicks, minTime);
+		vBox.getChildren().addAll(chi2Threshold, minClicks, minPercClicks, minTime);
 
 		return vBox;
 
 	}
+	
+	/**
+	 * Create the data selector. 
+	 * @return the data selector. 
+	 */
+	private Pane createDataSelectorPane() {
+		PamHBox hbox = new PamHBox();
+		hbox.setSpacing(5);
+		hbox.setAlignment(Pos.CENTER_LEFT);
+
+		dataSelectorButton = new PamButton();
+//		dataSelectorButton.setGraphic(PamGlyphDude.createPamGlyph(MaterialIcon.SETTINGS, PamGuiManagerFX.iconSize));
+		dataSelectorButton.setGraphic(PamGlyphDude.createPamIcon("mdi2c-cog", PamGuiManagerFX.iconSize));
+		dataSelectorButton.setOnAction((action)->{
+			showDataSelectorPane();
+		});
+		hbox.getChildren().addAll(dataSelectorButton);
+		return hbox; 
+	}
+	
+	
+	/**
+	 * Creates pane allowing the user to change fine scale things such as error limits. 
+	 * @return the pop over pane. 
+	 */
+	public void showDataSelectorPane() {
+		
+		if (popOver==null) {
+			popOver = new PopOver(); 
+			PamBorderPane holder = new PamBorderPane(simpleChi2Classifier.getDataSelector().getDialogPaneFX().getContentNode()); 
+			holder.setPadding(new Insets(5,5,5,5));
+			popOver.setContentNode(holder);
+		}
+
+		popOver.showingProperty().addListener((obs, old, newval)->{
+			if (newval) {
+//				System.out.println("Data Selector: "  + simpleChi2Classifier.getDataSelector());
+				simpleChi2Classifier.getDataSelector().getDialogPaneFX().setParams(true);
+			}
+			else {
+				simpleChi2Classifier.getDataSelector().getDialogPaneFX().getParams(true);
+			}
+		});
+		
+		popOver.show(dataSelectorButton);
+	} 
 
 	@Override
 	public Chi2ThresholdParams getParams(Chi2ThresholdParams currParams) {
+		//System.out.println("Get PERC spinner value; " + minPercClicks.getSpinner().getValue());
 		
 		currParams.chi2Threshold=chi2Threshold.getSpinner().getValue(); 
 		//HACK - for some reason Integer spinner is returning a double
 		currParams.minClicks=minClicks.getSpinner().getValue().intValue(); 
 		currParams.minTime=minTime.getSpinner().getValue(); 
+		currParams.minPercentage=minPercClicks.getSpinner().getValue()/100; 
+
+		if (simpleChi2Classifier!=null && simpleChi2Classifier.getDataSelector()!=null) {
+			simpleChi2Classifier.getDataSelector().getDialogPaneFX().getParams(true); 
+		}
 		
 		return currParams;
 	}
 
 	@Override
 	public void setParams(Chi2ThresholdParams input) {
+		
 		chi2Threshold.getSpinner().getValueFactory().setValue(input.chi2Threshold);
 		//HACK - for some reason Integer spinner is returning a double
 		minClicks.getSpinner().getValueFactory().setValue((double) input.minClicks);
 		minTime.getSpinner().getValueFactory().setValue(input.minTime);
+		minPercClicks.getSpinner().getValueFactory().setValue(input.minPercentage*100.);
 	}
 
 	@Override
@@ -164,6 +261,24 @@ public class SimpleCTClassifierPane extends SettingsPane<Chi2ThresholdParams>  {
 
 	}
 	
+	
+	StringConverter<Double> doubleConverter = new StringConverter<Double>() {
+		private final DecimalFormat df = new DecimalFormat("###.#");
+		@Override
+		public String toString(Double object) {
+		    if (object == null) {return "";}
+		    return df.format(object)+"%";}
+		@Override
+		public Double fromString(String string) {
+		    try {
+		        if (string == null) {return null;}
+		        string = string.trim();
+		        if (string.length() < 1) {return null;}     
+		        return df.parse(string).doubleValue();
+		    } catch (Exception ex) {throw new RuntimeException(ex);}
+		    }
+		};
+	
 
 
 

src/clickTrainDetector/layout/classification/templateClassifier/TemplateClassifierPane.java

@@ -118,6 +118,8 @@ public class TemplateClassifierPane extends SettingsPane<TemplateClassifierParam
 		spectrumPane.getChildren().addAll(spectrumthreshold, spectrumTemplatePane); 
 		spectrumPane.setPadding(new Insets(5,5,5,5));
 		
+		spectrumTemplatePane.prefWidthProperty().bind(spectrumPane.widthProperty());
+		
 		
 //		tabPane.setSide(Side.LEFT);
 		
@@ -136,6 +138,10 @@ public class TemplateClassifierPane extends SettingsPane<TemplateClassifierParam
 //		tabPane.minWidthProperty().bind(generalPane.widthProperty());
 //		tabPane.getTabs().addAll(tab1, tab2);
 		
+		
+		spectrumTemplatePane.drawCurrentUnit();
+
+		
 		return new PamVBox(generalPane, spectrumPane); 
 	}
 

src/clickTrainDetector/layout/classification/templateClassifier/TemplateSpectrumPane.java

@@ -91,7 +91,7 @@ public class TemplateSpectrumPane  extends PamBorderPane {
 
 		//now add the import button. 
 		Pane spectrumTemplate = createTemplatePane(templateDisplay);
-		
+				
 		
 		return spectrumTemplate; 
 	}
@@ -121,12 +121,14 @@ public class TemplateSpectrumPane  extends PamBorderPane {
 		stackPane.setMaxHeight(prefHeight);
 		stackPane.setMaxWidth(Double.MAX_VALUE);
 		stackPane.setPrefWidth(500); //need this for some reason to make the plot resize.
+	
 
 		//stackPane.setStyle("-fx-background-color: red;");
 
 		detectionPlot.prefWidthProperty().bind(stackPane.widthProperty());
 
 
+
 		PamVBox holder = new PamVBox(); 
 		holder.setSpacing(5);
 		holder.getChildren().addAll(stackPane); 
@@ -363,4 +365,9 @@ public class TemplateSpectrumPane  extends PamBorderPane {
 	}
 
 
+	public void drawCurrentUnit() {
+		templateDisplay.drawCurrentUnit();
+	}
+
+
 }

src/clickTrainDetector/layout/dataselector/CTDataSelectPanel.java

@@ -15,6 +15,7 @@ import PamView.dialog.PamDialog;
 import PamView.dialog.PamDialogPanel;
 import PamView.dialog.PamGridBagContraints;
 import PamguardMVC.dataSelector.DataSelectParams;
+import clickTrainDetector.classification.CTClassifierManager;
 import clickTrainDetector.dataselector.CTDataSelector;
 import clickTrainDetector.dataselector.CTSelectParams;
 import javafx.scene.control.CheckBox;
@@ -71,8 +72,15 @@ public class CTDataSelectPanel implements PamDialogPanel {
 	 */
 	private JTextField minUnitsField;
 
+	private JPanel classification;
+
+	private JCheckBox[] classifierCheckBoxes;
+
+	private JCheckBox unclassifiedCheckBox;
+
+	private JPanel classificationFilter;
+
 	public CTDataSelectPanel(CTDataSelector ctDataSelector, boolean allowScores) {
-		// TODO Auto-generated constructor stub
 		this.ctDataSelector=ctDataSelector; 
 		mainPanel = createPanel(); 
 	}
@@ -84,7 +92,7 @@ public class CTDataSelectPanel implements PamDialogPanel {
 	private JPanel createPanel() {
 		//panel for map options
 		JPanel dataFilter=new JPanel();
-		dataFilter.setBorder(new TitledBorder("ClickTrain Filter"));
+		dataFilter.setBorder(new TitledBorder("General"));
 		GridBagLayout layout = new GridBagLayout();
 		GridBagConstraints constraints = new PamGridBagContraints();
 		dataFilter.setLayout(layout);
@@ -106,11 +114,22 @@ public class CTDataSelectPanel implements PamDialogPanel {
 
 		constraints.gridx++;
 		PamDialog.addComponent(dataFilter, minUnitsField = new JTextField(4), constraints);
+		
+		
+		classificationFilter=new JPanel();
+		classificationFilter.setBorder(new TitledBorder("Species classification"));
+		layout = new GridBagLayout();
+		constraints = new PamGridBagContraints();
+		classificationFilter.setLayout(layout);
+		constraints.gridy = 0;
+		constraints.gridx = 0;
+		constraints.gridwidth=3;
+		PamDialog.addComponent(classificationFilter, classification = createClassificationPanel(), constraints);
 
 
 		//panel for map options
 		JPanel filterPanel=new JPanel(); 
-		filterPanel.setBorder(new TitledBorder("Sub Detection Filter"));
+		filterPanel.setBorder(new TitledBorder("Sub Detections"));
 		layout = new GridBagLayout();
 		constraints = new PamGridBagContraints();
 		filterPanel.setLayout(layout);
@@ -163,11 +182,120 @@ public class CTDataSelectPanel implements PamDialogPanel {
 		JPanel mainPanel = new JPanel(); 
 		mainPanel.setLayout(new BorderLayout());
 		mainPanel.add(dataFilter, BorderLayout.NORTH); //preferred
+		mainPanel.add(classificationFilter, BorderLayout.CENTER); //changes size. 
 		mainPanel.add(filterPanel, BorderLayout.SOUTH); //preferred
 
 		return mainPanel;
 	}
 
+	private JPanel createClassificationPanel() {
+		JPanel panel = new JPanel(); 
+		GridBagLayout layout = new GridBagLayout();
+		panel.setLayout(layout);
+
+		return panel;
+	}
+
+	/**
+	 * Set up the classification pane with the right species check boxes etc. 
+	 */
+	private void setClassificationPane() {
+		
+		GridBagConstraints constraints = new PamGridBagContraints();
+		constraints.gridy = 0;
+		constraints.gridx = 0;
+		constraints.gridwidth=3;
+		
+		classification.removeAll(); //clear all previous check boxes. 
+		
+		CTClassifierManager classifcationManager = ctDataSelector.getClickControl().getClassifierManager(); 
+		
+		if (classifcationManager.getCurrentClassifiers().size()<1) {
+			//don't show the classification pane if there are no classiifcations. 
+			this.classificationFilter.setVisible(false);
+		}
+		this.classificationFilter.setVisible(true);
+
+		
+		PamDialog.addComponent(classification,  unclassifiedCheckBox = new JCheckBox("All"), constraints);
+		unclassifiedCheckBox.addActionListener((action)->{
+			setCheckBoxEnable();
+		});
+		constraints.gridy++; 
+
+		classifierCheckBoxes = new JCheckBox[classifcationManager.getCurrentClassifiers().size()]; 
+		for (int i=0; i<classifcationManager.getCurrentClassifiers().size(); i++) {
+			//System.out.println("Classifications: " + i); 
+			PamDialog.addComponent(classification,  classifierCheckBoxes[i] = new JCheckBox(classifcationManager.getCurrentClassifiers().get(i).getParams().classifierName), constraints);
+			classifierCheckBoxes[i].setSelected(true); //default should be selected
+			constraints.gridy++; 
+		}	
+		classification.validate(); //make sure everything is laid out properly.
+		
+		setClassifierParams(); 
+		
+		setCheckBoxEnable(); 
+	}
+	
+	private void setCheckBoxEnable() {
+		if (classifierCheckBoxes!=null) {
+			for (int i=0; i<classifierCheckBoxes.length; i++) {
+				classifierCheckBoxes[i].setEnabled(!unclassifiedCheckBox.isSelected());
+			}
+		}
+	}
+	
+	
+	/**
+	 * Set the classifier parameters. 
+	 */
+	private void setClassifierParams() {
+		
+		unclassifiedCheckBox.setSelected(currentParams.needsClassification ); 
+
+		if (currentParams.classifier==null ) {
+			for (int i=0; i<classifierCheckBoxes.length; i++) {
+					classifierCheckBoxes[i].setSelected(true);
+			}
+			return; 
+		}
+		
+		for (int i=0; i<classifierCheckBoxes.length; i++) {
+			classifierCheckBoxes[i].setSelected(false);
+			for (int j=0; j<currentParams.classifier.length; j++) {
+				if (ctDataSelector.getClickControl().getClassifierManager().getCurrentClassifiers().get(i).getSpeciesID()==currentParams.classifier[j]) {
+					classifierCheckBoxes[i].setSelected(true);
+				}
+			}
+		}
+
+	}
+		
+	
+	/**
+	 * Get the parameters for the classifiers to  use. 	
+	 */
+	private void getClassifierParams() {
+			currentParams.needsClassification  = unclassifiedCheckBox.isSelected(); 
+			
+			int count = 0; 
+			for (int i=0; i<classifierCheckBoxes.length; i++) {
+				if (classifierCheckBoxes[i].isSelected()) {
+					count++; 				
+				}
+			}
+			
+//			System.out.println("No. count: " + count);
+			currentParams.classifier = new int[count];  
+			for (int i=0; i<classifierCheckBoxes.length; i++) {
+				if (classifierCheckBoxes[i].isSelected()) {
+					currentParams.classifier[i] = ctDataSelector.getClickControl().getClassifierManager().getCurrentClassifiers().get(i).getSpeciesID(); 				
+				}
+			}
+		
+	}
+
+	
 	@Override
 	public JComponent getDialogComponent() {
 		return mainPanel;
@@ -182,11 +310,17 @@ public class CTDataSelectPanel implements PamDialogPanel {
 			maxAngleField.setText(String.format("%.2f", Math.toDegrees(currentParams.maxAngleChange)));
 			maxTimeField.setText(String.format("%.2f", currentParams.maxTime/1000.));
 
-
 			//click train plotting
 			minUnitsField.setText(String.format("%d", currentParams.minSubDetections));
 			hasLoc.setSelected(currentParams.needsLoc);
+			
+//			System.out.println("No. set classiifers: " + currentParams.classifier.length);
+			
+			setClassificationPane(); 
+			
 		}
+		
+		
 	}
 
 	/**
@@ -206,6 +340,8 @@ public class CTDataSelectPanel implements PamDialogPanel {
 			currentParams = new CTSelectParams();
 		}
 		try {
+			//System.out.println("Get Params: ");
+
 			Double minTime  =  (Double.valueOf(minTimeField.getText())*1000.); //millis
 			Double maxTime  =  (Double.valueOf(maxTimeField.getText())*1000.); //millis
 			Double maxAngleChange  =  Double.valueOf(maxAngleField.getText()); 
@@ -217,6 +353,11 @@ public class CTDataSelectPanel implements PamDialogPanel {
 			//click train plotting
 			currentParams.minSubDetections = Integer.valueOf(minUnitsField.getText());
 			currentParams.needsLoc = hasLoc.isSelected();
+			
+			// get the classifier parameters.
+			getClassifierParams();
+			
+			//System.out.println("No. getParams classifiers: " + currentParams.classifier.length);
 
 			return true; 
 		}

src/clickTrainDetector/layout/mht/MHTSettingsPane.java

@@ -159,25 +159,25 @@ public class MHTSettingsPane extends SettingsPane<MHTParams> {
 		pruneStartSpinner.setEditable(true);
 		pruneBackSpinner.setTooltip(new Tooltip("The minimum number of detections before pruning starts."));
 		gridPane.add(pruneStartSpinner, 1, gridY); 
-		gridY++;
+		gridY=0;
 
-		gridPane.add(new Label("Max no. coasts"), 0, gridY); 
+		gridPane.add(new Label("  Max no. coasts"), 2, gridY); 
 		nCoastsSpinner = new PamSpinner<Integer>(0,Integer.MAX_VALUE,3,1); 
 		nCoastsSpinner.getStyleClass().add(Spinner.STYLE_CLASS_SPLIT_ARROWS_HORIZONTAL);
 		nCoastsSpinner.setPrefWidth(70);
 		nCoastsSpinner.setEditable(true);
 		nCoastsSpinner.setTooltip(new Tooltip("The maximum number of missing detections before a track is closed"));
 
-		gridPane.add(nCoastsSpinner, 1, gridY); 
+		gridPane.add(nCoastsSpinner, 3, gridY); 
 		gridY++; 
 
-		gridPane.add(new Label("Max no. trains"), 0, gridY); 
+		gridPane.add(new Label("  Max no. trains"), 2, gridY); 
 		nHoldSpinner = new PamSpinner<Integer>(0,1000,3,1); 
 		nHoldSpinner.getStyleClass().add(Spinner.STYLE_CLASS_SPLIT_ARROWS_HORIZONTAL);
 		nHoldSpinner.setPrefWidth(70);
 		nHoldSpinner.setEditable(true);
 		nHoldSpinner.setTooltip(new Tooltip("The maximum number of unique click trains that can be tracked at the same time."));
-		gridPane.add(nHoldSpinner, 1, gridY); 
+		gridPane.add(nHoldSpinner, 3, gridY); 
 
 		pamVBox.getChildren().addAll(label, gridPane); 
 

src/dataMap/DataMapControl.java

@@ -8,7 +8,6 @@ import java.util.ArrayList;
 import javax.swing.SwingUtilities;
 
 import pamScrollSystem.AbstractScrollManager;
-
 import generalDatabase.DBControlUnit;
 import binaryFileStorage.BinaryStore;
 import dataMap.layoutFX.DataMapGUIFX;
@@ -240,6 +239,32 @@ public class DataMapControl extends PamControlledUnit implements PamSettings {
 	public ArrayList<PamDataBlock> getMappedDataBlocks() {
 		return mappedDataBlocks;
 	}
+	
+	/**
+	 * Update a single data map. Useful when bringing in data 
+	 * from 'non standard' sources. Check overall time limits and 
+	 * redraw, but no total map creation. 
+	 * @param singleDataMap
+	 */
+	public void updateSingleDataMap(OfflineDataMap<?> singleDataMap) {
+		long newLastTime = singleDataMap.getLastDataTime();
+		long newFirstTime = singleDataMap.getFirstDataTime();
+		if (mappedDataBlocks == null) {
+			return;
+		}
+		for (PamDataBlock aBlock : mappedDataBlocks) {
+			int nMaps = aBlock.getNumOfflineDataMaps();
+			for (int iMap = 0; iMap < nMaps; iMap++) {
+				OfflineDataMap aMap = aBlock.getOfflineDataMap(iMap);
+				newFirstTime = Math.min(newFirstTime, aMap.getFirstDataTime());
+				newLastTime = Math.max(newLastTime, aMap.getLastDataTime());
+			}
+		}
+		firstTime = newFirstTime;
+		lastTime = newLastTime;
+		dataMapPanel.repaintAll();
+		dataMapPanel.getSummaryPanel().newDataSources();
+	}
 
 	/**
 	 * @return the firstTime for any data in any data block

src/dataMap/DataMapPanel.java

@@ -167,5 +167,12 @@ public class DataMapPanel extends PamBorderPanel implements PamTabPanel {
 		}
 		summaryPanel.newDataSources();
 	}
+
+	/**
+	 * @return the summaryPanel
+	 */
+	public SummaryPanel getSummaryPanel() {
+		return summaryPanel;
+	}
 	
 }

src/dataMap/SummaryPanel.java

@@ -99,8 +99,8 @@ public class SummaryPanel extends HidingDialogComponent {
 				dataEnds[i].setText(" ---No data---");
 			}
 			else {
-			dataStarts[i].setText(PamCalendar.formatDateTime2(dataExtent[0], true));
-			dataEnds[i].setText(PamCalendar.formatDateTime(dataExtent[1], true));
+				dataStarts[i].setText(PamCalendar.formatDateTime2(dataExtent[0], true));
+				dataEnds[i].setText(PamCalendar.formatDateTime(dataExtent[1], true));
 			}
 		}
 		for (int i = offlineDataStores.size(); i < maxDataSources; i++) {

src/detectionPlotFX/layout/DetectionPlotDisplay.java

@@ -447,6 +447,11 @@ public class DetectionPlotDisplay extends PamBorderPane implements UserDisplayNo
 	private void drawDataUnit(PamDataUnit newDataUnit) {
 		//Debug.out.println("DetectionPlotDisplay DrawDataUnit: " +newDataUnit);
 		if (currentDataInfo!=null){
+			//sometimes the axis just need a little push to make sure the pane and axis object bindings have been updated
+			for (int i=0; i<Side.values().length; i++) {
+				dDPlotPane.getAxisPane(Side.values()[i]).layout(); 
+			}
+
 			currentDataInfo.drawData(dDPlotPane.getPlotCanvas().getGraphicsContext2D(), 
 					new Rectangle(0,0,dDPlotPane.getPlotCanvas().getWidth(),dDPlotPane.getPlotCanvas().getHeight()), 
 					this.detectionPlotProjector, newDataUnit);

src/detectionPlotFX/plots/SpectrumPlot.java

@@ -326,7 +326,7 @@ public abstract class  SpectrumPlot <D extends PamDataUnit> implements Detection
 			}
 			g2.strokePolyline(scaledDataX, scaledDataY, scaledDataY.length-1);
 			if (fillSpectrum) {
-				//				System.out.println("Last point: " + x0 + "  y0 " + r.getHeight()); 
+				//System.out.println("Last point: " + x0 + "  y0 " + y0 + " " + scale + " " + clickLineData[iChan][0] + "  " + projector.getAxis(Side.LEFT).getMinVal() +  " " +projector.getAxis(Side.LEFT).getTotalPixels()); 
 				scaledDataX[scaledDataX.length-1]=x0; // the last x position
 				scaledDataY[scaledDataY.length-1]= r.getHeight() ; //return the line to zero for polygon drawing
 				//				PamUtils.PamArrayUtils.printArray(scaledDataY);

src/fileOfflineData/OfflineFileList.java

@@ -0,0 +1,88 @@
+package fileOfflineData;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.util.ArrayList;
+
+/**
+ * Make a list of files with the given file filter. 
+ * @author dg50
+ *
+ */
+public class OfflineFileList {
+	
+	private ArrayList<File> files = new ArrayList<>();
+	private String folder;
+	private FileFilter fileFilter;
+	private boolean includeSubFolders;
+
+	public OfflineFileList(String folder, FileFilter fileFilter, boolean includeSubFolders) {
+		this.folder = folder;
+		this.fileFilter = fileFilter;
+		this.includeSubFolders = includeSubFolders;
+		updateCatalog();
+	}
+	
+	public int updateCatalog() {
+		files.clear();
+		File current = new File(this.folder);
+		addFiles(current);
+		return files.size();
+	}
+
+	private void addFiles(File current) {
+		if (current.exists() == false) {
+			return;
+		}
+		if (current.isFile() && checkFilter(current)) {
+			/*
+			 * This can only really happen if the root passed in is a file, not a 
+			 * folder, since files within the folder structure will get 
+			 * added from the loop below. 
+			 */
+			files.add(current);
+		}
+		else if (current.isDirectory()) {
+			File[] filesList = current.listFiles();
+			if (filesList == null) {
+				return;
+			}
+			for (int i = 0; i < filesList.length; i++) {
+				File aFile = filesList[i];
+				if (aFile.isFile() && checkFilter(aFile)) {
+					files.add(aFile);
+				}
+				else if (aFile.isDirectory() && includeSubFolders) {
+					addFiles(aFile);
+				}
+			}
+		}
+	}
+
+	/**
+	 * Check that if there is a filter, the file is accepted. 
+	 * @param aFile
+	 * @return
+	 */
+	private boolean checkFilter(File aFile) {
+		if (fileFilter == null) {
+			return true;
+		}
+		return fileFilter.accept(aFile);
+	}
+
+	/**
+	 * Get a list of files in the catalog as a simple string list. 
+	 * @return files as strings
+	 */
+	public String[] asStringList() {
+		if (files == null) {
+			return null;
+		}
+		String[] str = new String[files.size()];
+		for (int i = 0; i < files.size(); i++) {
+			str[i] = files.get(i).getAbsolutePath();
+		}
+		return str;
+	}
+}

src/generalDatabase/PamTableItem.java

@@ -426,7 +426,11 @@ public class PamTableItem implements Cloneable {
 		return (Double) value;
 	}
 	
-	
+	/**
+	 * Get a float value, being aware that some DBMS may have
+	 * decided to store as a Double anyway. Return Float.NaN for null data
+	 * @return float value or NaN
+	 */
 	public float getFloatValue() {
 		if (value == null) {
 			return Float.NaN;

src/generalDatabase/backup/DatabaseBackupStream.java

@@ -120,6 +120,9 @@ public class DatabaseBackupStream extends FileBackupStream {
 
 	public FileLocation getSourceLocation() {
 		File dbFile = getDatabaesFile();
+		if (dbFile == null) {
+			return null;
+		}
 		FileLocation sl = new FileLocation();
 		sl.path = dbFile.getAbsolutePath();
 		sl.canEditMask = false;

src/offlineProcessing/OfflineTask.java

@@ -4,6 +4,7 @@ import generalDatabase.DBControlUnit;
 import generalDatabase.PamConnection;
 import generalDatabase.SQLLogging;
 import generalDatabase.SQLTypes;
+import generalDatabase.SuperDetLogging;
 import generalDatabase.clauses.FixedClause;
 import generalDatabase.clauses.FromClause;
 import generalDatabase.clauses.PAMSelectClause;
@@ -354,6 +355,7 @@ public abstract class OfflineTask<T extends PamDataUnit> {
 		}
 		aBlock.clearAll(); 
 
+		
 
 		SQLLogging logging = aBlock.getLogging();
 		if (logging == null) {
@@ -382,7 +384,15 @@ public abstract class OfflineTask<T extends PamDataUnit> {
 			System.out.println("Unknown data selection option in OfflineTask.deleteOldData: " + taskGroupParams.dataChoice);
 			return;
 		}
-		logging.deleteData(clause);
+		while (logging != null) {
+			logging.deleteData(clause);
+			if (logging instanceof SuperDetLogging) {
+				logging = ((SuperDetLogging) logging).getSubLogging();
+			}
+			else {
+				break;
+			}
+		}
 	}
 
 

src/pamScrollSystem/AbstractPamScroller.java

@@ -44,6 +44,14 @@ public abstract class AbstractPamScroller implements DataTimeLimits {
 	 */
 	protected double[] playSpeeds = {.1, 0.25, .5, 1.0, 2, 5, 10};
 
+//	private long realTimerStart;
+//
+//	private long timerStartPosition;
+
+	private long timerLastCurrentTime;
+
+//	private long timerTimeMillis;
+
 
 	public AbstractPamScroller(String name, int orientation, int stepSizeMillis, long defaultLoadTime, boolean hasMenu){
 
@@ -630,6 +638,8 @@ public abstract class AbstractPamScroller implements DataTimeLimits {
 					playTimerAction();
 				}
 			});
+			timerLastCurrentTime = System.currentTimeMillis();
+//			timeLastValue = getValueMillis();
 			playTimer.start();
 			playbackStarted();
 		}
@@ -671,11 +681,17 @@ public abstract class AbstractPamScroller implements DataTimeLimits {
 				stopPlayback();
 				return;
 			}
-			long step = Math.max((long) (timerInterval * scrollerData.getPlaySpeed()), 1);
-			setValueMillis(pos+step);
-			if (pos == getValueMillis()) {
-				playTimer.setDelay(playTimer.getDelay()*2);
-			}
+			/**
+			 * Since the action on setValue can take quite some time, the timer can run slow
+			 * if we just increment by what we think this delay is, so increment the value
+			 * based on how much system time has elapsed between the last call and now 
+			 */
+			long now = System.currentTimeMillis();
+			int elapsed = (int) (now - timerLastCurrentTime);
+			int toAdd = (int) (elapsed*scrollerData.getPlaySpeed());
+			timerLastCurrentTime = now;
+			
+			setValueMillis(getValueMillis()+toAdd);
 		}
 	}
 

src/pamViewFX/fxNodes/pamAxis/PamAxisPane2.java

@@ -93,7 +93,7 @@ public class PamAxisPane2 extends StackPane {
 		this.getChildren().add(mainPane);
 	}
 
-	private void layoutAxis(){
+	public void layoutAxis(){
 
 		mainPane.setCenter(null);
 

src/pamViewFX/fxNodes/utilityPanes/MinMaxPane.java

@@ -1,7 +1,6 @@
 package pamViewFX.fxNodes.utilityPanes;
 
 import java.io.Serializable;
-
 import javafx.geometry.Pos;
 import javafx.scene.control.CheckBox;
 import javafx.scene.control.Label;

src/rocca/RoccaControl.java

@@ -69,6 +69,11 @@ public class RoccaControl extends PamControlledUnit implements PamSettings {
      */
 	public static final String unitType = "Rocca";
 	
+	/*
+	 * Max max data keep time to avoid memory overflows. Currently at 15 minutes. 
+	 */
+	private static final int MAXMAXDATAKEEPTIME = 900000;
+	
 	/**
 	 * reference to the ClickControl module when it is loaded in Viewer mode
 	 */
@@ -193,6 +198,17 @@ public class RoccaControl extends PamControlledUnit implements PamSettings {
 		return 1;
 	}
     
+    /**
+     * A bit of a fudge to deal with some old code which kept doubling the 
+     * keep time of the raw data, which eventually led to raw data using too 
+     * much memory and bringing down PG. I don't fully understand that code so 
+     * have left as much of it as possible, but put this in as an absolute 
+     * maximum which cannot be exceeded. 
+     * @return max in milliseconds as int, which is what's used in PAMDataBlock. 
+     */
+    public int getMaxDataKeepTime() {
+    	return MAXMAXDATAKEEPTIME;
+    }
     /**
      * 
      * @param eventList
@@ -242,18 +258,21 @@ public class RoccaControl extends PamControlledUnit implements PamSettings {
 					(rcdb.getContour().get(RoccaContourStats.ParamIndx.SNR) > 35. ||
 							rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) < 0.005 ||
 							rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 0.6 )) {
+				rcdb.setNaturalLifetimeMillis(0);
 				return;
 			}
 			if (roccaParameters.roccaClassifierModelFilename.getName().equals("HIClick.model") &&
 					(rcdb.getContour().get(RoccaContourStats.ParamIndx.SNR) > 40. ||
 							rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) < 0.01 ||
 							rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 0.6 )) {
+				rcdb.setNaturalLifetimeMillis(0);
 				return;
 			}
 			if (roccaParameters.roccaClassifierModelFilename.getName().equals("NWAtlClick.model") &&
 					(rcdb.getContour().get(RoccaContourStats.ParamIndx.SNR) > 35. ||
 							rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) < 0.005 ||
 							rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 0.6 )) {
+				rcdb.setNaturalLifetimeMillis(0);
 				return;
 			}
 

src/rocca/RoccaProcess.java

@@ -363,6 +363,9 @@ public class RoccaProcess extends PamProcess {
 			
 			// 2017/12/4 set the natural lifetime to Integer.Max, so that we definitely keep all of the data
 			// units during this code block.  Set the lifetime back to 0 at the end of the block
+			/*
+			 * DG June '22 made sure this is the case when the function returns early !
+			 */
 			rcdb.setNaturalLifetimeMillis(Integer.MAX_VALUE);
 			rcdb.calculateStatistics();
 			
@@ -385,6 +388,7 @@ public class RoccaProcess extends PamProcess {
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 1.5 ||
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) < 2000. ||
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) > 28000. )) {
+					rcdb.setNaturalLifetimeMillis(0);
 					return;
 				}
 				if (roccaControl.roccaParameters.roccaClassifierModelFilename.getName().equals("HIWhist.model") &&
@@ -398,6 +402,7 @@ public class RoccaProcess extends PamProcess {
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) > 60000.  ||
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQRANGE) < 800. ||
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQRANGE) > 14000.  )) {
+					rcdb.setNaturalLifetimeMillis(0);
 					return;
 				}
 				if (roccaControl.roccaParameters.roccaClassifierModelFilename.getName().equals("NWAtlWhist.model") &&
@@ -407,6 +412,7 @@ public class RoccaProcess extends PamProcess {
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 2.5 ||
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) < 9100. ||
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) > 82000. )) {
+					rcdb.setNaturalLifetimeMillis(0);
 					return;
 				}
 			}
@@ -736,13 +742,15 @@ public class RoccaProcess extends PamProcess {
 				PamUtils.makeChannelMap(lowestChanList));
 		int firstIndx = prdb.getUnitIndex(firstRDU);
 		if (firstIndx==-1) {
-			System.out.println("RoccaProcess: Cannot determine firstIndx, raw data lifetime = " + prdb.getNaturalLifetimeMillis() + " ms");
 	        int newTime;
 	        if (prdb.getNaturalLifetimeMillis() > Integer.MAX_VALUE/2) {
 	        	newTime = Integer.MAX_VALUE;
 	        } else {
 	        	newTime = prdb.getNaturalLifetimeMillis()*2;
 	        }
+	        // stop it getting silly.
+	        newTime = Math.min(newTime, roccaControl.getMaxDataKeepTime());
+			System.out.println("RoccaProcess: Cannot determine firstIndx, raw data lifetime = " + prdb.getNaturalLifetimeMillis() + " ms");
 	        prdb.setNaturalLifetimeMillis(newTime); // increase the lifetime to try and prevent this from happening again
 			return null;
 		}
@@ -769,13 +777,14 @@ public class RoccaProcess extends PamProcess {
 				PamUtils.makeChannelMap(highestChanList));
 		int lastIndx = prdb.getUnitIndex(lastRDU);
 		if (lastIndx==-1) {
-	        System.out.println("RoccaProcess: Cannot determine lastIndx, raw data lifetime = " + prdb.getNaturalLifetimeMillis() + " ms");
 	        int newTime;
 	        if (prdb.getNaturalLifetimeMillis() > Integer.MAX_VALUE/2) {
 	        	newTime = Integer.MAX_VALUE;
 	        } else {
 	        	newTime = prdb.getNaturalLifetimeMillis()*2;
 	        }
+	        newTime = Math.min(newTime, roccaControl.getMaxDataKeepTime());
+	        System.out.println("RoccaProcess: Cannot determine lastIndx, raw data lifetime = " + prdb.getNaturalLifetimeMillis() + " ms");
 	        prdb.setNaturalLifetimeMillis(newTime); // increase the lifetime to try and prevent this from happening again
 	        return null;
 		}

src/rocca/RoccaSidePanel.java

@@ -114,7 +114,10 @@ public class RoccaSidePanel extends PamObserverAdapter implements PamSidePanel
         this.rsdb = new RoccaSightingDataBlock
                 (roccaControl.roccaProcess,
                 roccaControl.roccaParameters.getChannelMap());
+        
+        // this one probably OK to never delete ? 
         rsdb.setNaturalLifetimeMillis(Integer.MAX_VALUE);
+        
         rdl = new RoccaDetectionLogger(this, rsdb);
         rsdb.SetLogging(rdl);
         rsdb.setMixedDirection(PamDataBlock.MIX_INTODATABASE);

src/rocca/RoccaWhistleSelect.java

@@ -171,6 +171,8 @@ public class RoccaWhistleSelect extends PamProcess implements SpectrogramMarkObs
                         roccaControl.roccaSidePanel.sidePanel.addASighting(false);
                 // if the user hit cancel, just exit
                 if (dummy == RoccaSightingDataUnit.NONE) {
+                    selectedWhistle.setNaturalLifetimeMillis(0);
+                    selectedWhistleRaw.setNaturalLifetimeMillis(0);
                 	return;
                 }
             }
@@ -198,6 +200,14 @@ public class RoccaWhistleSelect extends PamProcess implements SpectrogramMarkObs
                     selectedWhistleRaw,
                     display,
                     channel);
+
+            /**
+             * DG June '22.
+             * I hope IT's K to set these back here. It's possible it's also 
+             * done elsewhere.  
+             */
+            selectedWhistle.setNaturalLifetimeMillis(0);
+            selectedWhistleRaw.setNaturalLifetimeMillis(0);
         }
 	}
 

src/spectrogramNoiseReduction/layoutFX/SpectrogramNoisePaneFX.java

@@ -3,12 +3,10 @@ package spectrogramNoiseReduction.layoutFX;
 
 import java.util.ArrayList;
 
-import org.controlsfx.control.ToggleSwitch;
-
 import pamViewFX.PamGuiManagerFX;
-import pamViewFX.fxNodes.PamBorderPane;
 import pamViewFX.fxNodes.PamHBox;
 import pamViewFX.fxNodes.PamVBox;
+import pamViewFX.fxNodes.utilityPanes.PamToggleSwitch;
 import pamViewFX.fxNodes.utilityPanes.SourcePaneFX;
 import spectrogramNoiseReduction.SpecNoiseMethod;
 import spectrogramNoiseReduction.SpectrogramNoiseProcess;
@@ -16,10 +14,8 @@ import spectrogramNoiseReduction.SpectrogramNoiseSettings;
 import javafx.geometry.Insets;
 import javafx.geometry.Pos;
 import javafx.scene.Node;
-import javafx.scene.control.CheckBox;
 import javafx.scene.control.Label;
 import javafx.scene.control.Tooltip;
-import javafx.scene.layout.Pane;
 import PamController.SettingsPane;
 import PamguardMVC.PamDataBlock;
 
@@ -39,7 +35,7 @@ public class SpectrogramNoisePaneFX extends SettingsPane<SpectrogramNoiseSetting
 	
 	private SpectrogramNoiseSettings spectrogramNoiseSettings=new SpectrogramNoiseSettings(); 
 
-	private ToggleSwitch[] enableMethod;
+	private PamToggleSwitch[] enableMethod;
 	
 	private PamDataBlock dataSource;
 	
@@ -58,7 +54,7 @@ public class SpectrogramNoisePaneFX extends SettingsPane<SpectrogramNoiseSetting
 		PamVBox methodPane;
 		SpecNoiseNodeFX dC;
 		Node node;
-		enableMethod = new ToggleSwitch[methods.size()];
+		enableMethod = new PamToggleSwitch[methods.size()];
 		
 
 		for (int i = 0; i < methods.size(); i++) {
@@ -66,13 +62,14 @@ public class SpectrogramNoisePaneFX extends SettingsPane<SpectrogramNoiseSetting
 			methodPane.setSpacing(10); 
 			//create name
 			Label title=new Label(methods.get(i).getName());
-			PamGuiManagerFX.titleFont2style(title);
 //			title.setFont(PamGuiManagerFX.titleFontSize2);
 			
 			PamHBox toggleHolder = new PamHBox();
 			toggleHolder.setSpacing(5);
 			toggleHolder.getChildren().addAll(enableMethod[i] = 
-					new ToggleSwitch(), title); 
+					new PamToggleSwitch(methods.get(i).getName())); 
+			PamGuiManagerFX.titleFont2style(enableMethod[i].getLabel());
+
 			enableMethod[i].setAlignment(Pos.CENTER_LEFT);
 			toggleHolder.setAlignment(Pos.CENTER_LEFT);
 			

src/warnings/SingleLineWarningDisplay.java

@@ -67,7 +67,8 @@ public class SingleLineWarningDisplay implements WarningDisplay {
 			lastWarning.setToolTipText(null);
 		}
 		else {
-			String str = String.format("Warning: %s-%s   ", w.getWarningSource(), w.getWarningMessage());
+			String str = w.getWarnignLevel() > 0 ? "Warning: " : "";
+			str += String.format("%s-%s   ", w.getWarningSource(), w.getWarningMessage());
 			lastWarning.setText(str);
 			lastWarning.setWarningLevel(w.getWarnignLevel());
 			lastWarning.setToolTipText(w.getWarningTip());