Merge branch 'main' of https://github.com/macster110/PAMGuard

.classpath

@@ -6,7 +6,7 @@
 			<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-21">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/Amazon Coretto 21">
 		<attributes>
 			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>

.settings/org.eclipse.core.resources.prefs

@@ -1,6 +1,5 @@
 eclipse.preferences.version=1
 encoding//src/rawDeepLearningClassifer/segmenter/SegmenterProcess.java=UTF-8
-encoding//src/test=UTF-8
 encoding//src/test/resources=UTF-8
 encoding/<project>=UTF-8
 encoding/src=UTF-8

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

@@ -1,9 +1,9 @@
 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=21
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=18
 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=21
+org.eclipse.jdt.core.compiler.compliance=18
 org.eclipse.jdt.core.compiler.debug.lineNumber=generate
 org.eclipse.jdt.core.compiler.debug.localVariable=generate
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
@@ -13,4 +13,4 @@ org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
 org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=warning
 org.eclipse.jdt.core.compiler.release=enabled
-org.eclipse.jdt.core.compiler.source=21
+org.eclipse.jdt.core.compiler.source=18

pom.xml

@@ -302,11 +302,7 @@
 		<version>0.0.57</version>
 	</dependency>
 
-	<!--jpam project - Deep learning java library 
+	<!--jpam project - Deep learning java library -->
-	DG has commented this out since there are problems with access to the maven repo
-	on JDJM's Github. For now a jar file is included in the build and we'll go back to 
-	Maven when we can ... DG 15 Jan 2022.
-	 	   Repo for jpam code- this used for deep learning [15:17] Jamie MacAulay-->
 	<dependency>
 		<groupId>io.github.macster110</groupId>
 		<artifactId>jdl4pam</artifactId>
@@ -372,7 +368,7 @@
            <version>${javafx.version}</version>
 	</dependency>
 	
-	<!-- Decorates JavaFX components-->
+	<!-- Decorates JavaFX components with error icons if inputs are incorrect-->
 	<dependency>
 		<groupId>net.synedra</groupId>
 		<artifactId>validatorfx</artifactId>
@@ -466,6 +462,13 @@
 		<version>12.3.1</version>
 	</dependency> 
 	
+	<!-- Icon symbol pack for swing icons . -->
+    <dependency>
+        <groupId>org.kordamp.ikonli</groupId>
+        <artifactId>ikonli-swing</artifactId>
+        <version>12.3.1</version>
+    </dependency>
+	
 	<!-- Ikonli MaterialDesign2 (Latest) font pack https://kordamp.org/ikonli/cheat-sheet-materialdesign2.html -->
 	<dependency>
 	    <groupId>org.kordamp.ikonli</groupId>
@@ -480,30 +483,28 @@
 	    <version>12.3.1</version>
 	</dependency>
 
-	<!-- https://mvnrepository.com/artifact/net.sf.geographiclib/GeographicLib-Java -->
+	<!-- https://mvnrepository.com/artifact/net.sf.geographiclib/GeographicLib-Java 
+	 Used in the video range module-->
 	<dependency>
 		<groupId>net.sf.geographiclib</groupId>
 		<artifactId>GeographicLib-Java</artifactId>
 		<version>1.50</version>
 	</dependency>
 	
-	<!-- https://mvnrepository.com/artifact/org.jogamp.gluegen/gluegen -->
+	<!-- https://mvnrepository.com/artifact/org.jogamp.gluegen/gluegen
 	<dependency>
 		<groupId>org.jogamp.gluegen</groupId>
 		<artifactId>gluegen-rt-main</artifactId>
 		<version>2.3.2</version>
-	</dependency>
+	</dependency>-->
-	
+		
-	<!-- https://mvnrepository.com/artifact/java3d/j3dutils -->
-	
-	<!-- https://mvnrepository.com/artifact/java3d/j3dcore -->
 
-	<!-- https://mvnrepository.com/artifact/com.healthmarketscience.jackcess/jackcess -->
+	<!-- https://mvnrepository.com/artifact/com.healthmarketscience.jackcess/jackcess
 	<dependency>
 		<groupId>com.healthmarketscience.jackcess</groupId>
 		<artifactId>jackcess</artifactId>
 		<version>3.0.1</version>
-	</dependency>
+	</dependency>-->
 	
 	<!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.core/jackson-databind -->
 	<dependency>
@@ -512,12 +513,12 @@
 		<version>2.10.1</version>
 	</dependency>
 	
-	<!-- https://mvnrepository.com/artifact/org.jogamp.jogl/jogl-all-main -->
+	<!-- https://mvnrepository.com/artifact/org.jogamp.jogl/jogl-all-main 
 	<dependency>
 		<groupId>org.jogamp.jogl</groupId>
 		<artifactId>jogl-all-main</artifactId>
 		<version>2.3.2</version>
-	</dependency>
+	</dependency>-->
 	
 	<!-- NOT SURE IF WE NEED THE JAXB LIBRARIES HERE - NO ERRORS WHEN REMOVED
 	<dependency>
@@ -654,7 +655,8 @@
 	    <version>42.2.24</version>
 	</dependency>
 
-	<!-- https://mvnrepository.com/artifact/org.renjin/renjin-script-engine -->
+	<!-- https://mvnrepository.com/artifact/org.renjin/renjin-script-engine
+	Used to export data to R structures-->
 	<dependency>
 	    <groupId>org.renjin</groupId>
 	    <artifactId>renjin-script-engine</artifactId>
@@ -669,8 +671,7 @@
 	    <version>1.8.0-beta4</version>
 	</dependency>
  	 
-	
+ 	 
-	
 	<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-nop
 	this one is only needed to get rid of an annoying warning that shows up during startup -->
 	<dependency>
@@ -906,7 +907,7 @@
 	</dependency>
 
 	
-		<!-- https://mvnrepository.com/artifact/it.sauronsoftware/jave -->
+	<!-- https://mvnrepository.com/artifact/it.sauronsoftware/jave -->
  	<dependency>
 	    <groupId>it.sauronsoftware</groupId>
 	    <artifactId>jave</artifactId>

src/PamModel/PamModel.java

@@ -45,7 +45,6 @@ import whistlesAndMoans.AbstractWhistleDataUnit;
 import fftManager.FFTDataUnit;
 import fftManager.PamFFTControl;
 import group3dlocaliser.Group3DLocaliserControl;
-import metadata.MetaDataContol;
 import meygenturbine.MeygenTurbine;
 import printscreen.PrintScreenControl;
 import rockBlock.RockBlockControl;
@@ -472,6 +471,7 @@ final public class PamModel implements PamSettings {
 			mi.setToolTipText("Interface to Tethys Database");
 			mi.setModulesMenuGroup(utilitiesGroup);
 			mi.setMaxNumber(1);
+			//mi.addGUICompatabilityFlag(PamGUIManager.FX); //has FX enabled GUI.
 			mi.setHidden(SMRUEnable.isEnable() == false);
 		}		
 		

src/PamView/PamGui.java

@@ -74,8 +74,11 @@ import javax.swing.event.MenuListener;
 
 import Acquisition.DaqSystemInterface;
 import annotation.tasks.AnnotationManager;
+import export.layoutFX.ExportOptions;
 import metadata.MetaDataContol;
+import pamViewFX.fxNodes.pamDialogFX.PamDialogFX2AWT;
 import performanceTests.PerformanceDialog;
+import rawDeepLearningClassifier.RawDLParams;
 import tipOfTheDay.TipOfTheDayManager;
 import Array.ArrayManager;
 //import Logging.LogDataObserver;
@@ -86,6 +89,7 @@ import PamController.PamControllerInterface;
 import PamController.PamSettingManager;
 import PamController.PamSettings;
 import PamController.PamguardVersionInfo;
+import PamController.SettingsPane;
 import PamController.settings.SettingsImport;
 import PamModel.CommonPluginInterface;
 import PamModel.PamModel;
@@ -668,6 +672,13 @@ public class PamGui extends PamView implements WindowListener, PamSettings {
 		startMenuEnabler.addMenuItem(menuItem);
 		fileMenu.add(menuItem);
 
+		//export items
+		menuItem = new JMenuItem("Export Data ...");
+		menuItem.addActionListener(new ExportOptionsListener(getGuiFrame()));
+		startMenuEnabler.addMenuItem(menuItem);
+		fileMenu.add(menuItem);
+		
+		
 		for (int i = 0; i < pamControllerInterface.getNumControlledUnits(); i++) {
 
 			menuItem = pamControllerInterface.getControlledUnit(i).createFileMenu(frame);
@@ -975,6 +986,20 @@ public class PamGui extends PamView implements WindowListener, PamSettings {
 		}
 	}
 	
+	class ExportOptionsListener implements ActionListener {
+		private JFrame parentFrame;
+
+		public ExportOptionsListener(JFrame parentFrame) {
+			super();
+			this.parentFrame = parentFrame;
+		}
+
+		public void actionPerformed(ActionEvent e) {
+			//show the export options dialog. 
+			ExportOptions.getInstance().showDialog(parentFrame);
+		}
+	}
+
 	class MenuGeneralXMLExport implements ActionListener {
 		private JFrame parentFrame;
 		public MenuGeneralXMLExport(JFrame parentFrame) {

src/dataMap/layoutFX/DataMapPaneFX.java

@@ -274,10 +274,7 @@ public class DataMapPaneFX extends PamBorderPane implements UserDisplayNodeFX {
 	 * @param timeEnd - the end of loaded data in millis. 
 	 */
 	public void selectedDataTime(Long timeStart, Long timeEnd) {
-		System.out.println("SELECTED DATA TIME:  " + timeStart + "  " + timeEnd);
 		summaryPane.setSelectedDataTime(timeStart, timeEnd);
-		dateAxis.setUpperBound(timeEnd);
-		dateAxis.setLowerBound(timeStart);
 	}
 
 

src/dataMap/layoutFX/DataStreamPaneFX.java

@@ -386,7 +386,7 @@ public class DataStreamPaneFX extends PamBorderPane {
 			
 			long time2 = System.currentTimeMillis();
 
-			System.out.println("Paint Canvas: " + this + "   " + System.currentTimeMillis() + "  " + (time2-time1));
+			//System.out.println("Paint Canvas: " + this + "   " + System.currentTimeMillis() + "  " + (time2-time1));
 
 		}
 		

src/dataMap/layoutFX/ScalePaneFX.java

@@ -9,12 +9,15 @@ import PamUtils.PamCalendar;
 import binaryFileStorage.BinaryStore;
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
+import javafx.geometry.Pos;
 import javafx.scene.Node;
 import javafx.scene.control.CheckBox;
 import javafx.scene.control.ComboBox;
 import javafx.scene.control.Label;
 import javafx.scene.control.Slider;
+import javafx.scene.layout.GridPane;
 import javafx.scene.layout.Pane;
+import javafx.util.StringConverter;
 import pamViewFX.PamGuiManagerFX;
 import pamViewFX.fxNodes.PamBorderPane;
 import pamViewFX.fxNodes.PamGridPane;
@@ -22,6 +25,7 @@ import pamViewFX.fxNodes.PamHBox;
 import pamViewFX.fxNodes.PamVBox;
 import pamViewFX.fxNodes.pamDialogFX.PamDialogFX;
 import pamViewFX.fxNodes.sliders.PamSlider;
+import pamViewFX.fxNodes.utilityPanes.PamToggleSwitch;
 
 /**
  * Allows uses to change the horizontal and vertical scales on the data map. 
@@ -59,14 +63,17 @@ public class ScalePaneFX extends PamBorderPane {
 	/**
 	 * Check box for log vertical scale. 
 	 */
-	private CheckBox logScaleBox;
+	private PamToggleSwitch logScaleBox;
 	
 	/**
 	 * The chosen time values. 
 	 */
 	private double[] timeScaleChoices = DataMapParameters.hScaleChoices;
 	
-	private Pane datagramPane;
+	/**
+	 * Combo box holding options to channge the datargam bin size
+	 */
+	private ComboBox<String> datagramBox;
 
 	/**
 	 * Holds a list of times for the datagram bin size. 
@@ -76,7 +83,14 @@ public class ScalePaneFX extends PamBorderPane {
 	/**
 	 * Holds everything. 
 	 */
-	private PamVBox holder; 
+	private PamVBox holder;
+
+	/**
+	 * Grid pane with settings for the data scales
+	 */
+	private PamGridPane scaleSettingsPane;
+
+	private Label dataGramLabel; 
 
 
 
@@ -84,9 +98,16 @@ public class ScalePaneFX extends PamBorderPane {
 		this.dataMapControl = dataMapControl;
 		this.dataMapPane = dataMapPane;
 		
+//		//create the holder pane. 
+//		PamVBox vBoxHolder=new PamVBox(); 
+//		vBoxHolder.setSpacing(5);
+//		Label title=new Label("Scales"); 
+//		PamGuiManagerFX.titleFont2style(title);
+//		vBoxHolder.getChildren().addAll(title, controlPane);
+		
 		holder=new PamVBox(); 
 		holder.setSpacing(20);
-		holder.getChildren().add(createScalePane());
+		holder.getChildren().add(scaleSettingsPane = createScalePane());
 		
 		this.setCenter(holder); 
 		
@@ -103,31 +124,28 @@ public class ScalePaneFX extends PamBorderPane {
 	public void checkDataGramPane(){
 		if (BinaryStore.findBinaryStoreControl()!=null){
 			DatagramManager dataGramManager=BinaryStore.findBinaryStoreControl().getDatagramManager();
-			if (dataGramManager!=null && datagramPane==null) {
+			if (dataGramManager!=null && datagramBox==null) {
-				datagramPane=createDatagramPane(dataGramManager);
+				datagramBox=createDatagramPane(dataGramManager);
-				holder.getChildren().add(datagramPane);
+				scaleSettingsPane.add(dataGramLabel= new Label("Datagram bin size"), 0, 2);
+				scaleSettingsPane.add(dataGramComboBox, 1, 2);
 			}
 		}
 		else {
-			holder.getChildren().remove(datagramPane);
+			scaleSettingsPane.getChildren().remove(dataGramLabel);
-			datagramPane=null; 
+			scaleSettingsPane.getChildren().remove(dataGramComboBox);
+
+			datagramBox=null; 
 		}
 	}
 
 	
 	/**
-	 * Create the pane to reset the datagram pane bin size. 
+	 * Create the a datagram combo box to change the size of the datagram
 	 * @param dataGramManager - the datagram manager for the current biinary store. 
-	 * @return
+	 * @return a combo box with datagram bin sizes. 
 	 */
-	private Pane createDatagramPane(DatagramManager dataGramManager){
+	private ComboBox<String> createDatagramPane(DatagramManager dataGramManager){
 
-		
-		PamGridPane dataGramOptions=new PamGridPane(); 
-		dataGramOptions.setHgap(5);
-		dataGramOptions.setVgap(5);
-		
-		dataGramOptions.add(new Label("Datagram Bin Size"),0,0);
 		dataGramComboBox=new ComboBox<String>(createDurationList(dataGramManager)); 
 		
 		dataGramComboBox.getSelectionModel().select(durationToString(dataGramManager.getDatagramSettings().datagramSeconds*1000L));
@@ -147,19 +165,7 @@ public class ScalePaneFX extends PamBorderPane {
 			}
 	     });
 		
-		dataGramOptions.add(dataGramComboBox,1,0);
+		return dataGramComboBox;
-
-		//create the holder pane. 
-		PamVBox vBoxHolder=new PamVBox(); 
-		vBoxHolder.setSpacing(5);
-		Label title=new Label("Datagram"); 
-//		title.setFont(PamGuiManagerFX.titleFontSize2);
-		PamGuiManagerFX.titleFont2style(title);
-
-		vBoxHolder.getChildren().addAll(title, dataGramOptions);
-
-		
-		return vBoxHolder;
 		
 	}
 	
@@ -184,19 +190,24 @@ public class ScalePaneFX extends PamBorderPane {
 	}
 
 	
-	private Node createScalePane() {
+	private PamGridPane createScalePane() {
 	
 		PamGridPane controlPane=new PamGridPane(); 
 		controlPane.setHgap(5);
 		controlPane.setVgap(5);
 		
 		//create time scale controls
-		controlPane.add(new Label("Time"),0,1);
+		controlPane.add(new Label("Time window"),0,1);
 		
 		//create time slider 
 		timeSlider=new Slider(0, timeScaleChoices.length-1, 1); 
 		timeSlider.setShowTickLabels(true);
 		timeSlider.setShowTickMarks(true);
+		timeSlider.setMajorTickUnit(1);
+		
+		timeSlider.setLabelFormatter(new ScaleStringConverter());
+		
+//		PamGridPane.setHalignment(timeSlider, Pos.BOTTOM_CENTER);
 
 		controlPane.add(timeSlider,1,1);
 		//add listener to time slider to change datamap. 
@@ -205,10 +216,11 @@ public class ScalePaneFX extends PamBorderPane {
 			dataMapPane.scaleChanged();
 		}); 
 		 
-		controlPane.add(timeScaleLabel=new Label(""),2,1);
+		controlPane.add(timeScaleLabel=new Label(""),3,1);
 		
 		//create vertical scale controls
-		controlPane.add(new Label("Data Counts"),0,0);
+		controlPane.add(new Label("Data counts"),0,0);
+		
 
 		scaleBox=new ComboBox<String> (); 
 		scaleBox.getItems().add("No Scaling");
@@ -217,28 +229,37 @@ public class ScalePaneFX extends PamBorderPane {
 		scaleBox.getItems().add("per Hour");
 		scaleBox.getItems().add("per Day");
 		controlPane.add(scaleBox,1,0);
+		scaleBox.setPrefWidth(200);
 
 		scaleBox.valueProperty().addListener((ov, oldVal, newVal)->{
 			dataMapPane.scaleChanged();
 		}); 
 
 		 
-		logScaleBox=new CheckBox("Log Scale"); 
+		logScaleBox=new PamToggleSwitch("Log Scale"); 
-		logScaleBox.setOnAction((action)->{
+		logScaleBox.selectedProperty().addListener((obsVal, oldVal, newVal)->{
 			dataMapPane.scaleChanged();
-		});;
+		});
-		controlPane.add(logScaleBox,2,0);
 		
-		//create the holder pane. 
+		
-		PamVBox vBoxHolder=new PamVBox(); 
+		controlPane.add(logScaleBox,3,0);
-		vBoxHolder.setSpacing(5);
-		Label title=new Label("Scales"); 
-		PamGuiManagerFX.titleFont2style(title);
-		vBoxHolder.getChildren().addAll(title, controlPane);
 			
 
+		return controlPane;
+	}
+	
+	class ScaleStringConverter extends StringConverter<Double> {
+
+		@Override
+		public String toString(Double object) {
+			return String.valueOf(timeScaleChoices[object.intValue()]);
+		}
+
+		@Override
+		public Double fromString(String string) {
+			return Double.valueOf(string);
+		}
 		
-		return vBoxHolder;
 	}
 	
 	/**

src/dataMap/layoutFX/ScrollingDataPaneFX.java

@@ -8,22 +8,19 @@ import PamUtils.PamCalendar;
 import javafx.animation.KeyFrame;
 import javafx.animation.Timeline;
 import javafx.geometry.Insets;
+import javafx.geometry.Side;
 import javafx.scene.Node;
 import javafx.scene.control.Label;
 import javafx.scene.control.ScrollBar;
-import javafx.scene.control.ScrollPane.ScrollBarPolicy;
 import javafx.scene.paint.Color;
-import javafx.scene.text.Text;
 import javafx.util.Duration;
 import PamguardMVC.PamDataBlock;
 import dataMap.DataMapControl;
-import pamViewFX.fxGlyphs.PamGlyphDude;
 import pamViewFX.fxNodes.PamBorderPane;
-import pamViewFX.fxNodes.PamButton;
 import pamViewFX.fxNodes.PamColorsFX;
 import pamViewFX.fxNodes.PamScrollPane;
 import pamViewFX.fxNodes.PamVBox;
-import pamViewFX.fxNodes.sashPane.SashPane;
+import pamViewFX.fxNodes.pamAxis.PamDateAxis;
 
 public class ScrollingDataPaneFX extends PamBorderPane {
 	
@@ -99,8 +96,10 @@ public class ScrollingDataPaneFX extends PamBorderPane {
 
 	private PamBorderPane holder;
 
-
+	/**
-
+	 * Axis which shows the current dates
+	 */
+	private PamDateAxis dateAxis;
 
 	/**
 	 * Constructor for the ScrollingDataPaneFX
@@ -162,6 +161,18 @@ public class ScrollingDataPaneFX extends PamBorderPane {
 			notifyScrollChange(300);
 		});
 		
+		
+		dateAxis = new PamDateAxis();
+		dateAxis.setAutoRanging(false);
+		dateAxis.setLabel("Time");
+		dateAxis.setSide(Side.TOP);
+		dateAxis.setAnimated(false);
+		dateAxis.setMinHeight(50);
+//		dateAxis.prefWidthProperty().bind(scrollingDataPanel.widthProperty());
+//		dateAxis.setStyle("-fx-background-color: ORANGE;");		 
+		dateAxis.setForceZeroInRange(false);
+		holder.setTop(dateAxis);
+		
 		return holder;
 	}
 	
@@ -204,6 +215,8 @@ public class ScrollingDataPaneFX extends PamBorderPane {
 			notifyScrollChange();
 		});
 		
+		timeScrollBar.setPrefHeight(20);
+		
 		holder.setCenter(timeScrollBar);
 		holder.setBottom(timeLabelPane);
 		
@@ -236,10 +249,13 @@ public class ScrollingDataPaneFX extends PamBorderPane {
 			dataStreamPanels.get(i).scrollChanged();
 		}
 		settingsStrip.scrollChanged();
+		
+		updateDateAxis();
 	}
 	
 	Timeline timeline; 
 	long lastTime = 0; 
+	
 	/**
 	 * Notify all panels and the settings strip that the scroll bar moved - but have a timer to wait to not call too often. 
 	 */
@@ -259,9 +275,19 @@ public class ScrollingDataPaneFX extends PamBorderPane {
 		}
 		
 		lastTime=currentTime;
+		
+		updateDateAxis();
 	
 	}
 
+	private void updateDateAxis() {
+		calcStartEndMillis();
+		dateAxis.setUpperBound(screenEndMillis);
+		dateAxis.setLowerBound(screenStartMillis);
+		double[] ticks = dateAxis.recalculateTicks();
+		System.out.println("Ticks: " + (ticks[3]/1000/3600) +  "hours");
+		dateAxis.setTickUnit(ticks[3]);	
+	}
 
 	/**
 	 * Create the data graphs to go into the pane. 
@@ -282,7 +308,7 @@ public class ScrollingDataPaneFX extends PamBorderPane {
 			for (int i = 0; i < dataBlocks.size(); i++) {
 				aStreamPanel = new DataStreamPaneFX(dataMapControl, this, dataBlocks.get(i));
 				dataStreamPanels.add(aStreamPanel);
-				dataStreamPanels.get(i).setPrefHeight(DATASTREAMPANE_HEIGHT);
+				dataStreamPanels.get(i).setMinHeight(DATASTREAMPANE_HEIGHT);
 				//now add to a split pane. 
 				//SplitPane.setResizableWithParent(aStreamPanel, true);
 				dataPanePanes.getChildren().add(aStreamPanel);

src/dataModelFX/connectionNodes/ModuleConnectionNode.java

@@ -637,6 +637,14 @@ public class ModuleConnectionNode extends StandardConnectionNode implements PAMC
 					removeConnectionPlug(getConnectionPlugs().get(i),false); 
 				}
 			}
+			
+			
+			Tooltip tooltip = ModuleToolTipFactory.getToolTip(pamControlledUnit);
+			
+			if (tooltip!=null) {
+			Tooltip. install(this, tooltip);
+			}
+			
 		}
 		
 		if (pamControlledUnit.getPamModuleInfo()!=null) {

src/dataModelFX/connectionNodes/ModuleIconFactory.java

@@ -36,7 +36,7 @@ public class ModuleIconFactory {
 	public enum ModuleIcon {
 		DATAMAP, NMEA, GPS, MAP, SOUND_AQ, SOUND_OUTPUT, FFT, FILTER, CLICK, CLICK_TRAIN, RECORDER, WHISTLE_MOAN,
 		NOISE_BAND, NOISE_FILT, DATABASE, BINARY, TIME_DISPLAY, DETECTION_DISPLAY, ARRAY, DEEP_LEARNING, MATCHED_CLICK_CLASSIFIER,
-		DECIMATOR, CPOD
+		DECIMATOR, CPOD, TETHYS
 	}
 
 	/**
@@ -130,14 +130,14 @@ public class ModuleIconFactory {
 		case CPOD:
 			iconNode = new Label("CPOD"); //TEMP
 			break;
+		case TETHYS:
+			iconNode = PamGlyphDude.createModuleIcon("file-codemeta"); 
+			break;
 		default:
 			break;
 		}
 		
 		long time2 = System.currentTimeMillis();
-
-		//System.out.println("GET MODULE ICON: " + icon + " load time: " + (time2-time1));
-
 		return iconNode;
 	}; 
 	
@@ -215,6 +215,7 @@ public class ModuleIconFactory {
 	 * @return the module icon enum
 	 */
 	public ModuleIcon getModuleIcon(String className) {
+		System.out.println("Get module icon: " + className);
 		ModuleIcon icon = null; 
 		switch (className) {
 		case "Acquisition.AcquisitionControl":
@@ -268,6 +269,9 @@ public class ModuleIconFactory {
 		case "cpod.CPODControl2":
 			icon=ModuleIcon.CPOD; 
 			break; 
+		case "MetaDataControl":
+			icon = ModuleIcon.TETHYS;
+			break;
 		}
 		return icon;
 	}

src/dataModelFX/connectionNodes/ModuleToolTipFactory.java

@@ -0,0 +1,16 @@
+package dataModelFX.connectionNodes;
+
+import PamController.PamControlledUnit;
+import javafx.scene.control.Tooltip;
+
+public class ModuleToolTipFactory {
+
+	public static Tooltip getToolTip(PamControlledUnit pamControlledUnit) {
+		
+		if (pamControlledUnit.getPamModuleInfo()==null) return null;
+		
+		return new Tooltip(pamControlledUnit.getPamModuleInfo().getToolTipText());
+		
+	}
+
+}

src/dataPlotsFX/TDControl.java

@@ -13,6 +13,7 @@ import dataPlots.TDParameters;
 import dataPlotsFX.data.TDDataInfoFX;
 import dataPlotsFX.layout.TDDisplayFX;
 import dataPlotsFX.layout.TDGraphFX;
+import detectiongrouplocaliser.DetectionGroupSummary;
 
 /**
  * The main class for the TDDisplay. 
@@ -222,5 +223,13 @@ public abstract class TDControl implements PamSettings {
 		this.uniqueDisplayName = uniqueName;
 	}
 
+	/**
+	 * A new detection group has been selected. 
+	 * @param detectionGroup - the detection group that has been selected
+	 */
+	public void newSelectedDetectionGroup(DetectionGroupSummary detectionGroup, TDGraphFX tdGraph) {
+		
+	}
+
 
 }

src/dataPlotsFX/TDControlFX.java

@@ -12,6 +12,8 @@ import dataPlotsFX.data.TDDataInfoFX;
 import dataPlotsFX.data.TDDataProviderFX;
 import dataPlotsFX.data.TDDataProviderRegisterFX;
 import dataPlotsFX.layout.TDDisplayFX;
+import dataPlotsFX.layout.TDGraphFX;
+import detectiongrouplocaliser.DetectionGroupSummary;
 import PamController.PamController;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
@@ -394,4 +396,10 @@ public class TDControlFX extends TDControl implements UserDisplayNodeFX {
 	public void setFrameHolder(PamInternalPane internalFrame) {
 		this.internalFrame=internalFrame; 
 	}
+	
+
+	@Override
+	public void newSelectedDetectionGroup(DetectionGroupSummary detectionGroup, TDGraphFX tdGraph) {
+		System.out.println("New selected detection group: " + detectionGroup);
+	}
 }

src/dataPlotsFX/TDDisplayController.java

@@ -9,10 +9,12 @@ import userDisplayFX.UserDisplayControlFX;
 import userDisplayFX.UserDisplayNodeFX;
 import PamController.PamController;
 import PamController.PamControllerInterface;
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.PamDataUnit;
 
 /**
- * The controller for the TD display. This is only used in the FX Gui where displays
+ * The controller for the TD display. This is only used in the FX GUI where displays
- * tend to have equality with modules. 
+ * tend to have equal parity with modules. 
  * 
  * @author Jamie Macaulay 
  *
@@ -30,6 +32,8 @@ public class TDDisplayController extends UserDisplayControlFX {
 	 */
 	private TDControlFX tdControlFX;
 	
+	private PamDataBlock selectedDataUnits;
+	
 	
 
 	public TDDisplayController(String unitName) {
@@ -37,13 +41,18 @@ public class TDDisplayController extends UserDisplayControlFX {
 		//set the compatible data units. 
 		 //indicate that this display can accept multiple parent data blocks at the same time. 
 		this.setMultiParent(true);
-		//set which PamDataUnits the display can show and therefore which datablocks it can accept as parents.
+		
+		//set which PamDataUnits the display can show and therefore which data blocks it can accept as parents.
 		setCompatibleDataUnits();
+		
+		selectedDataUnits = new PamDataBlock(PamDataUnit.class, "Selected Data Units", getUserDisplayProcess() , Integer.MAX_VALUE); //TODO
+		
+		getUserDisplayProcess().addOutputDataBlock(selectedDataUnits);
 	}
 	
 	/**
-	 * Set compatible data units in the process for this display. This allows the data model to determine if connections can
+	 * Set compatible data units in the process for this display. This allows the
-	 * be made to the display. 
+	 * data model to determine if connections can be made to the display.
 	 */
 	private void setCompatibleDataUnits(){
 		super.removeCompatibleDataUnits();
@@ -61,7 +70,6 @@ public class TDDisplayController extends UserDisplayControlFX {
 	 * @param dataBlocks - the parent datablocks to set. 
 	 */
 	protected void setParentDataBlocks(ArrayList<TDDataInfoFX> dataBlocks){
-//		System.out.println("Set parent datablocks: " + dataBlocks.size()); 
 		allowProcessNotify=false; 
 		
 		while (getUserDisplayProcess().getNumMuiltiplexDataBlocks()>0){
@@ -80,6 +88,7 @@ public class TDDisplayController extends UserDisplayControlFX {
 	
 	//disables notifications. 
 	boolean allowProcessNotify=true;
+	
 	@Override
 	public void notifyModelChanged(int type){
 //		System.out.println("---------------------------------" ); 

src/dataPlotsFX/overlaymark/DetectionGroupListener.java

@@ -0,0 +1,19 @@
+package dataPlotsFX.overlaymark;
+
+import detectiongrouplocaliser.DetectionGroupSummary;
+
+/**
+ * Listener for detection group. 
+ * 
+ * @author Jamie Macaulay
+ *
+ */
+public interface DetectionGroupListener {
+	
+	/**
+	 * A new detection group has been selected. 
+	 * @param detectionGroup - the detection group. 
+	 */
+	public void newSelectedGroup(DetectionGroupSummary detectionGroup);
+
+}

src/dataPlotsFX/overlaymark/OverlayMarkerManager.java

@@ -42,73 +42,6 @@ public class OverlayMarkerManager extends ExtMouseAdapter {
 		markerAdapters.add(new DragMarkerAdapter(tdGraphFX));
 	}
 	
-//	
-//	public void subscribePanel(TDPlotPanel fxPlot) {
-//		
-//		fxPlot.setOnMouseClicked(new MouseClicked());
-//		fxPlot.setOnMousePressed(new MousePressed());
-//		fxPlot.setOnMouseReleased(new MouseReleased());
-//		fxPlot.setOnMouseMoved(new MouseMoved());
-//		fxPlot.setOnMouseDragged(new MouseDragged());
-//		fxPlot.setOnMouseEntered(new MouseEntered());
-//		fxPlot.setOnMouseExited(new MouseExited());
-//
-//		for (TDOverlayMarker tdOverlayMarker: overlayMarkers){
-//			tdOverlayMarker.subscribePanel(fxPlot);
-//		}
-//	}
-//	
-//	class MouseClicked implements EventHandler<MouseEvent> {
-//		@Override
-//		public void handle(MouseEvent event) {
-////			System.out.println("Mouse Clicked: " + event.toString());
-//			overlayMarkers.get(currentMarker).mouseClicked(event);
-//		}
-//	}
-//	
-//	class MousePressed implements EventHandler<MouseEvent> {
-//		@Override
-//		public void handle(MouseEvent event) {
-////			System.out.println("Mouse Pressed: " + event.toString());
-//			overlayMarkers.get(currentMarker).mousePressed(event);
-//		}
-//	}
-//	class MouseReleased implements EventHandler<MouseEvent> {
-//		@Override
-//		public void handle(MouseEvent event) {
-////			System.out.println("Mouse Released: " + event.toString());
-//			overlayMarkers.get(currentMarker).mouseReleased(event);
-//		}
-//	}
-//	class MouseMoved implements EventHandler<MouseEvent> {
-//		@Override
-//		public void handle(MouseEvent event) {
-//			overlayMarkers.get(currentMarker).mouseMoved(event);
-//		}
-//	}
-//	class MouseDragged implements EventHandler<MouseEvent> {
-//		@Override
-//		public void handle(MouseEvent event) {
-//			overlayMarkers.get(currentMarker).mouseDragged(event);
-//		}
-//	}
-//	
-//	class MouseEntered implements EventHandler<MouseEvent> {
-//		@Override
-//		public void handle(MouseEvent event) {
-////			System.out.println("Mouse Entered: " + event.toString());
-//			overlayMarkers.get(currentMarker).mouseEntered(event);
-//		}
-//	}
-//	
-//	class MouseExited implements EventHandler<MouseEvent> {
-//		@Override
-//		public void handle(MouseEvent event) {
-////			System.out.println("Mouse Exited: " + event.toString());
-//			overlayMarkers.get(currentMarker).mouseExited(event);
-//		}
-//	}
-
 
 	public ArrayList<TDOverlayAdapter> getOverlayMarkers() {
 		return markerAdapters;

src/dataPlotsFX/overlaymark/TDMarkerAdapter.java

@@ -2,9 +2,15 @@ package dataPlotsFX.overlaymark;
 
 import java.util.List;
 
+import javax.swing.JPopupMenu;
+
+import PamView.GeneralProjector.ParameterType;
+import PamView.paneloverlay.overlaymark.MarkDataSelector;
 import PamView.paneloverlay.overlaymark.MarkRelationships;
 import PamView.paneloverlay.overlaymark.OverlayMark;
+import PamView.paneloverlay.overlaymark.OverlayMarkObserver;
 import PamView.paneloverlay.overlaymark.OverlayMarkProviders;
+import PamView.paneloverlay.overlaymark.OverlayMarker;
 import dataPlotsFX.layout.TDGraphFX;
 import dataPlotsFX.layout.TDGraphFX.TDPlotPane;
 import detectiongrouplocaliser.DetectionGroupSummary;
@@ -30,7 +36,7 @@ public class TDMarkerAdapter extends TDOverlayAdapter {
 	/**
 	 * The overlay marker with hooks into other modules which subscribe to the display.
 	 */
-	private StandardOverlayMarker pamMarker;
+	private TDMarkerFX pamMarker;
 
 	public TDMarkerAdapter(TDGraphFX tdGraphFX){
 		
@@ -51,16 +57,20 @@ public class TDMarkerAdapter extends TDOverlayAdapter {
 			MarkRelationships.getInstance().subscribeObservers(pamMarker);
 		}
 		pamMarker.setProjector(tdGraphFX.getGraphProjector());
+		
+		pamMarker.addDetectionGroupListener((detectionGroup)->{
+			tdGraphFX.getTDDisplay().getTDControl().newSelectedDetectionGroup(detectionGroup, tdGraphFX); 
+		});
 	}
 	
+
+	
 	/**
 	 * Get the selected detections
 	 * @return class containing selected detections
 	 */
 	public DetectionGroupSummary getSelectedDetectionGroup(){
 		//get the currently selected data units. 
-		
-		//System.out.println("Get selected detection group: " + pamMarker.getCurrentDetectionGroup());
 		return pamMarker.getCurrentDetectionGroup(); 
 	}
 	

src/dataPlotsFX/overlaymark/TDMarkerFX.java

@@ -1,6 +1,7 @@
 package dataPlotsFX.overlaymark;
 
 import java.awt.Point;
+import java.util.ArrayList;
 import java.util.List;
 
 import javax.swing.JPopupMenu;
@@ -36,17 +37,20 @@ public class TDMarkerFX extends StandardOverlayMarker  {
 	 * The current detection group. 
 	 */
 	private DetectionGroupSummary currentDetectionGroup;
+	
+	/**
+	 * The detection groups. 
+	 */
+	public ArrayList<DetectionGroupListener> detectionGroupListeners = new ArrayList<DetectionGroupListener>(); 
 
 	/**
 	 * The maximum distance a click can be from a data unit to be selected. 
 	 */
 	private static double maxMarkDistance=15; 
-
+	
-
 
 	public TDMarkerFX(TDGraphFX tdGraphFX) {
 		super(tdGraphFX);
-
 	}
 
 	/*
@@ -57,6 +61,23 @@ public class TDMarkerFX extends StandardOverlayMarker  {
 		return true; 
 	}
 
+	/**
+	 * Add the detection group listener. 
+	 * @param detectionGroupListener - the detection group listener
+	 */
+	public void addDetectionGroupListener(DetectionGroupListener detectionGroupListener) {
+		detectionGroupListeners.add(detectionGroupListener);
+	}
+
+	/**
+	 * Notify all listeners that there is a new detection group.
+	 * @param detectionGroup - the detection groups. 
+	 */
+	private void notifyNewDetectionGroup(DetectionGroupSummary detectionGroup) {
+		for (DetectionGroupListener aDetectionGroupListener : detectionGroupListeners) {
+			aDetectionGroupListener.newSelectedGroup(detectionGroup);
+		}
+	}
 
 	/**
 	 * Override to allow a highlighting of selected data units. 
@@ -110,7 +131,7 @@ public class TDMarkerFX extends StandardOverlayMarker  {
 
 		currentDetectionGroup = new DetectionGroupSummary(e, this, this.getCurrentMark(),
 				getSelectedMarkedDataUnits(this.getCurrentMark(), null) ); 
-
+		notifyNewDetectionGroup(currentDetectionGroup);
 		//		Debug.out.println("TDMarkerFX: Marked data units: " + currentDetectionGroup.getNumDataUnits()); 
 
 		this.setNowMarking(false);
@@ -160,6 +181,7 @@ public class TDMarkerFX extends StandardOverlayMarker  {
 			//System.out.println("PamMarkerFX: Found a data unit @ distance: " + foundDataUnit.distance + " "
 			//		+ PamCalendar.formatDateTime(foundDataUnit.dataUnit.getTimeMilliseconds()));
 			currentDetectionGroup =  new DetectionGroupSummary(e, this, this.getCurrentMark(), foundDataUnit.dataUnit);  
+			notifyNewDetectionGroup(currentDetectionGroup);
 			return true; 
 		}
 		else{
@@ -168,6 +190,7 @@ public class TDMarkerFX extends StandardOverlayMarker  {
 				//only do this if the primary mouse button. Otherwise we might be right clicking on a markout out area in which
 				//all saved markes will be removed and the pop up menu will show nothing. So the user can only use the primary button to select data units.
 				currentDetectionGroup =null; 
+				notifyNewDetectionGroup(currentDetectionGroup);
 			}
 			foundDataUnit=null; 
 			return false; 

src/dataPlotsFX/overlaymark/TDOverlayAdapter.java

@@ -9,7 +9,7 @@ import javafx.scene.canvas.GraphicsContext;
 import javafx.scene.control.Tooltip;
 
 /**
- * An overlay adapter essentially allows user mouse and touch interactions with the display. 
+ * An overlay adapter allows user mouse and touch interactions with the display. 
  * 
  * @author Jamie Macaulay
  *

src/export/MLExport/MLDetectionsManager.java

@@ -1,12 +1,11 @@
 package export.MLExport;
 
+import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
 
-import com.google.protobuf.compiler.PluginProtos.CodeGeneratorResponse.File;
-
 import PamguardMVC.PamDataUnit;
-import export.PamExportManager;
+import export.PamDataUnitExporter;
 import us.hebi.matlab.mat.format.Mat5;
 import us.hebi.matlab.mat.types.Struct;
 
@@ -16,7 +15,7 @@ import us.hebi.matlab.mat.types.Struct;
  * @author Jamie Macaulay 
  *
  */
-public class MLDetectionsManager implements PamExportManager {
+public class MLDetectionsManager implements PamDataUnitExporter {
 	
 	public static final String extension = "mat";
 
@@ -35,7 +34,15 @@ public class MLDetectionsManager implements PamExportManager {
 	
 	@Override
 	public boolean hasCompatibleUnits(Class dataUnitType) {
-		// TODO Auto-generated method stub
+		for (int i=0; i<mlDataUnitsExport.size(); i++){
+			//check whether the same. ;
+			//System.out.println(" dataUnits.get(j).getClass(): " + dataUnits.get(j).getClass());
+			//System.out.println(" mlDataUnitsExport.get(i).getUnitClass(): " + mlDataUnitsExport.get(i).getUnitClass());
+			if (mlDataUnitsExport.get(i).getUnitClass().isAssignableFrom(dataUnitType)) {
+				//System.out.println("FOUND THE DATA UNIT!");
+				return true; 
+			}
+		}
 		return false;
 	}
 
@@ -52,15 +59,7 @@ public class MLDetectionsManager implements PamExportManager {
 	public boolean hasCompatibleUnits(List<PamDataUnit> dataUnits) {
 		//first need to figure out how many data units there are. 
 		for (int j=0; j<dataUnits.size(); j++){
-			for (int i=0; i<mlDataUnitsExport.size(); i++){
+			if (hasCompatibleUnits(dataUnits.get(j).getClass())) return true;
-				//check whether the same. ;
-				//System.out.println(" dataUnits.get(j).getClass(): " + dataUnits.get(j).getClass());
-				//System.out.println(" mlDataUnitsExport.get(i).getUnitClass(): " + mlDataUnitsExport.get(i).getUnitClass());
-				if (mlDataUnitsExport.get(i).getUnitClass().isAssignableFrom(dataUnits.get(j).getClass())) {
-					//System.out.println("FOUND THE DATA UNIT!");
-					return true; 
-				}
-			}
 		}
 		return false; 
 	}
@@ -115,16 +114,12 @@ public class MLDetectionsManager implements PamExportManager {
 					n++; 
 					alreadyStruct[j] = true;
 				}
-
-
 			}
 
 			if (n>=1) {
 				list.set(mlDataUnitsExport.get(i).getName(),mlStructure);
 				list.set(mlDataUnitsExport.get(i).getName()+"_sR", Mat5.newScalar(sampleRate)); 
 			}
-
-
 		}
 
 		//now ready to save. 
@@ -137,6 +132,11 @@ public class MLDetectionsManager implements PamExportManager {
 		return extension;
 	}
 
+	@Override
+	public String getIconString() {
+		return "file-matlab"; 
+	}
+
 	
 
 

src/export/PamDataUnitExporter.java

@@ -1,15 +1,15 @@
 package export;
 
+import java.io.File;
 import java.util.List;
 
-import com.google.protobuf.compiler.PluginProtos.CodeGeneratorResponse.File;
 
 import PamguardMVC.PamDataUnit;
 
 /**
  * Manages the exporting of data units to a particular type of file e.g. CSV, MATLAB, R, WAV files 
  */
-public interface PamExportManager {
+public interface PamDataUnitExporter {
 	
 	/**
 	 * Check whether a particular data unit class is compatible
@@ -31,6 +31,13 @@ public interface PamExportManager {
 	 * Get the extension for the output file type
 	 * @return the extension for the file type e.g. "mat" 
 	 */
-	public String getFileExtension(); 
+	public String getFileExtension();
+
+	/**
+	 * Get the ikonli icon string for the exporter. 
+	 * @return the ikon string. 
+	 */
+	public String getIconString();
+
 
 }

src/export/PamExporter.java

@@ -1,26 +0,0 @@
-package export;
-
-import java.util.ArrayList;
-
-import export.MLExport.MLDetectionsManager;
-
-/**
- * Exports data to external files. 
- */
-public class PamExporter {
-	
-	/**
-	 * A list of the avilable exporters. 
-	 */
-	private ArrayList<PamExportManager> pamExporters;
-	
-	
-	public PamExporter() {
-		pamExporters = new ArrayList<PamExportManager>();
-		
-		//add the MATLAB export
-		pamExporters.add(new MLDetectionsManager());
-		
-	}
-
-}

src/export/PamExporterManager.java

@@ -0,0 +1,69 @@
+package export;
+
+import java.util.ArrayList;
+
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.PamDataUnit;
+import export.MLExport.MLDetectionsManager;
+import export.RExport.RExportManager;
+import export.wavExport.WavFileExportManager;
+
+/**
+ * Exports data to external files. Manages the file sizes and creates data buffers for 
+ * offline processing. 
+ */
+public class PamExporterManager {
+	
+	/**
+	 * A list of the avilable exporters. 
+	 */
+	private ArrayList<PamDataUnitExporter> pamExporters;
+	
+	
+	public PamExporterManager() {
+		pamExporters = new ArrayList<PamDataUnitExporter>();
+		
+		//add the MATLAB export
+		pamExporters.add(new MLDetectionsManager());
+		pamExporters.add(new RExportManager());
+		pamExporters.add(new WavFileExportManager());
+
+		
+	}
+
+	/** 
+	 * Add a data unit to the export list. 
+	 */
+	public void exportDataUnit(PamDataUnit<?, ?> dataUnit) {
+		// TODO Auto-generated method stub
+		
+	}
+	
+	public boolean canExportDataBlock(PamDataBlock dataBlock) {
+		for (PamDataUnitExporter exporter:pamExporters) {
+			if (exporter.hasCompatibleUnits(dataBlock.getUnitClass())) return true;
+		}
+		
+		return false;
+	}
+
+	/**
+	 * Get the number of data exporters. e.g. MAT files, CSV, Wav etc. 
+	 * @return the number of data exporters
+	 */
+	public int getNumExporters() {
+		return pamExporters.size();
+	}
+
+	/**
+	 * Get a specific exporter. 
+	 * @param i - the index of the exporter. 
+	 * @return the exporter. 
+	 */
+	public PamDataUnitExporter getExporter(int i) {
+		return pamExporters.get(i);
+		
+	}
+
+
+}

src/export/RExport/RExportManager.java

@@ -1,11 +1,14 @@
 package export.RExport;
 
+import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
 
 import org.renjin.sexp.ListVector;
 import org.renjin.sexp.PairList;
+
 import PamguardMVC.PamDataUnit;
+import export.PamDataUnitExporter;
 
 /**
  * Handles exporting pam data units into an rdata. 
@@ -13,7 +16,7 @@ import PamguardMVC.PamDataUnit;
  *
  */
 @SuppressWarnings("rawtypes")
-public class RExportManager {
+public class RExportManager implements PamDataUnitExporter {
 
 	/**
 	 * 
@@ -27,29 +30,34 @@ public class RExportManager {
 		mlDataUnitsExport.add(new RClickExport()); 
 		mlDataUnitsExport.add(new RWhistleExport()); 
 		mlDataUnitsExport.add(new RRawExport()); //should be last in case raw data holders have specific exporters
-
 	}
-	
+
 	/**
 	 * Check whether there are compatible data units to be exported. 
 	 * @param dataUnits - the data unit list
-	 * @return true if MATLAB export is possible for the current data units. 
+	 * @return true if r export is possible for the current data units. 
 	 */
 	public boolean hasCompatibleUnits(List<PamDataUnit> dataUnits) {
-		for (int i=0; i<mlDataUnitsExport.size(); i++){
+		//first need to figure out how many data units there are. 
-			//first need to figure out how many data units there are. 
+		for (int j=0; j<dataUnits.size(); j++){
-			for (int j=0; j<dataUnits.size(); j++){
+			if (hasCompatibleUnits(dataUnits.get(j).getClass())) return true;
-				//check whether the same. ;
-//				System.out.println(" dataUnits.get(j).getClass(): " + dataUnits.get(j).getClass());
-//				System.out.println(" mlDataUnitsExport.get(i).getUnitClass(): " + mlDataUnitsExport.get(i).getUnitClass());
-				if (mlDataUnitsExport.get(i).getUnitClass().isAssignableFrom(dataUnits.get(j).getClass())) {
-					return true; 
-				}
-			}
 		}
 		return false; 
 	}
 	
+	@Override
+	public boolean hasCompatibleUnits(Class dataUnitType) {
+		for (int i=0; i<mlDataUnitsExport.size(); i++){
+			//check whether the same. ;
+			//System.out.println(" dataUnits.get(j).getClass(): " + dataUnits.get(j).getClass());
+			//System.out.println(" mlDataUnitsExport.get(i).getUnitClass(): " + mlDataUnitsExport.get(i).getUnitClass());
+			if (mlDataUnitsExport.get(i).getUnitClass().isAssignableFrom(dataUnitType)) {
+				//System.out.println("FOUND THE DATA UNIT!");
+				return true; 
+			}
+		}
+		return false;
+	}
 	
 	/**
 	 * Sort a list of data units into lists of the same type of units. Convert to a list of structures. 
@@ -126,6 +134,24 @@ public class RExportManager {
 		public ArrayList<String> dataUnitTypes; 
 	}
 
+
+
+	@Override
+	public boolean exportData(File fileName, List<PamDataUnit> dataUnits) {
+		// TODO Auto-generated method stub
+		return false;
+	}
+
+	@Override
+	public String getFileExtension() {
+		return ".RData";
+	}
+
+	@Override
+	public String getIconString() {
+		return "file-r";
+	}
+
 	
 
 }

src/export/layoutFX/ExportOptions.java

@@ -0,0 +1,113 @@
+package export.layoutFX;
+
+import java.io.Serializable;
+import javax.swing.JFrame;
+
+import PamController.PamControlledUnitSettings;
+import PamController.PamSettingManager;
+import PamController.PamSettings;
+import PamController.StorageParameters;
+import export.PamExporterManager;
+import export.swing.ExportProcessDialog;
+
+/**
+ * Manages opening settings dialog and saving settings. 
+ * 
+ * @author Jamie Macaulay
+ *
+ */
+public class ExportOptions implements PamSettings {
+	
+	private static ExportOptions singleInstance;
+	
+	/**
+	 * Parameters for the exporter. 
+	 */
+	private ExportParams storageParameters = new ExportParams();
+
+	/**
+	 * Swing dialog for exporting data. 
+	 */
+	private ExportProcessDialog exportProcessDialog;
+	
+	/**
+	 * Reference to the export manager. This handles exporting data units. 
+	 */
+	private PamExporterManager exportManager = new PamExporterManager(); 
+
+	private ExportOptions() {
+		PamSettingManager.getInstance().registerSettings(this);
+	}
+	
+	public static ExportOptions getInstance() {
+		if (singleInstance == null) {
+			singleInstance = new ExportOptions();
+		}
+		return singleInstance;
+	}
+
+	
+	/**
+	 * Show the swing dialog. 
+	 * @param parentFrame - the parent frame. 
+	 * @return true if settings are OK on close
+	 */
+	public boolean showDialog(JFrame parentFrame) {
+		
+		if (exportProcessDialog==null) {
+			exportProcessDialog= new ExportProcessDialog(exportManager); 
+		}
+		this.exportProcessDialog.showOfflineDialog(parentFrame);
+		
+//		ExportParams newParams = StorageOptionsDialog.showDialog(parentFrame, storageParameters);
+//		if (newParams != null) {
+//			storageParameters = newParams.clone();
+//			return true;
+//		}
+//		else {
+//			return false;
+//		}
+		
+		return true;
+	}
+	
+	@Override
+	public Serializable getSettingsReference() {
+		return storageParameters;
+	}
+
+	@Override
+	public long getSettingsVersion() {
+		return StorageParameters.serialVersionUID;
+	}
+
+	@Override
+	public String getUnitName() {
+		return "PAMGUARD Export Options";
+	}
+
+	@Override
+	public String getUnitType() {
+		return "PAMGUARD Export Options";
+	}
+
+	@Override
+	public boolean restoreSettings(
+			PamControlledUnitSettings pamControlledUnitSettings) {
+		storageParameters = ((ExportParams) pamControlledUnitSettings.getSettings()).clone();
+		return true;
+	}
+
+	
+	public void setStorageParameters(ExportParams storageParameters) {
+		this.storageParameters = storageParameters;
+	}
+
+	/**
+	 * Get storage parameters settings. 
+	 * @return the storage paramters settings
+	 */
+	public ExportParams getStorageParameters() {
+		return storageParameters;
+	}
+}

src/export/layoutFX/ExportParams.java

@@ -0,0 +1,32 @@
+package export.layoutFX;
+
+import java.io.Serializable;
+
+
+/**
+ * Parameter for the exporter. 
+ * @author Jamie Macaulay
+ *
+ */
+public class ExportParams implements Serializable, Cloneable {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 1L;
+	
+	public int exportChoice;
+	
+	
+	@Override
+	public ExportParams clone()  {
+		try {
+			ExportParams newP = (ExportParams) super.clone();
+			return newP;
+		} catch (CloneNotSupportedException e) {
+			e.printStackTrace();
+			return null;
+		}
+	}
+
+}

src/export/layoutFX/ExporterPane.java

@@ -0,0 +1,53 @@
+package export.layoutFX;
+
+import PamController.SettingsPane;
+import javafx.scene.Node;
+import javafx.scene.control.Label;
+import pamViewFX.fxNodes.PamBorderPane;
+
+/**
+ * Create a pane to export data. 
+ * @author Jamie Macaulay
+ *
+ */
+public class ExporterPane extends SettingsPane<ExportParams>{
+	
+	PamBorderPane mainPane;
+
+	public ExporterPane(Object ownerWindow) {
+		super(ownerWindow);
+		mainPane = new PamBorderPane();
+		
+		mainPane.setTop(new Label("Hello")); 
+		mainPane.setCenter(new Label("Hello")); 
+	}
+
+	@Override
+	public ExportParams getParams(ExportParams currParams) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public void setParams(ExportParams input) {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public String getName() {
+		return "Export Settings";
+	}
+
+	@Override
+	public Node getContentNode() {
+		return mainPane;
+	}
+
+	@Override
+	public void paneInitialized() {
+		// TODO Auto-generated method stub
+		
+	}
+
+}

src/export/swing/ExportProcessDialog.java

@@ -0,0 +1,177 @@
+package export.swing;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Frame;
+import java.awt.Window;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+
+import javax.swing.ButtonGroup;
+import javax.swing.Icon;
+import javax.swing.JToggleButton;
+
+import org.kordamp.ikonli.Ikon;
+import org.kordamp.ikonli.fileicons.FileIcons;
+import org.kordamp.ikonli.materialdesign2.MaterialDesignA;
+import org.kordamp.ikonli.materialdesign2.MaterialDesignF;
+import org.kordamp.ikonli.swing.FontIcon;
+
+import PamController.PamController;
+import PamView.panel.PamPanel;
+import PamguardMVC.PamDataBlock;
+import export.PamExporterManager;
+import offlineProcessing.OLProcessDialog;
+import offlineProcessing.OfflineTaskGroup;
+
+/**
+ * Processes exportying data. 
+ * @author Jamie Macaulay
+ *
+ */
+public class ExportProcessDialog {
+
+
+	/**
+	 * The offline task group
+	 */
+	private OfflineTaskGroup dlOfflineGroup;
+
+	private OLProcessDialog mtOfflineDialog;
+
+	/**
+	 * Reference to the export manager. 
+	 */
+	private PamExporterManager exportManager;
+
+	public ExportProcessDialog(PamExporterManager exportManager) {
+		//create the offline task group. 
+		this.exportManager=exportManager;
+		dlOfflineGroup = new ExportTaskGroup("Export data");
+	}
+
+
+	public void createExportGroup() {
+		
+		//clear current tasks. 
+		dlOfflineGroup.clearTasks();
+
+		//go through every data block we have and check if we can export the data units...
+		ArrayList<PamDataBlock> dataBlocks= PamController.getInstance().getDataBlocks();
+		
+		for (int i=0; i<dataBlocks.size(); i++) {
+			if (exportManager.canExportDataBlock(dataBlocks.get(i))) {
+				dlOfflineGroup.addTask(new ExportTask(dataBlocks.get(i), exportManager));
+			}
+		}
+
+	}
+	////---Swing stuff----/// should not be here but this is how PG works. 
+
+	public void showOfflineDialog(Frame parentFrame) {
+
+		createExportGroup();
+		
+		//if null open the dialog- also create a new offlineTask group if the datablock has changed. 
+		if (mtOfflineDialog == null) {
+			mtOfflineDialog = new ExportOLDialog(parentFrame, 
+					dlOfflineGroup, "Export Data");
+			//batchLocaliseDialog.setModalityType(Dialog.ModalityType.MODELESS);
+		}
+		mtOfflineDialog.enableControls();
+		mtOfflineDialog.setVisible(true);
+	}
+
+	/**
+	 * Custom dialog which shows some extra options/ 
+	 * @author Jamie Macaulay
+	 *
+	 */
+	class ExportOLDialog extends OLProcessDialog {
+
+		/**
+		 * 
+		 */
+		private static final long serialVersionUID = 1L;
+
+		public ExportOLDialog(Window parentFrame, OfflineTaskGroup taskGroup, String title) {
+			super(parentFrame, taskGroup, title);
+			// TODO Auto-generated constructor stub
+
+			BorderLayout layout = new BorderLayout();
+			PamPanel mainPanel = new PamPanel();
+
+			ButtonGroup buttonGroup = new ButtonGroup();
+
+
+			PamPanel buttonPanel = new PamPanel();
+			ActionListener listener = actionEvent -> {
+				System.out.println(actionEvent.getActionCommand() + " Selected");
+			};
+
+			for (int i = 0; i < exportManager.getNumExporters(); i++) {
+				JToggleButton b = new JToggleButton();
+								
+				FontIcon icon = FontIcon.of(getIconFromString(exportManager.getExporter(i).getIconString()));
+				icon.setIconSize(25);
+				icon.setIconColor(Color.GRAY);
+				
+				
+				b.setIcon(icon);
+				
+				b.addActionListener(listener);
+				buttonGroup.add(b);
+				buttonPanel.add(b);
+			}
+
+			mainPanel.add(buttonPanel, BorderLayout.CENTER);
+
+			//add the main panel at a diffderent index. 
+			getMainPanel().add(buttonPanel, 1);
+		}
+		
+		private Ikon getIconFromString(String iconString) {
+			
+			Ikon icon = null;
+			/**
+			 * This is nasty but we won't have many exporters and this is the only
+			 * good way to get this to work in Swing. 
+			 */
+			switch (iconString) {
+			case "file-matlab":
+				icon=FileIcons.MATLAB;
+				break;
+			case "file-r":
+				icon=FileIcons.R;
+					break;
+			case "mdi2f-file-music":
+				icon=MaterialDesignF.FILE_MUSIC;
+				break;
+			}
+			
+			return icon;
+		
+		}
+		
+
+
+	}
+
+
+	class ExportTaskGroup extends OfflineTaskGroup{
+
+		public ExportTaskGroup(String settingsName) {
+			super(null, settingsName);
+			// TODO Auto-generated constructor stub
+
+		}
+
+		@Override
+		public String getUnitType() {
+			return "Export Data";
+		}
+	}
+
+
+
+}

src/export/swing/ExportTask.java

@@ -0,0 +1,48 @@
+package export.swing;
+
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.PamDataUnit;
+import dataMap.OfflineDataMapPoint;
+import export.PamExporterManager;
+import offlineProcessing.OfflineTask;
+
+/**
+ * Export data to a file type. 
+ * 
+ * @author Jamie Macaulay
+ *
+ */
+public class ExportTask extends OfflineTask<PamDataUnit<?,?>>{
+	
+	PamExporterManager exporter; 
+
+	public ExportTask(PamDataBlock<PamDataUnit<?, ?>> parentDataBlock, PamExporterManager exporter) {
+		super(parentDataBlock);
+		this.exporter = exporter; 
+		// TODO Auto-generated constructor stub
+	}
+
+	@Override
+	public String getName() {
+		return this.getDataBlock().getDataName();
+	}
+
+	@Override
+	public boolean processDataUnit(PamDataUnit<?, ?> dataUnit) {
+		exporter.exportDataUnit(dataUnit);
+		return true;
+	}
+
+	@Override
+	public void newDataLoad(long startTime, long endTime, OfflineDataMapPoint mapPoint) {
+		// TODO Auto-generated method stub
+		
+	}
+
+	@Override
+	public void loadedDataComplete() {
+		// TODO Auto-generated method stub
+		
+	}
+
+}

src/export/wavExport/WavFileExportManager.java

@@ -22,6 +22,7 @@ import PamguardMVC.PamRawDataBlock;
 import PamguardMVC.dataOffline.OfflineDataLoading;
 import dataMap.OfflineDataMapPoint;
 import detectiongrouplocaliser.DetectionGroupSummary;
+import export.PamDataUnitExporter;
 import wavFiles.Wav16AudioFormat;
 import wavFiles.WavFileWriter;
 
@@ -30,7 +31,7 @@ import wavFiles.WavFileWriter;
  * @author Jamie Macaulay
  *
  */
-public class WavFileExportManager {
+public class WavFileExportManager implements PamDataUnitExporter  {
 
 	/**
 	 * Successful writing of .wav file. 
@@ -420,6 +421,38 @@ public class WavFileExportManager {
 
 
 
+	@Override
+	public boolean hasCompatibleUnits(Class dataUnitType) {
+		// TODO Auto-generated method stub
+		return false;
+	}
+
+
+
+	@Override
+	public boolean exportData(File fileName,
+			List<PamDataUnit> dataUnits) {
+		// TODO Auto-generated method stub
+		return false;
+	}
+
+
+
+	@Override
+	public String getFileExtension() {
+		return "wav";
+	}
+
+
+
+	@Override
+	public String getIconString() {
+		// TODO Auto-generated method stub
+		return "mdi2f-file-music";
+	}
+
+
+
 
 
 	//	hello(){

src/metadata/MetaDataContol.java

@@ -7,11 +7,13 @@ import java.io.Serializable;
 import javax.swing.JFrame;
 import javax.swing.JMenuItem;
 
+import Array.ArrayManager;
 import PamController.PamControlledUnit;
 import PamController.PamControlledUnitSettings;
 import PamController.PamController;
 import PamController.PamSettingManager;
 import PamController.PamSettings;
+import PamModel.PamModuleInfo;
 import metadata.swing.MetaDataDialog;
 
 /**
@@ -44,12 +46,25 @@ public class MetaDataContol extends PamControlledUnit implements PamSettings {
 	public static MetaDataContol getMetaDataControl() {
 		if (singleInstance == null) {
 			singleInstance = new MetaDataContol(unitType);
+			singleInstance.addModuleInfo(); //needed for FX
 			// add this line to add it to the main modules list. Then it will get menu's, etc. 
 			PamController.getInstance().addControlledUnit(singleInstance);	
 		}
 		return singleInstance;
 	}
 	
+	
+	/**
+	 * Add module info to the array manager. Need to do this to add icon which is used in data model. 
+	 */
+	private void addModuleInfo(){
+		//need to add module info due to fact array manager is a special case
+		PamModuleInfo arrayModuleInfo=new PamModuleInfo("MetaDataControl", "Meta Data MANAGER", MetaDataContol.class); 
+		arrayModuleInfo.setCoreModule(true);
+		arrayModuleInfo.setToolTipText("Meta data manager");
+		this.setPamModuleInfo(arrayModuleInfo);
+	}
+	
 	/**
 	 * Get PAMGuard Metadata. This contains a nilus Deployment object wrapped up 
 	 * so that it can be serialised into other PAMGuard settings. 

src/offlineProcessing/OLProcessDialog.java

@@ -93,13 +93,18 @@ public class OLProcessDialog extends PamDialog {
 
 	TaskStatus currentStatus = TaskStatus.IDLE;
 
+	/**
+	 * Reference to the main panel
+	 */
+	private JPanel mainPanel;
+
 
 	public OLProcessDialog(Window parentFrame, OfflineTaskGroup taskGroup, String title) {
 		super(parentFrame, title, false);
 		this.taskGroup = taskGroup;
 		taskGroup.setTaskMonitor(new OLMonitor());
 
-		JPanel mainPanel = new JPanel();
+		mainPanel = new JPanel();
 		mainPanel.setLayout(new BoxLayout(mainPanel, BoxLayout.Y_AXIS));
 
 		JPanel dataSelectPanel = new PamAlignmentPanel(BorderLayout.WEST);
@@ -207,6 +212,14 @@ public class OLProcessDialog extends PamDialog {
 		setResizable(true);
 
 	}
+	
+	/**
+	 * Get the main panel. This can be used to add additional controls if needed. 
+	 * @return the main panel. 
+	 */
+	public JPanel getMainPanel() {
+		return mainPanel;
+	}
 
 	/**
 	 * Get the delete old data check box

src/offlineProcessing/OfflineTaskGroup.java

@@ -66,6 +66,7 @@ public class OfflineTaskGroup implements PamSettings {
 	private DataTimeLimits dataTimeLimits;
 
 	private volatile TaskStatus completionStatus = TaskStatus.IDLE;
+	
 	/**
 	 * PamControlledunit required in constructor since some bookkeeping will
 	 * be going on in the background which will need the unit type and name. 
@@ -76,7 +77,7 @@ public class OfflineTaskGroup implements PamSettings {
 	public OfflineTaskGroup(PamControlledUnit pamControlledUnit, String settingsName) {
 		super();
 		this.pamControlledUnit = pamControlledUnit;
-		pamControlledUnit.addOfflineTaskGroup(this);
+		if (pamControlledUnit!=null) pamControlledUnit.addOfflineTaskGroup(this);
 		this.settingsName = settingsName;
 		PamSettingManager.getInstance().registerSettings(this);
 	}
@@ -965,4 +966,14 @@ public class OfflineTaskGroup implements PamSettings {
 	public OfflineSuperDetFilter getSuperDetectionFilter() {
 		return superDetectionFilter;
 	}
+
+	/**
+	 * Clear all task from the task group. This also clears affected and required datablocks. 
+	 */
+	public void clearTasks() {
+		requiredDataBlocks.clear();
+		affectedDataBlocks.clear();
+		offlineTasks.clear();
+		
+	}
 }

src/pamViewFX/fxNodes/pamAxis/PamDateAxis.java

@@ -217,7 +217,7 @@ public class PamDateAxis extends ValueAxis<Long> {
         };
     }
 
-    private double[] recalculateTicks()
+    public double[] recalculateTicks()
     {
         final Side side = getSide();
         final boolean vertical = Side.LEFT.equals(side) || Side.RIGHT.equals(side);

src/rawDeepLearningClassifier/defaultModels/HumpbackWhaleAtlantic.java

@@ -5,8 +5,17 @@ import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
+import java.util.ArrayList;
 
+import org.jamdev.jdl4pam.transforms.DLTransformsFactory;
+import org.jamdev.jdl4pam.transforms.DLTransfromParams;
+import org.jamdev.jdl4pam.transforms.SimpleTransformParams;
+import org.jamdev.jdl4pam.transforms.DLTransform.DLTransformType;
+
+import rawDeepLearningClassifier.dlClassification.DLClassName;
 import rawDeepLearningClassifier.dlClassification.animalSpot.StandardModelParams;
+import rawDeepLearningClassifier.dlClassification.genericModel.GenericModelParams;
+import rawDeepLearningClassifier.layoutFX.exampleSounds.ExampleSoundFactory.ExampleSoundType;
 
 /**
  *
@@ -57,7 +66,31 @@ public class HumpbackWhaleAtlantic implements DLModel {
 
 	@Override
 	public void setParams(Serializable dlModelSettings) {
-		// TODO Auto-generated method stub
+		GenericModelParams genericModelParams = (GenericModelParams) dlModelSettings;
+		
+		//decimation value
+		float sr = 2000; 
+
+		//create the transforms. 
+		ArrayList<DLTransfromParams> dlTransformParamsArr = new ArrayList<DLTransfromParams>();
+
+		dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.DECIMATE_SCIPY, sr)); 
+
+		genericModelParams.dlTransfromParams = dlTransformParamsArr;
+		
+		genericModelParams.defaultSegmentLen =   3.8775*1000;
+		genericModelParams.binaryClassification = new boolean[] {true};
+		genericModelParams.classNames= new DLClassName[] {new DLClassName("Humpback whale", (short) 1)};
+		genericModelParams.numClasses = 1; 
+		
+		
+		genericModelParams.defaultShape= new Long[] {-1L,-1L,-1L,1L};
+		genericModelParams.shape= new Long[] {-1L,-1L,-1L,1L};
+
+		//create the transforms. 
+		genericModelParams.dlTransfroms = DLTransformsFactory.makeDLTransforms((ArrayList<DLTransfromParams>)genericModelParams.dlTransfromParams); 
+		
+		genericModelParams.setExampleSound(ExampleSoundType.HUMPBACK_WHALE);
 		
 	}
 	

src/rawDeepLearningClassifier/defaultModels/HumpbackWhaleGoogle.java

@@ -36,8 +36,8 @@ public class HumpbackWhaleGoogle implements DLModel {
 	@Override
 	public URI getModelURI() {
 		try {
-			return new URL("https://github.com/PAMGuard/deeplearningmodels/raw/master/humpback_whale_1/humpback_whale_1.zip").toURI();
+			return new URI("https://github.com/PAMGuard/deeplearningmodels/raw/master/humpback_whale_1/humpback_whale_1.zip");
-		} catch (MalformedURLException | URISyntaxException e) {
+		} catch (URISyntaxException e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}
@@ -52,8 +52,8 @@ public class HumpbackWhaleGoogle implements DLModel {
 	@Override
 	public URI getCitationLink() {
 		try {
-			return new URL("https://doi.org/10.3389/fmars.2021.607321").toURI();
+			return new URI("https://doi.org/10.3389/fmars.2021.607321");
-		} catch (MalformedURLException | URISyntaxException e) {
+		} catch (URISyntaxException e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
 			return null;
@@ -70,7 +70,7 @@ public class HumpbackWhaleGoogle implements DLModel {
 		//create the transforms. 
 		ArrayList<DLTransfromParams> dlTransformParamsArr = new ArrayList<DLTransfromParams>();
 
-		dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.DECIMATE, sr)); 
+		dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.DECIMATE_SCIPY, sr)); 
 
 		genericModelParams.dlTransfromParams = dlTransformParamsArr;
 		

src/rawDeepLearningClassifier/defaultModels/RightWhaleModel1.java

@@ -44,8 +44,8 @@ public class RightWhaleModel1 implements DLModel {
 	@Override
 	public URI getModelURI() {
 		try {
-			return new URL("https://github.com/PAMGuard/deeplearningmodels/raw/master/right_whale_1/model_lenet_dropout_input_conv_all.zip").toURI();
+			return new URI("https://github.com/PAMGuard/deeplearningmodels/raw/master/right_whale_1/model_lenet_dropout_input_conv_all.zip");
-		} catch (MalformedURLException | URISyntaxException e) {
+		} catch (URISyntaxException e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}

src/rawDeepLearningClassifier/dlClassification/genericModel/GenericModelWorker.java

@@ -44,7 +44,7 @@ public class GenericModelWorker extends DLModelWorker<GenericPrediction> {
 				waveStack[i] = transformedDataStack[i][0]; 
 			}
 			
-			//System.out.println("RUN GENERIC MODEL WAVE: " + transformedDataStack.length +  "  " + transformedDataStack[0].length);
+			//System.out.println("RUN GENERIC MODEL WAVE: " + waveStack.length +  "  " + waveStack[0].length +  " " + waveStack[0][0]);
 			results =  getModel().runModel(waveStack);
 		}
 		//System.out.println("GENERIC MODEL RESULTS: " + results== null ? null : results.length);

src/test/rawDeepLearningClassifier/GenericDLClassifierTest.java

@@ -3,6 +3,10 @@ package test.rawDeepLearningClassifier;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
 import java.io.IOException;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -14,6 +18,7 @@ import org.jamdev.jdl4pam.utils.DLUtils;
 import org.jamdev.jpamutils.wavFiles.AudioData;
 import org.junit.jupiter.api.Test;
 
+import rawDeepLearningClassifier.defaultModels.HumpbackWhaleAtlantic;
 import rawDeepLearningClassifier.defaultModels.RightWhaleModel1;
 import rawDeepLearningClassifier.dlClassification.genericModel.GenericModelParams;
 import rawDeepLearningClassifier.dlClassification.genericModel.GenericModelWorker;
@@ -29,10 +34,14 @@ import rawDeepLearningClassifier.segmenter.SegmenterProcess.GroupedRawData;
 public class GenericDLClassifierTest {
 
 	/**
-	 * Run a test on the Generic DL Classifier. This tests the worker can open and run a model 
+	 * Run a test on the Generic DL Classifier. This tests the worker can open and
+	 * run a model
 	 */
 	@Test
 	public void rightWhaleDLWorker() {
+
+		System.out.println("*****Generic DL: Right whale test*****"); 
+
 		//relative paths to the resource folders.
 		String relModelPath  =	"./src/test/resources/rawDeepLearningClassifier/Generic/right_whale/model_lenet_dropout_input_conv_all/saved_model.pb";
 		String relWavPath  =	"./src/test/resources/rawDeepLearningClassifier/Generic/right_whale/right_whale_example.wav";
@@ -63,18 +72,18 @@ public class GenericDLClassifierTest {
 
 			GroupedRawData groupedRawData = new GroupedRawData(0, 1, 0, duration, (int) duration);
 			groupedRawData.copyRawData(soundData.getScaledSampleAmplitudes(), 0, soundData.getScaledSampleAmplitudes().length, 0);
-			
+
 			ArrayList<GroupedRawData> groupedData = new ArrayList<GroupedRawData>();
-			
+
-			
+
 			groupedData.add(groupedRawData);
 
 			ArrayList<GenericPrediction> gwenericPrediciton = genericModelWorker.runModel(groupedData, soundData.sampleRate, 0);		
-			
+
 			float[] output = gwenericPrediciton.get(0).getPrediction();
-			
+
 			System.out.println("Right whale network output: " + output[0] + "  " + output[1]);
-			
+
 			//test the predicitons are true. 
 			assertTrue( output[0]<0.01 ); //noise
 			assertTrue( output[1]>0.98 ); //right whale
@@ -87,18 +96,98 @@ public class GenericDLClassifierTest {
 			assertEquals(false, true);
 		}
 	}
-	
+
-	
+
-	
+
 	/**
-	 * Test the ketos classifier and tests are working properly. This tests loading the ketos model and also using
+	 * Test the ketos classifier and tests are working properly. This tests loading
-	 * functions in KetosWorker.
+	 * the ketos model and also using functions in KetosWorker.
 	 */
 	@Test
 	public void humpbackWhaleTest() {
+
+		System.out.println("*****Generic DL: Humpback whale test*****"); 
+
+		//relative paths to the resource folders.
+		String relModelPath  =	"./src/test/resources/rawDeepLearningClassifier/Generic/humpback_whale_atlantic/FlatHBNA/saved_model.pb";
+		String relWavPath  =	"./src/test/resources/rawDeepLearningClassifier/Generic/humpback_whale_atlantic/SAMOSAS_EL1_humpback.wav";
+		String resultsPath  =	"./src/test/resources/rawDeepLearningClassifier/Generic/humpback_whale_atlantic/SAMOSAS_EL1_humpback_annotations.txt";
+
+		Path path = Paths.get(relModelPath);
+
+		GenericModelWorker genericModelWorker = new GenericModelWorker(); 
+
+		GenericModelParams genericModelParams = new GenericModelParams(); 
+
+		genericModelParams.modelPath =  path.toAbsolutePath().normalize().toString();
+
+		path = Paths.get(relWavPath);
+		String wavFilePath = path.toAbsolutePath().normalize().toString();
+
+		HumpbackWhaleAtlantic humpbackModel = new HumpbackWhaleAtlantic();
+		humpbackModel.setParams(genericModelParams);
 		
+		System.out.println(genericModelParams);
 		
+		//prep the model
+		genericModelWorker.prepModel(genericModelParams, null);
+
+		try {
+			//load audio
+			AudioData soundData = DLUtils.loadWavFile(wavFilePath);
+
+			
+			//load true predictions file. 
+			File file = new File(resultsPath);
+			FileReader fr = new FileReader(file);	
+			BufferedReader br = new BufferedReader(fr);
+			String line;
+			int ind=0; 
+			
+			while((line = br.readLine()) != null){
+				if (ind>0) {
+
+					//read the data from the text file
+					String[] data = line.split("\t");
+					int chunkID = Integer.valueOf(data[0]);
+
+					double startTimeS = Double.valueOf(data[1]);
+					double endTimeS = Double.valueOf(data[2]);
+					double prediction = Double.valueOf(data[5]);
+
+					int startChunk = (int) (soundData.sampleRate*startTimeS); //humpback whale call
+					int chunkSize = (int) Math.ceil((endTimeS-startTimeS)*soundData.sampleRate); 
+					
+					chunkSize=7755;
+
+					GroupedRawData groupedRawData = new GroupedRawData(0, 1, 0, chunkSize, chunkSize);
+					groupedRawData.copyRawData(soundData.getScaledSampleAmplitudes(), startChunk, chunkSize, 0);
+					
+
+					ArrayList<GroupedRawData> groupedData = new ArrayList<GroupedRawData>();
+
+					groupedData.add(groupedRawData);
+
+					ArrayList<GenericPrediction> genericPrediction = genericModelWorker.runModel(groupedData, soundData.sampleRate, 0);		
+
+					float[] output = genericPrediction.get(0).getPrediction();
+
+					System.out.println(String.format("Chunk %d %d Predicted output: %.2f true output: %.2f passed: %b", chunkID, startChunk,
+							output[0], prediction, output[0]>prediction*0.9 && output[0]<prediction*1.1)); 
+
+					//allow 10% scrumph to take account of slight differences in Java input. 
+					assertEquals(output[0], prediction, 0.1); //humpback whale detection
+
+
+				}
+				  ind++;
+				}
+			
+		} catch (Exception e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
 	}
-	
+
 
 }

src/test/resources/rawDeepLearningClassifier/Generic/humpback_whale_atlantic/SAMOSAS_EL1_humpback_annotations.txt

@@ -0,0 +1,216 @@
+Selection	Begin Time (s)	End Time (s)	High Freq (Hz)	Low Freq (Hz)	Prediction/Comments
+1	3.8775	7.755	1000	50	0.99972177
+2	7.755	11.6325	1000	50	0.89199716
+3	11.6325	15.51	1000	50	0.64813995
+4	15.51	19.3875	1000	50	0.9713266
+5	19.3875	23.265	1000	50	0.8342721
+6	23.265	27.142500000000002	1000	50	0.99634343
+7	31.02	34.8975	1000	50	0.9933128
+8	34.8975	38.775	1000	50	0.5325079
+9	42.6525	46.53	1000	50	0.9727334
+10	46.53	50.4075	1000	50	0.7700455
+11	54.285	58.162499999999994	1000	50	0.93229276
+12	58.1625	62.04	1000	50	0.5089565
+13	62.04	65.9175	1000	50	0.53604007
+14	65.9175	69.795	1000	50	0.6665228
+15	69.795	73.6725	1000	50	0.8109671
+16	73.6725	77.55	1000	50	0.9998325
+17	77.55	81.4275	1000	50	0.6296093
+18	81.4275	85.30499999999999	1000	50	0.99747694
+19	93.06	96.9375	1000	50	0.99976456
+20	96.9375	100.815	1000	50	0.53218305
+21	104.6925	108.57	1000	50	0.98100567
+22	112.4475	116.325	1000	50	0.91926867
+23	124.08	127.9575	1000	50	0.9990459
+24	127.9575	131.835	1000	50	0.6861532
+25	135.7125	139.59	1000	50	0.5737106
+26	143.4675	147.345	1000	50	0.9537415
+27	147.345	151.2225	1000	50	0.5592457
+28	151.2225	155.1	1000	50	0.97674406
+29	155.1	158.9775	1000	50	0.55292696
+30	166.7325	170.60999999999999	1000	50	0.86637044
+31	170.61	174.4875	1000	50	0.8887141
+32	174.4875	178.365	1000	50	0.65914917
+33	182.2425	186.12	1000	50	0.78331536
+34	189.9975	193.875	1000	50	0.51390845
+35	193.875	197.7525	1000	50	0.8545577
+36	197.7525	201.63	1000	50	0.99297434
+37	209.385	213.2625	1000	50	0.91762686
+38	217.14	221.01749999999998	1000	50	0.9865262
+39	221.0175	224.895	1000	50	0.9802332
+40	224.895	228.7725	1000	50	0.9038371
+41	228.7725	232.65	1000	50	0.9299754
+42	232.65	236.5275	1000	50	0.99995977
+43	236.5275	240.405	1000	50	0.75877947
+44	240.405	244.2825	1000	50	0.8074757
+45	244.2825	248.16	1000	50	0.57404643
+46	248.16	252.0375	1000	50	0.5844841
+47	252.0375	255.915	1000	50	0.77901065
+48	267.5475	271.425	1000	50	0.9999262
+49	283.0575	286.935	1000	50	0.91496134
+50	286.935	290.8125	1000	50	0.6016941
+51	290.8125	294.69	1000	50	0.5288352
+52	294.69	298.5675	1000	50	0.7803428
+53	298.5675	302.445	1000	50	0.9457351
+54	302.445	306.3225	1000	50	0.8809803
+55	314.0775	317.955	1000	50	0.76862615
+56	317.955	321.8325	1000	50	0.9179431
+57	321.8325	325.71	1000	50	0.64783925
+58	325.71	329.5875	1000	50	0.63720423
+59	333.465	337.3425	1000	50	0.9080041
+60	337.3425	341.21999999999997	1000	50	0.636528
+61	341.22	345.0975	1000	50	0.8285956
+62	348.975	352.8525	1000	50	0.5541101
+63	360.6075	364.485	1000	50	0.9939563
+64	364.485	368.3625	1000	50	0.5179203
+65	368.3625	372.24	1000	50	0.998485
+66	372.24	376.1175	1000	50	0.7255482
+67	379.995	383.8725	1000	50	0.6432554
+68	387.75	391.6275	1000	50	0.85360736
+69	395.505	399.3825	1000	50	0.63949126
+70	403.26	407.1375	1000	50	0.9875199
+71	407.1375	411.015	1000	50	0.63171786
+72	411.015	414.8925	1000	50	0.51271856
+73	414.8925	418.77	1000	50	0.8624972
+74	418.77	422.6475	1000	50	0.9287566
+75	422.6475	426.525	1000	50	0.79819566
+76	442.035	445.9125	1000	50	0.9992767
+77	445.9125	449.79	1000	50	0.85704327
+78	449.79	453.6675	1000	50	0.606248
+79	465.3	469.1775	1000	50	0.6945031
+80	469.1775	473.055	1000	50	0.91730964
+81	476.9325	480.81	1000	50	0.8548426
+82	480.81	484.6875	1000	50	0.8609153
+83	484.6875	488.565	1000	50	0.53578407
+84	492.4425	496.32	1000	50	0.6815063
+85	504.075	507.9525	1000	50	0.5493686
+86	511.83	515.7075	1000	50	0.57242775
+87	515.7075	519.585	1000	50	0.802748
+88	519.585	523.4625000000001	1000	50	0.75667137
+89	527.34	531.2175000000001	1000	50	0.6283601
+90	535.095	538.9725000000001	1000	50	0.58465177
+91	538.9725	542.85	1000	50	0.7337384
+92	546.7275	550.605	1000	50	0.6839575
+93	562.2375	566.115	1000	50	0.6672469
+94	593.2575	597.1350000000001	1000	50	0.5644848
+95	604.89	608.7675	1000	50	0.78537405
+96	624.2775	628.1550000000001	1000	50	0.52095556
+97	632.0325	635.9100000000001	1000	50	0.86063546
+98	635.91	639.7875	1000	50	0.7444124
+99	643.665	647.5425	1000	50	0.59704643
+100	647.5425	651.4200000000001	1000	50	0.9363932
+101	666.93	670.8075	1000	50	0.78785974
+102	678.5625	682.44	1000	50	0.99932384
+103	690.195	694.0725000000001	1000	50	0.7276663
+104	694.0725	697.95	1000	50	0.6033868
+105	697.95	701.8275000000001	1000	50	0.7666113
+106	705.705	709.5825000000001	1000	50	0.9996606
+107	709.5825	713.46	1000	50	0.87555915
+108	717.3375	721.215	1000	50	0.99977213
+109	721.215	725.0925000000001	1000	50	0.6706097
+110	728.97	732.8475000000001	1000	50	0.99964714
+111	736.725	740.6025000000001	1000	50	0.9942172
+112	740.6025	744.48	1000	50	0.99729407
+113	744.48	748.3575000000001	1000	50	0.98387647
+114	748.3575	752.235	1000	50	0.97733885
+115	756.1125	759.99	1000	50	0.9908622
+116	763.8675	767.745	1000	50	0.9963475
+117	775.5	779.3775	1000	50	0.9301784
+118	779.3775	783.2550000000001	1000	50	0.8671598
+119	783.255	787.1325	1000	50	0.8163382
+120	787.1325	791.0100000000001	1000	50	0.67742085
+121	794.8875	798.7650000000001	1000	50	0.9999998
+122	798.765	802.6425	1000	50	0.9092158
+123	802.6425	806.5200000000001	1000	50	0.5064141
+124	806.52	810.3975	1000	50	0.9245316
+125	810.3975	814.2750000000001	1000	50	0.9987917
+126	814.275	818.1525	1000	50	0.98765403
+127	818.1525	822.0300000000001	1000	50	0.7059854
+128	822.03	825.9075	1000	50	0.9687309
+129	825.9075	829.7850000000001	1000	50	0.99980175
+130	829.785	833.6625	1000	50	0.9667981
+131	833.6625	837.5400000000001	1000	50	0.6459364
+132	837.54	841.4175	1000	50	0.99052876
+133	845.295	849.1725	1000	50	0.98032534
+134	849.1725	853.0500000000001	1000	50	0.9769905
+135	864.6825	868.5600000000001	1000	50	0.9989409
+136	868.56	872.4375	1000	50	0.65797764
+137	876.315	880.1925000000001	1000	50	0.8667758
+138	880.1925	884.07	1000	50	0.8123294
+139	884.07	887.9475000000001	1000	50	0.9994879
+140	887.9475	891.825	1000	50	0.6211881
+141	895.7025	899.58	1000	50	0.9882314
+142	899.58	903.4575000000001	1000	50	0.988451
+143	903.4575	907.335	1000	50	0.8560532
+144	907.335	911.2125000000001	1000	50	0.8371353
+145	911.2125	915.09	1000	50	0.9963776
+146	918.9675	922.845	1000	50	0.99993306
+147	930.6	934.4775000000001	1000	50	0.98831177
+148	938.355	942.2325000000001	1000	50	0.6520295
+149	957.7425	961.62	1000	50	0.6918473
+150	961.62	965.4975000000001	1000	50	0.74858236
+151	965.4975	969.375	1000	50	0.97066724
+152	973.2525	977.1300000000001	1000	50	0.6426704
+153	981.0075	984.8850000000001	1000	50	0.8150208
+154	984.885	988.7625	1000	50	0.5683353
+155	988.7625	992.6400000000001	1000	50	0.581548
+156	992.64	996.5175	1000	50	0.77473736
+157	1000.395	1004.2725	1000	50	0.950805
+158	1004.2725	1008.1500000000001	1000	50	0.53004926
+159	1012.0275	1015.9050000000001	1000	50	0.9998928
+160	1015.905	1019.7825	1000	50	0.90716743
+161	1023.66	1027.5375	1000	50	0.9305084
+162	1031.415	1035.2925	1000	50	0.77918565
+163	1039.17	1043.0475000000001	1000	50	0.9984765
+164	1043.0475	1046.925	1000	50	0.5665361
+165	1050.8025	1054.68	1000	50	0.999446
+166	1054.68	1058.5575000000001	1000	50	0.5452138
+167	1062.435	1066.3125	1000	50	0.99469894
+168	1066.3125	1070.19	1000	50	0.5405148
+169	1074.0675	1077.9450000000002	1000	50	0.5739461
+170	1077.945	1081.8225	1000	50	0.5058043
+171	1081.8225	1085.7	1000	50	0.883449
+172	1089.5775	1093.4550000000002	1000	50	0.9999634
+173	1093.455	1097.3325	1000	50	0.6814424
+174	1097.3325	1101.21	1000	50	0.904202
+175	1105.0875	1108.9650000000001	1000	50	0.55364376
+176	1120.5975	1124.4750000000001	1000	50	0.719839
+177	1136.1075	1139.9850000000001	1000	50	0.57873297
+178	1147.74	1151.6175	1000	50	0.7904256
+179	1151.6175	1155.4950000000001	1000	50	0.88318896
+180	1178.76	1182.6375	1000	50	0.88804716
+181	1186.515	1190.3925000000002	1000	50	0.6625152
+182	1198.1475	1202.025	1000	50	0.9660911
+183	1205.9025	1209.78	1000	50	0.91225654
+184	1209.78	1213.6575	1000	50	0.7151032
+185	1221.4125	1225.29	1000	50	0.9564372
+186	1244.6775	1248.555	1000	50	0.722955
+187	1248.555	1252.4325000000001	1000	50	0.7033242
+188	1252.4325	1256.31	1000	50	0.72211057
+189	1256.31	1260.1875	1000	50	0.6124199
+190	1260.1875	1264.065	1000	50	0.7847693
+191	1264.065	1267.9425	1000	50	0.6674457
+192	1267.9425	1271.8200000000002	1000	50	0.76507866
+193	1271.82	1275.6975	1000	50	0.8226003
+194	1279.575	1283.4525	1000	50	0.5882834
+195	1283.4525	1287.3300000000002	1000	50	0.94607145
+196	1287.33	1291.2075	1000	50	0.5691646
+197	1295.085	1298.9625	1000	50	0.9842685
+198	1298.9625	1302.8400000000001	1000	50	0.9851393
+199	1310.595	1314.4725	1000	50	0.5915515
+200	1314.4725	1318.3500000000001	1000	50	0.56246245
+201	1318.35	1322.2275	1000	50	0.996443
+202	1326.105	1329.9825	1000	50	0.8811614
+203	1329.9825	1333.8600000000001	1000	50	0.9826125
+204	1337.7375	1341.615	1000	50	0.9936857
+205	1345.4925	1349.3700000000001	1000	50	0.997924
+206	1357.125	1361.0025	1000	50	0.88610935
+207	1364.88	1368.7575000000002	1000	50	0.5882369
+208	1388.145	1392.0225	1000	50	0.6528943
+209	1395.9	1399.7775000000001	1000	50	0.7434355
+210	1407.5325	1411.41	1000	50	0.53381926
+211	1438.5525	1442.43	1000	50	0.7328098
+212	1446.3075	1450.185	1000	50	0.65970933
+213	1465.695	1469.5725	1000	50	0.539152
+214	1485.0825	1488.96	1000	50	0.6864708
+215	1492.8375	1496.7150000000001	1000	50	0.6845237