Updates to exporter and data map in FX GUI

.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/jdk-21.0.2.13-hotspot">
+	<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"/>

src/dataMap/layoutFX/DataMapPaneFX.java

@@ -65,7 +65,7 @@ public class DataMapPaneFX extends PamBorderPane implements UserDisplayNodeFX {
 	/**
 	 * Pane which allows users to change scale on datamap. 
 	 */
-	private ScalePaneFX scalePane;
+	private DataMapSettingsPane dataMapSettingsPane;
 
 	private PamVBox settingsPane;
 
@@ -87,14 +87,14 @@ public class DataMapPaneFX extends PamBorderPane implements UserDisplayNodeFX {
 		//create all the different panes, 
 		summaryPane = new SummaryPaneFX(dataMapControl, this);
 		
-		scalePane=new ScalePaneFX(dataMapControl,this);
-
 		scrollingDataPanel= new ScrollingDataPaneFX(dataMapControl, this); 
 		
+		dataMapSettingsPane=new DataMapSettingsPane(dataMapControl,this);
+		
 		//create the setting spane
 		settingsPane=new PamVBox(); 
 //		settingsPane.getChildren().add(summaryPane);
-		settingsPane.getChildren().add(scalePane); 
+		settingsPane.getChildren().add(dataMapSettingsPane.getContentNode()); 
 		settingsPane.setPadding(new Insets(40,10,10,10));
 		settingsPane.setPrefWidth(HIDE_PANE_WIDTH);
 
@@ -178,12 +178,11 @@ public class DataMapPaneFX extends PamBorderPane implements UserDisplayNodeFX {
 	 * Called from ScalePanel when anything 
 	 * to do with scaling changes. 
 	 */
-	@Deprecated
 	public void scaleChanged() {
-		if (scalePane == null || scrollingDataPanel == null) {
+		if (dataMapSettingsPane == null || scrollingDataPanel == null) {
 			return;
 		}
-		scalePane.getParams(dataMapControl.dataMapParameters);
+		dataMapSettingsPane.getParams(dataMapControl.dataMapParameters);
 		//scrollingDataPanel.scaleChange();
 	}
 
@@ -228,24 +227,30 @@ public class DataMapPaneFX extends PamBorderPane implements UserDisplayNodeFX {
 		switch (changeType) {
 		case PamControllerInterface.INITIALIZATION_COMPLETE:
 			scrollingDataPanel.updateScrollBar();
-			scalePane.checkDataGramPane();
+			dataMapSettingsPane.setParams(dataMapControl.dataMapParameters);
 			this.repaintAll();
+			break;
 		case PamControllerInterface.CHANGED_OFFLINE_DATASTORE:
 			scrollingDataPanel.updateScrollBar();
-			scalePane.checkDataGramPane();
+			dataMapSettingsPane.checkDataGramPane();
+			dataMapSettingsPane.setParams(dataMapControl.dataMapParameters);
+			break;
 		case PamControllerInterface.ADD_CONTROLLEDUNIT:
-			scalePane.checkDataGramPane();
 		case PamControllerInterface.REMOVE_CONTROLLEDUNIT:
-			scalePane.checkDataGramPane();
+			dataMapSettingsPane.checkDataGramPane();
+			dataMapSettingsPane.setParams(dataMapControl.dataMapParameters);
+			break;
 		case PamControllerInterface.INITIALIZE_LOADDATA:
 		case PamControllerInterface.EXTERNAL_DATA_IMPORTED:
 			scrollingDataPanel.updateScrollBar();
-			scalePane.checkDataGramPane();
+			dataMapSettingsPane.checkDataGramPane();
+			dataMapSettingsPane.setParams(dataMapControl.dataMapParameters);
 			this.repaintAll();
 			break;
 		case PamControllerInterface.OFFLINE_DATA_LOADED:
 			scrollingDataPanel.updateScrollBar();
-			scalePane.checkDataGramPane();
+			dataMapSettingsPane.checkDataGramPane();
+			dataMapSettingsPane.setParams(dataMapControl.dataMapParameters);
 			this.repaintAll();
 			break;
 		case PamControllerInterface.DATA_LOAD_COMPLETE:
@@ -304,4 +309,22 @@ public class DataMapPaneFX extends PamBorderPane implements UserDisplayNodeFX {
 		return null;
 	}
 
+	/**
+	 * Get the current number of data stream panes
+	 * @return the number of data stream panes
+	 */
+	public int getNumDataStreamPanes() {
+		return this.scrollingDataPanel.getNumDataStreamPanes();
+	}
+	
+	/**
+	 * Get a data stream pane. 
+	 * @param n - the index of the data stream pane
+	 * @return the data stream pane or null if the index is out of bounds. 
+	 */
+	public DataStreamPaneFX getDataStreamPane(int n) {
+		return this.scrollingDataPanel.getDataSyreamPane( n);
+
+	}
+
 }

src/dataMap/layoutFX/DataMapSettingsPane.java

@@ -0,0 +1,489 @@
+package dataMap.layoutFX;
+
+import dataGram.DatagramManager;
+import dataGram.DatagramScaleInformation;
+import dataGram.DatagramSettings;
+import dataMap.DataMapControl;
+import dataMap.DataMapParameters;
+import PamController.PamController;
+import PamUtils.PamCalendar;
+import binaryFileStorage.BinaryStore;
+import javafx.beans.value.ChangeListener;
+import javafx.beans.value.ObservableValue;
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
+import javafx.geometry.Insets;
+import javafx.geometry.Orientation;
+import javafx.geometry.Pos;
+import javafx.scene.Node;
+import javafx.scene.control.ComboBox;
+import javafx.scene.control.Label;
+import javafx.scene.layout.BorderPane;
+import javafx.scene.layout.ColumnConstraints;
+import javafx.scene.layout.GridPane;
+import javafx.scene.layout.Pane;
+import javafx.scene.layout.Priority;
+import pamViewFX.PamGuiManagerFX;
+import pamViewFX.fxNodes.PamBorderPane;
+import pamViewFX.fxNodes.PamGridPane;
+import pamViewFX.fxNodes.PamVBox;
+import pamViewFX.fxNodes.comboBox.ColorComboBox;
+import pamViewFX.fxNodes.pamDialogFX.PamDialogFX;
+import pamViewFX.fxNodes.sliders.ColourRangeSlider;
+import pamViewFX.fxNodes.utilityPanes.PamToggleSwitch;
+import pamViewFX.fxNodes.utilsFX.ColourArray;
+import pamViewFX.fxNodes.utilsFX.ColourArray.ColourArrayType;
+import pamViewFX.fxSettingsPanes.DynamicSettingsPane;
+
+/**
+ * Settings pane which allows users to change settings for data maps. 
+ * 
+ * @author Jamie Macaulay
+ *
+ */
+public class DataMapSettingsPane extends DynamicSettingsPane<DataMapParameters> {
+
+	/*
+	 * Reference to the data map control. 
+	 */
+	private DataMapControl dataMapControl;
+
+	/**
+	 * Reference to the dataMapPane. 
+	 */
+	private DataMapPaneFX dataMapPane;
+
+//	/**
+//	 * The slider which determines time scale. 
+//	 */
+//	private Slider timeSlider;
+
+	/**
+	 * Shows the time scale in pix/hour
+	 */
+	private Label timeScaleLabel;
+
+	/**
+	 * Selects unit count on vertical scale
+	 */
+	private ComboBox<String> scaleBox;
+
+	/**
+	 * Check box for log vertical scale. 
+	 */
+	private PamToggleSwitch logScaleToggle;
+
+//	/**
+//	 * The chosen time values. 
+//	 */
+//	private double[] timeScaleChoices = DataMapParameters.hScaleChoices;
+
+	/**
+	 * Combo box holding options to channge the datargam bin size
+	 */
+	private ComboBox<String> datagramBox;
+
+	/**
+	 * Holds a list of times for the datagram bin size. 
+	 */
+	private ComboBox<String> dataGramComboBox;
+
+	/**
+	 * Holds everything. 
+	 */
+	private PamVBox holder;
+
+	/**
+	 * Grid pane with settings for the data scales
+	 */
+	private PamGridPane scaleSettingsPane;
+
+	private Label dataGramLabel;
+
+	private ComboBox<String> dataGramBox;
+
+	/**
+	 * Holdes datagram settings. 
+	 */
+	private PamVBox dataGramSettingsPane;
+
+	private DataGramColPane dataGramColPane;
+
+	private PamBorderPane mainPain; 
+
+
+
+	public DataMapSettingsPane(DataMapControl dataMapControl, DataMapPaneFX dataMapPane) {
+		super(null);
+		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);
+
+		//add the scale 
+		holder=new PamVBox(); 
+		holder.setSpacing(5);
+
+		Label scaleLabel = new Label("Data Scale");
+		PamGuiManagerFX.titleFont2style(scaleLabel);
+		holder.getChildren().add(scaleLabel);
+		holder.getChildren().add(scaleSettingsPane = createScalePane());
+
+		//adds the datagram settings pane which is dependent on binary storage. 
+		checkDataGramPane(); 
+
+		mainPain = new PamBorderPane(); 
+		mainPain.setCenter(holder); 
+
+		//set params for the pane		
+		setParams(dataMapControl.dataMapParameters);
+		checkDataGramPane(); // create datagram pane if a binary store already added. 
+		sayHScale();
+
+	}
+
+	/**
+	 * Adds a settings pane for the data gram if a binary store is present. 
+	 */
+	public void checkDataGramPane(){
+		if (BinaryStore.findBinaryStoreControl()!=null){
+			DatagramManager dataGramManager=BinaryStore.findBinaryStoreControl().getDatagramManager();
+			if (dataGramManager!=null && dataGramSettingsPane==null) {
+				PamVBox datagramholder =   new PamVBox(); 
+				datagramholder.setSpacing(5);
+				Label datagramLabel = new Label("Datagrams");
+				PamGuiManagerFX.titleFont2style(datagramLabel);
+				datagramholder.getChildren().add(datagramLabel);
+				datagramholder.getChildren().add(createDatagramPane(dataGramManager));
+
+				holder.getChildren().add(this.dataGramSettingsPane = datagramholder); 
+			}
+		}
+		else {
+			holder.getChildren().remove(this.dataGramSettingsPane);
+			datagramBox=null; 
+		}
+	}
+
+
+	/**
+	 * Create the a datagram combo box to change the size of the datagram
+	 * @param dataGramManager - the datagram manager for the current biinary store. 
+	 * @return a combo box with datagram bin sizes. 
+	 */
+	private ComboBox<String> createDataGramBinPane(DatagramManager dataGramManager){
+
+		dataGramComboBox=new ComboBox<String>(createDurationList(dataGramManager)); 
+
+		dataGramComboBox.getSelectionModel().select(durationToString(dataGramManager.getDatagramSettings().datagramSeconds*1000L));
+		dataGramComboBox.valueProperty().addListener(( ov,  t,  t1) -> {                
+			if (t==t1) return; 
+			else {
+				PamController.getInstance();
+				boolean ans=PamDialogFX.showWarning(PamController.getMainStage(), "Warning", "Recalculating the datagram for a large dataset may take a long time" +
+						"Are you sure you want to continue"); 
+				if (ans){
+					int index=dataGramComboBox.getSelectionModel().getSelectedIndex();
+					//messy- datagramSeconfds should be in millis but left for backwards compatibility. 
+					dataGramManager.getDatagramSettings().datagramSeconds=(int) (DatagramSettings.defaultDatagramSeconds[index]/1000);
+					dataGramManager.updateDatagrams();
+					dataMapPane.repaintAll();
+				}
+			}
+		});
+
+		return dataGramComboBox;
+
+	}
+
+	/**
+	 * Convert duration to string.
+	 * @param duration in  millis.
+	 */
+	private String durationToString(long duration){
+		return (" " + PamCalendar.formatDuration(duration));
+	}
+
+	/**
+	 * Create list of load times. 
+	 * @return list of load times duration. 
+	 */
+	private ObservableList<String> createDurationList(DatagramManager dataGramManager){
+		ObservableList<String> loadTimeList=FXCollections.observableArrayList();
+		for (int i=0; i<DatagramSettings.defaultDatagramSeconds.length; i++){
+			loadTimeList.add(durationToString(DatagramSettings.defaultDatagramSeconds[i]));
+		}
+		return loadTimeList;
+	}
+
+
+	private Pane createDatagramPane(DatagramManager dataGramManager) {
+
+		dataGramLabel= new Label("Datagram bin size");
+		ComboBox<String> datagramBinsBox = createDataGramBinPane(dataGramManager); 
+
+		//Pane for colouring datagrams. 
+		dataGramBox=new ComboBox<String> (); 
+
+		//find all datagrams. 
+		updateDataStreamBox();
+
+		dataGramBox.setOnAction((action)->{
+			dataGramColPane.setDataStreamPanel(dataMapPane.getDataStreamPane(dataGramBox.getSelectionModel().getSelectedIndex()));
+		});
+
+		//holds settings for the datagram
+		dataGramColPane = new DataGramColPane(); 
+
+		PamGridPane holder = new PamGridPane(); 
+		holder.setHgap(5);
+		holder.setVgap(5);
+		//holder.setGridLinesVisible(true);
+
+		int row = 0;
+		
+		holder.add(dataGramLabel, 0,row);
+		holder.add(datagramBinsBox, 1, row);
+		
+		row++;
+		
+		holder.add(new Label("Select datagram"), 0, row);
+		holder.add(dataGramBox, 1, row);
+		
+		row++;
+		
+		GridPane.setHgrow(dataGramColPane, Priority.ALWAYS);
+		holder.add(dataGramColPane, 0, row);
+		
+		//dunno why this always had to be set after the child has been added to work. 
+		GridPane.setColumnSpan(dataGramColPane, 3);
+		
+		//hack to make sure the third column of the gris expands to fit the pane
+        ColumnConstraints rightCol = new ColumnConstraints();
+        rightCol.setHgrow(Priority.ALWAYS);
+        holder.getColumnConstraints().addAll(new ColumnConstraints(),  new ColumnConstraints(), rightCol);
+
+		return holder; 
+
+	}
+	
+	private void updateDataStreamBox() {
+		System.out.println("UPDATE DATA STREAM BOX: " + this.dataMapPane.getNumDataStreamPanes());
+		for (int i=0; i<this.dataMapPane.getNumDataStreamPanes(); i++) {
+			if (dataMapPane.getDataStreamPane(i).getScaleType() == DatagramScaleInformation.PLOT_3D) {
+				dataGramBox.getItems().add(dataMapPane.getDataStreamPane(i).getDataName().getName()); 
+			}
+		}
+	}
+
+
+
+	/** 
+	 * Allows the user to change datagram colours. 
+	 * 
+	 */
+	public class DataGramColPane extends PamBorderPane {
+
+
+		private ColourRangeSlider colourSlider;
+
+		private Label ampLabel;
+
+		private ColorComboBox colorBox;
+
+		private ColourArrayType colorArray = ColourArrayType.HSV; 
+		
+		private DataStreamPaneFX dataStreamPane; 
+
+		public DataGramColPane() {
+
+			//create colour slider
+			//colour slider 
+			colourSlider=new ColourRangeSlider();
+			colourSlider.setShowTickMarks(false);
+			colourSlider.setShowTickLabels(false);
+			colourSlider.setOrientation(Orientation.HORIZONTAL);
+			//amplifier label
+			//				String dBRef = GlobalMedium.getdBRefString(PamController.getInstance().getGlobalMediumManager().getCurrentMedium());
+			Label ampLabel = new Label("Colour scale"); 
+			
+			colorBox=new ColorComboBox(ColorComboBox.COLOUR_ARRAY_BOX);
+			colorBox.setPrefWidth(80);
+			
+			colourSlider.highValueProperty().addListener((obsVal, oldVal, newVal)->{
+				
+			});
+
+			//Change the colour of the colour slider when combo box is changed. 
+			colorBox.valueProperty().addListener(new ChangeListener<String>() {
+				@Override public void changed(ObservableValue<? extends String> ov, String t, String t1) {                
+					//change the colour of the colour range slider.     
+					setColours();
+				}
+			});
+			
+
+			colorBox.setValue(ColourArray.getName(getColourArrayType()));
+
+			//need to set up alignment properly. //FIXME- a bit messy 
+			BorderPane.setAlignment(colorBox, Pos.CENTER);
+			//sliderPane.setPadding(new Insets(10,0,0,0));
+			BorderPane.setMargin(colorBox, new Insets(0,5,0,5));
+			
+			this.setCenter(colourSlider);
+			this.setRight(colorBox);
+		
+			//set up so the correct color
+			colorBox.setValue(ColourArray.getName(getColourArrayType()));
+			colourSlider.setColourArrayType(getColourArrayType()); 
+
+		}
+
+
+		public void setDataStreamPanel(DataStreamPaneFX selectedItem) {
+			this.dataStreamPane=selectedItem;
+			//TODO - set the colours here. 
+			
+		}
+
+
+		/**
+		 * Set colours depending on current colour selection in combo box. 
+		 */
+		private void setColours(){
+			this.setColourArrayType(ColourArray.getColourArrayType(colorBox.getValue()));
+			colourSlider.setColourArrayType(getColourArrayType());
+		}
+		
+	
+		public ColourArrayType getColourArrayType() {
+			return colorArray;
+		}
+
+		public void setColourArrayType(ColourArrayType colourArrayType) {
+			this.colorArray = colourArrayType; 
+		}
+
+
+	}
+
+
+	/**
+	 * Create a pane to change vertical scales. 
+	 * @return pamne with controls to change vertical scales. 
+	 */
+	private PamGridPane createScalePane() {
+
+		PamGridPane controlPane=new PamGridPane(); 
+		controlPane.setHgap(5);
+		controlPane.setVgap(5);
+
+		//		//create time scale controls
+		//		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. 
+		//		timeSlider.valueProperty().addListener((ov, oldVal, newVal)->{
+		//			sayHScale();
+		//			dataMapPane.scaleChanged();
+		//		}); 
+		//		 
+		//		controlPane.add(timeScaleLabel=new Label(""),3,1);
+
+		//create vertical scale controls
+		
+		scaleBox=new ComboBox<String> (); 
+		scaleBox.getItems().add("No Scaling");
+		scaleBox.getItems().add("per Second");
+		scaleBox.getItems().add("per Minute");
+		scaleBox.getItems().add("per Hour");
+		scaleBox.getItems().add("per Day");
+		
+		controlPane.add(new Label("Show detections "),0,0);
+		controlPane.add(scaleBox,1,0);
+//		scaleBox.setPrefWidth(200);
+
+		scaleBox.valueProperty().addListener((ov, oldVal, newVal)->{
+			dataMapPane.scaleChanged();
+		}); 
+
+
+		logScaleToggle=new PamToggleSwitch("Log Scale"); 
+		logScaleToggle.selectedProperty().addListener((obsVal, oldVal, newVal)->{
+			dataMapPane.scaleChanged();
+		});
+
+
+		controlPane.add(logScaleToggle,0,1);
+
+
+		return controlPane;
+	}
+
+	/**
+	 * Show the horizontal scale. 
+	 */
+	private void sayHScale() {
+//		double hChoice = timeScaleChoices[this.];
+//		timeScaleLabel.setText(String.format("%s pixs/hour", new Double(timeScaleChoices[(int) hChoice]).toString()));
+	}
+
+	//HACK use setting flag to avoid immediate callback which overwrites changes 2 and 3 ! 
+	boolean setting = false;
+
+	public void setParams(DataMapParameters dataMapParameters) {
+		setting = true;
+//		timeSlider.setValue(dataMapParameters.hScaleChoice);
+		scaleBox.getSelectionModel().select(dataMapParameters.vScaleChoice);
+		logScaleToggle.setSelected(dataMapParameters.vLogScale);
+			
+		//make sure the combo box has correct datastreams
+		updateDataStreamBox();
+		
+		setting = false;
+	}
+
+
+	public DataMapParameters getParams(DataMapParameters dataMapParameters) {
+		if (setting) return dataMapParameters;
+//		dataMapParameters.hScaleChoice = (int) timeSlider.getValue(); 
+		dataMapParameters.vScaleChoice = scaleBox.getSelectionModel().getSelectedIndex();
+		dataMapParameters.vLogScale = logScaleToggle.isSelected();
+		
+		return dataMapParameters;
+	}
+
+	@Override
+	public String getName() {
+		return "Datamap settings";
+	}
+
+	@Override
+	public Node getContentNode() {
+		// TODO Auto-generated method stub
+		return mainPain;
+	}
+
+	@Override
+	public void paneInitialized() {
+		// TODO Auto-generated method stub
+		
+	}
+
+
+}

src/dataMap/layoutFX/DataStreamPaneFX.java

@@ -138,6 +138,7 @@ public class DataStreamPaneFX extends PamBorderPane {
 		dataGraph = new DataGraphFX();
 		dataGraph.setupAxis();
 		dataName = new DataName();
+		dataName.setName(dataBlock.getDataName()); 
 		
 		this.setTop(topPane=createTopPane());
 		this.setCenter(dataGraph);
@@ -990,6 +991,16 @@ public class DataStreamPaneFX extends PamBorderPane {
 	}
 	
 	public class DataName {
+
+		private String name;
+
+		public String getName() {
+			return name;
+		}
+
+		public void setName(String dataName) {
+			this.name=dataName;
+		}
 		
 	}
 	

src/dataMap/layoutFX/ScalePaneFX.java

@@ -1,293 +0,0 @@
-package dataMap.layoutFX;
-
-import dataGram.DatagramManager;
-import dataGram.DatagramSettings;
-import dataMap.DataMapControl;
-import dataMap.DataMapParameters;
-import PamController.PamController;
-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;
-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. 
- * 
- * @author Jamie Macaulay
- *
- */
-public class ScalePaneFX extends PamBorderPane {
-	
-	/*
-	 * Reference to the data map control. 
-	 */
-	private DataMapControl dataMapControl;
-	
-	/**
-	 * Reference to the dataMapPane. 
-	 */
-	private DataMapPaneFX dataMapPane;
-
-	/**
-	 * The slider which determines time scale. 
-	 */
-	private Slider timeSlider;
-
-	/**
-	 * Shows the time scale in pix/hour
-	 */
-	private Label timeScaleLabel;
-
-	/**
-	 * Selects unit count on vertical scale
-	 */
-	private ComboBox<String> scaleBox;
-
-	/**
-	 * Check box for log vertical scale. 
-	 */
-	private PamToggleSwitch logScaleBox;
-	
-	/**
-	 * The chosen time values. 
-	 */
-	private double[] timeScaleChoices = DataMapParameters.hScaleChoices;
-	
-	/**
-	 * Combo box holding options to channge the datargam bin size
-	 */
-	private ComboBox<String> datagramBox;
-
-	/**
-	 * Holds a list of times for the datagram bin size. 
-	 */
-	private ComboBox<String> dataGramComboBox;
-
-	/**
-	 * Holds everything. 
-	 */
-	private PamVBox holder;
-
-	/**
-	 * Grid pane with settings for the data scales
-	 */
-	private PamGridPane scaleSettingsPane;
-
-	private Label dataGramLabel; 
-
-
-
-	public ScalePaneFX(DataMapControl dataMapControl, DataMapPaneFX dataMapPane) {
-		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(scaleSettingsPane = createScalePane());
-		
-		this.setCenter(holder); 
-		
-		//set params for the pane		
-		setParams(dataMapControl.dataMapParameters);
-		checkDataGramPane(); // create datagram pane if a binary store already added. 
-		sayHScale();
-		
-	}
-
-	/**
-	 * Adds a settings pane for the datagram if a binary store is present. 
-	 */
-	public void checkDataGramPane(){
-		if (BinaryStore.findBinaryStoreControl()!=null){
-			DatagramManager dataGramManager=BinaryStore.findBinaryStoreControl().getDatagramManager();
-			if (dataGramManager!=null && datagramBox==null) {
-				datagramBox=createDatagramPane(dataGramManager);
-				scaleSettingsPane.add(dataGramLabel= new Label("Datagram bin size"), 0, 2);
-				scaleSettingsPane.add(dataGramComboBox, 1, 2);
-			}
-		}
-		else {
-			scaleSettingsPane.getChildren().remove(dataGramLabel);
-			scaleSettingsPane.getChildren().remove(dataGramComboBox);
-
-			datagramBox=null; 
-		}
-	}
-
-	
-	/**
-	 * Create the a datagram combo box to change the size of the datagram
-	 * @param dataGramManager - the datagram manager for the current biinary store. 
-	 * @return a combo box with datagram bin sizes. 
-	 */
-	private ComboBox<String> createDatagramPane(DatagramManager dataGramManager){
-
-		dataGramComboBox=new ComboBox<String>(createDurationList(dataGramManager)); 
-		
-		dataGramComboBox.getSelectionModel().select(durationToString(dataGramManager.getDatagramSettings().datagramSeconds*1000L));
-		dataGramComboBox.valueProperty().addListener(( ov,  t,  t1) -> {                
-			if (t==t1) return; 
-			else {
-				PamController.getInstance();
-				boolean ans=PamDialogFX.showWarning(PamController.getMainStage(), "Warning", "<html>Recalculating the datagram for a large dataset may take a long time<br>" +
-						"Are you sure you want to continue ?</html>"); 
-				if (ans){
-					int index=dataGramComboBox.getSelectionModel().getSelectedIndex();
-					//messy- datagramSeconfds should be in millis but left for backwards compatibility. 
-					dataGramManager.getDatagramSettings().datagramSeconds=(int) (DatagramSettings.defaultDatagramSeconds[index]/1000);
-					dataGramManager.updateDatagrams();
-					dataMapPane.repaintAll();
-				}
-			}
-	     });
-		
-		return dataGramComboBox;
-		
-	}
-	
-	/**
-	 * Convert duration to string.
-	 * @param duration in  millis.
-	 */
-	private String durationToString(long duration){
-		return (" " + PamCalendar.formatDuration(duration));
-	}
-	
-	/**
-	 * Create list of load times. 
-	 * @return list of load times duration. 
-	 */
-	private ObservableList<String> createDurationList(DatagramManager dataGramManager){
-		ObservableList<String> loadTimeList=FXCollections.observableArrayList();
-		for (int i=0; i<DatagramSettings.defaultDatagramSeconds.length; i++){
-			loadTimeList.add(durationToString(DatagramSettings.defaultDatagramSeconds[i]));
-		}
-		return loadTimeList;
-	}
-
-	
-	private PamGridPane createScalePane() {
-	
-		PamGridPane controlPane=new PamGridPane(); 
-		controlPane.setHgap(5);
-		controlPane.setVgap(5);
-		
-		//create time scale controls
-		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. 
-		timeSlider.valueProperty().addListener((ov, oldVal, newVal)->{
-			sayHScale();
-			dataMapPane.scaleChanged();
-		}); 
-		 
-		controlPane.add(timeScaleLabel=new Label(""),3,1);
-		
-		//create vertical scale controls
-		controlPane.add(new Label("Data counts"),0,0);
-		
-
-		scaleBox=new ComboBox<String> (); 
-		scaleBox.getItems().add("No Scaling");
-		scaleBox.getItems().add("per Second");
-		scaleBox.getItems().add("per Minute");
-		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 PamToggleSwitch("Log Scale"); 
-		logScaleBox.selectedProperty().addListener((obsVal, oldVal, newVal)->{
-			dataMapPane.scaleChanged();
-		});
-		
-		
-		controlPane.add(logScaleBox,3,0);
-			
-
-		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);
-		}
-		
-	}
-	
-	/**
-	 * Show the horizontal scale. 
-	 */
-	private void sayHScale() {
-		double hChoice = timeSlider.getValue();
-		timeScaleLabel.setText(String.format("%s pixs/hour", new Double(timeScaleChoices[(int) hChoice]).toString()));
-	}
-	
-	//HACK use setting flag to avoid immediate callback which overwrites changes 2 and 3 ! 
-	boolean setting = false;
-	
-	public void setParams(DataMapParameters dataMapParameters) {
-		setting = true;
-		timeSlider.setValue(dataMapParameters.hScaleChoice);
-		scaleBox.getSelectionModel().select(dataMapParameters.vScaleChoice);
-		logScaleBox.setSelected(dataMapParameters.vLogScale);
-		setting = false;
-	}
-	
-	
-	public void getParams(DataMapParameters dataMapParameters) {
-		if (setting) return;
-		dataMapParameters.hScaleChoice = (int) timeSlider.getValue(); 
-		dataMapParameters.vScaleChoice = scaleBox.getSelectionModel().getSelectedIndex();
-		dataMapParameters.vLogScale = logScaleBox.isSelected();
-	}
-
-
-}

src/dataMap/layoutFX/ScrollingDataPaneFX.java

@@ -28,7 +28,7 @@ public class ScrollingDataPaneFX extends PamBorderPane {
 
 	/**
 	 * Standard millis to wait for repaint. 
-	 * Do not ake this too high i.e. above 50 or the display gets very jerky
+	 * Do not make this too high i.e. above 50 or the display gets very jerky
 	 */
 	public static final long REPAINTMILLIS = 50;
 
@@ -496,4 +496,24 @@ public class ScrollingDataPaneFX extends PamBorderPane {
 //		this.notifyScrollChange();
 //	}
 
+	/**
+	 * Get the current number of data stream panes
+	 * @return the number of data stream panes
+	 */
+	public int getNumDataStreamPanes() {
+		return this.dataStreamPanels.size();
+	}
+	
+	/**
+	 * Get a data stream pane. 
+	 * @param n - the index of the data stream pane
+	 * @return the data stream pane or null if the index is out of bounds. 
+	 */
+	public DataStreamPaneFX getDataSyreamPane(int n) {
+		if (n<this.dataStreamPanels.size()) {
+			return dataStreamPanels.get(n);
+		}
+		else return null;
+	}
+	
 }

src/dataPlotsFX/overlaymark/menuOptions/WavExportOverlayMenu.java

@@ -7,16 +7,13 @@ import PamView.paneloverlay.overlaymark.OverlayMark;
 import PamguardMVC.PamDataUnit;
 import PamguardMVC.PamRawDataBlock;
 import detectiongrouplocaliser.DetectionGroupSummary;
-import export.wavExport.WavFileExportManager;
+import export.wavExport.WavDetExport;
-import javafx.animation.Timeline;
 import javafx.application.Platform;
 import javafx.scene.control.Labeled;
 import javafx.scene.control.Tooltip;
-import javafx.scene.effect.ColorInput;
 import javafx.scene.text.Text;
 import pamViewFX.fxGlyphs.PamGlyphDude;
 import pamViewFX.fxNodes.PamButton;
-import wavFiles.WavFileWriter;
 
 /**
  * Export a .wav clip. 
@@ -27,27 +24,27 @@ public class WavExportOverlayMenu  extends ExportOverlayMenu {
 
 	private Text wavFileGlyph;
 
-	/**
+//	/**
-	 * The wav file write
+//	 * The wav file write
-	 */
+//	 */
-	private WavFileWriter wavFile;
+//	private WavFileWriter wavFile;
+//
+//	private String defaultPath;
+//
+//	private String currentFolder;
 
-	private String defaultPath;
+	private WavDetExport wavExportManager;
 
-	private String currentFolder;
+//	private ColorInput shadow;
-
+//
-	private WavFileExportManager wavExportManager;
+//	private Timeline timline;
-
-	private ColorInput shadow;
-
-	private Timeline timline;
 
 	private PamButton pamButton; 
 
 	public WavExportOverlayMenu(){
 //		wavFileGlyph=PamGlyphDude.createPamGlyph(MaterialDesignIcon.FILE_MUSIC, standardIconSize);
 		wavFileGlyph=PamGlyphDude.createPamIcon("mdi2f-file-music", standardIconSize+14);
-		wavExportManager= new WavFileExportManager(); 
+		wavExportManager= new WavDetExport(); 
 
 		//set a callback when saving is finsihed. 
 		wavExportManager.setOnWavSaved((saveFile, flag)->{
@@ -132,7 +129,7 @@ public class WavExportOverlayMenu  extends ExportOverlayMenu {
 	 */
 	private void writeWavFile(DetectionGroupSummary foundDataUnits, int selectedIndex, OverlayMark mark) {
 		//		 animateButton() ; //start button animation. 
-		wavExportManager.dataUnits2Wav(foundDataUnits, selectedIndex, mark);
+		wavExportManager.writeOverlayMarkWav(foundDataUnits, selectedIndex, mark);
 	}		
 
 
@@ -148,7 +145,7 @@ public class WavExportOverlayMenu  extends ExportOverlayMenu {
 			rawDataBlock=foundDataUnits.getDataList().get(0).getParentDataBlock().getRawSourceDataBlock();
 		}
 		//is there available raw data
-		if (mark!=null && WavFileExportManager.haveRawData(rawDataBlock, (long) mark.getLimits()[0], (long) mark.getLimits()[1])) {
+		if (mark!=null && WavDetExport.haveRawData(rawDataBlock, (long) mark.getLimits()[0], (long) mark.getLimits()[1])) {
 			return true;
 		} 
 

src/dataPlotsFX/overlaymark/popUpMenu/TDMenuPane.java

@@ -12,7 +12,7 @@ import dataPlotsFX.layout.TDGraphFX.TDPlotPane;
 import dataPlotsFX.overlaymark.menuOptions.OverlayMenuItem;
 import dataPlotsFX.overlaymark.menuOptions.OverlayMenuManager;
 import detectiongrouplocaliser.DetectionGroupSummary;
-import export.wavExport.WavFileExportManager;
+import export.wavExport.WavDetExport;
 import javafx.geometry.Insets;
 import javafx.geometry.Orientation;
 import javafx.geometry.Pos;
@@ -546,7 +546,7 @@ public class TDMenuPane extends PamBorderPane {
 			PamRawDataBlock pamRawBlock =  findRawSourceBlock(); 
 			//			System.out.println("Pam raw data block: " +  pamRawBlock); 
 			
-			if (WavFileExportManager.haveRawData(pamRawBlock, (long) overlayMarker.getCurrentMark().getLimits()[0], (long) overlayMarker.getCurrentMark().getLimits()[1])) {
+			if (WavDetExport.haveRawData(pamRawBlock, (long) overlayMarker.getCurrentMark().getLimits()[0], (long) overlayMarker.getCurrentMark().getLimits()[1])) {
 				//System.out.println("Overaly Marker start X: " +  overlayMarker.getCurrentMark().getLimits()[0] + "  end: " +  overlayMarker.getCurrentMark().getLimits()[1]);
 				//System.out.println("Overlay Marker start Y: " +  overlayMarker.getCurrentMark().getLimits()[2] + "  end: " +  overlayMarker.getCurrentMark().getLimits()[3]);
 				groupDetectionDisplay.showRawData(pamRawBlock, overlayMarker.getCurrentMark().getLimits(), overlayMarker.getCurrentMark().getMarkChannels());

src/dataPlotsFX/scrollingPlot2D/Scrolling2DPlotDataFX.java

@@ -925,6 +925,8 @@ public class Scrolling2DPlotDataFX {
 
 		//reset transform in case of other drawings on base canvas. 
 		if (orientation == Orientation.VERTICAL) g2d.setTransform(horzAffine);
+		
+		
 
 	}
 	

src/dataPlotsFX/spectrogramPlotFX/SpectrogramControlPane.java

@@ -22,9 +22,13 @@ import javafx.scene.layout.Pane;
 import javafx.scene.paint.Color;
 
 /**
- * A general pane with a frequency slider, colour bar slider and colour combo box. These nodes are interconnected so when colour combo box is changed colours change. 
+ * A general pane with a frequency slider, colour bar slider and colour combo
- * Other than that this pane does nothing but all slider value properties are available to be used in another class or subclass. This means this control pane should be 
+ * box. These nodes are interconnected so when colour combo box is changed
- * available to be used for any spectrogram/3D colour image. 
+ * colours change. Other than that this pane does nothing but all slider value
+ * properties are available to be used in another class or subclass. This means
+ * this control pane should be available to be used for any spectrogram/3D
+ * colour image.
+ * 
  * @author Jamie Macaulay
  *
  */

src/export/MLExport/MLDataUnitExport.java

@@ -48,8 +48,12 @@ public abstract class MLDataUnitExport<T extends PamDataUnit<?, ?>> {
 		//UID for the detection.
 		Matrix UID =  Mat5.newScalar(dataUnit.getUID()); 
 
-		//the start sample.
+		Matrix startSample = Mat5.newScalar(0); 
-		Matrix startSample = Mat5.newScalar(dataUnit.getStartSample()); 
+		if (dataUnit.getStartSample()!=null) {
+			//the start sample.
+			 startSample = Mat5.newScalar(dataUnit.getStartSample()); 
+		}
+		
 
 		//the duration of the detection in samples.
 		Matrix sampleDuration = Mat5.newScalar(dataUnit.getSampleDuration()); 

src/export/PamExporterManager.java

@@ -11,7 +11,7 @@ import PamguardMVC.PamDataUnit;
 import export.CSVExport.CSVExportManager;
 import export.MLExport.MLDetectionsManager;
 import export.RExport.RExportManager;
-import export.wavExport.WavFileExportManager;
+import export.wavExport.WavDetExportManager;
 
 /**
  * Exports data to external files. Manages the file sizes and creates data buffers for 
@@ -61,7 +61,7 @@ public class PamExporterManager {
 		//add the MATLAB export
 		pamExporters.add(new MLDetectionsManager());
 		pamExporters.add(new RExportManager(this));
-		pamExporters.add(new WavFileExportManager());
+		pamExporters.add(new WavDetExportManager());
 //		pamExporters.add(new CSVExportManager());
 	}
 

src/export/swing/ExportProcessDialog.java

@@ -37,6 +37,7 @@ import PamguardMVC.PamDataBlock;
 import export.ExportParams;
 import export.PamExporterManager;
 import offlineProcessing.OLProcessDialog;
+import offlineProcessing.OLProcessDialog.OLMonitor;
 import offlineProcessing.OfflineTaskGroup;
 import offlineProcessing.TaskMonitor;
 import offlineProcessing.TaskMonitorData;
@@ -359,7 +360,7 @@ public class ExportProcessDialog {
 
 
 		public void setParams(ExportParams params) {
-			System.out.println("EXPORT: SET PARAMS: " +params);
+//			System.out.println("EXPORT: SET PARAMS: " +params);
 
 			if (params ==null) currentParams = new ExportParams(); 
 			currentParams = params.clone(); 
@@ -367,46 +368,87 @@ public class ExportProcessDialog {
 			buttonGroup.clearSelection();
 			exportButtons[params.exportChoice].setSelected(true);
 
-			System.out.println("EXPORT: SET PARAMS: " +currentParams.folder);
+//			System.out.println("EXPORT: SET PARAMS: " +currentParams.folder);
 			exportTo.setText(currentParams.folder);
 
 			spinner.setValue(currentParams.maximumFileSize);
 			
 			enableTasks();
 		}
+		
+		
+		/**
+		 * Ok, this is a bit of a hack but because we run tasks for multiple data blocks 
+		 * we have to run a new task whenever the previous task is finished. So we use a task monitor
+		 * to deetct when the task is finsihed and then, instead of finishing we run a new task. 
+		 */
+		class ExportTaskMonitor extends OLMonitor {
+
+			private int taskIndex;
+
+			private ExportTaskGroup exportTaskGroup;
+
+			private boolean started = false;
+
+			private int activeTasks;
+
+			public ExportTaskMonitor(int i, ExportTaskGroup exportTaskGroup) {
+				super();
+				this.taskIndex = i;
+				this.exportTaskGroup = exportTaskGroup;
+				
+				this.activeTasks = 0; 
+				for (int i1=0; i1<exportTaskGroup.getNTasks(); i1++) {
+					if (exportTaskGroup.getTask(i1).isDoRun()) {
+					activeTasks++;
+					}
+				}
+				
+			}
 
 
-
+			@Override
-	}
+			public void setTaskStatus(TaskMonitorData taskMonitorData) {
-
+				
-	class ExportTaskMonitor implements TaskMonitor {
+				switch (taskMonitorData.taskStatus) {
-
+				case COMPLETE:
-		private int taskIndex;
+					if (taskIndex<exportTaskGroup.getNTasks() && !started) {
-
+						exportTaskGroup.runTaskFrom(taskIndex+1);
-		private ExportTaskGroup exportTaskGroup;
+						started = true;
-
+					}
-		private boolean started = false;
+					break;
-
+				default:
-		public ExportTaskMonitor(int i, ExportTaskGroup exportTaskGroup) {
+					super.setTaskStatus(taskMonitorData);
-			this.taskIndex = i;
+				}
-			this.exportTaskGroup = exportTaskGroup;
+				
-		}
+				//A hack which sets the global 
-
+				switch (taskMonitorData.taskActivity) {
-
+				case LINKING:
-		@Override
+				case LOADING:
-		public void setTaskStatus(TaskMonitorData taskMonitorData) {
+					
-			if (taskMonitorData.taskStatus== TaskStatus.COMPLETE && !started) {
+					//the progress of one datablocks
-				System.out.println(" TASK COMPLETE:");
+					double progress = ((double) taskMonitorData.progValue)/taskMonitorData.progMaximum;
-				if (taskIndex<exportTaskGroup.getNTasks()) {
+					double totalProgress = ((double) taskIndex)/activeTasks + progress/activeTasks;
-					exportTaskGroup.runTaskFrom(taskIndex+1);
+//					System.out.println("Total progress: " + taskMonitorData.progValue + " of "  + taskMonitorData.progMaximum + " - " + totalProgress + "%" + "  " + progress + "  " + activeTasks + " " + taskIndex);
-					started = true;
+					//needs to be added to the overall progress
+					int max = getGlobalProgress().getMaximum();
+					getGlobalProgress().setValue((int) (totalProgress*max));
+				default:
+					break;
 				}
 			}
+
 		}
+		
+		public ExportTaskMonitor newExportTaskMonitor(int i, ExportTaskGroup exportTaskGroup) {
+			return new ExportTaskMonitor(i, exportTaskGroup);
+		}
+		
 
 	}
 
 
+
 	/**
 	 * Export task
 	 */
@@ -428,12 +470,12 @@ public class ExportProcessDialog {
 		 * @param i - the index
 		 */
 		public void runTaskFrom(int i) {
-			System.out.println("RUN TASK FROM :" + i);
 
+			//sets the porimary datablock to that of the relevent task. 
 			this.setPrimaryDataBlock(getTask(i).getDataBlock());
 			if (i<getNTasks()-1) {
 				//will start a new thread after this one has finished
-				this.setTaskMonitor(new ExportTaskMonitor(i, this));
+				this.setTaskMonitor(mtOfflineDialog.newExportTaskMonitor(i, this));
 			}
 			super.runTasks();
 		}

src/export/swing/ExportTask.java

@@ -56,7 +56,7 @@ public class ExportTask extends OfflineTask<PamDataUnit<?,?>>{
 				//System.out.println("Data selector null: " + this.getDataBlock().getDataName() + "  " + dataUnit);
 				exporter.exportDataUnit(dataUnit, false);
 			}
-			else if (dataSelector.scoreData(dataUnit)>0 && dataSelector.getParams().getCombinationFlag()  != DataSelectParams.DATA_SELECT_DISABLE) {
+			else if (dataSelector.scoreData(dataUnit)>0 || dataSelector.getParams().getCombinationFlag()  == DataSelectParams.DATA_SELECT_DISABLE) {
 				//System.out.println("Data selector OK: " + this.getDataBlock().getDataName() + "  " + dataUnit);
 				exporter.exportDataUnit(dataUnit, false);
 			}
@@ -73,7 +73,7 @@ public class ExportTask extends OfflineTask<PamDataUnit<?,?>>{
 
 	@Override
 	public void loadedDataComplete() {
-		System.out.println("EXPORTER: loaded data complete"); 
+//		System.out.println("EXPORTER: loaded data complete"); 
 		//force the exporter so save any renaming data units in the buffer
 		exporter.exportDataUnit(null,  true);
 		exporter.close();

src/export/wavExport/WavDetExport.java

@@ -1,6 +1,5 @@
 package export.wavExport;
 
-import java.awt.Component;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -20,46 +19,36 @@ import PamguardMVC.PamObservable;
 import PamguardMVC.PamObserver;
 import PamguardMVC.PamObserverAdapter;
 import PamguardMVC.PamRawDataBlock;
-import PamguardMVC.RawDataHolder;
 import PamguardMVC.dataOffline.OfflineDataLoading;
 import dataMap.OfflineDataMapPoint;
 import detectiongrouplocaliser.DetectionGroupSummary;
-import export.PamDataUnitExporter;
-import javafx.scene.layout.Pane;
 import wavFiles.Wav16AudioFormat;
 import wavFiles.WavFileWriter;
 
-/**
+public class WavDetExport {
- * Manages .wav file writing based on what type of data unit is selected and whether raw data is available.
+	
- * <p>
- * There are two primary use cases; 
- * <br>
- * 1) Order raw data from an overlay mark and save as a wav file
- * <br>
- * 2) Save a list of data units to wav files - either a single file with zero pads, a concatonated file or seperate files. 
- * 
- * @author Jamie Macaulay
- *
- */
-public class WavFileExportManager implements PamDataUnitExporter  {
-
 	/**
 	 * Successful writing of .wav file. 
 	 */
-	public static final int SUCCESS_WAV=0; 
+//	public static final int SUCCESS_WAV=0; 
 
 	/**
 	 * Successful writing of .wav file from data contained in detections. 
 	 */
-	public static final int SUCCESS_DET_WAV=1; 
+//	public static final int SUCCESS_DET_WAV=1; 
 
 	/**
 	 * General failure in wav file writing 
 	 */
-	public static final int FAILURE_WAV=2; 
+//	public static final int FAILURE_WAV=2; 
 
 
-	public static final int LOADING_WAV=2;
+//	public static final int LOADING_WAV=2;
+
+	/**
+	 * The maximum allowed size
+	 */
+	private static final double MAX_ZEROPAD_SIZE_MEGABYTES = 1024; //MB
 
 	/**
 	 * The default path to write files to
@@ -80,7 +69,7 @@ public class WavFileExportManager implements PamDataUnitExporter  {
 
 	private WavOptionsPanel wavOptionsPanel; 
 
-	public WavFileExportManager() {
+	public WavDetExport() {
 		wavDataUnitExports.add(new RawHolderWavExport());	
 
 		defaultPath=FileSystemView.getFileSystemView().getDefaultDirectory().getPath();
@@ -179,7 +168,7 @@ public class WavFileExportManager implements PamDataUnitExporter  {
 	 * @param selectedIndex  - the currently selected data unit.
 	 * @param mark           - overlay mark.
 	 */
-	public int dataUnits2Wav(DetectionGroupSummary foundDataUnits, int selectedIndex, OverlayMark mark) {
+	public int writeOverlayMarkWav(DetectionGroupSummary foundDataUnits, int selectedIndex, OverlayMark mark) {
 		System.out.println("Data units 2 wav");
 		//this order for .wav files. 
 		//if there is a mark then save limits of mark. If there is one data unit then set limits of data units
@@ -224,15 +213,18 @@ public class WavFileExportManager implements PamDataUnitExporter  {
 
 		int flag=-1; 
 
+		String currentFileS = createFileName(foundDataUnits.getFirstTimeMillis()); 
+		File file = new File(currentFileS);
+
 		if (hasAllWavClips) {
-			flag = saveDataUnitWav(foundDataUnits); 
+			flag = writeDetGroupWav(foundDataUnits, file, false); 
 		}
 		else if (!hasAllWavClips && haveRawData) {
 			//no raw data
 			flag = saveRawWav(start, end, rawDataBlock); 
 		}
 		else {
-			flag = saveDataUnitWav(foundDataUnits); 
+			flag = writeDetGroupWav(foundDataUnits, file, false); 
 		}
 
 		return flag; 
@@ -263,47 +255,129 @@ public class WavFileExportManager implements PamDataUnitExporter  {
 	/**
 	 * Save wav data from a data unit instead of from the raw file store. 
 	 * @param foundDataUnits - the list of found data units. 
+	 * @param currentFile - path to current file to save to. 
+	 * @param zeroPad - if true will zeroPad detections. 
 	 * @return the number of data units that were saved. 
 	 */
-	private int saveDataUnitWav(DetectionGroupSummary foundDataUnits) {
+	public int writeDetGroupWav(DetectionGroupSummary foundDataUnits, File filename, boolean zeroPad) {
-		return saveDataUnitWav(foundDataUnits.getDataList());
+		return writeDataUnitWav(foundDataUnits.getDataList(), filename, zeroPad);
 	}
 	
+	
 	/**
-	 * Save data units which contain raw data to a wav file. Note that this assumed
+	 * Save data units which contain raw data to individual wav files within a folder. 
-	 * the data units all contain raw data and are in order.
+	 * @param foundDataUnits - list of data units to save.
-	 * 
+	 * @param currentFile - the current folder. If this is a file name the parent directory will be used. 
-	 * @param foundDataUnits - data units containing raw data.
+	 * @return the number of data units saved
-	 * @return the number of data units saved - this should be the same as the size
-	 *         of the data unit list.
 	 */
-	private int saveDataUnitWav(List<PamDataUnit> foundDataUnits) {
+	public int writeDataUnitWavs(List<PamDataUnit> foundDataUnits, File currentFile) {
 		int n=0; 
 		WavFileWriter wavWrite = null; 
 		for (PamDataUnit fnDataUnit: foundDataUnits){
-
+			
-			String currentFile = createFileName(fnDataUnit.getTimeMilliseconds()); 
-
 			AudioFormat audioFormat = new Wav16AudioFormat(fnDataUnit.getParentDataBlock().getSampleRate(), PamUtils.getNumChannels(fnDataUnit.getChannelBitmap()));
 
-			System.out.println("Save detection wav." + foundDataUnits.size());
+			String currentFileS = createFileName(fnDataUnit.getTimeMilliseconds()); 
-			
+
+			//System.out.println("Save detection wav." + foundDataUnits.size());
 			for (int i=0; i<wavDataUnitExports.size(); i++) {
 				if (wavDataUnitExports.get(i).getUnitClass().isAssignableFrom(fnDataUnit.getClass())) {
 					
-					wavWrite= new WavFileWriter(currentFile, audioFormat); 
+					wavWrite= new WavFileWriter(currentFileS, audioFormat); 
 
-					System.out.println("Append wav." + foundDataUnits.size());
+					System.out.println("Write individual wav." + foundDataUnits.size());
 					//save the wav file of detection
 					wavWrite.append(wavDataUnitExports.get(i).getWavClip(fnDataUnit)); 
 					n++; 
 					
 					wavWrite.close();
+					
 					break; 
 				}
 			}
 		}
 		
+		return n;
+	}
+
+	/**
+	 * Save data units which contain raw data to a wav file. Note that this assumed
+	 * the data units all contain raw data, the raw data is at the same sample rate and number of channels 
+	 * and the data units are in order. This will APPEND to the wav file if it currently exists. 
+	 * 
+	 * @param foundDataUnits - data units containing raw data.
+	 * @param currentFile - path to current file to save to. 
+	 * @param zeroPad - if true will zeroPad detections. 
+	 * @return the number of data units saved - this should be the same as the size
+	 *         of the data unit list.
+	 */
+	public int writeDataUnitWav(List<PamDataUnit> foundDataUnits, File currentFile, boolean zeroPad) {
+		int n=0; 
+		WavFileWriter wavWrite = null; 
+		PamDataUnit lastfnDataUnit = null;
+		
+		if (foundDataUnits==null || foundDataUnits.size()<=0) {
+			return 0;
+		}
+		
+		//System.out.println("Save detection wav." + foundDataUnits.size());
+		AudioFormat audioFormat = new Wav16AudioFormat(foundDataUnits.get(0).getParentDataBlock().getSampleRate(), PamUtils.getNumChannels(foundDataUnits.get(0).getChannelBitmap())); 
+		
+		wavWrite= new WavFileWriter(currentFile.getAbsolutePath(), audioFormat);
+				
+		for (PamDataUnit fnDataUnit: foundDataUnits){
+			
+			for (int i=0; i<wavDataUnitExports.size(); i++) {
+				if (wavDataUnitExports.get(i).getUnitClass().isAssignableFrom(fnDataUnit.getClass())) {
+					
+					System.out.println("Append wav. data unit: " + n + " samples: " + wavDataUnitExports.get(i).getWavClip(fnDataUnit)[0].length + " zeroPad: " + zeroPad);
+					
+					if (zeroPad && lastfnDataUnit!=null) {
+						//we need to append zero samples between the detections. 
+						long timeMillisDiff = fnDataUnit.getTimeMilliseconds() - lastfnDataUnit.getTimeMilliseconds();
+						
+						long sampleDiff =  fnDataUnit.getStartSample()  - lastfnDataUnit.getStartSample();
+						
+						int samplesPad;
+						//are the two similar? - are they within 5 milliseconds
+						if (Math.abs(((sampleDiff/audioFormat.getSampleRate())*1000.) - timeMillisDiff)<5){
+							//use the sample diff
+							samplesPad =  (int) sampleDiff;
+						}
+						else {
+							//use time millis for padding. May indicate that data units are from different wav files. 
+							samplesPad =  (int) ((((double) timeMillisDiff)/1000.)*audioFormat.getSampleRate());
+						}
+						
+						//now safety check - is this more than one GB of data. Each sample is 16bits but the input double array is 64 bits each. 
+						double size = samplesPad*16*audioFormat.getChannels()/1024/1024;
+						
+						//
+						if (size>MAX_ZEROPAD_SIZE_MEGABYTES) {
+							wavWrite.close();
+							System.err.println(String.format("WavExportManager: A zero padding of %.2f MB was requested. The maximum allowed size is %.2f - "
+									+ "the .wav file was closed and any additional data units have not been written %s", size, MAX_ZEROPAD_SIZE_MEGABYTES, currentFile));
+							return n;
+						}
+						
+						System.out.println("Append wav. zero pad" + samplesPad);
+
+						wavWrite.append(new double[audioFormat.getChannels()][samplesPad]);
+					}
+					
+					//save the wav file of detection
+					if (wavWrite.append(wavDataUnitExports.get(i).getWavClip(fnDataUnit))) { 
+						n++; 
+					}					
+					lastfnDataUnit = fnDataUnit;
+					break; 
+				}
+			}
+		}
+		
+		wavWrite.close();
+
+		
 		//send a message that the wav file has saved
 		if (wavWrite!=null && saveCallback!=null) saveCallback.wavSaved(wavWrite.getFileName(), 0);
 		
@@ -340,85 +414,6 @@ public class WavFileExportManager implements PamDataUnitExporter  {
 	}
 
 
-
-	@Override
-	public boolean hasCompatibleUnits(Class dataUnitType) {
-//        boolean implementsInterface = Arrays.stream(dataUnitType.getInterfaces()).anyMatch(i -> i == RawDataHolder.class);
-		if ( RawDataHolder.class.isAssignableFrom(dataUnitType)) return true;
-		return false;
-	}
-
-
-
-	@Override
-	public boolean exportData(File fileName,
-			List<PamDataUnit> dataUnits, boolean append) {
-	
-		
-		//should we zeropad? 
-		saveDataUnitWav(dataUnits); 
-	
-		return true; 
-		
-		
-	}
-
-
-
-	@Override
-	public String getFileExtension() {
-		return "wav";
-	}
-
-
-
-	@Override
-	public String getIconString() {
-		return "mdi2f-file-music";
-	}
-
-
-
-	@Override
-	public String getName() {
-		return "raw sound";
-	}
-
-
-
-	@Override
-	public void close() {
-		// TODO Auto-generated method stub
-	}
-
-
-
-	@Override
-	public boolean isNeedsNewFile() {
-		return false;
-	}
-
-
-
-	@Override
-	public Component getOptionsPanel() {
-		if (this.wavOptionsPanel==null) {
-			this.wavOptionsPanel = new WavOptionsPanel(); 
-		}
-		return wavOptionsPanel;
-	}
-
-
-
-	@Override
-	public Pane getOptionsPane() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-
-
-
 	/**
 	 * Observes incoming raw data and saves to a wav file 
 	 *
@@ -528,70 +523,4 @@ public class WavFileExportManager implements PamDataUnitExporter  {
 	}
 
 
-	//	hello(){
-	//
-	//
-	//		if (mark==null) {
-	//			start= foundDataUnits.getFirstTimeMillis();
-	//			end= foundDataUnits.getLastTimeMillis(); 
-	//		}
-	//
-	//		File folder = new File(currentFolder); 
-	//
-	//		//save a .wav file clip. 
-	//		if (!folder.exists()){
-	//			if (!folder.mkdir()){
-	//				//TODO- warning message. 
-	//				return;
-	//			}
-	//		}
-	//
-	//		String currentPath = PamCalendar.formatFileDateTime();
-	//		//add data types to the filen,ae
-	//		for (int i=0 ;i<mlData.size(); i++ ){
-	//			currentPath=currentPath + "_" + mlData.get(i).getName(); 
-	//		}
-	//		//add correct file type.	
-	//		currentPath = currentPath + ".mat";
-	//		currentPath = currentFolder+"\\"+currentPath;
-	//
-	//
-	//		if (append && clipControl.clipSettings.storageOption == ClipSettings.STORE_WAVFILES) {
-	//			wavFile.append(rawData);
-	//			lastClipDataUnit.setSampleDuration(rawEnd-lastClipDataUnit.getStartSample());
-	//			clipDataBlock.updatePamData(lastClipDataUnit, dataUnit.getTimeMilliseconds());
-	//			//			System.out.println(String.format("%d samples added to file", rawData[0].length));
-	//		}
-	//		else {
-	//			ClipDataUnit clipDataUnit;
-	//			long startMillis = dataUnit.getTimeMilliseconds() - (long) (clipGenSetting.preSeconds*1000.);
-	//			if (clipControl.clipSettings.storageOption == ClipSettings.STORE_WAVFILES) {
-	//				String folderName = getClipFileFolder(dataUnit.getTimeMilliseconds(), true);
-	//				String fileName = getClipFileName(startMillis);
-	//				AudioFormat af = new Wav16AudioFormat(getSampleRate(), rawData.length);
-	//				wavFile = new WavFileWriter(folderName+fileName, af);
-	//				wavFile.write(rawData);
-	//				wavFile.close();
-	//				// make a data unit to go with it. 
-	//				clipDataUnit = new ClipDataUnit(startMillis, dataUnit.getTimeMilliseconds(), rawStart,
-	//						(int)(rawEnd-rawStart), channelMap, fileName, dataBlock.getDataName(), rawData, getSampleRate());
-	//			}
-	//			else {
-	//				clipDataUnit = new ClipDataUnit(startMillis, dataUnit.getTimeMilliseconds(), rawStart,
-	//						(int)(rawEnd-rawStart), channelMap, "", dataBlock.getDataName(), rawData, getSampleRate());
-	//			}
-	//			clipDataUnit.setFrequency(dataUnit.getFrequency());
-	//			lastClipDataUnit = clipDataUnit;
-	//			if (bearingLocaliser != null) {
-	//				localiseClip(clipDataUnit, bearingLocaliser, hydrophoneMap);
-	//			}				
-	//			clipDataBlock.addPamData(clipDataUnit);
-	//		}
-	//
-	//		return 0; // no error. 
-	//	}
-	//
-	//	}
-	//	}
-
 }

src/export/wavExport/WavDetExportManager.java

@@ -0,0 +1,229 @@
+package export.wavExport;
+
+import java.awt.Component;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.sound.sampled.AudioFormat;
+import javax.swing.filechooser.FileSystemView;
+
+import PamController.PamController;
+import PamDetection.RawDataUnit;
+import PamUtils.PamCalendar;
+import PamUtils.PamUtils;
+import PamView.paneloverlay.overlaymark.OverlayMark;
+import PamguardMVC.LoadObserver;
+import PamguardMVC.PamDataUnit;
+import PamguardMVC.PamObservable;
+import PamguardMVC.PamObserver;
+import PamguardMVC.PamObserverAdapter;
+import PamguardMVC.PamRawDataBlock;
+import PamguardMVC.RawDataHolder;
+import PamguardMVC.dataOffline.OfflineDataLoading;
+import dataMap.OfflineDataMapPoint;
+import detectiongrouplocaliser.DetectionGroupSummary;
+import export.PamDataUnitExporter;
+import javafx.scene.layout.Pane;
+import wavFiles.Wav16AudioFormat;
+import wavFiles.WavFileWriter;
+
+/**
+ * Writes data units and/or ordered raw data to a wav file. Has functions to
+ * handle .wav file writing based on overlay marks and detection groups with
+ * functions to make decisions based on what type of data unit is selected and
+ * whether raw data is available.
+ * <p>
+ * There are two primary use cases; <br>
+ * 1) Order raw data from an overlay mark and save as a wav file <br>
+ * 2) Save a list of data units to wav files - either a single file with zero
+ * pads, a concatenated file or separate files.
+ * 
+ * @author Jamie Macaulay
+ *
+ */
+public class WavDetExportManager implements PamDataUnitExporter  {
+
+	/**
+	 * Options for exporting wav files. 
+	 */
+	private WavExportOptions wavFileoptions = new WavExportOptions(); 
+
+	/**
+	 * Settings panel for wav file exporting
+	 */
+	private WavOptionsPanel wavOptionsPanel; 
+
+	/**
+	 * Exporter of wav files. 
+	 */
+	private WavDetExport wavDetExport = new WavDetExport();
+
+	public WavDetExportManager() {
+
+	}
+
+	@Override
+	public boolean hasCompatibleUnits(Class dataUnitType) {
+		//        boolean implementsInterface = Arrays.stream(dataUnitType.getInterfaces()).anyMatch(i -> i == RawDataHolder.class);
+		if ( RawDataHolder.class.isAssignableFrom(dataUnitType)) return true;
+		return false;
+	}
+
+
+
+	@Override
+	public boolean exportData(File fileName,
+			List<PamDataUnit> dataUnits, boolean append) {
+
+		//make sure we have the latest options. 
+		if (wavOptionsPanel!=null) {
+			//means the options panel has been opened. 
+			wavFileoptions = wavOptionsPanel.getParams(wavFileoptions);
+		}
+
+		//should we zeropad? 
+		//saveDataUnitWav(dataUnits); 		
+		switch (wavFileoptions.wavSaveChoice) {
+		case WavExportOptions.SAVEWAV_CONCAT:
+			wavDetExport.writeDataUnitWav(dataUnits, fileName, false);
+			break;
+		case WavExportOptions.SAVEWAV_INDIVIDUAL:
+			//here the filename will not be used but the parent folder will be used instead to write
+			//lots of wav files to. 
+			wavDetExport.writeDataUnitWavs(dataUnits, fileName);
+			break;
+		case WavExportOptions.SAVEWAV_ZERO_PAD:
+			wavDetExport.writeDataUnitWav(dataUnits, fileName, true);
+			break;
+		}
+		
+		return true; 
+	}
+
+
+
+	@Override
+	public String getFileExtension() {
+		return "wav";
+	}
+
+
+
+	@Override
+	public String getIconString() {
+		return "mdi2f-file-music";
+	}
+
+
+
+	@Override
+	public String getName() {
+		return "raw sound";
+	}
+
+
+
+	@Override
+	public void close() {
+		// TODO Auto-generated method stub
+	}
+
+
+
+	@Override
+	public boolean isNeedsNewFile() {
+		return false;
+	}
+
+
+
+	@Override
+	public Component getOptionsPanel() {
+		if (this.wavOptionsPanel==null) {
+			this.wavOptionsPanel = new WavOptionsPanel(); 
+		}
+		wavOptionsPanel.setParams(this.wavFileoptions) ;
+		return wavOptionsPanel;
+	}
+
+
+
+	@Override
+	public Pane getOptionsPane() {
+		// TODO - make FX version of settings. 
+		return null;
+	}
+
+
+
+
+
+	//	hello(){
+	//
+	//
+	//		if (mark==null) {
+	//			start= foundDataUnits.getFirstTimeMillis();
+	//			end= foundDataUnits.getLastTimeMillis(); 
+	//		}
+	//
+	//		File folder = new File(currentFolder); 
+	//
+	//		//save a .wav file clip. 
+	//		if (!folder.exists()){
+	//			if (!folder.mkdir()){
+	//				//TODO- warning message. 
+	//				return;
+	//			}
+	//		}
+	//
+	//		String currentPath = PamCalendar.formatFileDateTime();
+	//		//add data types to the filen,ae
+	//		for (int i=0 ;i<mlData.size(); i++ ){
+	//			currentPath=currentPath + "_" + mlData.get(i).getName(); 
+	//		}
+	//		//add correct file type.	
+	//		currentPath = currentPath + ".mat";
+	//		currentPath = currentFolder+"\\"+currentPath;
+	//
+	//
+	//		if (append && clipControl.clipSettings.storageOption == ClipSettings.STORE_WAVFILES) {
+	//			wavFile.append(rawData);
+	//			lastClipDataUnit.setSampleDuration(rawEnd-lastClipDataUnit.getStartSample());
+	//			clipDataBlock.updatePamData(lastClipDataUnit, dataUnit.getTimeMilliseconds());
+	//			//			System.out.println(String.format("%d samples added to file", rawData[0].length));
+	//		}
+	//		else {
+	//			ClipDataUnit clipDataUnit;
+	//			long startMillis = dataUnit.getTimeMilliseconds() - (long) (clipGenSetting.preSeconds*1000.);
+	//			if (clipControl.clipSettings.storageOption == ClipSettings.STORE_WAVFILES) {
+	//				String folderName = getClipFileFolder(dataUnit.getTimeMilliseconds(), true);
+	//				String fileName = getClipFileName(startMillis);
+	//				AudioFormat af = new Wav16AudioFormat(getSampleRate(), rawData.length);
+	//				wavFile = new WavFileWriter(folderName+fileName, af);
+	//				wavFile.write(rawData);
+	//				wavFile.close();
+	//				// make a data unit to go with it. 
+	//				clipDataUnit = new ClipDataUnit(startMillis, dataUnit.getTimeMilliseconds(), rawStart,
+	//						(int)(rawEnd-rawStart), channelMap, fileName, dataBlock.getDataName(), rawData, getSampleRate());
+	//			}
+	//			else {
+	//				clipDataUnit = new ClipDataUnit(startMillis, dataUnit.getTimeMilliseconds(), rawStart,
+	//						(int)(rawEnd-rawStart), channelMap, "", dataBlock.getDataName(), rawData, getSampleRate());
+	//			}
+	//			clipDataUnit.setFrequency(dataUnit.getFrequency());
+	//			lastClipDataUnit = clipDataUnit;
+	//			if (bearingLocaliser != null) {
+	//				localiseClip(clipDataUnit, bearingLocaliser, hydrophoneMap);
+	//			}				
+	//			clipDataBlock.addPamData(clipDataUnit);
+	//		}
+	//
+	//		return 0; // no error. 
+	//	}
+	//
+	//	}
+	//	}
+
+}

src/export/wavExport/WavExportOptions.java

@@ -25,7 +25,7 @@ public class WavExportOptions implements Serializable, Cloneable {
 	public static final int SAVEWAV_INDIVIDUAL = 2;
 
 	/**
-	 * Flag to indicuate how to save files
+	 * Flag to indicate how to save files
 	 */
 	public int wavSaveChoice = SAVEWAV_CONCAT;
 

src/export/wavExport/WavOptionsPanel.java

@@ -38,17 +38,17 @@ public class WavOptionsPanel extends PamPanel {
 		
 		this.setLayout((new GridBagLayout()));
 
-		addComponent(this, zeroPad = new JRadioButton("Concat"), c);
+		addComponent(this, zeroPad = new JRadioButton("Zero Pad"), c);
 		
 		c.gridx++;
 		
-		addComponent(this, noZeroPad = new JRadioButton("Zero pad"), c);
+		addComponent(this, noZeroPad = new JRadioButton("Concatonate"), c);
 
 		c.gridx++;
 		addComponent(this, indvidualWav = new JRadioButton("Individual"), c);
 		
-		c.gridx++;
+//		c.gridx++;
-		addComponent(this, new JLabel(" wav"), c);
+//		addComponent(this, new JLabel(" wav"), c);
 		
 		 // Initialization of object of "ButtonGroup" class. 
 		ButtonGroup buttonGroup = new ButtonGroup(); 
@@ -97,8 +97,8 @@ public class WavOptionsPanel extends PamPanel {
 	public WavExportOptions getParams(WavExportOptions wavExportOptions) {
 		
 		if (zeroPad.isSelected()) wavExportOptions.wavSaveChoice = WavExportOptions.SAVEWAV_ZERO_PAD;
-		if (noZeroPad.isSelected()) wavExportOptions.wavSaveChoice = WavExportOptions.SAVEWAV_ZERO_PAD;
+		if (noZeroPad.isSelected()) wavExportOptions.wavSaveChoice = WavExportOptions.SAVEWAV_CONCAT;
-		if (indvidualWav.isSelected()) wavExportOptions.wavSaveChoice = WavExportOptions.SAVEWAV_ZERO_PAD;
+		if (indvidualWav.isSelected()) wavExportOptions.wavSaveChoice = WavExportOptions.SAVEWAV_INDIVIDUAL;
 
 		return wavExportOptions; 
 	}

src/offlineProcessing/OLProcessDialog.java

@@ -63,6 +63,7 @@ public class OLProcessDialog extends PamDialog {
 	private JButton[] settingsButton;
 	private JLabel status, currFile;
 	private JProgressBar globalProgress; // file by file progress 1: nFiles
+
 	private JProgressBar loadedProgress; // progress throgh loaded data
 	private JCheckBox deleteOldData;
 	private JLabel dataInfo;
@@ -723,7 +724,7 @@ public class OLProcessDialog extends PamDialog {
 	 * @author Doug Gillespie
 	 *
 	 */
-	class OLMonitor implements TaskMonitor {
+	public class OLMonitor implements TaskMonitor {
 
 		@Override
 		public void setTaskStatus(TaskMonitorData taskMonitorData) {
@@ -734,6 +735,7 @@ public class OLProcessDialog extends PamDialog {
 			else {
 				currFile.setText(taskMonitorData.fileOrStatus);
 			}
+			
 			switch (taskMonitorData.taskActivity) {
 			case LINKING:
 			case LOADING:
@@ -755,6 +757,7 @@ public class OLProcessDialog extends PamDialog {
 			default:
 				break;
 			}
+			
 			switch (taskMonitorData.taskStatus) {
 			case COMPLETE:
 				globalProgress.setValue(100);
@@ -878,6 +881,11 @@ public class OLProcessDialog extends PamDialog {
 	public void setNeedaNote(boolean isNeedaNote) {
 		this.isNeedaNote = isNeedaNote;
 	}
+	
+	public JProgressBar getGlobalProgress() {
+		return globalProgress;
+	}
+
 
 
 

src/pamViewFX/PamGuiFX.java

@@ -43,29 +43,29 @@ import org.controlsfx.control.ToggleSwitch;
  *
  */
 public class PamGuiFX extends StackPane implements PamViewInterface {
-	
+
 	/**
 	 * This is essentially one PAMGuard stage. PAMGuard may have multiple stages in which case it will have multiple PAMGuiFX instances. 
 	 */
 	private PamTabPane mainTabPane; 
-	
+
 	/**
 	 * The preferred width of the side pane. 
 	 */
 	public static final double SIDE_PANE_PREF_WIDTH = 250;
-	
+
-//	/**
+	//	/**
-//	 * Icon for menu
+	//	 * Icon for menu
-//	 */
+	//	 */
-//	public Image menuIconGrey=new Image(getClass().getResourceAsStream("/Resources/MenuButton.png"));
+	//	public Image menuIconGrey=new Image(getClass().getResourceAsStream("/Resources/MenuButton.png"));
-//	
+	//	
-//	public Image showButtonGrey=new Image(getClass().getResourceAsStream("/Resources/SidePanelShow2Grey.png"));
+	//	public Image showButtonGrey=new Image(getClass().getResourceAsStream("/Resources/SidePanelShow2Grey.png"));
-//	
+	//	
-//	public Image hideButtonGrey=new Image(getClass().getResourceAsStream("/Resources/SidePanelHide2Grey.png"));
+	//	public Image hideButtonGrey=new Image(getClass().getResourceAsStream("/Resources/SidePanelHide2Grey.png"));
-//
+	//
-//	public Image recordStart=new Image(getClass().getResourceAsStream("/Resources/recordStart.png"));
+	//	public Image recordStart=new Image(getClass().getResourceAsStream("/Resources/recordStart.png"));
-//
+	//
-//	public Image playPause=new Image(getClass().getResourceAsStream("/Resources/playStart.png"));
+	//	public Image playPause=new Image(getClass().getResourceAsStream("/Resources/playStart.png"));
 
 	/**
 	 * A reference to the stage this PAMGUIFX belongs to. 
@@ -81,18 +81,18 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 	 * Hiding side pane. 
 	 */
 	private HidingPane hidingSidePane;
-	
+
 	/**
 	 * The Pane which holds everything that sits in hide pane. 
 	 */
 	private  PamVBox sidePaneContent;
-	
+
 
 	/**
 	 * Pane which holds main PAMGUARD settings
 	 */
 	private PamVBox settingsPane; 
-	
+
 	/**
 	 * Hiding pane which holds settings
 	 */
@@ -121,34 +121,34 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 	 * @param pamGuiManagerFX - the GUI manager. 
 	 */
 	public PamGuiFX (PamTabPane mainTabPane, Stage stage, PamGuiManagerFX pamGuiManagerFX){
-		
+
 		this.stage=stage; 
 		this.pamGuiManagerFX=pamGuiManagerFX; 
-        this.mainTabPane = mainTabPane;
+		this.mainTabPane = mainTabPane;
-		
+
-        Node layout=createMainPane(mainTabPane, stage); 
+		Node layout=createMainPane(mainTabPane, stage); 
 
 		//add main pane to PamGui
 		this.getChildren().add(layout);
 
 	}
-	
+
 	public PamGuiFX (Stage stage, PamGuiManagerFX pamGuiManagerFX){
-		
+
 		this.stage=stage; 
 		this.pamGuiManagerFX=pamGuiManagerFX; 
-		
+
 		//create the main tab pane. 
-        this.mainTabPane = new PamTabPane();
+		this.mainTabPane = new PamTabPane();
-       		
+
-        Node layout=createMainPane(mainTabPane, stage); 
+		Node layout=createMainPane(mainTabPane, stage); 
-	   
+
-	    //add main pane to PamGui
+		//add main pane to PamGui
-	    this.getChildren().add(layout);
+		this.getChildren().add(layout);
 
 	}
-	
+
-	
+
 	/**
 	 * Create the pane which sits inside stage and holds tabs, side pane. 
 	 * @param mainTabPane - the main tab pane for the scene. 
@@ -174,7 +174,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 		//create the button which shows the hiding panel. Although we get this button from the hiding pane, where to place
 		//it and what colour it is etc has to be set for whatever pane it is to be located in. 
 		PamButton showButtonRight=hidingSidePane.getShowButton();
-//		showButtonRight.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.CHEVRON_LEFT, PamGuiManagerFX.iconColor, PamGuiManagerFX.iconSize));
+		//		showButtonRight.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.CHEVRON_LEFT, PamGuiManagerFX.iconColor, PamGuiManagerFX.iconSize));
 		showButtonRight.setGraphic(PamGlyphDude.createPamIcon("mdi2c-chevron-left", PamGuiManagerFX.iconColor, PamGuiManagerFX.iconSize));
 		//showLeftButton.setText(PamFontAwesome.ICON_CHEVRON_LEFT);
 		showButtonRight.getStyleClass().add("close-button-left-trans");
@@ -183,10 +183,10 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 		//alter animations to remove/add showButton to tab pane. 
 		//TODO- tried to have animation here to hide buttons but didn't appear to work. 
 		//Maybe an issue with running another animation from animation thread?
-//		showButton.prefWidthProperty().addListener((listener)->{
+		//		showButton.prefWidthProperty().addListener((listener)->{
-//			mainTabPane.layout(); //Don't need this
+		//			mainTabPane.layout(); //Don't need this
-//		});
+		//		});
-				
+
 		hidingSidePane.getTimeLineShow().setOnFinished((value)->{
 			showButtonRight.setPrefWidth(1);
 			showButtonRight.setVisible(false);
@@ -203,55 +203,55 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 
 		PamButton closeButtonLeft=hidingSidePane.getHideButton();
 		closeButtonLeft.getStyleClass().add("close-button-right-trans");
-//		closeButtonLeft.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.CHEVRON_RIGHT, Color.DARKGRAY.darker(), PamGuiManagerFX.iconSize));
+		//		closeButtonLeft.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.CHEVRON_RIGHT, Color.DARKGRAY.darker(), PamGuiManagerFX.iconSize));
 		closeButtonLeft.prefHeightProperty().bind(mainTabPane.getHeaderHeightProperty());
-		
+
 		//add hiding pane to main pane. 
 		layout.setRight(hidingSidePane);
-				
+
 		/**create settings pane. This allows access to primary PAMGUARD settings.**/
 		settingsPane=new PamSettingsMenuPane();
 		settingsPane.setPrefWidth(250);
 		hidingPaneLeft=new HidingPane(Side.LEFT, settingsPane, this, false);
 		hidingPaneLeft.showHidePane(false);
-		
+
 		hidingPaneLeft.getStylesheets().addAll(pamGuiManagerFX.getPamSettingsCSS());
 
 		PamButton showButtonLeft=hidingPaneLeft.getShowButton();
-//		showButtonLeft.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.BARS, Color.LIGHTGRAY, PamGuiManagerFX.iconSize));
+		//		showButtonLeft.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.BARS, Color.LIGHTGRAY, PamGuiManagerFX.iconSize));
 		showButtonLeft.setGraphic(PamGlyphDude.createPamIcon("mdi2m-menu", Color.LIGHTGRAY, PamGuiManagerFX.iconSize));
 		showButtonLeft.getStyleClass().add("close-button-right-trans");
 		showButtonLeft.setStyle(" -fx-background-radius: 0 0 0 0;");
-		
+
 		PamButton closeRightButton=hidingPaneLeft.getHideButton();
 		closeRightButton.setPrefWidth(40);
 		closeRightButton.getStyleClass().add("close-button-left-trans");
-//		closeRightButton.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.CHEVRON_LEFT, Color.WHITE, PamGuiManagerFX.iconSize));
+		//		closeRightButton.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.CHEVRON_LEFT, Color.WHITE, PamGuiManagerFX.iconSize));
 		closeRightButton.setGraphic(PamGlyphDude.createPamIcon("mdi2c-chevron-left", Color.WHITE, PamGuiManagerFX.iconSize));
 		closeRightButton.prefHeightProperty().bind(mainTabPane.getHeaderHeightProperty());
-		
+
 		//add hiding pane to main pane. 
 		layout.setLeft(hidingPaneLeft);
-		
+
-//		//Create a button which sits at end of tab pane
+		//		//Create a button which sits at end of tab pane
-//		settingsButton  = new PamButton();
+		//		settingsButton  = new PamButton();
-//		settingsButton.setMinWidth(Control.USE_PREF_SIZE);
+		//		settingsButton.setMinWidth(Control.USE_PREF_SIZE);
-//		settingsButton.setGraphic(Glyph.create("FontAwesome|BARS").size(22).color(Color.DARKGREY.darker()));
+		//		settingsButton.setGraphic(Glyph.create("FontAwesome|BARS").size(22).color(Color.DARKGREY.darker()));
-//		settingsButton.getStyleClass().add("transparent-button");
+		//		settingsButton.getStyleClass().add("transparent-button");
-////		settingsButton.setPadding(new Insets(0,10,0,10));
+		////		settingsButton.setPadding(new Insets(0,10,0,10));
-//		settingsButton.setOnAction(e -> { 
+		//		settingsButton.setOnAction(e -> { 
-//			//TODO-open settings menu
+		//			//TODO-open settings menu
-//		});
+		//		});
 
 		mainTabPane.setTabEndRegion(showButtonRight);
 		mainTabPane.setTabStartRegion(showButtonLeft);
-//		mainTabPane.getStyleClass().add(Styles.TABS_FLOATING);
+		//		mainTabPane.getStyleClass().add(Styles.TABS_FLOATING);
 
 		mainTabPane.getAddTabButton().setOnAction((value)->{
-		    addPamTab(new TabInfo("Display " + (this.getNumTabs()+1)), null ,true); 
+			addPamTab(new TabInfo("Display " + (this.getNumTabs()+1)), null ,true); 
-		    mainTabPane.layout();
+			mainTabPane.layout();
 		});
-		
+
 		//now have a holder - add the loading pane. 
 		/**create left hiding pane**/
 		loadPane=new PamLoadingPane(this.pamGuiManagerFX);
@@ -259,14 +259,14 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 		hidingLoadPane.setPrefHeight(110);
 		hidingLoadPane.removeHideButton();
 		hidingLoadPane.showHidePane(false);
-		
+
 		PamBorderPane layoutHolder=new PamBorderPane(layout);
 		layoutHolder.setTop(hidingLoadPane);
 
-	    return  layoutHolder; 
+		return  layoutHolder; 
-	    
+
 	}
-	
+
 	/**
 	 * Get the load pane for the PamGuiFX- shows loading data and other status updates. 
 	 * @return the PamLoadingf Pane
@@ -281,79 +281,79 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 	public void show(){
 		stage.show(); 
 	}
-	
+
-		
+
 	/**
 	 * Convenience function to add a closable tab to the display with a new UserDisplayNodeFX.
 	 * @param name- tab name.
 	 * @param content- content to add to the tab. Can be null; 
 	 */
 	public PamGuiTabFX addPamTab(TabInfo tabInfo, UserDisplayNodeFX content, boolean detachable ){        
-        //create holder pane and add to tab
+		//create holder pane and add to tab
 		PamGuiTabFX newTab = new PamGuiTabFX(tabInfo, this);
-		
+
 		newTab.setToolbar(new ToolBarPane(newTab));
-		
+
 		//static displays have non closable tabs and non resizable displays
-        if (content!=null){
+		if (content!=null){
-        	newTab.setClosable(!content.isStaticDisplay());
+			newTab.setClosable(!content.isStaticDisplay());
-        	newTab.setResizableDisplays(!content.isStaticDisplay());
+			newTab.setResizableDisplays(!content.isStaticDisplay());
 
-        	if (content.isStaticDisplay()){
+			if (content.isStaticDisplay()){
-        		//if static, then add to center. 
+				//if static, then add to center. 
-        		newTab.getContentHolder().setCenter(content.getNode());
+				newTab.getContentHolder().setCenter(content.getNode());
-        	}
+			}
-        	else{
+			else{
-        		//add content- will not add and return null if content is null 
+				//add content- will not add and return null if content is null 
-        		newTab.addInternalPane(content);
+				newTab.addInternalPane(content);
-        	}
+			}
-        }
+		}
-        
-        newTab.setOnClosed((action)->{
-        	//when a tab is closer. 
-        	for (int i=0; i<newTab.getInternalPanes().size(); i++) {
-        		System.out.println("REMOVE TAB: " + newTab.getInternalPanes().size());
 
-	        	newTab.getInternalPanes().get(i).getUserDisplayNode().closeNode();
+		newTab.setOnClosed((action)->{
-	        	if (newTab.getInternalPanes().get(i).getUserDisplayNode().getUserDisplayControl()!=null) {
+			//when a tab is closer. 
-	        		System.out.println("REMOVE CONTROLLED DISPLAY UNIT: " + newTab.getInternalPanes().get(i).getUserDisplayNode().getUserDisplayControl());
+			for (int i=0; i<newTab.getInternalPanes().size(); i++) {
-	        		//the display is a standalone display and so remove the tab means the controlled unit should be removed from the data model 
+				System.out.println("REMOVE TAB: " + newTab.getInternalPanes().size());
-	        		PamController.getInstance().removeControlledUnt(newTab.getInternalPanes().get(i).getUserDisplayNode().getUserDisplayControl());
+
-	        		PamGuiManagerFX.getInstance().getDataModelFX().dataModeltoPamModel();
+				newTab.getInternalPanes().get(i).getUserDisplayNode().closeNode();
-	        	}
+				if (newTab.getInternalPanes().get(i).getUserDisplayNode().getUserDisplayControl()!=null) {
-        	}
+					System.out.println("REMOVE CONTROLLED DISPLAY UNIT: " + newTab.getInternalPanes().get(i).getUserDisplayNode().getUserDisplayControl());
-        });
+					//the display is a standalone display and so remove the tab means the controlled unit should be removed from the data model 
-        
+					PamController.getInstance().removeControlledUnt(newTab.getInternalPanes().get(i).getUserDisplayNode().getUserDisplayControl());
-        newTab.setDetachable(detachable);
+					PamGuiManagerFX.getInstance().getDataModelFX().dataModeltoPamModel();
-   
+				}
-        //add tab
+			}
-        mainTabPane.getTabs().add(newTab);
+		});
-        
+
-        return newTab;
+		newTab.setDetachable(detachable);
+
+		//add tab
+		mainTabPane.getTabs().add(newTab);
+
+		return newTab;
 	}
-		
+
 	/**
 	 * Add a tab for the data model. 
 	 * @param dataModelPaneFX - the data model 
 	 */
 	public DataModelPaneFX addDataModelTab() {
-		
+
 		PamGuiTabFX newTab = new PamGuiTabFX(new TabInfo("Data Model"), this);
 		newTab.setToolbar(new ToolBarPane(newTab));
-		
+
-        newTab.setClosable(false); //can't close a data model
+		newTab.setClosable(false); //can't close a data model
-        newTab.setDetachable(false);
+		newTab.setDetachable(false);
-        mainTabPane.getTabs().add(newTab);
+		mainTabPane.getTabs().add(newTab);
-        DataModelPaneFX dataModelPaneFX=new DataModelPaneFX(); 
+		DataModelPaneFX dataModelPaneFX=new DataModelPaneFX(); 
-        
+
-        //create controls in the tool bar for the data model 
+		//create controls in the tool bar for the data model 
-        dataModelPaneFX.createToolbarControls(newTab); 
+		dataModelPaneFX.createToolbarControls(newTab); 
-        
+
-        newTab.setMainContent(dataModelPaneFX);
+		newTab.setMainContent(dataModelPaneFX);
-        return dataModelPaneFX; 
+		return dataModelPaneFX; 
-		
+
 	}
-	
+
 	/**
 	 * Get all tabs for this PamGuiFX
 	 * @return list of tabs in the PamGuiFX
@@ -365,7 +365,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 		}
 		return tabs;
 	}
-	
+
 	/**
 	 * Add a tab to the tab pane.
 	 * @param pamGuiTabFX - the tab to add
@@ -374,7 +374,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 		// add a tab.
 		mainTabPane.getTabs().add(pamGuiTabFX);
 	}
-	
+
 	/**
 	 * Add tabs to the tab pane.
 	 * @param pamGuiTabFX - the tabs to add
@@ -383,7 +383,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 		// add a tab.>
 		mainTabPane.getTabs().addAll(pamGuiTabFXs);
 	}
-	
+
 	/**
 	 * Get the number of tabs currently open.
 	 * @return the number of tabs.
@@ -391,7 +391,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 	public int getNumTabs(){
 		return mainTabPane.getTabs().size();
 	}
-	
+
 	/**
 	 * Get a tab
 	 * @param i - tab index
@@ -400,16 +400,16 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 	public PamGuiTabFX getTab(int i){
 		return (PamGuiTabFX) mainTabPane.getTabs().get(i);
 	}
-	
+
 	/**
 	 * Select a tab
 	 * @param j - index 
 	 */
 	public void selectTab(int j) {
 		this.mainTabPane.getSelectionModel().select(j);
-		
+
 	}
-	
+
 
 	/**
 	 * Create the tool bar pane. The top of each tab content node contains a tool
@@ -423,24 +423,24 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 	 *
 	 */
 	public class ToolBarPane extends PamBorderPane {
-		
+
-		
+
 		/**
 		 * Record/batch process button. In real time starts/stops data acquisition. In viewer mode
 		 * opens the batch run manager to allow batch processing of data e.g. reclassifying clicks. 
 		 */
 		private PamButton recordButton;
-		
+
 		/**
 		 *Play/pause button. Plays back sound in real time/viewer mode. 
 		 */
 		private PamButton playButton;
-		
+
 		/**
 		 * Holds all extra controls in the toolbar. 
 		 */
 		private PamHBox centerHBox;
-		
+
 		/**
 		 * Height of the toolbar. 
 		 */
@@ -466,59 +466,76 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 		 * Button to select what autosort option for windows. 
 		 */
 		private MenuButton autoSortChoice;
-	
+
 		public ToolBarPane(PamGuiTabFX pamGuiTab){
 			super();
-			
-			this.pamGuiTab=pamGuiTab;
-		
-			//create record and play buttons. 
-			PamHBox playControls=new PamHBox();
-			recordButton=new PamButton();
-//			recordButton.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.CIRCLE, Color.LIMEGREEN, PamGuiManagerFX.iconSize));
-			recordButton.setGraphic(PamGlyphDude.createPamIcon("mdi2r-record-circle", Color.RED, PamGuiManagerFX.iconSize));
-			recordButton.getStyleClass().add("transparent-button");
-			
-			//recordButton.setStyle(" -fx-background-radius: 50;");
-			
-			recordButton.setOnAction((action)->{
-				if (PamController.getInstance().getPamStatus()==PamController.PAM_RUNNING){
-					PamController.getInstance().pamStop();
-					pamGuiManagerFX.setPamRunning(false);
-				}
-				else {
-					PamController.getInstance().pamStart();
-					pamGuiManagerFX.setPamRunning(true);
-					
-				}
-			});
 
-			playButton=new PamButton();
+			this.pamGuiTab=pamGuiTab;
-//			playButton.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.PLAY, Color.BLACK, PamGuiManagerFX.iconSize));
+
-			playButton.setGraphic(PamGlyphDude.createPamIcon("mdi2p-play", Color.BLACK, PamGuiManagerFX.iconSize));
+			PamHBox analysisControls=new PamHBox();
-			playButton.getStyleClass().add("transparent-button");
+			analysisControls.setSpacing(10);
-			//playButton.setStyle(" -fx-background-radius: 50;");
+			analysisControls.setPadding(new Insets(0,10,0,20));
-			playButton.setOnAction((action)->{
+			//			playControls.getStyleClass().add("pane-opaque");
-				//TODO
+			analysisControls.setPrefHeight(prefHeight);
-				//start pamguard
+			analysisControls.setAlignment(Pos.CENTER);
-				//PamController.getInstance().pamStart();
+
-			});
+			if (PamController.getInstance().getRunMode() == PamController.RUN_PAMVIEW) {
-			
+				
-			
+				//in PMAGUard viewer mode we want a reporcess button 
-			playControls.getChildren().addAll(recordButton,playButton);
+
-			playControls.setSpacing(10);
+				PamButton reProcessButton=new PamButton("Reprocess...");
-			playControls.setPadding(new Insets(0,10,0,20));
+				reProcessButton.setGraphic(PamGlyphDude.createPamIcon("mdi2c-cog-transfer", PamGuiManagerFX.iconSize));
-//			playControls.getStyleClass().add("pane-opaque");
+				reProcessButton.setOnAction((action->{
-			playControls.setPrefHeight(prefHeight);
+					
-			playControls.setAlignment(Pos.CENTER);
+				}));
-			
+
+				
+				analysisControls.getChildren().addAll(reProcessButton);
+
+			}
+			else {
+				//real time mode
+				//create record and play buttons. 
+				recordButton=new PamButton();
+				//			recordButton.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.CIRCLE, Color.LIMEGREEN, PamGuiManagerFX.iconSize));
+				recordButton.setGraphic(PamGlyphDude.createPamIcon("mdi2r-record-circle", Color.RED, PamGuiManagerFX.iconSize));
+				recordButton.getStyleClass().add("transparent-button");
+				recordButton.setStyle("-fx-padding: 0 10 0 10;"); 
+				//recordButton.setStyle(" -fx-background-radius: 50;");
+
+				recordButton.setOnAction((action)->{
+					if (PamController.getInstance().getPamStatus()==PamController.PAM_RUNNING){
+						PamController.getInstance().pamStop();
+						pamGuiManagerFX.setPamRunning(false);
+					}
+					else {
+						PamController.getInstance().pamStart();
+						pamGuiManagerFX.setPamRunning(true);
+					}
+				});
+
+				//			playButton=new PamButton();
+				////			playButton.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.PLAY, Color.BLACK, PamGuiManagerFX.iconSize));
+				//			playButton.setGraphic(PamGlyphDude.createPamIcon("mdi2p-play", Color.BLACK, PamGuiManagerFX.iconSize));
+				//			playButton.getStyleClass().add("transparent-button");
+				//			//playButton.setStyle(" -fx-background-radius: 50;");
+				//			playButton.setOnAction((action)->{
+				//				//TODO
+				//				//start pamguard
+				//				//PamController.getInstance().pamStart();
+				//			});
+
+				analysisControls.getChildren().addAll(recordButton);
+
+			}
+
 			//create window editing button. This holds a toggle to edit windows and options. 
 			rightHBox=new PamHBox();
 			rightHBox.setAlignment(Pos.CENTER_LEFT);
 			rightHBox.setPadding(new Insets(0,10,0,20));
 			rightHBox.setSpacing(5);
-//			rightHBox.getStyleClass().add("pane-opaque");
+			//			rightHBox.getStyleClass().add("pane-opaque");
-			
+
 			editWindows=new ToggleSwitch("Resize"); 
 			//HACK,
 			editWindows.setPadding(new Insets(8,0,0,0));
@@ -527,56 +544,56 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 				boolean editable=!pamGuiTab.getEditable();
 				pamGuiTab.setPanesEditable(editable);
 			});
-			
+
 			//add a choice box to allow users to automatically resize windows. 
 			autoSortChoice=new MenuButton();
 			autoSortChoice.getStyleClass().add("transparent-button");
-//			autoSortChoice.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.ELLIPSIS_V, 
+			//			autoSortChoice.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.ELLIPSIS_V, 
 			autoSortChoice.setGraphic(PamGlyphDude.createPamIcon("mdi2d-dots-vertical", 
 					Color.DARKGRAY, PamGuiManagerFX.iconSize));
-			
+
 			MenuItem tile=new MenuItem("Tile");
 			tile.setOnAction((action)->{
 				pamGuiTab.autoSortPanes(PamGuiTabFX.SORT_TILE);
 			});
-			
+
 			MenuItem vertical=new MenuItem("Horizontal");
 			vertical.setOnAction((action)->{
 				pamGuiTab.autoSortPanes(PamGuiTabFX.SORT_HORIZONTAL);
 			});
-			
+
 			MenuItem horizontal=new MenuItem("Vertical");
 			horizontal.setOnAction((action)->{
 				pamGuiTab.autoSortPanes(PamGuiTabFX.SORT_VERTICAL);
 			});
-			
+
 			autoSortChoice.getItems().addAll(tile, vertical, horizontal); 
-			
+
 			rightHBox.getChildren().addAll(editWindows, autoSortChoice);
 
-			
+
 			//create content hboc for extra controls.
 			centerHBox=new PamHBox();
 			centerHBox.setSpacing(10);
 			//need to set this style to prevent the pane form being transparent. 
 			//centerHBox.getStyleClass().add("pane-opaque");
 			centerHBox.setPrefHeight(prefHeight);
-			
+
 			this.setCenter(centerHBox);
-			this.setLeft(playControls);
+			this.setLeft(analysisControls);
 			this.setRight(rightHBox);
-			
+
 			this.setPrefHeight(prefHeight);
 			this.getStyleClass().add("pane-opaque");
 
 
 			//this.setPadding(new Insets(0,0,0,0));
-			
+
 			this.toFront();
 
 		}
-		
+
-		
+
 		/**
 		 * Get the content HBox. This holds any extra controls in the top tool bar. 
 		 * @return HBox to add extra toolbar content to. 
@@ -584,7 +601,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 		public PamHBox getCenterHBox(){
 			return centerHBox;
 		}
-		
+
 		/**
 		 * Add a node to the content area of the toolbar. 
 		 * @param node - node to add. 
@@ -592,7 +609,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 		public void addToolbarNode(Node node){
 			centerHBox.getChildren().add(node);
 		}
-		
+
 		/**
 		 * Get the button which starts and stops PAMGUARD. 
 		 * @return the button. 
@@ -600,7 +617,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 		public Button getRecordButton(){
 			return recordButton; 
 		}
-		
+
 		/**
 		 * Get the HBox on the right hand side of the toolbar. 
 		 * @return hbox on right hand side of display. 
@@ -616,7 +633,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 
 
 		/**
-		 * Show the controls which allows manula resizing of the pane. 
+		 * Show the controls which allows manual resizing of the pane. 
 		 * @param resize. 
 		 */
 		public void showResizableControl(boolean resize) {
@@ -627,7 +644,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 		}
 
 	}
-	
+
 	/**
 	 * Get all record buttons from the different toolbars in this stage.
 	 * @return list of record buttons. 
@@ -640,7 +657,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 		}
 		return buttons; 
 	}
-	
+
 	/**
 	 * Remove an internal pane if it is contained within any tabs within the PamGuiFX
 	 * @param removeNode - remove the pane if it contains this node. 
@@ -651,7 +668,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 			tabs.get(i).removeInternalPane(removeNode);
 		}
 	}
-	
+
 	/**
 	 * Show the PamLoadPnae- this shows the pane that contains progress bars for loading data.
 	 * @param show - true to show pane. 
@@ -676,13 +693,13 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 	 * @param pamTaskUpdate - information on a thread which s currently doing some work. 
 	 */
 	public void notifyLoadProgress(PamTaskUpdate pamTaskUpdate) {
-		 Platform.runLater (() -> this.loadPane.updateLoadPane(pamTaskUpdate));
+		Platform.runLater (() -> this.loadPane.updateLoadPane(pamTaskUpdate));
 	}
 
 	@Override
 	public void pamStarted() {
 		this.pamGuiManagerFX.pamStarted();
-		
+
 	}
 
 	@Override
@@ -693,19 +710,19 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 	@Override
 	public void modelChanged(int changeType) {
 		// TODO Auto-generated method stub
-		
+
 	}
 
 	@Override
 	public void addControlledUnit(PamControlledUnit unit) {
 		this.pamGuiManagerFX.addControlledUnit(unit);
-		
+
 	}
 
 	@Override
 	public void removeControlledUnit(PamControlledUnit unit) {
 		this.pamGuiManagerFX.removeControlledUnit(unit);
-		
+
 	}
 
 	@Override
@@ -716,7 +733,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 	@Override
 	public void setTitle(String title) {
 		// TODO Auto-generated method stub
-		
+
 	}
 
 	@Override
@@ -733,7 +750,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 	@Override
 	public void enableGUIControl(boolean enable) {
 		// TODO Auto-generated method stub
-		
+
 	}
 
 	/**
@@ -769,7 +786,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 	public PamVBox getSidePane() {
 		return sidePaneContent;
 	}
-	
+
 	/**
 	 * Show the side pane. The side pane holds extra quick access
 	 * controls for modules. 
@@ -778,7 +795,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 	public void showSidePane(boolean show) {
 		this.hidingSidePane.showHidePane(show);
 	}
-	
+
 	/**
 	 * Rename a tab at a selected index. 
 	 * @param selectedItem - the new name

src/pamViewFX/PamLauncherPane.java

@@ -1,15 +1,9 @@
 package pamViewFX;
 
 import java.net.MalformedURLException;
-import java.net.URL;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
-import atlantafx.base.controls.ToggleSwitch;
-import atlantafx.base.theme.PrimerDark;
-import atlantafx.base.theme.PrimerLight;
-import javafx.application.Application;
-import javafx.application.Platform;
 import javafx.geometry.Insets;
 import javafx.geometry.Pos;
 import javafx.scene.control.ContentDisplay;
@@ -96,7 +90,16 @@ public class PamLauncherPane extends PamBorderPane {
 //        this.getStylesheets().add(getClass().getResource(primerPAMGuard).toExternalForm());
 //        this.getStylesheets().add(getClass().getResource(new PrimerDark().getUserAgentStylesheet()).toExternalForm());
 		PamStylesManagerFX.getPamStylesManagerFX().setCurStyle(new PamDefaultStyle());
-		
+	}
+	
+	private void setStyle(boolean PAMGuardFX) {
+		this.getStylesheets().clear();
+
+		if (PAMGuardFX) {
+			PamStylesManagerFX.getPamStylesManagerFX().setCurStyle(new PamAtlantaStyle());
+	        this.getStylesheets().addAll(PamStylesManagerFX.getPamStylesManagerFX().getCurStyle().getDialogCSS());
+	        this.setStyle("-fx-background-color: -fx-darkbackground");
+		}
 
 	}
 

src/pamViewFX/PamSettingsMenuPane.java

@@ -42,7 +42,6 @@ import javafx.scene.control.ToggleButton;
 import javafx.scene.control.ToggleGroup;
 import javafx.scene.control.Tooltip;
 import javafx.scene.layout.Priority;
-import javafx.scene.paint.Color;
 
 /**
  * Pane which holds settings menu. All primary settings are accessed from this pane which sits in a hiding pane to the right 

src/pamViewFX/fxStyles/PamAtlantaStyle.java

@@ -4,6 +4,8 @@ import java.util.ArrayList;
 
 import PamView.ColourScheme;
 import PamView.PamColors;
+import atlantafx.base.theme.CupertinoDark;
+import atlantafx.base.theme.CupertinoLight;
 import atlantafx.base.theme.PrimerDark;
 import atlantafx.base.theme.PrimerLight;
 
@@ -53,6 +55,7 @@ public class PamAtlantaStyle extends PamDefaultStyle {
 	// private String guiCSS = new NordDark().getUserAgentStylesheet();
 //	protected String primerlight = "/Resources/css/primer-light.css";
 	protected String primerlight = new PrimerLight().getUserAgentStylesheet();
+//	protected String primerlight = new CupertinoLight().getUserAgentStylesheet();
 
 	/**
 	 * Relative location of the CSS style sheet to be used for the Pamguard standard
@@ -62,6 +65,7 @@ public class PamAtlantaStyle extends PamDefaultStyle {
 	// private String dialogCSS = new PrimerDark().getUserAgentStylesheet();
 //	protected String primerdark = "/Resources/css/primer-dark.css";
 	protected String primerdark = new PrimerDark().getUserAgentStylesheet();
+//	protected String primerdark = new CupertinoDark().getUserAgentStylesheet();
 
 	
 	/**

src/test/rawDeepLearningClassifier/ClickDLTest.java

@@ -7,6 +7,7 @@ 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.jpamutils.wavFiles.AudioData;
 import org.jamdev.jdl4pam.transforms.DLTransform.DLTransformType;
 import org.junit.jupiter.api.Test;
 
@@ -31,7 +32,7 @@ public class ClickDLTest {
 		System.out.println("*****Click classification Deep Learning C*****"); 
 
 		//relative paths to the resource folders.		
-		String relModelPath  =	"./src/test/resources/rawDeepLearningClassifier/Generic/risso_click/updated_model/saved_model.pb";
+		String relModelPath  =	"./src/test/resources/rawDeepLearningClassifier/Generic/risso_click/uniform_model/saved_model.pb";
 		String clicksPath  =	"./src/test/resources/rawDeepLearningClassifier/Generic/risso_click/clicks.mat";
 
 		Path path = Paths.get(relModelPath);
@@ -45,14 +46,17 @@ public class ClickDLTest {
 		//create the transforms. 
 		ArrayList<DLTransfromParams> dlTransformParamsArr = new ArrayList<DLTransfromParams>();
 
-		dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.NORMALISE_WAV)); 
+		//waveform transforms. 
-				
+		dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.DECIMATE_SCIPY, 248000.)); 
+		dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.PEAK_TRIM, 128, 1)); 
+		dlTransformParamsArr.add(new SimpleTransformParams(DLTransformType.NORMALISE_WAV, 0., 1, AudioData.ZSCORE)); 
+		
 		genericModelParams.dlTransfromParams = dlTransformParamsArr;
 		genericModelParams.dlTransfroms = DLTransformsFactory.makeDLTransforms((ArrayList<DLTransfromParams>)genericModelParams.dlTransfromParams); 
 		
 		//create the clicks. 
 		path = Paths.get(clicksPath);
-		ArrayList<GroupedRawData> clicks = importClicks(path.toAbsolutePath().normalize().toString(),  SAMPLE_RATE); 
+		ArrayList<PredGroupedRawData> clicks = importClicks(path.toAbsolutePath().normalize().toString(),  SAMPLE_RATE); 
 		
 		//prep the model
 		genericModelWorker.prepModel(genericModelParams, null);
@@ -61,20 +65,22 @@ public class ClickDLTest {
 
 		ArrayList<GroupedRawData> groupedData = new ArrayList<GroupedRawData>();
 		
-		int i=0;
+		for (int i=0; i<1; i++) {
 		
-		float prediction = 0; 
+			float prediction = (float) clicks.get(i).getPrediction()[0]; 
-
+	
-		groupedData.add(clicks.get(i)); //TODO for loop
+			groupedData.add(clicks.get(i)); //TODO for loop
-
+	
-		System.out.println("Waveform input: " + groupedData.get(i).getRawData().length + " " + groupedData.get(i).getRawData()[0].length);
+			//System.out.println("Waveform input: " + groupedData.get(i).getRawData().length + " " + groupedData.get(i).getRawData()[0].length);
+			
+			ArrayList<StandardPrediction> genericPrediction = genericModelWorker.runModel(groupedData,SAMPLE_RATE, 0);		
+	
+			float[] output = genericPrediction.get(i).getPrediction();
+			
+			System.out.println(String.format("Click %d Predicted output: %.2f true output: %.2f passed: %b", clicks.get(i).getUID(),
+					output[0], prediction, output[0]>prediction*0.9 && output[0]<prediction*1.1)); 
 		
-		ArrayList<StandardPrediction> genericPrediction = genericModelWorker.runModel(groupedData,SAMPLE_RATE, 0);		
+		}
-
-		float[] output = genericPrediction.get(0).getPrediction();
-		
-		System.out.println(String.format("Click %d Predicted output: %.2f true output: %.2f passed: %b", clicks.get(i).getUID(),
-				output[0], prediction, output[0]>prediction*0.9 && output[0]<prediction*1.1)); 
 
 		
 	}
@@ -82,7 +88,7 @@ public class ClickDLTest {
 	/**
 	 * Import a bunch of clicks from a .mat file
 	 */
-	public static ArrayList<GroupedRawData> importClicks(String filePath, float sR) {
+	public static ArrayList<PredGroupedRawData> importClicks(String filePath, float sR) {
 
 		try {
 			 Mat5File mfr = Mat5.readFromFile(filePath);
@@ -91,9 +97,9 @@ public class ClickDLTest {
 			Struct mlArrayRetrived = mfr.getStruct( "clickpreds" );
 
 			int numClicks= mlArrayRetrived.getNumCols();
-			ArrayList<GroupedRawData> clicks = new ArrayList<GroupedRawData>(numClicks); 
+			ArrayList<PredGroupedRawData> clicks = new ArrayList<PredGroupedRawData>(numClicks); 
 
-			GroupedRawData clickData;
+			PredGroupedRawData clickData;
 			for (int i=0; i<numClicks; i++) {
 				Matrix clickWav= mlArrayRetrived.get("wave", i);
 				
@@ -107,10 +113,12 @@ public class ClickDLTest {
 				Matrix channelMap= mlArrayRetrived.get("channelMap", i);
 				Matrix startSample= mlArrayRetrived.get("startSample", i);
 				Matrix sampleDuration= mlArrayRetrived.get("sampleDuration", i);
+				Matrix pred= mlArrayRetrived.get("pred", i);
 
-				clickData = new GroupedRawData(clickmillis.getLong(0), channelMap.getInt(0), startSample.getLong(0), sampleDuration.getLong(0), sampleDuration.getInt(0));
+				clickData = new PredGroupedRawData(clickmillis.getLong(0), channelMap.getInt(0), startSample.getLong(0), sampleDuration.getLong(0), sampleDuration.getInt(0));
 				clickData.setUID(clickUID.getLong(0));
 				clickData.setRawData(clickwaveform);
+				clickData.setPrediction(new double[] {pred.getDouble(0), pred.getDouble(1)});
 				
 				clicks.add(clickData); 
 			}
@@ -124,5 +132,25 @@ public class ClickDLTest {
 		}
 	}
 	
+	public static class PredGroupedRawData extends GroupedRawData {
+		
+		private double[] prediction;
+		
+		public double[] getPrediction() {
+			return prediction;
+		}
+
+		public void setPrediction(double[] prediction) {
+			this.prediction = prediction;
+		}
+
+		public PredGroupedRawData(long timeMilliseconds, int channelBitmap, long startSample, long duration, int samplesize) {
+			super(timeMilliseconds,  channelBitmap,  startSample,  duration,  samplesize);
+		}
+		
+		
+		
+	}
+	
 	
 }

src/test/rawDeepLearningClassifier/DelphinIDTest.java

@@ -218,8 +218,7 @@ public class DelphinIDTest {
 				//the values for the whistle detector.
 				double[][] pamguardWhistleImage = 	whistleScatter2Image(whistleValues);
 	
-				
+				//System.out.println("Size python: " + compressedWhistleImage.length + " x " + compressedWhistleImage[0].length);
-				System.out.println("Size python: " + compressedWhistleImage.length + " x " + compressedWhistleImage[0].length);
 				
 				float[][][] input = new float[1][][];
 				input[0] =  JamArr.doubleToFloat(compressedWhistleImage);
@@ -255,7 +254,6 @@ public class DelphinIDTest {
 		
 		System.out.println("DelphinID mode test end");
 
-
 	}
 
 

src/wavFiles/WavFile.java

@@ -1,23 +1,10 @@
 package wavFiles;
 
-import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.io.RandomAccessFile;
-
 import javax.swing.JOptionPane;
 
-//import org.kc7bfi.jflac.util.ByteData;
-import org.jflac.util.ByteData;
-
 import clickDetector.WindowsFile;
-import java.io.ByteArrayInputStream;
-import java.util.Arrays;
-
-import javax.sound.sampled.AudioFileFormat;
 import javax.sound.sampled.AudioFormat;
-import javax.sound.sampled.AudioInputStream;
-import javax.sound.sampled.AudioSystem;
 
 public class WavFile {