Fixed display bug.

Fixed several display bugs including predictions not showing on PAMGuard stop start.

.classpath

@@ -6,8 +6,9 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-21">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jdk-21.0.2.13-hotspot">
 		<attributes>
+			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>

src/PamModel/PamModel.java

@@ -502,7 +502,8 @@ final public class PamModel implements PamSettings {
 		mi.setModulesMenuGroup(sensorsGroup);
 		mi.setToolTipText("Imports CPOD data");
 		mi.setHidden(SMRUEnable.isEnable() == false);
-		
+		mi.addGUICompatabilityFlag(PamGUIManager.FX); //has FX enabled GUI.
+
 		/*
 		 * ************* Start Displays  Group *******************
 		 */

src/Resources/css/primer-pamguard.css

@@ -234,7 +234,8 @@
 .popover > .content {
     -fx-background-color: -fx-darkbackground;     
     -fx-background-radius: 5;
-    -fx-border-radius: 5;                   
+    -fx-border-radius: 5;       
+    -fx-padding: 0 0 0 0;               
 }
 
 .popover > .arrow {

src/cpod/dataPlotFX/CPODDDDataInfo.java

@@ -60,7 +60,12 @@ public class CPODDDDataInfo extends DDDataInfo<CPODClick> {
 		public void setupAxis(PamDataUnit data, double sR, DetectionPlotProjector plotProjector) {
 			super.setupAxis(data, sR, plotProjector);
 			
+
 			CPODClick click = (CPODClick) data;
+			if (click.getWaveData()==null) {
+				return;
+			}
+			
 			double lenMS = (1000.*click.getWaveData()[0].length)/FPODReader.FPOD_WAV_SAMPLERATE;
 			//set the scroller minimum and maximum 
 			plotProjector.setMinScrollLimit(0);
@@ -68,7 +73,6 @@ public class CPODDDDataInfo extends DDDataInfo<CPODClick> {
 			plotProjector.setMaxScrollLimit(lenMS);
 			plotProjector.setEnableScrollBar(true);
 			
-			
 			plotProjector.setAxisMinMax(0, 250, Side.BOTTOM);
 		}
 
@@ -89,7 +93,6 @@ public class CPODDDDataInfo extends DDDataInfo<CPODClick> {
 
 		public CPODWaveformPlot(DetectionPlotDisplay detectionPlotDisplay) {
 			super(detectionPlotDisplay);
-			// TODO Auto-generated constructor stub
 		}
 
 		@Override

src/cpod/dataPlotFX/CPODPlotInfoFX.java

@@ -325,7 +325,6 @@ public class CPODPlotInfoFX extends GenericDataPlotInfo {
 				y2= tdProjector.getYPix(nycl); 
 
 				break; 
-
 			}
 
 			if (tdProjector.getOrientation()==Orientation.VERTICAL){
@@ -381,12 +380,14 @@ public class CPODPlotInfoFX extends GenericDataPlotInfo {
 		@Override
 		public PamSymbolFX getPamSymbol(PamDataUnit dataUnit, int type) {
 			PamSymbolFX symbol =  super.getPamSymbol(dataUnit, type);
+			
 			if (((CPODClick) dataUnit).getWaveData()!=null && type!=TDSymbolChooserFX.HIGHLIGHT_SYMBOL) {
 				symbol.setLineColor(symbol.getFillColor().darker());
 				symbol.setHeight(symbol.getHeight()*1.5);
 				symbol.setWidth(symbol.getWidth()*1.5);
+				return symbol;
 			}
-			
+						
 			return symbol;
 
 		}

src/cpod/dataPlotFX/CPODTDSettingsPane.java

@@ -46,7 +46,7 @@ public class CPODTDSettingsPane implements TDSettingsPane {
 	public CPODTDSettingsPane(CPODPlotInfoFX cpodPlotInfoFX) {
 		this.cpodPlotInfoFX=cpodPlotInfoFX; 
 		mainPane = createMainPane(); 
-		mainPane.setPrefWidth(330);
+		mainPane.setPrefWidth(400);
 	}
 
 	/**

src/cpod/fx/CPODGUIFX.java

@@ -10,12 +10,12 @@ import pamViewFX.PamControlledGUIFX;
 public class CPODGUIFX extends PamControlledGUIFX {
 	
 	/**
-	 * The dl control. 
+	 * Reference to the CPOD control. 
 	 */
-	private CPODControl2 dlControl;
+	private CPODControl2 cpodControl;
 
 	public CPODGUIFX(CPODControl2 cpodControl2) {
-		// TODO Auto-generated constructor stub
+		cpodControl = cpodControl2; 
 	}
 
 	
@@ -27,19 +27,19 @@ public class CPODGUIFX extends PamControlledGUIFX {
 	 * @return a Pane containing controls to change settings for module.
 	 */
 	public SettingsPane<?> getSettingsPane(){
-		dlControl.getSettingsPane().setParams(dlControl.getCPODParam());
+		cpodControl.getSettingsPane().setParams(cpodControl.getCPODParam());
-		return dlControl.getSettingsPane();
+		return cpodControl.getSettingsPane();
 	}
 	
 	
 	@Override
 	public void updateParams() {
-		CPODParams newParams=dlControl.getSettingsPane().getParams(dlControl.getCPODParam()); 
+		CPODParams newParams=cpodControl.getSettingsPane().getParams(cpodControl.getCPODParam()); 
 		if (newParams!=null) {
-			dlControl.setCPODParams(newParams);
+			cpodControl.setCPODParams(newParams);
 		}
 		//setup the controlled unit. 
-		dlControl.setupControlledUnit(); 
+		cpodControl.setupControlledUnit(); 
 	}
 	
 	@Override

src/dataGram/DatagramManager.java

@@ -539,6 +539,8 @@ public class DatagramManager {
 			else {
 				PamController.getInstance().notifyTaskProgress(
 						new SimplePamTaskUpdate("Finished Datagram Mapping", PamTaskUpdate.STATUS_DONE));
+				publish(new DatagramProgress(PamTaskUpdate.STATUS_DONE, 1, 1));
+
 			}
 		}
 

src/dataGram/DatagramProgress.java

@@ -77,8 +77,7 @@ public class DatagramProgress extends PamTaskUpdate {
 	}
 
 	@Override
-	public double getProgress() {
+	public double getProgress2() {
-		System.out.println("DatagramProgress: " + processedUnits + " tot: " + totalUnits); 
 		double progress= ProgressIndicator.INDETERMINATE_PROGRESS;
 		switch(getStatus()) {
 		case DatagramProgress.STATUS_BLOCKCOUNT:
@@ -95,13 +94,17 @@ public class DatagramProgress extends PamTaskUpdate {
 			else progress=0; 
 			break;
 		}
+		
+		//System.out.println("DatagramProgress: " + processedUnits + " tot: " + totalUnits + " progress: " + progress); 
+
 		return progress;
 	}
 	
 	@Override
-	public double getProgress2(){
+	public double getProgress(){
+		//seems like the current point is simply the percentage done...
 		double progress;
-		if (pointsToUpdate>0) progress=((double)currentPoint)/pointsToUpdate;
+		if (pointsToUpdate>0) progress=((double)currentPoint)/100.;
 		else progress=0; 
 		switch(getStatus()) {
 		case DatagramProgress.STATUS_BLOCKCOUNT:
@@ -110,14 +113,16 @@ public class DatagramProgress extends PamTaskUpdate {
 			progress=0; 
 			break;
 		case DatagramProgress.STATUS_STARTINGFILE:
-			progress=((double)currentPoint)/pointsToUpdate;
+			progress=((double)currentPoint)/100.;
 			break;
 		case DatagramProgress.STATUS_ENDINGFILE:
-			progress=((double)currentPoint)/pointsToUpdate;
+			progress=((double)currentPoint)/100.;
 			break;
 		case DatagramProgress.STATUS_UNITCOUNT:	
 			break;
 		}
+		//System.out.println("DatagramProgress2: " + currentPoint + " tot: " + pointsToUpdate + " progress: " + progress); 
+
 		return progress;
 	}
 	

src/dataModelFX/connectionNodes/ModuleIconFactory.java

@@ -2,6 +2,7 @@ package dataModelFX.connectionNodes;
 
 import dataModelFX.DataModelStyle;
 import javafx.scene.Node;
+import javafx.scene.control.Label;
 import javafx.scene.image.Image;
 import javafx.scene.image.ImageView;
 import javafx.scene.layout.StackPane;
@@ -35,7 +36,7 @@ public class ModuleIconFactory {
 	public enum ModuleIcon {
 		DATAMAP, NMEA, GPS, MAP, SOUND_AQ, SOUND_OUTPUT, FFT, FILTER, CLICK, CLICK_TRAIN, RECORDER, WHISTLE_MOAN,
 		NOISE_BAND, NOISE_FILT, DATABASE, BINARY, TIME_DISPLAY, DETECTION_DISPLAY, ARRAY, DEEP_LEARNING, MATCHED_CLICK_CLASSIFIER,
-		DECIMATOR
+		DECIMATOR, CPOD
 	}
 
 	/**
@@ -126,6 +127,9 @@ public class ModuleIconFactory {
 		case DECIMATOR:
 			iconNode = getSVGIcon("/Resources/modules/decimator.svg"); 
 			break;
+		case CPOD:
+			iconNode = new Label("CPOD"); //TEMP
+			break;
 		default:
 			break;
 		}
@@ -261,6 +265,9 @@ public class ModuleIconFactory {
 		case "decimator.DecimatorControl":
 			icon=ModuleIcon.DECIMATOR; 
 			break; 
+		case "cpod.CPODControl2":
+			icon=ModuleIcon.CPOD; 
+			break; 
 		}
 		return icon;
 	}

src/dataPlotsFX/data/TDDataInfoFX.java

@@ -12,6 +12,7 @@ import javafx.scene.canvas.GraphicsContext;
 import javafx.scene.shape.Polygon;
 import PamController.PamController;
 import PamUtils.Coordinate3d;
+import PamUtils.PamCalendar;
 import PamUtils.PamUtils;
 import PamView.HoverData;
 import PamView.GeneralProjector.ParameterType;
@@ -373,8 +374,8 @@ public abstract class TDDataInfoFX {
 	 */
 	public void drawAllDataUnits(int plotNumber, GraphicsContext g, double scrollStart, TDProjectorFX tdProjector) {
 		
-//		System.out.println("Max double value: " +  PamCalendar.formatDateTime((long)  Double.MAX_EXPONENT)); 
+//		System.out.println("Max double value: " + this.getDataName() +  PamCalendar.formatDateTime((long)  Double.MAX_EXPONENT)); 
-//		System.out.println("Max long value: " +  PamCalendar.formatDateTime((long)  Long.MAX_VALUE)); 
+//		System.out.println("Max long value: " + this.getDataName() + PamCalendar.formatDateTime((long)  Long.MAX_VALUE)); 
 
 		
 		PamDataUnit dataUnit = null;
@@ -391,7 +392,10 @@ public abstract class TDDataInfoFX {
 //			scrollStart = PamCalendar.getTimeInMillis();
 			//work out start and stop times
 			long loopEnd = (long) (scrollStart + (tdProjector.getVisibleTime() * 1.5));
-			long loopStart = (long) (scrollStart - (tdProjector.getVisibleTime() * .5));
+			long loopStart = (long) (scrollStart - (tdProjector.getVisibleTime() * 1.5));
+			
+//			System.out.println("Loop start: " + this.getDataName() +  PamCalendar.formatDateTime((long)  loopStart)); 
+//			System.out.println("Loop end: " + this.getDataName() + PamCalendar.formatDateTime((long)  loopEnd)); 
 
 			//find a number close to the index start, 			
 			ListIterator<PamDataUnit> it = getUnitIterator( loopStart,  plotNumber);
@@ -402,6 +406,7 @@ public abstract class TDDataInfoFX {
 				dataUnit = it.next();
 				count++; 
 				if (dataUnit!=null && shouldDraw(plotNumber, dataUnit)) {
+					
 					if (dataUnit.getEndTimeInMilliseconds() < loopStart) {
 						continue;
 					}
@@ -409,11 +414,13 @@ public abstract class TDDataInfoFX {
 						break;
 					}
 					
+					drawCalls++;
 					drawDataUnit(plotNumber, dataUnit, g,  scrollStart, 
 							tdProjector ,TDSymbolChooserFX.NORMAL_SYMBOL);
 				}
 			}
 			
+//			System.out.println("Found: " + drawCalls + "  " + this.getDataName() + "  to draw"); 
 			lastUnitDrawn(g, scrollStart, tdProjector, plotNumber); 
 		}
 		//System.out.println("Total data units: " + count+ " draw calls: " +drawCalls );

src/dataPlotsFX/data/generic/GenericLinePlotInfo.java

@@ -2,6 +2,7 @@ package dataPlotsFX.data.generic;
 
 import PamController.PamController;
 import PamUtils.Coordinate3d;
+import PamUtils.PamCalendar;
 import PamView.GeneralProjector;
 import PamView.HoverData;
 import PamView.symbol.PamSymbolChooser;
@@ -47,21 +48,18 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
 	}
 
 
-	
-
 	/* (non-Javadoc)
 	 * @see dataPlotsFX.data.TDDataInfoFX#drawDataUnit(int, PamguardMVC.PamDataUnit, javafx.scene.canvas.GraphicsContext, long, dataPlotsFX.projector.TDProjectorFX, int)
 	 */
 	@Override
 	public Polygon drawDataUnit(int plotNumber, PamDataUnit pamDataUnit, GraphicsContext g, double scrollStart,
 			TDProjectorFX tdProjector, int type) {
-
 			return drawPredicition(plotNumber, pamDataUnit, g, scrollStart, tdProjector, type);
-
 	}
 
+	
 	/**
-	 * Get the line data. Each double[] is a seperate line with N evenly spaced data points. 
+	 * Get the line data. Each double[] is a separate line with N evenly spaced data points. 
 	 * @param pamDataUnit - the pam data unit containing the data. 
 	 * @return the line data. 
 	 */
@@ -98,15 +96,12 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
 		double timeMillis = pamDataUnit.getTimeMilliseconds()+pamDataUnit.getDurationInMilliseconds()/2; 
 		double tC=tdProjector.getTimePix(timeMillis-scrollStart);
 
-
 		//draws lines so tc should be some slop in pixels. 
 		if (tC < -1000 || tC>tdProjector.getWidth()+1000) {
+			//System.out.println("Line is outside display " + tC);
 			return null;
 		}
 
-		//TODO -must sort out wrap
-		//dlControl.getDLParams().sampleHop; 
-
 		double dataPixel; 
 		Coordinate3d c; 
 		Color color;
@@ -128,16 +123,13 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
 				
 					//brighten the colour up. 
 					//color = Color.color(color.getRed()*0.8, color.getGreen()*0.8, color.getBlue()*0.8); 
-	
+//					System.out.println("TDDataInfoFX: tc: "+tC+ " dataUnitTime: "+PamCalendar.formatTime((long) timeMillis)+" scrollStart: "
-					//System.out.println("TDDataInfoFX: tc: "+tC+ " dataUnitTime: "+PamCalendar.formatTime(timeMillis)+" scrollStart: "
+//					+PamCalendar.formatTime((long) scrollStart)+" (timeMillis-scrollStart)/1000. "+((timeMillis-scrollStart)/1000.));
-					//+PamCalendar.formatTime((long) scrollStart)+" (timeMillis-scrollStart)/1000. "+((timeMillis-scrollStart)/1000.));
+				
-					
-	
 					c = tdProjector.getCoord3d(timeMillis, detData[i][j], 0);
 	
 					dataPixel = tdProjector.getYPix(detData[i][j]);
 	
-	
 					if (lastUnits[chan][i]==null) {
 						lastUnits[chan][i] = new Point2D(tC, dataPixel); 
 						g.fillOval(tC, dataPixel, 5,5);
@@ -147,7 +139,6 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
 						if (tC>lastUnits[chan][i].getX() && (!this.getTDGraph().isWrap() || 
 								(tC<tdProjector.getWidth()) && tC>=0 && lastUnits[chan][i].getX()<tdProjector.getWidth() && lastUnits[chan][i].getX()>0)) {
 							//in wrap mode we can get some weird effects with tC co-ordintates. Still have not quite cracked this...
-							
 //							if (Math.abs(tC - lastUnits[chan][i].getX())>100) {
 //								System.out.println("tC: " + tC + " lastUnits[i].getX(): " + lastUnits[chan][i].getX() 
 //										+ "  " + tdProjector. getTimeAxis().getPosition((timeMillis-scrollStart)/1000.) + "  " + tdProjector.getWidth());
@@ -155,12 +146,9 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
 							g.strokeLine(tC, dataPixel, lastUnits[chan][i].getX(), lastUnits[chan][i].getY());		
 						}
 						lastUnits[chan][i] = new Point2D(tC, dataPixel); 
-
 					}
 					tdProjector.addHoverData(new HoverData(c , pamDataUnit, 0, plotNumber));
-
 				}
-
 				//getSymbolChooser().getPamSymbol(pamDataUnit,type).draw(g, new Point2D(tC, dataPixel));
 			}
 		}
@@ -192,7 +180,8 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
 	 * @return the color for that prediciton
 	 */
 	public abstract LineInfo getColor(int i);
-
+	
+	
 	@Override
 	public Double getDataValue(PamDataUnit pamDataUnit) {
 		//this is not used because we have overridden the super drawing class. 
@@ -206,15 +195,13 @@ public abstract class GenericLinePlotInfo extends TDDataInfoFX {
 	 * @param changeType - notification flag.
 	 */
 	public void notifyChange(int changeType) {
-		//System.out.println("Prediction NOTIFYMODELCHANGED: "); 
+//	System.out.println("Prediction NOTIFYMODELCHANGED: " + changeType); 
 		switch (changeType) {
 		case PamController.CHANGED_PROCESS_SETTINGS:
 			lastUnits  = new Point2D[PamConstants.MAX_CHANNELS][];
-; 
 			break;
 		case PamController.RUN_NORMAL:
 			lastUnits  = new Point2D[PamConstants.MAX_CHANNELS][];
-
 			break;
 		case PamController.PAM_STOPPING:
 			lastUnits = new Point2D[PamConstants.MAX_CHANNELS][];

src/dataPlotsFX/layout/TDDisplayFX.java

@@ -615,9 +615,10 @@ public class TDDisplayFX extends PamBorderPane {
 	 * @param milliSeconds - the master clock position. 
 	 */
 	public void scrollDisplayEnd(long milliSeconds) {
+		
 
-		if (!isViewer() && milliSeconds <= lastUpdate && milliSeconds > lastUpdate - tdParametersFX.visibleTimeRange) {
+		if (!isViewer() && lastUpdate>0 && milliSeconds <= lastUpdate && milliSeconds > lastUpdate - tdParametersFX.visibleTimeRange) {
-			//System.out.println("milliSeconds <= lastUpdate && milliSeconds > lastUpdate - visibleRange");
+//			System.out.println("milliSeconds <= lastUpdate && milliSeconds > lastUpdate - visibleRange");
 			return;
 		}
 
@@ -849,7 +850,6 @@ public class TDDisplayFX extends PamBorderPane {
 
 		@Override
 		public void scrollValueChanged(AbstractPamScroller pamScroller) {
-			//			System.out.println("TDDisplayFX: Scroll Value changed: " +  System.currentTimeMillis());
 			//			System.out.println(String.format("Scroller value changed get start %s, End %s, pos %s", PamCalendar.formatTime(timeScrollerFX.getMinimumMillis()),
 			//					PamCalendar.formatTime(timeScrollerFX.getMaximumMillis()),PamCalendar.formatTime(timeScrollerFX.getValueMillis())));
 			//have to set the repaint wait millis param to zero or else when scroll bar is moved quickly painting does not occur correctly. 
@@ -1183,11 +1183,15 @@ public class TDDisplayFX extends PamBorderPane {
 			break;
 		}
 
+		//forces a repaint after any changes. 
+		lastUpdate=-1;
+		
 		if (tdGraphs != null) {
 			for (TDGraphFX tdg:tdGraphs) {
 				tdg.notifyModelChanged(changeType);
 			}
 		}
+		
 	}
 
 	/**

src/dataPlotsFX/layout/TDGraphFX.java

@@ -1124,7 +1124,7 @@ public class TDGraphFX extends PamBorderPane {
 		 * 
 		 */
 		public synchronized void repaint(long tm, int flag) {
-
+			
 			// clear the current canvas's
 			if (hasCanvas(flag, BASE_CANVAS)) {
 				baseCanvas.getGraphicsContext2D().clearRect(0, 0, baseCanvas.getWidth(), baseCanvas.getHeight());
@@ -1151,16 +1151,18 @@ public class TDGraphFX extends PamBorderPane {
 			boolean hasBase = false; 
 			synchronized (dataList) {
 				for (TDDataInfoFX dataInfo : dataList) {
+					
 					base = false;
+					
 					if (!dataInfo.isShowing()) {
-						// System.out.println("dataInfo.isShowing(): " + dataInfo.getDataName());
+						System.out.println("!dataInfo.isShowing(): " + dataInfo.getDataName());
 						continue;
 					}
 
 					scaleInfo = dataInfo.getScaleInfo();
 					if (scaleInfo == null) {
-						// System.out.println("scale info null " + dataInfo.getDataName() + "index:
+//						 System.out.println("scale info null " + dataInfo.getDataName() + "index:
-						// "+dataInfo.getScaleInfoIndex());
+//						 "+dataInfo.getScaleInfoIndex());
 						continue;
 					}
 
@@ -1183,7 +1185,7 @@ public class TDGraphFX extends PamBorderPane {
 					}
 					;
 
-					// ok so only repaint if we have the right CANVAS
+					// OK so only repaint if we have the right CANVAS
 					if (base && hasCanvas(flag, BASE_CANVAS)) {
 						paintDataUnits(gc, dataInfo, false);
 					} else if (!base && hasCanvas(flag, FRONT_CANVAS)) {
@@ -1287,6 +1289,7 @@ public class TDGraphFX extends PamBorderPane {
 			// PamDataBlock<PamDataUnit> dataBlock = dataInfo.getDataBlock();
 
 			// scroll start is the end of the display i.e. the last visible time in the past
+			
 			// in real time mode.
 			scrollStart = tdDisplay.getTimeScroller().getValueMillisD();
 
@@ -1524,7 +1527,7 @@ public class TDGraphFX extends PamBorderPane {
 	 * @param tm- if within millis of last repaint don't repaint
 	 */
 	public synchronized void repaint(long tm, int flag) {
-
+				
 		// Start of block moved over from the panel repaint(tm) function.
 		long currentTime = System.currentTimeMillis();
 		if (currentTime - lastTime < tm) {

src/dataPlotsFX/overlaymark/popUpMenu/TDPopUpMenuAdv.java

@@ -66,7 +66,8 @@ public class TDPopUpMenuAdv implements ExtPopMenu {
 		}
 		
 		if (PamGUIManager.isFX()) {
-			popOver.show(tdGraphFX.getScene().getWindow(), e.getScreenX(), e.getScreenY()); //FX
+			//TODO - need to shift by the distance to arrow- not arbitrary 40 pixels
+			popOver.show(tdGraphFX.getScene().getWindow(), e.getScreenX(), e.getScreenY()-40); //FX
 		}
 		else {
 			popOver.show(tdGraphFX, e.getScreenX(), e.getScreenY()); //Swing 

src/detectionPlotFX/rawDDPlot/RawSpectrumPlot.java

@@ -54,30 +54,7 @@ public class RawSpectrumPlot extends SpectrumPlot<PamDataUnit> {
 		plotProjector.setEnableScrollBar(true);
 	}
 
-
+	
-//	@Override
-//	public double[][] getPowerSpectrum(PamDataUnit data) {
-//		return ((RawDataHolder) data).getDataTransforms().getPowerSpectrum(((RawDataHolder) data).getWaveData()[0].length); 
-//	}
-//	@Override
-//	public double[][] getCepstrum(PamDataUnit data) {
-//		return ((RawDataHolder) data).getDataTransforms().getCepstrum(((RawDataHolder) data).getWaveData()[0].length); 
-//		//return data.getRawDataTransforms().getCepstrum(channel, cepLength)
-//	}
-
-
-
-//
-//	public ClickSpectrumPlot(DetectionPlotDisplay displayPlot) {
-//		super(displayPlot);
-//	}
-//	
-//	
-//	@Override
-//	public String getName() {
-//		return "Spectrum";
-//	}
-//	
 	/**
 	 * New click added to the display. 
 	 * @param newClick
@@ -169,18 +146,16 @@ public class RawSpectrumPlot extends SpectrumPlot<PamDataUnit> {
 	
 	@Override
 	public void paintPlot(PamDataUnit data, GraphicsContext gc, Rectangle rectangle, DetectionPlotProjector projector, int flag) {
-//		this.lastDataUnit=data;
+		
-		//System.out.println("Paint plot projector: "+ projector);
+		if (((RawDataHolder) data).getWaveData()==null) {
+			gc.clearRect(0, 0, rectangle.getWidth(), rectangle.getHeight());
+			return;
+		}
+		
 		if (flag== DetectionPlot.SCROLLPANE_DRAW) {
 			
-			
 			double[][] waveformTemp =  ((RawDataHolder) data).getWaveData();
 			
-			if (waveformTemp==null) return;
-			
-//			System.out.println("Spectrum plot: " +  "  "  + projector.getMinScrollLimit()  + "  " 
-//			+ projector.getMaxScrollLimit() + "  " + projector.getAxis(Side.TOP).getMaxVal() + "  wvfrm: " + WaveformPlot.getYScale(waveformTemp));
-			
 			WaveformPlot.paintWaveform(waveformTemp, data.getSequenceBitmap(),  gc,  rectangle,  0, waveformTemp[0].length,
 					WaveformPlot.getYScale(waveformTemp), null, true,  false);	
 		}

src/pamScrollSystem/LoadQueueProgressData.java

@@ -34,11 +34,13 @@ public class LoadQueueProgressData extends PamTaskUpdate {
 		this.loadEnd = loadEnd;
 		this.loadCurrent = loadCurrent;
 		this.nLoaded = nLoaded;
+		setDualProgressUpdate(true);
 	}
 	
 	public LoadQueueProgressData(int status) {
 		super();
 		this.setStatus(PamTaskUpdate.STATUS_DONE);
+		setDualProgressUpdate(true);
 	}
 
 
@@ -119,6 +121,7 @@ public class LoadQueueProgressData extends PamTaskUpdate {
 
 	@Override
 	public double getProgress() {		
+//		System.out.println( getStreamName() + " progress: " + iStream + " of " + totalStreams);
 		if (getStreamName() != null) {
 			return (double )iStream/ (double) totalStreams;
 		}
@@ -127,6 +130,7 @@ public class LoadQueueProgressData extends PamTaskUpdate {
 
 	@Override
 	public String getProgressString() {
+
 		if (getState() == LoadQueueProgressData.STATE_LINKINGSUBTABLE) {
 			return String.format("Linking subtable data %d of %d", 
 					getIStream(), getTotalStreams());
@@ -141,13 +145,15 @@ public class LoadQueueProgressData extends PamTaskUpdate {
 	} 
 	
 	@Override
-	public double getProgress2() {		
+	public double getProgress2() {	
+//		System.out.println( getStreamName() + " progress2: " + getLoadStart() );
 		long interval =getLoadEnd() - getLoadStart();
-		if (interval == 0) {
+		if (interval <= 0) {
 			return ProgressIndicator.INDETERMINATE_PROGRESS; 
 		}
 		else {
 			long done =getLoadCurrent() - getLoadStart();
+//			System.out.println( getStreamName() + " progress2: " + done + " " + interval + " start " + getLoadStart() + " end " + getLoadEnd())
 			return ((double) done )/ interval;
 		}
 	}

src/pamViewFX/PamGuiFX.java

@@ -252,7 +252,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 		/**create left hiding pane**/
 		loadPane=new PamLoadingPane(this.pamGuiManagerFX);
 		hidingLoadPane=new HidingPane(Side.TOP, loadPane, this, false);
-		hidingLoadPane.setPrefHeight(90);
+		hidingLoadPane.setPrefHeight(110);
 		hidingLoadPane.removeHideButton();
 		hidingLoadPane.showHidePane(false);
 		

src/rawDeepLearningClassifier/dataPlotFX/DLPredictionPlotInfoFX.java

@@ -210,7 +210,7 @@ public class DLPredictionPlotInfoFX extends GenericLinePlotInfo {
 	public Polygon drawDataUnit(int plotNumber, PamDataUnit pamDataUnit, GraphicsContext g, double scrollStart,
 			TDProjectorFX tdProjector, int type) {
 
-		//System.out.println("Get data type: " + getScaleInfo().getDataType()); 
+//		System.out.println("Get prediciton data type: " + getScaleInfo().getDataType()); 
 		if (getScaleInfo().getDataType().equals(ParameterType.FREQUENCY)) { // frequency data !
 			return drawFrequencyData(plotNumber, pamDataUnit, g, scrollStart, tdProjector, type);
 		}

src/rawDeepLearningClassifier/dlClassification/archiveModel/ArchiveModelWorker.java

@@ -113,8 +113,8 @@ public class ArchiveModelWorker extends GenericModelWorker {
 
 			//HACK there seems to be some sort of bug in ketos where the params input shape is correct but the model input shape is wrong. 
 			if (dlModel.getInputShape()==null || !dlModel.getInputShape().equals(modelParams.defaultInputShape)) {
-				System.out.println("Model input shape: " + modelParams.defaultInputShape);
+				System.err.println("Model input shape does not match: params: " + modelParams.defaultInputShape + " model: " + dlModel.getInputShape());
-				WarnOnce.showWarning("Model shape", "The model shape does not match the model metadata. \n Metadata shape will be used used.", WarnOnce.OK_OPTION);
+				//WarnOnce.showWarning("Model shape", "The model shape does not match the model metadata. \n Metadata shape will be used used.", WarnOnce.OK_OPTION);
 				dlModel.setInputShape(modelParams.defaultInputShape);
 			}
 

src/rawDeepLearningClassifier/dlClassification/genericModel/GenericPrediction.java

@@ -39,6 +39,12 @@ public class GenericPrediction implements PredictionResult {
 	public double analysisTime=0; 
 	
 
+	/**
+	 * Constructor for a typical generic prediciton. 
+	 * @param prob - the probability for each class. 
+	 * @param classNameID - the ID's of the class names.
+	 * @param isBinary - true if the model result passed a binary test (usually one species above a threshold)
+	 */
 	public GenericPrediction(float[] prob, short[] classNameID, boolean isBinary) {
 		this.prob=prob; 
 		this.classNameID = classNameID;

src/rawDeepLearningClassifier/logging/ModelResultBinaryFactory.java

@@ -115,7 +115,6 @@ public class ModelResultBinaryFactory {
 		try {
 
 			//System.out.println("Make model result: "); 
-
 			int type = dis.readByte(); 
 			boolean isBinary = dis.readBoolean(); 
 			double scale = dis.readFloat();
@@ -150,9 +149,7 @@ public class ModelResultBinaryFactory {
 				result = new GenericPrediction(data, isBinary); 
 				break; 
 			}
-
 			//System.out.println("New model result: "+ type); 
-
 			return result; 
 
 		} catch (IOException e) {