Rw improvement (#16)

* Update .project

* RWE imporvement to peak detection and dealing with smoothing.

* Make improvements to MARW edge detector so that it doesn't merge
harmonics, by using a threshold down from the peak as well as up from
the noise

.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-11">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
 		<attributes>
+			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>

.project

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
-	<name>PamGuard Main</name>
+	<name>PamGuard Main DG</name>
 	<comment></comment>
 	<projects>
 	</projects>

src/Acquisition/filedate/StandardFileDate.java

@@ -264,7 +264,8 @@ public class StandardFileDate implements FileDate, PamSettings {
 //			System.out.println(d);
 		} catch (ParseException e) {
 			// TODO Auto-generated catch block
-			e.printStackTrace();
+//			e.printStackTrace();
+			System.out.println(e.getMessage());
 		}  //throws ParseException if no match
 		setLastFormat(forcedDateFormat);
 		return d.getTime();

src/RightWhaleEdgeDetector/RWEControl.java

@@ -10,6 +10,7 @@ import javax.swing.JMenuItem;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 
+import KernelSmoothing.KernelSmoothingProcess;
 import PamController.PamControlledUnit;
 import PamController.PamControlledUnitSettings;
 import PamController.PamController;
@@ -20,6 +21,8 @@ import PamUtils.PamUtils;
 import PamView.GroupedDataSource;
 import PamView.GroupedSourceParameters;
 import PamView.dialog.GroupedSourcePanel;
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.ProcessAnnotation;
 
 /**
  * Exact implementation of the 2003 Right Whale detector I developed when I was 
@@ -85,6 +88,19 @@ public class RWEControl extends PamControlledUnit implements PamSettings {
 			rweProcess.setupProcesses();
 		}
 	}
+	
+	/**
+	 * Check that the input process has implemented kernel smoothing.
+	 * @param inputBlock input data block (should be fft data).  
+	 * @return true if kernel smoothing is in place. 
+	 */
+	protected boolean hasKernelSmoothing(PamDataBlock inputBlock) {
+		if (inputBlock == null) {
+			return false;
+		}
+		ProcessAnnotation an = inputBlock.findAnnotation(KernelSmoothingProcess.processType, KernelSmoothingProcess.processName);
+		return an != null;
+	}
 
 
 	@Override

src/RightWhaleEdgeDetector/RWEDialog.java

@@ -5,6 +5,7 @@ import java.awt.GridBagConstraints;
 import java.awt.GridBagLayout;
 import java.awt.Window;
 
+import javax.swing.JCheckBox;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JTabbedPane;
@@ -29,11 +30,15 @@ public class RWEDialog extends PamDialog {
 	private static RWEDialog singleInstance;
 	private SourcePanel sourcePanel;
 	
+	private RWEControl rweControl;
+	
 	private JTextField startFreq, endFreq, thresholdDB;
 	private JTextField minSoundType;
+	private JCheckBox downThreshold;
 		
-	private RWEDialog(Window parentFrame) {
+	private RWEDialog(RWEControl rweControl, Window parentFrame) {
 		super(parentFrame, "Right Whale Edge Detector Settings", true);
+		this.rweControl = rweControl;
 		sourcePanel = new SourcePanel(this, "Source and Channels", 
 				FFTDataUnit.class, true, true);
 		sourcePanel.setSourceToolTip("Data source should be the output of a Spectrogram Smmothing Kernel");
@@ -67,6 +72,11 @@ public class RWEDialog extends PamDialog {
 		addComponent(det, thresholdDB = new JTextField(5), c);
 		c.gridx++;
 		addComponent(det, new JLabel(" dB", SwingConstants.RIGHT), c);
+		c.gridy++;
+		c.gridx = 0;
+		addComponent(det, new JLabel("Appy down threshold ", SwingConstants.RIGHT), c);
+		c.gridx++;
+		addComponent(det, downThreshold = new JCheckBox(), c);
 
 		JPanel cl = new JPanel(new GridBagLayout());
 		cl.setBorder(new TitledBorder("Detection"));
@@ -85,6 +95,7 @@ public class RWEDialog extends PamDialog {
 		}
 		txt += "</html>";
 		minSoundType.setToolTipText(txt);
+		downThreshold.setToolTipText("Applies threshold as dB down from the peak, as well as up from the noise floor");
 		
 		pp.add(BorderLayout.NORTH, det);
 		pp.add(BorderLayout.CENTER, cl);
@@ -96,8 +107,8 @@ public class RWEDialog extends PamDialog {
 	}
 	
 	public static RWEParameters showDialog(Window frame, RWEControl rweControl) {
-		if (singleInstance == null || frame != singleInstance.getOwner()) {
-			singleInstance = new RWEDialog(frame);
+		if (singleInstance == null || frame != singleInstance.getOwner() || rweControl != singleInstance.rweControl) {
+			singleInstance = new RWEDialog(rweControl, frame);
 		}
 		singleInstance.rweParameters = rweControl.rweParameters.clone();
 		singleInstance.setParams();
@@ -113,6 +124,7 @@ public class RWEDialog extends PamDialog {
 		endFreq.setText(String.format("%3.1f", rweParameters.endFreq));
 		double thDB = 10. * Math.log10(rweParameters.threshold);
 		thresholdDB.setText(String.format("%3.1f", thDB));
+		downThreshold.setSelected(rweParameters.downThreshold);
 		minSoundType.setText(String.format("%d", rweParameters.minSoundType));
 	}
 
@@ -120,6 +132,7 @@ public class RWEDialog extends PamDialog {
 	public boolean getParams() {
 		rweParameters.channelMap = sourcePanel.getChannelList();
 		rweParameters.dataSourceName = sourcePanel.getSource().getDataName();
+		rweParameters.downThreshold = downThreshold.isSelected();
 		if (rweParameters.dataSourceName == null) {
 			return showWarning("You must select a valid input data source");
 		}
@@ -137,26 +150,13 @@ public class RWEDialog extends PamDialog {
 		catch (NumberFormatException e) {
 			return showWarning("Invalid detection or classification parameter");
 		}
-		boolean gok = checkInputProcessing();
-		if (gok == false) {
-			return showWarning("Right whale detector input must include Gaussian Kernel Smoothing as part of the FFT module, or a stand alone smoothing module");
-		}
+//		boolean gok = rweControl.hasKernelSmoothing(sourcePanel.getSource());
+//		if (gok == false) {
+//			return showWarning("Right whale detector input must include Gaussian Kernel Smoothing as part of the FFT module, or a stand alone smoothing module");
+//		}
 		return true;
 	}
 
-	/**
-	 * Check that the input process has implemented kernel smoothing. 
-	 * @return
-	 */
-	private boolean checkInputProcessing() {
-		PamDataBlock db = sourcePanel.getSource();
-		if (db == null) {
-			return false;
-		}
-		ProcessAnnotation an = db.findAnnotation(KernelSmoothingProcess.processType, KernelSmoothingProcess.processName);
-		return an != null;
-	}
-
 	@Override
 	public void cancelButtonPressed() {
 		rweParameters = null;

src/RightWhaleEdgeDetector/RWEParameters.java

@@ -27,6 +27,8 @@ public class RWEParameters implements Serializable, Cloneable, ManagedParameters
 	
 	public int minSoundType = 5;
 	
+	public boolean downThreshold = false;
+	
 	@Override
 	protected RWEParameters clone() {
 		try {

src/RightWhaleEdgeDetector/RWEProcess.java

@@ -16,6 +16,7 @@ import fftManager.Complex;
 import fftManager.FFTDataBlock;
 import fftManager.FFTDataUnit;
 import networkTransfer.receive.BuoyStatusDataUnit;
+import spectrogramNoiseReduction.kernelSmoothing.KernelSmoothing;
 import whistlesAndMoans.WhistleBearingInfo;
 import PamController.PamController;
 import PamDetection.AbstractLocalisation;
@@ -43,6 +44,11 @@ public class RWEProcess extends PamProcess {
 		
 	private Hashtable<Integer, BearingLocaliser> bearingLocalisers;
 	private StandardSymbolManager symbolManager;
+	/**
+	 * Already has Kernel smoothing applied to input data. 
+	 */
+	private boolean isPreSmoothed;
+	private KernelSmoothing kernelSmoothing;
 	
 	public RWEProcess(RWEControl rweControl) {
 		super(rweControl, null);
@@ -96,6 +102,18 @@ public class RWEProcess extends PamProcess {
 		if (sourceDataBlock == null) {
 			return;
 		}
+		/**
+		 * work out if the fft source has already run the Guassian smoothing or not
+		 */
+		isPreSmoothed = rweControl.hasKernelSmoothing(sourceDataBlock);
+		if (isPreSmoothed) {
+			kernelSmoothing = null;
+		}
+		else {
+			kernelSmoothing = new KernelSmoothing();
+			kernelSmoothing.initialise(sourceDataBlock.getChannelMap());
+		}
+//		sourceDataBlock.findAnnotation(null);
 //		rweDataBlock.setChannelMap(rweControl.rweParameters.channelMap);
 		rweDataBlock.sortOutputMaps(sourceDataBlock.getChannelMap(), sourceDataBlock.getSequenceMapObject(), rweControl.rweParameters.channelMap);
 		if (db == null) {
@@ -135,6 +153,7 @@ public class RWEProcess extends PamProcess {
 		private int numOT; // number of bins in last analysed slice over threshold
 		private int minSoundType;
 		private RWClassifier classifier = new RWStandardClassifier();
+		
 		public RWEChannelProcess(RWEProcess rweProcess, int iChannel) {
 			this.rweProcess = rweProcess;
 			this.iChannel = iChannel;
@@ -160,6 +179,15 @@ public class RWEProcess extends PamProcess {
 		
 		
 		public void newData(FFTDataUnit fftDataUnit) {
+			if (!isPreSmoothed) {
+				FFTDataUnit newFFTUnit = new FFTDataUnit(fftDataUnit.getTimeMilliseconds(), fftDataUnit.getChannelBitmap(), 
+						fftDataUnit.getStartSample(), fftDataUnit.getSampleDuration(), null, fftDataUnit.getFftSlice());
+				newFFTUnit.setSequenceBitmap(fftDataUnit.getSequenceBitmapObject());
+				newFFTUnit.setFftData(fftDataUnit.getFftData().clone());
+				kernelSmoothing.runNoiseReduction(newFFTUnit);
+				fftDataUnit = newFFTUnit;
+			}
+			
 			RWEDetectionPeak[] newPeaks = findPeaks(fftDataUnit.getFftData());
 			RWESound[] newSounds = findSounds(fftDataUnit.getTimeMilliseconds(), newPeaks);
 			if (newSounds == null) {
@@ -197,6 +225,7 @@ public class RWEProcess extends PamProcess {
 			RWEDetectionPeak[] detectedPeaks = null;
 			int nPeaks = 0;
 			int nOver = 0;
+			double onDown = rweControl.rweParameters.downThreshold ? 1 : 0;
 			for (int i = searchBin1; i <= searchBin2; i++) {
 				magData[i] = complexArray.magsq(i);
 			}
@@ -239,7 +268,8 @@ public class RWEProcess extends PamProcess {
 					// do nothing it it's still off !
 				}
 				else {
-					if (oTh[i]) { // continue peak
+					// if downThreshold == false then onDown is 0, so second threshold is always on since magData always > 0
+					if (oTh[i] && magData[i] > newPeak.maxAmp*onDown/threshold) { // continue peak
 						newPeak.bin2 = i;
 						if (magData[i] > newPeak.maxAmp) {
 							newPeak.maxAmp = magData[i];
@@ -258,6 +288,16 @@ public class RWEProcess extends PamProcess {
 						detectedPeaks[nPeaks++] = newPeak;
 						newPeak = new RWEDetectionPeak(0);
 						peakOn = false;
+						// now trim off the start of the peak if it's too wide. 
+						if (onDown > 0) {
+							for (int ip = newPeak.bin1; ip < newPeak.peakBin; ip++) {
+								if (magData[ip] < newPeak.maxAmp/threshold) {
+									newPeak.bin1 = ip+1;
+									newPeak.signal -= magData[ip];
+									newPeak.noise -= backgroundData[ip];
+								}
+							}
+						}
 					}
 				}
 			}

src/binaryFileStorage/BinaryStorageDialogPanel.java

@@ -91,7 +91,7 @@ public class BinaryStorageDialogPanel {
 		JPanel qb = new JPanel(new BorderLayout());
 		qb.add(BorderLayout.WEST, q);
 		qb.setBorder(new TitledBorder("Options"));
-		qb.setVisible(PamController.getInstance().getRunMode() != PamController.RUN_PAMVIEW);
+//		qb.setVisible(PamController.getInstance().getRunMode() != PamController.RUN_PAMVIEW);
 		
 		p.add(BorderLayout.CENTER, qb);