Merge from DG (#145)

* Localization output

* update localiser output

src/Localiser/LocalisationAlgorithm.java

@@ -1,5 +1,7 @@
 package Localiser;
 
+import java.io.Serializable;
+
 import PamDetection.LocContents;
 import PamDetection.LocalisationInfo;
 
@@ -12,10 +14,9 @@ import PamDetection.LocalisationInfo;
 public interface LocalisationAlgorithm {
 
 	/**
-	 * Get the likely content flags for this localiser. 
-	 * @see LocalisationInfo
-	 * @see LocContents
-	 * @return localisation flags. 
+	 * Get information about the localisation algorithm. 
+	 * @return algorithm information. 
 	 */
-	public int getLocalisationContents();
+	public LocalisationAlgorithmInfo getAlgorithmInfo();
+	
 }

src/Localiser/LocalisationAlgorithmInfo.java

@@ -0,0 +1,31 @@
+package Localiser;
+
+import java.io.Serializable;
+
+import PamDetection.LocContents;
+import PamDetection.LocalisationInfo;
+
+public interface LocalisationAlgorithmInfo {
+	
+	/**
+	 * Get the likely content flags for this localiser. 
+	 * @see LocalisationInfo
+	 * @see LocContents
+	 * @return localisation flags. 
+	 */
+	public int getLocalisationContents();
+	
+	/**
+	 * Get the algorithm name
+	 * @return algorithm name
+	 */
+	public String getAlgorithmName();
+	
+	/**
+	 * Get the algorithm parameters. Something else 
+	 * can turn these into xml for Tethys. 
+	 * @return algorithm parameters object. Might be null;
+	 */
+	public Serializable getParameters();
+	
+}

src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/BearingLocaliser.java

@@ -1,6 +1,7 @@
 package Localiser.algorithms.timeDelayLocalisers.bearingLoc;
 
 import Localiser.LocalisationAlgorithm;
+import Localiser.LocalisationAlgorithmInfo;
 import pamMaths.PamVector;
 
 /**
@@ -9,7 +10,7 @@ import pamMaths.PamVector;
  * @author Doug Gillespie
  *
  */
-public interface BearingLocaliser extends LocalisationAlgorithm {
+public interface BearingLocaliser extends LocalisationAlgorithm, LocalisationAlgorithmInfo {
 
 	/**
 	 * Do any preparation necessary (e.g. creation of look up tables)

src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/CombinedBearingLocaliser.java

@@ -1,8 +1,12 @@
 package Localiser.algorithms.timeDelayLocalisers.bearingLoc;
 
+import java.io.Serializable;
+
+import Localiser.LocalisationAlgorithmInfo;
 import PamDetection.LocContents;
 import pamMaths.PamVector;
 
+@Deprecated
 public class CombinedBearingLocaliser implements BearingLocaliser {
 	
 	private BearingLocaliser firstLocaliser;
@@ -67,4 +71,19 @@ public class CombinedBearingLocaliser implements BearingLocaliser {
 		return res2;
 	}
 
+	@Override
+	public String getAlgorithmName() {
+		return "Combined Simplex bearing localiser";
+	}
+
+	@Override
+	public Serializable getParameters() {
+		return null;
+	}
+
+	@Override
+	public LocalisationAlgorithmInfo getAlgorithmInfo() {
+		return this;
+	}
+
 }

src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/LSQBearingLocaliser.java

@@ -1,10 +1,13 @@
 package Localiser.algorithms.timeDelayLocalisers.bearingLoc;
 
+import java.io.Serializable;
+
 import Array.ArrayManager;
 import Array.PamArray;
 import Jama.LUDecomposition;
 import Jama.Matrix;
 import Jama.QRDecomposition;
+import Localiser.LocalisationAlgorithmInfo;
 import PamDetection.LocContents;
 import PamUtils.PamUtils;
 import pamMaths.PamVector;
@@ -14,7 +17,7 @@ public class LSQBearingLocaliser implements BearingLocaliser {
 	private int hydrophoneBitMap;
 	private long timeMillis;
 	private double timingError;
-	
+
 	private Matrix weightedHydrophoneVectors;
 	private Matrix hydrophoneVectors;
 	private Matrix hydrophoneErrorVectors;
@@ -35,7 +38,7 @@ public class LSQBearingLocaliser implements BearingLocaliser {
 	public int getLocalisationContents() {
 		return LocContents.HAS_BEARING | LocContents.HAS_AMBIGUITY;
 	}
-	
+
 	@Override
 	public void prepare(int[] arrayElements, long timeMillis, double timingError) {
 		/*
@@ -49,7 +52,7 @@ public class LSQBearingLocaliser implements BearingLocaliser {
 		arrayType = arrayManager.getArrayShape(currentArray, hydrophoneBitMap);
 
 		arrayAxis = arrayManager.getArrayDirections(currentArray, hydrophoneBitMap);
-		
+
 		int nHyd = arrayElements.length;
 		int nDelay = (nHyd*(nHyd-1))/2;
 		weightedHydrophoneVectors = new Matrix(nDelay, 3);
@@ -77,12 +80,12 @@ public class LSQBearingLocaliser implements BearingLocaliser {
 					weightedHydrophoneVectors.set(iRow, e, v.getElement(e)/c*fitWeights[iRow]);
 					hydrophoneVectors.set(iRow, e, v.getElement(e)/c);
 					hydrophoneErrorVectors.set(iRow, e, errorVec.getElement(e)/c);
-//					hydrophoneUnitVectors.set(iRow, e, uv.getElement(e));
+					//					hydrophoneUnitVectors.set(iRow, e, uv.getElement(e));
 				}
 				iRow++;
 			}
 		}
-//		luHydrophoneUnitMatrix = new LUDecomposition(hydrophoneUnitVectors);
+		//		luHydrophoneUnitMatrix = new LUDecomposition(hydrophoneUnitVectors);
 		qrHydrophones = new QRDecomposition(weightedHydrophoneVectors);
 	}
 
@@ -100,71 +103,71 @@ public class LSQBearingLocaliser implements BearingLocaliser {
 	public PamVector[] getArrayAxis() {
 		return arrayAxis;
 	}	 
-	
+
 	/* 
 	 * @return true if a new grid needs to be created
 	 */
 	private boolean resetArray(long timeMillis){
-		
+
 		if (currentArray == null || (this.timeMillis!=timeMillis && currentArray.getHydrophoneLocator().isChangeable())){
 			prepare(PamUtils.getChannelArray(hydrophoneBitMap), timeMillis, 1e-6);
 			this.timeMillis = timeMillis;
 			return true;
 		}
-			
+
 		return false; 
 	}
 
 	@Override
 	public double[][] localise(double[] delays, long timeMillis) {
 		resetArray(timeMillis);
-//		qrHydrophones = new QRDecomposition(hydrophoneVectors);
+		//		qrHydrophones = new QRDecomposition(hydrophoneVectors);
 		Matrix normDelays = new Matrix(delays.length, 1);
 		for (int i = 0; i < delays.length; i++) {
 			normDelays.set(i, 0, -delays[i]*fitWeights[i]);
 		}
-//		Matrix soln = luHydrophoneUnitMatrix.solve(normDelays);
+		//		Matrix soln = luHydrophoneUnitMatrix.solve(normDelays);
 		Matrix soln2 = qrHydrophones.solve(normDelays);
 		double[][] angs = new double[2][2];
 		PamVector v = new PamVector(soln2.get(0, 0), soln2.get(1,0), soln2.get(2, 0));
-//		System.out.printf("Vector Norm = %4.3f: ", v.norm());
+		//		System.out.printf("Vector Norm = %4.3f: ", v.norm());
 		double m = v.normalise();
 		angs[0][0] = Math.PI/2. - Math.atan2(v.getElement(0),v.getElement(1));
 		angs[0][1] = Math.asin(v.getElement(2));
-		
-//		timingError = 1e-5;
+
+		//		timingError = 1e-5;
 		// now take a look at angle errors
 		double oneDeg = Math.PI/180.;
-		
+
 		double testDeg = 5;
 		double[][] er = new double[2][20];
 		for (int i = 0; i < 20; i++) {
 			testDeg = 1+i;
-		// pick points testDeg degrees either side of angs and change one at a time
-		double aDiff = testDeg * oneDeg;
-		double a;
-		double l1, l2, l3, l1a, l3a;
-		l1 = logLikelihood(delays, angs[0][0] - aDiff, angs[0][1]);
-		l2 = logLikelihood(delays, angs[0][0], angs[0][1]);
-		l3 = logLikelihood(delays, angs[0][0] + aDiff, angs[0][1]);
-		er[0][i] = angs[1][0] = Math.sqrt(1./(l1+l3-2*l2))*aDiff;
-		l1a = logLikelihood(delays, angs[0][0], angs[0][1] - aDiff);
-//		l2 = logLikelihood(delays, angs[0][0], angs[0][1]);
-		l3a = logLikelihood(delays, angs[0][0], angs[0][1] + aDiff);
-		er[1][i] = angs[1][1] = Math.sqrt(1./(l1a+l3a-2*l2))*aDiff;
+			// pick points testDeg degrees either side of angs and change one at a time
+			double aDiff = testDeg * oneDeg;
+			double a;
+			double l1, l2, l3, l1a, l3a;
+			l1 = logLikelihood(delays, angs[0][0] - aDiff, angs[0][1]);
+			l2 = logLikelihood(delays, angs[0][0], angs[0][1]);
+			l3 = logLikelihood(delays, angs[0][0] + aDiff, angs[0][1]);
+			er[0][i] = angs[1][0] = Math.sqrt(1./(l1+l3-2*l2))*aDiff;
+			l1a = logLikelihood(delays, angs[0][0], angs[0][1] - aDiff);
+			//		l2 = logLikelihood(delays, angs[0][0], angs[0][1]);
+			l3a = logLikelihood(delays, angs[0][0], angs[0][1] + aDiff);
+			er[1][i] = angs[1][1] = Math.sqrt(1./(l1a+l3a-2*l2))*aDiff;
 		}
-		
-		
-		
-		
-//		double ll[] = new double[21];
-//		double a[] = new double[2];
-//		timingError = 1.e-4;
-//		a[1] = angs[0][1];
-//		for (int i = 0; i < ll.length; i++) {
-//			a[0] = angs[0][0] + (-10 + i)*oneDeg;
-//			ll[i] = logLikelihood(delays, a);
-//		}
+
+
+
+
+		//		double ll[] = new double[21];
+		//		double a[] = new double[2];
+		//		timingError = 1.e-4;
+		//		a[1] = angs[0][1];
+		//		for (int i = 0; i < ll.length; i++) {
+		//			a[0] = angs[0][0] + (-10 + i)*oneDeg;
+		//			ll[i] = logLikelihood(delays, a);
+		//		}
 		return angs;
 	}
 	/**
@@ -181,7 +184,7 @@ public class LSQBearingLocaliser implements BearingLocaliser {
 		whaleVec.set(2, 0, Math.sin(angle1));
 		return logLikelihood(delays, whaleVec);
 	}
-	
+
 	/**
 	 * Calculate a log likelihood for a given pair of angles
 	 * @param delays actual delays
@@ -190,11 +193,11 @@ public class LSQBearingLocaliser implements BearingLocaliser {
 	 */
 	public double logLikelihood(double[] delays, double[] angles) {
 		return logLikelihood(delays, angles[0], angles[1]);
-//		Matrix whaleVec = new Matrix(3,1);
-//		whaleVec.set(0, 0, Math.cos(angles[1])*Math.cos(angles[0]));
-//		whaleVec.set(1, 0, Math.cos(angles[1])*Math.sin(angles[0]));
-//		whaleVec.set(2, 0, Math.sin(angles[1]));
-//		return logLikelihood(delays, whaleVec);
+		//		Matrix whaleVec = new Matrix(3,1);
+		//		whaleVec.set(0, 0, Math.cos(angles[1])*Math.cos(angles[0]));
+		//		whaleVec.set(1, 0, Math.cos(angles[1])*Math.sin(angles[0]));
+		//		whaleVec.set(2, 0, Math.sin(angles[1]));
+		//		return logLikelihood(delays, whaleVec);
 	}
 	/**
 	 * Calculate a log likelihood for a given whale vector. 
@@ -215,5 +218,18 @@ public class LSQBearingLocaliser implements BearingLocaliser {
 		}
 		return chi/2;
 	}
+	
+	@Override
+	public String getAlgorithmName() {
+		return "Least Squares bearing localiser";
+	}
 
+	@Override
+	public Serializable getParameters() {
+		return null;
+	}
+	@Override
+	public LocalisationAlgorithmInfo getAlgorithmInfo() {
+		return this;
+	}
 }

src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/MLGridBearingLocaliser.java

@@ -1,10 +1,12 @@
 package Localiser.algorithms.timeDelayLocalisers.bearingLoc;
 
+import java.io.Serializable;
 import java.util.Arrays;
 
 import Array.ArrayManager;
 import Array.PamArray;
 import Jama.Matrix;
+import Localiser.LocalisationAlgorithmInfo;
 import Localiser.algorithms.Correlations;
 import PamDetection.LocContents;
 import PamUtils.ArrayDump;
@@ -635,6 +637,19 @@ public class MLGridBearingLocaliser implements BearingLocaliser {
 	public int getHydrophoneMap() {
 		return hydrophoneMap;
 	}
-	
 
+	@Override
+	public String getAlgorithmName() {
+		return "Maximum likelyhood grid bearing localiser";
+	}
+
+	@Override
+	public Serializable getParameters() {
+		return null;
+	}
+
+	@Override
+	public LocalisationAlgorithmInfo getAlgorithmInfo() {
+		return this;
+	}
 }

src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/MLGridBearingLocaliser2.java

@@ -1,10 +1,12 @@
 package Localiser.algorithms.timeDelayLocalisers.bearingLoc;
 
+import java.io.Serializable;
 import java.util.Arrays;
 
 import Array.ArrayManager;
 import Array.PamArray;
 import Jama.Matrix;
+import Localiser.LocalisationAlgorithmInfo;
 import Localiser.algorithms.Correlations;
 import Localiser.algorithms.PeakPosition2D;
 import Localiser.algorithms.PeakSearch;
@@ -13,6 +15,7 @@ import PamUtils.ArrayDump;
 import PamUtils.PamUtils;
 import PamUtils.SystemTiming;
 import pamMaths.PamVector;
+import tethys.pamdata.AutoTethysProvider;
 
 /**
  * Revamp of the earlier MLGridBearingLocaliser but with a more sensible 
@@ -743,5 +746,36 @@ public class MLGridBearingLocaliser2 implements BearingLocaliser {
 	public double[][] getLikelihoodLUT() {
 		return likelihoodLUT;
 	}
+
+	@Override
+	public String getAlgorithmName() {
+		return "Maximum likelyhood grid bearing localiser V2";
+	}
+
+	@Override
+	public Serializable getParameters() {
+		return new LocaliserParams(this.thetaStep, this.phiStep);
+	}
 	
+	@Override
+	public LocalisationAlgorithmInfo getAlgorithmInfo() {
+		return this;
+	}
+	
+	/**
+	 * For passing to Tethys output. 
+	 * @author dg50
+	 *
+	 */
+	public class LocaliserParams implements Serializable {
+		private static final long serialVersionUID = 1L;
+		public double thetaStep, phiStep;
+		public LocaliserParams(double thetaStep, double phiStep) {
+			super();
+			this.thetaStep = Math.toDegrees(thetaStep);
+			this.phiStep = Math.toDegrees(phiStep);
+			this.thetaStep = AutoTethysProvider.roundDecimalPlaces(this.thetaStep, 2);
+			this.phiStep = AutoTethysProvider.roundDecimalPlaces(this.phiStep, 2);
+		}
+	}
 }

src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/PairBearingLocaliser.java

@@ -1,11 +1,13 @@
 package Localiser.algorithms.timeDelayLocalisers.bearingLoc;
 
+import java.io.Serializable;
 import java.util.Arrays;
 
 import Array.ArrayManager;
 import Array.PamArray;
 import Jama.Matrix;
 import Jama.QRDecomposition;
+import Localiser.LocalisationAlgorithmInfo;
 import PamDetection.LocContents;
 import PamUtils.PamUtils;
 import pamMaths.PamVector;
@@ -294,4 +296,17 @@ public class PairBearingLocaliser implements BearingLocaliser {
 		return speedOfSound;
 	}
 
+	@Override
+	public String getAlgorithmName() {
+		return "Pair bearing localiser";
+	}
+
+	@Override
+	public Serializable getParameters() {
+		return null;
+	}
+	@Override
+	public LocalisationAlgorithmInfo getAlgorithmInfo() {
+		return this;
+	}
 }

src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/SimplexBearingLocaliser.java

@@ -1,5 +1,6 @@
 package Localiser.algorithms.timeDelayLocalisers.bearingLoc;
 
+import java.io.Serializable;
 import java.util.Arrays;
 
 import org.apache.commons.math.FunctionEvaluationException;
@@ -14,10 +15,12 @@ import Array.ArrayManager;
 import Array.PamArray;
 import Jama.Matrix;
 import Jama.QRDecomposition;
+import Localiser.LocalisationAlgorithmInfo;
 import PamDetection.LocContents;
 import PamUtils.PamUtils;
 import pamMaths.PamVector;
 
+@Deprecated
 public class SimplexBearingLocaliser implements BearingLocaliser {
 	private int arrayType;
 	private Matrix hydrophoneVectors;
@@ -236,7 +239,21 @@ public class SimplexBearingLocaliser implements BearingLocaliser {
 	public void setFirstStep(double[] firstStep) {
 		this.firstStep = firstStep;
 	}
-	
+
+	@Override
+	public String getAlgorithmName() {
+		return "Simplex bearing localiser";
+	}
+
+	@Override
+	public LocalisationAlgorithmInfo getAlgorithmInfo() {
+		return this;
+	}
+
+	@Override
+	public Serializable getParameters() {
+		return null;
+	}
 //	private class BearingConvergence implements RealConvergenceChecker {
 //
 //		@Override

src/PamguardMVC/PamDataBlock.java

@@ -49,6 +49,7 @@ import org.w3c.dom.Element;
 
 import Acquisition.AcquisitionControl;
 import Acquisition.AcquisitionProcess;
+import Localiser.LocalisationAlgorithm;
 import pamScrollSystem.ViewLoadObserver;
 import tethys.TethysControl;
 import tethys.pamdata.AutoTethysProvider;
@@ -2530,6 +2531,42 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
 	public void addLocalisationContents(int localisationContents) {
 		this.localisationContents.addLocContent(localisationContents);
 	}
+	
+	/**
+	 * Find localisation algorithm for this data. 
+	 * This may be within the owning module, or a downstream algorithm. 
+	 * @return first found localisation algorithm or null;
+	 */
+	public LocalisationAlgorithm getLocalisationAlgorithm() {
+		/*
+		 *  first check downstream modules. If these are in use, they
+		 *  probably override anything internal, so look for these first.  
+		 */
+		List<PamObserver> instObs = getInstantObservers();
+		for (PamObserver obs : instObs) {
+			if (obs instanceof LocalisationAlgorithm) {
+				return (LocalisationAlgorithm) obs;
+			}
+			if (obs instanceof PamProcess) {
+				PamProcess proc = (PamProcess) obs;
+				PamControlledUnit pcu = proc.getPamControlledUnit();
+				if (pcu == null) {
+					continue;
+				}
+				if (pcu instanceof LocalisationAlgorithm) {
+					return (LocalisationAlgorithm) pcu;
+				}
+			}
+		}
+		// if nothing downstream, then check the owning module
+		PamProcess proc = getParentProcess();
+		if (proc == null) return null;
+		PamControlledUnit pcu = proc.getPamControlledUnit();
+		if (pcu instanceof LocalisationAlgorithm) {
+			return (LocalisationAlgorithm) pcu;
+		}		
+		return null;
+	}
 
 	public static final int ITERATOR_END = -1;
 

src/PamguardMVC/PamObservable.java

@@ -562,6 +562,20 @@ public class PamObservable {//extends PanelOverlayDraw {
 		return PamModel.getPamModel().getPamModelSettings().getThreadingJitterMillis();
 	}
 
+	/**
+	 * @return the pamObservers
+	 */
+	protected List<PamObserver> getPamObservers() {
+		return pamObservers;
+	}
+
+	/**
+	 * @return the instantObservers
+	 */
+	protected List<PamObserver> getInstantObservers() {
+		return instantObservers;
+	}
+
 	//	@Override
 	//	public boolean hasOptionsDialog(GeneralProjector generalProjector) {
 	//		if (overlayDraw != null) {

src/bearinglocaliser/BearingLocaliserControl.java

@@ -10,14 +10,18 @@ import java.util.List;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 
+import Localiser.LocalisationAlgorithm;
+import Localiser.LocalisationAlgorithmInfo;
 import PamController.PamControlledUnit;
 import PamController.PamControlledUnitSettings;
 import PamController.PamController;
 import PamController.PamSettingManager;
 import PamController.PamSettings;
+import PamDetection.LocContents;
 import PamUtils.SimpleObservable;
 import PamguardMVC.PamDataUnit;
 import beamformer.algorithms.BeamAlgorithmProvider;
+import bearinglocaliser.algorithms.BearingAlgorithm;
 import bearinglocaliser.algorithms.BearingAlgorithmProvider;
 import bearinglocaliser.annotation.BearingAnnotationType;
 import bearinglocaliser.beamformer.BeamFormBearingWrapper;
@@ -30,7 +34,7 @@ import offlineProcessing.OfflineTaskGroup;
 import pamViewFX.fxNodes.pamDialogFX.PamDialogFX2AWT;
 import userDisplay.UserDisplayControl;
 
-public class BearingLocaliserControl extends PamControlledUnit implements PamSettings {
+public class BearingLocaliserControl extends PamControlledUnit implements PamSettings, LocalisationAlgorithm, LocalisationAlgorithmInfo {
 	
 	public static final String unitType = "Bearing Calculator";
 	
@@ -228,4 +232,46 @@ public class BearingLocaliserControl extends PamControlledUnit implements PamSet
 	public String getHelpPoint() {
 		return helpPoint;
 	}
+
+	@Override
+	public LocalisationAlgorithmInfo getAlgorithmInfo() {
+		return this;
+	}
+
+	
+	private BearingAlgorithm findAlgorithm() {
+		BearingAlgorithmGroup[] groups = bearingProcess.getBearingAlgorithmGroups();
+		if (groups == null) {
+			return null;
+		}
+		for (int i = 0; i < groups.length; i++) {
+			BearingAlgorithm ba = groups[i].bearingAlgorithm;
+			if (ba != null) {
+				return ba;
+			}
+		}
+		return null;
+	}
+	
+	@Override
+	public int getLocalisationContents() {
+		int cont = LocContents.HAS_BEARING | LocContents.HAS_BEARINGERROR;
+		// work out if we should also add ambiguity. How to work that out ? 
+		return cont;
+	}
+
+	@Override
+	public String getAlgorithmName() {
+//		BearingAlgorithm ba = findAlgorithm();
+//		if (ba == null) {
+//			return null;
+//		}
+//		ba.getParams().
+		return getUnitType();
+	}
+
+	@Override
+	public Serializable getParameters() {
+		return bearingLocaliserParams;
+	}
 }

src/clickDetector/ClickControl.java

@@ -44,6 +44,8 @@ import targetMotionOld.TargetMotionLocaliser;
 import binaryFileStorage.BinaryStore;
 import Filters.FilterDialog;
 import Filters.FilterParams;
+import Localiser.LocalisationAlgorithm;
+import Localiser.LocalisationAlgorithmInfo;
 import Localiser.detectionGroupLocaliser.GroupDetection;
 import PamController.PamConfiguration;
 import PamController.PamControlledUnit;
@@ -112,7 +114,7 @@ import offlineProcessing.OfflineTaskGroup;
  * 
  */
 
-public class ClickControl extends PamControlledUnit implements PamSettings {
+public class ClickControl extends PamControlledUnit implements PamSettings, LocalisationAlgorithm {
 
 	protected ClickDetector clickDetector;
 
@@ -1293,5 +1295,10 @@ public class ClickControl extends PamControlledUnit implements PamSettings {
 		return clickFFTDataOrganiser;
 	}
 
+	@Override
+	public LocalisationAlgorithmInfo getAlgorithmInfo() {
+		return clickDetector.getLocaliserInfo();
+	}
+
 
 }

src/clickDetector/ClickDetector.java

@@ -42,6 +42,7 @@ import Filters.Filter;
 import Filters.FilterMethod;
 import Filters.FilterType;
 import Localiser.DelayMeasurementParams;
+import Localiser.LocalisationAlgorithmInfo;
 import Localiser.algorithms.Correlations;
 import Localiser.algorithms.DelayGroup;
 import Localiser.algorithms.TimeDelayData;
@@ -2109,4 +2110,22 @@ public class ClickDetector extends PamProcess {
 		super.destroyProcess();
 		newClickMonitor.destroyProcess();
 	}
+
+	/**
+	 * Get information about the internal bearing localiser. Will have to do 
+	 * just for the first sub detector. 
+	 * @return
+	 */
+	public LocalisationAlgorithmInfo getLocaliserInfo() {
+		if (channelGroupDetectors == null || channelGroupDetectors.length == 0) {
+			return null;
+		}
+		BearingLocaliser bl = channelGroupDetectors[0].bearingLocaliser;
+		if (bl == null) {
+			return null;
+		}
+		else {
+			return bl.getAlgorithmInfo();
+		}
+	}
 }

src/clickDetector/tethys/ClickEventTethysDataProvider.java

@@ -31,6 +31,7 @@ public class ClickEventTethysDataProvider extends AutoTethysProvider {
 		GranularityEnumType[] allowed = {GranularityEnumType.GROUPED};
 		return allowed;
 	}
+	
 	@Override
 	public Detection createDetection(PamDataUnit dataUnit, TethysExportParams tethysExportParams,
 			StreamExportParams streamExportParams) {

src/rawDeepLearningClassifier/tethys/DLTethysDataProvider.java

@@ -1,22 +1,20 @@
 package rawDeepLearningClassifier.tethys;
 
-import java.io.Serializable;
+import java.util.ArrayList;
 
-import javax.xml.bind.JAXBException;
 
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
 import nilus.Detection;
 import nilus.Detection.Parameters;
 import rawDeepLearningClassifier.DLControl;
-import rawDeepLearningClassifier.RawDLParams;
-import rawDeepLearningClassifier.dlClassification.DLClassiferModel;
 import rawDeepLearningClassifier.dlClassification.DLDetection;
+import rawDeepLearningClassifier.dlClassification.PredictionResult;
+import rawDeepLearningClassifier.logging.DLAnnotation;
 import tethys.TethysControl;
 import tethys.output.StreamExportParams;
 import tethys.output.TethysExportParams;
 import tethys.pamdata.AutoTethysProvider;
-import tethys.pamdata.TethysParameterPacker;
 
 public class DLTethysDataProvider extends AutoTethysProvider {
 
@@ -35,6 +33,26 @@ public class DLTethysDataProvider extends AutoTethysProvider {
 			return null;
 		}
 		DLDetection dlDetection = (DLDetection) dataUnit;
+		
+		// try to find the score which is burried in the annotation
+		DLAnnotation annotation = (DLAnnotation) dlDetection.findDataAnnotation(DLAnnotation.class) ;
+		if (annotation != null) {
+			double bestScore = 0;
+			ArrayList<PredictionResult> results = annotation.getModelResults();
+			for (PredictionResult res : results) {
+				float[] resres = res.getPrediction();
+				if (resres != null)  for (int i = 0; i < resres.length; i++) {
+					double aRes = resres[i];
+					if (aRes > bestScore) {
+						bestScore = aRes;
+					}
+				}
+			}
+			bestScore = roundSignificantFigures(bestScore, 4);
+			detection.getParameters().setScore(bestScore);
+		}
+//		ds = getPamDataBlock().
+		
 	
 //		result = 
 		String annotSummary = dlDetection.getAnnotationsSummaryString();

src/tethys/TethysControl.java

@@ -570,16 +570,22 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 		for (DatablockSynchInfo synchInfo : dataBlockSynchInfos) {
 //			dataPrefixes[i] = DetectionsHandler.getDetectionsDocIdPrefix(deplData.getProject(), synchInfo.getDataBlock());
 			int detectionCount = 0;
-			int documentCount = 0;
+			int locDocumentCount = 0;
+			int detDocumentCount = 0;
 			for (PDeployment pDepl : matchedDeployments) {
 				detectionCount += dbxmlQueries.countData(synchInfo.getDataBlock(), pDepl.getDocumentId());
 				ArrayList<String> detectionsNames = getDbxmlQueries().getDetectionsDocuments(synchInfo.getDataBlock(), pDepl.getDocumentId());
 				if (detectionsNames != null) {
-					documentCount += detectionsNames.size();
+					detDocumentCount += detectionsNames.size();
+				}
+				ArrayList<String> locDocNames = getDbxmlQueries().getLocalizationDocuments(synchInfo.getDataBlock(), pDepl.getDocumentId());
+				if (locDocNames != null) {
+					locDocumentCount += locDocNames.size();
 				}
 			}
 			synchInfo.setDataCount(detectionCount);
-			synchInfo.setDetectionDocumentCount(documentCount);
+			synchInfo.setDetectionDocumentCount(detDocumentCount);
+			synchInfo.setLocalizationDocumentCount(locDocumentCount);
 			
 			i++;
 		}

src/tethys/detection/DetectionsHandler.java

@@ -10,6 +10,8 @@ import javax.swing.SwingWorker;
 import javax.xml.datatype.DatatypeConstants;
 import javax.xml.datatype.XMLGregorianCalendar;
 
+import Localiser.LocalisationAlgorithm;
+import Localiser.LocalisationAlgorithmInfo;
 import PamController.PamControlledUnit;
 import PamController.PamController;
 import PamController.PamguardVersionInfo;
@@ -665,7 +667,7 @@ public class DetectionsHandler extends CollectionHandler {
 		AlgorithmType algorithm = detections.getAlgorithm();
 
 		if (dataProvider != null) {
-			algorithm = dataProvider.getAlgorithm();
+			algorithm = dataProvider.getAlgorithm(Collection.Detections);
 			//			detections.setAlgorithm(algorithm);
 		}
 		algorithm.setMethod(getMethodString(dataBlock));
@@ -750,10 +752,20 @@ public class DetectionsHandler extends CollectionHandler {
 		AlgorithmType algorithm = localisations.getAlgorithm();
 
 		if (dataProvider != null) {
-			algorithm = dataProvider.getAlgorithm();
+			algorithm = dataProvider.getAlgorithm(Collection.Localizations);
 			//			detections.setAlgorithm(algorithm);
 		}
-		algorithm.setMethod(getMethodString(dataBlock));
+		LocalisationAlgorithm locAlgorithm = dataBlock.getLocalisationAlgorithm();
+		LocalisationAlgorithmInfo locAlgoinfo = null;
+		if (locAlgorithm != null) {
+			locAlgoinfo = locAlgorithm.getAlgorithmInfo();
+		}
+		if (locAlgoinfo != null) {
+			algorithm.setMethod(locAlgoinfo.getAlgorithmName());
+		}
+		else {
+			algorithm.setMethod(getMethodString(dataBlock));
+		}
 		algorithm.setSoftware(getSoftwareString(dataBlock));
 		algorithm.setVersion(getVersionString(dataBlock));
 

src/tethys/detection/GranularityHandler.java

@@ -1,7 +1,5 @@
 package tethys.detection;
 
-import java.util.List;
-import java.util.ListIterator;
 
 import javax.xml.datatype.DatatypeConstants;
 import javax.xml.datatype.XMLGregorianCalendar;
@@ -9,7 +7,6 @@ import javax.xml.datatype.XMLGregorianCalendar;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
 import nilus.Detection;
-import nilus.DetectionGroup;
 import nilus.Detections;
 import nilus.GranularityEnumType;
 import tethys.TethysControl;

src/tethys/localization/LocalizationHandler.java

@@ -3,6 +3,8 @@ package tethys.localization;
 import java.math.BigInteger;
 import java.util.ArrayList;
 
+import Localiser.detectionGroupLocaliser.GroupLocResult;
+import Localiser.detectionGroupLocaliser.GroupLocalisation;
 import PamDetection.AbstractLocalisation;
 import PamDetection.LocContents;
 import PamUtils.LatLong;
@@ -17,7 +19,8 @@ import nilus.LocalizationType;
 import nilus.LocalizationType.References;
 import nilus.LocalizationType.References.Reference;
 import nilus.Localize;
-import nilus.SpeciesIDType
+import nilus.SpeciesIDType;
+import pamMaths.PamVector;
 import nilus.Localize.Effort.CoordinateReferenceSystem;
 import tethys.Collection;
 import tethys.CollectionHandler;
@@ -37,13 +40,13 @@ public class LocalizationHandler extends CollectionHandler {
 		super(tethysControl, Collection.Localizations);
 	}
 
-//	public LocalizationType getLoc() {
-//		LocalizationType lt = new LocalizationType();
-//		CylindricalCoordinateType cct = new CylindricalCoordinateType();
-////		cct.set
-//		CoordinateReferenceSystem cr;
-//		return null;
-//	}
+	//	public LocalizationType getLoc() {
+	//		LocalizationType lt = new LocalizationType();
+	//		CylindricalCoordinateType cct = new CylindricalCoordinateType();
+	////		cct.set
+	//		CoordinateReferenceSystem cr;
+	//		return null;
+	//	}
 
 	/**
 	 * Get a list of Localization documents associated with a particular data block for all deployments
@@ -55,7 +58,7 @@ public class LocalizationHandler extends CollectionHandler {
 		ArrayList<PDeployment> deployments = tethysControl.getDeploymentHandler().getMatchedDeployments();
 		return getStreamLocalizations(dataBlock, deployments);
 	}
-	
+
 	/**
 	 * Get a list of Localization documents associated with a particular data block for the list of deployments
 	 * documents. Group them by abstract or something
@@ -72,14 +75,14 @@ public class LocalizationHandler extends CollectionHandler {
 			if (someNames == null) {
 				continue;
 			}
-//			// no have a list of all the Detections documents of interest for this datablock.
+			//			// no have a list of all the Detections documents of interest for this datablock.
 			for (String aDoc : someNames) {
 				Localize localize = tethysControl.getDbxmlQueries().getLocalizationDocInfo(aDoc);
 				int count = tethysControl.getDbxmlQueries().countLocalizations2(aDoc);
 				PLocalization pLocalize = new PLocalization(localize, dataBlock, aDep, count);
 				localizeDocs.add(pLocalize);
-//				PDetections pDetections = new PDetections(detections, dataBlock, aDep, count);
-//				detectionsDocs.add(pDetections);
+				//				PDetections pDetections = new PDetections(detections, dataBlock, aDep, count);
+				//				detectionsDocs.add(pDetections);
 			}
 		}
 		return new StreamDetectionsSummary(localizeDocs);
@@ -137,7 +140,7 @@ public class LocalizationHandler extends CollectionHandler {
 			break;
 		default:
 			break;
-		
+
 		}
 		return locEl;
 	}
@@ -150,7 +153,7 @@ public class LocalizationHandler extends CollectionHandler {
 			e.printStackTrace();
 		}
 		locType.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(dataUnit.getTimeMilliseconds()));
-		
+
 		DataBlockSpeciesManager spManager = dataBlock.getDatablockSpeciesManager();
 		if (spManager != null) {
 			SpeciesMapItem speciesStuff = spManager.getSpeciesItem(dataUnit);
@@ -160,7 +163,7 @@ public class LocalizationHandler extends CollectionHandler {
 				locType.setSpeciesId(species);
 			}
 		}
-		
+
 		References references = locType.getReferences();
 		if (references == null) {
 			references = new References();
@@ -175,7 +178,7 @@ public class LocalizationHandler extends CollectionHandler {
 		reference.setIndex(BigInteger.valueOf(dataUnit.getUID()));
 		reference.setEventRef("UID");
 		locType.getReferences().getReference().add(reference);
-		
+
 		return locType;
 	}
 
@@ -194,6 +197,22 @@ public class LocalizationHandler extends CollectionHandler {
 		return deg;
 	}
 
+	/**
+	 * Convert a vertical angle from radians to degrees and round. 
+	 * @param radians
+	 * @return
+	 */
+	private double toSlantAngle(double radians) {
+		/*
+		 * these really need to be constrained to -90 to 90, but I don't see what to do if
+		 * they are outside that range.
+		 */
+		double deg = Math.toDegrees(radians);
+		deg= PamUtils.constrainedAngle(deg, 180);
+		deg = AutoTethysProvider.roundDecimalPlaces(deg, 2);
+		return deg;				
+	}
+
 	private LocalizationType createWGS84Loc(Localize localiseDocument, PamDataBlock dataBlock, PamDataUnit dataUnit,
 			StreamExportParams streamExportParams) {
 		AbstractLocalisation loc = dataUnit.getLocalisation();
@@ -209,9 +228,32 @@ public class LocalizationHandler extends CollectionHandler {
 		coord.setX(latlong.getLongitude());
 		coord.setY(latlong.getLatitude());
 		coord.setZ(latlong.getHeight());
-				
+
+		PamVector planarVec = loc.getPlanarVector();
 		locType.setCoordinate(coord);
-		
+
+		// see if it's possible to get a beam measurement. 
+		if (loc instanceof GroupLocalisation) {
+			GroupLocalisation groupLoc = (GroupLocalisation) loc;
+			GroupLocResult groupLocResult = groupLoc.getGroupLocaResult(0);
+			Double perpDist = groupLocResult.getPerpendicularDistance();
+			Long beamTime = groupLocResult.getBeamTime();
+			if (perpDist != null && beamTime != null) {
+				AngularCoordinateType acType = new AngularCoordinateType();
+				acType.setAngle1(90);
+				acType.setDistanceM(AutoTethysProvider.roundDecimalPlaces(perpDist,1));
+				locType.setAngularCoordinate(acType);
+				locType.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(beamTime));
+				locType.setCoordinate(null);
+			}
+			//			groupLoc.getp
+		}
+
+		/*
+		 * Try to also add a range loc. 
+		 */
+		//		loc.
+
 		return locType;
 	}
 
@@ -241,7 +283,10 @@ public class LocalizationHandler extends CollectionHandler {
 		BearingType angType = new BearingType();
 		angType.setAngle1(constrainRadianAngle(angles[0]));
 		if (angles.length >= 2) {
-			angType.setAngle2(constrainRadianAngle(angles[1]));
+			angType.setAngle2(toSlantAngle(angles[1]));
+			//			if (angType.getAngle2() > 360) {
+			//				angType.setAngle2(Math.toDegrees(angles[1]));
+			//			}
 		}
 		locType.setBearing(angType);
 
@@ -254,7 +299,7 @@ public class LocalizationHandler extends CollectionHandler {
 			}
 			locType.setBearingError(angErrType);
 		}
-		
+
 		return locType;
 	}
 	private LocalizationType createPolarLoc(Localize localiseDocument, PamDataBlock dataBlock, PamDataUnit dataUnit,
@@ -264,7 +309,7 @@ public class LocalizationHandler extends CollectionHandler {
 			return null;
 		}
 		if (loc.hasLocContent(LocContents.HAS_RANGE) == false) {
-			
+
 			// do the more basic bearing type instead. 
 			return createBearingLoc(localiseDocument, dataBlock, dataUnit, streamExportParams);
 		}
@@ -277,6 +322,9 @@ public class LocalizationHandler extends CollectionHandler {
 		angType.setAngle1(constrainRadianAngle(angles[0]));
 		if (angles.length >= 2) {
 			angType.setAngle2(constrainRadianAngle(angles[1]));
+			if (angType.getAngle2() > 360) {
+				angType.setAngle2(toSlantAngle(angles[1]));
+			}
 		}
 		if (loc.hasLocContent(LocContents.HAS_RANGE)) {
 			angType.setDistanceM(loc.getRange(0));
@@ -295,10 +343,10 @@ public class LocalizationHandler extends CollectionHandler {
 			}
 			locType.setAngularCoordinateError(angErrType);
 		}
-		
+
 		return locType;
 	}
-	
+
 	private LocalizationType createPerpRange(Localize localiseDocument, PamDataBlock dataBlock, PamDataUnit dataUnit,
 			StreamExportParams streamExportParams) {
 		// TODO Auto-generated method stub

src/tethys/output/DatablockSynchInfo.java

@@ -28,6 +28,8 @@ public class DatablockSynchInfo {
 	 */
 	private int detectionDocumentCount;
 	
+	private int localizationDocumentCount;
+	
 
 	public DatablockSynchInfo(TethysControl tethysControl, PamDataBlock dataBlock) {
 		super();
@@ -68,5 +70,19 @@ public class DatablockSynchInfo {
 	public void setDetectionDocumentCount(int detectionDocumentCount) {
 		this.detectionDocumentCount = detectionDocumentCount;
 	}
+
+	/**
+	 * @return the localizationDocumentCount
+	 */
+	public int getLocalizationDocumentCount() {
+		return localizationDocumentCount;
+	}
+
+	/**
+	 * @param localizationDocumentCount the localizationDocumentCount to set
+	 */
+	public void setLocalizationDocumentCount(int localizationDocumentCount) {
+		this.localizationDocumentCount = localizationDocumentCount;
+	}
 	
 }

src/tethys/output/StreamExportParams.java

@@ -79,6 +79,9 @@ public class StreamExportParams implements Serializable {
 		if (detectionDescription == null) {
 			detectionDescription = new WrappedDescriptionType();
 		}
+//		if (detectionDescription.getMethod() == null) {
+//			
+//		}
 		return detectionDescription;
 	}
 
@@ -87,6 +90,29 @@ public class StreamExportParams implements Serializable {
 		this.longDataName = dataBlock.getLongDataName();
 		autoFill(tethysControl, dataBlock);
 	}
+	
+	/**
+	 * Used to get the description data back in again if it's changes
+	 * as PAMGuard updates. This object can't store references to the 
+	 * TethysControl or the datablock since they aren't serializable. 
+	 * Normally, the description is auto filled at constructoin, but once
+	 * serialized, this can no longer happen, so can call this function to 
+	 * sort it all out.  
+	 */
+	public void checkDescription() {
+		TethysControl tethysControl = (TethysControl) PamController.getInstance().findControlledUnit(TethysControl.class, null);
+		PamDataBlock dataBlock = PamController.getInstance().getDataBlockByLongName(longDataName);
+		if (tethysControl == null || dataBlock == null) {
+			return; // probably impossible for this to happen, but just in case.  
+		}
+		DescriptionType desc = getNilusDetectionDescription();
+		if (desc == null) {
+			detectionDescription.setDescription(desc = new DescriptionType());
+		}
+		if (desc.getMethod() == null || desc.getMethod().length() == 0) {
+			autoFill(tethysControl, dataBlock);
+		}
+	}
 
 	/**
 	 * Try to put some information automatically into the Methods. 

src/tethys/pamdata/AutoTethysProvider.java

@@ -9,6 +9,8 @@ import org.w3c.dom.Element;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 
+import Localiser.LocalisationAlgorithm;
+import Localiser.LocalisationAlgorithmInfo;
 import PamController.PamControlledUnit;
 import PamController.PamSettings;
 import PamController.PamguardVersionInfo;
@@ -35,6 +37,7 @@ import nilus.DetectionEffortKind;
 import nilus.GranularityEnumType;
 import nilus.Helper;
 import nilus.SpeciesIDType;
+import tethys.Collection;
 import tethys.TethysControl;
 import tethys.TethysTimeFuncs;
 import tethys.detection.DetectionsHandler;
@@ -101,7 +104,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 	}
 
 	@Override
-	public AlgorithmType getAlgorithm() {
+	public AlgorithmType getAlgorithm(Collection collection) {
 		/**
 		 * Probably need to split this to provide detection algorithm parameters and 
 		 * localisation algorithm parameters, or pass in the document type as a function 
@@ -113,14 +116,64 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 		} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
 			e.printStackTrace();
 		}
+		// do the parameters as normal whether it's dets or locs. 
 		nilus.AlgorithmType.Parameters algoParameters = this.getAlgorithmParameters();
 		if (algoParameters != null) {
 			algorithm.setParameters(algoParameters);
 		}
+		if (collection == Collection.Localizations) {
+			nilus.AlgorithmType.Parameters locParameters = this.getLocalisationParameters();
+			if (algoParameters == null) {
+				algorithm.setParameters(locParameters);
+			}
+			else if (locParameters != null) {
+				// merge the two sets, putting the localisation information first.  
+				List<Element> mainList = algoParameters.getAny();
+				List<Element> locList = locParameters.getAny();
+				if (mainList != null && locList != null) {
+					for (int i = 0; i < locList.size(); i++) {
+						mainList.add(i, locList.get(i));
+					}
+				}
+			}
+		}
+		else {
+		}
 
 		return algorithm;
 	}
 
+	public nilus.AlgorithmType.Parameters getLocalisationParameters() {
+		LocalisationAlgorithm algo = pamDataBlock.getLocalisationAlgorithm();
+		if (algo == null) {
+			return null;
+		}
+		LocalisationAlgorithmInfo algoInfo = algo.getAlgorithmInfo();
+		if (algoInfo == null) {
+			return null;
+		}
+		Object params = algoInfo.getParameters();
+		if (params == null) {
+			return null;
+		}
+		// pack the params object
+		TethysParameterPacker paramPacker = null;
+		try {
+			paramPacker = new TethysParameterPacker(tethysControl);
+		} catch (JAXBException e) {
+			e.printStackTrace();
+		}
+		Element paramEl = paramPacker.packObject(params, "localizer");
+		if (paramEl == null) {
+			return null;
+		}
+		nilus.AlgorithmType.Parameters parameters = new nilus.AlgorithmType.Parameters();
+		List<Element> paramList = parameters.getAny();
+		paramList.add(paramEl);
+		
+		return parameters;
+	}
+
 	@Override
 	public nilus.AlgorithmType.Parameters getAlgorithmParameters() {
 		if (pamControlledUnit instanceof PamSettings == false) {
@@ -536,6 +589,13 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 			return new TethysLocalisationInfo(pamDataBlock);
 		}
 	}
+
+	/**
+	 * @return the pamDataBlock
+	 */
+	protected PamDataBlock getPamDataBlock() {
+		return pamDataBlock;
+	}
 	
 
 

src/tethys/pamdata/TethysDataProvider.java

@@ -11,6 +11,7 @@ import nilus.DescriptionType;
 import nilus.Detection;
 import nilus.DetectionEffortKind;
 import nilus.GranularityEnumType;
+import tethys.Collection;
 import tethys.localization.TethysLocalisationInfo;
 import tethys.niluswraps.PDeployment;
 import tethys.output.StreamExportParams;
@@ -62,9 +63,10 @@ public interface TethysDataProvider {
 
 	/**
 	 * Get Algorithm information for a Tethys Detections document
+	 * @param collection Detections or Localisations may have different parameter sets. 
 	 * @return Algorithm information
 	 */
-	public AlgorithmType getAlgorithm();
+	public AlgorithmType getAlgorithm(Collection collection);
 	
 	/**
 	 * Get a list of allowed granularity types for this output 

src/tethys/pamdata/TethysParameterPacker.java

@@ -24,6 +24,7 @@ import PamController.settings.output.xml.PamguardXMLWriter;
 import PamModel.parametermanager.ManagedParameters;
 import PamModel.parametermanager.PamParameterData;
 import PamModel.parametermanager.PamParameterSet;
+import PamModel.parametermanager.SimplePamParameterData;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamProcess;
 import PamguardMVC.dataSelector.DataSelectParams;
@@ -125,16 +126,13 @@ public class TethysParameterPacker {
 						e1.printStackTrace();
 					}  
 					Element elf = docf.getDocumentElement();
-					elList.add(elf);/**
+					elList.add(elf);
+					/**
 					 * Is there a data filter ? If so, write it's 
 					 * XML parameters out here. 
 					 */
 					Element pEl = xmlWriter.writeObjectData(docf, elf, filterParams, null);
 				}
-				//				if (pEl != null) {
-////					filterEl.appendChild(pEl);
-//					elf.appendChild(filterEl);
-//				}
 			}
 		}
 		if (paramOption == TethysExportParams.DETECTOR_DATASELECTOR) {
@@ -177,6 +175,27 @@ public class TethysParameterPacker {
 		return elList;
 	}
 	
+	public Element packObject(Object data) {
+		return packObject(data, "parameters");
+	}
+
+	public Element packObject(Object data, String elementName) {
+		Document doc = null;
+		QName qname = new QName(MarshalXML.schema, elementName, "ty");
+		JAXBElement<String> jaxel = new JAXBElement<String>(
+				qname, String.class, data.getClass().getCanonicalName());
+
+		
+		try {
+			doc = marshaller.marshalToDOM(jaxel);
+		} catch (JAXBException | ParserConfigurationException e1) {
+			e1.printStackTrace();
+		}  
+		Element el = doc.getDocumentElement();
+		Element pEl = xmlWriter.writeObjectData(doc, el, data, null);
+		return pEl;
+	}
+
 	/**
 	 * Get a list of parent modules of the datablock, including it's own. 
 	 * @param dataBlock
@@ -199,7 +218,7 @@ public class TethysParameterPacker {
 		return chain;
 	}
 
-	private boolean createElement(Document document, Element parentEl, Object paramData, PamParameterData pamParam, ArrayList<Object> objectHierarchy) {
+	private Element createElement(Document document, Element parentEl, Object paramData, PamParameterData pamParam, ArrayList<Object> objectHierarchy) {
 		Class<? extends Object> javaClass = paramData.getClass();
 		if (PamguardXMLWriter.isWritableType(javaClass)) {
 			String name = pamParam.getFieldName();
@@ -209,63 +228,20 @@ public class TethysParameterPacker {
 			el.setTextContent(value);
 			parentEl.appendChild(el);
 			
-
-//			QName qname = new QName(MarshalXML.schema, name, "ty");
-//			JAXBElement<String> jaxel = new JAXBElement<String>(
-//					qname, String.class, value);
-//			
-//
-//			try {
-//				jxbm.marshal(jaxel, dom);
-//			} catch (JAXBException e) {
-//				e.printStackTrace();
-//			}
-//			Document doc = null;
-//			try {
-//				doc = marshaller.marshalToDOM(jaxel);
-//			} catch (JAXBException e) {
-//				e.printStackTrace();
-//			} catch (ParserConfigurationException e) {
-//				e.printStackTrace();
-//			}  
-//			Element el = doc.getDocumentElement();
-//			return el;
-			return true;
+			return el;
 		}
 		if (javaClass.isArray()) {
 			return writeArray(document, parentEl, paramData, pamParam, objectHierarchy);
 			
 		}
-		/*
-		 * 
-		if (javaClass.isArray()) {
-			return writeArray(doc, el, data, pamParam, objectHierarchy);
-		}
-		if (List.class.isAssignableFrom(javaClass)){
-			return writeList(doc, el, data, pamParam, objectHierarchy);
-		}
-		if (Map.class.isAssignableFrom(javaClass)){
-			return writeMap(doc, el, data, pamParam, objectHierarchy);
-		}
-		if (File.class.isAssignableFrom(javaClass)) {
-			return writeFile(doc, el, data, pamParam);
-		}
-		
-		else {
-			Element e = makeElement(doc, pamParam.getFieldName(), data.getClass().getName());
-			el.appendChild(e);
-			writeObjectData(doc, e, data, objectHierarchy);
-			return e;
-		}
-		 */
-		return false;
+		return null;
 	}
 
 
-	private boolean writeArray(Document document, Element parentEl, Object paramData, PamParameterData pamParam,
+	private Element writeArray(Document document, Element parentEl, Object paramData, PamParameterData pamParam,
 			ArrayList<Object> objectHierarchy) {
 		if (paramData.getClass().isArray() == false) {
-			return false;
+			return null;
 		}
 		String name = pamParam.getFieldName();
 		Element el = document.createElement(name);
@@ -274,10 +250,10 @@ public class TethysParameterPacker {
 		boolean ok = true;
 		for (int i = 0; i < n; i++) {
 			Object arrayEl = Array.get(paramData, i);
-			ok &= createElement(document, el, arrayEl, pamParam, objectHierarchy);
+			ok &= (createElement(document, el, arrayEl, pamParam, objectHierarchy) != null);
 		}
 		// TODO Auto-generated method stub
-		return ok;
+		return el;
 	}
 
 

src/tethys/swing/DatablockDetectionsPanel.java

@@ -1,5 +1,7 @@
 package tethys.swing;
 
+import static org.mockito.Mockito.RETURNS_DEEP_STUBS;
+
 import java.awt.BorderLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -105,24 +107,55 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 		//        if (rowIndex < 0) {
 		//        	return null;
 		//        }
+		NilusDataWrapper doc = detectionsForRow(rowIndex);
 		int colIndex = table.columnAtPoint(p);
 		switch (colIndex) {
 		case 0:
-			return "Tethys Detections document name";
+			if (doc != null) {
+				return "Tethys Detections document Id: " + doc.getDocumentId();
+			}
+			return "Tethys Detections document Id";
 		case 1:
+			if (dataBlock != null) {
+				return "Name of PAMGuard data stream: " + dataBlock.getLongDataName();
+			}
 			return "Name of PAMGuard data stream";
 		case 2:
-			return "Effort period";
+			return "Deployment type";
 		case 3:
-			return "Output granularity";
+			return "Output type and granularity ";
 		case 4:
-			return "Number of detection elements in document";
+			return "Effort period";
 		case 5:
-			return "Document abstract";
+			return "Number of detection or localization elements in document";
+		case 6:
+			DescriptionType desc = findDescription(rowIndex);
+			if (desc != null) {
+				String str = "Document abstract: " + desc.getAbstract();
+				return str;
+			}
+			else {
+				return "Document abstract";
+			}
 
 		}
 		return "No tip";
 	}
+	
+	
+	private DescriptionType findDescription(int rowIndex) {
+		NilusDataWrapper doc = detectionsForRow(rowIndex);
+		if (doc == null) {
+			return null;
+		}
+		Object desc = doc.getGotObject("getDescription");
+		if (desc instanceof DescriptionType) {
+			return (DescriptionType) desc;
+		}
+		else {
+			return null;
+		}
+	}
 
 	@Override
 	public JComponent getComponent() {
@@ -362,7 +395,7 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 
 	private class TableModel extends AbstractTableModel {
 
-		private String[] colNames = {"Document", "Detector", "Deployment", "Type", "Effort", "Granularity", "Count", "Abstract"};
+		private String[] colNames = {"Document", "Detector", "Deployment", "Type (Granularity)", "Effort", "Count", "Abstract"};
 
 		@Override
 		public int getRowCount() {
@@ -413,7 +446,10 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 					return dataSource.getDeploymentId();
 				}
 			case 3:
-				return pDets.getCollection();
+//				String col = pDets.getCollection().collectionName();
+//				
+//				return pDets.getCollection();
+				return getType(pDets);
 			case 4:
 //				XMLGregorianCalendar start = dets.getEffort().getStart();
 //				XMLGregorianCalendar stop = dets.getEffort().getEnd();
@@ -421,27 +457,8 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 				XMLGregorianCalendar stop = pDets.getEffortEnd();
 				return start + " to " + stop;
 			case 5:
-				Object effort = pDets.getGotObjects("getEffort");
-				if (effort instanceof DetectionEffort) {
-					DetectionEffort detectionEffort = (DetectionEffort) effort;
-					List<DetectionEffortKind> kinds = detectionEffort.getKind();
-					if (kinds == null) {
-						return null;
-					}
-					for (DetectionEffortKind kind : kinds) {
-						if (kind.getGranularity() != null) {
-							GranularityType granularity = kind.getGranularity();
-							return PDeployment.formatGranularity(granularity);
-							//						if (granularity != null) {
-							//							return granularity.getValue();
-							//						}
-						}
-					}
-				}
-				break;
-			case 6:
 				return pDets.count;
-			case 7:
+			case 6:
 				DescriptionType desc = pDets.getDescription();
 				if (desc != null) {
 					return desc.getAbstract();
@@ -451,4 +468,31 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 		}
 
 	}
+	
+	private String getType(NilusDataWrapper<PDetections> pDets) {
+		String type;
+		if (pDets == null || pDets.nilusObject == null) {
+			return null;
+		}
+		type = pDets.getCollection().collectionName();
+		
+		// if it's a detection, also get the granularity. 
+		Object effort = pDets.getGotObjects("getEffort");
+		if (effort instanceof DetectionEffort) {
+			DetectionEffort detectionEffort = (DetectionEffort) effort;
+			List<DetectionEffortKind> kinds = detectionEffort.getKind();
+			if (kinds == null) {
+				return type;
+			}
+			for (DetectionEffortKind kind : kinds) {
+				if (kind.getGranularity() != null) {
+					GranularityType granularity = kind.getGranularity();
+					if (granularity != null) {
+						type += " (" + granularity.getValue() + ")";
+					}
+				}
+			}
+		}
+		return type;
+	}
 }

src/tethys/swing/DatablockSynchPanel.java

@@ -299,7 +299,7 @@ public class DatablockSynchPanel extends TethysExportPanel {
 				long stop = synchInfo.getDataBlock().getPrimaryDataMap().getLastDataTime();
 				return String.format("%s - %s", PamCalendar.formatDBDateTime(start), PamCalendar.formatDBDateTime(stop));
 			case 3:
-				return synchInfo.getDetectionDocumentCount();
+				return synchInfo.getDetectionDocumentCount() +  synchInfo.getLocalizationDocumentCount();
 			}
 			return null;
 		}

src/tethys/swing/XMLStringView.java

@@ -2,8 +2,12 @@ package tethys.swing;
 
 import java.awt.BorderLayout;
 import java.awt.Window;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 
+import javax.swing.JMenuItem;
 import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
 import javax.swing.JScrollPane;
 import javax.swing.JTextArea;
 
@@ -26,11 +30,34 @@ public class XMLStringView extends PamDialog {
 		textArea.setEditable(false);
 		textArea.setCaretPosition(0);
 		
+		JPopupMenu popMenu = new JPopupMenu();
+		textArea.setComponentPopupMenu(popMenu);
+		JMenuItem copyItem = new JMenuItem("Copy");
+		copyItem.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				textArea.copy();
+			}
+		});
+		JMenuItem selItem = new JMenuItem("Select All");
+		selItem.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				textArea.selectAll();
+			}
+		});
+		
+		popMenu.add(copyItem);
+		popMenu.addSeparator();
+		popMenu.add(selItem);
+		
 		getCancelButton().setVisible(false);
 		setModal(false);
 		
 		getOkButton().setText("Close");
 		getOkButton().setToolTipText("Close window");
+		
+		setModal(false);
 	}
 	
 	public static void showDialog(Window parent, String collection, String documentId, String xmlString) {

src/tethys/swing/export/DescriptionTypePanel.java

@@ -101,12 +101,23 @@ public class DescriptionTypePanel {
 			tMethod.setText(null);
 		}
 		else {
+			checkDescription(description);
 			tObjectives.setText(description.getObjectives());
 			tAbstract.setText(description.getAbstract());
 			tMethod.setText(description.getMethod());
 		}
 	}
 	
+	/**
+	 * Auto fill some of the description fields. 
+	 * @param description
+	 */
+	private void checkDescription(DescriptionType description) {
+		if (description.getMethod() == null || description.getMethod().length() == 0) {
+			
+		}
+	}
+
 	public boolean getParams(DescriptionType description) {
 		Window f = PamGui.findComponentWindow(mainPanel);
 		if (checkField(requireObjective, tObjectives) == false) {

src/tethys/swing/export/DetectionsExportWizard.java

@@ -81,6 +81,7 @@ public class DetectionsExportWizard extends PamWizard {
 			granularityCard.setParams(streamExportParams);
 		}
 		if (wizardCard == descriptionCard) {
+			streamExportParams.checkDescription();
 			 descriptionCard.setParams(streamExportParams.getNilusDetectionDescription());
 		}
 		if (wizardCard == algorithmCard) {

src/whistlesAndMoans/WhistleMoanControl.java

@@ -10,6 +10,8 @@ import javax.swing.JMenuItem;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 
+import Localiser.LocalisationAlgorithm;
+import Localiser.LocalisationAlgorithmInfo;
 import dataPlots.data.TDDataProviderRegister;
 import dataPlotsFX.data.TDDataProviderRegisterFX;
 import dataPlotsFX.whistlePlotFX.WhistleMoanProviderFX;
@@ -30,7 +32,7 @@ import PamController.PamSettings;
 import PamView.PamSidePanel;
 import PamView.WrapperControlledGUISwing;
 
-public class WhistleMoanControl extends PamControlledUnit implements PamSettings {
+public class WhistleMoanControl extends PamControlledUnit implements PamSettings, LocalisationAlgorithm {
 
 	private WhistleToneConnectProcess whistleToneProcess;
 
@@ -229,4 +231,9 @@ public class WhistleMoanControl extends PamControlledUnit implements PamSettings
 	public String getModuleSummary(boolean clear) {
 		return whistleToneProcess.getModuleSummary(clear);
 	}
+	
+	@Override
+	public LocalisationAlgorithmInfo getAlgorithmInfo() {
+		return whistleToneProcess.getLocAlgorithmInfo();
+	}
 }

src/whistlesAndMoans/WhistleToneConnectProcess.java

@@ -15,6 +15,7 @@ import fftManager.FFTDataUnit;
 import generalDatabase.PamDetectionLogging;
 import generalDatabase.SQLLogging;
 import Array.ArrayManager;
+import Localiser.LocalisationAlgorithmInfo;
 import Localiser.algorithms.Correlations;
 import Localiser.algorithms.timeDelayLocalisers.bearingLoc.BearingLocaliser;
 import Localiser.algorithms.timeDelayLocalisers.bearingLoc.BearingLocaliserSelector;
@@ -1088,4 +1089,23 @@ public class WhistleToneConnectProcess extends PamProcess {
 		return sumText;
 	}
 
+
+	/**
+	 * Get info on current localisation algorithm. Grab the BL from the
+	 * first group that has one. 
+	 * @return
+	 */
+	public LocalisationAlgorithmInfo getLocAlgorithmInfo() {
+		if (shapeConnectors == null) {
+			return null;
+		}
+		for (int i = 0; i < shapeConnectors.length; i++) {
+			BearingLocaliser bl = shapeConnectors[i].bearingLocaliser;
+			if (bl != null && bl.getAlgorithmInfo() != null) {
+				return bl.getAlgorithmInfo();
+			}
+		}
+		return null;
+	}
+
 }