Tethys updates

And get rid of some other files that had got into the repo by accident

README.files/colorschememapping.xml

@@ -1,2 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<a:clrMap xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" bg1="lt1" tx1="dk1" bg2="lt2" tx2="dk2" accent1="accent1" accent2="accent2" accent3="accent3" accent4="accent4" accent5="accent5" accent6="accent6" hlink="hlink" folHlink="folHlink"/>

buildconfigurations/readme.txt

@@ -1,16 +0,0 @@
-To build an executable jar file from the PAMGuard source using Eclipse, you need to use this build configuration
-'Build PAMGuard.launch'
-You cannot simply export the project as a runnable jar file, or you will not get the required Maven dependencies. 
-To use this with Eclipse, from your workspace, select File, then import, then in the list of things to be imported select 
-Run/Debug Launch Configurations, hit Next
-Then in the Import Launch Configurations panel, browse to this folder. Select the folder (not a specific file)
-then in the left panel, select the folder, then in the right panel the configuration you wish to import 
-(i.e. Build PAMGuard.launch) and hit Finish
-Then go to 'Run Configurations' and find the launch in the 'Maven Builds' section. You'll probably have to change the 
-Base directory at the top of the panel to select the right project within your workspace. 
-Once that's done, you can Run the configuration. It will take a while to get all the Maven dependencies and will output 
-a runnable jar file into the 'targets' folder in your workspace. 
-The name and version number of the created files are taken from the POM.xml file, so edit that if you want a different name.
-For unknown reasons, it makes three files. They are all the same, you can delete the ones starting with 'original-' and 
-ending with '-shared'
-

src/RightWhaleEdgeDetector/species/RWTethysDataProvider.java

@@ -14,6 +14,7 @@ public class RWTethysDataProvider extends AutoTethysProvider {
 
 	public RWTethysDataProvider(TethysControl tethysControl, PamDataBlock pamDataBlock) {
 		super(tethysControl, pamDataBlock);
+		setAddFrequencyInfo(true);
 	}
 
 	@Override

src/clickDetector/ClickClassifiers/ClickBlockSpeciesManager.java

@@ -15,8 +15,8 @@ public class ClickBlockSpeciesManager extends DataBlockSpeciesManager<ClickDetec
 	public ClickBlockSpeciesManager(ClickControl clickControl, ClickDataBlock clickDataBlock) {
 		super(clickDataBlock);
 		this.clickControl = clickControl;
-		setDefaultDefaultSpecies(new SpeciesMapItem(ITISTypes.OTHER, "Unknown", "Unknown"));
+		setDefaultDefaultSpecies(new SpeciesMapItem(ITISTypes.CETACEAN, "Click", "Click"));
-		setDefaultSpeciesCode("Unknown");
+		setDefaultSpeciesCode("Click");
 	}
 
 	@Override

src/targetMotionOld/tethys/TMALocalizationCreator.java

@@ -12,25 +12,25 @@ import PamDetection.LocContents;
 import PamUtils.LatLong;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
-import nilus.AngularCoordinateType;
+import nilus.Helper;
 import nilus.LocalizationType;
 import nilus.Localize;
 import nilus.WGS84CoordinateType;
-import nilus.LocalizationType.Angular;
 import nilus.LocalizationType.Parameters;
 import nilus.LocalizationType.WGS84;
 import nilus.LocalizationType.Parameters.TargetMotionAnalysis;
 import nilus.Localize.Effort;
 import nilus.Localize.Effort.CoordinateReferenceSystem;
+import nilus.Localize.Effort.CoordinateReferenceSystem.ReferenceFrame;
 import pamMaths.PamVector;
 import targetMotionOld.TargetMotionLocaliser;
 import tethys.TethysTimeFuncs;
+import tethys.localization.Anchor;
 import tethys.localization.CoordinateName;
 import tethys.localization.LocalizationBuilder;
 import tethys.localization.LocalizationCreator;
 import tethys.localization.LocalizationSubTypes;
 import tethys.localization.LocalizationTypes;
-import tethys.localization.ReferenceFrame;
 import tethys.localization.TimeReference;
 import tethys.pamdata.AutoTethysProvider;
 
@@ -38,7 +38,7 @@ public class TMALocalizationCreator implements LocalizationCreator {
 
 
 	int maxDimension = 2;
-	
+
 	public TMALocalizationCreator(TargetMotionLocaliser targetMotionLocaliser) {
 		// TODO Auto-generated constructor stub
 	}
@@ -53,12 +53,36 @@ public class TMALocalizationCreator implements LocalizationCreator {
 		locTypes.add(LocalizationTypes.Point.toString());
 		locTypes.add(LocalizationTypes.PerpendicularRange.toString());
 
+		/**
+		 * Currently, TMA is only outputing as WGS84. Future release will have 
+		 * options to put out local xyz coordinates instead, in which case this 
+		 * will be Engineering and the referenceFrame will become instrument. 
+		 */
 		CoordinateReferenceSystem coordRefs = locEffort.getCoordinateReferenceSystem();
 		coordRefs.setName(CoordinateName.WGS84.toString());
 		coordRefs.setSubtype(LocalizationSubTypes.Geographic.toString());
-		
+
+		ReferenceFrame refFrame = localizationBuilder.getDefaultReferenceFrame(CoordinateName.WGS84, LocalizationSubTypes.Geographic);
+		if (refFrame != null) {
+			coordRefs.setReferenceFrame(refFrame);
+		}
+//		/**
+//		 * TMA is always references to the earth. 
+//		 */
+//		ReferenceFrame refFrame = coordRefs.getReferenceFrame();
+//		if (refFrame == null) {
+//			refFrame = new ReferenceFrame();
+//			try {
+//				Helper.createRequiredElements(refFrame);
+//			} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
+//				e.printStackTrace();
+//			}
+//			coordRefs.setReferenceFrame(refFrame);
+//		}
+//		refFrame.setAnchor(Anchor.WGS84.toString());
+
 		locEffort.setDimension(2);		
-		
+
 		return true;
 	}
 
@@ -115,19 +139,19 @@ public class TMALocalizationCreator implements LocalizationCreator {
 		 * Needs a bit of work to get errors in correct direction (needs import
 		 * of track data for this value ?) and conversion to latlong units.  
 		 */
-//		if (errorVec != null && errorVec.length >= 2) {
+		//		if (errorVec != null && errorVec.length >= 2) {
-//			wgsErr = new WGS84CoordinateType();
+		//			wgsErr = new WGS84CoordinateType();
-//			wgsErr.setLongitude(errorVec[0]);
+		//			wgsErr.setLongitude(errorVec[0]);
-//			wgsErr.setLatitude(errorVec[1]);
+		//			wgsErr.setLatitude(errorVec[1]);
-//			if (hasDepth && errorVec.length >= 3) {
+		//			if (hasDepth && errorVec.length >= 3) {
-//				wgsErr.setElevationM(errorVec[2]);
+		//				wgsErr.setElevationM(errorVec[2]);
-//			}
+		//			}
-//			wgs84.setCoordinateError(wgsErr);
+		//			wgs84.setCoordinateError(wgsErr);
-//		}
+		//		}
-		
+
-		
+
 		loc.setWGS84(wgs84);
-		
+
 		// set the TMA information
 		Parameters params = loc.getParameters();
 		if (params == null) {
@@ -142,31 +166,31 @@ public class TMALocalizationCreator implements LocalizationCreator {
 		if (timeAbeam != null) {
 			loc.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(timeAbeam));
 		}
-				
+
-//		 now also output a perpendicular distance.
+		//		 now also output a perpendicular distance.
 		Double perp = groupLocResult.getPerpendicularDistance();
 		if (perp != null) {
 			loc.setPerpendicularRangeM(AutoTethysProvider.roundDecimalPlaces(perp, 2));
 		}
-		
-		
-		// con only output one type. 
-//		if (perp != null) {
-//			AngularCoordinateType acType = new AngularCoordinateType();
-//			acType.setAngle1(90);
-//			acType.setDistanceM(AutoTethysProvider.roundDecimalPlaces(perp,1));
-//			Angular angular = new Angular();
-//			angular.setCoordinate(acType);
-//			if (errors != null) {
-//				AngularCoordinateType angErr = new AngularCoordinateType();
-//				angErr.setDistanceM(errors.norm());
-//				angular.setCoordinateError(angErr);
-//			}
-//			loc.setAngular(angular);
-//		}
 
-		
+
-		
+		// con only output one type. 
+		//		if (perp != null) {
+		//			AngularCoordinateType acType = new AngularCoordinateType();
+		//			acType.setAngle1(90);
+		//			acType.setDistanceM(AutoTethysProvider.roundDecimalPlaces(perp,1));
+		//			Angular angular = new Angular();
+		//			angular.setCoordinate(acType);
+		//			if (errors != null) {
+		//				AngularCoordinateType angErr = new AngularCoordinateType();
+		//				angErr.setDistanceM(errors.norm());
+		//				angular.setCoordinateError(angErr);
+		//			}
+		//			loc.setAngular(angular);
+		//		}
+
+
+
 		return loc;
 	}
 

src/tethys/deployment/DeploymentHandler.java

@@ -87,6 +87,7 @@ import tethys.dbxml.TethysException;
 import tethys.deployment.swing.DeploymentWizard;
 import tethys.deployment.swing.EffortProblemDialog;
 import tethys.deployment.swing.RecordingGapDialog;
+import tethys.localization.TethysLatLong;
 import tethys.niluswraps.PDeployment;
 import tethys.output.TethysExportParams;
 import tethys.pamdata.AutoTethysProvider;
@@ -909,8 +910,8 @@ public class DeploymentHandler extends CollectionHandler implements TethysStateO
 			GpsData gpsData = gpsDataUnit.getGpsData();
 			Point gpsPoint = new Point();
 			gpsPoint.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(gpsDataUnit.getTimeMilliseconds()));
-			gpsPoint.setLatitude(gpsData.getLatitude());
+			gpsPoint.setLatitude(TethysLatLong.formatLatitude(gpsData.getLatitude()));
-			gpsPoint.setLongitude(PamUtils.constrainedAngle(gpsData.getLongitude()));
+			gpsPoint.setLongitude(TethysLatLong.formatLongitude(gpsData.getLongitude()));
 			CourseOverGroundDegN cog = gpsPoint.getCourseOverGroundDegN();
 			if (cog == null) {
 				cog = new CourseOverGroundDegN();
@@ -1080,8 +1081,8 @@ public class DeploymentHandler extends CollectionHandler implements TethysStateO
 			double recLat = deploymentData.getRecoveryDetails().getLatitude();
 			double recLong = deploymentData.getRecoveryDetails().getLongitude();
 			if (recLat != 0 & recLong != 0.) {
-				deployment.getRecoveryDetails().setLatitude(recLat);
+				deployment.getRecoveryDetails().setLatitude(TethysLatLong.formatLatitude(recLat));
-				deployment.getRecoveryDetails().setLongitude(PamUtils.constrainedAngle(recLong));
+				deployment.getRecoveryDetails().setLongitude(TethysLatLong.formatLongitude(recLong));
 			}
 		}
 		

src/tethys/detection/DetectionsHandler.java

@@ -620,7 +620,7 @@ public class DetectionsHandler extends CollectionHandler {
 		 * Check the document name isn't already used and increment id as necessary.
 		 */
 		while (true) {
-			fullId = String.format("%s_%d", prefix, uniqueDetectionsId++);
+			fullId = String.format("%s_D_%d", prefix, uniqueDetectionsId++);
 			if (!tethysControl.getDbxmlQueries().documentExists(Collection.Detections.toString(), fullId)) {
 				break;
 			}

src/tethys/localization/Anchor.java

@@ -0,0 +1,10 @@
+package tethys.localization;
+
+/**
+ * Anchors for localization effort coordinate system.
+ * @author dg50
+ *
+ */
+public enum Anchor {
+UTMZone, WGS84, instrument;
+}

src/tethys/localization/LocalizationBuilder.java

@@ -3,6 +3,18 @@ package tethys.localization;
 import java.math.BigInteger;
 import java.util.List;
 
+import javax.xml.bind.JAXBException;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.w3c.dom.Element;
+
+import Array.ArrayManager;
+import Array.PamArray;
+import Array.Streamer;
+import Array.streamerOrigin.OriginSettings;
+import Array.streamerOrigin.StaticOriginSettings;
+import GPS.GpsData;
+import GPS.GpsDataUnit;
 import Localiser.LocalisationAlgorithm;
 import Localiser.LocalisationAlgorithmInfo;
 import Localiser.detectionGroupLocaliser.GroupLocResult;
@@ -14,6 +26,7 @@ import PamUtils.LatLong;
 import PamUtils.PamUtils;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
+import binaryFileStorage.DataUnitFileInformation;
 import nilus.AlgorithmType;
 import nilus.AngularCoordinateType;
 import nilus.BearingType;
@@ -31,10 +44,12 @@ import nilus.LocalizationType.Parameters;
 import nilus.LocalizationType.References;
 import nilus.LocalizationType.WGS84;
 import nilus.LocalizationType.Parameters.TargetMotionAnalysis;
+import nilus.LocalizationType.Parameters.UserDefined;
 import nilus.LocalizationType.References.Reference;
 import nilus.Localize.Effort;
 import nilus.Localize.Effort.CoordinateReferenceSystem;
 import nilus.Localize.Effort.ReferencedDocuments;
+import nilus.Localize.Effort.CoordinateReferenceSystem.ReferenceFrame;
 import nilus.Localize.Effort.ReferencedDocuments.Document;
 import pamMaths.PamVector;
 import tethys.Collection;
@@ -68,6 +83,8 @@ public class LocalizationBuilder {
 	private Localize currentDocument;
 	private LocalizationCreator localisationCreator;
 	private TethysDataProvider dataProvider;
+	
+	private Helper helper;
 
 	public LocalizationBuilder(TethysControl tethysControl, PDeployment deployment, Detections detectionsDocument, PamDataBlock dataBlock,
 			StreamExportParams exportParams) {
@@ -76,6 +93,11 @@ public class LocalizationBuilder {
 		this.dataBlock = dataBlock;
 		this.streamExportParams = exportParams;
 		this.tethysControl = tethysControl;
+		try {
+			helper = new Helper();
+		} catch (JAXBException e) {
+			e.printStackTrace();
+		}
 		dataProvider = dataBlock.getTethysDataProvider(tethysControl);
 		localisationHandler = tethysControl.getLocalizationHandler();
 		localisationAlgorithm = dataBlock.getLocalisationAlgorithm();
@@ -123,13 +145,13 @@ public class LocalizationBuilder {
 			}
 			Document detectsDoc = new Document();
 			detectsDoc.setId(detectionsDocument.getId());
-			detectsDoc.setType(Collection.Localizations.collectionName());
+			detectsDoc.setType(Collection.Detections.collectionName());
 			detectsDoc.setIndex(BigInteger.ZERO);
 			eff.getReferencedDocuments().getDocument().add(detectsDoc);
 		}
 
 
-		String prefix = deployment.nilusObject.getId() + "_" + dataProvider.getDetectionsName();
+		String prefix = deployment.nilusObject.getId() + "_" + dataProvider.getDetectionsName() + "_L";
 		String fullId = localisationHandler.getLocalisationdocId(prefix);
 		currentDocument.setId(fullId);
 		//		detections.setDescription(dataProvider.getDescription(deployment, tethysExportParams));
@@ -185,6 +207,54 @@ public class LocalizationBuilder {
 		return done;
 	}
 	
+	/**
+	 * Get a default reference frame for the header of a localization document. This is very dependent
+	 * on the localization subtype. Also on whether the array is fixed or moving. It it's fixed, then
+	 * we also need to add the instrument lat long. 
+	 * @param coordinateName
+	 * @param subType
+	 * @return
+	 */
+	public ReferenceFrame getDefaultReferenceFrame(CoordinateName coordinateName, LocalizationSubTypes subType) {
+		ReferenceFrame referenceFrame = new ReferenceFrame();
+		switch (subType) {
+		case Derived:
+			referenceFrame.setAnchor(Anchor.UTMZone.toString()); // i never use this on. If I do, this will need work !
+			break;
+		case Engineering:
+			referenceFrame.setAnchor(Anchor.instrument.toString()); 
+			break;
+		case Geographic:
+			referenceFrame.setAnchor(Anchor.WGS84.toString()); 
+			break;
+		default:
+			break;
+		}
+		/*
+		 * And see if it's a fixed or moving array. Will just have to look at the 
+		 * first streamer here. Hard to copy with multiples !
+		 */
+		PamArray array = ArrayManager.getArrayManager().getCurrentArray();
+		Streamer streamer = array.getStreamer(0);
+		if (streamer != null) {
+			OriginSettings origin = streamer.getOriginSettings();
+			if (origin instanceof StaticOriginSettings) {
+				StaticOriginSettings staticOrigin = (StaticOriginSettings) origin;
+				GpsDataUnit ll = staticOrigin.getStaticPosition();
+				if (ll != null) {
+					GpsData pos = ll.getGpsData();
+					if (pos != null) {
+						referenceFrame.setLatitude(TethysLatLong.formatLatitude(pos.getLatitude()));
+						referenceFrame.setLongitude(TethysLatLong.formatLongitude(pos.getLongitude()));
+						referenceFrame.setDatum(String.format("Altitude %3.2fm", pos.getHeight()));
+					}
+				}
+			}
+		}
+		
+		return referenceFrame;
+	}
+	
 	public boolean sortStandardCoordinates(PamDataBlock dataBlock) {
 		LocalisationInfo locInfo = dataBlock.getLocalisationContents();
 		Effort locEffort = currentDocument.getEffort();
@@ -202,6 +272,7 @@ public class LocalizationBuilder {
 //		List<String> locTypes = locEffort.getLocalizationType();
 		boolean ambiguity = locInfo.hasLocContent(LocContents.HAS_AMBIGUITY);
 		CoordinateReferenceSystem coordRefs = locEffort.getCoordinateReferenceSystem();		
+		ReferenceFrame referenceFrame = null;
 		List<String> locTypes = locEffort.getLocalizationType();
 		if (locInfo.getLocContent() == 0) {
 			return false;
@@ -217,6 +288,7 @@ public class LocalizationBuilder {
 			else {
 				locEffort.setDimension(2);
 			}
+			referenceFrame = getDefaultReferenceFrame(CoordinateName.WGS84, LocalizationSubTypes.Geographic);
 //			locEffort.set
 		}
 		else if (locInfo.hasLocContent(LocContents.HAS_XYZ)) {
@@ -224,12 +296,14 @@ public class LocalizationBuilder {
 			coordRefs.setSubtype(LocalizationSubTypes.Engineering.toString());
 			locTypes.add(LocalizationTypes.Point.toString());
 			locEffort.setDimension(3);
+			referenceFrame = getDefaultReferenceFrame(CoordinateName.Cartesian, LocalizationSubTypes.Engineering);
 		}
 		else if (locInfo.hasLocContent(LocContents.HAS_XY)) {
 			coordRefs.setName(CoordinateName.Cartesian.toString());
 			coordRefs.setSubtype(LocalizationSubTypes.Engineering.toString());
 			locTypes.add(LocalizationTypes.Point.toString());
 			locEffort.setDimension(2);
+			referenceFrame = getDefaultReferenceFrame(CoordinateName.Cartesian, LocalizationSubTypes.Engineering);
 		}
 		else if (locInfo.hasLocContent(LocContents.HAS_BEARING)) {
 			coordRefs.setName(CoordinateName.Polar.toString());
@@ -241,10 +315,12 @@ public class LocalizationBuilder {
 			else {
 				locEffort.setDimension(2);
 			}
+			referenceFrame = getDefaultReferenceFrame(CoordinateName.Polar, LocalizationSubTypes.Engineering);
 		}
 		else {
 			return false;
 		}
+		coordRefs.setReferenceFrame(referenceFrame);
 		
 		return true;
 	}
@@ -329,21 +405,41 @@ public class LocalizationBuilder {
 					locType.setSpeciesId(species);
 				}
 			}
-
+			
-			References references = locType.getReferences();
+			/*
-			if (references == null) {
+			 * Add references back to PAMGuard data as for Detections. 
-				references = new References();
+			 * Same code as in Detections, but classes are different (though with the same fields). 
-				try {
+			 */
-					Helper.createRequiredElements(references);
+			Parameters params = getParameters(locType);
-				} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
+			String uid = BigInteger.valueOf(dataUnit.getUID()).toString();
-					e.printStackTrace();
+			Element el = addUserDefined(params,"PAMGuardUID", uid);
-				}
+			DataUnitFileInformation fileInf = dataUnit.getDataUnitFileInformation();
-				locType.setReferences(references);
+			if (fileInf != null) {
+				el.setAttribute("BinaryFile", fileInf.getShortFileName(2048));
+				el.setAttribute("FileIndex", Long.valueOf(fileInf.getIndexInFile()).toString());
 			}
-			Reference reference = new Reference();
+			if (dataUnit.getDatabaseIndex() > 0) {
-			reference.setIndex(BigInteger.valueOf(dataUnit.getUID()));
+				// only write the database index if it's > 0, i.e. is used.
-			reference.setEventRef("UID");
+				addUserDefined(params, "DatabaseId", String.format("%d", dataUnit.getDatabaseIndex()));
-			locType.getReferences().getReference().add(reference);
+			}
+
+			/*
+			 * Not needed. something to do with references to Detection docs. 
+			 */
+//			References references = locType.getReferences();
+//			if (references == null) {
+//				references = new References();
+//				try {
+//					Helper.createRequiredElements(references);
+//				} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
+//					e.printStackTrace();
+//				}
+//				locType.setReferences(references);
+//			}
+//			Reference reference = new Reference();
+//			reference.setIndex(BigInteger.valueOf(dataUnit.getUID()));
+//			reference.setEventRef("UID");
+//			locType.getReferences().getReference().add(reference);
 
 			return locType;
 		}
@@ -405,11 +501,7 @@ public class LocalizationBuilder {
 			locType.setWGS84(wgs84);
 			
 //			locType.setParameters(null);
-			Parameters params = locType.getParameters();
+			Parameters params = getParameters(locType);
-			if (params == null) {
-				params = new Parameters();
-				locType.setParameters(params);
-			}
 			TargetMotionAnalysis tma = new TargetMotionAnalysis();
 			tma.setStart(TethysTimeFuncs.xmlGregCalFromMillis(dataUnit.getTimeMilliseconds()));
 			tma.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(dataUnit.getEndTimeInMilliseconds()));
@@ -442,6 +534,40 @@ public class LocalizationBuilder {
 
 			return locType;
 		}
+		
+		/**
+		 * Convenience method to get the Parameters object for a localisation and
+		 * to automatically create it if it doesn't exist. 
+		 * @param localization
+		 * @return
+		 */
+		public Parameters getParameters(LocalizationType localization) {
+			Parameters params = localization.getParameters();
+			if (params == null) {
+				params = new Parameters();
+				localization.setParameters(params);
+			}
+			return params;
+		}
+		
+		public Element addUserDefined(Parameters parameters, String parameterName, String parameterValue) {
+			UserDefined userDefined = parameters.getUserDefined();
+			if (userDefined == null) {
+				userDefined = new UserDefined();
+				parameters.setUserDefined(userDefined);
+			}
+			Element el = null;
+			try {
+				el = helper.AddAnyElement(userDefined.getAny(), parameterName, parameterValue);
+			} catch (JAXBException e) {
+				e.printStackTrace();
+				return null;
+			} catch (ParserConfigurationException e) {
+				e.printStackTrace();
+				return null;
+			}
+			return el;
+		}
 
 		public LocalizationType createSphericalLoc(PamDataUnit dataUnit) {
 			// TODO Auto-generated method stub

src/tethys/localization/LocalizationHandler.java

@@ -2,17 +2,8 @@ package tethys.localization;
 
 import java.util.ArrayList;
 
-import Localiser.detectionGroupLocaliser.GroupLocResult;
-import Localiser.detectionGroupLocaliser.GroupLocalisation;
-import PamDetection.AbstractLocalisation;
-import PamDetection.LocContents;
-import PamUtils.LatLong;
-import PamUtils.PamUtils;
 import PamguardMVC.PamDataBlock;
 import nilus.Localize;
-import nilus.SpeciesIDType;
-import pamMaths.PamVector;
-import nilus.Localize.Effort.CoordinateReferenceSystem;
 import tethys.Collection;
 import tethys.CollectionHandler;
 import tethys.TethysControl;

src/tethys/localization/TethysLatLong.java

@@ -0,0 +1,122 @@
+package tethys.localization;
+
+import PamUtils.PamUtils;
+import tethys.pamdata.AutoTethysProvider;
+
+/**
+ * Static formatting (rounding and range checking) functions for latlong values. 
+ * @author dg50
+ *
+ */
+public class TethysLatLong {
+
+	/*
+	 * A degree is 60 minutes and a minute is one mile = 1852m. 
+	 * Therefore one metre of latitude is 9e-6 degrees. 
+	 * One mm of latitude is therefore 9e-9 degrees. 
+	 * GPS Accuracy is generally <3m, so 6dp generally OK for track data. however, 
+	 * localisations around a small static array may want mm accuracy, so need 8dp. 
+	 * For a double precision number, resolution at 360 degrees is 14dp
+	 * 
+	 */
+	
+	/**
+	 * Number of decimal places for metre accuracy
+	 */
+	public static int metreDecimalPlaces = 6;
+	
+	/**
+	 * Number of decimal places for mm accuracy. 
+	 */
+	public static int mmDecimalPlaces = 9;
+	
+	/**
+	 * Check range of  a latitude value. 
+	 * This function does absolutely nothing, but is here for completeness. 
+	 * @param latitude
+	 * @return
+	 */
+	public static Double formatLatitude(Double latitude) {
+		if (latitude == null) {
+			return null;
+		}
+		return latitude;
+	}
+	
+	/**
+	 * Check range and round a latitude value to a set number of decimal places. 
+	 * @param latitude
+	 * @param decimalPlaces
+	 * @return
+	 */
+	public static Double formatLatitude(Double latitude, int decimalPlaces) {
+		if (latitude == null) {
+			return null;
+		}
+		return AutoTethysProvider.roundDecimalPlaces(latitude, decimalPlaces);
+	}
+	
+	/**
+	 * format a latitude to metre accuracy
+	 * @param latitude
+	 * @return
+	 */
+	public static Double formatLatitude_m(Double latitude) {
+		return formatLatitude(latitude, metreDecimalPlaces);
+	}
+	
+	/**
+	 * format a latitude to mm accuracy
+	 * @param latitude
+	 * @return
+	 */
+	public static Double formatLatitude_mm(Double latitude) {
+		return formatLatitude(latitude, mmDecimalPlaces);
+	}
+	
+	/**
+	 * Check range of a longitude value which must be between 0 and 360. 
+	 * This function does absolutely nothing, but is here for completeness. 
+	 * @param latitude
+	 * @return
+	 */
+	public static Double formatLongitude(Double longitude) {
+		if (longitude == null) {
+			return null;
+		}
+		return PamUtils.constrainedAngle(longitude);
+	}
+	
+	/**
+	 * Check range and round a longitude value to a set number of decimal places. 
+	 * @param latitude
+	 * @param decimalPlaces
+	 * @return
+	 */
+	public static Double formatLongitude(Double longitude, int decimalPlaces) {
+		if (longitude == null) {
+			return null;
+		}
+		longitude = formatLongitude(longitude); // constrain first.  
+		return AutoTethysProvider.roundDecimalPlaces(longitude, decimalPlaces);
+	}
+	
+	/**
+	 * format a longitude value to m accuracy. 
+	 * @param latitude
+	 * @return
+	 */
+	public static Double formatLongitude_m(Double longitude) {
+		return formatLongitude(longitude, metreDecimalPlaces);
+	}
+	
+	/**
+	 * format a longitude value to mm accuracy. 
+	 * @param latitude
+	 * @return
+	 */
+	public static Double formatLongitude_mm(Double longitude) {
+		return formatLongitude(longitude, mmDecimalPlaces);
+	}
+
+}

src/tethys/pamdata/AutoTethysProvider.java

@@ -1,32 +1,34 @@
 package tethys.pamdata;
 
+import java.io.StringReader;
 import java.math.BigInteger;
 import java.util.ArrayList;
 import java.util.List;
 
+import javax.xml.bind.JAXBException;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.Source;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMResult;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamSource;
+
 import org.w3c.dom.Document;
 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;
-import PamController.settings.output.xml.PamguardXMLWriter;
 import PamDetection.LocalisationInfo;
-import PamUtils.XMLUtils;
 import PamguardMVC.DataAutomationInfo;
-import PamguardMVC.DataUnitBaseData;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
 import PamguardMVC.PamProcess;
 import PamguardMVC.TFContourData;
 import PamguardMVC.TFContourProvider;
 import binaryFileStorage.DataUnitFileInformation;
-import generalDatabase.DBSchemaWriter;
-import generalDatabase.SQLLogging;
 import nilus.AlgorithmType;
 import nilus.Deployment;
 import nilus.DescriptionType;
@@ -52,23 +54,11 @@ import tethys.species.SpeciesMapItem;
 import tethys.swing.export.ExportWizardCard;
 import whistleClassifier.WhistleContour;
 
-import javax.xml.bind.JAXBException;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.*;
-import javax.xml.transform.dom.DOMResult;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-import javax.xml.transform.stream.StreamSource;
-import java.io.File;
-import java.io.IOException;
-import java.io.StringReader;
-import java.net.URISyntaxException;
-
 /**
- * Automatically provides Tethys data for a PAMGuard datablock. 
+ * Automatically provides Tethys data for a PAMGuard datablock.
  * Does most of what needs to be done, though individual modules
- * will want to override this, call the base createDetection function and then add a 
+ * will want to override this, call the base createDetection function and then add a
- * few more bespoke elements. 
+ * few more bespoke elements.
  * @author dg50
  *
  */
@@ -79,6 +69,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 	private PamControlledUnit pamControlledUnit;
 	private TethysControl tethysControl;
 	private Helper helper;
+	private boolean addFrequencyInfo  = false;
 
 	public AutoTethysProvider(TethysControl tethysControl, PamDataBlock pamDataBlock) {
 		this.tethysControl = tethysControl;
@@ -91,7 +82,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 			e.printStackTrace();
 		}
 	}
-	
+
 	@Override
 	public DescriptionType getDescription(Deployment deployment, TethysExportParams tethysExportParams) {
 		DescriptionType description = new DescriptionType();
@@ -106,9 +97,9 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 	@Override
 	public AlgorithmType getAlgorithm(Collection collection) {
 		/**
-		 * Probably need to split this to provide detection algorithm parameters and 
+		 * Probably need to split this to provide detection algorithm parameters and
-		 * localisation algorithm parameters, or pass in the document type as a function 
+		 * localisation algorithm parameters, or pass in the document type as a function
-		 * argument. 
+		 * argument.
 		 */
 		AlgorithmType algorithm = new AlgorithmType();
 		try {
@@ -116,7 +107,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 		} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
 			e.printStackTrace();
 		}
-		// do the parameters as normal whether it's dets or locs. 
+		// do the parameters as normal whether it's dets or locs.
 		nilus.AlgorithmType.Parameters algoParameters = this.getAlgorithmParameters();
 		if (algoParameters != null) {
 			algorithm.setParameters(algoParameters);
@@ -125,7 +116,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 			nilus.AlgorithmType.Parameters locParameters = this.getLocalisationParameters();
 			if (locParameters == null) {
 				/*
-				 * It seems Tethys MUST have parameters, so make an empty one if needed. 
+				 * It seems Tethys MUST have parameters, so make an empty one if needed.
 				 */
 				locParameters = new nilus.AlgorithmType.Parameters();
 			}
@@ -133,7 +124,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 				algorithm.setParameters(locParameters);
 			}
 			else if (locParameters != null) {
-				// merge the two sets, putting the localisation information first.  
+				// merge the two sets, putting the localisation information first.
 				List<Element> mainList = algoParameters.getAny();
 				List<Element> locList = locParameters.getAny();
 				if (mainList != null && locList != null) {
@@ -150,7 +141,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 	}
 
 	/**
-	 * Localisation parameters. Some localisers don't actually have any parameters, 
+	 * Localisation parameters. Some localisers don't actually have any parameters,
 	 * but Tethys requires a parameters element, so if there aren't any, set a dummy
 	 * @return
 	 */
@@ -181,13 +172,13 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 		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) {
+		if (!(pamControlledUnit instanceof PamSettings)) {
 			return null;
 		}
 		PamSettings pamSettings = (PamSettings) pamControlledUnit;
@@ -211,7 +202,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 
 	/**
 	 * Not used. Was an attempt to automatically add name spaces to the PAMGuard settings
-	 * XML I generate, but we found a better way. 
+	 * XML I generate, but we found a better way.
 	 * @param doc
 	 * @param settingsEl
 	 * @param xmlNameSpace
@@ -270,7 +261,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 
 			DOMSource source = new DOMSource(doc);
 
-			//            Result 
+			//            Result
 			//			Source text = new StreamSource(new File("input.xml"));
 			DOMResult result = new DOMResult();
 			transformer.transform(source, result);
@@ -294,8 +285,8 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 	}
 
 	/**
-	 * Algorithm method. Default is the module name. Can change to a paper citation 
+	 * Algorithm method. Default is the module name. Can change to a paper citation
-	 * by overriding this 
+	 * by overriding this
 	 * @return
 	 */
 	private String getAlgorithmMethod() {
@@ -335,16 +326,21 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 		}
 		detection.setSpeciesId(species);
 		/*
-		 * NOTE: I use channel bitmaps throughout since detections are often made on multiple channels. 
+		 * NOTE: I use channel bitmaps throughout since detections are often made on multiple channels.
 		 */
 		detection.setChannel(BigInteger.valueOf(dataUnit.getChannelBitmap()));
 
 		nilus.Detection.Parameters detParams = new nilus.Detection.Parameters();
 		detection.setParameters(detParams);
-		double[] freqs = dataUnit.getFrequency();
+		if (addFrequencyInfo) {
-		if (freqs != null && freqs[1] != 0) {
+			/**
-			detParams.setMinFreqHz(freqs[0]);
+			 * Don't add by default.
-			detParams.setMaxFreqHz(freqs[1]);
+			 */
+			double[] freqs = dataUnit.getFrequency();
+			if (freqs != null && freqs[1] != 0) {
+				detParams.setMinFreqHz(freqs[0]);
+				detParams.setMaxFreqHz(freqs[1]);
+			}
 		}
 		double ampli = dataUnit.getAmplitudeDB();
 		ampli = roundDecimalPlaces(ampli, 1);
@@ -359,7 +355,8 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 			el.setAttribute("BinaryFile", fileInf.getShortFileName(2048));
 			el.setAttribute("FileIndex", Long.valueOf(fileInf.getIndexInFile()).toString());
 		}
-		if (dataUnit.getDatabaseIndex() >= 0) {
+		if (dataUnit.getDatabaseIndex() > 0) {
+			// only write the database index if it's > 0, i.e. is used.
 			addUserDefined(detParams, "DatabaseId", String.format("%d", dataUnit.getDatabaseIndex()));
 		}
 
@@ -387,7 +384,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 
 	/**
 	 * Get tonal sounds contour. Sadly there are two slightly different interfaces in use
-	 * in PAMGuard, so try them both. 
+	 * in PAMGuard, so try them both.
 	 * @param detParams
 	 * @return true if a contour was added
 	 */
@@ -402,7 +399,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 				List<Double> offsetS = tonal.getOffsetS();
 				List<Double> hz = tonal.getHz();
 				for (int i = 0; i < tMillis.length; i++) {
-					offsetS.add(roundSignificantFigures((double) (tMillis[i]-tMillis[0]) / 1000., 4));
+					offsetS.add(roundSignificantFigures((tMillis[i]-tMillis[0]) / 1000., 4));
 					hz.add(roundSignificantFigures(fHz[i], 4));
 				}
 				detParams.setTonal(tonal);
@@ -485,7 +482,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 			kind.setCall(mapItem.getCallType());
 
 
-			effortKinds.add(kind);		
+			effortKinds.add(kind);
 
 		}
 
@@ -495,7 +492,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 	public String getDetectionsMethod() {
 		/*
 		 *  could really do with knowing what type of detector we're dealing with, i.e. if it's
-		 *  automatic or manual. For most blocks this is fixed, though some may have a mixture of both ! 
+		 *  automatic or manual. For most blocks this is fixed, though some may have a mixture of both !
 		 */
 		DataAutomationInfo dataAutomation = pamDataBlock.getDataAutomationInfo();
 		String method;
@@ -524,7 +521,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 		String blockName = pamDataBlock.getDataName();
 		String documentName;
 		/**
-		 * If the datablock name is the same as the unit name, no need to repeat onesself. 
+		 * If the datablock name is the same as the unit name, no need to repeat onesself.
 		 */
 		if (pcuName.equals(blockName)) {
 			documentName = new String(pcuName); // copy it, since we're about to modify it!
@@ -539,7 +536,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 	public static double roundDecimalPlaces(double value, int decPlaces) {
 		double scale = Math.pow(10, decPlaces);
 		long longVal = Math.round(value*scale);
-		return (double) longVal/scale;
+		return longVal/scale;
 	}
 
 	public static double roundSignificantFigures(double value, int sigFigs) {
@@ -551,7 +548,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 		double scale = sigFigs-Math.floor(Math.log10(value));
 		scale = Math.pow(10, scale);
 		long longVal = Math.round(value*scale);
-		return sign*(double) longVal/scale;
+		return sign*longVal/scale;
 	}
 
 	@Override
@@ -571,7 +568,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 		return true;
 	}
 
-	
+
 	@Override
 	public boolean canExportLocalisations(GranularityEnumType granularityType) {
 		LocalisationInfo locCont = pamDataBlock.getLocalisationContents();
@@ -582,7 +579,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 	}
 
 	/**
-	 * Granularity is OK for export. 
+	 * Granularity is OK for export.
 	 * @param granularityType
 	 * @return
 	 */
@@ -607,7 +604,21 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 	protected PamDataBlock getPamDataBlock() {
 		return pamDataBlock;
 	}
-	
+
+	/**
+	 * @return the addFrequencyInfo
+	 */
+	public boolean isAddFrequencyInfo() {
+		return addFrequencyInfo;
+	}
+
+	/**
+	 * @param addFrequencyInfo the addFrequencyInfo to set
+	 */
+	public void setAddFrequencyInfo(boolean addFrequencyInfo) {
+		this.addFrequencyInfo = addFrequencyInfo;
+	}
+
 
 
 }

src/tethys/species/ITISTypes.java

@@ -7,8 +7,14 @@ package tethys.species;
  */
 public class ITISTypes {
 
+	/*
+	 * A few that get used in defaults copied from itis.gov for convenience. 
+	 */
 	public static final int OTHER = -10;
 	public static final int ANTHROPOGENIC = 1758;
+	public static final int CETACEAN = 180403;
+	public static final int ODONTOCETE = 180404;
+	public static final int MYSTICETE = 552298;
 	
 	public static final String getName(int code) {
 		switch (code) {

src/whistlesAndMoans/species/WhistleMoanTethysProvider.java

@@ -8,6 +8,7 @@ public class WhistleMoanTethysProvider extends AutoTethysProvider {
 
 	public WhistleMoanTethysProvider(TethysControl tethysControl, PamDataBlock pamDataBlock) {
 		super(tethysControl, pamDataBlock);
+		setAddFrequencyInfo(true);
 	}
 
 }