Refactoring Tethys

A lot of refactoring of Nilus wrappers with more useful Objects for PAMGUard to work with.

.classpath

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

pom.xml

@@ -888,7 +888,7 @@
 	<dependency>
 		<groupId>tethys.org</groupId>
 		<artifactId>nilus</artifactId>
-		<version>3.0</version>
+		<version>3.1</version>
 	</dependency>
 
 	<dependency>

repo/tethys/org/nilus/3.1/_remote.repositories

@@ -0,0 +1,4 @@
+#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
+#Tue Jul 16 19:29:56 BST 2024
+nilus-3.1.jar>=
+nilus-3.1.pom>=

repo/tethys/org/nilus/3.1/nilus-3.1.pom

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>tethys.org</groupId>
+  <artifactId>nilus</artifactId>
+  <version>3.1</version>
+  <description>POM was created from install:install-file</description>
+</project>

src/PamView/dialog/PamDialog.java

@@ -306,6 +306,9 @@ abstract public class PamDialog extends JDialog {
 	 * put the dialog near the mouse location. 
 	 */
 	public void moveToMouseLocation() {
+		if (MouseInfo.getPointerInfo() == null) {
+			return;
+		}
 		Point mouse = MouseInfo.getPointerInfo().getLocation();
 		moveToLocation(mouse);
 	}

src/Spectrogram/SpectrogramDisplay.java

@@ -2929,7 +2929,7 @@ InternalFrameListener, DisplayPanelContainer, SpectrogramParametersUser, PamSett
 			String name = spectrogramDisplay.getDataSelectorName(panelId);
 			DataSelector dataSelector = usedDataBlock.getDataSelector(name, false);
 			
-			if (dataSelector.getParams().getCombinationFlag() == DataSelectParams.DATA_SELECT_DISABLE) {
+			if (dataSelector != null && dataSelector.getParams().getCombinationFlag() == DataSelectParams.DATA_SELECT_DISABLE) {
 				dataSelector = null;
 			}
 			directDrawProjector.setDataSelector(dataSelector);

src/tethys/Collection.java

@@ -89,7 +89,7 @@ public enum Collection {
 			return Calibrations;
 		case "nilus.Ensemble":
 			return Ensembles;
-		case "nilus.Localization":
+		case "nilus.Localize":
 			return Localizations;
 		case "nilus.SpeciesAbbreviation":
 			return SpeciesAbbreviations;

src/tethys/TethysControl.java

@@ -49,6 +49,7 @@ import tethys.dbxml.TethysException;
 import tethys.dbxml.TethysQueryException;
 import tethys.deployment.DeploymentHandler;
 import tethys.detection.DetectionsHandler;
+import tethys.localization.LocalizationHandler;
 import tethys.niluswraps.PDeployment;
 import tethys.output.DatablockSynchInfo;
 import tethys.output.TethysExportParams;
@@ -91,6 +92,7 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 	private DeploymentHandler deploymentHandler;
 	private DetectionsHandler detectionsHandler;
 	private CalibrationHandler calibrationHandler;
+	private LocalizationHandler localizationHandler;
 	
 	private ITISFunctions itisFunctions;
 
@@ -102,6 +104,7 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 		deploymentHandler = new DeploymentHandler(this);
 		detectionsHandler = new DetectionsHandler(this);
 		calibrationHandler = new CalibrationHandler(this);
+		localizationHandler = new LocalizationHandler(this);
 		
 		serverCheckTimer = new Timer(10000, new ActionListener() {
 			@Override
@@ -569,8 +572,8 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 			int detectionCount = 0;
 			int documentCount = 0;
 			for (PDeployment pDepl : matchedDeployments) {
-				detectionCount += dbxmlQueries.countData(synchInfo.getDataBlock(), pDepl.deployment.getId());
+				detectionCount += dbxmlQueries.countData(synchInfo.getDataBlock(), pDepl.getDocumentId());
-				ArrayList<String> detectionsNames = getDbxmlQueries().getDetectionsDocuments(synchInfo.getDataBlock(), pDepl.deployment.getId());
+				ArrayList<String> detectionsNames = getDbxmlQueries().getDetectionsDocuments(synchInfo.getDataBlock(), pDepl.getDocumentId());
 				if (detectionsNames != null) {
 					documentCount += detectionsNames.size();
 				}

src/tethys/TethysMenuActions.java

@@ -26,14 +26,14 @@ public class TethysMenuActions {
 	}
 
 	public void deploymentMouseActions(MouseEvent e, PDeployment pDeployment) {
-		ArrayList<String> detDocNames = tethysControl.getDbxmlQueries().getDetectionsDocuments(pDeployment.deployment.getId());
+		ArrayList<String> detDocNames = tethysControl.getDbxmlQueries().getDetectionsDocuments(pDeployment.nilusObject.getId());
 //		System.out.println("Detections for deployment " + pDeployment.deployment.getId());
 //		for (String detName : detDocNames) {
 //			System.out.println(detName);
 //		}
 		JPopupMenu menu = new JPopupMenu();
 		if (detDocNames.size() == 0) {
-			JMenuItem menuItem = new JMenuItem("Delete deployment " + pDeployment.deployment.getId());
+			JMenuItem menuItem = new JMenuItem("Delete deployment " + pDeployment.nilusObject.getId());
 			menuItem.addActionListener(new ActionListener() {
 				@Override
 				public void actionPerformed(ActionEvent e) {
@@ -47,7 +47,7 @@ public class TethysMenuActions {
 			menu.add(menuItem);
 		}
 		else {
-			String str = String.format("Delete deployment %s and %d Detections documents", pDeployment.deployment.getId(), detDocNames.size());
+			String str = String.format("Delete deployment %s and %d Detections documents", pDeployment.nilusObject.getId(), detDocNames.size());
 			JMenuItem menuItem = new JMenuItem(str);
 			menuItem.addActionListener(new ActionListener() {
 				@Override
@@ -65,6 +65,6 @@ public class TethysMenuActions {
 	}
 
 	protected void deleteDeployment(PDeployment pDeployment) throws TethysException {
-		tethysControl.getDbxmlConnect().deleteDeployment(pDeployment.deployment.getId());
+		tethysControl.getDbxmlConnect().deleteDeployment(pDeployment.nilusObject.getId());
 	}
 }

src/tethys/calibration/CalibrationHandler.java

@@ -420,10 +420,24 @@ public class CalibrationHandler extends CollectionHandler implements TethysState
 			calibration.setSensitivityDBFS(fullScale);
 		}
 		FrequencyResponse frs = calibration.getFrequencyResponse();
+		if (frs == null) {
+			frs = new FrequencyResponse();		
+			try {
+				Helper.createRequiredElements(frs);
+			} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
+				e.printStackTrace();
+			}
+			calibration.setFrequencyResponse(frs);
+		}
 		List<Double> hz = frs.getHz();
 		List<Double> db = frs.getDB();
+//		if (hz == null) {
+//			
+//		}
+		if (hz != null && db != null) {
 		hz.add(Double.valueOf(0));
 		db.add(Double.valueOf(hSens+preampGain));
+		}
 		
 		if (NilusChecker.isEmpty(calibration.getResponsibleParty())) {
 			calibration.setResponsibleParty(null);

src/tethys/dbxml/DBXMLConnect.java

@@ -515,7 +515,7 @@ C:\Users\dg50\AppData\Local\Temp\PAMGuardTethys\20080311_2DSimplex_0.xmlnot: 0 b
 	 * @param nilusObject
 	 * @return document Id for any type of document, or null if the document doesn't have a getID function
 	 */
-	private String getDocumentId(Object nilusObject) {
+	public static String getDocumentId(Object nilusObject) {
 		String tempName = null;
 		Class nilusClass = nilusObject.getClass();
 		Method getId;

src/tethys/dbxml/DBXMLQueries.java

@@ -561,6 +561,63 @@ public class DBXMLQueries {
 		}
 		return detectionsNames;
 	}
+	/**
+	 * Get a list of Localization documents which associate with a datablock and a deploymentId.
+	 * @param dataBlock
+	 * @param deploymentId can be null to get all docs for data block
+	 * @return
+	 */
+	public ArrayList<String> getLocalizationDocuments(PamDataBlock dataBlock, String deploymentId) {
+		/**
+		 * first query for Detections documents associated with this deployment and datablock.
+		 * updated May 23
+		 */
+		if (dataBlock == null) {
+			return null;
+		}
+		String queryNoDepl = "{\"species\":{\"query\":{\"op\":\"lib:completename2tsn\",\"optype\":\"function\",\"operands\":[\"%s\"]},\"return\":{\"op\":\"lib:tsn2completename\",\"optype\":\"function\",\"operands\":[\"%s\"]}},\"return\":[\"Localize/Id\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Localize/Algorithm/Software\",\"LongDataName\"],\"optype\":\"binary\"}],\"enclose\":1}";
+		String queryWithDepl = "{\"species\":{\"query\":{\"op\":\"lib:completename2tsn\",\"optype\":\"function\",\"operands\":[\"%s\"]},\"return\":{\"op\":\"lib:tsn2completename\",\"optype\":\"function\",\"operands\":[\"%s\"]}},\"return\":[\"Localize/Id\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Localize/DataSource/DeploymentId\",\"TheDeploymentId\"],\"optype\":\"binary\"},{\"op\":\"=\",\"operands\":[\"Localize/Algorithm/Software\",\"LongDataName\"],\"optype\":\"binary\"}],\"enclose\":1}";
+		String query;
+		if (deploymentId == null) {
+			query = queryNoDepl;
+		}
+		else {
+			query = queryWithDepl.replace("TheDeploymentId", deploymentId);
+		}
+		query = query.replace("LongDataName", dataBlock.getLongDataName());
+		DBQueryResult queryResult = null;
+		try {
+			queryResult = executeQuery(query);
+		} catch (TethysQueryException e1) {
+			tethysControl.showException(e1);
+			return null;
+		}
+		if (queryResult ==null) {
+			return null;
+		}
+		Document doc;
+		try {
+			doc = queryResult.getDocument();
+		} catch (ParserConfigurationException | SAXException | IOException e) {
+			e.printStackTrace();
+			return null;
+		}
+		if (doc == null) {
+			return null;
+		}
+		ArrayList<String> detectionsNames = new ArrayList();
+		int count = 0;
+		NodeList returns = doc.getElementsByTagName("Localize");
+		//		if (returns.getLength() == 0) {
+		//			returns = doc.getElementsByTagName("Result");
+		//		}
+		for (int i = 0; i < returns.getLength(); i++) {
+			Node aNode = returns.item(i);
+			String docName = aNode.getTextContent();
+			detectionsNames.add(docName);
+		}
+		return detectionsNames;
+	}
 
 
 	/**

src/tethys/deployment/DeploymentHandler.java

@@ -492,7 +492,7 @@ public class DeploymentHandler extends CollectionHandler implements TethysStateO
 		PDeployment exDeploymnet = onePeriod.getMatchedTethysDeployment();
 		try {
 			if (exDeploymnet != null) {
-				deployment.setId(exDeploymnet.deployment.getId());
+				deployment.setId(exDeploymnet.nilusObject.getId());
 				dbxmlConnect.updateDocument(deployment);
 			}
 			else {
@@ -522,7 +522,7 @@ public class DeploymentHandler extends CollectionHandler implements TethysStateO
 			String id = String.format("%s_%d", exportParams.getDatasetName(), i);
 			if (exDeploymnet != null) {
 				deployment = createDeploymentDocument(freeId, recordPeriod, id);
-				deployment.setId(exDeploymnet.deployment.getId());
+				deployment.setId(exDeploymnet.nilusObject.getId());
 			}
 			if (deployment == null) {
 				deployment = createDeploymentDocument(freeId++, recordPeriod, id);
@@ -646,7 +646,7 @@ public class DeploymentHandler extends CollectionHandler implements TethysStateO
 		}
 		ArrayList<PInstrument> instruments = new ArrayList<>();
 		for (PDeployment aDepl : projectDeployments) {
-			Instrument intr = aDepl.deployment.getInstrument();
+			Instrument intr = aDepl.nilusObject.getInstrument();
 			if (intr == null) {
 				continue;
 			}
@@ -764,7 +764,7 @@ public class DeploymentHandler extends CollectionHandler implements TethysStateO
 		int firstFree = 0;
 		if (projectDeployments != null) {
 			for (PDeployment dep : projectDeployments) {
-				firstFree = Math.max(firstFree, dep.deployment.getDeploymentId()+1);
+				firstFree = Math.max(firstFree, dep.nilusObject.getDeploymentId()+1);
 			}
 		}
 		return firstFree;

src/tethys/detection/DetectionsHandler.java

@@ -12,6 +12,8 @@ import javax.xml.datatype.XMLGregorianCalendar;
 import PamController.PamControlledUnit;
 import PamController.PamController;
 import PamController.PamguardVersionInfo;
+import PamDetection.LocContents;
+import PamDetection.LocalisationInfo;
 import PamModel.PamPluginInterface;
 import PamUtils.PamCalendar;
 import PamView.dialog.PamDialog;
@@ -26,6 +28,8 @@ import dataMap.OfflineDataMap;
 import dataMap.OfflineDataMapPoint;
 import nilus.AlgorithmType;
 import nilus.AlgorithmType.SupportSoftware;
+import nilus.Localize.Effort;
+import nilus.Localize.Effort.CoordinateReferenceSystem;
 import nilus.Localize.Localizations;
 import nilus.DataSourceType;
 import nilus.Deployment;
@@ -36,6 +40,7 @@ import nilus.DetectionGroup;
 import nilus.Detections;
 import nilus.GranularityEnumType;
 import nilus.Helper;
+import nilus.Localize;
 import tethys.Collection;
 import tethys.CollectionHandler;
 import tethys.TethysControl;
@@ -43,6 +48,9 @@ import tethys.TethysTimeFuncs;
 import tethys.dbxml.DBXMLConnect;
 import tethys.dbxml.TethysException;
 import tethys.deployment.DeploymentHandler;
+import tethys.localization.CoordinateName;
+import tethys.localization.LocalizationSubType;
+import tethys.localization.LocalizationType;
 import tethys.niluswraps.PDeployment;
 import tethys.niluswraps.PDetections;
 import tethys.output.StreamExportParams;
@@ -87,6 +95,7 @@ public class DetectionsHandler extends CollectionHandler {
 	 */
 	public StreamDetectionsSummary getStreamDetections(PamDataBlock dataBlock) {
 		ArrayList<PDeployment> deployments = tethysControl.getDeploymentHandler().getMatchedDeployments();
+//		getStreamLocalizations(dataBlock, deployments);
 		return getStreamDetections(dataBlock, deployments);
 	}
 
@@ -102,7 +111,7 @@ public class DetectionsHandler extends CollectionHandler {
 
 		ArrayList<PDetections> detectionsDocs = new ArrayList<>();
 		for (PDeployment aDep : deployments) {
-			ArrayList<String> someNames = tethysControl.getDbxmlQueries().getDetectionsDocuments(dataBlock, aDep.deployment.getId());
+			ArrayList<String> someNames = tethysControl.getDbxmlQueries().getDetectionsDocuments(dataBlock, aDep.nilusObject.getId());
 			if (someNames == null) {
 				continue;
 			}
@@ -117,6 +126,7 @@ public class DetectionsHandler extends CollectionHandler {
 		return new StreamDetectionsSummary(detectionsDocs);
 	}
 
+
 	/**
 	 * Get the Detection Effort part of a Detections document
 	 * @param pDeployment
@@ -126,7 +136,7 @@ public class DetectionsHandler extends CollectionHandler {
 	 */
 	private DetectionEffort getDetectorEffort(PDeployment pDeployment, PamDataBlock dataBlock, StreamExportParams exportParams) {
 		DetectionEffort effort = new DetectionEffort();
-		Deployment deployment = pDeployment.deployment;
+		Deployment deployment = pDeployment.nilusObject;
 		Long effortStart = pDeployment.getAudioStart();
 		Long effortEnd = pDeployment.getAudioEnd();
 		effort.setStart(TethysTimeFuncs.xmlGregCalFromMillis(effortStart));
@@ -404,8 +414,9 @@ public class DetectionsHandler extends CollectionHandler {
 		 * The main documents for both dets and locs. 
 		 */
 		Detections detectionsDocument = null;
-		Localizations localisationsDocument = null;
+		Localize localiseDocument = null;
 		DetectionGroup onEffortDetections = null;
+		Localizations localisations = null;
 
 		OfflineDataMap dataMap = dataBlock.getPrimaryDataMap();
 		DataSelector dataSelector = dataBlock.getDataSelector(tethysControl.getDataSelectName(), false);
@@ -432,6 +443,8 @@ public class DetectionsHandler extends CollectionHandler {
 			exportObserver.update(prog);
 			granularityHandler.prepare(deployment.getAudioStart());
 			
+			List<Detection> detectionList;
+
 			// export everything in that deployment.
 			// need to loop through all map points in this interval.
 			List<OfflineDataMapPoint> mapPoints = dataMap.getMapPoints();
@@ -448,12 +461,23 @@ public class DetectionsHandler extends CollectionHandler {
 					detectionsDocument = startDetectionsDocument(deployment, dataBlock, streamExportParams);
 					detectionsDocument.getEffort().setStart(TethysTimeFuncs.xmlGregCalFromMillis(deployment.getAudioStart()));
 					onEffortDetections = detectionsDocument.getOnEffort();
+					detectionList = onEffortDetections.getDetection();
+//					if {detectionList == null) {
+//						onEffortDetections.
+//					}
 				}
 				else {
 					onEffortDetections = null;
+					detectionList = null;
 				}
-				if (localisationsDocument == null && streamExportParams.exportLocalisations) {
+				if (localiseDocument == null && streamExportParams.exportLocalisations) {
-					localisationsDocument = startLocalisationDocument(deployment, dataBlock, streamExportParams);
+					localiseDocument = startLocalisationDocument(deployment, dataBlock, streamExportParams);
+					Effort eff = localiseDocument.getEffort();
+					localiseDocument.getEffort().setStart(TethysTimeFuncs.xmlGregCalFromMillis(deployment.getAudioStart()));
+					localisations = localiseDocument.getLocalizations();
+				}
+				else {
+					localisations = null;
 				}
 
 				if (mapPoint.getEndTime() < deployment.getAudioStart()) {
@@ -476,10 +500,14 @@ public class DetectionsHandler extends CollectionHandler {
 							exportCount++;
 							documentCount++;
 							if (streamExportParams.exportDetections) {
-								onEffortDetections.getDetection().add(dets[dd]);
+								detectionList.add(dets[dd]);
+							}
+							if (streamExportParams.exportLocalisations) {
+								// convert the dets into localisations and add them. 
 							}
 						}
 					}
+
 					if (exportCount % 100 == 0) {
 						prog = new DetectionExportProgress(deployment, detectionsDocument, totalMapPoints, doneMapPoints,
 								lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_GATHERING);
@@ -508,6 +536,17 @@ public class DetectionsHandler extends CollectionHandler {
 						}
 						detectionsDocument = null;
 					}
+					if (localiseDocument != null) {
+						closeLocaliseDocument(localiseDocument, mapPoint.getEndTime());
+						try {
+							if (checkLocaliseDocument(localiseDocument, granularityHandler)) {
+								dbxmlConnect.postAndLog(localiseDocument);
+							}
+						} catch (TethysException e) {
+							tethysControl.showException(e);
+						}
+						localiseDocument = null;
+					}
 				}
 
 				if (viewerLoadPolicy == ViewerLoadPolicy.LOAD_ALWAYS_EVERYTHING) {
@@ -543,6 +582,27 @@ public class DetectionsHandler extends CollectionHandler {
 				}
 				detectionsDocument = null;
 			}
+			if (localiseDocument != null) {
+				Detection dets[] = granularityHandler.cleanup(deployment.getAudioEnd());
+				if (dets != null) {
+					for (int dd = 0; dd < dets.length; dd++) {
+						exportCount++;
+						documentCount++;
+						//						localiseDocument.getOnEffort().getDetection().add(dets[dd]);
+					}
+				}
+				prog = new DetectionExportProgress(deployment, detectionsDocument,totalMapPoints, doneMapPoints,
+						lastUnitTime, totalCount, exportCount, skipCount, DetectionExportProgress.STATE_WRITING);
+				closeLocaliseDocument(localiseDocument, deployment.getAudioEnd());
+				try {
+					if (checkLocaliseDocument(localiseDocument, granularityHandler)) {
+						dbxmlConnect.postAndLog(localiseDocument);
+					}
+				} catch (TethysException e) {
+					tethysControl.showException(e);
+				}
+				localiseDocument = null;
+			}
 		}
 
 		prog = new DetectionExportProgress(null, null,totalMapPoints, totalMapPoints,
@@ -551,20 +611,6 @@ public class DetectionsHandler extends CollectionHandler {
 		return DetectionExportProgress.STATE_COMPLETE;
 	}
 
-	private Localizations startLocalisationDocument(PDeployment deployment, PamDataBlock dataBlock,
-			StreamExportParams streamExportParams) {
-		Localizations localisations = new Localizations();
-		try {
-			Helper.createRequiredElements(localisations);
-		} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
-			e.printStackTrace();
-			return null;
-		}
-		
-		return localisations;
-	}
-
-
 	/**
 	 * Start a new detections document for the deployment and datablock. <br>
 	 * Add all the standard information to the top of the Document
@@ -584,7 +630,7 @@ public class DetectionsHandler extends CollectionHandler {
 		}
 		TethysDataProvider dataProvider = dataBlock.getTethysDataProvider(tethysControl);
 
-		String prefix = deployment.deployment.getId() + "_" + dataProvider.getDetectionsName();
+		String prefix = deployment.nilusObject.getId() + "_" + dataProvider.getDetectionsName();
 		String fullId = "";
 		/*
 		 * Check the document name isn't already used and increment id as necessary.
@@ -599,7 +645,7 @@ public class DetectionsHandler extends CollectionHandler {
 		//		detections.setDescription(dataProvider.getDescription(deployment, tethysExportParams));
 		detections.setDescription(exportParams.getNilusDetectionDescription());
 		DataSourceType dataSource = new DataSourceType();
-		dataSource.setDeploymentId(deployment.deployment.getId());
+		dataSource.setDeploymentId(deployment.nilusObject.getId());
 		//		dataSource.setEnsembleId(""); ToDo
 		detections.setDataSource(dataSource);
 		AlgorithmType algorithm = detections.getAlgorithm();
@@ -624,6 +670,141 @@ public class DetectionsHandler extends CollectionHandler {
 		return detections;
 	}
 
+	private Localize startLocalisationDocument(PDeployment deployment, PamDataBlock dataBlock,
+			StreamExportParams exportParams) {
+		Localize localisations = new Localize();
+		try {
+			Helper.createRequiredElements(localisations);
+		} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
+			e.printStackTrace();
+			return null;
+		}		
+		if (localisations.getEffort() == null) {
+			Effort eff = new Effort();
+			try {
+				Helper.createRequiredElements(eff);
+			} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
+				e.printStackTrace();
+				return null;
+			}		
+			localisations.setEffort(eff);
+		}
+		TethysDataProvider dataProvider = dataBlock.getTethysDataProvider(tethysControl);
+
+		String prefix = deployment.nilusObject.getId() + "_" + dataProvider.getDetectionsName();
+		String fullId = "";
+		/*
+		 * Check the document name isn't already used and increment id as necessary.
+		 */
+		while (true) {
+			fullId = String.format("%s_%d", prefix, uniqueDetectionsId++);
+			if (!tethysControl.getDbxmlQueries().documentExists(Collection.Localizations.toString(), fullId)) {
+				break;
+			}
+		}
+		localisations.setId(fullId);
+		//		detections.setDescription(dataProvider.getDescription(deployment, tethysExportParams));
+		localisations.setDescription(exportParams.getNilusDetectionDescription());
+		DataSourceType dataSource = new DataSourceType();
+		dataSource.setDeploymentId(deployment.nilusObject.getId());
+		//		dataSource.setEnsembleId(""); ToDo
+		localisations.setDataSource(dataSource);
+		AlgorithmType algorithm = localisations.getAlgorithm();
+
+		if (dataProvider != null) {
+			algorithm = dataProvider.getAlgorithm();
+			//			detections.setAlgorithm(algorithm);
+		}
+		algorithm.setMethod(getMethodString(dataBlock));
+		algorithm.setSoftware(getSoftwareString(dataBlock));
+		algorithm.setVersion(getVersionString(dataBlock));
+
+		List<SupportSoftware> supSoft = algorithm.getSupportSoftware();
+		SupportSoftware supportSoft = new SupportSoftware();
+		supportSoft.setSoftware(getSupportSoftware(dataBlock));
+		supportSoft.setVersion(getSupportSoftwareVersion(dataBlock));
+		supSoft.add(supportSoft);
+		localisations.setAlgorithm(algorithm);
+
+		localisations.setUserId("PAMGuard user");
+		//		localisations.setEffort(getLocaliserEffort(deployment, dataBlock, exportParams));
+		sortLocaliseCoordinates(dataBlock, localisations);
+
+		// sort out coordinate system. 
+
+		return localisations;
+	}
+	
+	private boolean sortLocaliseCoordinates(PamDataBlock dataBlock, Localize localisations) {
+		LocalisationInfo locInfo = dataBlock.getLocalisationContents();
+		Effort locEffort = localisations.getEffort();
+		if (locEffort == null) {
+			locEffort = new Effort();
+			localisations.setEffort(locEffort);
+		}
+		try {
+			Helper.createRequiredElements(locEffort);
+		} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
+			e.printStackTrace();
+			return false;
+		}
+		locEffort.setTimeReference("relative");
+//		List<String> locTypes = locEffort.getLocalizationType();
+		boolean ambiguity = locInfo.hasLocContent(LocContents.HAS_AMBIGUITY);
+		CoordinateReferenceSystem coordRefs = locEffort.getCoordinateReferenceSystem();		
+		if (locInfo.getLocContent() == 0) {
+			return false;
+		}
+		else if (locInfo.hasLocContent(LocContents.HAS_LATLONG)) {
+			coordRefs.setName(CoordinateName.WGS84.toString());
+			coordRefs.setSubtype(LocalizationSubType.Geographic.toString());
+			locEffort.setLocalizationType(LocalizationType.Point.toString());
+//			locEffort.set
+			if (locInfo.hasLocContent(LocContents.HAS_DEPTH)) {
+				locEffort.setDimension(3);
+			}
+			else {
+				locEffort.setDimension(2);
+			}
+//			locEffort.set
+		}
+		else if (locInfo.hasLocContent(LocContents.HAS_XYZ)) {
+			coordRefs.setName(CoordinateName.Cartesian.toString());
+			coordRefs.setSubtype(LocalizationSubType.Engineering.toString());
+			locEffort.setLocalizationType(LocalizationType.Point.toString());
+			locEffort.setDimension(3);
+		}
+		else if (locInfo.hasLocContent(LocContents.HAS_XY)) {
+			coordRefs.setName(CoordinateName.Cartesian.toString());
+			coordRefs.setSubtype(LocalizationSubType.Engineering.toString());
+			locEffort.setLocalizationType(LocalizationType.Point.toString());
+			locEffort.setDimension(2);
+		}
+		else if (locInfo.hasLocContent(LocContents.HAS_BEARING)) {
+			coordRefs.setName(CoordinateName.Polar.toString());
+			coordRefs.setSubtype(LocalizationSubType.Engineering.toString());
+			locEffort.setLocalizationType(LocalizationType.Bearing.toString());
+			if (ambiguity) {
+				locEffort.setDimension(1);
+			}
+			else {
+				locEffort.setDimension(2);
+			}
+		}
+		else {
+			return false;
+		}
+		
+		return true;
+	}
+
+
+	private nilus.Localize.Effort getLocaliserEffort(PDeployment deployment, PamDataBlock dataBlock, StreamExportParams exportParams) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+
 	/**
 	 * Close a detections document. This basically just means rewriting the end time and it's only
 	 * important in the event that a document got too big and has to be restarted.
@@ -634,6 +815,11 @@ public class DetectionsHandler extends CollectionHandler {
 		detections.getEffort().setEnd(TethysTimeFuncs.xmlGregCalFromMillis(audioEnd));
 	}
 
+	private void closeLocaliseDocument(Localize localiseDocument, long endTime) {
+		localiseDocument.getEffort().setEnd(TethysTimeFuncs.xmlGregCalFromMillis(endTime));
+	}
+
+
 	/**
 	 * Run some checks on the Detections document prior to submission. <br>
 	 * Currently, is is just a check that the detections are within the effort times.   
@@ -678,6 +864,11 @@ public class DetectionsHandler extends CollectionHandler {
 		return true;
 	}
 
+	private boolean checkLocaliseDocument(Localize localiseDocument, GranularityHandler granularityHandler) {
+		// TODO Auto-generated method stub
+		return true;
+	}
+
 	/**
 	 * Worker thread for exporting detections. 
 	 * Currently, it counts them first, then checks the user wants to export 

src/tethys/localization/CoordinateName.java

@@ -0,0 +1,11 @@
+package tethys.localization;
+
+/**
+ * Enumeration of the Name field in nilus.Localize.Effort.CoordinateReferenceSystem<br>
+ * Within Tethys, these are only ever used in their String form. 
+ * @author dg50
+ *
+ */
+public enum CoordinateName {
+	WGS84, UTM, Cartesian, Polar, Spherical, Cylindrical, Range, PerpindicularRange;
+}

src/tethys/localization/LocalizationHandler.java

@@ -1,17 +1,63 @@
 package tethys.localization;
 
+import java.util.ArrayList;
+
+import PamguardMVC.PamDataBlock;
 import nilus.CylindricalCoordinateType;
 import nilus.LocalizationType;
 import nilus.Localize.Effort.CoordinateReferenceSystem;
+import tethys.Collection;
+import tethys.CollectionHandler;
+import tethys.TethysControl;
+import tethys.detection.StreamDetectionsSummary;
+import tethys.niluswraps.PDeployment;
 
-public class LocalizationHandler {
+public class LocalizationHandler extends CollectionHandler {
 
+	public LocalizationHandler(TethysControl tethysControl) {
+		super(tethysControl, Collection.Localizations);
+		// TODO Auto-generated constructor stub
+	}
 
-	public LocalizationType getLoc() {
+//	public LocalizationType getLoc() {
-		LocalizationType lt = new LocalizationType();
+//		LocalizationType lt = new LocalizationType();
-		CylindricalCoordinateType cct = new CylindricalCoordinateType();
+//		CylindricalCoordinateType cct = new CylindricalCoordinateType();
-//		cct.set
+////		cct.set
-		CoordinateReferenceSystem cr;
+//		CoordinateReferenceSystem cr;
+//		return null;
+//	}
+	
+	/**
+	 * Get a list of Localization documents associated with a particular data block for the list of deployments
+	 * documents. Group them by abstract or something
+	 * @param dataBlock
+	 * @param deployments
+	 * @return
+	 */
+	public StreamDetectionsSummary getStreamLocalizations(PamDataBlock dataBlock, ArrayList<PDeployment> deployments) {
+		// get the basic data for each document including it's Description.
+
+//		ArrayList<PDetections> detectionsDocs = new ArrayList<>();
+		for (PDeployment aDep : deployments) {
+			ArrayList<String> someNames = tethysControl.getDbxmlQueries().getLocalizationDocuments(dataBlock, aDep.getDocumentId());
+			if (someNames == null) {
+				continue;
+			}
+//			// no have a list of all the Detections documents of interest for this datablock.
+//			for (String aDoc : someNames) {
+//				Detections detections = tethysControl.getDbxmlQueries().getDetectionsDocInfo(aDoc);
+//				int count = tethysControl.getDbxmlQueries().countDetections2(aDoc);
+//				PDetections pDetections = new PDetections(detections, dataBlock, aDep, count);
+//				detectionsDocs.add(pDetections);
+//			}
+		}
+//		return new StreamDetectionsSummary(detectionsDocs);
+		return null;
+	}
+
+	@Override
+	public String getHelpPoint() {
+		// TODO Auto-generated method stub
 		return null;
 	}
 }

src/tethys/localization/LocalizationSubType.java

@@ -0,0 +1,10 @@
+package tethys.localization;
+/**
+ * Enumeration of the ReferenceFrame field in nilus.Localize.Effort.CoordinateReferenceSystem.Subtype <br>
+ * Within Tethys, these are only ever used in their String form. 
+ * @author dg50
+ *
+ */
+public enum LocalizationSubType {
+	Geographic, Derived, Engineering;
+}

src/tethys/localization/LocalizationType.java

@@ -0,0 +1,11 @@
+package tethys.localization;
+
+/**
+ * Enumeration of the ReferenceFrame field in nilus.Localize.Effort.CoordinateReferenceSystem.Subtype <br>
+ * Within Tethys, these are only ever used in their String form. 
+ * @author dg50
+ *
+ */
+public enum LocalizationType {
+	Bearing, PerpindicularRange, Point, Range, Track;
+}

src/tethys/localization/ReferenceFrame.java

@@ -0,0 +1,11 @@
+package tethys.localization;
+
+/**
+ * Enumeration of the ReferenceFrame field in nilus.Localize.Effort.CoordinateReferenceSystem <br>
+ * Within Tethys, these are only ever used in their String form. 
+ * @author dg50
+ *
+ */
+public enum ReferenceFrame {
+	UTMZone, WGS84, instrument;
+}

src/tethys/localization/TimeReference.java

@@ -0,0 +1,10 @@
+package tethys.localization;
+/**
+ * Enumeration of the ReferenceFrame field in nilus.Localize.Effort.TimeReference <br>
+ * Within Tethys, these are only ever used in their String form. 
+ * @author dg50
+ *
+ */
+public enum TimeReference {
+	absolute, channel, relative;
+}

src/tethys/niluswraps/NilusDataWrapper.java

@@ -0,0 +1,27 @@
+package tethys.niluswraps;
+
+import PamguardMVC.PamDataBlock;
+
+/**
+ * Wrapper for Nilus data objects. This means Detections and Localization documents which 
+ * should have an associated datablock, a deployment wrapper and a data count. 
+ * @author dg50
+ *
+ * @param <T>
+ */
+public class NilusDataWrapper<T> extends NilusDocumentWrapper<T> {
+
+	public Integer count;
+	
+	public PDeployment deployment;
+
+	public PamDataBlock dataBlock;
+
+	public NilusDataWrapper(T nilusObject, PamDataBlock dataBlock, PDeployment deployment, Integer count) {
+		super(nilusObject);
+		this.dataBlock = dataBlock;
+		this.deployment = deployment;
+		this.count = count;
+	}
+
+}

src/tethys/niluswraps/NilusDocumentWrapper.java

@@ -0,0 +1,24 @@
+package tethys.niluswraps;
+
+import PamguardMVC.PamDataBlock;
+import tethys.dbxml.DBXMLConnect;
+
+public class NilusDocumentWrapper<T> {
+
+	public T nilusObject;
+	
+	public String documentName;
+	
+	public NilusDocumentWrapper(T nilusDocument) {
+		super();
+		this.nilusObject = nilusDocument;
+	}
+	
+	public String getDocumentId() {
+		if (nilusObject == null) {
+			return null;
+		}
+		return DBXMLConnect.getDocumentId(nilusObject);
+	}
+	
+}

src/tethys/niluswraps/PDeployment.java

@@ -12,18 +12,16 @@ import tethys.deployment.RecordingPeriod;
  * @author dg50
  *
  */
-public class PDeployment {
+public class PDeployment extends NilusDocumentWrapper<Deployment>{
 	
-	public Deployment deployment;
 	private RecordingPeriod matchedPAMGaurdPeriod;
 
 	public PDeployment(Deployment deployment) {
-		super();
+		super(deployment);
-		this.deployment = deployment;
 	}
 	
 	public Long getAudioStart() {
-		DeploymentRecoveryDetails detail = deployment.getDeploymentDetails();
+		DeploymentRecoveryDetails detail = nilusObject.getDeploymentDetails();
 		if (detail == null || detail.getAudioTimeStamp() == null) {
 			return null;
 		}
@@ -31,7 +29,7 @@ public class PDeployment {
 	}
 	
 	public Long getAudioEnd() {
-		DeploymentRecoveryDetails detail = deployment.getRecoveryDetails();
+		DeploymentRecoveryDetails detail = nilusObject.getRecoveryDetails();
 		if (detail == null || detail.getAudioTimeStamp() == null) {
 			return null;
 		}
@@ -40,7 +38,7 @@ public class PDeployment {
 
 	@Override
 	public String toString() {
-		return String.format("%s:%d; %s - %s", deployment.getId(), deployment.getDeploymentId(), 
+		return String.format("%s:%d; %s - %s", nilusObject.getId(), nilusObject.getDeploymentId(), 
 				PamCalendar.formatDBDateTime(getAudioStart()), PamCalendar.formatDBDateTime(getAudioEnd()));
 	}
 
@@ -55,10 +53,10 @@ public class PDeployment {
 	public String getShortDescription() {
 		Long audioStart = getAudioStart();
 		if (audioStart == null) {
-			return String.format("%s %s", deployment.getId(), "unknown start");
+			return String.format("%s %s", nilusObject.getId(), "unknown start");
 		}
 		else {
-			return String.format("%s %s", deployment.getId(), PamCalendar.formatDBDate(getAudioStart()));
+			return String.format("%s %s", nilusObject.getId(), PamCalendar.formatDBDate(getAudioStart()));
 		}
 	}
 	

src/tethys/niluswraps/PDetections.java

@@ -3,24 +3,29 @@ package tethys.niluswraps;
 import PamguardMVC.PamDataBlock;
 import nilus.Detections;
 
-public class PDetections {
+public class PDetections extends NilusDataWrapper<Detections>{
-	
-	public Detections detections;
-	
-	public Integer count;
-	
-	public PDeployment deployment;
-
-	public PamDataBlock dataBlock;
 
 	public PDetections(Detections detections, PamDataBlock dataBlock, PDeployment deployment, Integer count) {
-		super();
+		super(detections, dataBlock, deployment, count);
-		this.dataBlock = dataBlock;
+		// TODO Auto-generated constructor stub
-		this.detections = detections;
-		this.deployment = deployment;
-		this.count = count;
 	}
 	
+//	public Detections nilusObject;
+//	
+//	public Integer count;
+//	
+//	public PDeployment deployment;
+//
+//	public PamDataBlock dataBlock;
+//
+//	public PDetections(Detections detections, PamDataBlock dataBlock, PDeployment deployment, Integer count) {
+//		super();
+//		this.dataBlock = dataBlock;
+//		this.nilusObject = detections;
+//		this.deployment = deployment;
+//		this.count = count;
+//	}
+	
 	
 	
 

src/tethys/swing/DatablockDetectionsPanel.java

@@ -62,7 +62,7 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 	public DatablockDetectionsPanel(TethysControl tethysControl) {
 		super(tethysControl);
 		mainPanel = new JPanel(new BorderLayout());
-		mainPanel.add(BorderLayout.NORTH, dataBlockName = new JLabel("PAMGUard data stream", JLabel.LEFT));
+		mainPanel.add(BorderLayout.NORTH, dataBlockName = new JLabel("PAMGuard data stream", JLabel.LEFT));
 		mainPanel.setBorder(new TitledBorder("Data stream Tethys Detections documents"));
 
 		tableModel = new TableModel();
@@ -193,7 +193,7 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 		JMenuItem menuItem;
 		if (rows.length == 1) {
 			
-			menuItem = new JMenuItem("Display document " + pDets.detections.getId());
+			menuItem = new JMenuItem("Display document " + pDets.getDocumentId());
 			menuItem.addActionListener(new ActionListener() {
 				@Override
 				public void actionPerformed(ActionEvent e) {
@@ -202,7 +202,7 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 			});
 			popMenu.add(menuItem);
 
-			menuItem = new JMenuItem("Export document " + pDets.detections.getId());
+			menuItem = new JMenuItem("Export document " + pDets.getDocumentId());
 			menuItem.addActionListener(new ActionListener() {
 				@Override
 				public void actionPerformed(ActionEvent e) {
@@ -212,7 +212,7 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 			popMenu.add(menuItem);
 			
 			popMenu.addSeparator();
-			menuItem = new JMenuItem("Delete document " + pDets.detections.getId());
+			menuItem = new JMenuItem("Delete document " + pDets.getDocumentId());
 			menuItem.addActionListener(new ActionListener() {
 				@Override
 				public void actionPerformed(ActionEvent e) {
@@ -255,7 +255,7 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 			if (pDets == null) {
 				continue;
 			}
-			toDelete.add(pDets.detections);
+			toDelete.add(pDets.nilusObject);
 		}
 		DeleteDocs dd = new DeleteDocs(toDelete);
 		PamWorker<Integer> worker = new PamWorker(dd, getTethysControl().getGuiFrame(), 1, "Deleting Detections documents");
@@ -293,13 +293,13 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 	}
 
 	protected void deleteDocument(PDetections pDets) {
-		String msg = String.format("Are you sure you want to delete the Detections document %s ?", pDets.detections.getId());
+		String msg = String.format("Are you sure you want to delete the Detections document %s ?", pDets.getDocumentId());
 		int ans = WarnOnce.showWarning(PamGui.findComponentWindow(mainPanel), "Delete Document", msg, WarnOnce.OK_CANCEL_OPTION);
 		if (ans != WarnOnce.OK_OPTION) {
 			return;
 		}
 		try {
-			getTethysControl().getDbxmlConnect().deleteDocument(pDets.detections);
+			getTethysControl().getDbxmlConnect().deleteDocument(pDets.nilusObject);
 		} catch (TethysException e) {
 			getTethysControl().showException(e);
 		}
@@ -308,12 +308,12 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 	}
 
 	private void displayDocument(PDetections pDets) {
-		getTethysControl().displayDocument(Collection.Detections.collectionName(), pDets.detections.getId());
+		getTethysControl().displayDocument(Collection.Detections.collectionName(), pDets.getDocumentId());
 
 	}
 
 	private void exportDocument(PDetections pDets) {
-		getTethysControl().exportDocument(Collection.Detections.toString(), pDets.detections.getId());
+		getTethysControl().exportDocument(Collection.Detections.toString(), pDets.getDocumentId());
 
 	}
 
@@ -359,7 +359,7 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 			if (pDets == null) {
 				return null;
 			}
-			Detections dets = pDets.detections;
+			Detections dets = pDets.nilusObject;
 			if (dets == null) {
 				return "Error in doc";
 			}

src/tethys/swing/DeploymentExportPanel.java

@@ -124,10 +124,10 @@ public class DeploymentExportPanel extends TethysGUIPanel implements DeploymentT
 			return;
 		}
 		PDeployment deployment = tethysDeploys.get(row);
-		String msg = "Do you want to copy settings from deploymnet document " + deployment.deployment.getId();
+		String msg = "Do you want to copy settings from deploymnet document " + deployment.nilusObject.getId();
 		int ans = WarnOnce.showWarning("Deployment data", msg, WarnOnce.OK_CANCEL_OPTION);
 		if (ans == WarnOnce.OK_OPTION) {
-			copyDeploymentData(deployment.deployment);
+			copyDeploymentData(deployment.nilusObject);
 		}
 	}
 

src/tethys/swing/PAMGuardDeploymentsTable.java

@@ -229,14 +229,14 @@ private RecordingList masterList;
 			return;
 		}
 		for (PDeployment depl : matchedDeployments) {
-			if (depl.deployment == null) {
+			if (depl.nilusObject == null) {
 				continue;
 			}
 			try {
-				if (checkDetections(depl.deployment) == false) {
+				if (checkDetections(depl.nilusObject) == false) {
 					continue;
 				}
-				boolean gone = getTethysControl().getDbxmlConnect().deleteDocument(depl.deployment);
+				boolean gone = getTethysControl().getDbxmlConnect().deleteDocument(depl.nilusObject);
 			} catch (TethysException e) {
 				getTethysControl().showException(e);
 			}
@@ -279,7 +279,7 @@ private RecordingList masterList;
 	}
 
 	protected void deleteDeployment(PDeployment pDeployment) {
-		Deployment dep = pDeployment.deployment;
+		Deployment dep = pDeployment.nilusObject;
 		if (dep == null) {
 			return;
 		}
@@ -300,11 +300,11 @@ private RecordingList masterList;
 	}
 
 	protected void exportDeployment(PDeployment pDeployment) {
-		getTethysControl().exportDocument(Collection.Deployments.collectionName(), pDeployment.deployment.getId());
+		getTethysControl().exportDocument(Collection.Deployments.collectionName(), pDeployment.nilusObject.getId());
 	}
 
 	protected void displayDeployment(PDeployment pDeployment) {
-		getTethysControl().displayDocument(Collection.Deployments.collectionName(), pDeployment.deployment.getId());
+		getTethysControl().displayDocument(Collection.Deployments.collectionName(), pDeployment.nilusObject.getId());
 	}
 
 	@Override
@@ -443,7 +443,7 @@ private RecordingList masterList;
 						if (deployment == null) {
 							return null;
 						}
-						return deployment.deployment.getId();
+						return deployment.nilusObject.getId();
 //						return makeDeplString(period, deployment);
 					case 8:
 						if (deployment == null) {

src/tethys/swing/TethysConnectionPanel.java

@@ -226,7 +226,7 @@ public class TethysConnectionPanel extends TethysGUIPanel {
 		 */
 		ArrayList<PDeployment> projectDeployments = getTethysControl().getDeploymentHandler().getProjectDeployments();
 		if (projectDeployments != null && projectDeployments.size() > 0) {
-			Deployment dep = projectDeployments.get(0).deployment;
+			Deployment dep = projectDeployments.get(0).nilusObject;
 			globDeployment.setProject(dep.getProject());
 			globDeployment.setRegion(dep.getRegion());
 			getTethysControl().sendStateUpdate(new TethysState(TethysState.StateType.NEWPROJECTSELECTION));