Merge branch 'main' of https://github.com/douggillespie/PAMGuardTethys

src/PamController/settings/output/xml/PamguardXMLWriter.java

@@ -437,7 +437,7 @@ public class PamguardXMLWriter implements PamSettings {
 	 * @param pamSettingsUnit 
 	 * @return xml element
 	 */
-	private Element writeUnitSettings(Document doc, Element parent, PamSettings pamSettingsUnit) {
+	public Element writeUnitSettings(Document doc, Element parent, PamSettings pamSettingsUnit) {
 
 		int[] settingInds = findSettings(null, pamSettingsUnit.getUnitName());
 		PamSettings[] settingsObjects = null;
@@ -462,7 +462,7 @@ public class PamguardXMLWriter implements PamSettings {
 	 * can be temporary settings objects when writing temporary settings from dialogs. 
 	 * @return new XML element. 
 	 */
-	private Element writeUnitSettings(Document doc, Element parent, PamSettings pamSettingsUnit, PamSettings[] toWrite) {
+	public Element writeUnitSettings(Document doc, Element parent, PamSettings pamSettingsUnit, PamSettings[] toWrite) {
 		Element moduleData = doc.createElement("MODULE");
 		moduleData.setAttribute("Java.class", pamSettingsUnit.getClass().getName());
 		moduleData.setAttribute("UnitType", pamSettingsUnit.getUnitType());

src/PamguardMVC/PamDataBlock.java

@@ -3055,7 +3055,7 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
 	
 	/**
 	 * Gets a data provider for Tethys. These will probably need
-	 * to be bespoke, but for now will autogenerate based on the SALLogging information. 
+	 * to be bespoke, but for now will autogenerate based on the SQLLogging information. 
 	 * @return the tethysDataProvider
 	 */
 	public TethysDataProvider getTethysDataProvider() {

src/tethys/TethysControl.java

@@ -11,6 +11,7 @@ import javax.swing.JMenuItem;
 import PamController.PamControlledUnit;
 import PamController.PamController;
 import PamguardMVC.PamDataBlock;
+import tethys.dbxml.DBXMLConnect;
 //import nilus.Deployment;
 //import nilus.Deployment.Instrument;
 import tethys.output.StreamExportParams;
@@ -33,9 +34,20 @@ public class TethysControl extends PamControlledUnit {
 
 	private TethysExportParams tethysExportParams = new TethysExportParams();
 	
+	private DBXMLConnect dbxmlConnect;
 
 	public TethysControl(String unitName) {
 		super(unitType, unitName);
+		dbxmlConnect = new DBXMLConnect(this);
+	}
+
+	/**
+	 * Get DBXML Connector. This class contains all the functions that are needed
+	 * to talk to the database. 
+	 * @return DBXML functions. 
+	 */
+	public DBXMLConnect getDbxmlConnect() {
+		return dbxmlConnect;
 	}
 
 	@Override

src/tethys/dbxml/DBXMLConnect.java

@@ -2,6 +2,12 @@ package tethys.dbxml;
 
 import tethys.TethysControl;
 
+/**
+ * Class containing functions for managing the database connection. Opening, closing,
+ * writing, keeping track of performance, etc. 
+ * @author Doug Gillespie, Katie O'Laughlin
+ *
+ */
 public class DBXMLConnect {
 
 	private TethysControl tethysControl;
@@ -19,6 +25,6 @@ public class DBXMLConnect {
 		
 	}
 	
-	// add whatever calls are necessary to set up schema's etc. 
+	// add whatever calls are necessary ... 
 
 }

src/tethys/deployment/DeploymentHandler.java

@@ -67,8 +67,8 @@ public class DeploymentHandler {
 		 * Realistically, this list is always 0,1,2,etc or it goes horribly wrong !
 		 */
 		// so write functions here to get information from the daqParams. 
-		System.out.printf("Sample regime: %s input with rate %3.1fHz, %d channels, gain %3.1fdB, ADCp-p %3.1fV\n", daqParams.getDaqSystemType(),
-				daqParams.getSampleRate(), daqParams.getNChannels(), daqParams.preamplifier.getGain(), daqParams.voltsPeak2Peak);
+//		System.out.printf("Sample regime: %s input with rate %3.1fHz, %d channels, gain %3.1fdB, ADCp-p %3.1fV\n", daqParams.getDaqSystemType(),
+//				daqParams.getSampleRate(), daqParams.getNChannels(), daqParams.preamplifier.getGain(), daqParams.voltsPeak2Peak);
 		/**
 		 * then there is the actual sampling. This is a bit harder to find. I thought it would be in the data map
 		 * but the datamap is a simple count of what's in the databasase which is not quite what we want.  
@@ -207,8 +207,8 @@ public class DeploymentHandler {
 		 * Realistically, this list is always 0,1,2,etc or it goes horribly wrong !
 		 */
 		// so write functions here to get information from the daqParams. 
-		System.out.printf("Sample regime: %s input with rate %3.1fHz, %d channels, gain %3.1fdB, ADCp-p %3.1fV\n", daqParams.getDaqSystemType(),
-				daqParams.getSampleRate(), daqParams.getNChannels(), daqParams.preamplifier.getGain(), daqParams.voltsPeak2Peak);
+//		System.out.printf("Sample regime: %s input with rate %3.1fHz, %d channels, gain %3.1fdB, ADCp-p %3.1fV\n", daqParams.getDaqSystemType(),
+//				daqParams.getSampleRate(), daqParams.getNChannels(), daqParams.preamplifier.getGain(), daqParams.voltsPeak2Peak);
 		/**
 		 * then there is the actual sampling. This is a bit harder to find. I thought it would be in the data map
 		 * but the datamap is a simple count of what's in the databasase which is not quite what we want.  
@@ -242,8 +242,8 @@ public class DeploymentHandler {
 				}
 			}
 			
-			System.out.printf("Input map of sound data indicates data from %s to %s with %d starts and %d stops over %d files\n", 
-					PamCalendar.formatDateTime(dataStart), PamCalendar.formatDateTime(dataEnd), nStart, nStop, nFile+1);
+//			System.out.printf("Input map of sound data indicates data from %s to %s with %d starts and %d stops over %d files\n", 
+//					PamCalendar.formatDateTime(dataStart), PamCalendar.formatDateTime(dataEnd), nStart, nStop, nFile+1);
 			
 		}
 		

src/tethys/detection/DetectionGranularity.java

@@ -0,0 +1,34 @@
+package tethys.detection;
+
+/**
+ * Class to help define what the granularity of exported detections 
+ * documents should be. The entire document will be in memory, so it
+ * may be necessary to add many detections documents into the database 
+ * for a single Deployment. 
+ * @author dg50
+ *
+ */
+public class DetectionGranularity {
+
+	public enum GRANULARITY {NONE, BINARYFILE, TIME};
+	
+	/**
+	 * Type of granularity. Are data all in one lump, split by binary file or by time. 
+	 */
+	GRANULARITY granularity = GRANULARITY.NONE;
+	
+	/**
+	 * Granularity interval in seconds. Output system will try to round these
+	 * to something with sensible boundaries. 
+	 * This field is only needed when using the GRANULARITY.TIME option.  
+	 */
+	public long granularityIntervalSeconds;
+
+	public DetectionGranularity(GRANULARITY granularity, long granularityIntervalSeconds) {
+		super();
+		this.granularity = granularity;
+		this.granularityIntervalSeconds = granularityIntervalSeconds;
+	}
+	
+	
+}

src/tethys/detection/DetectionsHandler.java

@@ -0,0 +1,191 @@
+package tethys.detection;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import PamUtils.PamCalendar;
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.PamDataUnit;
+import PamguardMVC.dataSelector.DataSelector;
+import dataMap.OfflineDataMap;
+import dataMap.OfflineDataMapPoint;
+import nilus.DataSourceType;
+import nilus.Deployment;
+import nilus.Detection;
+import nilus.DetectionEffort;
+import nilus.DetectionEffortKind;
+import nilus.DetectionGroup;
+import nilus.Detections;
+import tethys.TethysControl;
+import tethys.TethysTimeFuncs;
+import tethys.detection.DetectionGranularity.GRANULARITY;
+import tethys.output.StreamExportParams;
+import tethys.output.TethysExportParams;
+import tethys.pamdata.TethysDataProvider;
+
+public class DetectionsHandler {
+
+
+	private TethysControl tethysControl;
+	
+	public DetectionsHandler(TethysControl tethysControl) {
+		super();
+		this.tethysControl = tethysControl;
+	}
+
+	/**
+	 * Here is where we export data for a specific data stream to Tethys.
+	 *
+	 * @param aDataBlock
+	 * @param aDeployment 
+	 * @param tethysExportParams
+	 * @param streamExportParams
+	 */
+	public boolean exportDetections(PamDataBlock aDataBlock, Deployment deployment, DetectionGranularity granularity, TethysExportParams tethysExportParams,
+			StreamExportParams streamExportParams) {
+		if (granularity == null || granularity.granularity == null) {
+			granularity = new DetectionGranularity(GRANULARITY.TIME, 3600);
+		}
+		switch (granularity.granularity) {
+		case BINARYFILE:
+			return exportByBinaryFile(aDataBlock, deployment, tethysExportParams, streamExportParams);
+		case NONE:
+			return exportEverything(aDataBlock, deployment, tethysExportParams, streamExportParams);
+		case TIME:
+			return exportByTimeChunk(aDataBlock, deployment, granularity.granularityIntervalSeconds, tethysExportParams, streamExportParams);
+		default:
+			break;
+		}
+
+		return false;
+	
+
+	}
+
+	private boolean exportByBinaryFile(PamDataBlock dataBlock, Deployment deployment,
+			TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
+		long deploymentStart = TethysTimeFuncs.millisFromGregorianXML(deployment.getDeploymentDetails().getAudioTimeStamp());
+		long deploymentStop = TethysTimeFuncs.millisFromGregorianXML(deployment.getRecoveryDetails().getAudioTimeStamp());
+		/*
+		 *  there should be a pretty good correspondence between the start of a binary file and the deploymentStart
+		 *  since they all derived from the same start clock. 
+		 */
+		OfflineDataMap dataMap = dataBlock.getPrimaryDataMap();
+		if (dataMap == null) {
+			return false;
+		}
+		List<OfflineDataMapPoint> mapPoints = dataMap.getMapPoints();
+		boolean ok = true;
+		for (OfflineDataMapPoint mapPoint : mapPoints) {
+			if (mapPoint.getEndTime() < deploymentStart) {
+				continue;
+			}
+			if (mapPoint.getStartTime() >= deploymentStop) {
+				continue;
+			}
+			ok &= loadAndExport(dataBlock, deployment, Math.max(deploymentStart, mapPoint.getStartTime()), 
+					Math.min(deploymentStop, mapPoint.getEndTime()), tethysExportParams, streamExportParams);
+		}
+		
+		
+		return ok;
+	}
+
+	private boolean exportEverything(PamDataBlock dataBlock, Deployment deployment,
+			TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
+		long deploymentStart = TethysTimeFuncs.millisFromGregorianXML(deployment.getDeploymentDetails().getAudioTimeStamp());
+		long deploymentStop = TethysTimeFuncs.millisFromGregorianXML(deployment.getRecoveryDetails().getAudioTimeStamp());
+		return loadAndExport(dataBlock, deployment, deploymentStart, deploymentStop, tethysExportParams, streamExportParams);
+	}
+
+	private boolean exportByTimeChunk(PamDataBlock dataBlock, Deployment deployment, long granularityIntervalSeconds,
+			TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
+
+		long deploymentStart = TethysTimeFuncs.millisFromGregorianXML(deployment.getDeploymentDetails().getAudioTimeStamp());
+		long deploymentStop = TethysTimeFuncs.millisFromGregorianXML(deployment.getRecoveryDetails().getAudioTimeStamp());
+		long chunkMillis = granularityIntervalSeconds*1000;
+		long exportStart = deploymentStart / chunkMillis;
+		exportStart *= chunkMillis;
+		boolean ok = true;
+		while (exportStart < deploymentStop) {
+			ok &= loadAndExport(dataBlock, deployment, Math.max(deploymentStart, exportStart), 
+					Math.min(deploymentStop, exportStart + chunkMillis), tethysExportParams, streamExportParams);
+			exportStart += chunkMillis;
+		}
+		
+		return ok;
+	}
+
+/**
+	 * Load and export data for a given time period. This may be a complete deployment, it may be a short section. Do as told !
+	 * Hopefully data interval is small enough to hold all in memory - it needs to be if the document will fit in mempory, so should be OK
+	 * @param dataBlock
+	 * @param deployment
+	 * @param max
+	 * @param min
+	 * @param tethysExportParams
+	 * @param streamExportParams
+	 */
+	private boolean loadAndExport(PamDataBlock dataBlock, Deployment deployment, long startTimeMillis, long endTimeMillis,
+			TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
+		// load the data
+		dataBlock.loadViewerData(startTimeMillis, endTimeMillis, null);
+		DataSelector dataSelector = dataBlock.getDataSelector(tethysControl.getDataSelectName(), false);
+		/*
+		 *  for easier synching, get a copy of the data and also apply the data selector right away so that
+		 *  we've a list of exactly the right data.  
+		 */
+		ArrayList<PamDataUnit> data = dataBlock.getDataCopy(startTimeMillis, endTimeMillis, true, dataSelector);
+		/*
+		 * Here, make Detection object and add the DetectionEffort data. 
+		 */
+		TethysDataProvider dataProvider = dataBlock.getTethysDataProvider();
+		Detections detections = new Detections();
+		detections.setId(deployment.getId());
+		detections.setDescription(dataProvider.getDescription(deployment, tethysExportParams));
+		DataSourceType dataSource = new DataSourceType();
+		dataSource.setDeploymentId(deployment.getId());
+//		dataSource.setEnsembleId(""); ToDo
+		detections.setDataSource(dataSource);
+		detections.setAlgorithm(dataProvider.getAlgorithm());
+		detections.setUserId("Unknown user");
+		detections.setEffort(getDetectorEffort(deployment, startTimeMillis, endTimeMillis));
+		DetectionGroup detectionGroup = new DetectionGroup();
+		detections.setOnEffort(detectionGroup);
+		List<Detection> detectionList = detectionGroup.getDetection();
+		for (int i = 0; i < data.size(); i++) {
+			PamDataUnit dataUnit = data.get(i);
+			Detection detection = dataProvider.createDetection(dataUnit, tethysExportParams, streamExportParams);
+			if (detection != null) {
+				detectionList.add(detection);
+			}
+		}
+		System.out.printf("Exporting %d %s detections for time period %s to %s\n", detectionList.size(), dataBlock.getDataName(), 
+				detections.getEffort().getStart().toString(), detections.getEffort().getEnd().toString());
+		/*
+		 * We should now have a fully populated Detections object, so write it to the database
+		 * using functions in DBXMLConnect 
+		 */
+		tethysControl.getDbxmlConnect(); // call whatever you need to call in here to write the Detections. 
+		
+		
+		return true;
+		
+	}
+
+//	private boolean exportByTimeChunk(PamDataBlock aDataBlock, Deployment deployment, long granularityIntervalSeconds,
+//			TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
+//		// TODO Auto-generated method stub
+//		return false;
+//	}
+
+	private DetectionEffort getDetectorEffort(Deployment deployment, long effortStart, long effortEnd) {
+		DetectionEffort effort = new DetectionEffort();
+		effort.setStart(TethysTimeFuncs.xmlGregCalFromMillis(effortStart));
+		effort.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(effortEnd));
+//		effort.set // no setter for DetectionEffortKind
+		List<DetectionEffortKind> effortKinds = effort.getKind();
+		return effort;
+	}
+
+}

src/tethys/output/TethysExporter.java

@@ -35,6 +35,9 @@ import tethys.TethysControl;
 import tethys.dbxml.DBXMLConnect;
 import tethys.deployment.DeploymentHandler;
 import tethys.deployment.DeploymentRecoveryPair;
+import tethys.detection.DetectionGranularity;
+import tethys.detection.DetectionGranularity.GRANULARITY;
+import tethys.detection.DetectionsHandler;
 import tethys.pamdata.TethysDataProvider;
 import tethys.pamdata.TethysSchema;
 
@@ -202,6 +205,7 @@ public class TethysExporter {
 			return false;
 		}
 
+		ArrayList<Deployment> deploymentDocs = new ArrayList<>();
 		/*
 		 * This will become the main loop over deployment documents
 		 */
@@ -210,7 +214,7 @@ public class TethysExporter {
 
 			Deployment deployment = deploymentHandler.createDeploymentDocument(i++, drd);
 //			System.out.println(deployment.toString());
-
+			deploymentDocs.add(deployment);
 
 		}
 
@@ -220,13 +224,21 @@ public class TethysExporter {
 		 * go through the export params and call something for every data block that's
 		 * enabled.
 		 */
+		DetectionsHandler detectionsHandler = new DetectionsHandler(tethysControl);
 		ArrayList<PamDataBlock> allDataBlocks = PamController.getInstance().getDataBlocks();
-		for (PamDataBlock aDataBlock : allDataBlocks) {
-			StreamExportParams streamExportParams = tethysExportParams.getStreamParams(aDataBlock);
-			if (streamExportParams == null || !streamExportParams.selected) {
-				continue; // not interested in this one.
+		/**
+		 * Outer loop is through deployemnt documents. Will then export detections within each 
+		 * deployment detector by detector
+		 */
+		for (Deployment aDeployment : deploymentDocs) {
+			for (PamDataBlock aDataBlock : allDataBlocks) {
+				StreamExportParams streamExportParams = tethysExportParams.getStreamParams(aDataBlock);
+				if (streamExportParams == null || !streamExportParams.selected) {
+					continue; // not interested in this one.
+				}
+				detectionsHandler.exportDetections(aDataBlock, aDeployment, 
+						new DetectionGranularity(GRANULARITY.TIME, 3600), tethysExportParams, streamExportParams);
 			}
-			exportDataStream(aDataBlock, tethysExportParams, streamExportParams);
 		}
 		/*
 		 * Then do whatever else is needed to complete the document.
@@ -297,9 +309,9 @@ public class TethysExporter {
 			for (int iPhone = 0; iPhone < hydrophones.size(); iPhone++) {
 				Hydrophone aPhone = hydrophones.get(iPhone);
 				double totalCal = -daqProcess.rawAmplitude2dB(1, iPhone, false);
-				System.out.printf(
-						"hydrophone %d has sensitivity %3.1fdB + gain %3.1fdB. Total calibration is %3.1fdB re1U/uPa\n",
-						iPhone, aPhone.getSensitivity(), aPhone.getPreampGain(), totalCal);
+//				System.out.printf(
+//						"hydrophone %d has sensitivity %3.1fdB + gain %3.1fdB. Total calibration is %3.1fdB re1U/uPa\n",
+//						iPhone, aPhone.getSensitivity(), aPhone.getPreampGain(), totalCal);
 			}
 		}
 
@@ -308,112 +320,4 @@ public class TethysExporter {
 
 
 
-	/**
-	 * Here is where we export data for a specific data stream to Tethys.
-	 *
-	 * @param aDataBlock
-	 * @param tethysExportParams
-	 * @param streamExportParams
-	 */
-	private void exportDataStream(PamDataBlock aDataBlock, TethysExportParams tethysExportParams,
-			StreamExportParams streamExportParams) {
-		/**
-		 * This will probably need to be passed additional parameters and may also want
-		 * to return something other than void in order to build a bigger Tethys
-		 * document.
-		 */
-		/*
-		 * Some examples of how to do whatever is needed to get schema and data out of
-		 * PAMGuard.
-		 */
-		/*
-		 * first we'll probably want a reference to the module containing the data. in
-		 * principle this can't get null, since the datablock was found be searching in
-		 * the other direction.
-		 */
-		PamControlledUnit pamControlledUnit = aDataBlock.getParentProcess().getPamControlledUnit();
-
-		TethysDataProvider dataProvider = aDataBlock.getTethysDataProvider();
-
-		PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
-
-		if (dataProvider == null) {
-			return;
-		}
-
-		TethysSchema tethysSchema = dataProvider.getSchema();
-		/*
-		 * the schema should have a Document object in it. If we wanted to turn that
-		 * into an XML string we can ... (though I'd assume that having the Document is
-		 * more useful)
-		 */
-		String schemaXMLString = pamXMLWriter.getAsString(tethysSchema.getXsd(), false);
-		System.out.printf("Schema for %s is %s\n", aDataBlock.getDataName(), schemaXMLString);
-
-		/*
-		 * Get the XML settings for that datablock. This is (or should be the parameters
-		 * that were controlling that module, with adequate data about upstream
-		 * modules). I think this has to go somewhere into the Detections document.
-		 */
-		Document doc = pamXMLWriter.writeOneModule((PamSettings) pamControlledUnit, System.currentTimeMillis());
-		String moduleXML = null;
-		if (doc != null) {
-			// this string should be XML of all the settings for the module controlling this
-			// datablock.
-			moduleXML = pamXMLWriter.getAsString(doc, true); // change to false to get smaller xml
-			System.out.printf("Module settings for datablock %s are:\n", moduleXML);
-			System.out.println(moduleXML);
-		}
-
-		/**
-		 * Now can go through the data. Probably, we'll want to go through all the data
-		 * in the project, but we can hold off on that for now and just go for data that
-		 * are in memory. We'll also have to think a lot about updating parts of the
-		 * database which have been reprocessed - what we want to do, should eventually
-		 * all be options set in the dialog and available within TethysExportParams For
-		 * now though, we're just going to export data that are in memory. Once basic
-		 * export is working, I can easily enough write something which will go through
-		 * an entire data set, go through between two times, etc.
-		 */
-		// so this is a way of iterating through the data that are in memory, which will
-		// do for now ..
-		// do it with a data copy which can avoid synchronising the entire block for
-		// what may be a long time
-		// the copy function is itself synched, and is quite fast, so easier and safe
-		// this way
-		ArrayList<PamDataUnit> dataCopy = aDataBlock.getDataCopy();
-		DataSelector dataSelector = aDataBlock.getDataSelector(tethysControl.getDataSelectName(), false);
-		int nSkipped = 0;
-		int nExport = 0;
-
-		for (PamDataUnit aData : dataCopy) {
-			/*
-			 * see if we want this data unit. PAMGuard has a complicated system of data
-			 * selectors specific to each data type. These are centrally managed so you
-			 * don't need to worry too much about them. They are identified by name for each
-			 * data stream and the behaviour here should follow the selections you made in
-			 * the dialog. the data selection system allows different displays to show
-			 * different data, so a stream can have many differently named selectors active
-			 * at any one time, all doing different things in different parts of PAMGuard.
-			 */
-			if (dataSelector != null) {
-				if (dataSelector.scoreData(aData) <= 0) {
-					nSkipped++;
-					continue; // don't want this one.
-				}
-			}
-
-			/*
-			 * then we do whatever we need to do to convert this into something for Tethys
-			 * this might happen in the tethysSchema object for each data stream ????
-			 */
-
-			nExport++;
-		}
-
-		System.out.printf("Exported %d data units and skipped %d in %s", nExport, nSkipped,
-				aDataBlock.getLongDataName());
-
-	}
-
 }

src/tethys/pamdata/AutoTethysProvider.java

@@ -1,11 +1,32 @@
 package tethys.pamdata;
 
-import org.w3c.dom.Document;
+import java.math.BigInteger;
+import java.util.List;
 
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import PamController.PamControlledUnit;
+import PamController.PamSettings;
+import PamController.PamguardVersionInfo;
+import PamController.settings.output.xml.PamguardXMLWriter;
+import PamUtils.XMLUtils;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
+import PamguardMVC.PamProcess;
 import generalDatabase.DBSchemaWriter;
 import generalDatabase.SQLLogging;
+import nilus.AlgorithmType;
+import nilus.AlgorithmType.Parameters;
+import nilus.Deployment;
+import nilus.DescriptionType;
+import nilus.Detection;
+import nilus.SpeciesIDType;
+import tethys.TethysTimeFuncs;
+import tethys.output.StreamExportParams;
+import tethys.output.TethysExportParams;
 
 /**
  * Automatically provides Tethys data based on the SQL database interface 
@@ -16,9 +37,13 @@ import generalDatabase.SQLLogging;
 public class AutoTethysProvider implements TethysDataProvider {
 
 	private PamDataBlock pamDataBlock;
+	private PamProcess pamProcess;
+	private PamControlledUnit pamControlledUnit;
 
 	public AutoTethysProvider(PamDataBlock pamDataBlock) {
 		this.pamDataBlock = pamDataBlock;
+		pamProcess = pamDataBlock.getParentProcess();
+		pamControlledUnit = pamProcess.getPamControlledUnit();
 	}
 
 	@Override
@@ -39,4 +64,131 @@ public class AutoTethysProvider implements TethysDataProvider {
 		return null;
 	}
 
+	@Override
+	public DescriptionType getDescription(Deployment deployment, TethysExportParams tethysExportParams) {
+		DescriptionType description = new DescriptionType();
+		String fullUnitName = pamControlledUnit.getUnitType() + " " + pamControlledUnit.getUnitName();
+		description.setAbstract(fullUnitName);
+		description.setObjectives(fullUnitName);
+		description.setMethod(pamControlledUnit.getUnitType());
+		
+		return description;
+	}
+
+	@Override
+	public AlgorithmType getAlgorithm() {
+		AlgorithmType algorithm = new AlgorithmType();
+		algorithm.setMethod(this.getAlgorithmMethod());
+		algorithm.setSoftware("PAMGuard");
+		algorithm.setVersion(PamguardVersionInfo.version);
+		algorithm.setParameters(this.getAlgorithmParameters());
+		
+		return algorithm;
+	}
+
+	private Parameters getAlgorithmParameters() {
+		if (pamControlledUnit instanceof PamSettings == false) {
+			return null;
+		}
+		PamSettings pamSettings = (PamSettings) pamControlledUnit;
+		Parameters parameters = new Parameters();
+		List<Element> paramList = parameters.getAny();
+		Document doc = XMLUtils.createBlankDoc();
+		PamguardXMLWriter pamXMLWriter = PamguardXMLWriter.getXMLWriter();
+		Element dummyEl = doc.createElement("MODULES");
+		doc.appendChild(dummyEl);
+		PamSettings[] settingsObjs = getSettingsObjects();
+		if (settingsObjs == null) {
+			return null;
+		}
+		Element settingsEl = pamXMLWriter.writeUnitSettings(doc, dummyEl, pamSettings, settingsObjs);
+		if (settingsEl == null) {
+			return null;
+		}
+		dummyEl.appendChild(settingsEl);
+		NodeList childs = settingsEl.getChildNodes();
+		for (int i = 0; i < childs.getLength(); i++) {
+			Node el = childs.item(i);
+//			System.out.println(el.getNodeName());
+			if (el instanceof Element) {
+				paramList.add((Element) el);
+			}
+		}
+
+//		Document doc = pamXMLWriter.writeOneModule((PamSettings) pamControlledUnit, System.currentTimeMillis());
+//		String moduleXML = null;
+		if (doc != null) {
+			// this string should be XML of all the settings for the module controlling this
+			// datablock.
+//			moduleXML = pamXMLWriter.getAsString(doc, true); // change to false to get smaller xml
+//			System.out.printf("Module settings for datablock %s are:\n", moduleXML);
+//			System.out.println(moduleXML);
+//			Element pamguard = doc.get("PAMGUARD");
+//			Element modules = (Element) pamguard.getElementsByTagName("MODULES");
+//			doc.get
+//			NodeList childs = doc.getChildNodes();
+//			for (int i = 0; i < childs.getLength(); i++) {
+//				Node el = childs.item(i);
+//				System.out.println(el.getNodeName());
+//				if (el instanceof Element) {
+//					paramList.add((Element) el);
+//				}
+//			}
+//			String moduleXML = pamXMLWriter.getAsString(doc, true); // change to false to get smaller xml
+//			System.out.printf("Module settings for datablock %s are:\n%s", this.pamDataBlock.getDataName(), moduleXML);
+		}
+		
+//		// try the old say
+//		Document doc2 = pamXMLWriter.writeOneModule((PamSettings) pamControlledUnit, System.currentTimeMillis());
+//		String moduleXML = null;
+//		if (doc2 != null) {
+//			// this string should be XML of all the settings for the module controlling this
+//			// datablock.
+//			moduleXML = pamXMLWriter.getAsString(doc2, true); // change to false to get smaller xml
+//			System.out.printf("Module settings for datablock %s are:\n%s", pamDataBlock.getDataName(),moduleXML);
+//		}
+//		
+		
+		return parameters;
+	}
+	
+	private PamSettings[] getSettingsObjects() {
+		if (pamControlledUnit instanceof PamSettings) {
+			PamSettings[] settings = new PamSettings[1];
+			settings[0] = (PamSettings) pamControlledUnit;
+			return settings;
+		}
+		return null;
+	}
+
+	/**
+	 * Algorithm method. Default is the module name. Can change to a paper citation 
+	 * by overriding this 
+	 * @return
+	 */
+	private String getAlgorithmMethod() {
+		return pamControlledUnit.getUnitType();
+	}
+
+	@Override
+	public Detection createDetection(PamDataUnit dataUnit, TethysExportParams tethysExportParams,
+			StreamExportParams streamExportParams) {
+		Detection detection = new Detection();
+		detection.setStart(TethysTimeFuncs.xmlGregCalFromMillis(dataUnit.getTimeMilliseconds()));
+		detection.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(dataUnit.getEndTimeInMilliseconds()));
+		detection.setSpeciesId(getSpeciesIdType());
+		/*
+		 * NOTE: I use channel bitmaps throughout since detections are often made on multiple channels. 
+		 */
+		detection.setChannel(BigInteger.valueOf(dataUnit.getChannelBitmap()));
+		
+		return detection;
+	}
+
+	private SpeciesIDType getSpeciesIdType() {
+		SpeciesIDType species = new SpeciesIDType();
+//		species.s
+		return species;
+	}
+
 }

src/tethys/pamdata/TethysDataProvider.java

@@ -1,6 +1,12 @@
 package tethys.pamdata;
 
 import PamguardMVC.PamDataUnit;
+import nilus.AlgorithmType;
+import nilus.Deployment;
+import nilus.DescriptionType;
+import nilus.Detection;
+import tethys.output.StreamExportParams;
+import tethys.output.TethysExportParams;
 
 /**
  * Any PAMGuard data stream which can provide Detection data to PAMGuard will 
@@ -29,4 +35,32 @@ public interface TethysDataProvider {
 	 */
 	public TethysDataPoint getDataPoint(PamDataUnit pamDataUnit);
 
+
+	/**
+	 * Get DescriptionType object to include in a Tethys Detections document. 
+	 * @param deployment
+	 * @param tethysExportParams
+	 * @return Tethys DescriptionType object, which contains infromation about detections
+	 */
+	public DescriptionType getDescription(Deployment deployment, TethysExportParams tethysExportParams);
+
+
+	/**
+	 * Get Algorithm information for a Tethys Detections document
+	 * @return Algorithm information
+	 */
+	public AlgorithmType getAlgorithm();
+
+
+	/**
+	 * Create a Tethys Detection object from a PamDataUnit.<br>
+	 * It's OK for this to return null if for some reason the unit shouldn't be stored. 
+	 * @param dataUnit PAMGuard data unit
+	 * @param tethysExportParams 
+	 * @param streamExportParams
+	 * @return Detection Tethys Detection object. 
+	 */
+	public Detection createDetection(PamDataUnit dataUnit, TethysExportParams tethysExportParams,
+			StreamExportParams streamExportParams);
+	
 }