Detections Document ready to go

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(),
+//		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);
+//				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(),
+//		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);
+//				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", 
+//			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);
+//					PamCalendar.formatDateTime(dataStart), PamCalendar.formatDateTime(dataEnd), nStart, nStop, nFile+1);
 			
 		}
 		

src/tethys/detection/DetectionsHandler.java

@@ -3,11 +3,7 @@ package tethys.detection;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.w3c.dom.Document;
+import PamUtils.PamCalendar;
-
-import PamController.PamControlledUnit;
-import PamController.PamSettings;
-import PamController.settings.output.xml.PamguardXMLWriter;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
 import PamguardMVC.dataSelector.DataSelector;
@@ -15,8 +11,10 @@ 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;
@@ -24,7 +22,6 @@ import tethys.detection.DetectionGranularity.GRANULARITY;
 import tethys.output.StreamExportParams;
 import tethys.output.TethysExportParams;
 import tethys.pamdata.TethysDataProvider;
-import tethys.pamdata.TethysSchema;
 
 public class DetectionsHandler {
 
@@ -58,35 +55,9 @@ public class DetectionsHandler {
 			return exportByTimeChunk(aDataBlock, deployment, granularity.granularityIntervalSeconds, tethysExportParams, streamExportParams);
 		default:
 			break;
-		
 		}
-		/**
-		 * 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.
-		 */
-		/*
-		 * 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();
+		return false;
-
-		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));
-		
-		return true;
 	
 
 	}
@@ -168,13 +139,34 @@ public class DetectionsHandler {
 		/*
 		 * 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);
-			// add many Detecion objects
+			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(), 
-//		write to database
+				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;
@@ -187,10 +179,10 @@ public class DetectionsHandler {
 //		return false;
 //	}
 
-	private DetectionEffort getDetectorEffort(Deployment deployment) {
+	private DetectionEffort getDetectorEffort(Deployment deployment, long effortStart, long effortEnd) {
 		DetectionEffort effort = new DetectionEffort();
-		effort.setStart(deployment.getDeploymentDetails().getAudioTimeStamp());
+		effort.setStart(TethysTimeFuncs.xmlGregCalFromMillis(effortStart));
-		effort.setEnd(deployment.getRecoveryDetails().getAudioTimeStamp());
+		effort.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(effortEnd));
 //		effort.set // no setter for DetectionEffortKind
 		List<DetectionEffortKind> effortKinds = effort.getKind();
 		return effort;

src/tethys/output/TethysExporter.java

@@ -216,7 +216,7 @@ public class TethysExporter {
 
 			Deployment deployment = deploymentHandler.createDeploymentDocument(i++, drd);
 //			System.out.println(deployment.toString());
-			deploymentDocs.add(deployment1);
+			deploymentDocs.add(deployment);
 
 		}
 
@@ -311,9 +311,9 @@ 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(
+//				System.out.printf(
-						"hydrophone %d has sensitivity %3.1fdB + gain %3.1fdB. Total calibration is %3.1fdB re1U/uPa\n",
+//						"hydrophone %d has sensitivity %3.1fdB + gain %3.1fdB. Total calibration is %3.1fdB re1U/uPa\n",
-						iPhone, aPhone.getSensitivity(), aPhone.getPreampGain(), totalCal);
+//						iPhone, aPhone.getSensitivity(), aPhone.getPreampGain(), totalCal);
 			}
 		}
 

src/tethys/pamdata/AutoTethysProvider.java

@@ -1,5 +1,6 @@
 package tethys.pamdata;
 
+import java.math.BigInteger;
 import java.util.List;
 
 import org.w3c.dom.Document;
@@ -21,6 +22,10 @@ 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;
 
 /**
@@ -104,7 +109,7 @@ public class AutoTethysProvider implements TethysDataProvider {
 		NodeList childs = settingsEl.getChildNodes();
 		for (int i = 0; i < childs.getLength(); i++) {
 			Node el = childs.item(i);
-			System.out.println(el.getNodeName());
+//			System.out.println(el.getNodeName());
 			if (el instanceof Element) {
 				paramList.add((Element) el);
 			}
@@ -165,4 +170,25 @@ public class AutoTethysProvider implements TethysDataProvider {
 		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

@@ -4,6 +4,8 @@ import PamguardMVC.PamDataUnit;
 import nilus.AlgorithmType;
 import nilus.Deployment;
 import nilus.DescriptionType;
+import nilus.Detection;
+import tethys.output.StreamExportParams;
 import tethys.output.TethysExportParams;
 
 /**
@@ -34,9 +36,31 @@ 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);
 	
 }