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

src/Array/MovingHydrophoneLocator.java

@@ -16,5 +16,10 @@ abstract public class MovingHydrophoneLocator extends SimpleHydrophoneLocator {
 		super(pamArray, streamer);
 	}
 
+	@Override
+	public boolean isChangeable() {
+		return true;
+	}
+
 
 }

src/PamModel/PamModel.java

@@ -464,7 +464,7 @@ final public class PamModel implements PamModelInterface, PamSettings {
 
 
 		mi = PamModuleInfo.registerControlledUnit(MetaDataContol.class.getName(), MetaDataContol.unitType);
-		mi.setToolTipText("Deployment Meta Data");
+		mi.setToolTipText("Project Meta Data");
 		mi.setModulesMenuGroup(utilitiesGroup);
 		mi.setMaxNumber(1); 
 		

src/RightWhaleEdgeDetector/RWEBinaryDataSource.java

@@ -218,7 +218,7 @@ public class RWEBinaryDataSource extends BinaryDataSource {
 		binaryObjectData.getDataUnitBaseData().setSampleDuration(duration);
 //		rweDataUnit = new RWEDataUnit(aSound.timeMilliseconds, channelMap, 
 //				startSample, duration, aSound);
-		rweDataUnit = new RWEDataUnit(binaryObjectData.getDataUnitBaseData(), aSound);
+		rweDataUnit = new RWEDataUnit(rweProcess, binaryObjectData.getDataUnitBaseData(), aSound);
 		rweDataUnit.setSequenceBitmap(sequenceMap);
 		double f[] = new double[2];
 		f[0] = aSound.minFreq * rweDataBlock.getSampleRate()/rweDataBlock.getFftLength();

src/RightWhaleEdgeDetector/RWEDataUnit.java

@@ -6,26 +6,31 @@ import whistlesAndMoans.AbstractWhistleDataUnit;
 public class RWEDataUnit extends AbstractWhistleDataUnit {
 
 	public RWESound rweSound;
+	private RWEProcess rweProcess;
 	
-	public RWEDataUnit(long timeMilliseconds, int channelBitmap,
+	public RWEDataUnit(RWEProcess rweProcess, long timeMilliseconds, int channelBitmap,
 			long startSample, long duration,  RWESound rweSound) {
 		super(timeMilliseconds, channelBitmap, startSample, duration);
 		this.rweSound = rweSound;
+		this.rweProcess = rweProcess;
 		// TODO Auto-generated constructor stub
 	}
 
-	public RWEDataUnit(DataUnitBaseData basicData,  RWESound rweSound) {
+	public RWEDataUnit(RWEProcess rweProcess, DataUnitBaseData basicData,  RWESound rweSound) {
 		super(basicData);
 		this.rweSound = rweSound;
+		this.rweProcess = rweProcess;
 	}
 
-	double[] freqsHz;
 	@Override
 	public double[] getFreqsHz() {
-		if (freqsHz == null) {
-			freqsHz = new double[rweSound.sliceCount];
+		double[] f = new double[rweSound.sliceCount];
+		RWEDataBlock rweDataBlock = rweProcess.getRweDataBlock();
+		double binToHz = rweDataBlock.getSampleRate() / rweDataBlock.getFftLength();
+		for (int i = 0; i < f.length; i++) {
+			f[i] = (double) rweSound.peakFreq[i] * binToHz;
 		}
-		return null;
+		return f;
 	}
 
 	@Override
@@ -35,9 +40,17 @@ public class RWEDataUnit extends AbstractWhistleDataUnit {
 
 	@Override
 	public double[] getTimesInSeconds() {
-		// TODO Auto-generated method stub
+		if (rweSound == null) {
 			return null;
 		}
+		double[] t = new double[rweSound.sliceCount];
+		RWEDataBlock rweDataBlock = rweProcess.getRweDataBlock();
+		double binToT = rweDataBlock.getFftHop() / rweDataBlock.getSampleRate();
+		for (int i = 0; i < t.length; i++) {
+			t[i] = (double) rweSound.sliceList[i] * binToT;
+		}
+		return t;
+	}
 
 	@Override
 	public String getSummaryString() {

src/RightWhaleEdgeDetector/RWEProcess.java

@@ -42,6 +42,10 @@ public class RWEProcess extends PamProcess {
 	private FFTDataBlock sourceDataBlock;
 	private RWEDataBlock rweDataBlock;
 		
+	public RWEDataBlock getRweDataBlock() {
+		return rweDataBlock;
+	}
+
 	private Hashtable<Integer, BearingLocaliser> bearingLocalisers;
 	private StandardSymbolManager symbolManager;
 	/**
@@ -211,7 +215,7 @@ public class RWEProcess extends PamProcess {
 //					System.out.println(String.format("Detected sound type %d on channel %d", 
 //							soundType, this.iChannel));
 					duration = sourceDataBlock.getFftHop() * aSound.duration;
-					rweDataUnit = new RWEDataUnit(aSound.timeMilliseconds, 
+					rweDataUnit = new RWEDataUnit(RWEProcess.this, aSound.timeMilliseconds, 
 							1<<iChannel, fftDataUnit.getStartSample()-duration, duration, aSound);
 					rweDataUnit.sortOutputMaps(sourceDataBlock.getChannelMap(), sourceDataBlock.getSequenceMapObject(), 1<<iChannel);
 					f[0] = aSound.minFreq * getSampleRate()/sourceDataBlock.getFftLength();

src/tethys/deployment/DeploymentHandler.java

@@ -1,6 +1,5 @@
 package tethys.deployment;
 
-import java.io.Serializable;
 import java.math.BigInteger;
 import java.util.ArrayList;
 import java.util.List;
@@ -16,23 +15,26 @@ import Acquisition.DaqStatusDataUnit;
 import Acquisition.DaqSystem;
 import Array.ArrayManager;
 import Array.Hydrophone;
+import Array.HydrophoneLocator;
 import Array.PamArray;
+import Array.Streamer;
+import Array.ThreadingHydrophoneLocator;
 import PamController.PamControlledUnit;
 import PamController.PamController;
-import PamUtils.PamCalendar;
-import PamUtils.PamUtils;
 import PamguardMVC.PamDataBlock;
+import metadata.MetaDataContol;
+import metadata.deployment.DeploymentData;
 import nilus.Audio;
 import nilus.ChannelInfo;
 import nilus.ChannelInfo.Sampling;
 import nilus.ChannelInfo.Sampling.Regimen;
 import nilus.Deployment;
+import nilus.Deployment.Instrument;
 import nilus.Deployment.SamplingDetails;
 import nilus.Deployment.Sensors;
 import nilus.DeploymentRecoveryDetails;
 import nilus.GeometryTypeM;
 import nilus.Helper;
-import nilus.MarshalXML;
 import pamMaths.PamVector;
 import tethys.TethysLocationFuncs;
 import tethys.TethysTimeFuncs;
@@ -52,7 +54,7 @@ public class DeploymentHandler {
 	public DeploymentOverview createOverview() {
 		// first find an acquisition module.
 		PamControlledUnit aModule = PamController.getInstance().findControlledUnit(AcquisitionControl.class, null);
-		if (aModule instanceof AcquisitionControl == false) {
+		if (!(aModule instanceof AcquisitionControl)) {
 			// will return if it's null. Impossible for it to be the wrong type.
 			// but it's good practice to check anyway before casting.
 			return null;
@@ -192,7 +194,7 @@ public class DeploymentHandler {
 
 		// first find an acquisition module.
 		PamControlledUnit aModule = PamController.getInstance().findControlledUnit(AcquisitionControl.class, null);
-		if (aModule instanceof AcquisitionControl == false) {
+		if (!(aModule instanceof AcquisitionControl)) {
 			// will return if it's null. Impossible for it to be the wrong type.
 			// but it's good practice to check anyway before casting.
 			return null;
@@ -289,6 +291,8 @@ public class DeploymentHandler {
 
 		TethysLocationFuncs.getTrackAndPositionData(deployment);
 
+		getProjectData(deployment);
+
 		getSamplingDetails(deployment);
 
 		getSensorDetails(deployment);
@@ -305,6 +309,58 @@ public class DeploymentHandler {
 		return deployment;
 	}
 
+	/**
+	 * Add project Metadata to a Deploymnet document. This is currently being
+	 * made available in the MetaDataControl module which should be added to PAMGuard
+	 * as well as the Tethys output module.
+	 * @param deployment
+	 */
+	private boolean getProjectData(Deployment deployment) {
+		PamControlledUnit aUnit = PamController.getInstance().findControlledUnit(MetaDataContol.class, null);
+		if (aUnit instanceof MetaDataContol == false) {
+			return false;
+		}
+		MetaDataContol metaControl = (MetaDataContol) aUnit;
+		DeploymentData deploymentData = metaControl.getDeploymentData();
+		deployment.setProject(deploymentData.getProject());
+		deployment.setDeploymentAlias(deploymentData.getDeploymentAlias());
+		deployment.setSite(deploymentData.getSite());
+		deployment.setCruise(deploymentData.getCruise());
+		deployment.setPlatform(deploymentData.getPlatform());
+		deployment.setRegion(deploymentData.getRegion());
+		Instrument instrument = new Instrument();
+		instrument.setType(deploymentData.getInstrumentType());
+		instrument.setInstrumentId(deploymentData.getInstrumentId());
+		// get the geometry type from the array manager. 
+		String geomType = getGeometryType();
+		instrument.setGeometryType(geomType);
+		deployment.setInstrument(instrument);
+		return true;
+	}
+
+	/**
+	 * Get a geometry type string for Tethys based on information in the array manager. 
+	 * @return
+	 */
+	private String getGeometryType() {
+		PamArray array = ArrayManager.getArrayManager().getCurrentArray();
+		int nStreamer = array.getStreamerCount();
+		for (int i = 0; i < nStreamer; i++) {
+			Streamer streamer = array.getStreamer(i);
+			HydrophoneLocator locator = streamer.getHydrophoneLocator();
+			if (locator == null) {
+				continue;
+			}
+			if (locator instanceof ThreadingHydrophoneLocator) {
+				return "cabled";
+			}
+			else {
+				return "rigid";
+			}
+		}
+		return "unknown";
+	}
+
 	private boolean getSensorDetails(Deployment deployment) {
 		PamArray array = ArrayManager.getArrayManager().getCurrentArray();
 		Sensors sensors = new Sensors();
@@ -385,7 +441,7 @@ public class DeploymentHandler {
 			channelInfo.setEnd(deployment.getRecoveryDetails().getAudioTimeStamp());
 
 			BigIntegerConverter biCon = new BigIntegerConverter();
-			BigInteger chanNum = BigInteger.valueOf((long) i);
+			BigInteger chanNum = BigInteger.valueOf(i);
 			channelInfo.setChannelNumber(chanNum);
 			if (hydroMap != null) {
 				channelInfo.setSensorNumber(hydroMap[i]);

src/tethys/pamdata/AutoTethysProvider.java

@@ -13,9 +13,12 @@ import PamController.PamSettings;
 import PamController.PamguardVersionInfo;
 import PamController.settings.output.xml.PamguardXMLWriter;
 import PamUtils.XMLUtils;
+import PamguardMVC.DataUnitBaseData;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
 import PamguardMVC.PamProcess;
+import PamguardMVC.TFContourData;
+import PamguardMVC.TFContourProvider;
 import generalDatabase.DBSchemaWriter;
 import generalDatabase.SQLLogging;
 import nilus.AlgorithmType;
@@ -27,6 +30,7 @@ import nilus.SpeciesIDType;
 import tethys.TethysTimeFuncs;
 import tethys.output.StreamExportParams;
 import tethys.output.TethysExportParams;
+import whistleClassifier.WhistleContour;
 
 /**
  * Automatically provides Tethys data based on the SQL database interface 
@@ -182,9 +186,64 @@ public class AutoTethysProvider implements TethysDataProvider {
 		 */
 		detection.setChannel(BigInteger.valueOf(dataUnit.getChannelBitmap()));
 		
+		nilus.Detection.Parameters detParams = new nilus.Detection.Parameters();
+		detection.setParameters(detParams);
+		double[] freqs = dataUnit.getFrequency();
+		if (freqs != null) {
+			detParams.setMinFreqHz(freqs[0]);
+			detParams.setMaxFreqHz(freqs[1]);
+		}
+		double ampli = dataUnit.getAmplitudeDB();
+		detParams.setReceivedLevelDB(ampli);
+//		DataUnitBaseData basicData = dataUnit.getBasicData();
+		gotTonalContour(dataUnit, detParams);
+		
 		return detection;
 	}
 
+	/**
+	 * Get tonal sounds contour. Sadly there are two slightly different interfaces in use
+	 * in PAMGuard, so try them both. 
+	 * @param detParams
+	 * @return true if a contour was added
+	 */
+	private boolean gotTonalContour(PamDataUnit dataUnit, nilus.Detection.Parameters detParams) {
+		if (dataUnit instanceof TFContourProvider) {
+			TFContourProvider tfcp = (TFContourProvider) dataUnit;
+			TFContourData cd = tfcp.getTFContourData();
+			if (cd != null) {
+				long[] tMillis = cd.getContourTimes();
+				double[] fHz = cd.getRidgeFrequency();
+				nilus.Detection.Parameters.Tonal tonal = new nilus.Detection.Parameters.Tonal();
+				List<Double> offsetS = tonal.getOffsetS();
+				List<Double> hz = tonal.getHz();
+				for (int i = 0; i < tMillis.length; i++) {
+					offsetS.add((double) (tMillis[i]-tMillis[0]) / 1000.);
+					hz.add(fHz[i]);
+				}
+				detParams.setTonal(tonal);
+				return true;
+			}
+		}
+		if (dataUnit instanceof WhistleContour) {
+			WhistleContour wc = (WhistleContour) dataUnit;
+			double[] t = wc.getTimesInSeconds();
+			double[] f = wc.getFreqsHz();
+			if (t != null && f != null) {
+				nilus.Detection.Parameters.Tonal tonal = new nilus.Detection.Parameters.Tonal();
+				List<Double> offsetS = tonal.getOffsetS();
+				List<Double> hz = tonal.getHz();
+				for (int i = 0; i < t.length; i++) {
+					offsetS.add(t[i]-t[0]);
+					hz.add(f[i]);
+				}
+				detParams.setTonal(tonal);
+				return true;
+			}
+		}
+		return false;
+	}
+
 	private SpeciesIDType getSpeciesIdType() {
 		SpeciesIDType species = new SpeciesIDType();
 //		species.s

src/whistlesAndMoans/AbstractWhistleDataUnit.java

@@ -7,8 +7,7 @@ import PamguardMVC.DataUnitBaseData;
 import PamguardMVC.PamDataUnit;
 import PamguardMVC.TFContourProvider;;
 
-public abstract class AbstractWhistleDataUnit 
-	extends PamDataUnit<PamDataUnit, PamDataUnit> 
+public abstract class AbstractWhistleDataUnit extends PamDataUnit<PamDataUnit, PamDataUnit> 
 	implements WhistleContour, PamDetection {
 
 	public AbstractWhistleDataUnit(long timeMilliseconds, int channelBitmap,