Added Tethys output to DL module

.gitignore

@@ -109,3 +109,5 @@ settings.xml
 .classpath
 .classpath
 .classpath
+.classpath
+.settings/org.eclipse.jdt.core.prefs

src/PamController/PamController.java

@@ -1456,13 +1456,14 @@ public class PamController implements PamControllerInterface, PamSettings {
 		for (int iU = 0; iU < pamControlledUnits.size(); iU++) {
 			pamControlledUnits.get(iU).pamHasStopped();
 		}
-		guiFrameManager.pamEnded();
 		
 		long stopTime = PamCalendar.getTimeInMillis();
 		saveEndSettings(stopTime);
 
 		setPamStatus(PAM_IDLE);
 		
+		guiFrameManager.pamEnded();
+		
 		// no good having this here since it get's called at the end of every file. 
 //		if (GlobalArguments.getParam(PamController.AUTOEXIT) != null) {
 ////			can exit here, since we've auto started, can auto exit.

src/PamController/PamguardVersionInfo.java

@@ -31,12 +31,12 @@ public class PamguardVersionInfo {
 	 * Version number, major version.minorversion.sub-release.
 	 * Note: can't go higher than sub-release 'f'
 	 */
-	static public final String version = "2.02.10bd";
+	static public final String version = "2.02.11c";
 	
 	/**
 	 * Release date
 	 */
-	static public final String date = "23 April 2024";
+	static public final String date = "29 April 2024";
 	
 //	/**
 //	 * Release type - Beta or Core

src/PamModel/PamModel.java

@@ -472,7 +472,7 @@ final public class PamModel implements PamSettings {
 			mi.setModulesMenuGroup(utilitiesGroup);
 			mi.setMaxNumber(1);
 			//mi.addGUICompatabilityFlag(PamGUIManager.FX); //has FX enabled GUI.
-			mi.setHidden(SMRUEnable.isEnable() == false);
+//			mi.setHidden(SMRUEnable.isEnable() == false);
 		}		
 		
 		/*

src/PamguardMVC/dataOffline/OfflineDataLoading.java

@@ -189,11 +189,11 @@ public class OfflineDataLoading<T extends PamDataUnit> {
 						switch (offlineDataInfo.getInterrupt()) {
 						case OFFLINE_DATA_INTERRUPT:
 							//						System.out.println("Request order cancelling");
-
+							int giveUp = 0;
 
 							if (orderData.cancelOrder()) {			
 
-								while (orderData!=null || !orderData.isDone()) {
+								while ((orderData!=null || !orderData.isDone()) & giveUp++ < 300) {
 									try {
 										Thread.sleep(10);
 									} catch (InterruptedException e) {

src/RightWhaleEdgeDetector/RWEControl.java

@@ -7,22 +7,19 @@ import java.io.Serializable;
 
 import javax.swing.JMenuItem;
 
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-
 import KernelSmoothing.KernelSmoothingProcess;
 import PamController.PamControlledUnit;
 import PamController.PamControlledUnitSettings;
-import PamController.PamController;
 import PamController.PamControllerInterface;
 import PamController.PamSettingManager;
 import PamController.PamSettings;
 import PamUtils.PamUtils;
-import PamView.GroupedDataSource;
 import PamView.GroupedSourceParameters;
 import PamView.dialog.GroupedSourcePanel;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.ProcessAnnotation;
+import RightWhaleEdgeDetector.graphics.RWEDataPlotProviderFX;
+import dataPlotsFX.data.TDDataProviderRegisterFX;
 
 /**
  * Exact implementation of the 2003 Right Whale detector I developed when I was 
@@ -43,6 +40,7 @@ public class RWEControl extends PamControlledUnit implements PamSettings {
 		super("RW Edge Detector", unitName);
 		rweProcess = new RWEProcess(this);
 		addPamProcess(rweProcess);
+		
 		PamSettingManager.getInstance().registerSettings(this);
 	}
 

src/RightWhaleEdgeDetector/RWEProcess.java

@@ -12,6 +12,7 @@ import Localiser.algorithms.timeDelayLocalisers.bearingLoc.BearingLocaliser;
 import Localiser.algorithms.timeDelayLocalisers.bearingLoc.BearingLocaliserSelector;
 import annotation.calcs.snr.SNRAnnotationType;
 import autecPhones.AutecGraphics;
+import dataPlotsFX.data.TDDataProviderRegisterFX;
 import fftManager.Complex;
 import fftManager.FFTDataBlock;
 import fftManager.FFTDataUnit;
@@ -33,6 +34,7 @@ import PamguardMVC.PamDataUnit;
 import PamguardMVC.PamObservable;
 import PamguardMVC.PamProcess;
 import PamguardMVC.debug.Debug;
+import RightWhaleEdgeDetector.graphics.RWEDataPlotProviderFX;
 import RightWhaleEdgeDetector.graphics.RWESymbolManager;
 
 public class RWEProcess extends PamProcess {
@@ -53,6 +55,7 @@ public class RWEProcess extends PamProcess {
 	 */
 	private boolean isPreSmoothed;
 	private KernelSmoothing kernelSmoothing;
+	private RWEDataPlotProviderFX fxPlotProvider;
 	
 	public RWEProcess(RWEControl rweControl) {
 		super(rweControl, null);
@@ -71,6 +74,9 @@ public class RWEProcess extends PamProcess {
 		rweDataBlock.setCanClipGenerate(true);
 		rweDataBlock.SetLogging(new RWESQLLogging(rweControl, rweDataBlock));
 		rweDataBlock.addDataAnnotationType(new SNRAnnotationType());
+
+		fxPlotProvider = new RWEDataPlotProviderFX(this, rweDataBlock);
+		TDDataProviderRegisterFX.getInstance().registerDataInfo(fxPlotProvider);
 	}
 	
 	@Override

src/RightWhaleEdgeDetector/graphics/RWEDataPlotProviderFX.java

@@ -0,0 +1,25 @@
+package RightWhaleEdgeDetector.graphics;
+
+import RightWhaleEdgeDetector.RWEDataBlock;
+import RightWhaleEdgeDetector.RWEProcess;
+import dataPlotsFX.data.TDDataInfoFX;
+import dataPlotsFX.data.TDDataProviderFX;
+import dataPlotsFX.layout.TDGraphFX;
+
+public class RWEDataPlotProviderFX extends TDDataProviderFX {
+
+	private RWEDataBlock rweDataBlock;
+	private RWEProcess rweProcess;
+
+	public RWEDataPlotProviderFX(RWEProcess rweProcess, RWEDataBlock rweDataBlock) {
+		super(rweDataBlock);
+		this.rweProcess = rweProcess;
+		this.rweDataBlock = rweDataBlock;
+	}
+
+	@Override
+	public TDDataInfoFX createDataInfo(TDGraphFX tdGraph) {
+		return new RWEDataPlotinfoFX(this, rweProcess, tdGraph, rweDataBlock);
+	}
+
+}

src/RightWhaleEdgeDetector/graphics/RWEDataPlotinfoFX.java

@@ -0,0 +1,133 @@
+package RightWhaleEdgeDetector.graphics;
+
+import PamUtils.Coordinate3d;
+import PamView.GeneralProjector.ParameterType;
+import PamView.GeneralProjector.ParameterUnits;
+import PamguardMVC.PamDataUnit;
+import RightWhaleEdgeDetector.RWEDataBlock;
+import RightWhaleEdgeDetector.RWEDataUnit;
+import RightWhaleEdgeDetector.RWEProcess;
+import RightWhaleEdgeDetector.RWESound;
+import dataPlotsFX.TDSymbolChooserFX;
+import dataPlotsFX.data.TDDataInfoFX;
+import dataPlotsFX.data.TDScaleInfo;
+import dataPlotsFX.layout.TDGraphFX;
+import dataPlotsFX.projector.TDProjectorFX;
+import fftManager.FFTDataBlock;
+import javafx.scene.canvas.GraphicsContext;
+import javafx.scene.shape.Polygon;
+
+public class RWEDataPlotinfoFX extends TDDataInfoFX {
+
+	private RWEDataBlock rweDataBlock;
+	private TDScaleInfo bearingScaleInfo;
+	private TDScaleInfo frequencyInfo;
+	private RWEProcess rweProcess;
+
+	public RWEDataPlotinfoFX(RWEDataPlotProviderFX tdDataProvider, RWEProcess rweProcess, TDGraphFX tdGraph, RWEDataBlock rweDataBlock) {
+		super(tdDataProvider, tdGraph, rweDataBlock);
+		this.rweProcess = rweProcess;
+		this.rweDataBlock = rweDataBlock;
+
+		bearingScaleInfo = new TDScaleInfo(0,180, ParameterType.BEARING, ParameterUnits.DEGREES);
+		bearingScaleInfo.setReverseAxis(true); //set the axis to be reverse so 0 is at top of graph
+		frequencyInfo = new TDScaleInfo(0, 1, ParameterType.FREQUENCY, ParameterUnits.HZ);
+		this.getScaleInfos().add(bearingScaleInfo);
+		this.getScaleInfos().add(frequencyInfo);
+
+		//set correct frequency range based on nyquist. 
+		frequencyInfo.setMaxVal(rweDataBlock.getSampleRate()/2.);
+		
+	}
+
+	@Override
+	public Double getDataValue(PamDataUnit pamDataUnit) {
+		if (pamDataUnit.getLocalisation() == null) {
+			return null;
+		}
+		double[] angles = pamDataUnit.getLocalisation().getAngles();
+		if (angles != null && angles.length > 0) {
+			return Math.toDegrees(angles[0]);
+		}
+		return null;
+	}
+
+	@Override
+	public TDScaleInfo getScaleInfo() {
+
+		setNPlotPanes(frequencyInfo, this.getDataBlock(), false); 
+
+		double min = Math.min(bearingScaleInfo.getMinVal(), bearingScaleInfo.getMaxVal());
+		double max = Math.max(bearingScaleInfo.getMinVal(), bearingScaleInfo.getMaxVal());
+
+		bearingScaleInfo.setMaxVal(max);
+		bearingScaleInfo.setMinVal(min);
+
+		return super.getScaleInfo();
+	}
+	
+	@Override
+	public TDSymbolChooserFX getSymbolChooser() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public Polygon drawDataUnit(int plotNumber, PamDataUnit pamDataUnit, GraphicsContext g, double scrollStart, TDProjectorFX tdProjector,int type) {
+		// if drawing FFT then need to use slight more complex drawing functions.
+		if (getScaleInfoIndex()==1) {
+			return drawRWContour(plotNumber, pamDataUnit, g, scrollStart, tdProjector, type);
+		}
+		else {
+			return super.drawDataUnit(plotNumber, pamDataUnit, g, scrollStart, tdProjector ,type);
+		}
+//		return null;
+	}
+
+	private Polygon drawRWContour(int plotNumber, PamDataUnit pamDataUnit, GraphicsContext g, double scrollStart,
+			TDProjectorFX tdProjector, int type) {
+		if (!shouldDraw(plotNumber, pamDataUnit)){
+			//System.out.println("Cannot plot whistle");
+//			iCol++;
+			return null; 
+		}
+		RWEDataUnit rweDataUnit = (RWEDataUnit) pamDataUnit;
+		RWESound rweSound = rweDataUnit.rweSound;
+		int[] hf = rweSound.highFreq;
+		int[] lf = rweSound.lowFreq;
+		int[] pf = rweSound.peakFreq;
+
+		FFTDataBlock dataSource = (FFTDataBlock) rweProcess.getParentDataBlock();
+		if (dataSource == null) {
+			return null;
+		}
+		double fs = dataSource.getSampleRate();
+		int fftLen = dataSource.getFftLength();
+		int fftHop = dataSource.getFftHop();
+		
+//		Polygon outer = new Poly
+		int nOut = hf.length*2;
+		double[] outsideX = new double[nOut];
+		double[] outsideY = new double[nOut];
+		for (int i = 0; i < hf.length; i++) {
+			long t = (long) (i*1000*fftHop/fs)+rweDataUnit.getTimeMilliseconds();
+			double f  = lf[i]*fs/fftLen;
+			double tdPix = tdProjector.getTimePix(t-scrollStart);
+			double fPix = tdProjector.getYPix(f);
+//			Coordinate3d coord = tdProjector.getCoord3d(i, t, f);
+			outsideX[i] =  tdPix;
+			outsideY[i] =  fPix;
+
+			f  = hf[i]*fs/fftLen;
+//			coord = tdProjector.getCoord3d(i, t, f);
+			fPix = tdProjector.getYPix(f);
+			outsideX[nOut-1-i] =  tdPix;
+			outsideY[nOut-1-i] =  fPix;
+			
+		}
+		g.strokePolygon(outsideX, outsideY, nOut);
+		
+		
+		return null;
+	}
+}

src/rawDeepLearningClassifier/dlClassification/DLClassifyProcess.java

@@ -494,6 +494,39 @@ public class DLClassifyProcess extends PamInstantProcess {
 	}
 
 
+	/**
+	 * Get the result with the highest score. 
+	 * @return model result with the highest score. 
+	 */
+	public PredictionResult getBestModelResult(DLDetection dlDetection) {
+		ArrayList<PredictionResult> results = dlDetection.getModelResults();
+		if (results == null || results.size() == 0) {
+			return null;
+		}
+		/*
+		 *  probably need to improve this function to only look at results
+		 *  that are in a list of used results or something crazy ? 
+		 */
+		
+//		dlControl.getDLModel().;
+		PredictionResult bestResult = null;
+		float bestScore = 0;
+		for (PredictionResult pred : results) {
+			float[] scores = pred.getPrediction();
+			if (scores == null) {
+				continue;
+			}
+			for (int i = 0; i < scores.length; i++) {
+				if (scores[i] > bestScore) {
+					bestScore = scores[i];
+					bestResult = pred;
+				}
+			}
+		}
+		
+		return bestResult;
+	}
+
 	/**
 	 * Clear the data unit buffer. 
 	 */
@@ -596,4 +629,8 @@ public class DLClassifyProcess extends PamInstantProcess {
 		return this.dlControl.getDLParams();
 	}
 
+	public DLControl getDLControl() {
+		return dlControl;
+	}
+
 }

src/rawDeepLearningClassifier/dlClassification/DLDetection.java

@@ -134,7 +134,6 @@ public class DLDetection extends PamDataUnit implements PamDetection, RawDataHol
 	}
 	
 	
-	
 	/**
 	 * Get the wave data for a specified channel. 
 	 * @param channel

src/rawDeepLearningClassifier/dlClassification/DLDetectionDataBlock.java

@@ -3,6 +3,11 @@ package rawDeepLearningClassifier.dlClassification;
 import PamView.GroupedDataSource;
 import PamView.GroupedSourceParameters;
 import PamguardMVC.AcousticDataBlock;
+import rawDeepLearningClassifier.tethys.DLSpeciesManager;
+import rawDeepLearningClassifier.tethys.DLTethysDataProvider;
+import tethys.TethysControl;
+import tethys.pamdata.TethysDataProvider;
+import tethys.species.DataBlockSpeciesManager;
 
 /**
  * Holds classified data units from deep learning model. 
@@ -13,6 +18,8 @@ import PamguardMVC.AcousticDataBlock;
 public class DLDetectionDataBlock extends AcousticDataBlock<DLDetection> implements GroupedDataSource {
 
 	private DLClassifyProcess dlClassifyProcess;
+	private DLTethysDataProvider dlTethysDataProvider;
+	private DLSpeciesManager dlSpeciesManager;
 
 	public DLDetectionDataBlock(String dataName, DLClassifyProcess parentProcess, int channelMap) {
 		super(DLDetection.class, dataName, parentProcess, channelMap);
@@ -24,5 +31,21 @@ public class DLDetectionDataBlock extends AcousticDataBlock<DLDetection> impleme
 		return dlClassifyProcess.getDLParams().groupedSourceParams;
 	}
 
+	@Override
+	public TethysDataProvider getTethysDataProvider(TethysControl tethysControl) {
+		if (dlTethysDataProvider == null) {
+			dlTethysDataProvider = new DLTethysDataProvider(tethysControl, this);
+		}
+		return dlTethysDataProvider;
+	}
+
+	@Override
+	public DataBlockSpeciesManager<DLDetection> getDatablockSpeciesManager() {
+		if (dlSpeciesManager == null) {
+			dlSpeciesManager = new DLSpeciesManager(dlClassifyProcess.getDLControl(), this);
+		}
+		return dlSpeciesManager;
+	}
+
 
 }

src/rawDeepLearningClassifier/tethys/DLSpeciesManager.java

@@ -0,0 +1,105 @@
+package rawDeepLearningClassifier.tethys;
+
+import java.util.ArrayList;
+
+import PamUtils.PamArrayUtils;
+import PamguardMVC.PamDataBlock;
+import annotation.DataAnnotation;
+import rawDeepLearningClassifier.DLControl;
+import rawDeepLearningClassifier.dlClassification.DLClassName;
+import rawDeepLearningClassifier.dlClassification.DLClassiferModel;
+import rawDeepLearningClassifier.dlClassification.DLDetection;
+import rawDeepLearningClassifier.dlClassification.PredictionResult;
+import rawDeepLearningClassifier.logging.DLAnnotation;
+import tethys.species.DataBlockSpeciesCodes;
+import tethys.species.DataBlockSpeciesManager;
+
+public class DLSpeciesManager extends DataBlockSpeciesManager<DLDetection> {
+
+	private DLControl dlControl;
+	
+	private static final String unknown = "Unknown";
+
+	public DLSpeciesManager(DLControl dlControl, PamDataBlock<DLDetection> dataBlock) {
+		super(dataBlock);
+		this.dlControl = dlControl;
+	}
+
+	@Override
+	public DataBlockSpeciesCodes getSpeciesCodes() {
+		DLClassName[] classNames = getClassNames();
+		String[] classStrings = getClassStrings(classNames);
+		return new DataBlockSpeciesCodes(unknown, classStrings);
+	}
+	
+	/**
+	 * Get just the strings of the class names. 
+	 * @param classNames
+	 * @return
+	 */
+	private String[] getClassStrings(DLClassName[] classNames) {
+		if (classNames == null) {
+			return null;
+		}
+		String[] classStrings = new String[classNames.length];
+		for (int i = 0; i < classStrings.length; i++) {
+			classStrings[i] = classNames[i].className;
+		}
+		return classStrings;
+	}
+	
+	/**
+	 * Get the list of class names, or make a single unknown category. 
+	 * @return
+	 */
+	private DLClassName[] getClassNames() {
+		DLClassiferModel currentModel = dlControl.getDLModel();
+		DLClassName[] classNames = null;
+		if (currentModel != null) {
+			classNames = currentModel.getClassNames();
+		}
+		if (classNames == null) {
+			classNames = new DLClassName[1];
+			classNames[0] = new DLClassName(unknown, (short) 0);
+		}
+		return classNames;
+	}
+	
+	
+
+	@Override
+	public String getSpeciesCode(DLDetection dlDetection) {
+		int nAnnot = dlDetection.getNumDataAnnotations();
+		if (nAnnot == 0) {
+			return unknown;
+		}
+//		DataAnnotation annot = dlDetection.getDataAnnotation(0);
+//		ArrayList<PredictionResult> results = null;
+//		if (annot instanceof DLAnnotation) {
+//			DLAnnotation dlAnnot = (DLAnnotation) annot;
+//			results = dlAnnot.getModelResults();
+//		}
+		PredictionResult result = dlControl.getDLClassifyProcess().getBestModelResult(dlDetection);
+		if (result == null) {
+			return unknown;
+		}
+		int resInd = 0;
+		float bestScore = 0;
+		float[] scores = result.getPrediction();
+		if (scores == null || scores.length == 0) {
+			return unknown;
+		}
+		for (int i = 0; i < scores.length; i++) {
+			if (scores[i] > bestScore) {
+				bestScore = scores[i];
+				resInd = i;
+			}
+		}
+		String[] names = getClassStrings(getClassNames());
+		if (resInd < names.length) {
+			return names[resInd];
+		}
+		return unknown;
+	}
+
+}

src/rawDeepLearningClassifier/tethys/DLTethysDataProvider.java

@@ -0,0 +1,38 @@
+package rawDeepLearningClassifier.tethys;
+
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.PamDataUnit;
+import nilus.Detection;
+import nilus.Detection.Parameters;
+import rawDeepLearningClassifier.dlClassification.DLDetection;
+import tethys.TethysControl;
+import tethys.output.StreamExportParams;
+import tethys.output.TethysExportParams;
+import tethys.pamdata.AutoTethysProvider;
+
+public class DLTethysDataProvider extends AutoTethysProvider {
+
+	public DLTethysDataProvider(TethysControl tethysControl, PamDataBlock pamDataBlock) {
+		super(tethysControl, pamDataBlock);
+		// TODO Auto-generated constructor stub
+	}
+
+	@Override
+	public Detection createDetection(PamDataUnit dataUnit, TethysExportParams tethysExportParams,
+			StreamExportParams streamExportParams) {
+		Detection detection =  super.createDetection(dataUnit, tethysExportParams, streamExportParams);
+		if (detection == null) {
+			return null;
+		}
+		DLDetection dlDetection = (DLDetection) dataUnit;
+	
+//		result = 
+		String annotSummary = dlDetection.getAnnotationsSummaryString();
+		if (annotSummary != null) {
+			Parameters parameters = detection.getParameters();
+			addUserDefined(parameters, "Annotation", annotSummary);
+		}
+	
+		return detection;
+	}
+}

src/tethys/dbxml/DBXMLConnect.java

@@ -197,15 +197,15 @@ public class DBXMLConnect {
 			marshal.marshal(nilusObject, tempFile.toString());
 			// above lines have made a file. Are now going to gzip it before sending to Tethys
 			File zipFile = null;
-			try {
-				zipFile = zipOutputFile(tempFile);
-			}
-			catch (FileNotFoundException e1){
-				System.out.println(e1.getMessage());
-			}
-			catch (IOException e2) {
-				System.out.println(e2.getMessage());
-			}
+//			try {
+//				zipFile = zipOutputFile(tempFile);
+//			}
+//			catch (FileNotFoundException e1){
+//				System.out.println(e1.getMessage());
+//			}
+//			catch (IOException e2) {
+//				System.out.println(e2.getMessage());
+//			}
 			String finalName;
 			if (zipFile == null) {
 				finalName = bodgeName;