Merge pull request #38 from PAMGuard/main

Merge in from main

.classpath

@@ -6,7 +6,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/Java 17">
 		<attributes>
 			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>

.gitignore

@@ -40,3 +40,4 @@ settings.xml
 .classpath
 .classpath
 .classpath
+.classpath

dependency-reduced-pom.xml

@@ -4,7 +4,7 @@
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
   <name>Pamguard Java12+</name>
-  <version>2.02.07b</version>
+  <version>2.02.07f</version>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
   <url>www.pamguard.org</url>
   <organization>

pom.xml

@@ -4,7 +4,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
-  <version>2.02.07b</version>
+  <version>2.02.07f</version>
   <name>Pamguard Java12+</name>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
 	<url>www.pamguard.org</url>

src/Acquisition/FolderInputSystem.java

@@ -50,6 +50,7 @@ import PamView.dialog.PamGridBagContraints;
 import PamView.dialog.PamLabel;
 import PamView.panel.PamPanel;
 import PamView.panel.PamProgressBar;
+import PamguardMVC.debug.Debug;
 
 /**
  * Read multiple files in sequence. Options exist to either pause and
@@ -118,7 +119,7 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 		if (folderInputParameters == null)
 			setFolderInputParameters(new FolderInputParameters(getSystemType()));
 		//		PamSettingManager.getInstance().registerSettings(this); //calling super already registers this in the FileInputSystem constructor
-		checkComandLine();
+//		checkComandLine();
 		makeSelFileList();
 		newFileTimer = new Timer(1000, new RestartTimer());
 		newFileTimer.setRepeats(false);
@@ -128,21 +129,24 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 	/**
 	 * Check to see if acquisition source folder was set in the command line. 
 	 */
-	private void checkComandLine() {
+	private String[] checkComandLineFolder() {
 		String globalFolder = GlobalArguments.getParam(GlobalWavFolderArg);
+		Debug.out.println("Checking -wavfilefolder option: is " + globalFolder);
 		if (globalFolder == null) {
-			return;
+			return null;
 		}
 		// see if it at least exists, though will we want to do this for Network folders ? 
 		File aFile = new File(globalFolder);
 		if (aFile.exists() == false) {
-			System.err.println("Command line folder does not exist: " + globalFolder);
+			System.err.printf("Command line wav folder \"%s\" does not exist", globalFolder);
+//			return null;
 		}
 		String[] selList = {globalFolder};
-		folderInputParameters.setSelectedFiles(selList);
+//		folderInputParameters.setSelectedFiles(selList);
 		// need to immediately make the allfiles list since it's about to get used by the reprocess manager
 		// need to worry about how to wait for this since it's starting in a different thread. 
-		makeSelFileList();
+		//makeSelFileList();
+		return selList;
 	}
 
 	/**
@@ -295,15 +299,24 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 	}
 
 	/**
-	 * Make a list of wav files within a folder. 
+	 * Make a list of wav files within a folder. In some circumstances this can be a list 
+	 * of actual files in a folder. Also needs to handle the possibility of it using 
+	 * a globally set folder name. 
 	 * @return flag to indicate...nothing?
 	 */
 	public int makeSelFileList() {
 
-		if (fileInputParameters.recentFiles == null || fileInputParameters.recentFiles.size() < 1) {
+		String[] selection = checkComandLineFolder();
-			return 0;
+		
+		if (selection == null) {
+			if (fileInputParameters.recentFiles == null || fileInputParameters.recentFiles.size() < 1) {
+				return 0;
+			}
+			selection = folderInputParameters.getSelectedFiles();
+		}
+		if (selection.length > 0) {
+			System.out.println("FolderInputSystem.makeSelFileList(): Searching for sound files in " + selection[0]);
 		}
-		String[] selection = folderInputParameters.getSelectedFiles();
 		return makeSelFileList(selection);
 	}
 	

src/Acquisition/filedate/StandardFileDate.java

@@ -284,9 +284,12 @@ public class StandardFileDate implements FileDate, PamSettings {
 		} catch (ParseException e) {
 			// TODO Auto-generated catch block
 //			e.printStackTrace();
-			System.out.println(e.getMessage());
+			System.out.println("StandardfileDate.forcedDataFormat:" + e.getMessage());
 		}  //throws ParseException if no match
 		setLastFormat(forcedDateFormat);
+		if (d == null) {
+			return 0;
+		}
 		return d.getTime();
 	}
 

src/IshmaelLocator/IshLocProcess.java

@@ -368,7 +368,7 @@ abstract public class IshLocProcess extends PamProcess implements SpectrogramMar
 			selectionSams =	daqBlock.getSamples(startSam, (int)durationSam, channelMap);
 		}
 		catch (RawDataUnavailableException e) {
-			System.out.println(e.getMessage());
+			System.out.println("RawDataUnavailableException in IshLocProcess:" + e.getMessage());
 
 			// if the raw data has already been discarded, adjust the natural lifetime to try and avoid this in the future
 			int newTime;

src/JSSHTerminal/SSHSession.java

@@ -287,7 +287,7 @@ public final class SSHSession implements UserInfo {
         out.write(k);
         out.flush();
       } catch (IOException e) {
-        System.out.println(e.getMessage());
+        System.out.println("IOException in SSHSession.write: " + e.getMessage());
       }
     }
 
@@ -349,7 +349,7 @@ public final class SSHSession implements UserInfo {
           }
         }
       } catch (IOException e) {
-        System.out.println(e.getMessage());
+        System.out.println("Error in SSHSession.pump: " + e.getMessage());
       } finally {
         closeQuietly(in);
         closeQuietly(out);

src/NMEA/AcquireNmeaData.java

@@ -203,7 +203,7 @@ public class AcquireNmeaData extends PamProcess implements ActionListener, Modul
 		try {
 			pjSerialComm = PJSerialComm.openSerialPort(params.serialPortName, params.serialPortBitsPerSecond);
 		} catch (PJSerialException e) {
-			System.out.println(e.getMessage());
+			System.out.println("PJSerialException in AcquireNMEAData" + e.getMessage());
 //			WarnOnce.sho
 			return;
 		}

src/PamController/PamController.java

@@ -1314,7 +1314,12 @@ public class PamController implements PamControllerInterface, PamSettings {
 
 		@Override
 		public void run() {
+			long t1 = System.currentTimeMillis();
 			while (checkRunStatus()) {
+				long t2 = System.currentTimeMillis();
+				if (t2 - t1 > 5000) {
+					System.out.printf("Stopping, but stuck in loop for CheckRunStatus for %3.1fs\n", (double) (t2-t1)/1000.);
+				}
 				try {
 					Thread.sleep(10);
 				} catch (InterruptedException e) {

src/PamController/PamSettingManager.java

@@ -1752,10 +1752,10 @@ public class PamSettingManager {
 			fIs.close();
 			fOs.close();
 		} catch (FileNotFoundException e) {
-			System.out.println(e.getMessage());
+			System.out.println("FileNotFound exception in PamSettingsManager: " + e.getMessage());
 			return false;
 		} catch (IOException e) {
-			System.out.println(e.getMessage());
+			System.out.println("IO exception in PamSettingsManager: " + e.getMessage());
 			return false;
 		}
 		return true;

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 = "2.02.07b";
+	static public final String version = "2.02.07f";
 	
 	/**
 	 * Release date
 	 */
-	static public final String date = "19 January 2023";
+	static public final String date = "4 April 2023";
 	
 //	/**
 //	 * Release type - Beta or Core

src/PamController/extern/ExternalCapture.java

@@ -46,7 +46,7 @@ public class ExternalCapture extends ExternalController {
 				}
 			}
 		} catch (IOException e) {
-			System.out.println(e.getMessage());
+			System.out.println("IOError in ExternalCapture.readInputStream: " + e.getMessage());
 		}
 	}
 

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

@@ -662,7 +662,7 @@ public class PamguardXMLWriter implements PamSettings {
 			}
 		}
 		catch (Exception e) {
-			System.out.println(e.getMessage());
+			System.out.println("Error in PamguardXMLWriter.writeArray: " + e.getMessage());
 		}
 		return null;
 	}
@@ -704,7 +704,7 @@ public class PamguardXMLWriter implements PamSettings {
 			return e;
 		}
 		catch (Exception e) {
-			System.out.println(e.getMessage());
+			System.out.println("Error in PamguardXMLWriter.writeObjectArray: " + e.getMessage());
 		}
 		return null;
 	}
@@ -729,7 +729,7 @@ public class PamguardXMLWriter implements PamSettings {
 			//			el.appendChild(e);
 		}
 		catch (Exception e) {
-			System.out.println(e.getMessage());
+			System.out.println("Error in PamguardXMLWriter.writePrimativeArray: " + e.getMessage());
 		}
 		return null;
 	}

src/PamUtils/FileFunctions.java

@@ -108,7 +108,7 @@ public class FileFunctions {
 		return attrib;
 		}
 		catch (Error e) {
-			System.out.println(e.getMessage());
+			System.out.println("Error in FileFunctions.getAttributes: " + e.getMessage());
 			return 0;
 		}
 	}

src/PamUtils/worker/filelist/FileListWorker.java

@@ -8,6 +8,7 @@ import PamUtils.PamFileFilter;
 import PamUtils.worker.PamWorkProgressMessage;
 import PamUtils.worker.PamWorkWrapper;
 import PamUtils.worker.PamWorker;
+import PamguardMVC.debug.Debug;
 
 /**
  * Class to list files in one or more directories. 
@@ -64,6 +65,9 @@ public abstract class FileListWorker<T extends File> implements PamWorkWrapper<F
 		this.fileList = rootList;
 		this.subFolders = subFolders;
 		this.useOldIfPossible = useOldIfPossible;
+		for (int i = 0; i < rootList.length; i++) {
+			Debug.out.println(">>>>>>>>Starting file search in " + rootList[i]);
+		}
 		if (noChange(rootList, subFolders, useOldIfPossible)) {
 			SwingUtilities.invokeLater(new Runnable() {
 				@Override
@@ -162,6 +166,7 @@ public abstract class FileListWorker<T extends File> implements PamWorkWrapper<F
 	private void addFiles(PamWorker<FileListData<T>> pamWorker, FileListData<T> newFileList, File folder) {
 		newFileList.addFolder();
 		pamWorker.update(new PamWorkProgressMessage(-1, "Searching folder " + folder.getAbsolutePath()));
+		Debug.out.println(">>>> Searching for files in abs path " + folder.getAbsolutePath());
 		//		System.out.println(folder.getAbsolutePath());
 		File[] moreFiles = folder.listFiles(fileFilter);
 		if (moreFiles == null) {

src/Resources/css/primer-dark.css

@@ -3699,7 +3699,7 @@ Text {
 
 
 #label-title1 {
-    -fx-font: bold 16pt  -fx-font-family;
+    -fx-font: bold 14pt  -fx-font-family;
 }
 
 #label-title2 {

src/alarm/AlarmProcess.java

@@ -225,6 +225,11 @@ public class AlarmProcess extends PamProcess {
 	}
 
 
+	@Override
+	public void updateData(PamObservable o, PamDataUnit arg) {
+		newData(o, arg);
+	}
+
 	public boolean setupAlarm() {
 		dataSource = PamController.getInstance().getDataBlock(PamDataUnit.class, alarmControl.alarmParameters.dataSourceName);
 		if (dataSource == null) {

src/alarm/actions/sound/PlaySound.java

@@ -94,7 +94,7 @@ public class PlaySound extends AlarmAction implements PamSettings {
 			double secs = fl/sr*1000;
 		}
 		catch (Exception e) {
-			System.out.println(e.getMessage());
+			System.out.println("Error in PlaySound.playSound:" + e.getMessage());
 			return false;
 		}
 		return true;
@@ -114,10 +114,10 @@ public class PlaySound extends AlarmAction implements PamSettings {
 			System.out.println(f.getMessage());
 			return currentClip = null;
 		} catch (IOException e) {
-			System.out.println(e.getMessage());
+			System.out.println("IOError in PlaySound.prepareClip: " + e.getMessage());
 			return currentClip = null;
 		} catch (LineUnavailableException e) {
-			System.out.println(e.getMessage());
+			System.out.println("LineUnavailableException in PlaySound.prepareClip: " + e.getMessage());
 			return currentClip = null;
 		}
 		currentFile = soundFile;		

src/backupmanager/stream/BackupStream.java

@@ -118,7 +118,7 @@ public abstract class BackupStream implements PamSettings, BackupFunction {
 				try {
 					ok = doAction(backupManager, action, item);
 				} catch (BackupException e) {
-					System.out.println(e.getMessage());
+					System.out.println("Error in BackupStream.runAction:" + e.getMessage());
 					backupManager.updateProgress(new BackupProgress(this, action, STATE.PROBLEM, toDoList.size(), 
 							iDone, "Error " + e.getMessage()));
 					ok = false; //otherwise, OK stays true! This will leave a true null entry in the database, so file will be selected next time around

src/binaryFileStorage/BinaryDataSource.java

@@ -41,6 +41,8 @@ public abstract class BinaryDataSource {
 	private boolean saveUpdates = false;
 	
 	private BackgroundBinaryWriter backgroundBinaryWriter;
+	
+	public static final Object packSynchObject = new Object();
 
 	/**
 	 * Create a binary data source. These are used both to store data in binary 
@@ -224,11 +226,13 @@ public abstract class BinaryDataSource {
 		 * Then pack the data
 		 */
 		BinaryObjectData data;
-		if (pamDataUnit instanceof BackgroundDataUnit) {
+		synchronized (packSynchObject) {
-			data = getBackgroundBinaryWriter().packBackgroundData((BackgroundDataUnit) pamDataUnit);
+			if (pamDataUnit instanceof BackgroundDataUnit) {
-		}
+				data = getBackgroundBinaryWriter().packBackgroundData((BackgroundDataUnit) pamDataUnit);
-		else {
+			}
-			data = getPackedData(pamDataUnit);
+			else {
+				data = getPackedData(pamDataUnit);
+			}
 		}
 		/*
 		 * Then put it back to how it was a moment ago.

src/clickDetector/ClickDetector.java

@@ -1809,7 +1809,7 @@ public class ClickDetector extends PamProcess {
 						newClick.setStartSample(newClick.getStartSample() - firstFilterDelay - secondFilterDelay);
 						waveDataError = false;
 					} catch (RawDataUnavailableException e) {
-						System.out.println("RawDataUnavailableException");
+						System.out.println(" Click Detector RawDataUnavailableException");
 						System.out.println(e.getMessage());
 					}
 					for (int k = 0; k < nChannels; k++) {

src/clickDetector/layoutFX/clickClassifiers/SweepClassifierSetPaneFX.java

@@ -51,11 +51,18 @@ import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JTextField;
 
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JPanel;
 import PamController.SettingsPane;
 import PamUtils.PamUtils;
 import PamView.PamSymbol;
 import PamView.dialog.PamGridBagContraints;
 import PamView.symbol.SymbolData;
+import clickDetector.ClickControl;
 import clickDetector.ClickClassifiers.basicSweep.CodeHost;
 import clickDetector.ClickClassifiers.basicSweep.SweepClassifier;
 import clickDetector.ClickClassifiers.basicSweep.SweepClassifierSet;
@@ -237,11 +244,10 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
 			//create holder pane
 			borderPane=new PamBorderPane();
 			this.setCenter(borderPane);
-
+			
 			PamHBox hBox = new PamHBox();
 			hBox.setSpacing(5);
 
-
 			if (borderTitle != null) {
 				label=new Label(borderTitle); 
 
@@ -764,6 +770,8 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
 		 */
 		PamSpinner<Double> threshold;
 
+		private PamVBox vboxholder;
+
 
 		ClickLengthBox() {
 			super("Click Length", true);
@@ -882,10 +890,11 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
 
 		@Override
 		protected void disbleControls(boolean disable) {
-			smoothing.setDisable(disable);
+			vboxholder.setDisable(disable);
-			minLengthms.setDisable(disable);
+//			smoothing.setDisable(disable);
-			maxLengthms.setDisable(disable);
+//			minLengthms.setDisable(disable);
-			threshold.setDisable(disable);
+//			maxLengthms.setDisable(disable);
+//			threshold.setDisable(disable);
 		}
 
 	}
@@ -929,13 +938,13 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
 			pamGridPane.setVgap(5);
 
 			Label freqLabel=new Label("Frequency (Hz)");
-			pamGridPane.add(freqLabel, 0, 0);
+////			gridPaneHolder.add(freqLabel, 0, 0);
-			pamGridPane.add(new Label("Threshold (dB)"), 2, 0);
+////			gridPaneHolder.add(new Label("Threshold (dB)"), 2, 0);
-			PamGridPane.setHalignment(freqLabel, HPos.CENTER);
+//			PamGridPane.setHalignment(freqLabel, HPos.CENTER);
-			PamGridPane.setColumnSpan(pamGridPane, 2);
+//			PamGridPane.setColumnSpan(gridPaneHolder, 2);
-
+//
-			//test band
+//			//test band
-			pamGridPane.add(new Label("Test Band"), 0, 1);
+//			gridPaneHolder.add(new Label("Test Band"), 0, 1);
 
 			testBandFreqPane=new FreqBandPane(Orientation.HORIZONTAL);
 			testBandFreqPane.setBandText("");
@@ -1094,6 +1103,9 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
 		private PamSpinner<Double> threshold;
 		private FreqBandPane searchRange;
 		private FreqBandPane meanFreq;
+		
+		//the main holder pane. 
+		private PamGridPane gridPaneHolder;
 
 		FrequencySearchBlock() {
 			super("Peak and Mean Frequency", true);
@@ -1176,14 +1188,12 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
 			addValidatorFreqCheck(getValidator(), peakWidthPane, "peak width ",  "peak_width");
 
 			gridy++;
-
 			pamGridPane.add(new Label(""), 1,gridy);
 
 			threshold=new PamSpinner<Double>(1., 300., 6.,1.);
 			threshold.getStyleClass().add(Spinner.STYLE_CLASS_SPLIT_ARROWS_HORIZONTAL);
 			threshold.setPrefWidth(100);
 			GridPane.setMargin(threshold, new Insets(0,0,0,5)); //bit of a hack to make sure everything lines up nicely with the frequency pane. 
-
 			pamGridPane.add(threshold,2,gridy); 
 
 			pamGridPane.add(new Label("dB"), 3,gridy);
@@ -1216,8 +1226,6 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
 		@Override
 		protected void setParams() {
 			setEnableBox(sweepClassifierSet.enableEnergyBands);
-
-
 		}
 
 		@Override
@@ -1227,6 +1235,22 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
 		}
 
 		@Override
+//		protected void disbleControls(boolean disable) {
+//			this.gridPaneHolder.setDisable(disable);
+			
+//			peakFreqCheckBox.setDisable(enable);
+//			peakWidthCheckBox.setDisable(enable);
+//			meanFreqCheckBox.setDisable(enable);
+//
+//
+//			/**
+//			 * Pane to set frequency band range		 */
+//			peakFreqPane.setDisable(enable);
+//			smoothing.setDisable(enable);
+//			peakWidthPane.setDisable(enable);
+//			threshold.setDisable(enable);
+//			searchRange.setDisable(enable);
+//			meanFreq.setDisable(enable);
 		protected void disbleControls(boolean enable) {
 			peakFreqCheckBox.setDisable(enable);
 			peakWidthCheckBox.setDisable(enable);
@@ -1274,6 +1298,11 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
 		 */
 		private PamSpinner<Double> freqZeroMax;
 
+		/**
+		 * The main holder
+		 */
+		private PamGridPane gridPaneHolder;
+
 		ZeroCrossingsBox() {
 			super("Zero Crossings", true);
 			this.getHolderPane().setCenter(createZeroCrossPane());
@@ -1600,6 +1629,7 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
 			p.setLayout(new GridBagLayout());
 			GridBagConstraints c = new PamGridBagContraints();
 			
+
 //			c.gridx = 0;
 //			addComponent(p, enableBearings, c);
 //			c.gridx += c.gridwidth;
@@ -1832,12 +1862,19 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
 	}
 
 
-
 	private boolean showWarning(String string, String string2) {
 		//PamController.getInstance();
 		PamDialogFX.showWarning(null, string, string2);
 		return false;
 	}
+	
+	/**
+	 * Get the click control associated with the classifier. 
+	 * @return the click control. 
+	 */
+	public ClickControl getClickControl() {
+		return this.sweepClassifier.getClickDetector().getClickControl();
+	}
 
 
 	/**
@@ -1862,4 +1899,4 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
 	private boolean isPaneShowing() {
 		return sweepClassifier.getClassifierPane().getFlipPane().isBackVisible();
 	}
-}
+}

src/clipgenerator/ClipProcess.java

@@ -291,7 +291,7 @@ public class ClipProcess extends SpectrogramMarkProcess {
 		try {
 			rawData = rawDataBlock.getSamples(startSample, numSamples, channelMap);
 		} catch (RawDataUnavailableException e) {
-			System.out.println(e.getMessage());
+			System.out.println("RawDataUnavailableException in ClipProcess.spectrogramNotification  :" + e.getMessage());
 			return false;
 		}
 		if (rawData == null) {

src/dbht/DbHtDialog.java

@@ -199,7 +199,7 @@ public class DbHtDialog extends PamDialog {
 			params.calculateFilterThings(currentSampleRate);
 		}
 		catch (DbHtException e) {
-			System.out.println(e.getMessage());
+			System.out.println("Error in DbHtDialog.updateEverything: " + e.getMessage());
 			return;
 		}
 		double[] f = params.getFilterFrequencies(currentSampleRate);

src/difar/DifarProcess.java

@@ -1110,7 +1110,7 @@ public class DifarProcess extends PamProcess {
 				rawData[0] = rawDataAll[0]; // is fine since getSamples was fed a channel map. 
 			}
 		} catch (RawDataUnavailableException e) {
-			System.out.println(e.getMessage());
+			System.out.println("Error in DifarProcess.difarTrigger" + e.getMessage());
 			return;
 		}
 		if (rawData[0] == null) {

src/difar/demux/NativeDemux.java

@@ -98,7 +98,7 @@ public class NativeDemux extends GreenridgeDemux {
 			return true;
 		}
 		catch (UnsatisfiedLinkError e) {
-			System.out.println(e.getMessage());
+			System.out.println("Error in NativeDemux.loadLibrary" + e.getMessage());
 			return false; 
 		}
 	}

src/generalDatabase/DBSpeedTest.java

@@ -190,7 +190,7 @@ public class DBSpeedTest {
 				dropStmt.execute();
 			} catch (SQLException e) {
 				//			e.printStackTrace();
-				System.out.println(e.getMessage());
+				System.out.println("Error in DBSpeedTest testSpeed2:" + e.getMessage());
 			}
 		}
 		try {

src/gpl/contour/ContourFinder.java

@@ -261,7 +261,13 @@ public class ContourFinder {
 		 * Note that binData is padded, whiteData isn't. 
 		 */
 		GPLContour newContour = new GPLContour(iT-1, iF-1+gplProcess.binLo, whiteData[iT-1][iF-1], energyData[iT-1][iF-1]);
-		findAdjacentPoints(newContour, iT, iF, binData, whiteData, energyData, con);
+		try {
+			findAdjacentPoints(newContour, iT, iF, binData, whiteData, energyData, con);
+		}
+		catch (StackOverflowError e) {
+			System.out.println("Stack overflow in GPLContour.findRegion for bloated contour size " + newContour.getArea());
+			System.out.println("The contour is incomplete, but has not been discarded");
+		}
 		return newContour;
 	}
 
@@ -282,6 +288,10 @@ public class ContourFinder {
 		 * Separate loops to get above and to sides, NOT diagonal matches. 
 		 * could also easily change to connect 8 instead of connect 4. 
 		 */
+		if (newContour.getArea() >= 500) {
+			System.out.println("GPL Contour size exceeds maximum value of 500 points so ceasing to grow it");
+			return;
+		}
 		binData[currT][currF] = 0; // set current point to 0 so it doesn't get found again
 		int nX = binData.length-1;
 		int nY = binData[0].length-1;

src/group3dlocaliser/algorithm/hyperbolic/HyperbolicLocaliser.java

@@ -217,7 +217,7 @@ public class HyperbolicLocaliser extends TOADBaseAlgorithm {
 //			answer2 = rightMatrix.times(leftInverse.transpose());
 		}
 		catch (Exception e) {
-			System.out.println(e.getMessage());
+			System.out.println("Error in HyperbolicLocaliser.processTOADsPlane: " + e.getMessage());
 //			Matrix m = leftMatrix.transpose();
 //			m = m.inverse();
 			return null;
@@ -254,7 +254,7 @@ public class HyperbolicLocaliser extends TOADBaseAlgorithm {
 			
 		}
 		catch (Exception e) {
-			System.out.println(e.getMessage());
+			System.out.println("Error2 in HyperbolicLocaliser.processTOADsPlane: " + e.getMessage());
 		}
 		
 		// now need to rotate back from the plane that we're in to get back to the original position. 
@@ -736,7 +736,7 @@ public class HyperbolicLocaliser extends TOADBaseAlgorithm {
 			
 		}
 		catch (Exception e) {
-			System.out.println(e.getMessage());
+			System.out.println("Error in HyperbolicLocaliser.processTOADs3D: " + e.getMessage());
 		}
 		
 		LatLong pos = geometry.getReferenceGPS().addDistanceMeters(centre.getCoordinate(0)+answer.get(0,0), 

src/group3dlocaliser/algorithm/toadsimplex/ToadSimplexLocaliser.java

@@ -146,7 +146,7 @@ public class ToadSimplexLocaliser extends TOADBaseAlgorithm {
 			try {
 				result = optimiser.optimize(chiFunc, goal, start);
 			} catch (OptimizationException | FunctionEvaluationException | IllegalArgumentException e) {
-				System.out.println(e.getMessage());
+				System.out.println("Error in TOADSimplexLocaliser.processTOADs: " + e.getMessage());
 				nFails++;
 				System.out.printf("%d  fails out of %d = %3.2f%%\n", nFails, nCalls, (double) nFails * 100. / nCalls);
 				resultChiData[iStart] = null;

src/networkTransfer/emulator/EmulatorStream.java

@@ -129,7 +129,7 @@ public class EmulatorStream {
 		try {
 			emSocket.getOutputStream().write(data);
 		} catch (IOException e) {
-			System.out.println(e.getMessage());
+			System.out.println("Error in EmulatorStream.sendPamCommand: " + e.getMessage());
 		}
 	}
 	private boolean openSocket() {
@@ -137,9 +137,9 @@ public class EmulatorStream {
 		try {
 			emSocket = new Socket(sktParams.ipAddress, sktParams.portNumber);
 		} catch (UnknownHostException e) {
-			System.out.println(e.getMessage());
+			System.out.println("UnknownHostException in EmulatorStream.sendPamCommand: " + e.getMessage());
 		} catch (IOException e) {
-			System.out.println(e.getMessage());
+			System.out.println("IOException in EmulatorStream.sendPamCommand: " + e.getMessage());
 		}
 		if (emSocket != null) {
 			status.socketStatus = emSocket.isConnected();

src/networkTransfer/receive/NetworkReceiver.java

@@ -458,7 +458,7 @@ public class NetworkReceiver extends PamControlledUnit implements PamSettings, N
 //					checkExistingThreads(clientSocket, rxThread);
 				}
 			} catch (IOException e) {
-				System.out.println(e.getMessage());
+				System.out.println("IOException in NeetworkReceiver" + e.getMessage());
 			}
 
 		}

src/networkTransfer/send/NetworkObjectPacker.java

@@ -75,7 +75,10 @@ public class NetworkObjectPacker {
 		BinaryDataSource binarySource = dataBlock.getBinaryDataSource();
 		int dataType2 = dataBlock.getQuickId();
 		
-		BinaryObjectData packedObject = binarySource.getPackedData(dataUnit);
+		BinaryObjectData packedObject = null;
+		synchronized (BinaryDataSource.packSynchObject) {
+			packedObject = binarySource.getPackedData(dataUnit);
+		}
 		byte[] data = packedObject.getData();
 		int duDataLength = data.length + 12;
 		DataUnitBaseData baseData = dataUnit.getBasicData();

src/networkTransfer/send/NetworkSender.java

@@ -23,10 +23,12 @@ import javax.swing.SwingWorker;
 
 import networkTransfer.emulator.NetworkEmulator;
 import networkTransfer.receive.NetworkReceiver;
+import pamguard.GlobalArguments;
 
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 
+import Acquisition.FolderInputSystem;
 import PamController.PamControlledUnit;
 import PamController.PamControlledUnitSettings;
 import PamController.PamController;
@@ -44,6 +46,11 @@ import PamguardMVC.PamDataBlock;
  *
  */
 public class NetworkSender extends PamControlledUnit implements PamSettings {
+	
+	public static final String ADDRESS = "-netSend.address";
+	public static final String PORT = "-netSend.port";
+	public static final String ID1 = "-netSend.id1";
+	public static final String ID2 = "-netSend.id2";
 
 	protected NetworkSendParams networkSendParams = new NetworkSendParams();
 	private NetworkEmulator networkEmulator;
@@ -169,6 +176,28 @@ public class NetworkSender extends PamControlledUnit implements PamSettings {
 	public boolean restoreSettings(
 			PamControlledUnitSettings pamControlledUnitSettings) {
 		networkSendParams = ((NetworkSendParams) pamControlledUnitSettings.getSettings()).clone();
+		
+		String address = GlobalArguments.getParam(ADDRESS);
+		String portString = GlobalArguments.getParam(PORT);
+		String id1String = GlobalArguments.getParam(ID1);
+		String id2String = GlobalArguments.getParam(ID2);
+	
+		if (address != null) {
+			networkSendParams.ipAddress = address; // remember it. 
+		}
+		
+		if(portString != null) {
+			networkSendParams.portNumber = Integer.valueOf(portString);
+		}
+		
+		if(id1String!=null) {
+			networkSendParams.stationId1 = Integer.valueOf(id1String);
+		}
+		
+		if(id2String!=null) {
+			networkSendParams.stationId1 = Integer.valueOf(id2String);
+		}
+		
 		return (networkSendParams != null);
 	}
 
@@ -452,7 +481,7 @@ public class NetworkSender extends PamControlledUnit implements PamSettings {
 			return true;
 		} catch (IOException e) {
 //			e.printStackTrace();
-			System.out.println(e.getMessage());
+			System.out.println("IOException in NeetworkSender.writeByteData: " + e.getMessage());
 			currStatus = "Socket Closed";
 			return false;
 		}
@@ -465,7 +494,7 @@ public class NetworkSender extends PamControlledUnit implements PamSettings {
 			return true;
 		} catch (IOException e) {
 //			e.printStackTrace();
-			System.out.println(e.getMessage());
+			System.out.println("IOException in NeetworkSender.writeStringData" + e.getMessage());
 			currStatus = "Socket Closed";
 			return false;
 		}
@@ -513,7 +542,7 @@ public class NetworkSender extends PamControlledUnit implements PamSettings {
 			tcpWriter.close();
 		} catch (IOException e) {
 //			e.printStackTrace();
-			System.out.println(e.getMessage());
+			System.out.println("IOException in NeetworkSender.closeconnection" + e.getMessage());
 		}
 		tcpSocket = null;
 		tcpWriter = null;

src/nmeaEmulator/SerialOutput.java

@@ -68,7 +68,7 @@ public class SerialOutput {
 					SerialPort.NO_PARITY,
 					SerialPort.FLOW_CONTROL_DISABLED); // disable flow control, since this is the RXTX default and it's not specified above
 		} catch (PJSerialException e) {
-			System.out.println(e.getMessage());
+			System.out.println("PJSerialException in SerialOutput: " + e.getMessage());
 			e.printStackTrace();
 			return false;
 		}

src/offlineProcessing/DataCopyTask.java

@@ -21,8 +21,6 @@ import dataMap.OfflineDataMapPoint;
  * @param <T>
  */
 public class DataCopyTask<T extends PamDataUnit> extends OfflineTask<T> {
-
-	private PamDataBlock<T> pamDataBlock;
 	
 	private SQLLogging sqlLogging;
 	
@@ -40,7 +38,6 @@ public class DataCopyTask<T extends PamDataUnit> extends OfflineTask<T> {
 	 */
 	public DataCopyTask(PamDataBlock<T> pamDataBlock) {
 		super(pamDataBlock);
-		this.pamDataBlock = pamDataBlock;
 		this.sqlLogging = pamDataBlock.getLogging();
 		this.binaryDataSource = pamDataBlock.getBinaryDataSource();
 		setParentDataBlock(pamDataBlock);
@@ -77,7 +74,7 @@ public class DataCopyTask<T extends PamDataUnit> extends OfflineTask<T> {
 
 	@Override
 	public String getName() {
-		return "Copy " + pamDataBlock.getDataName() + " To database";
+		return "Copy " + getDataBlock().getDataName() + " To database";
 	}
 
 	@Override

src/offlineProcessing/OfflineTask.java

@@ -458,5 +458,4 @@ public abstract class OfflineTask<T extends PamDataUnit> {
 	}
 
 
-
 }

src/pamViewFX/fxNodes/pamAxis/PamAxisPane2.java

@@ -250,7 +250,7 @@ public class PamAxisPane2 extends StackPane {
 //				}
 			}
 			catch (Exception e) {
-				System.out.println(e.getMessage());
+				System.out.println("Exception in PamAxisPanel2.ScaledNumberFormatter: " + e.getMessage());
 				e.printStackTrace();
 				return "Err";
 			}

src/pamViewFX/fxNodes/utilityPanes/GroupedSourcePaneFX.java

@@ -109,7 +109,7 @@ public class GroupedSourcePaneFX extends SourcePaneFX {
 		channelPanel.setSpacing(5);
 		
 		Label channelLabel = new Label("Channels");
-//		channelLabel.setFont(PamGuiManagerFXAWT.titleFontSize2);
+		PamGuiManagerFX.titleFont2style(channelLabel);
 		sourcePane.add(channelLabel,0,2);
 		
 		//create radio buttons to allow user to quickly select type of grouping. 

src/pamViewFX/fxNodes/utilityPanes/SimpleFilterPaneFX.java

@@ -238,11 +238,13 @@ public class SimpleFilterPaneFX extends DynamicSettingsPane<FFTFilterParams>{
 	 * @param disable - true to disable the pane
 	 */
 	public void setDisableFilterPane(boolean disable){
-		highPass.setDisable(disable);
+		mainPane.setDisable(disable);
-		lowPass.setDisable(disable);
+		
-		bandPass.setDisable(disable);
+//		highPass.setDisable(disable);
-		bandStop.setDisable(disable);
+//		lowPass.setDisable(disable);
-		freqPane.setDisableFreqPane(disable);
+//		bandPass.setDisable(disable);
+//		bandStop.setDisable(disable);
+//		freqPane.setDisableFreqPane(disable);
 	}
 	
 	public double getSampleRate() {

src/pamguard/Pamguard.java

@@ -43,6 +43,7 @@ import PamguardMVC.debug.Debug;
 import binaryFileStorage.BinaryStore;
 import dataPlotsFX.JamieDev;
 import generalDatabase.DBControl;
+import networkTransfer.send.NetworkSender;
 import rocca.RoccaDev;
 
 import java.io.BufferedReader;
@@ -122,6 +123,7 @@ public class Pamguard {
 
 		int runMode = PamController.RUN_NORMAL;
 		String InputPsf = "NULL";
+		
 
 
 		// set up the system to output to both a log file and the console window.  Also
@@ -137,6 +139,14 @@ public class Pamguard {
 //		TimeZone.setDefault(PamCalendar.defaultTimeZone);
 
 		System.out.println("**********************************************************");
+		// print out the entire command line
+		if (args != null && args.length > 0) {
+			System.out.printf("Command line options: ");
+			for (int i = 0; i < args.length; i++) {
+				System.out.printf("\"%s\" ", args[i]);
+			}
+			System.out.printf("\n");
+		}
 		try {
 			// get the java runnable file name. 
 			//	    	http://stackoverflow.com/questions/4294522/jar-file-name-form-java-code
@@ -210,6 +220,7 @@ public class Pamguard {
 				}
 				else if (anArg.equalsIgnoreCase("-nogui")) {
 					PamGUIManager.setType(PamGUIManager.NOGUI);
+					System.out.println("no gui operation.");
 				}
 				///////////////
 				else if (anArg.equalsIgnoreCase("-psf")) {
@@ -219,13 +230,16 @@ public class Pamguard {
 				}
 				else if (anArg.equalsIgnoreCase("-port")) {
 					// port id to open a udp port to receive commands
-					pamBuoyGlobals.setNetworkControlPort(Integer.parseInt(args[iArg++]));
+					String port = args[iArg++];
+					pamBuoyGlobals.setNetworkControlPort(Integer.parseInt(port));
+					System.out.println("Setting UDP control port " + port);
 				}
 				else if (anArg.equalsIgnoreCase("-mport")) {
 					// multicast control (for multiple PAMGuards) 
 					String mAddr = args[iArg++];
 					int mPort = Integer.parseInt(args[iArg++]);
 					pamBuoyGlobals.setMultiportConfig(mAddr, mPort);
+					System.out.printf("Setting multiport control addr %s port %d\n", mAddr, mPort);
 				}
 				else if (anArg.equalsIgnoreCase("-nolog")) {
 					System.out.println("Disabling log file from command line switch...");
@@ -233,23 +247,47 @@ public class Pamguard {
 				}
 				else if (anArg.equalsIgnoreCase(BinaryStore.GlobalFolderArg)) {
 					// output folder for binary files. 
-					GlobalArguments.setParam(BinaryStore.GlobalFolderArg, args[iArg++]);
+					String binFolder = args[iArg++];
+					GlobalArguments.setParam(BinaryStore.GlobalFolderArg, binFolder);
+					System.out.println("Setting output folder for binary files to " + binFolder);
 				}
 				else if (anArg.equalsIgnoreCase(DBControl.GlobalDatabaseNameArg)) {
 					// database file name
-					GlobalArguments.setParam(DBControl.GlobalDatabaseNameArg, args[iArg++]);
+					String dbName = args[iArg++];
+					GlobalArguments.setParam(DBControl.GlobalDatabaseNameArg, dbName);
+					System.out.println("Setting output database file to " + dbName);
 				}
 				else if (anArg.equalsIgnoreCase(FolderInputSystem.GlobalWavFolderArg)) {
 					// source folder for wav files (or other supported sound files)
-					GlobalArguments.setParam(FolderInputSystem.GlobalWavFolderArg, args[iArg++]);
+					String wavFolder = args[iArg++];
+					GlobalArguments.setParam(FolderInputSystem.GlobalWavFolderArg, wavFolder);
+					System.out.println("Setting input wav file folder to " + wavFolder);
 				}
 				else if (anArg.equalsIgnoreCase(PamController.AUTOSTART)) {
 					// auto start processing. 
 					GlobalArguments.setParam(PamController.AUTOSTART, PamController.AUTOSTART);
+					System.out.println("Setting autostart ON");
 				}
 				else if (anArg.equalsIgnoreCase(PamController.AUTOEXIT)) {
 					// auto exit at end of processing. 
 					GlobalArguments.setParam(PamController.AUTOEXIT, PamController.AUTOEXIT);
+					System.out.println("Setting autoexit ON");
+				}
+				else if (anArg.equalsIgnoreCase(NetworkSender.ADDRESS)) {
+					// auto exit at end of processing. 
+					GlobalArguments.setParam(NetworkSender.ADDRESS, args[iArg++]);
+				}
+				else if (anArg.equalsIgnoreCase(NetworkSender.ID1)) {
+					// auto exit at end of processing. 
+					GlobalArguments.setParam(NetworkSender.ID1, args[iArg++]);
+				}
+				else if (anArg.equalsIgnoreCase(NetworkSender.ID2)) {
+					// auto exit at end of processing. 
+					GlobalArguments.setParam(NetworkSender.ID2, args[iArg++]);
+				}
+				else if (anArg.equalsIgnoreCase(NetworkSender.PORT)) {
+					// auto exit at end of processing. 
+					GlobalArguments.setParam(NetworkSender.PORT, args[iArg++]);
 				}
 				else if (anArg.equalsIgnoreCase(ReprocessStoreChoice.paramName)) {
 					String arg = args[iArg++];

src/rawDeepLearningClassifier/dataPlotFX/DLPredictionPlotInfoFX.java

@@ -317,10 +317,12 @@ public class DLPredictionPlotInfoFX extends GenericLinePlotInfo {
 
 	@Override
 	public double[][] getDetData(PamDataUnit pamDataUnit) {
-		double[] data = PamArrayUtils.float2Double(((DLDataUnit) pamDataUnit).getPredicitionResult().getPrediction());
 		
+		double[] data = PamArrayUtils.float2Double(((DLDataUnit) pamDataUnit).getPredicitionResult().getPrediction());
+
 		double[][] dataD = new double[data.length][]; 
 		for (int i=0; i<data.length; i++) {
+
 			dataD[i] = new double[] {data[i]};
 		}
 		

src/rawDeepLearningClassifier/dlClassification/DLClassifyProcess.java

@@ -375,7 +375,7 @@ public class DLClassifyProcess extends PamInstantProcess {
 					//Need to go by the parent data unit for merging data not the segments. Note that we may still add multiple
 					//predicitions to a single data unit depending on how many segments it contains. 
 
-				    System.out.println("New model data " + pamRawData.getParentDataUnit().getUID() + " " + groupDataBuffer[i].size() + " " + modelResultDataBuffer[i].size()); 
+				    //System.out.println("New model data " + pamRawData.getParentDataUnit().getUID() + " " + groupDataBuffer[i].size() + " " + modelResultDataBuffer[i].size()); 
 
 					if (pamRawData.getParentDataUnit()!=lastParentDataUnit[i]) {
 						//save any data

src/rawDeepLearningClassifier/layoutFX/dlTransfroms/DLImageTransformPane.java

@@ -75,79 +75,81 @@ public class DLImageTransformPane  extends PamBorderPane {
 		if (getDLTransforms()==null) return;
 
 		//System.out.println("Set transforms: " + sampleRate);
+		
+		/****This was way too much hassle in bugs than it was worth****/
 
 		//OK so when we change samplerates massively e.g. from bat to right whale we could technically use the 
 		//same transforms but this can cause weird issues - for example upsampling a 2s right whale call to 256000 Hz is 
 		//not pretty. So just be nice to the user and set a few default 
 
-		ArrayList<DLTransform> transforms =  getDLTransforms(); 
+//		ArrayList<DLTransform> transforms =  getDLTransforms(); 
-		WaveTransform waveTransForm ;
+//		WaveTransform waveTransForm ;
-		FreqTransform freqTranform ;
+//		FreqTransform freqTranform ;
 
-		//extra things that may need changed...
+//		//extra things that may need changed...
-		for (DLTransform dlTransfrom:  transforms) {
+//		for (DLTransform dlTransfrom:  transforms) {
-			switch (dlTransfrom.getDLTransformType()) {
+//			switch (dlTransfrom.getDLTransformType()) {
-			case DECIMATE:
+//			case DECIMATE:
-				waveTransForm = ((WaveTransform)  dlTransfrom);
+//				waveTransForm = ((WaveTransform)  dlTransfrom);
-				
+//				
-				//change if the example sample rate is higher to if there is a large differenc in sample rates and decimation. 
+//				//change if the example sample rate is higher to if there is a large differenc in sample rates and decimation. 
-				if (exampleSound.getSampleRate()<waveTransForm.getParams()[0].floatValue() 
+//				if (exampleSound.getSampleRate()<waveTransForm.getParams()[0].floatValue() 
-						|| exampleSound.getSampleRate()/waveTransForm.getParams()[0].floatValue()>4) {
+//						|| exampleSound.getSampleRate()/waveTransForm.getParams()[0].floatValue()>4) {
-					waveTransForm.setParams(new Number[] {exampleSound.getSampleRate()}); //set the correct samplerate
+//					waveTransForm.setParams(new Number[] {exampleSound.getSampleRate()}); //set the correct samplerate
-					dlTransformPane.getDLTransformPanes().get(transforms.indexOf(dlTransfrom)).setParams(waveTransForm);
+//					dlTransformPane.getDLTransformPanes().get(transforms.indexOf(dlTransfrom)).setParams(waveTransForm);
-				}
+//				}
-				break;
+//				break;
-			case PREEMPHSIS:
+//			case PREEMPHSIS:
-				waveTransForm = ((WaveTransform)  dlTransfrom);
+//				waveTransForm = ((WaveTransform)  dlTransfrom);
-				if (exampleSound.getSampleRate()<10000 && waveTransForm.getParams()[0].doubleValue()>0.1) {
+//				if (exampleSound.getSampleRate()<10000 && waveTransForm.getParams()[0].doubleValue()>0.1) {
-					waveTransForm.setParams(new Number[] {0.1}); //set the correct samplerate
+//					waveTransForm.setParams(new Number[] {0.1}); //set the correct samplerate
-					dlTransformPane.getDLTransformPanes().get(transforms.indexOf(dlTransfrom)).setParams(waveTransForm);
+//					dlTransformPane.getDLTransformPanes().get(transforms.indexOf(dlTransfrom)).setParams(waveTransForm);
-				}
+//				}
-				break;
+//				break;
-			case SPEC2DB:
+//			case SPEC2DB:
-				break;
+//				break;
-			case SPECCLAMP:
+//			case SPECCLAMP:
-				break;
+//				break;
-			case SPECCROPINTERP:
+//			case SPECCROPINTERP:
-
+//
-				freqTranform = ((FreqTransform)  dlTransfrom);
+//				freqTranform = ((FreqTransform)  dlTransfrom);
-				Number[] params = freqTranform.getParams();
+//				Number[] params = freqTranform.getParams();
-				
+//				
-				double highestFreq = exampleSound.getSampleRate()/2; //nyquist
+//				double highestFreq = exampleSound.getSampleRate()/2; //nyquist
-
+//
-				if (params[0].doubleValue()>=highestFreq) params[0]=0.0;
+//				if (params[0].doubleValue()>=highestFreq) params[0]=0.0;
-
+//
-				//this will break stuff if interp frequency is greater than nyquist
+//				//this will break stuff if interp frequency is greater than nyquist
-				if (params[1].doubleValue()>highestFreq) {
+//				if (params[1].doubleValue()>highestFreq) {
-//					System.out.println("----HERE 1----");
+////					System.out.println("----HERE 1----");
-					params[1]=highestFreq; //nyquist
-				}
-				//if we switch to a high frequency want to the interp not to just select the lowest band
-				
-//				else if (params[1].doubleValue()<highestFreq/10) {
-////					System.out.println("----HERE 2----" + exampleSound.getSampleRate()/10.0 + "  " + params[1].doubleValue());
 //					params[1]=highestFreq; //nyquist
 //				}
-
+//				//if we switch to a high frequency want to the interp not to just select the lowest band
-				//System.out.println("Interp params: " + params[0] + "  " + params[1] + "  " + params[2]); 
+//				
-				freqTranform.setParams(params);
+////				else if (params[1].doubleValue()<highestFreq/10) {
-
+//////					System.out.println("----HERE 2----" + exampleSound.getSampleRate()/10.0 + "  " + params[1].doubleValue());
-				dlTransformPane.getDLTransformPanes().get(transforms.indexOf(dlTransfrom)).setParams(freqTranform);
+////					params[1]=highestFreq; //nyquist
-
+////				}
-				break;
+//
-			case SPECNORMALISE:
+//				//System.out.println("Interp params: " + params[0] + "  " + params[1] + "  " + params[2]); 
-				break;
+//				freqTranform.setParams(params);
-			case SPECNORMALISEROWSUM:
+//
-				break;
+//				dlTransformPane.getDLTransformPanes().get(transforms.indexOf(dlTransfrom)).setParams(freqTranform);
-			case SPECTROGRAM:
+//
-				break;
+//				break;
-			case TRIM:
+//			case SPECNORMALISE:
-				break;
+//				break;
-			default:
+//			case SPECNORMALISEROWSUM:
-				break;
+//				break;
-
+//			case SPECTROGRAM:
-			}
+//				break;
-		}
+//			case TRIM:
+//				break;
+//			default:
+//				break;
+//
+//			}
+//		}
 	}
 
 

src/rocca/RoccaContour.java

@@ -192,7 +192,7 @@ public class RoccaContour {
             	(currentStartSample, fftLength, channelMap );
             }
             catch (RawDataUnavailableException e) {
-            	System.out.println(e.getMessage());	
+            	System.out.println("RawDataUnavailableException in ROCCAContour.generateContour: " + e.getMessage());	
             	currentRawData = null;
             }
             /* every now and then the FFTDataUnit start sample doesn't match up
@@ -237,7 +237,7 @@ public class RoccaContour {
                 	nextRawData = rawDataBlockIn.getSamples(nextStartSample, fftLength, channelMap );
                 }
                 catch (RawDataUnavailableException e) {
-                	System.out.println(e.getMessage());
+                	System.out.println("RawDataUnavailableException (2) in ROCCAContour.generateContour: " + e.getMessage());
                 	nextRawData = null;
                 }
                 nextFFT = nextFFTDataUnit.getFftData();

src/rocca/RoccaSpecPopUp.java

@@ -2333,7 +2333,7 @@ public class RoccaSpecPopUp extends javax.swing.JPanel {
         	}
         }
         catch (RawDataUnavailableException e) {
-        	System.out.println(e.getMessage());	
+        	System.out.println("RawDataUnavailableException in ROCCASpecPopUp: " + e.getMessage());	
         }
 
         if (rawDataValues==null) {

src/rocca/RoccaWhistleSelect.java

@@ -205,9 +205,12 @@ public class RoccaWhistleSelect extends PamProcess implements SpectrogramMarkObs
              * DG June '22.
              * I hope IT's K to set these back here. It's possible it's also 
              * done elsewhere.  
+             * 
+             * MO Jan '23
+             * These are set to 0 in the RoccaSpecPopUp class, before the user closes the window.  If set here, the objects are cleared before the user can trace the whistle and throws an exception
              */
-            selectedWhistle.setNaturalLifetimeMillis(0);
+//            selectedWhistle.setNaturalLifetimeMillis(0);
-            selectedWhistleRaw.setNaturalLifetimeMillis(0);
+//            selectedWhistleRaw.setNaturalLifetimeMillis(0);
         }
 	}
 

src/rockBlock/RockBlockProcess2.java

@@ -280,7 +280,7 @@ public class RockBlockProcess2 extends PamProcess implements ModuleStatusManager
 					timeDelays[0] = rockBlockControl.getParams().getCommTiming();
 					initializeRockBlock();
 				} catch (Exception e) {
-					System.out.println(e.getMessage());
+					System.out.println("Exception in rockBlockProcess: " + e.getMessage());
 					rbStatus.setPortError(e.getMessage());
 					rbStatus.setCommReady(false);
 					commReady = false;

src/soundtrap/DWVConverter.java

@@ -219,7 +219,7 @@ public class DWVConverter {
 					}
 				}
 				catch (Exception e) {
-					System.out.println(e.getMessage());
+					System.out.println("Exception 1 in DWVConverter.effortLine: " + e.getMessage());
 				}
 				binaryStream.openOutputFiles(bclLine.getMilliseconds());
 				binaryStream.writeHeader(bclLine.getMilliseconds(), System.currentTimeMillis());
@@ -234,7 +234,7 @@ public class DWVConverter {
 							PamCalendar.formatDBDateTime(wavFileStop), PamCalendar.formatDBDateTime(bclLine.getMilliseconds()));
 				}
 				catch (Exception e) {
-					System.out.println(e.getMessage());
+					System.out.println("Exception 2 in DWVConverter.effortLine: " + e.getMessage());
 				}
 				binaryStream.writeModuleFooter();
 				binaryStream.writeFooter(bclLine.getMilliseconds(), System.currentTimeMillis(), BinaryFooter.END_UNKNOWN);