Merge branch 'main' of https://github.com/douggillespie/PAMGuard.git into main

.classpath

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

.gitignore

@@ -39,3 +39,4 @@ settings.xml
 .classpath
 .classpath
 .classpath
+.classpath

src/PamguardMVC/PamObservable.java

@@ -400,7 +400,7 @@ public class PamObservable {//extends PanelOverlayDraw {
 		}
 	}
 
-	private Timer t = new Timer(1000, new ActionListener() {
+	private Timer t = new Timer(4321, new ActionListener() {
 		public void actionPerformed(ActionEvent evt) {
 			long now = System.currentTimeMillis();
 			if (cpuUsage == null) return;
@@ -413,6 +413,16 @@ public class PamObservable {//extends PanelOverlayDraw {
 		}
 	});
 	
+	
+	/**
+	 * Had some issues with the Timer holding a reference to the underlying PamDataBlock 
+	 * (RoccaContourDataBlock, in this case) and not releasing it for garbage collection.
+	 * Added in this method to force the timer to stop and release it's hold.
+	 */
+	public void stopTimer() {
+		t.stop();
+	}
+
 	public double getCPUPercent(int objectIndex) {
 		if (objectIndex < 0 || objectIndex >= cpuPercent.length) return -1;
 		return cpuPercent[objectIndex];

src/pamguard/Pamguard.java

@@ -23,17 +23,14 @@ package pamguard;
 import javax.swing.SwingUtilities;
 import javax.swing.UIManager;
 
-import Acquisition.AcquisitionControl;
 import Acquisition.FolderInputSystem;
 import PamController.PamController;
 import PamController.PamGUIManager;
 import PamController.PamSettingManager;
 import PamController.PamguardVersionInfo;
 import PamController.pamBuoyGlobals;
-import PamController.command.TerminalController;
 import PamModel.SMRUEnable;
 import PamUtils.FileFunctions;
-import PamUtils.PamCalendar;
 import PamUtils.PamExceptionHandler;
 import PamUtils.PlatformInfo;
 import PamUtils.Splash;
@@ -45,6 +42,7 @@ import PamguardMVC.debug.Debug;
 import binaryFileStorage.BinaryStore;
 import dataPlotsFX.JamieDev;
 import generalDatabase.DBControl;
+import rocca.RoccaDev;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -190,6 +188,10 @@ public class Pamguard {
 					JamieDev.setEnabled(true);
 					System.out.println("Enabling Jamie Macaulay modifications.");
 				}
+				else if (anArg.equalsIgnoreCase("-rocca")) {
+					RoccaDev.setEnabled(true);
+					System.out.println("Enabling Rocca development mode");
+				}
 				else if (anArg.equalsIgnoreCase(Debug.flag)) {
 					Debug.setPrintDebug(true);
 					Debug.out.println("Enabling debug terminal output.");

src/rocca/RoccaClassifier.java

@@ -408,6 +408,10 @@ public class RoccaClassifier {
 
     	// load the whistle classifier
     	if (roccaControl.roccaParameters.isClassifyWhistles()) {
+    		if (roccaControl.roccaParameters.roccaClassifierModelFilename==null) {
+    			roccaControl.roccaParameters.setClassifyWhistles(false);
+    		}
+    		else {
 		        String fname = roccaControl.roccaParameters.roccaClassifierModelFilename.getAbsolutePath();
 		        File f = new File(fname);
 		        if (f.exists() == false) {
@@ -450,9 +454,14 @@ public class RoccaClassifier {
 		        	}
 		        }
 	    	}
+    	}
         
         // serialVersionUID=24 2016/08/10 added to load click classifier
     	if (roccaControl.roccaParameters.isClassifyClicks()) {
+    		if (roccaControl.roccaParameters.roccaClickClassifierModelFilename==null) {
+    			roccaControl.roccaParameters.setClassifyClicks(false);
+    		}
+    		else {
 		        String fname = roccaControl.roccaParameters.roccaClickClassifierModelFilename.getAbsolutePath();
 		        File f = new File(fname);
 		        if (f.exists() == false) {
@@ -495,6 +504,7 @@ public class RoccaClassifier {
 		        	}
 	    		}
 	    	}
+    	}
     	
         // if we didn't load either classifier, don't bother loading trying to load an encounter
     	// classifier because it relies on the species.  Just reset the side panel and return
@@ -505,6 +515,10 @@ public class RoccaClassifier {
         
         // serialVersionUID=24 2016/08/10 added to load event classifier
     	if (roccaControl.roccaParameters.isClassifyEvents()) {
+       		if (roccaControl.roccaParameters.roccaEventClassifierModelFilename==null) {
+    			roccaControl.roccaParameters.setClassifyEvents(false);
+    		}
+    		else {
 		        String fname = roccaControl.roccaParameters.roccaEventClassifierModelFilename.getAbsolutePath();
 		        File f = new File(fname);
 		        if (f.exists() == false) {
@@ -543,6 +557,7 @@ public class RoccaClassifier {
 		        	}
 		        }
 	    	}
+    	}
 
         resetSidePanel();
         return true;

src/rocca/RoccaDev.java

@@ -0,0 +1,27 @@
+package rocca;
+
+/**
+ * Global flag set at runtime for Rocca development flags. 
+ * @author mo55
+ *
+ */
+public class RoccaDev {
+
+	
+	private static boolean enabled = false;
+
+	/**
+	 * @return the enabled
+	 */
+	public static boolean isEnabled() {
+		return enabled;
+	}
+
+	/**
+	 * @param enabled the enabled to set
+	 */
+	public static void setEnabled(boolean enabled) {
+		RoccaDev.enabled = enabled;
+	}
+
+}

src/rocca/RoccaParametersDialog.java

@@ -26,7 +26,6 @@ import java.awt.Frame;
 import java.awt.GridBagConstraints;
 import java.awt.GridBagLayout;
 import java.awt.GridLayout;
-import java.awt.Point;
 import java.util.ArrayList;
 import java.util.Objects;
 import java.util.Vector;
@@ -48,8 +47,6 @@ import PamUtils.PamFileChooser;
 import PamView.dialog.PamDialog;
 import PamView.dialog.SourcePanel;
 import PamguardMVC.PamDataBlock;
-import PamguardMVC.PamDataUnit;
-
 import java.awt.Dimension;
 import java.awt.Insets;
 import java.awt.event.ActionEvent;
@@ -60,20 +57,14 @@ import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.FileReader;
-import java.io.IOException;
-
 import javax.swing.Box;
 import javax.swing.BoxLayout;
-import javax.swing.ButtonGroup;
 import javax.swing.DefaultComboBoxModel;
 import javax.swing.GroupLayout;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
-import javax.swing.JComponent;
-import javax.swing.JFrame;
 import javax.swing.JRadioButton;
 import javax.swing.JFileChooser;
 import javax.swing.JScrollPane;
@@ -87,7 +78,6 @@ import javax.swing.border.EtchedBorder;
 import clickDetector.ClickControl;
 import clickDetector.ClickDetection;
 import clickDetector.NoiseDataBlock;
-import weka.classifiers.AbstractClassifier;
 import weka.core.Attribute;
 import weka.core.Instances;
 import weka.core.SerializationHelper;
@@ -523,7 +513,13 @@ public class RoccaParametersDialog extends PamDialog implements ActionListener,
         reclassifyButton.addActionListener(this);
         reclassifyButton.setToolTipText("Load the whistle data from the contour stats output file, and run it through the current Classifier");
         reclassifyButton.setVisible(true);
-        extraButtonsSubPanel.setVisible(true);		// ******** THIS LINES CONTROLS THE VISIBILITY ********
+        
+        // ******** THIS LINES CONTROLS THE VISIBILITY ********
+        if (RoccaDev.isEnabled()) {
+        	extraButtonsSubPanel.setVisible(true);
+        } else {
+        	extraButtonsSubPanel.setVisible(false);
+        }
         GroupLayout extraPanelLayout = new GroupLayout(extraButtonsSubPanel);
         extraButtonsSubPanel.setLayout(extraPanelLayout);
         extraPanelLayout.setAutoCreateGaps(true);

src/rocca/RoccaProcess.java

@@ -388,7 +388,9 @@ public class RoccaProcess extends PamProcess {
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 1.5 ||
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) < 2000. ||
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) > 28000. )) {
-					rcdb.setNaturalLifetimeMillis(0);
+//					rcdb.setNaturalLifetimeMillis(0);
+			        rcdb.stopTimer();
+					rcdb = null;
 					return;
 				}
 				if (roccaControl.roccaParameters.roccaClassifierModelFilename.getName().equals("HIWhist.model") &&
@@ -402,7 +404,9 @@ public class RoccaProcess extends PamProcess {
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) > 60000.  ||
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQRANGE) < 800. ||
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQRANGE) > 14000.  )) {
-					rcdb.setNaturalLifetimeMillis(0);
+//					rcdb.setNaturalLifetimeMillis(0);
+			        rcdb.stopTimer();
+					rcdb = null;
 					return;
 				}
 				if (roccaControl.roccaParameters.roccaClassifierModelFilename.getName().equals("NWAtlWhist.model") &&
@@ -412,7 +416,9 @@ public class RoccaProcess extends PamProcess {
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 2.5 ||
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) < 9100. ||
 						 rcdb.getContour().get(RoccaContourStats.ParamIndx.FREQABSSLOPEMEAN) > 82000. )) {
-					rcdb.setNaturalLifetimeMillis(0);
+//					rcdb.setNaturalLifetimeMillis(0);
+			        rcdb.stopTimer();
+					rcdb = null;
 					return;
 				}
 			}
@@ -431,7 +437,9 @@ public class RoccaProcess extends PamProcess {
 	        saveContourPoints(rcdb, rcdb.getChannelMap(), ++numDetections, sNum);
 	        saveContourStats(rcdb, rcdb.getChannelMap(), numDetections, sNum);
 	        saveContour(rcdb, rcdb.getChannelMap(), numDetections, sNum);
-			rcdb.setNaturalLifetimeMillis(0);
+//			rcdb.setNaturalLifetimeMillis(0);
+	        rcdb.stopTimer();
+			rcdb = null;
 
 	    /* if this is a click detection (signal, not noise) */
 		} else if (o==manClickSourceData || o==autoClickSourceData) {
@@ -499,18 +507,24 @@ public class RoccaProcess extends PamProcess {
 							(rcdb.getContour().get(RoccaContourStats.ParamIndx.SNR) > 35. ||
 							 rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) < 0.005 ||
 							 rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 0.6 )) {
+				        rcdb.stopTimer();
+						rcdb = null;
 						return;
 					}
 					if (roccaControl.roccaParameters.roccaClassifierModelFilename.getName().equals("HIClick.model") &&
 							(rcdb.getContour().get(RoccaContourStats.ParamIndx.SNR) > 40. ||
 							 rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) < 0.01 ||
 							 rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 0.6 )) {
+				        rcdb.stopTimer();
+						rcdb = null;
 						return;
 					}
 					if (roccaControl.roccaParameters.roccaClassifierModelFilename.getName().equals("NWAtlClick.model") &&
 							(rcdb.getContour().get(RoccaContourStats.ParamIndx.SNR) > 35. ||
 							 rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) < 0.005 ||
 							 rcdb.getContour().get(RoccaContourStats.ParamIndx.DURATION) > 0.6 )) {
+				        rcdb.stopTimer();
+						rcdb = null;
 						return;
 					}
 				}
@@ -529,7 +543,9 @@ public class RoccaProcess extends PamProcess {
 		        // add call to update side panel.  Set the isClick flag to True
 		        updateSidePanel(rcdb, true);
 		        saveContourStats(rcdb, rcdb.getChannelMap(), numDetections, sNum);
-		        rcdb.setNaturalLifetimeMillis(0);
+//		        rcdb.setNaturalLifetimeMillis(0);
+		        rcdb.stopTimer();
+		        rcdb = null;
 			}