Merge remote-tracking branch 'origin/main' into Tethys

src/PamController/PSFXReadWriter.java

@@ -198,6 +198,7 @@ public class PSFXReadWriter {
 		BinaryHeader bh = new BinaryHeader();
 		bh.readHeader(dis);
 		PamSettingsGroup psg = new PamSettingsGroup(bh.getDataDate());
+		ArrayList<ModuleNameObject> moduleNames = new ArrayList<ModuleNameObject>();
 		/*
 		 * 
 			dos.writeInt(totalLen);
@@ -217,6 +218,7 @@ public class PSFXReadWriter {
 				dis.read(data);
 				if (objectId == ModuleNameObject.typeId) {
 					ModuleNameObject mno = new ModuleNameObject(data);
+					moduleNames.add(mno);
 				}
 				else if (objectId == 2) {
 					PamControlledUnitSettings pcsu = PamControlledUnitSettings.createFromNamedByteArray(data);

src/PamController/PamConfiguration.java

@@ -26,7 +26,7 @@ import offlineProcessing.OfflineTaskGroup;
  * them, but for some of the batch processing control, we need to be able to load and
  * manipulate a second set of modules, which do nothing within the running 
  * configuration, but are there to allow us to set up a configuration to send to 
- * other batch processes in viewer mode. 
+ * other batch processes in viewer mode. This is also being used in an improved module import system. 
  * @author dg50
  *
  */

src/PamController/PamController.java

@@ -142,6 +142,12 @@ public class PamController implements PamControllerInterface, PamSettings {
 	// flag used in main() to indicate that pamguard should exit as soon as processing ends. 
 	public static final String AUTOEXIT = "-autoexit";
 
+	/**
+	 * Never changed. Needed to identify settings for list of modules in prfx files. 
+	 */
+	public static final String unitName = "Pamguard Controller";
+	public static final String unitType = "PamController";
+
 	/**
 	 * The pam model. 
 	 */
@@ -1862,15 +1868,15 @@ public class PamController implements PamControllerInterface, PamSettings {
 	public long getSettingsVersion() {
 		return 0;
 	}
-
+	
 	@Override
 	public String getUnitName() {
-		return "Pamguard Controller";
+		return unitName;
 	}
 
 	@Override
 	public String getUnitType() {
-		return "PamController";
+		return unitType;
 	}
 
 	@Override

src/PamController/PamSettingsGroup.java

@@ -33,9 +33,7 @@ public class PamSettingsGroup implements Comparable<PamSettingsGroup> {
 	 * @param settingsTime settings time in milliseconds. 
 	 */
 	public PamSettingsGroup(long settingsTime) {
-		super();
-		this.settingsTime = settingsTime;
-		unitSettings = new ArrayList<PamControlledUnitSettings>();
+		this(settingsTime, new ArrayList<PamControlledUnitSettings>());
 	}
 	
 	/**

src/PamController/UsedModuleInfo.java

@@ -8,7 +8,8 @@ import PamModel.parametermanager.PamParameterSet.ParameterSetType;
 
 /**
  * Very simple class used in an ArrayList of used modules that 
- * get's saved between runs.
+ * get's saved between runs. This forms the core of the settings system
+ * so don't f*** with it !
  * @author Doug
  *
  */

src/PamController/settings/SettingsImport.java

@@ -15,10 +15,12 @@ import PamController.PamController;
 import PamController.PamSettingManager;
 import PamController.PamSettings;
 import PamController.PamSettingsGroup;
+import PamController.UsedModuleInfo;
 import PamModel.PamModel;
 import PamModel.PamModuleInfo;
 import PamModel.SMRUEnable;
 import PamView.dialog.PamFileBrowser;
+import PamView.dialog.warn.WarnOnce;
 
 /**
  * Class to handle the import of settings from other psf files. 
@@ -180,9 +182,16 @@ public class SettingsImport {
 		/**
 		 * Now make a new Pamcontrolled unit with the given name ...
 		 */
+		// need to find the module information in the PamModel
+//		PamModel pamModel = PamModel.getPamModel();
+//		pamModel.
+		PamModuleInfo moduleInfo = PamModuleInfo.findModuleInfo(importGroup.getUsedModuleInfo().className);
 		// find the module info for this one
-		PamModuleInfo moduleInfo = importGroup.getModuleInfo();
+//		PamModuleInfo moduleInfo = importGroup.getUsedModuleInfo();
 		if (moduleInfo == null) {
+			String msg = String.format("Unable to find module information for type %s main class %s in model",
+					importGroup.getUsedModuleInfo().getUnitType(), importGroup.getUsedModuleInfo().className);
+			WarnOnce.showWarning("Module creating error!", msg, WarnOnce.WARNING_MESSAGE);
 			return null;
 		}
 
@@ -206,6 +215,7 @@ public class SettingsImport {
 			}
 		}
 		loadSubUnitSettings(importGroup, unit.getUnitName());
+		unit.setupControlledUnit();
 		return unit;
 	}
 
@@ -215,45 +225,64 @@ public class SettingsImport {
 	 * @return
 	 */
 	ArrayList<SettingsImportGroup> organiseSettingsGroups(ArrayList<PamControlledUnitSettings> settings) {
+		/**
+		 * this needs rewriting for psfx files which are organised differently. first we need to find 
+		 * a list of PAMGuard modules by finding the settings group of the PAMController. 
+		 */	
+		
 		ArrayList<SettingsImportGroup> groupedSettings = new ArrayList<>();
-		// first pull out the settings for PamControlledNnits. 
-		boolean[] used = new boolean[settings.size()];
-		for (int i = 0; i < settings.size(); i++) {
-			PamControlledUnitSettings aSet = settings.get(i);
-			if (aSet.getOwnerClassName() == null) {
-				continue;
-			}
-			Class ownerClass = null;
-			try {
-				ownerClass = Class.forName(aSet.getOwnerClassName());
-			} catch (ClassNotFoundException e) {
-				// TODO Auto-generated catch block
-//				e.printStackTrace();
-				// this is happening since the ownerclassname is not set correctly in psfx files
-				// so we have to deserialise the data to find the class. 
-//				ownerClass = getClassFromData(aSet.getSerialisedByteArray());
-//				ownerClass = PamModuleInfo.findModuleClass(aSet.getUnitType());
-			}
-			if (ownerClass == null) {
-				continue;
-			}
-			if (PamControlledUnit.class.isAssignableFrom(ownerClass)) {
-				PamModuleInfo moduleInfo = PamModuleInfo.findModuleInfo(aSet.getOwnerClassName());
-				groupedSettings.add(new SettingsImportGroup(aSet, moduleInfo));
-				used[i] = true;
-			}
+		ArrayList<UsedModuleInfo> usedModules = findPamControllerSettings(settings);
+		// make the group list based on the list of modules. 
+		for (UsedModuleInfo usedModule : usedModules) {
+			groupedSettings.add(new SettingsImportGroup(usedModule));
 		}
+			
+		
+//		// first pull out the settings for PamControlledNnits. 
+		boolean[] used = new boolean[settings.size()];
+//		for (int i = 0; i < settings.size(); i++) {
+//			PamControlledUnitSettings aSet = settings.get(i);
+//			if (aSet.getOwnerClassName() == null) {
+//				continue;
+//			}
+//			Class ownerClass = null;
+//			try {
+//				ownerClass = Class.forName(aSet.getOwnerClassName());
+//			} catch (ClassNotFoundException e) {
+//				// TODO Auto-generated catch block
+////				e.printStackTrace();
+//				// this is happening since the ownerclassname is not set correctly in psfx files
+//				// so we have to deserialise the data to find the class. 
+////				ownerClass = getClassFromData(aSet.getSerialisedByteArray());
+////				ownerClass = PamModuleInfo.findModuleClass(aSet.getUnitType());
+//			}
+//			if (ownerClass == null) {
+//				continue;
+//			}
+//			if (PamControlledUnit.class.isAssignableFrom(ownerClass)) {
+//				PamModuleInfo moduleInfo = PamModuleInfo.findModuleInfo(aSet.getOwnerClassName());
+//				groupedSettings.add(new SettingsImportGroup(moduleInfo));
+//				used[i] = true;
+//			}
+//		}
 
 		// now match all the remaining settings into the first set based on ModuleName. 
 		for (int i = 0; i < settings.size(); i++) {
 			PamControlledUnitSettings aSet = settings.get(i);
-			if (used[i]) continue;
+//			if (used[i]) continue;
 			SettingsImportGroup mainGroup = findGroup(groupedSettings, aSet.getUnitName());
 			if (mainGroup != null) {
-				mainGroup.addSubSettings(aSet);
+				// main settings will have same type as well as same name. 
+				boolean mainType = isMainType(mainGroup, aSet);
+				if (mainType) {
+					mainGroup.setMainSettings(aSet);
+				}
+				else {
+					mainGroup.addSubSettings(aSet);
+				}
 				used[i] = true;
-				System.out.println(String.format("Adding %s-%s to %s-%s group", aSet.getUnitType(), aSet.getUnitName(), 
-						mainGroup.getMainSettings().getUnitType(), mainGroup.getMainSettings().getUnitName()));
+//				System.out.println(String.format("Adding %s-%s to %s-%s group", aSet.getUnitType(), aSet.getUnitName(), 
+//						mainGroup.getMainSettings().getUnitType(), mainGroup.getMainSettings().getUnitName()));
 			}
 		}
 		
@@ -272,6 +301,34 @@ public class SettingsImport {
 		return groupedSettings;
 	}
 	
+	/**
+	 * IS this the main settings group for this module ? If it is, it should have the same 
+	 * type as well as the same name. 
+	 * @param mainGroup
+	 * @param aSet
+	 * @return
+	 */
+	private boolean isMainType(SettingsImportGroup mainGroup, PamControlledUnitSettings aSet) {
+		boolean isMain = mainGroup.getUsedModuleInfo().getUnitType().equals(aSet.getUnitType());
+		return isMain;
+	}
+
+	private ArrayList<UsedModuleInfo> findPamControllerSettings(ArrayList<PamControlledUnitSettings> settings) {
+		if (settings == null) {
+			return null;
+		}
+		for (PamControlledUnitSettings aSet : settings) {
+			if (aSet.getUnitName().equals(PamController.unitName) && 
+					aSet.getUnitType().equals(PamController.unitType)) {
+				Object sets = aSet.getSettings();
+				if (sets instanceof ArrayList) {
+					return (ArrayList<UsedModuleInfo>) sets;
+				}
+			}
+		}
+		return null;
+	}
+
 	private Class getClassFromData(byte[] data) {
 		try {
 			ObjectInputStream ois = new ObjectInputStream(new ByteArrayInputStream(data));
@@ -285,7 +342,7 @@ public class SettingsImport {
 
 	private SettingsImportGroup findGroup(ArrayList<SettingsImportGroup> groupedSettings, String unitName) {
 		for (SettingsImportGroup iG:groupedSettings) {
-			if (iG.getMainSettings().getUnitName().equals(unitName)) {
+			if (iG.getUsedModuleInfo().unitName.equals(unitName)) {
 				return iG;
 			}
 		}

src/PamController/settings/SettingsImportDialog.java

@@ -17,6 +17,7 @@ import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JTable;
 import javax.swing.border.EmptyBorder;
+import javax.swing.border.TitledBorder;
 import javax.swing.event.ListSelectionEvent;
 import javax.swing.event.ListSelectionListener;
 import javax.swing.table.AbstractTableModel;
@@ -66,6 +67,7 @@ public class SettingsImportDialog extends PamDialog {
 		moduleTable.getColumnModel().getColumn(2).setPreferredWidth(200);
 
 		JPanel mainPanel = new JPanel(new BorderLayout());
+		mainPanel.setBorder(new TitledBorder("Module import selection"));
 		JScrollPane scrollPanel = new JScrollPane(moduleTable);
 		mainPanel.add(BorderLayout.CENTER, scrollPanel);
 		mainPanel.setPreferredSize(new Dimension(600,  250));

src/PamController/settings/SettingsImportGroup.java

@@ -5,6 +5,7 @@ import java.util.ArrayList;
 import PamController.PamControlledUnit;
 import PamController.PamControlledUnitSettings;
 import PamController.PamController;
+import PamController.UsedModuleInfo;
 import PamModel.PamModuleInfo;
 
 /**
@@ -20,19 +21,26 @@ public class SettingsImportGroup {
 	
 	private ArrayList<PamControlledUnitSettings> subSettings = new ArrayList<>();
 
-	private PamModuleInfo moduleInfo;
+	private UsedModuleInfo usedModuleInfo;
 
 	private ArrayList<ImportChoice> importChoices;
 	
 	private ImportChoice importChoice;
+
+
+	public SettingsImportGroup(UsedModuleInfo moduleInfo) {
+		super();
+		this.usedModuleInfo = moduleInfo;
+	}
+	
 	/**
 	 * Constructor takes the main settings
 	 * @param mainSettings
 	 * @param moduleInfo 
 	 */
-	public SettingsImportGroup(PamControlledUnitSettings mainSettings, PamModuleInfo moduleInfo) {
+	public SettingsImportGroup(PamControlledUnitSettings mainSettings, UsedModuleInfo moduleInfo) {
 		this.mainSettings = mainSettings;
-		this.moduleInfo = moduleInfo;
+		this.usedModuleInfo = moduleInfo;
 	}
 
 	/**
@@ -72,7 +80,7 @@ public class SettingsImportGroup {
 		importChoices.add(importChoice = new ImportChoice(ImportChoice.DONT_IMPORT, null));
 		Class ownerClass = null;
 		try {
-			ownerClass = Class.forName(mainSettings.getOwnerClassName());
+			ownerClass = Class.forName(usedModuleInfo.className);
 		} catch (ClassNotFoundException e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
@@ -80,8 +88,9 @@ public class SettingsImportGroup {
 		ArrayList<PamControlledUnit> existingModules = 
 				PamController.getInstance().findControlledUnits(ownerClass);
 		int maxnumber = 1; // this will only ever be used by the Array Manager which doesn't have a moduleInfo. 
-		if (this.moduleInfo != null) {
-			maxnumber = moduleInfo.getMaxNumber();
+		PamModuleInfo pamModuleInfo = getPamModuleInfo();
+		if (pamModuleInfo != null) {
+			maxnumber = pamModuleInfo.getMaxNumber();
 		}
 		if (existingModules != null) {
 			for (int i = 0; i < existingModules.size(); i++) {
@@ -111,10 +120,29 @@ public class SettingsImportGroup {
 	}
 
 	/**
+	 * This is the information from an existing module, which may not
+	 * have the full class name, but does have the type and name of the 
+	 * module being imported. 
 	 * @return the moduleInfo
 	 */
-	public PamModuleInfo getModuleInfo() {
-		return moduleInfo;
+	public UsedModuleInfo getUsedModuleInfo() {
+		return usedModuleInfo;
+	}
+	
+	/**
+	 * this is the module information held in the PamModel which 
+	 * is used to create a module. 
+	 * @return
+	 */
+	public PamModuleInfo getPamModuleInfo() {
+		return PamModuleInfo.findModuleInfo(usedModuleInfo.className);
+	}
+
+	/**
+	 * @param mainSettings the mainSettings to set
+	 */
+	public void setMainSettings(PamControlledUnitSettings mainSettings) {
+		this.mainSettings = mainSettings;
 	}
 	
 	

src/alarm/AlarmControl.java

@@ -17,6 +17,7 @@ import alarm.actions.AlarmAction;
 import alarm.actions.email.SendEmailAction;
 import alarm.actions.serial.AlarmSerialAction;
 import alarm.actions.sound.PlaySound;
+import alarm.actions.tast.TastAction;
 import alarm.actions.udp.AlarmUDPAction;
 import userDisplay.UserDisplayComponent;
 import userDisplay.UserDisplayControl;
@@ -54,6 +55,7 @@ public class AlarmControl extends PamControlledUnit implements PamSettings {
 		alarmActions.add(new AlarmSerialAction(this));
 		alarmActions.add(new SendEmailAction(this));
 		alarmActions.add(new AlarmUDPAction(this));
+//		alarmActions.add(new TastAction(this)); // uncomment when alarm action string ready
 	}
 
 	/* (non-Javadoc)

src/alarm/actions/tast/TastAction.java

@@ -0,0 +1,26 @@
+package alarm.actions.tast;
+
+import alarm.AlarmControl;
+import alarm.AlarmDataUnit;
+import alarm.actions.serial.AlarmSerialAction;
+
+public class TastAction extends AlarmSerialAction {
+
+	public TastAction(AlarmControl alarmControl) {
+		super(alarmControl);
+	}
+
+	@Override
+	public String getActionName() {
+		return "TAST Trigger";
+	}
+
+
+	@Override
+	protected String createAlarmString(AlarmDataUnit alarmDataUnit) {
+		// TODO. To define serial string to send to TAST device once we hear back 
+		// from GenusWave. 
+		return null;
+	}
+
+}

src/clickDetector/offlineFuncs/EchoDetectionTask.java

@@ -24,7 +24,7 @@ public class EchoDetectionTask extends OfflineTask<ClickDetection> {
 		this.clickControl = clickControl;
 		echoDetectionSystem = clickControl.getEchoDetectionSystem();
 		setParentDataBlock(clickControl.getClickDataBlock());
-//		addAffectedDataBlock(clickControl.getClickDataBlock());
+		addAffectedDataBlock(clickControl.getClickDataBlock());
 	}
 
 	@Override

src/offlineProcessing/OfflineTask.java

@@ -301,6 +301,21 @@ public abstract class OfflineTask<T extends PamDataUnit> {
 	public PamDataBlock getAffectedDataBlock(int iBlock) {
 		return affectedDataBlocks.get(iBlock);
 	}
+	
+	/**
+	 * Get a formatted string list of affected data blocks  
+	 * @return
+	 */
+	public String getAffectedBlocksList() {
+		if (affectedDataBlocks == null || affectedDataBlocks.size() == 0) {
+			return null;
+		}
+		String blocks = affectedDataBlocks.get(0).getDataName();
+		for (int i = 1; i < affectedDataBlocks.size(); i++) {
+			blocks += "; " + affectedDataBlocks.get(i).getDataName();
+		}
+		return blocks;
+	}
 
 	/**
 	 * Return whether or not the task SHOULD be run - i.e. if it is selected in