Merge from DG (#124)

* claspath update

* Batch processing

Adding functionality for offline task batch processing.

.classpath

@@ -6,8 +6,9 @@
 			<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/JavaSE-11">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
 		<attributes>
+			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>

src/PamController/PamControlledUnit.java

@@ -31,12 +31,8 @@ import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 
-import offlineProcessing.OfflineTask;
 import offlineProcessing.OfflineTaskGroup;
 
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-
 import PamController.status.ModuleStatus;
 import PamController.status.ModuleStatusManager;
 import PamController.status.ProcessCheck;
@@ -848,6 +844,16 @@ public abstract class PamControlledUnit implements SettingsNameProvider {
 		}
 		return worstStatus;
 	}
+	
+	/**
+	 * Get the offline state of this module. This can generally
+	 * be idle, but can be a higher state when map making at startup
+	 * and when running an offline task. 
+	 * @return
+	 */
+	public int getOfflineState() {
+		return PamController.PAM_IDLE;
+	}
 
 //	/**
 //	 * Get a list of available offline tasks for this module. This is mostly used for tasks that 

src/PamController/PamController.java

@@ -37,6 +37,7 @@ import javax.swing.ToolTipManager;
 import com.jcraft.jsch.ConfigRepository.Config;
 import com.sun.xml.bind.v2.TODO;
 
+import Acquisition.AcquisitionControl;
 import Acquisition.AcquisitionProcess;
 
 //import com.sun.org.apache.xerces.internal.dom.DocumentImpl;
@@ -65,6 +66,7 @@ import PamController.command.TerminalController;
 import PamController.command.WatchdogComms;
 import PamController.fileprocessing.ReprocessManager;
 import PamController.masterReference.MasterReferencePoint;
+import PamController.settings.BatchViewSettingsImport;
 import PamController.settings.output.xml.PamguardXMLWriter;
 import PamController.settings.output.xml.XMLWriterDialog;
 import PamController.soundMedium.GlobalMediumManager;
@@ -124,6 +126,8 @@ public class PamController implements PamControllerInterface, PamSettings {
 	public static final int PAM_INITIALISING = 4;
 	public static final int PAM_STOPPING = 5;
 	public static final int PAM_COMPLETE = 6;
+	public static final int PAM_MAPMAKING = 7;
+	public static final int PAM_OFFLINETASK = 8;
 
 	// status' for RunMode = RUN_PAMVIEW
 	public static final int PAM_LOADINGDATA = 2;
@@ -235,6 +239,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 */
 	private Thread statusCheckThread;
 	private WaitDetectorThread detectorEndThread;
+	private boolean firstDataLoadComplete;
 
 
 	private PamController(int runMode, Object object) {
@@ -437,7 +442,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 		//			addModule(mi, "Temporary Database");	
 		//		}
 
-		// Add a note to the putput console for the user to ignore the SLF4J warning (see http://www.slf4j.org/codes.html#StaticLoggerBinder
+		// Add a note to the output console for the user to ignore the SLF4J warning (see http://www.slf4j.org/codes.html#StaticLoggerBinder
 		// for details).  I spent a few hours trying to get rid of this warning, but without any luck.  If you do a google search
 		// there are a lot of forum suggestions on how to fix, but none seemed to work for me.  Added both slf4j-nop and
 		// slf4j-simple to dependency list, neither made a difference.  Changed order of dependencies, ran purges and updates,
@@ -492,17 +497,31 @@ public class PamController implements PamControllerInterface, PamSettings {
 			addView(guiFrameManager.initPrimaryView(this, pamModelInterface)); 
 		}
 
+		/**
+		 * Calling this will cause a callback to this.restoreSettings which 
+		 * includes a list of modules which will then get created, and in turn
+		 * load all of their own settings from the settings manager. 
+		 */
 		PamSettingManager.getInstance().registerSettings(this);
+		
+		/**
+		 * For offline batch processing a few funnies happen here. We'll be open 
+		 * in viewer mode, but it's likely a psf will have been passed as an input argument. 
+		 * We will therefore have to extract all the modules from that psfx as well and either 
+		 * add them as new modules, or get their settings and use those to update existing settings 
+		 * That should probably be done here before the final calls to setup processes, etc. 
+		 */
+		if (getRunMode() == RUN_PAMVIEW && PamSettingManager.remote_psf != null) {
+			loadOtherSettings(PamSettingManager.remote_psf);
+		}
 
+		/*
+		 * Get any other required modules for this run mode. 
+		 */
 		pamModelInterface.startModel();
 
 		setupProcesses();
 
-		//				if (getRunMode() == RUN_PAMVIEW) {
-		//					createViewerStatusBar();			
-		//					pamControlledUnits.add(new OfflineProcessingControlledUnit("OfflineProcessing"));
-		//				}
-
 		/*
 		 * We are running as a remote application, start process straight away!
 		 */
@@ -573,6 +592,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 		//		});
 	}
 	
+
 	/**
 	 * Clear all data selectors and symbol managers. Required since some of these will have loaded as various modules were created, 
 	 * but may also require additional data selectors and symbol managers from super detections which were not availble. 
@@ -585,6 +605,11 @@ public class PamController implements PamControllerInterface, PamSettings {
 		
 	}
 
+	/**
+	 * This gets called after other data initialisation tasks (such as data mapping). 
+	 * @author dg50
+	 *
+	 */
 	class DataInitialised implements Runnable {
 		@Override
 		public void run() {
@@ -1792,6 +1817,10 @@ public class PamController implements PamControllerInterface, PamSettings {
 		if (moduleChange(changeType)) {
 			clearSelectorsAndSymbols();
 		}
+		
+		if (changeType == DATA_LOAD_COMPLETE) {
+			firstDataLoadComplete = true;
+		}
 
 	}
 	
@@ -1928,12 +1957,75 @@ public class PamController implements PamControllerInterface, PamSettings {
 
 	public void setPamStatus(int pamStatus) {
 		this.pamStatus = pamStatus;
+		/*
+		 * This only get's called once when set idle at viewer mode startup. 
+		 */
+//		System.out.printf("*******   PamController.setPamStatus to %d, real status is %d\n",  pamStatus, getRealStatus());
 		if (getRunMode() != RUN_PAMVIEW) {
 			TopToolBar.enableStartButton(pamStatus == PAM_IDLE);
 			TopToolBar.enableStopButton(pamStatus == PAM_RUNNING);
 		}
 		showStatusWarning(pamStatus);
 	}
+
+	/**
+	 * This was within the StatusCommand class, but useful to have it here since it's needed
+	 * in more than one place. In viewer mode at startup there are a number of things going on 
+	 * in different threads, such as the creation of datamaps, and this can (hopefully) handle those bespoke
+	 * goings on. 
+	 * @return program status for multithreaded statup tasks. 
+	 */
+	public int getRealStatus() {
+		PamController pamController = PamController.getInstance();
+		if (pamController.isInitializationComplete() == false) {
+			return PamController.PAM_INITIALISING;
+		}
+		int runMode = PamController.getInstance().getRunMode();
+		if (runMode == PamController.RUN_NETWORKRECEIVER) {
+			return PamController.PAM_RUNNING;
+		}
+		int status = pamController.getPamStatus();
+		if (status == PamController.PAM_IDLE) {
+			status = PamController.PAM_IDLE;
+		}
+		else {
+			ArrayList<PamControlledUnit> daqs = PamController.getInstance().findControlledUnits(AcquisitionControl.unitType);
+			if (daqs != null) for (int i = 0; i < daqs.size(); i++) {
+				try {
+					AcquisitionControl daq = (AcquisitionControl) daqs.get(i);
+					if (daq.isStalled()) {
+						status = PamController.PAM_STALLED;
+					}
+				}
+				catch (Exception e) {
+					e.printStackTrace();
+				}
+			}
+		}
+		WatchdogComms watchdogComms = PamController.getInstance().getWatchdogComms();
+		status = watchdogComms.getModifiedWatchdogState(status);
+		/*
+		 * This function is now being used in batch processing of offline data, where it may be necessary
+		 * to get status information from many different modules, for example when executing offline tasks
+		 * or just at startup while generating datamaps and datagrams. 
+		 * So go through all modules and get the highest state of any of them. 
+		 */
+		if (getRunMode() == RUN_PAMVIEW) {
+			if (firstDataLoadComplete == false) {
+				status = PAM_INITIALISING;
+			}
+			try {
+				for (PamControlledUnit aUnit : pamConfiguration.getPamControlledUnits()) {
+					status = Math.max(status, aUnit.getOfflineState());
+				}
+			}
+			catch (Exception e) {
+				//just incase there is a concurrent modification at startup. 
+			}
+		}
+		
+		return status;
+	}
 	
 	/**
 	 * show a warning when we're waiting for detectors to stop
@@ -2218,6 +2310,31 @@ public class PamController implements PamControllerInterface, PamSettings {
 	private boolean manualStop;
 
 
+	/**
+	 * Used when in viewer mode and planning batch processing with a modified
+	 * configuration, i.e. the command line has been supplied a normal viewer mode
+	 * database and also a psfx file. The settings from the database will already have 
+	 * been loaded, this will load any modules that weren't there and will override all the 
+	 * settings in other modules with these ones (except some specials such as data storage locations)
+	 * @param psfxFile Name of additional psfx file. 
+	 */
+	private boolean loadOtherSettings(String psfxName) {
+		
+		File psfxFile = new File(psfxName);
+		if (psfxFile.exists() == false) {
+			return false;
+		}
+
+		PamSettingsGroup settingsGroup = PSFXReadWriter.getInstance().loadFileSettings(psfxFile);
+		if (settingsGroup == null) {
+			return false;
+		}
+		
+		BatchViewSettingsImport importer = new BatchViewSettingsImport(this, settingsGroup);
+		importer.importSettings();
+		return true;
+	}
+	
 	/**
 	 * Called to load a specific set of PAMGUARD settings in 
 	 * viewer mode, which were previously loaded in from a 

src/PamController/PamSettingManager.java

@@ -44,6 +44,7 @@ import javax.swing.plaf.FontUIResource;
 
 import pamViewFX.fxNodes.utilsFX.PamUtilsFX;
 import pamViewFX.fxSettingsPanes.SettingsFileDialogFX;
+import pamguard.GlobalArguments;
 
 //XMLSettings
 //import org.jdom.Document;
@@ -492,7 +493,7 @@ public class PamSettingManager {
 	/**
 	 * Call just before PAMGUARD exits to save the settings
 	 * either to psf and / or database tables.
-	 * @return true if settings saved sucessfully.
+	 * @return true if settings saved successfully.
 	 */
 	public boolean saveFinalSettings() {
 		int runMode = PamController.getInstance().getRunMode();
@@ -1029,8 +1030,9 @@ public class PamSettingManager {
 		loadingLocalSettings = true;
 
 		loadSettingsFileData();
+		
 
-		if (PamSettingManager.RUN_REMOTE == false) {
+		if (PamSettingManager.RUN_REMOTE == false && GlobalArguments.isBatch() == false) {
 			if (settingsFileData != null) {
 				TipOfTheDayManager.getInstance().setShowAtStart(settingsFileData.showTipAtStartup);
 				if (settingsFileData.showTipAtStartup) {

src/PamController/command/BatchStatusCommand.java

@@ -2,6 +2,7 @@ package PamController.command;
 
 import Acquisition.AcquisitionControl;
 import PamController.PamController;
+import offlineProcessing.OfflineTaskManager;
 import pamViewFX.PamControlledGUIFX;
 
 /**
@@ -21,6 +22,19 @@ public class BatchStatusCommand extends ExtCommand {
 
 	@Override
 	public String execute(String command) {
+		if (PamController.getInstance().getRunMode() == PamController.RUN_NORMAL) {
+			return getNormalModeStatus(command);
+		}
+		else {
+			return getViewerModeStatus(command);
+		}
+	}
+
+	private String getViewerModeStatus(String command) {
+		return OfflineTaskManager.getManager().getBatchStatus();
+	}
+
+	private String getNormalModeStatus(String command) {
 		AcquisitionControl daqControl = (AcquisitionControl) PamController.getInstance().findControlledUnit(AcquisitionControl.class, null);
 		if (daqControl == null) {
 			return null;

src/PamController/command/StatusCommand.java

@@ -31,33 +31,7 @@ public class StatusCommand extends ExtCommand {
 	
 	private int getRealStatus() {
 		PamController pamController = PamController.getInstance();
-		if (pamController.isInitializationComplete() == false) {
-			return PamController.PAM_INITIALISING;
-		}
-		int runMode = PamController.getInstance().getRunMode();
-		if (runMode == PamController.RUN_NETWORKRECEIVER) {
-			return PamController.PAM_RUNNING;
-		}
-		int status = pamController.getPamStatus();
-		if (status == PamController.PAM_IDLE) {
-			status = PamController.PAM_IDLE;
-		}
-		else {
-			ArrayList<PamControlledUnit> daqs = PamController.getInstance().findControlledUnits(AcquisitionControl.unitType);
-			if (daqs != null) for (int i = 0; i < daqs.size(); i++) {
-				try {
-					AcquisitionControl daq = (AcquisitionControl) daqs.get(i);
-					if (daq.isStalled()) {
-						status = PamController.PAM_STALLED;
-					}
-				}
-				catch (Exception e) {
-					e.printStackTrace();
-				}
-			}
-		}
-		WatchdogComms watchdogComms = PamController.getInstance().getWatchdogComms();
-		return watchdogComms.getModifiedWatchdogState(status);
+		return pamController.getRealStatus();
 	}
 
 

src/PamController/settings/BatchViewSettingsImport.java

@@ -0,0 +1,155 @@
+package PamController.settings;
+
+import java.util.ArrayList;
+
+import PamController.DataInputStore;
+import PamController.OfflineDataStore;
+import PamController.OfflineFileDataStore;
+import PamController.PamControlledUnit;
+import PamController.PamControlledUnitSettings;
+import PamController.PamController;
+import PamController.PamSettingManager;
+import PamController.PamSettings;
+import PamController.PamSettingsGroup;
+import PamController.UsedModuleInfo;
+import PamModel.PamModuleInfo;
+
+/**
+ * A set of functions to handle importing and overriding settings imported from a psfx during 
+ * batch mode processing in viewer mode. Some of this is quite similar to code in SettingsImport
+ * but different enough that it's easier to have in a separate set of functions. 
+ * @author dg50
+ *
+ */
+public class BatchViewSettingsImport {
+
+	private PamController pamController;
+	private PamSettingsGroup settingsGroup;
+	private SettingsImport settingsImport;
+
+	public BatchViewSettingsImport(PamController pamController, PamSettingsGroup settingsGroup) {
+		this.pamController = pamController;
+		this.settingsGroup = settingsGroup;
+		settingsImport = new SettingsImport(pamController);
+	}
+	
+	public boolean importSettings() {
+		
+		// first organise by controlled unit
+		ArrayList<SettingsImportGroup> moduleGroups = settingsImport.organiseSettingsGroups(settingsGroup.getUnitSettings());
+		// can now go through those modules and see which exist and which need to be added. Not asking questions, just doing it!
+		for (SettingsImportGroup moduleGroup : moduleGroups) {
+			UsedModuleInfo moduleInfo = moduleGroup.getUsedModuleInfo();
+			PamControlledUnit exModule = pamController.findControlledUnit(moduleInfo.getUnitType(), moduleInfo.getUnitName());
+			boolean existingStore = false;
+			if (exModule != null) {
+				existingStore = isDataStore(exModule);
+				System.out.printf("Module %s:%s already exists in model (data store: %s)\n", moduleInfo.getUnitType(), moduleInfo.getUnitName(), Boolean.valueOf(existingStore));
+			}
+			else {
+				System.out.printf("Module %s:%s will be added to model\n", moduleInfo.getUnitType(), moduleInfo.getUnitName());
+				// add the module. No questions asked. 
+				PamModuleInfo pamModuleInfo = moduleGroup.getPamModuleInfo();
+				if (pamModuleInfo == null) {
+					System.out.printf("Module %s:%s is not available to this PAMGuard installation\n", moduleInfo.getUnitType(), moduleInfo.getUnitName());
+					continue;
+				}
+				exModule = pamController.addModule(pamModuleInfo, moduleInfo.getUnitName());
+			}
+			// set the settings for that module, but only if it's NOT a data storage module. 
+			if (exModule == null) {
+				continue;
+			}
+//			if (exModule.getUnitName().contains("Noise")) {
+//				System.out.printf("restoring settings for %s, %s\n", exModule.getUnitType(), exModule.getUnitName());
+//				
+//			}
+			if (isDataStore(exModule)) {
+				System.out.printf("Skip restoring settings for %s, %s\n", exModule.getUnitType(), exModule.getUnitName());
+				continue;
+			}
+			restoreSettings(moduleGroup.getMainSettings());
+			ArrayList<PamControlledUnitSettings> subSets = moduleGroup.getSubSettings();
+			if (subSets != null) {
+				for (PamControlledUnitSettings aSet : subSets) {
+					restoreSettings(aSet);
+				}
+			}
+//			exModule.notifyModelChanged(PamController.INITIALIZATION_COMPLETE);
+//			if (exModule.getTabPanel() != null) {
+////				exModule.getTabPanel()
+//			}
+		}
+		/*
+		 * Don't need to call this here since it get's called shortly 
+		 * from PAMController once all modules are in place. 
+		 */
+//		pamController.notifyModelChanged(PamController.INITIALIZATION_COMPLETE);
+		
+		// send out an initialisation complete to help restore settings
+//		ArrayList<PamControlledUnitSettings> allSettings = settingsGroup.getUnitSettings();
+//		for (PamControlledUnitSettings aSet : allSettings) {
+//			PamSettings owner = PamSettingManager.getInstance().findSettingsOwner(aSet.getUnitType(), aSet.getUnitName(), null);
+//			if (owner == null) {
+//				System.out.printf("Cannot find owner for %s, %s, %s\n", aSet.getUnitType(), aSet.getUnitName(), aSet.getOwnerClassName());
+//			}
+//			else {
+//				owner.restoreSettings(aSet);
+//			}
+//		}
+		
+		return true;		
+	}
+	
+	/**
+	 * Find the owner of these settings and send it it's new settings. 
+	 * @param aSet
+	 * @return true if found and set sucessfully. 
+	 */
+	private boolean restoreSettings(PamControlledUnitSettings aSet) {
+		PamSettings owner = PamSettingManager.getInstance().findSettingsOwner(aSet.getUnitType(), aSet.getUnitName(), null);
+		if (owner == null) {
+			System.out.printf("Cannot find owner for %s, %s, %s\n", aSet.getUnitType(), aSet.getUnitName(), aSet.getOwnerClassName());
+			return false;
+		}
+		else {
+			try {
+				owner.restoreSettings(aSet);
+			}
+			catch (Exception e) {
+				System.out.printf("Exception restoring settings %s, %s, %s\n", aSet.getUnitType(), aSet.getUnitName(), aSet.getOwnerClassName());
+				e.printStackTrace();
+				return false;
+			}
+		}
+		return true;
+	}
+	
+	
+
+	/**
+	 * Is the module a data store. If it is, we probably won't want to copy over it's settings. 
+	 * @param controlledUnit PAMGuard module
+	 * @return true if it's data output or input. 
+	 */
+	private boolean isDataStore(PamControlledUnit controlledUnit) {
+		return isDataStore(controlledUnit.getClass());
+	}
+
+	/**
+	 * Is the class a data store. If it is, we probably won't want to copy over it's settings. 
+	 * @param moduleClass module class
+	 * @return true if it's data output or input. 
+	 */
+	private boolean isDataStore(Class<? extends PamControlledUnit> moduleClass) {
+		//OfflineFileDataStore, DataInputStore
+		if (OfflineDataStore.class.isAssignableFrom(moduleClass)) {
+			return true;
+		}
+		if (DataInputStore.class.isAssignableFrom(moduleClass)) {
+			return true;
+		}
+		return false;
+	}
+
+}

src/PamController/settings/SettingsImport.java

@@ -29,7 +29,10 @@ import PamView.dialog.warn.WarnOnce;
  */
 public class SettingsImport {
 
+	private PamController pamController;
+
 	public SettingsImport(PamController pamController) {
+		this.pamController = pamController;
 	}
 
 	/**
@@ -235,7 +238,7 @@ public class SettingsImport {
 	 * @param settings
 	 * @return
 	 */
-	ArrayList<SettingsImportGroup> organiseSettingsGroups(ArrayList<PamControlledUnitSettings> settings) {
+	public 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. 

src/PamModel/PamModel.java

@@ -944,14 +944,17 @@ final public class PamModel implements PamSettings {
 		
 	}
 
-	/* (non-Javadoc)
-	 * @see PamModel.PamModelInterface#startModel()
+
+
+	/**
+	 * Add any remaining REQUIRED modules.<br>
+	 * this get's called after the PamController has loaded it's main settings. 
+	 * So at this point, go through all the PamModuleInfo's and check that 
+	 * all have at least the minimum number required 
+	 * @return true
 	 */
 	public synchronized boolean startModel() {
 		/*
-		 * this get's called after the PamController has loaded it's main settings. 
-		 * So at this point, go through all the PamModuleInfo's and check that 
-		 * all have at least the minimum number required 
 		 */
 
 		PamSettingManager.getInstance().registerSettings(this);
@@ -968,11 +971,11 @@ final public class PamModel implements PamSettings {
 		
 //		writeModuleList();
 		
-		return false;
+		return true;
 	}
 
 	/**
-	 * Really just debu goutput to make a list of all modules ...
+	 * Really just debug output to make a list of all modules ...
 	 */
 	private void writeModuleList() {
 		ArrayList<PamModuleInfo> moduleInfoList = PamModuleInfo.getModuleList();

src/Spectrogram/SpectrogramDisplay.java

@@ -77,6 +77,7 @@ import pamScrollSystem.PamScrollerData;
 import pamScrollSystem.RangeSpinner;
 import pamScrollSystem.RangeSpinnerListener;
 import pamScrollSystem.jumping.ScrollJumper;
+import pamguard.GlobalArguments;
 import soundPlayback.PlaybackControl;
 import soundPlayback.PlaybackProgressMonitor;
 import userDisplay.UserDisplayControl;
@@ -274,7 +275,8 @@ InternalFrameListener, DisplayPanelContainer, SpectrogramParametersUser, PamSett
 		// this should result in settings being loaded if they exist. 
 		PamSettingManager.getInstance().registerSettings(this); // always need to register, even if we're using old parameters
 		//		}
-		if (spectrogramParameters == null) {
+		boolean isBatch = GlobalArguments.getParam("-batch") != null;
+		if (spectrogramParameters == null && isBatch == false) {
 			this.spectrogramParameters = new SpectrogramParameters();
 			PamView view = userDisplayControl.getPamView();
 			if (view != null) {
@@ -285,6 +287,14 @@ InternalFrameListener, DisplayPanelContainer, SpectrogramParametersUser, PamSett
 				}
 			}
 		}
+		if (spectrogramParameters == null) {
+			/*
+			 *  this can happen in batch mode if a display was added.
+			 *  Hopefully not a problem, but may need to set some parameters to 
+			 *  set display up correctly.  
+			 */
+			spectrogramParameters = new SpectrogramParameters();
+		}
 
 		spectrogramDisplay = this;
 

src/binaryFileStorage/BinaryStore.java

@@ -155,6 +155,8 @@ PamSettingsSource, DataOutputStore {
 	private PamControlledGUISwing binaryStoreGUISwing;
 
 	private BackupInformation backupInformation;
+
+	private BinaryDataMapMaker dataMapMaker;
 	
 	public static int getCurrentFileFormat() { 
 		return CURRENT_FORMAT;
@@ -424,6 +426,25 @@ PamSettingsSource, DataOutputStore {
 		}
 		return true;
 	}
+	
+	public boolean checkCommandLine() {
+		/*
+		 * check to see if there is a command line override of the currently stored folder name. 
+		 */
+		String globFolder = GlobalArguments.getParam(GlobalFolderArg);
+		if (globFolder == null) {
+			return false;
+		}
+		boolean ok = checkGlobFolder(globFolder);
+		if (ok) {
+			binaryStoreSettings.setStoreLocation(globFolder); // remember it. 
+			return true;
+		}
+		else {
+			System.err.println("Unable to set binary storage folder " + globFolder);
+			return false;
+		}
+	}
 
 	/**
 	 * Set and create if necessary the global folder. 
@@ -601,7 +622,8 @@ PamSettingsSource, DataOutputStore {
 
 		// this first operation should be fast enough that it doesn't
 		// need rethreading. 
-		if (isViewer()) {
+		boolean hasCommandLine = checkCommandLine();
+		if (isViewer() && !hasCommandLine) {
 			BinaryStoreSettings newSettings = null;
 			if (PamGUIManager.isSwing()) {
 				//open the swing dialog.
@@ -790,8 +812,8 @@ PamSettingsSource, DataOutputStore {
 		 *  updates to the dialog to display progress, then close the 
 		 *  dialog. 
 		 */
-		BinaryDataMapMaker bdmm = new BinaryDataMapMaker(this);
-		AWTScheduler.getInstance().scheduleTask(bdmm);
+		dataMapMaker = new BinaryDataMapMaker(this);
+		AWTScheduler.getInstance().scheduleTask(dataMapMaker);
 
 	}
 
@@ -923,6 +945,7 @@ PamSettingsSource, DataOutputStore {
 			}
 			PamController.getInstance().notifyModelChanged(PamControllerInterface.CHANGED_OFFLINE_DATASTORE);
 //			System.out.println("BinaryDataMapMaker really done " + this);
+			dataMapMaker = null;
 		}
 
 		@Override
@@ -2554,6 +2577,18 @@ PamSettingsSource, DataOutputStore {
 		return storeDeleter.deleteDataFrom(timeMillis);
 	}
 	@Override
+	public int getOfflineState() {
+		int state = super.getOfflineState();
+		if (dataMapMaker != null) {
+			System.out.println("Binary store is map making");
+			state = Math.max(state, PamController.PAM_MAPMAKING);
+		}
+		if (datagramManager != null & datagramManager.getStatus()) {
+			state = Math.max(state, PamController.PAM_MAPMAKING);
+			System.out.println("Binary store is creating datagram");
+		}
+		return state;
+		
 	public String getDataLocation() {
 		return binaryStoreSettings.getStoreLocation();
 	}

src/dataGram/DatagramManager.java

@@ -12,6 +12,7 @@ import javax.swing.SwingWorker;
 import javafx.concurrent.Task;
 import pamViewFX.pamTask.PamTaskUpdate;
 import pamViewFX.pamTask.SimplePamTaskUpdate;
+import pamguard.GlobalArguments;
 import dataMap.OfflineDataMap;
 import dataMap.OfflineDataMapPoint;
 import binaryFileStorage.BinaryOfflineDataMap;
@@ -68,10 +69,11 @@ public class DatagramManager {
 	public ArrayList<PamDataBlock> checkAllDatagrams() {
 		ArrayList<PamDataBlock> grammedDataBlocks = getDataBlocks();
 		ArrayList<PamDataBlock> updateBlocks = new ArrayList<PamDataBlock>();
+		boolean isBatch = GlobalArguments.getParam("-batch") != null;
 		/**
 		 * Check to see if any of the blocks have an existing datagram
 		 */
-		if (datagramSettings.validDatagramSettings == false) {
+		if (datagramSettings.validDatagramSettings == false && isBatch == false) {
 			/*
 			 *  this is the first time this has been run, so ask
 			 *  the user what datagram size they want.  
@@ -169,6 +171,8 @@ public class DatagramManager {
 
 	private volatile DatagramProgressDialog datagramProgressDialog;
 
+	private volatile DatagramCreator datagramCreator;
+
 
 	/**
 	 * update a list of datagrams. This should be done in a 
@@ -176,9 +180,17 @@ public class DatagramManager {
 	 * @param updateList
 	 */
 	public void updateDatagrams(ArrayList<PamDataBlock> updateList) {
-		DatagramCreator datagramCreator = new DatagramCreator(updateList);
+		datagramCreator = new DatagramCreator(updateList);
 		AWTScheduler.getInstance().scheduleTask(datagramCreator);
 	}
+	
+	/**
+	 * Get true if the datagram worker is running. 
+	 * @return
+	 */
+	public boolean getStatus() {
+		return datagramCreator != null;
+	}
 
 
 	class DatagramCreatorTask extends Task<Integer> {
@@ -540,6 +552,7 @@ public class DatagramManager {
 				PamController.getInstance().notifyTaskProgress(
 						new SimplePamTaskUpdate("Finished Datagram Mapping", PamTaskUpdate.STATUS_DONE));
 			}
+			datagramCreator = null;
 		}
 
 		@Override

src/generalDatabase/DBControlUnit.java

@@ -50,6 +50,7 @@ public class DBControlUnit extends DBControl implements DataOutputStore {
 	private boolean initialisationComplete;
 	
 	private BackupInformation backupInformation;
+	private CreateDataMap createDataMap;
 
 	public DBControlUnit(String unitName) {
 		this(null, unitName);
@@ -188,8 +189,8 @@ public class DBControlUnit extends DBControl implements DataOutputStore {
 			pamDataBlocks.get(i).removeOfflineDataMap(THIS);
 			updateDataBlocks.add(pamDataBlocks.get(i));
 		}
-		
-		AWTScheduler.getInstance().scheduleTask(new CreateDataMap(updateDataBlocks));
+		createDataMap = new CreateDataMap(updateDataBlocks);
+		AWTScheduler.getInstance().scheduleTask(createDataMap);
 		
 	}
 	
@@ -258,6 +259,7 @@ public class DBControlUnit extends DBControl implements DataOutputStore {
 		 */
 		public CreateDataMap(ArrayList<PamDataBlock> loggingBlocks) {
 			super();
+			createDataMap = this;
 			this.loggingBlocks = loggingBlocks;
 		}
 
@@ -379,6 +381,7 @@ public class DBControlUnit extends DBControl implements DataOutputStore {
 			PamController.getInstance().notifyTaskProgress(new CreateMapInfo(PamTaskUpdate.STATUS_DONE));
 			PamController.getInstance().notifyModelChanged(PamControllerInterface.CHANGED_OFFLINE_DATASTORE);
 //			System.out.println("Create datamap point: DONE2"); 
+			createDataMap = null;
 		}
 
 		/* (non-Javadoc)
@@ -513,5 +516,13 @@ public class DBControlUnit extends DBControl implements DataOutputStore {
 		return getDbProcess().deleteDataFrom(timeMillis);
 	}
 
+	@Override
+	public int getOfflineState() {
+		int state = super.getOfflineState();
+		if (createDataMap != null) {
+			state = Math.max(state, PamController.PAM_MAPMAKING);
+		}
+		return state;
+	}
 
 }

src/noiseMonitor/NoiseControl.java

@@ -13,6 +13,7 @@ import org.w3c.dom.Element;
 
 import PamController.PamControlledUnit;
 import PamController.PamControlledUnitSettings;
+import PamController.PamController;
 import PamController.PamSettingManager;
 import PamController.PamSettings;
 import PamView.PamTabPanel;
@@ -298,4 +299,15 @@ public class NoiseControl extends PamControlledUnit implements PamSettings {
 	public NoiseSettings getNoiseSettings() {
 		return noiseSettings;
 	}
+
+	@Override
+	public void notifyModelChanged(int changeType) {
+		super.notifyModelChanged(changeType);
+		switch (changeType) {
+		case PamController.INITIALIZATION_COMPLETE:
+			noiseProcess.setupProcess();
+			sortBandEdges();
+		}
+	}
+
 }

src/noiseMonitor/NoiseTabPanel.java

@@ -789,7 +789,7 @@ private void setAxisLabels() {
 			double[][] noiseData, lastNoisedata = null;
 			int chan;
 			int nMeasures = noiseDataBlock.getNumMeasurementBands();
-			int x1, x2=0, y1, y2;
+			int x1, x2=0, y1=0, y2;
 			int xWin = getWidth() / 10;
 			synchronized (noiseDataBlock.getSynchLock()) {
 				noiseIterator = noiseDataBlock.getListIterator(0);
@@ -812,15 +812,22 @@ private void setAxisLabels() {
 						lastNoisedata = lastUnit.getNoiseBandData();
 					}
 					nMeasures = noiseData.length;
+					
 					for (int i = 0; i < nMeasures; i++) {
 						if (noiseDisplaySettings.isSelectData(i) == false) {
 							continue;
 						}
+						nStats = noiseData[i].length;
 						for (int m = 0; m < nStats; m++) {
 							if ((noiseDisplaySettings.selectedStats & noiseDataBlock.statIndexToBit(m)) == 0) {
 								continue;
 							}
+							try {
 							y1 = dBToYPix(noiseData[i][m]+bandCorrection[i]);
+							}
+							catch (Exception e) {
+								e.printStackTrace();
+							}
 							setSymbol(symbol, chan, i, m);
 							symbol.draw(g, new Point(x1, y1));
 							if (lastNoisedata != null && lastNoisedata.length > i) {

src/offlineProcessing/OfflineTask.java

@@ -123,6 +123,16 @@ public abstract class OfflineTask<T extends PamDataUnit> {
 		}
 	}
 
+	/**
+	 * Get a uniquely identifyng name for the task which consists of the 
+	 * pamControlledUnit type and name as well as the tasks shorter name from getName();
+	 * @return a long name which should be unique within a configuration. 
+	 */
+	public String getLongName() {
+		PamControlledUnit tcu = getTaskControlledUnit();
+		String str = String.format("%s:%s:%s", tcu.getUnitType(), tcu.getUnitName(), getName());
+		return str;
+	}
 	/**
 	 * 
 	 * @return a name for the task, to be displayed in the dialog. 

src/offlineProcessing/OfflineTaskManager.java

@@ -17,6 +17,10 @@ public class OfflineTaskManager {
 	
 	private ArrayList<OfflineTask> globalTaskList = new ArrayList();
 	
+	public static final String commandFlag = "-offlinetask";
+	
+	public ArrayList<String> commandLineTasks = new ArrayList();
+	
 	public static OfflineTaskManager getManager() {
 		if (singleInstance == null) {
 			singleInstance = new OfflineTaskManager();
@@ -116,8 +120,9 @@ public class OfflineTaskManager {
 	 * @param offlineTask
 	 * @return matching task or null. 
 	 */
+	@SuppressWarnings("rawtypes")
 	public OfflineTask findOfflineTask(OfflineTask offlineTask) {
-		return findOfflineTask(offlineTask.getUnitType(), offlineTask.getUnitName(), offlineTask.getName());
+		return findOfflineTask(offlineTask.getLongName());
 	}
 	
 	/**
@@ -128,6 +133,7 @@ public class OfflineTaskManager {
 	 * @param taskName
 	 * @return matching task or null. 
 	 */
+	@SuppressWarnings("rawtypes")
 	public OfflineTask findOfflineTask(String unitType, String unitName, String taskName) {
 		// could possibly also do a check on class type ????
 		for (OfflineTask aTask : globalTaskList) {
@@ -143,4 +149,51 @@ public class OfflineTaskManager {
 		}
 		return null;
 	}
+	
+	/**
+	 * Another way of finding offline tasks based on their long name. This is basically
+	 * the three names unitType, unitName and taskName concatenated together. Get's used
+	 * for some task management such as passing batch processing instructions. 
+	 * @param taskLongName 
+	 * @return matching task or null. 
+	 */
+	@SuppressWarnings("rawtypes")
+	public OfflineTask findOfflineTask(String taskLongName) {
+		for (OfflineTask aTask : globalTaskList) {
+			if (aTask.getLongName().equals(taskLongName)) {
+				return aTask;
+			}
+		}
+		return null;
+	}
+
+	/**
+	 * Add a task listed in the command line when PAMGuard was started. 
+	 * @param taskLongName
+	 */
+	public void addCommandLineTask(String taskLongName) {
+		commandLineTasks.add(taskLongName);
+	}
+
+	/**
+	 * The list of tasks from the command line. 
+	 * @return the commandLineTasks
+	 */
+	public ArrayList<String> getCommandLineTasks() {
+		return commandLineTasks;
+	}
+
+	/**
+	 * Get the status of jobs to pass back to the batch process controller. 
+	 * @return
+	 */
+	public String getBatchStatus() {
+		/**
+		 * this needs to largely follow the format of the data in folderinputsystem:
+		 * String bs = String.format("%d,%d,%d,%s", nFiles,currentFile,generalStatus,currFile);
+		 */
+		int generalStatus = PamController.getInstance().getRealStatus();
+		String bs = String.format("%d,%d,%d,%s", commandLineTasks.size(), 0, generalStatus, "Processing");
+		return bs;
+	}
 }

src/pamguard/GlobalArguments.java

@@ -9,6 +9,11 @@ import java.util.HashMap;
  *
  */
 public class GlobalArguments {
+	
+	/**
+	 * Put some common flags here for convenience. 
+	 */
+	public static final String BATCHFLAG = "-batch";
 
 	static HashMap<String, String> globalFlags = new HashMap<>();
 	
@@ -43,4 +48,12 @@ public class GlobalArguments {
 		return Integer.valueOf(val);
 	}
 	
+	/**
+	 * Is the batch flag set ?
+	 * @return
+	 */
+	public static boolean isBatch() {
+		return getParam(BATCHFLAG) != null;
+	}
+	
 }

src/pamguard/Pamguard.java

@@ -44,6 +44,7 @@ import binaryFileStorage.BinaryStore;
 import dataPlotsFX.JamieDev;
 import generalDatabase.DBControl;
 import networkTransfer.send.NetworkSender;
+import offlineProcessing.OfflineTaskManager;
 import rocca.RoccaDev;
 
 import java.io.BufferedReader;
@@ -176,6 +177,11 @@ public class Pamguard {
 				else if (anArg.equalsIgnoreCase("-nosplash")) {
 					showSplash = false;
 				}
+				else if (anArg.equalsIgnoreCase(GlobalArguments.BATCHFLAG)) {
+					// flag to say we're in batch processing mode. Can be used
+					// to avoid one or two dialogs that pop up in Viewer mode. 
+					GlobalArguments.setParam(GlobalArguments.BATCHFLAG, Boolean.TRUE.toString());
+				}
 
 				//	removed SEICHE switch when the two SEICHE modules were converted to plugins				
 				//				else if (anArg.equalsIgnoreCase("-seiche")) {
@@ -244,6 +250,10 @@ public class Pamguard {
 					pamBuoyGlobals.setMultiportConfig(mAddr, mPort);
 					System.out.printf("Setting multicast control addr %s port %d\n", mAddr, mPort);
 				}
+				else if (anArg.equalsIgnoreCase(OfflineTaskManager.commandFlag)) {
+					String taskName = args[iArg++];
+					OfflineTaskManager.getManager().addCommandLineTask(taskName);
+				}
 				else if (anArg.equalsIgnoreCase("-nolog")) {
 					System.out.println("Disabling log file from command line switch...");
 					ProxyPrintStream.disableLogFile();