Merge branch 'main' of https://github.com/douggillespie/PAMGuard 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">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>

dependency-reduced-pom.xml

@@ -4,7 +4,7 @@
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
   <name>Pamguard Java12+</name>
-  <version>2.02.07ab</version>
+  <version>2.02.08</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>2.02.07ab</version>
+  <version>2.02.08</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

@@ -861,7 +861,19 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 			long[] allFileStarts = new long[allFiles.size()];
 			for (int i = 0; i < allFiles.size(); i++) {
 				allFileStarts[i] = getFileStartTime(allFiles.get(i).getAbsoluteFile());
+				if (allFileStarts[i] < firstFileStart) {
+//					System.out.printf("Swap first file from %s to %s\n", firstFile.getName(), allFiles.get(i).getName());
+					firstFile = allFiles.get(i);
+					firstFileStart = allFileStarts[i];
 				}
+				if (allFileStarts[i] > lastFileEnd) {
+//					System.out.printf("Swap last file from %s to %s\n", lastFile.getName(), allFiles.get(i).getName());
+					lastFile = allFiles.get(i);
+					lastFileEnd = allFileStarts[i] + (long) (lastFile.getDurationInSeconds()*1000.);
+				}
+			}
+			storeInfo.setFirstFileStart(firstFileStart); // just incase changed. 
+			storeInfo.setLastFileEnd(lastFileEnd); // just incase changed
 			storeInfo.setFileStartTimes(allFileStarts);
 		}
 		return storeInfo;

src/Map/GebcoMapFile.java

@@ -11,6 +11,7 @@ import java.util.Vector;
 import javax.swing.JFileChooser;
 import javax.swing.JOptionPane;
 
+import PamController.PamController;
 import PamUtils.LatLong;
 import PamUtils.PamFileChooser;
 import PamView.dialog.warn.WarnOnce;
@@ -118,10 +119,19 @@ public class GebcoMapFile implements MapFileManager {
 		int pointCount;
 		int depth;
 		MapContour mapContour;
+		boolean error = false;
 		try {
+			int iLine = 0;
 			while((line = reader.readLine())!=null){
+				iLine++;
 				line = line.trim();
 				spaceIndex = line.indexOf(' ');
+				if (spaceIndex < 0) {
+					String msg = String.format("Error in map file at line %d \"%s\"", iLine, line);
+					WarnOnce.showNamedWarning("Gebco Map File Warning", PamController.getMainFrame(), gebcoFile.getName(), msg, WarnOnce.WARNING_MESSAGE);
+					error = true;
+					break;
+				}
 				num1 = line.substring(0,spaceIndex).trim();
 				num2 = line.substring(spaceIndex).trim();
 				depth = Integer.valueOf(num1);
@@ -152,11 +162,22 @@ public class GebcoMapFile implements MapFileManager {
 		}
 		catch (NumberFormatException nex) {
 			nex.printStackTrace();
-			return false;
+			error = true;
+		}
+		catch (IndexOutOfBoundsException iex) {
+			iex.printStackTrace();
+			error = true;
+		}
+		if (reader != null) {
+			try {
+				reader.close();
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
 		}
 		Collections.sort(mapContours);
 		Collections.sort(availableContours);
-		return true;
+		return !error;
 	}
 	
 	

src/PamController/InputStoreInfo.java

@@ -76,6 +76,27 @@ public class InputStoreInfo {
 		return fileStartTimes;
 	}
 
+	/**
+	 * @param firstFileStart the firstFileStart to set
+	 */
+	public void setFirstFileStart(long firstFileStart) {
+		this.firstFileStart = firstFileStart;
+	}
+
+	/**
+	 * @param lastFileStart the lastFileStart to set
+	 */
+	public void setLastFileStart(long lastFileStart) {
+		this.lastFileStart = lastFileStart;
+	}
+
+	/**
+	 * @param lastFileEnd the lastFileEnd to set
+	 */
+	public void setLastFileEnd(long lastFileEnd) {
+		this.lastFileEnd = lastFileEnd;
+	}
+	
 
 
 }

src/PamController/PamSettingManager.java

@@ -520,9 +520,15 @@ public class PamSettingManager {
 		if (initializationComplete == false) {
 			// if PAMGAURD hasn't finished loading, then don't save the settings
 			// or the file will get wrecked (bug tracker 2269579)			
+			String msg = "There was an error loading settings from this configuration, so the configuration"
+					+ " may be incomplete. <p>Do you want to save anyway ? <p>"
+					+ " If you have added new modules, the answer is probably \"Yes\"";
+			int ans = WarnOnce.showWarning("Confuguration file warning", msg, WarnOnce.YES_NO_OPTION);
+			if (ans == WarnOnce.CANCEL_OPTION) {
 				System.out.println("Settings have not yet loaded. Don't save file");
 				return false;
 			}
+		}
 
 		saveGlobalSettings();
 		//		saveSettingToDatabase();

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 = "2.02.07f";
+	static public final String version = "2.02.08";
 	
 	/**
 	 * Release date
 	 */
-	static public final String date = "4 April 2023";
+	static public final String date = "9 May 2023";
 	
 //	/**
 //	 * Release type - Beta or Core

src/PamController/command/StopCommand.java

@@ -4,8 +4,10 @@ import PamController.PamController;
 
 public class StopCommand extends ExtCommand {
 	
+	public static final String commandId = "stop";
+
 	public StopCommand() {
-		super("stop", false);
+		super(commandId, false);
 	}
 
 	@Override

src/PamView/dialog/warn/WarnOnce.java

@@ -24,6 +24,7 @@ import javafx.scene.control.Alert.AlertType;
 public class WarnOnce implements PamSettings {
 
 	public static final int OK_CANCEL_OPTION = JOptionPane.OK_CANCEL_OPTION;
+	public static final int YES_NO_OPTION = JOptionPane.YES_NO_OPTION;
 	public static final int WARNING_MESSAGE = JOptionPane.DEFAULT_OPTION;
 	public static final int OK_OPTION = JOptionPane.OK_OPTION;
 	public static final int CANCEL_OPTION = JOptionPane.CANCEL_OPTION;

src/PamView/dialog/warn/WarnOnceDialog.java

@@ -92,12 +92,17 @@ public class WarnOnceDialog extends PamDialog {
 		}
 		
 		// if the message type is OK_OPTION, hide the cancel button
-		if (messageType == WarnOnce.OK_OPTION) {
+		if (messageType == WarnOnce.YES_NO_OPTION) {
+			getOkButton().setText("Yes");
+			getCancelButton().setText("No");
+		}
+		else if (messageType == WarnOnce.OK_OPTION) {
 			getCancelButton().setVisible(false);
 		} else {
 			getCancelButton().setVisible(true);
 		}
 		
+		
 		// change the button text to custom text, if needed
 		if (okButtonText!=null) {
 			getOkButton().setText(okButtonText);

src/PamguardMVC/PamDataBlock.java

@@ -849,6 +849,30 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
 		return unitsInInterval;
 	}
 	
+	/**
+	 * Do data exist which cover the given time range ?  
+	 * @param startMillis
+	 * @param endMillis
+	 * @return true if data exist covering that time range. 
+	 */
+	public boolean hasDataRange(long startMillis, long endMillis) {
+		PamDataUnit first = null, last = null;
+		synchronized (synchronizationLock) {
+			first = getFirstUnit();
+			last = getLastUnit();
+		}
+		if (first == null || last == null) {
+			return false;
+		}
+		if (first.getTimeMilliseconds() > startMillis) {
+			return false;
+		}
+		if (last.getEndTimeInMilliseconds() < endMillis) {
+			return false;
+		}
+		return true;
+	}
+
 	// recursive search for the correct unit
 	// private Tunit searchFirstUnitAfter(int i1, int i2, long timems) {
 	// /*
@@ -1019,6 +1043,9 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
 	 * @return true if we need to reload offline data.
 	 */
 	public boolean needViewerDataLoad(OfflineDataLoadInfo offlineDataLoadInfo) {
+		if (pamDataUnits.size() == 0) {
+			return true;
+		}
 		if (offlineDataLoadInfo.getStartMillis() == currentViewDataStart
 				&& offlineDataLoadInfo.getEndMillis() == currentViewDataEnd) {
 			return false;

src/PamguardMVC/dataOffline/OfflineDataLoading.java

@@ -527,7 +527,10 @@ public class OfflineDataLoading<T extends PamDataUnit> {
 	public void notifyOfflineObservers(T pamDataUnit) {
 		if (requestingObservers != null) {
 			for (int i = 0; i < requestingObservers.size(); i++) {
-				requestingObservers.get(i).addData(pamDataBlock, pamDataUnit);
+				PamObserver obs = requestingObservers.get(i);
+				if (obs != null) {
+					obs.addData(pamDataBlock, pamDataUnit);
+				}
 			}
 		}
 

src/analogarraysensor/AnalogArraySensorDataUnit.java

@@ -60,7 +60,7 @@ public class AnalogArraySensorDataUnit extends PamDataUnit implements Array.sens
 	}
 
 	private Double getFieldVal(int iVal) {
-		if (sensorData == null || sensorData.length <= iVal) {
+		if (sensorData == null || sensorData.length <= iVal || iVal < 0) {
 			return null;
 		}
 		AnalogSensorData sensDat = sensorData[iVal];

src/analoginput/swing/AnalogDiagnosticsDisplay.java

@@ -225,7 +225,8 @@ public class AnalogDiagnosticsDisplay extends UserDisplayComponentAdapter implem
 				}
 				break;
 			case 4:
-				if (allItemData[rowIndex] != null) {
+				ItemAllData data = allItemData[rowIndex];
+				if (data != null) {
 					return allItemData[rowIndex].getIntValue();
 				}
 				break;

src/bearinglocaliser/offline/BLOfflineTask.java

@@ -4,6 +4,7 @@ import java.util.ListIterator;
 
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
+import PamguardMVC.dataOffline.OfflineDataLoadInfo;
 import bearinglocaliser.BearingLocaliserControl;
 import bearinglocaliser.BearingProcess;
 import dataMap.OfflineDataMapPoint;
@@ -28,6 +29,9 @@ public class BLOfflineTask extends OfflineTask {
 
 	@Override
 	public String getName() {
+		if (bearingLocaliserControl == null) {
+			return null;
+		}
 		return bearingLocaliserControl.getUnitName();
 	}
 
@@ -67,15 +71,21 @@ public class BLOfflineTask extends OfflineTask {
 		if (rawOrFFTBlock == null) {
 			return;
 		}
-		ListIterator it = rawOrFFTBlock.getListIterator(dataUnit.getTimeMilliseconds(), rawOrFFTBlock.getChannelMap(), 
-				PamDataBlock.MATCH_BEFORE, PamDataBlock.POSITION_BEFORE);
-		if (it == null || it.hasNext() == false) {
 		long dataStart = dataUnit.getTimeMilliseconds();
 		long dataEnd = dataUnit.getEndTimeInMilliseconds();
-			if (dataEnd-dataStart <= 0) {
-				dataEnd = dataStart + 1000;
-			}
-			rawOrFFTBlock.loadViewerData(dataStart, dataEnd, null);
+		boolean haveData = rawOrFFTBlock.hasDataRange(dataStart, dataEnd);
+		if (haveData == false) {
+//		ListIterator it = rawOrFFTBlock.getListIterator(dataUnit.getTimeMilliseconds(), rawOrFFTBlock.getChannelMap(), 
+//				PamDataBlock.MATCH_BEFORE, PamDataBlock.POSITION_BEFORE);
+//		if (it == null || it.hasNext() == false) {
+//			if (dataEnd-dataStart <= 0) {
+//				dataEnd = dataStart + 1000;
+//			}
+			OfflineDataLoadInfo offlineLoadInfo = new OfflineDataLoadInfo(dataStart, dataEnd);
+			offlineLoadInfo.setLoadKeepLayers(2);
+			rawOrFFTBlock.getOfflineData(offlineLoadInfo);
+//			System.out.printf("Loaded some FFT data I hope\n");
+//			rawOrFFTBlock.loadViewerData(dataStart, dataEnd, null);
 		}
 		
 	}

src/dataMap/ScrollingDataPanel.java

@@ -391,6 +391,9 @@ public class ScrollingDataPanel extends PamBorderPanel {
 	public void scrollToData(PamDataBlock dataBlock) {
 		long startTime = dataBlock.getCurrentViewDataStart();
 		int val = (int) ((startTime - getScreenStartMillis())/1000 - getScreenSeconds()/5)  ;
+		val += hScrollBar.getValue();
+//		System.out.printf("Scroll bar %d to %d set %d\n", hScrollBar.getMinimum(), 
+//				hScrollBar.getMaximum(), val);
 		hScrollBar.setValue(val);
 	}
 

src/fftManager/fftorganiser/FFTDataOrganiser.java

@@ -4,6 +4,7 @@ import java.util.Arrays;
 import java.util.List;
 import java.util.ListIterator;
 
+import PamController.PamController;
 import PamController.SettingsNameProvider;
 import PamDetection.RawDataUnit;
 import PamUtils.PamUtils;
@@ -143,6 +144,11 @@ public class FFTDataOrganiser {
 		if (rawOrFFTData == null) {
 			return null;
 		}
+		
+//		if (PamController.getInstance().getRunMode() == PamController.RUN_PAMVIEW) {
+//			checkOfflineDataLoad(rawOrFFTData, pamDataUnit.getTimeMilliseconds(), pamDataUnit.getEndTimeInMilliseconds());
+//		}
+		
 		switch (inputType) {
 		case FFTData:
 			return createFromFFTData(pamDataUnit, sampleRate, channelMap);
@@ -157,6 +163,52 @@ public class FFTDataOrganiser {
 		}
 	}
 
+	/**
+	 * Called when running offline to try to ensure required raw or fft data are in memory. 
+	 * @param sourceData
+	 * @param timeMilliseconds
+	 * @param endTimeInMilliseconds
+	 */
+	private boolean checkOfflineDataLoad(PamDataBlock sourceData, long startMilliseconds, long endMilliseconds) {
+		if (sourceData == null) {
+			return false;
+		}
+		boolean needData = needOfflineDataLoad(sourceData, startMilliseconds, endMilliseconds);
+		if (needData) {
+			sourceData.loadViewerData(startMilliseconds, endMilliseconds, null);
+		}
+		return needOfflineDataLoad(sourceData, startMilliseconds, endMilliseconds);		
+	}
+	
+	/**
+	 * Test to see if we still need to load offline data. 
+	 * @param sourceData
+	 * @param startMilliseconds
+	 * @param endMilliseconds
+	 * @return
+	 */
+	private boolean needOfflineDataLoad(PamDataBlock sourceData, long startMilliseconds, long endMilliseconds) {
+		if (sourceData == null) {
+			return false;
+		}
+		synchronized (sourceData.getSynchLock()) {
+			PamDataUnit first = sourceData.getFirstUnit();
+			PamDataUnit last = sourceData.getLastUnit();
+			if (first == null || last == null) {
+				return true;
+			}
+			if (first.getTimeMilliseconds() > startMilliseconds) {
+				return true;
+			}
+			if (last.getEndTimeInMilliseconds() < endMilliseconds) {
+				return true;
+			}
+		}
+		return false;
+	}
+	
+	
+
 	/**
 	 * Get FFT data units matching in time from the source 
 	 * @param pamDataUnit data unit we need FFT data for (can be anything, just needs it's times)

src/fileOfflineData/OfflineFileList.java

@@ -3,6 +3,8 @@ package fileOfflineData;
 import java.io.File;
 import java.io.FileFilter;
 import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
 
 /**
  * Make a list of files with the given file filter. 
@@ -30,6 +32,21 @@ public class OfflineFileList {
 		return files.size();
 	}
 	
+	public void sortByFileName() {
+		if (files == null || files.size() == 0) {
+			return;
+		}
+		Collections.sort(files, new Comparator<File>() {
+
+			@Override
+			public int compare(File file1, File file2) {
+				String n1 = file1.getName();
+				String n2 = file2.getName();
+				return n1.compareTo(n2);
+			}
+		});
+	}
+
 	private void addFiles(File current) {
 		if (current.exists() == false) {
 			return;

src/modbustcp/brainbox/BBED549.java

@@ -140,7 +140,7 @@ public class BBED549 {
 	public static double hexToEngineering(int range, int data) {
 		/**
 		 * convert integer data to engineering units. 
-		 * @param range range on device, asumed the same for all channels. 
+		 * @param range range on device, assumed the same for all channels. 
 		 * @param data data array
 		 * @return
 		 */

src/nidaqdev/NIFilePlayback.java

@@ -127,7 +127,8 @@ public class NIFilePlayback implements FilePlaybackDevice, PamSettings {
 
 	@Override
 	public boolean preparePlayback(PlaybackParameters playbackParameters) {
-		if (niDeviceLUT == null || niDeviceLUT.length <= playbackParameters.deviceNumber) {
+		if (niDeviceLUT == null || niDeviceLUT.length <= playbackParameters.deviceNumber
+				|| playbackParameters.deviceNumber < 0) {
 			return false;
 		}
 		int bn = niDeviceLUT[playbackParameters.deviceNumber];