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

.classpath

@@ -8,6 +8,7 @@
 	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
 		<attributes>
+			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>

dependency-reduced-pom.xml

@@ -4,7 +4,7 @@
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
   <name>Pamguard Java12+</name>
-  <version>2.02.09b</version>
+  <version>2.02.09c</version>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
   <url>www.pamguard.org</url>
   <organization>

pom.xml

@@ -786,7 +786,7 @@ C:\Users\*yourusername*\.m2\repository\pamguard\org\x3\2.2.2-->
  	<dependency>
 	    <groupId>pamguard.org</groupId>
 	    <artifactId>x3</artifactId>
-	    <version>2.2.3</version>
+	    <version>2.2.6</version>
 	</dependency>
 
 	

repo/pamguard/org/x3/2.2.6/_remote.repositories

@@ -0,0 +1,4 @@
+#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
+#Wed Nov 15 12:43:42 GMT 2023
+x3-2.2.6.jar>=
+x3-2.2.6.pom>=

repo/pamguard/org/x3/2.2.6/x3-2.2.6.pom

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>pamguard.org</groupId>
+  <artifactId>x3</artifactId>
+  <version>2.2.6</version>
+  <description>POM was created from install:install-file</description>
+</project>

src/Acquisition/pamAudio/SudAudioFile.java

@@ -7,27 +7,39 @@ import java.util.Arrays;
 
 import javax.sound.sampled.AudioInputStream;
 import javax.sound.sampled.UnsupportedAudioFileException;
+import javax.swing.SwingUtilities;
+
+import org.pamguard.x3.sud.ChunkHeader;
+import org.pamguard.x3.sud.SudMapListener;
+
+import PamController.PamController;
+import PamUtils.worker.PamWorkProgressMessage;
+import PamUtils.worker.PamWorkWrapper;
+import PamUtils.worker.PamWorker;
 
 /**
  * Opens a .sud audio file.
  * <p>
- * Sud files contain X3 compressed audio data. The sud
- * file reader opens files, creating a map of the file and saving
- * the map as a.sudx file so it can be read more rapidly when the file
- * is next accessed. 
+ * Sud files contain X3 compressed audio data. The sud file reader opens files,
+ * creating a map of the file and saving the map as a.sudx file so it can be
+ * read more rapidly when the file is next accessed.
  * <p>
- * The SudioAudioInput stream fully implements AudioInputStream and so 
- * sud files can be accessed using much of the same code as .wav files. 
+ * The SudioAudioInput stream fully implements AudioInputStream and so sud files
+ * can be accessed using much of the same code as .wav files.
  *
  * @author Jamie Macaulay
  *
  */
 public class SudAudioFile extends WavAudioFile {
 
+	private Object conditionSync = new Object();
+
+	private volatile PamWorker<AudioInputStream> worker;
+	private volatile SudMapWorker sudMapWorker;
 
 	public SudAudioFile() {
 		super();
-		fileExtensions = new ArrayList<String>(Arrays.asList(new String[]{".sud"})); 
+		fileExtensions = new ArrayList<String>(Arrays.asList(new String[] { ".sud" }));
 	}
 
 	@Override
@@ -35,29 +47,174 @@ public class SudAudioFile extends WavAudioFile {
 		return "SUD";
 	}
 
-	
 	@Override
 	public AudioInputStream getAudioStream(File soundFile) {
+
+		synchronized (conditionSync) {
+
+			// System.out.println("Get SUD getAudioStream : " + soundFile.getName());
+
 			if (soundFile.exists() == false) {
 				System.err.println("The sud file does not exist: " + soundFile);
 				return null;
 			}
 			if (soundFile != null) {
+
+				if (new File(soundFile.getAbsolutePath() + "x").exists()) {
+//				System.out.println("----NO NEED TO MAP SUD FILE-----"  + soundFile);
 					try {
 						return new SudAudioFileReader().getAudioInputStream(soundFile);
+					} catch (UnsupportedAudioFileException | IOException e) {
+						// TODO Auto-generated catch block
+						e.printStackTrace();
 					}
-				// don't do anything and it will try the built in Audiosystem
-			catch (UnsupportedAudioFileException e) {
-				System.err.println("UnsupportedAudioFileException: Could not open sud file: not a supported file " + soundFile.getName()); 
+				} else {
+
+//				System.out.println("----MAP SUD FILE ON OTHER THREAD-----" + soundFile);
+
+					/**
+					 * We need to map the sud file. But we don't want this o just freeze the current
+					 * GUI thread. Therefore add a listener to the mapping process and show a
+					 * blocking dialog to indicate that something is happening. The mapping is put
+					 * on a separate thread and blocks stuff from happening until the mapping
+					 * process has completed.
+					 */
+					if (sudMapWorker == null || !sudMapWorker.getSudFile().equals(soundFile)) {
+
+						sudMapWorker = new SudMapWorker(soundFile);
+						worker = new PamWorker<AudioInputStream>(sudMapWorker,
+								PamController.getInstance().getMainFrame(), 1,
+								"Mapping sud file: " + soundFile.getName());
+//					System.out.println("Sud Audio Stream STARTED: " + soundFile.getName());
+
+						SwingUtilities.invokeLater(() -> {
+							worker.start();
+						});
+						// this should block AWT thread but won't block if called on another thread..
+					}
+
+					// this is only ever called if this function is called on another thread other
+					// than the event dispatch thread.
+					while (sudMapWorker == null || !sudMapWorker.isDone()) {
+						// do nothing
+//						System.out.println("Waiting for the SUD file map: " + soundFile.getName() + " worker: " + worker);
+						try {
+//						Thread.sleep(100);
+							Thread.sleep(100);
+						} catch (InterruptedException e) {
+							// TODO Auto-generated catch block
+							e.printStackTrace();
+						}
+					}
+
+					AudioInputStream stream = sudMapWorker.getSudAudioStream();
+
+//				sudMapWorker= null;
+//				worker = null;
+
+//				System.out.println("----RETURN SUD FILE ON OTHER THREAD-----" + stream);
+
+					return stream;
+
+				}
+			}
+		}
+
+		return null;
+	}
+
+	public class SudMapProgress implements SudMapListener {
+
+		PamWorker<AudioInputStream> sudMapWorker;
+
+		public SudMapProgress(PamWorker<AudioInputStream> sudMapWorker) {
+			this.sudMapWorker = sudMapWorker;
+		}
+
+		@Override
+		public void chunkProcessed(ChunkHeader chunkHeader, int count) {
+			// System.out.println("Sud Map Progress: " + count);
+			if (count % 500 == 0) {
+				// don't update too often or everything just freezes
+				sudMapWorker.update(new PamWorkProgressMessage(-1, ("Mapped " + count + " sud file chunks")));
+			}
+			if (count == -1) {
+				sudMapWorker.update(new PamWorkProgressMessage(-1, ("Mapping sud file finished")));
+			}
+		}
+
+	}
+
+	/**
+	 * Opens an sud file on a different thread and adds a listener for a mapping.
+	 * This allows a callback to show map progress.
+	 * 
+	 * @author Jamie Macaulay
+	 *
+	 */
+	public class SudMapWorker implements PamWorkWrapper<AudioInputStream> {
+
+		private File soundFile;
+
+		private SudMapProgress sudMapListener;
+
+		private volatile boolean done = false;
+
+		private AudioInputStream result;
+
+		public SudMapWorker(File soundFile) {
+			this.soundFile = soundFile;
+		}
+
+		public File getSudFile() {
+			return soundFile;
+		}
+
+		public AudioInputStream getSudAudioStream() {
+			return result;
+		}
+
+		@Override
+		public AudioInputStream runBackgroundTask(PamWorker<AudioInputStream> pamWorker) {
+			AudioInputStream stream;
+			try {
+//				System.out.println("START OPEN SUD FILE:");
+
+				this.sudMapListener = new SudMapProgress(pamWorker);
+				stream = new SudAudioFileReader().getAudioInputStream(soundFile, sudMapListener);
+
+//				System.out.println("END SUD FILE:");
+
+				// for some reason - task finished may not be called on other
+				// thread so put this here.
+				this.result = stream;
+				this.done = true;
+
+				return stream;
+			} catch (UnsupportedAudioFileException e) {
+				System.err.println("UnsupportedAudioFileException: Could not open sud file: not a supported file "
+						+ soundFile.getName());
 				System.err.println(e.getMessage());
-//				e.printStackTrace();
+				// e.printStackTrace();
 			} catch (IOException e) {
 				System.err.println("Could not open sud file: IO Exception: " + soundFile.getName());
 
 				e.printStackTrace();
 			}
-		}
 			return null;
 		}
 
+		@Override
+		public void taskFinished(AudioInputStream result) {
+//			System.out.println("TASK FINSIHED:");
+			this.result = result;
+			this.done = true;
+		}
+
+		public boolean isDone() {
+			return done;
+		}
+
+	}
+
 }

src/Acquisition/pamAudio/SudAudioFileReader.java

@@ -30,8 +30,9 @@ public class SudAudioFileReader {
 		 sudParams = new SudParams();
 		 //set up the sud params for default. i.e. just read files and
 		 //don't save any decompressed or meta data.
-		 sudParams.saveWav = false; 
-		 sudParams.saveMeta = false; 
+//		 sudParams.saveWav = false;
+//		 sudParams.saveMeta = false;
+		 sudParams.setFileSave(false, false, false, false);
 		 sudParams.zeroPad = true;
 	} 
 	
@@ -51,5 +52,25 @@ public class SudAudioFileReader {
 		} 
 		return sudAudioInputStream;
 	}
+	/**
+	 * Get the audio input stream for a sud file.
+	 * @param file - the .sud file to open.
+	 * @param mapListener- a listener for the sud file maps - can be null.
+	 * @return the sud AudioStream.
+	 * @throws UnsupportedAudioFileException
+	 * @throws IOException
+	 */
+	public AudioInputStream getAudioInputStream(File file, SudMapListener mapListener) throws UnsupportedAudioFileException, IOException {
+		
+//		System.out.println("Get SUD getAudioInputStream");
+ 
+		try {
+			sudAudioInputStream = SudAudioInputStream.openInputStream(file, sudParams, mapListener, false);
+		} catch (Exception e) {
+			String msg = String.format("Corrupt sud file %s: %s", file.getName(), e.getMessage());
+			throw new UnsupportedAudioFileException(msg);
+		}
+		return sudAudioInputStream;
+	}
 
 }

src/Acquisition/sud/SUDFileTime.java

@@ -2,17 +2,11 @@ package Acquisition.sud;
  
 import java.io.File;
  
-import org.pamguard.x3.sud.ChunkHeader;
 import org.pamguard.x3.sud.SudAudioInputStream;
-import org.pamguard.x3.sud.SudFileMap;
-import org.pamguard.x3.sud.SudParams;
-
-import PamUtils.PamCalendar;
  
 public class SUDFileTime {
  
 	private static long sudTime;
-	
 	private static String lastFilePath = "";
 	/**
 	 * Temp measure to get the time from the first available sud record. 
@@ -20,6 +14,7 @@ public class SUDFileTime {
 	 * @return
 	 */
 	public static long getSUDFileTime(File file) {
+		//System.out.println("Get sud file time: " + file.getName()); 
 		if (file == null || file.exists() == false) {
 			return Long.MIN_VALUE;
 		}
@@ -36,22 +31,26 @@ public class SUDFileTime {
 		 */
 //		long t1 = System.currentTimeMillis();
 		sudTime = Long.MIN_VALUE;
-		SudParams sudParams = new SudParams();
-		sudParams.saveMeta = false;
-		sudParams.saveWav = false;
+//		SudParams sudParams = new SudParams();
+//		sudParams.saveMeta = false;
+//		sudParams.saveWav = false;
 		try {
-			SudAudioInputStream sudAudioInputStream = SudAudioInputStream.openInputStream(file, sudParams, false);
-			if (sudAudioInputStream == null) {
-				return Long.MIN_VALUE;
-			}
-			SudFileMap sudMap = sudAudioInputStream.getSudMap();
-			if (sudMap == null) {
-				return Long.MIN_VALUE;
-			}
-			long t = sudMap.getFirstChunkTimeMillis();
+//			
+//			SudAudioInputStream sudAudioInputStream = SudAudioInputStream.openInputStream(file, sudParams, false);
+//			if (sudAudioInputStream == null) {
+//				return Long.MIN_VALUE;
+//			}
+//			SudFileMap sudMap = sudAudioInputStream.getSudMap();
+//			if (sudMap == null) {
+//				return Long.MIN_VALUE;
+//			}
+//			long t = sudMap.getFirstChunkTimeMillis();
+			long t = SudAudioInputStream.quickFileTime(file);
+			t=t/1000; //turn to milliseconds. 
 			if (t != 0) {
 				sudTime = t;
 			}
+
 //			sudAudioInputStream.addSudFileListener((chunkID, sudChunk)->{
 //				ChunkHeader chunkHead = sudChunk.chunkHeader;
 //				if (chunkHead == null || sudTime != Long.MIN_VALUE) {
@@ -70,14 +69,13 @@ public class SUDFileTime {
 //				sudAudioInputStream.read();
 //			}
 //			
-			sudAudioInputStream.close();
+//			sudAudioInputStream.close();
 //			long t2 = System.currentTimeMillis();
 //			System.out.printf("SUD file time %s extracted in %d milliseconds\n", PamCalendar.formatDBDateTime(sudTime), t2-t1);
-			
 		} catch (Exception e) {
-			System.err.println("Error getting time from SUD file: " + e.getMessage());
+			System.err.println("Error getting time from SUD file: " + file + "  " + e.getMessage());
+			e.printStackTrace();
 		}
-		
 		return sudTime;
 	}
  

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 = "2.02.09b";
+	static public final String version = "2.02.09c";
 	
 	/**
 	 * Release date
 	 */
-	static public final String date = "29 June 2023";
+	static public final String date = "10 November 2023";
 	
 //	/**
 //	 * Release type - Beta or Core

src/analogarraysensor/ArraySensorParams.java

@@ -10,7 +10,7 @@ public class ArraySensorParams implements Serializable, Cloneable, ManagedParame
 
 	public static final long serialVersionUID = 1L;
 	
-	public int readIntervalMillis = 1000;
+	public volatile int readIntervalMillis = 1000;
 	
 	private ArrayDisplayParameters arrayDisplayParameters;
 	

src/analogarraysensor/ArraySensorProcess.java

@@ -45,7 +45,8 @@ public class ArraySensorProcess extends PamProcess {
 			while(true) {
 				readData();
 				try {
-					Thread.sleep(analogSensorControl.getAnalogSensorParams().readIntervalMillis);
+					int slptime = analogSensorControl.getAnalogSensorParams().readIntervalMillis;
+					Thread.sleep(slptime);
 				} catch (InterruptedException e) {
 					e.printStackTrace();
 				}

src/analoginput/brainboxes/BrainBoxDevices.java

@@ -139,7 +139,7 @@ public class BrainBoxDevices  implements AnalogDeviceType, PamSettings{
 			double sensData = BBED549.hexToEngineering(bbRanges[item], sensInts);
 			double paramValue = calibration.rawToValue(sensData, calibrationData[item]);
 			analogDevicesManager.notifyData(new ItemAllData(item, sensInts, sensData, paramValue));
-//			System.out.printf("Read item %d, chan %d, int %d, real %3.5f, param %3.5f\n", iChan, chan, sensInts, sensData, paramValue);
+//			System.out.printf("Read item %d, chan %d, int %d, real %3.5f, param %3.5f\n", 0, chan, sensInts, sensData, paramValue);
 			sayError(null);
 			return new AnalogSensorData(sensData, paramValue);
 			

src/analoginput/swing/AnalogDiagnosticsDisplay.java

@@ -221,7 +221,7 @@ public class AnalogDiagnosticsDisplay extends UserDisplayComponentAdapter implem
 				break;
 			case 3:
 				if (lastUpdate[rowIndex] > 0) {
-					return PamCalendar.formatTime(lastUpdate[rowIndex]);
+					return PamCalendar.formatTime(lastUpdate[rowIndex], true);
 				}
 				break;
 			case 4:

src/bearinglocaliser/offline/BLOfflineTask.java

@@ -22,6 +22,7 @@ public class BLOfflineTask extends OfflineTask {
 		this.bearingLocaliserControl = bearingLocaliserControl;
 		bearingProcess = bearingLocaliserControl.getBearingProcess();
 		this.addRequiredDataBlock(rawOrFFTBlock = bearingProcess.getParentDataBlock());
+		addAffectedDataBlock(detectionBlock);
 //		PamDataBlock detectionSource = bearingLocaliserControl.getDetectionMonitor().getParentDataBlock();
 //		this.setParentDataBlock(detectionSource);
 //		setParentDataBlock(bearingProcess.getParentDataBlock());

src/group3dlocaliser/offline/Group3DOfflineTask.java

@@ -26,6 +26,10 @@ public class Group3DOfflineTask extends OfflineTask<PamDataUnit>{
 		this.group3DControl = group3DControl;
 		group3DProcess = group3DControl.getGroup3dProcess();
 		addAffectedDataBlock(group3DProcess.getGroup3dDataBlock());
+		PamDataBlock parentData = group3DProcess.getParentDataBlock();
+		if (parentData != null) {
+			this.addRequiredDataBlock(parentData);
+		}
 	}
 
 	@Override

src/rocca/RoccaClassifyThis.java

@@ -32,6 +32,7 @@ import java.io.IOException;
 import java.util.EnumMap;
 
 import javax.swing.JFileChooser;
+import javax.swing.filechooser.FileNameExtensionFilter;
 
 import PamUtils.PamCalendar;
 
@@ -126,31 +127,34 @@ public class RoccaClassifyThis {
     /** the field in the RoccaContourStats object which contains all the stats measures */
     private EnumMap<RoccaContourStats.ParamIndx, Double> contourStats;
 
-	private String dirIn;
-
-	/** the input filename */
-	private String csvIn;
-	
-	/** the input file */
-	private File statsFileIn;
-	
-	/** the output filename */
-	private String csvOut;
-
-	/** the output file */
-	private File statsFileOut;
-	
-	/** Constructor */	
+	/** 
+	 * Constructor used when allowing user to select training dataset
+	 * */	
 	public RoccaClassifyThis(RoccaProcess roccaProcess) {
+		File statsFileIn = getTheFile();
+		if (statsFileIn!=null) {
+			runTheClassifier(statsFileIn, roccaProcess);
+		}
+	}
 
-		// initialize the BufferedReader
-		BufferedReader inputFile = null;
+	/**
+	 * Constructor when we pass in the training dataset
+	 */
+	public RoccaClassifyThis() {
+	}
 
+
+	/**
+	 * Ask the user to select the file containing the testing dataset
+	 * 
+	 * @return File the csv file containing the testing dataset
+	 */
+	public File getTheFile() {
 		// set the directory
 //		this.dirIn = new String("C:\\Users\\Mike\\Documents\\Work\\Java\\EclipseWorkspace\\testing\\RoccaClassifyThis_testing");
 //		this.dirIn = new String("C:\\Users\\Mike\\Documents\\Work\\Tom\\Atlantic Classifier\\manual 2-stage data");
 //		this.dirIn = new String("C:\\Users\\Mike\\Documents\\Work\\Tom\\Hawaii dataset problems");
-		this.dirIn = new String("C:\\Users\\SCANS\\Documents\\Work\\Biowaves\\ONR classifier");
+//		this.dirIn = new String("C:\\Users\\SCANS\\Documents\\Work\\Biowaves\\ONR classifier");
 		
 		// Define the input and output filenames
 		// Hard-coded for now.  To Do: query the user for the filename
@@ -158,28 +162,44 @@ public class RoccaClassifyThis {
 //		this.csvIn = new String("Manual_5sp_April 9 2013.csv");
 //		this.csvIn = new String("CombinedContourStats-fixed.csv");
 //		this.csvOut = new String("RoccaContourStatsReclassified.csv");
-		this.csvIn = new String("Atl_TestDFNoTrain_Call_W_160831.csv");
-		statsFileIn = new File(dirIn, csvIn);
-		this.csvOut = new String("Atl_TestDFNoTrain_Call_W_160829-classified.csv");
-		statsFileOut = new File(dirIn, csvOut);
-
-		
-//		JFileChooser fileChooser = new JFileChooser();
-//        fileChooser.setDialogTitle("Select spreadsheet to recalculate...");
-//        fileChooser.setFileHidingEnabled(true);
-//        fileChooser.setApproveButtonText("Select");
-//        fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
-//
-//		int state = fileChooser.showOpenDialog(this.dirIn);
-//		if (state == JFileChooser.APPROVE_OPTION) {
-		
-		
-		
-		
-		
+//		this.csvIn = new String("Atl_TestDFNoTrain_Call_W_160831.csv");
+//		statsFileIn = new File(dirIn, csvIn);
+//		this.csvOut = new String("Atl_TestDFNoTrain_Call_W_160829-classified.csv");
+//		statsFileOut = new File(dirIn, csvOut);
+
+        // let the user select the arff file
+		JFileChooser fileChooser = new JFileChooser();
+        fileChooser.setDialogTitle("Select spreadsheet to recalculate...");
+        fileChooser.setFileHidingEnabled(true);
+        fileChooser.setApproveButtonText("Select");
+        fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
+        FileNameExtensionFilter restrict = new FileNameExtensionFilter("Only .csv files", "csv");
+        fileChooser.addChoosableFileFilter(restrict);
+
+		int state = fileChooser.showOpenDialog(null);
+		File statsFileIn = null;
+		if (state == JFileChooser.APPROVE_OPTION) {
+
+		    // load the file
+			statsFileIn = fileChooser.getSelectedFile();
+			return statsFileIn;
+			
+		} else {
+			return null;
+		}
+	}
 	
 	
+	/**
+	 * Run the classifier
+	 * @param statsFileIn the File containing the testing dataset
+	 * @param roccaProcess the RoccaProcess instance
+	 */
+	public void runTheClassifier(File statsFileIn, RoccaProcess roccaProcess) {
 		
+		int index = statsFileIn.getAbsolutePath().lastIndexOf(".");
+        String csvOut = statsFileIn.getAbsolutePath().substring(0,index) + "-classified.csv";
+		File statsFileOut = new File(csvOut);
 				
 		
 		// load the classifier
@@ -187,6 +207,9 @@ public class RoccaClassifyThis {
         roccaProcess.setClassifierLoaded
         (roccaProcess.roccaClassifier.setUpClassifier());
 			
+		// initialize the BufferedReader
+		BufferedReader inputFile = null;
+		
 		// open the input file
 		try {
 			System.out.println("Opening input file "+statsFileIn);
@@ -263,12 +286,45 @@ public class RoccaClassifyThis {
 			contourStats.put(RoccaContourStats.ParamIndx.FREQPOSSLOPEMEAN, Double.parseDouble(dataArray[34]));
 			contourStats.put(RoccaContourStats.ParamIndx.FREQNEGSLOPEMEAN, Double.parseDouble(dataArray[35]));
 			contourStats.put(RoccaContourStats.ParamIndx.FREQSLOPERATIO, Double.parseDouble(dataArray[36]));
-			contourStats.put(RoccaContourStats.ParamIndx.FREQBEGSWEEP, Double.parseDouble(dataArray[37]));
-			//contourStats.put(RoccaContourStats.ParamIndx.FREQBEGUP, Double.parseDouble(dataArray[38]));
-			//contourStats.put(RoccaContourStats.ParamIndx.FREQBEGDWN, Double.parseDouble(dataArray[39]));
-			contourStats.put(RoccaContourStats.ParamIndx.FREQENDSWEEP, Double.parseDouble(dataArray[40]));
-			//contourStats.put(RoccaContourStats.ParamIndx.FREQENDUP, Double.parseDouble(dataArray[41]));
-			//contourStats.put(RoccaContourStats.ParamIndx.FREQENDDWN, Double.parseDouble(dataArray[42]));
+			
+			// Note that we have to modify the FREQBEGSWEEP value.  Weka is trained with the FREQBEGSWEEP param
+			// as -1=down, 0=flat and 1=up, and that would be how the test data comes through as well.  HOWEVER,
+			// Weka assumes that for nominal parameters, the value is the index location (0,1 or 2) and NOT the actual trained
+			// value (-1,0 or 1).  So if the whistle has a down sweep, Weka needs the FREQBEGSWEEP value to be 0 indicating the 
+			// first location in the array (which was 'down').  If it was up, the value would need to be 2 indicating the third 
+			// location in the array (which was 'up').
+			// Ideally we would map the values in the test data to the positions in the training array, but as a quick and
+			// dirty hack we'll simply add 1 to the value since the difference between the nominal values (-1,0,1) and the
+			/// index positions (0,1,2) is an offset of 1
+			// Note also that we don't have to do the same thing for FREQBEGUP and FREQBEGDWN since, by coincidence, the training
+			// values of 0 and 1 happen to match the index locations of 0 and 1
+			//contourStats.put(RoccaContourStats.ParamIndx.FREQBEGSWEEP, Double.parseDouble(dataArray[37]));
+			double tempVal = Double.parseDouble(dataArray[37]);
+			tempVal++;
+			contourStats.put(RoccaContourStats.ParamIndx.FREQBEGSWEEP, tempVal);
+			contourStats.put(RoccaContourStats.ParamIndx.FREQBEGUP, Double.parseDouble(dataArray[38]));
+			contourStats.put(RoccaContourStats.ParamIndx.FREQBEGDWN, Double.parseDouble(dataArray[39]));
+			
+			// Note that we have to modify the FREQENDSWEEP value.  Weka is trained with the FREQENDSWEEP param
+			// as -1=down, 0=flat and 1=up, and that would be how the test data comes through as well.  HOWEVER,
+			// Weka assumes that for nominal parameters, the value is the index location (0,1 or 2) and NOT the actual trained
+			// value (-1,0 or 1).  So if the whistle has a down sweep, Weka needs the FREQENDSWEEP value to be 0 indicating the 
+			// first location in the array (which was 'down').  If it was up, the value would need to be 2 indicating the third 
+			// location in the array (which was 'up').
+			// Ideally we would map the values in the test data to the positions in the training array, but as a quick and
+			// dirty hack we'll simply add 1 to the value since the difference between the nominal values (-1,0,1) and the
+			/// index positions (0,1,2) is an offset of 1
+			// Note also that we don't have to do the same thing for FREQENDUP and FREQENDDWN since, by coincidence, the training
+			// values of 0 and 1 happen to match the index locations of 0 and 1
+			//contourStats.put(RoccaContourStats.ParamIndx.FREQENDSWEEP, Double.parseDouble(dataArray[40]));
+			tempVal = Double.parseDouble(dataArray[40]);
+			tempVal++;
+			contourStats.put(RoccaContourStats.ParamIndx.FREQENDSWEEP, tempVal);
+			contourStats.put(RoccaContourStats.ParamIndx.FREQENDUP, Double.parseDouble(dataArray[41]));
+			contourStats.put(RoccaContourStats.ParamIndx.FREQENDDWN, Double.parseDouble(dataArray[42]));
+			// end of hack
+			
+			
 			contourStats.put(RoccaContourStats.ParamIndx.NUMSWEEPSUPDWN, Double.parseDouble(dataArray[43]));
 			contourStats.put(RoccaContourStats.ParamIndx.NUMSWEEPSDWNUP, Double.parseDouble(dataArray[44]));
 			contourStats.put(RoccaContourStats.ParamIndx.NUMSWEEPSUPFLAT, Double.parseDouble(dataArray[45]));
@@ -285,8 +341,8 @@ public class RoccaClassifyThis {
 			contourStats.put(RoccaContourStats.ParamIndx.INFLMEANDELTA, Double.parseDouble(dataArray[56]));
 			contourStats.put(RoccaContourStats.ParamIndx.INFLSTDDEVDELTA, Double.parseDouble(dataArray[57]));
 			contourStats.put(RoccaContourStats.ParamIndx.INFLMEDIANDELTA, Double.parseDouble(dataArray[58]));
-			contourStats.put(RoccaContourStats.ParamIndx.INFLDUR, Double.parseDouble(dataArray[59]));
-			contourStats.put(RoccaContourStats.ParamIndx.STEPDUR, Double.parseDouble(dataArray[60]));	
+			//contourStats.put(RoccaContourStats.ParamIndx.INFLDUR, Double.parseDouble(dataArray[59]));
+			//contourStats.put(RoccaContourStats.ParamIndx.STEPDUR, Double.parseDouble(dataArray[60]));	
 			
 			// Run the classifier
 	        roccaProcess.roccaClassifier.classifyContour2(rcdb);

src/rocca/RoccaParametersDialog.java

@@ -169,6 +169,7 @@ public class RoccaParametersDialog extends PamDialog implements ActionListener,
     JButton classifier2Button;
     JButton recalcButton;
     JButton reclassifyButton;
+    JButton trainThenTestButton;
     JButton clearClassifier;
     JComboBox<DefaultComboBoxModel<Vector<String>>> stage1Classes;
     DefaultComboBoxModel<Vector<String>> stage1ClassModel;
@@ -513,6 +514,10 @@ 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);
+        trainThenTestButton = new JButton("Train then Test");
+        trainThenTestButton.addActionListener(this);
+        trainThenTestButton.setToolTipText("Train a classifier on a set of training data, then test it with a set of testing data");
+        trainThenTestButton.setVisible(true);
         
         // ******** THIS LINES CONTROLS THE VISIBILITY ********
         if (RoccaDev.isEnabled()) {
@@ -528,13 +533,15 @@ public class RoccaParametersDialog extends PamDialog implements ActionListener,
         		extraPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
         		.addGroup(extraPanelLayout.createSequentialGroup()
         				.addComponent(recalcButton)
-        				.addComponent(reclassifyButton))
+        				.addComponent(reclassifyButton)
+        				.addComponent(trainThenTestButton))
         		);
         extraPanelLayout.setVerticalGroup(
         		extraPanelLayout.createSequentialGroup()
         		.addGroup(extraPanelLayout.createParallelGroup(GroupLayout.Alignment.BASELINE)
         				.addComponent(recalcButton)
-        				.addComponent(reclassifyButton))
+        				.addComponent(reclassifyButton)
+        				.addComponent(trainThenTestButton))
         		);
 		classifierPanel.add(extraButtonsSubPanel);
 		        
@@ -892,7 +899,9 @@ public class RoccaParametersDialog extends PamDialog implements ActionListener,
         } else if (e.getSource() == recalcButton) {
         	RoccaFixParams recalc = new RoccaFixParams(roccaControl.roccaProcess);
         } else if (e.getSource() == reclassifyButton) {
-        	RoccaClassifyThisEvent reclassify = new RoccaClassifyThisEvent(roccaControl.roccaProcess);
+        	RoccaClassifyThis reclassify = new RoccaClassifyThis(roccaControl.roccaProcess);
+        } else if (e.getSource() == trainThenTestButton) {
+        	RoccaTrainThenTest trainThenTest = new RoccaTrainThenTest(roccaControl.roccaProcess);
         } else if (e.getSource() == fftButton) {
         	roccaParameters.setUseFFT(true);
         	this.enableTheCorrectSource();

src/rocca/RoccaRFModel.java

@@ -145,6 +145,7 @@ public class RoccaRFModel implements java.io.Serializable {
             
         } catch (Exception ex) {
             System.err.println("1st Classification failed: " + ex.getMessage());
+            ex.printStackTrace();
             rcdb.setClassifiedAs("Err");
         }
  	}

src/rocca/RoccaTrainClassifier.java

@@ -24,10 +24,14 @@
 package rocca;
 
 import java.io.BufferedReader;
+import java.io.File;
 import java.io.FileReader;
 import java.util.Date;
 import java.util.Enumeration;
 
+import javax.swing.JFileChooser;
+import javax.swing.filechooser.FileNameExtensionFilter;
+
 import weka.classifiers.trees.RandomForest;
 import weka.core.Instances;
 import weka.core.SerializationHelper;
@@ -42,13 +46,64 @@ import weka.core.SerializationHelper;
  */
 public class RoccaTrainClassifier {
 
+	
+	/**
+	 * Standalone implementation
+	 * 
+	 * @param args
+	 */
     public static void main(String[] args) {
+    	
+    	RoccaTrainClassifier rtc = new RoccaTrainClassifier();
+    	File arffFile = rtc.getArff();
+    	if (arffFile!=null) {
+    		String modelName = rtc.trainClassifier(arffFile);
+    	}
+    }
+    
+    
+    /**
+     * Let user choose arff file training dataset
+     * 
+     * @return File the arff file containing the training dataset
+     */
+    public File getArff() {
+//        String arffFile = "C:\\Users\\SCANS\\Documents\\Work\\Biowaves\\ONR classifier\\TP_TrainEvtDF_170408";
+        
+        // let the user select the arff file
+		JFileChooser fileChooser = new JFileChooser();
+        fileChooser.setDialogTitle("Select arff file containing training data");
+        fileChooser.setFileHidingEnabled(true);
+        fileChooser.setApproveButtonText("Select");
+        fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
+        FileNameExtensionFilter restrict = new FileNameExtensionFilter("Only .arff files", "arff");
+        fileChooser.addChoosableFileFilter(restrict);
+        File arffFile;
+
+ 		int state = fileChooser.showOpenDialog(null);
+		if (state == JFileChooser.APPROVE_OPTION) {
+
+		    // load the file
+            arffFile = fileChooser.getSelectedFile();
+            return arffFile;
+            
+		} else {
+			return null;
+		}
+    }
+
+    
+    /**
+     * Actual code to train the classifier
+     * 
+     */
+    public String trainClassifier(File arffFile) {
+
         RandomForest model = new RandomForest ();
         Instances trainData = null;
-        String arffFile = "C:\\Users\\SCANS\\Documents\\Work\\Biowaves\\ONR classifier\\TP_TrainEvtDF_170408";
 
         // load the ARFF file containing the training set
-        System.out.println("Loading data...");
+        System.out.println("Loading data..." + arffFile.getAbsolutePath());
         try {
             trainData = new Instances
                     (new BufferedReader
@@ -56,10 +111,13 @@ public class RoccaTrainClassifier {
 //                    ("C:\\Users\\Mike\\Documents\\Work\\Java\\WEKA\\allwhists 12 vars 8sp update 1-28-10.arff")));
 //                    ("C:\\Users\\Mike\\Documents\\Work\\Java\\WEKA\\weka vs R\\ETP_orcawale_whists2 modified-subset110perspecies-no_harm_ratios.arff")));
 //                      ("C:\\Users\\SCANS\\Documents\\Work\\Biowaves\\ONR classifier\\Atl_TrainDF_Event_160829.arff")));
-                      (arffFile + ".arff")));
+//                      (arffFile + ".arff")));
+                    	(arffFile)));
             trainData.setClassIndex(trainData.numAttributes()-1);
         } catch (Exception ex) {
             System.out.println("Error Loading...");
+    		ex.printStackTrace();
+    		return null;
         }
         
         // set the classifier parameters
@@ -78,6 +136,8 @@ public class RoccaTrainClassifier {
             model.setOptions(options);
         } catch (Exception ex) {
             System.out.println("Error setting options...");
+    		ex.printStackTrace();
+    		return null;
         }
 
         // train the classifier
@@ -90,23 +150,29 @@ public class RoccaTrainClassifier {
                     new Date());
         } catch (Exception ex) {
             System.out.println("Error training classifier...");
+    		ex.printStackTrace();
+    		return null;
         }
 
         // save the classifier
-        String[] curOptions = model.getOptions();
-        Enumeration test = model.listOptions();
-        System.out.println("Saving Classifier...");
+//        String[] curOptions = model.getOptions();
+//        Enumeration test = model.listOptions();
         Instances header = new Instances(trainData,0);
+        int index = arffFile.getAbsolutePath().lastIndexOf(".");
+        String modelName = arffFile.getAbsolutePath().substring(0,index) + ".model";
+        System.out.println("Saving Classifier..." + modelName);
         try {
             SerializationHelper.writeAll
 //                ("C:\\Users\\Mike\\Documents\\Work\\Java\\WEKA\\weka vs R\\RF_8sp_54att_110whistle-subset.model",
-                  (arffFile + ".model",
+//                  (arffFile + ".model",
+            	(modelName,
                 new Object[]{model,header});
+            System.out.println("Finished!");
+            return modelName;
         } catch (Exception ex) {
             System.out.println("Error saving classifier...");
+    		ex.printStackTrace();
         }
-        
-        System.out.println("Finished!");
+        return null;
     }
-
 }

src/rocca/RoccaTrainThenTest.java

@@ -0,0 +1,109 @@
+/*
+ *  PAMGUARD - Passive Acoustic Monitoring GUARDianship.
+ * To assist in the Detection Classification and Localisation
+ * of marine mammals (cetaceans).
+ *
+ * Copyright (C) 2006
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+ */
+
+package rocca;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+
+import javax.swing.JFileChooser;
+import javax.swing.filechooser.FileNameExtensionFilter;
+
+public class RoccaTrainThenTest {
+	
+	RoccaTrainClassifier roccaTrainClassifier;
+	
+	RoccaClassifyThis roccaClassifyThis;
+	
+	
+	/**
+	 * Main Constructor
+	 * @param roccaProcess
+	 */
+	public RoccaTrainThenTest(RoccaProcess roccaProcess) {
+		
+		
+        // let the user select the csv file containing the training and testing dataset(s)
+		JFileChooser fileChooser = new JFileChooser();
+        fileChooser.setDialogTitle("Select csv file with the training/testing pairs");
+        fileChooser.setFileHidingEnabled(true);
+        fileChooser.setApproveButtonText("Select");
+        fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
+        FileNameExtensionFilter restrict = new FileNameExtensionFilter("Only .csv files", "csv");
+        fileChooser.addChoosableFileFilter(restrict);
+
+		int state = fileChooser.showOpenDialog(null);
+		if (state == JFileChooser.APPROVE_OPTION) {
+
+		    // load the file
+			try {
+				File csvDataPairs = fileChooser.getSelectedFile();
+				BufferedReader br = new BufferedReader(new FileReader(csvDataPairs));
+		        String curPath = csvDataPairs.getParent();
+				
+				// main loop
+				// read through the csv file one line at a time.  The first column should contain the training dataset filename,
+				// and the second column the testing dataset filename.  Paths should be relative to the path containing
+				// the csv file
+				String line = "";  
+				String splitBy = ",";  
+				while ((line=br.readLine())!=null) {
+					
+					String[] filenames = line.split(splitBy);
+					
+					// train the classifier
+					File arffFile = new File(curPath + File.separator + filenames[0]);
+					roccaTrainClassifier = new RoccaTrainClassifier();
+					String modelName = roccaTrainClassifier.trainClassifier(arffFile);
+					if (modelName == null) {
+						System.out.println("ERROR: could not create classifier model from "+arffFile);
+						continue;
+					}
+										
+					// set the classifier as the current one in RoccaParameters
+					roccaProcess.roccaControl.roccaParameters.setRoccaClassifierModelFilename(new File(modelName));
+					
+					
+					// test the classifier with the testing dataset
+					File testFile = new File(curPath + File.separator + filenames[1]);
+					roccaClassifyThis = new RoccaClassifyThis();
+					roccaClassifyThis.runTheClassifier(testFile, roccaProcess);
+					
+				}
+				
+				
+			} catch (FileNotFoundException e) {
+				e.printStackTrace();
+				return;
+			} catch (IOException e) {
+				e.printStackTrace();
+				return;
+			}
+		} else {
+			return;
+		}
+	}
+
+}