Batch and X3 updates (#105)

* Update FileListWorker.java

* Support batch processing

Multicast controller and a couple of additional commands to work with
the batch processing plugin.

* Database float unpack

Better unpacking checks of floats coming back from the database

* Batch changes

Changes in support of batch processing

* Small changes for batch processing

* update X3 to get Detector parameters

X3 and PAMguard updated to get and save the SoundTrap click detector
parameters.

.classpath

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

pom.xml

@@ -784,7 +784,7 @@
  	<dependency>
 	    <groupId>pamguard.org</groupId>
 	    <artifactId>x3</artifactId>
-	    <version>2.2.1</version>
+	    <version>2.2.2</version>
 	</dependency>
 	
 		<!-- https://mvnrepository.com/artifact/it.sauronsoftware/jave -->

src/soundtrap/ImportBCLDialog.java

@@ -453,12 +453,18 @@ public class ImportBCLDialog extends PamDialog {
 		int nFiles = 0;
 		int nCDET = 0;
 		int nDWV = 0;
+
+		STClickControl clickControl = (STClickControl) PamController.getInstance().findControlledUnit(STClickControl.STUNITTYPE, stToolsParams.clickDetName);
+		
 		for (File xmlFile:xmlFiles) {
 			Debug.out.println("Opening xml file " + xmlFile.getAbsolutePath());
-			if (xmlFile.getAbsolutePath().equals("E:\\STOctober2016\\335839252\\335839252.161031002807.log.xml")) {
+//			if (xmlFile.getAbsolutePath().equals("E:\\STOctober2016\\335839252\\335839252.161031002807.log.xml")) {
-				System.out.println("Opening xml file " + xmlFile.getAbsolutePath());
+//				System.out.println("Opening xml file " + xmlFile.getAbsolutePath());
-			}
+//			}
 			STXMLFile xmlFileInfo = STXMLFile.openXMLFile(xmlFile, customDateTimeFormat.getText());
+			if (clickControl != null && xmlFileInfo.getSudDetectorInfo() != null) {
+				clickControl.setSudClickDetectorInfo(xmlFileInfo.getSudDetectorInfo());
+			}
 			
 			if (xmlFileInfo == null || xmlFileInfo.getDwvInfo() == null) {
 				String title = "Error with Soundtrap file";

src/soundtrap/STClickControl.java

@@ -25,19 +25,26 @@
 package soundtrap;
 
 import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.Serializable;
 import java.util.ArrayList;
 
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
+import javax.swing.JSeparator;
+
+import org.pamguard.x3.sud.SUDClickDetectorInfo;
 
 import Acquisition.AcquisitionControl;
-import Acquisition.sud.SUDNotificationManager;
+import PamController.PamControlledUnitSettings;
 import PamController.PamController;
 import PamguardMVC.PamRawDataBlock;
 import clickDetector.ClickBTDisplay;
 import clickDetector.ClickControl;
 import clickDetector.ClickDisplay;
 import clickDetector.ClickDisplayManager;
+import soundtrap.sud.SUDParamsDialog;
 import soundtrap.sud.SudFileDWVHandler;
 
 /**
@@ -46,6 +53,8 @@ import soundtrap.sud.SudFileDWVHandler;
  */
 public class STClickControl extends ClickControl {
 	
+	private SUDClickDetectorInfo sudClickDetectorInfo;
+	
 	public static final String STUNITTYPE = "SoundTrap Click Detector";
 
 	/**
@@ -117,9 +126,23 @@ public class STClickControl extends ClickControl {
 			}
 		}
 		
+		JMenuItem sudItem = new JMenuItem("Sound Trap settings ...");
+		sudItem.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				showSudParameters(parentFrame);
+			}
+		});
+		newMenu.add(sudItem, 0);
+		newMenu.add(new JSeparator(), 1);
+		
 		return newMenu;
 	}
 
+	protected void showSudParameters(Frame parentFrame) {
+		SUDParamsDialog.showDialog(parentFrame, this);
+	}
+
 	@Override
 	public void pamStart() {
 		sudFileDWVHandler.pamStart();
@@ -157,6 +180,43 @@ public class STClickControl extends ClickControl {
 			}
 		}
 	}
+
+	@Override
+	public long getSettingsVersion() {
+		return SUDClickDetectorInfo.serialVersionUID;
+	}
+
+	@Override
+	public Serializable getSettingsReference() {
+		return getSudClickDetectorInfo();
+	}
+
+	@Override
+	public boolean restoreSettings(PamControlledUnitSettings pamControlledUnitSettings) {
+		Object o = pamControlledUnitSettings.getSettings();
+		if (o instanceof SUDClickDetectorInfo) {
+			sudClickDetectorInfo = (SUDClickDetectorInfo) o;
+			return true;
+		}
+		return false;
+	}
+
+	/**
+	 * @return the sudClickDetectorInfo
+	 */
+	public SUDClickDetectorInfo getSudClickDetectorInfo() {
+		if (sudClickDetectorInfo == null) {
+			sudClickDetectorInfo  = new SUDClickDetectorInfo();
+		}
+		return sudClickDetectorInfo;
+	}
+
+	/**
+	 * @param sudClickDetectorInfo the sudClickDetectorInfo to set
+	 */
+	public void setSudClickDetectorInfo(SUDClickDetectorInfo sudClickDetectorInfo) {
+		this.sudClickDetectorInfo = sudClickDetectorInfo;
+	}
 	
 
 }

src/soundtrap/STXMLFile.java

@@ -12,6 +12,8 @@ import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 
+import org.pamguard.x3.sud.SUDClickDetectorInfo;
+import org.pamguard.x3.sud.SUDXMLUtils;
 import org.w3c.dom.Document;
 import org.w3c.dom.NamedNodeMap;
 import org.w3c.dom.Node;
@@ -41,6 +43,7 @@ public class STXMLFile {
 	private WAVInfo wavInfo;
 	private String soundTrapId;
 	private	String dateFormat = defaultDateFormat;
+	private SUDClickDetectorInfo sudDetectorInfo;
 
 	
 	public static void main(String[] args) {
@@ -70,6 +73,9 @@ public class STXMLFile {
 	}
 	
 	private void unpackXMLDoc() throws Exception{
+		// try to get the new format complete settings as has been developed for the 
+		// SUD direct reader. 		
+		
 		cfgNodes = doc.getElementsByTagName("CFG");
 		NodeList procEvents = doc.getElementsByTagName("PROC_EVENT");
 		
@@ -231,8 +237,14 @@ public class STXMLFile {
 			return null;
 		}
 		doc.getDocumentElement().normalize();
+		
+		STXMLFile stXMLFile = new STXMLFile(doc, xmlFile, dateTimeFormat);
+
+		SUDXMLUtils sudXml = new SUDXMLUtils();
+		SUDClickDetectorInfo detectorInfo = sudXml.extractDetectorInfo(doc);
+		stXMLFile.setSudDetectorInfo(detectorInfo);
 	
-		return new STXMLFile(doc, xmlFile, dateTimeFormat);
+		return stXMLFile;
 	}
 
 	/**
@@ -299,4 +311,18 @@ public class STXMLFile {
 		}
 		return null;
 	}
+
+	/**
+	 * @return the sudDetectorInfo
+	 */
+	public SUDClickDetectorInfo getSudDetectorInfo() {
+		return sudDetectorInfo;
+	}
+
+	/**
+	 * @param sudDetectorInfo the sudDetectorInfo to set
+	 */
+	public void setSudDetectorInfo(SUDClickDetectorInfo sudDetectorInfo) {
+		this.sudDetectorInfo = sudDetectorInfo;
+	}
 }

src/soundtrap/sud/SUDParamsDialog.java

@@ -0,0 +1,107 @@
+package soundtrap.sud;
+
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Window;
+
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.border.TitledBorder;
+
+import org.pamguard.x3.sud.SUDClickDetectorInfo;
+
+import PamView.dialog.PamDialog;
+import PamView.dialog.PamGridBagContraints;
+import soundtrap.STClickControl;
+
+/**
+ * Display ST detection parameters. These cannot be changed so all boxes are disabled. 
+ * @author dg50
+ *
+ */
+public class SUDParamsDialog extends PamDialog {
+
+	private STClickControl stClickControl;
+	
+	private JTextField sampleRate, channels, threshold, blanking, preSamps, postSamps, len;
+	
+	private static SUDParamsDialog singleInstance;
+
+	private SUDParamsDialog(Window parentFrame, STClickControl stClickControl) {
+		super(parentFrame, stClickControl.getUnitName(), false);
+		this.stClickControl = stClickControl;
+		JPanel mainPanel = new JPanel(new GridBagLayout());
+		mainPanel.setBorder(new TitledBorder("SoundTrap Detector Configuration"));
+		GridBagConstraints c = new PamGridBagContraints();
+		sampleRate = addThing(mainPanel, "Sample Rate", "Hz", c);
+		channels = addThing(mainPanel, "Num Channels", null, c);
+		threshold = addThing(mainPanel, "Threshold", "dB", c);
+		blanking = addThing(mainPanel, "Blanking", "samples", c);
+		preSamps = addThing(mainPanel, "Pre Samples", "samples", c);
+		postSamps = addThing(mainPanel, "Post Samples", "samples", c);
+		len = addThing(mainPanel, "Length", "samples", c);
+		
+		setDialogComponent(mainPanel);
+	}
+	
+	public static void showDialog(Window parent, STClickControl stClickControl) {
+//		if (singleInstance == null) {
+			singleInstance = new SUDParamsDialog(parent, stClickControl);
+//		}
+		singleInstance.setParams(stClickControl.getSudClickDetectorInfo());
+		singleInstance.setVisible(true);
+		return;
+	}
+
+	private void setParams(SUDClickDetectorInfo sudClickDetectorInfo) {
+		sampleRate.setText(String.format("%d", sudClickDetectorInfo.sampleRate));
+		channels.setText(String.format("%d", sudClickDetectorInfo.nChan));
+		threshold.setText(String.format("%3.1f", sudClickDetectorInfo.detThr));
+		blanking.setText(String.format("%d", sudClickDetectorInfo.blankingSamples));
+		preSamps.setText(String.format("%d", sudClickDetectorInfo.preSamples));
+		postSamps.setText(String.format("%d", sudClickDetectorInfo.postSamples));
+		len.setText(String.format("%d", sudClickDetectorInfo.lenSamples));
+	}
+
+	private JTextField addThing(JPanel mainPanel, String title, String postTit, GridBagConstraints c) {
+		c.gridx = 0;
+		mainPanel.add(new JLabel(title, JLabel.RIGHT), c);
+		c.gridx++;
+		STField field = new STField(5);
+		mainPanel.add(field, c);
+		if (postTit != null) {
+			c.gridx++;
+			mainPanel.add(new JLabel(postTit, JLabel.LEFT), c);
+		}
+		c.gridy++;
+		return field;
+	}
+
+	@Override
+	public boolean getParams() {
+		return true;
+	}
+
+	@Override
+	public void cancelButtonPressed() {
+		// TODO Auto-generated method stub
+
+	}
+
+	@Override
+	public void restoreDefaultSettings() {
+		// TODO Auto-generated method stub
+
+	}
+	
+	private class STField extends JTextField {
+
+		public STField(int columns) {
+			super(columns);
+			setEditable(false);
+		}
+		
+	}
+
+}

src/soundtrap/sud/SudFileDWVHandler.java

@@ -10,6 +10,7 @@ import java.util.List;
 import org.pamguard.x3.sud.Chunk;
 import org.pamguard.x3.sud.SudAudioInputStream;
 import org.pamguard.x3.sud.SudDataInputStream;
+import org.pamguard.x3.sud.SudFileMap;
 
 import Acquisition.AcquisitionControl;
 import Acquisition.sud.SUDNotificationHandler;
@@ -73,7 +74,15 @@ public class SudFileDWVHandler implements SUDNotificationHandler {
 		// this is the wav sample rate, not the detector sample rate, so don't use it
 //		sampleRate = sudAudioInputStream.getFormat().getFrameRate();
 		// this is the right one
-		sampleRate = sudAudioInputStream.getSudMap().clickDetSampleRate;
+		SudFileMap sudMap = sudAudioInputStream.getSudMap();
+		sampleRate = 0;
+		if (sudMap.detectorInfo != null) {
+			sampleRate = sudMap.detectorInfo.sampleRate;
+			stClickControl.setSudClickDetectorInfo(sudMap.detectorInfo);
+		}
+		if (sampleRate == 0) {
+			sampleRate = sudAudioInputStream.getSudMap().clickDetSampleRate;
+		}
 		fileStartMicros = sudAudioInputStream.getSudMap().getFirstChunkTimeMicros();
 		stClickControl.findRawDataBlock().setChannelMap(1);
 		stClickControl.findRawDataBlock().setSampleRate((float) sampleRate, true);
@@ -81,7 +90,7 @@ public class SudFileDWVHandler implements SUDNotificationHandler {
 		stClickControl.getSTAcquisition().acquisitionParameters.voltsPeak2Peak = STAcquisitionControl.SOUNDTRAPVP2P;
 		stClickControl.getSTAcquisition().getAcquisitionProcess().setSampleRate((float) sampleRate, true);
 //		System.out.printf("Open input stream fs = %3.1f\n", sampleRate);
-		
+
 	}
 
 	@Override
@@ -104,10 +113,10 @@ public class SudFileDWVHandler implements SUDNotificationHandler {
 		String chunkName = "Unknown";
 		int chunkSize = sudChunk.buffer.length;
 		if (sudAudioInputStream.getChunkIDString(chunkID).equals("wav")) {
-			
+
 			long millis = sudChunk.getChunkHeader().getMillisTime();
 			stClickControl.updateDisplayScrollers(millis);
-			
+
 			if (sudAudioInputStream.isChunkIDWav(chunkID)) {
 //				chunkName = "RECORDINGS";
 				// System.out.printf("Chunk ID %d, size %d, type %s\n", chunkID, chunkSize,