Add zero pad option for sud files.

src/Acquisition/FolderInputSystem.java

@@ -256,11 +256,11 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 		addComponent(p, skipSecondsField = new JTextField(4), constraints);
 		constraints.gridx++;
 		addComponent(p,  new JLabel("seconds"), constraints);
-		constraints.anchor = GridBagConstraints.EAST;
 		//		}
 
 
 		//panel to show bespoke settings for certain audio loaders. 
+		constraints.anchor = GridBagConstraints.WEST;
 		constraints.gridx = 0;
 		constraints.gridy++;
 		constraints.gridwidth = 3;
@@ -618,6 +618,7 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 //					System.out.println("ADD AUDIO PANEL: " +loader.getSettingsPane().getAudioLoaderPanel());
 					//gridbag layout
 					addComponent(audioLoaderHolder, loader.getSettingsPane().getAudioLoaderPanel(), constraints);
+					loader.getSettingsPane().setParams();
 					constraints.gridy++;
 				}
 			}
@@ -823,6 +824,17 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 				return false; 
 			}
 		}
+		
+		//get bespoke paramters from selected audio loaders. 
+		ArrayList<PamAudioFileLoader> loaders = PamAudioFileManager.getInstance().getAudioFileLoaders(allFiles);
+
+	
+		for (PamAudioFileLoader loader : loaders) {
+			if (loader.getSettingsPane()!=null) {
+				loader.getSettingsPane().getParams();
+			}
+		}
+		
 		return super.dialogGetParams();
 	}
 
@@ -1005,6 +1017,8 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 		String bs = String.format("%d,%d,%d,%s", nFiles,currentFile,generalStatus,currFile);
 		return bs;
 	}
+	
+	
 
 
 }

src/Acquisition/pamAudio/PamAudioFileLoader.java

@@ -53,6 +53,7 @@ public interface PamAudioFileLoader {
 	 * @return settings pane for audio loader - can be null. 
 	 */
 	public PamAudioSettingsPane getSettingsPane();
+
 	
 
 }

src/Acquisition/pamAudio/PamAudioFileManager.java

@@ -9,6 +9,8 @@ import javax.sound.sampled.UnsupportedAudioFileException;
 
 import org.codehaus.plexus.util.FileUtils;
 
+import Acquisition.sud.SudAudioFile;
+
 /**
  * Central class for opening sound files.
  * <p>

src/Acquisition/pamAudio/PamAudioSettingsPane.java

@@ -3,6 +3,9 @@ package Acquisition.pamAudio;
 import PamView.panel.PamPanel;
 import javafx.scene.layout.Pane;
 
+/**
+ * User controls to change bespoke settings for audio loaders. 
+ */
 public interface PamAudioSettingsPane {
 	
 	/**
@@ -17,5 +20,15 @@ public interface PamAudioSettingsPane {
 	 */
 	public PamPanel getAudioLoaderPanel();
 
+	/**
+	 * Get the parameters. This called whenever the settings dialog or pane is closed. 
+	 */
+	public void getParams();
+
+	/**
+	 * Set parameters. This is called when the dialog or pane is opened. 
+	 */
+	public void setParams();
+
 
 }

src/Acquisition/pamAudio/PamAudioSystem.java

@@ -10,6 +10,8 @@ import javax.sound.sampled.UnsupportedAudioFileException;
 //import org.kc7bfi.jflac.sound.spi.FlacAudioFileReader;
 import org.jflac.sound.spi.FlacAudioFileReader;
 
+import Acquisition.sud.SudAudioFileReader;
+
 /**
  * Now replaced with PamAudioFileManager.
  * 

src/Acquisition/sud/PamSudParams.java

@@ -0,0 +1,33 @@
+package Acquisition.sud;
+
+import java.io.Serializable;
+
+
+/**
+ * Parameters for sud file extraction. 
+ */
+public class PamSudParams implements Serializable, Cloneable {
+
+	public static final long serialVersionUID = 1L;
+	
+	/**
+	 * Zero padding fills gaps in sud files with zeros - these gaps are usually due
+	 * to errors in the recording hardware.Without zero pad then time drift within a
+	 * file can be difficult to predict, however zero padding means the sample
+	 * numbers in other files e.g. csv sensor files will not align.
+	 */
+	public boolean zeroPad = true; 
+
+	@Override
+	public PamSudParams clone() {
+		try {
+			PamSudParams ap = (PamSudParams) super.clone();
+			
+			return ap;
+		}
+		catch (CloneNotSupportedException Ex) {
+			Ex.printStackTrace();
+		}
+		return null;
+	}
+}

src/Acquisition/sud/SudAudioFile.java

@@ -1,7 +1,8 @@
-package Acquisition.pamAudio;
+package Acquisition.sud;
 
 import java.io.File;
 import java.io.IOException;
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Arrays;
 
@@ -12,8 +13,13 @@ import javax.swing.SwingUtilities;
 import org.pamguard.x3.sud.ChunkHeader;
 import org.pamguard.x3.sud.SudMapListener;
 
-import Acquisition.sud.SudAudioSettingsPane;
+import Acquisition.AcquisitionParameters;
+import Acquisition.pamAudio.PamAudioSettingsPane;
+import Acquisition.pamAudio.WavAudioFile;
+import PamController.PamControlledUnitSettings;
 import PamController.PamController;
+import PamController.PamSettingManager;
+import PamController.PamSettings;
 import PamUtils.worker.PamWorkProgressMessage;
 import PamUtils.worker.PamWorkWrapper;
 import PamUtils.worker.PamWorker;
@@ -31,21 +37,32 @@ import PamUtils.worker.PamWorker;
  * @author Jamie Macaulay
  *
  */
-public class SudAudioFile extends WavAudioFile {
+public class SudAudioFile extends WavAudioFile implements PamSettings {
 
 	private Object conditionSync = new Object();
 
 	private volatile PamWorker<AudioInputStream> worker;
+	
 	private volatile SudMapWorker sudMapWorker;
 
 	/**
 	 * Settings pane to allow users to set some additional options.  
 	 */
 	private SudAudioSettingsPane sudAudioSettingsPane;
+	
+	/**
+	 * Parameters for the sud file. TODO Note: PamAudioManager is always a single
+	 * instance referenced globally from PAMGuard. Having parameters is therefore
+	 * slightly problematic because they will apply across SoundAcquisition modules.
+	 * So in the case that someone is using two or more Sound Acquisition modules
+	 * then selecting zero and non -zero pad would be impossible
+	 */
+	private PamSudParams sudParams = new PamSudParams(); 
 
 	public SudAudioFile() {
 		super();
 		fileExtensions = new ArrayList<String>(Arrays.asList(new String[] { ".sud" }));
+		PamSettingManager.getInstance().registerSettings(this);
 	}
 
 	@Override
@@ -69,7 +86,7 @@ public class SudAudioFile extends WavAudioFile {
 				if (new File(soundFile.getAbsolutePath() + "x").exists()) {
 //				System.out.println("----NO NEED TO MAP SUD FILE-----"  + soundFile);
 					try {
-						return new SudAudioFileReader().getAudioInputStream(soundFile);
+						return new SudAudioFileReader(sudParams.zeroPad).getAudioInputStream(soundFile);
 					} catch (UnsupportedAudioFileException | IOException e) {
 						// TODO Auto-generated catch block
 						e.printStackTrace();
@@ -187,7 +204,7 @@ public class SudAudioFile extends WavAudioFile {
 //				System.out.println("START OPEN SUD FILE:");
 
 				this.sudMapListener = new SudMapProgress(pamWorker);
-				stream = new SudAudioFileReader().getAudioInputStream(soundFile, sudMapListener);
+				stream = new SudAudioFileReader(sudParams.zeroPad).getAudioInputStream(soundFile, sudMapListener);
 
 //				System.out.println("END SUD FILE:");
 
@@ -231,4 +248,42 @@ public class SudAudioFile extends WavAudioFile {
 		return sudAudioSettingsPane;
 	}
 
+	@Override
+	public String getUnitName() {
+		return "PamAudioManager";
+	}
+
+	@Override
+	public String getUnitType() {
+		return "sud_files";
+	}
+
+	@Override
+	public Serializable getSettingsReference() {
+		return sudParams;
+	}
+
+	@Override
+	public long getSettingsVersion() {
+		return PamSudParams.serialVersionUID;
+	}
+
+
+	@Override
+	public boolean restoreSettings(PamControlledUnitSettings pamControlledUnitSettings) {
+			try {
+				sudParams = ((PamSudParams) pamControlledUnitSettings.getSettings()).clone();
+				
+				return true;
+			}
+			catch (ClassCastException e) {
+				e.printStackTrace();
+			}
+			return false;
+	}
+
+	public PamSudParams getSudParams() {
+		return this.sudParams;
+	}
+
 }

src/Acquisition/sud/SudAudioFileReader.java

@@ -1,4 +1,4 @@
-package Acquisition.pamAudio;
+package Acquisition.sud;
 
 import java.io.File;
 import java.io.IOException;
@@ -25,15 +25,32 @@ public class SudAudioFileReader {
 	 */
 	SudParams sudParams; 
 
-
+	/**
+	 * Constructor to create an Sud Audio reader with a
+	 * default true to zeropad sud files. 
+	 * */
 	public SudAudioFileReader() {
+		this(true); 
+	} 
+	
+	
+	/**
+	 * Constructor to create an Sud Audio reader. Allows the option of zero padding.
+	 * Zero padding fills gaps in sud files with zeros - these gaps are usually due
+	 * to errors in the recording hardware.Without zero pad then time drift within a
+	 * file can be difficult to predict, however zero padding means the sample
+	 * numbers in other files e.g. csv sensor files will not align.
+	 * 
+	 * @param zeroPad - true to zero pad sud files.
+	 */
+	public SudAudioFileReader(boolean zeroPad) {
 		 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.setFileSave(false, false, false, false);
-		 sudParams.zeroPad = true;
+		 sudParams.zeroPad = zeroPad;
 	} 
 	
 	/**

src/Acquisition/sud/SudAudioSettingsPane.java

@@ -1,17 +1,25 @@
 package Acquisition.sud;
 
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+
+import javax.swing.JCheckBox;
 import javax.swing.JLabel;
+import javax.swing.JPanel;
 
 import Acquisition.pamAudio.PamAudioSettingsPane;
-import Acquisition.pamAudio.SudAudioFile;
+import PamView.dialog.PamGridBagContraints;
 import PamView.panel.PamPanel;
 import javafx.scene.layout.Pane;
 
+/**
+ * Some Swing and FX controls to allow a user to chnage sud parameters. 
+ */
 public class SudAudioSettingsPane implements PamAudioSettingsPane {
-	
+
 	private SudAudioFile sudAudioFile;
-	
-	private PamPanel sudAudioPanel;
+
+	private SudSettingsPanel sudAudioPanel;
 
 	public SudAudioSettingsPane(SudAudioFile sudAudioFile) {
 		this.sudAudioFile=sudAudioFile; 
@@ -32,10 +40,69 @@ public class SudAudioSettingsPane implements PamAudioSettingsPane {
 	}
 
 	private void createSudAudioPanel() {
-		sudAudioPanel = new PamPanel(); 
+		sudAudioPanel = new SudSettingsPanel(); 
+	}
+
+	public void setParams(PamSudParams sudParams) {
+		//System.out.println("Set SUD PARAMS: " + sudParams + "  " + sudParams.zeroPad); 
+		if (sudAudioPanel!=null) sudAudioPanel.setParams(sudParams);; 
+
+	}
+	
+	public PamSudParams getParams(PamSudParams sudParams) {
+		//System.out.println("Get SUD PARAMS: " + sudParams + "  " + sudParams.zeroPad); 
+
+		if (sudAudioPanel!=null)  return sudAudioPanel.getParams(sudParams);; 
+		return null;
+	}
+
+
+	/**
+	 * The sud settings panel. 
+	 */
+	public class SudSettingsPanel extends PamPanel {
 		
-		sudAudioPanel.add(new JLabel("Hello"));
+		private static final long serialVersionUID = 1L;
 		
+		private JCheckBox zeroPadSud; 
+
+		public SudSettingsPanel() {
+			
+			this.setLayout(new GridBagLayout());
+//			soundTrapDate.setPreferredSize(tzPanel.getPreferredSize());
+			GridBagConstraints c = new PamGridBagContraints();
+			c.gridy = 0;
+			c.gridx = 0;
+			c.gridwidth = 1;
+			
+			zeroPadSud = new JCheckBox("Zero pad sud files"); 
+			zeroPadSud.setToolTipText("Zero pad sud files. Zero padding replaces sections of sud files \n"
+									+ "with corrupt or no data with zeros. This can improve time drift. ");
+						
+			this.add(zeroPadSud,c);
+		}
+		
+		public void setParams(PamSudParams sudParams) {
+			this.zeroPadSud.setSelected(sudParams.zeroPad);
+		}
+		
+		
+		public PamSudParams getParams(PamSudParams sudParams) {
+			sudParams.zeroPad = zeroPadSud.isSelected();
+			return sudParams;
+		}
+
+	}
+
+
+	@Override
+	public void getParams() {
+		getParams(sudAudioFile.getSudParams());
+	}
+
+	@Override
+	public void setParams() {
+		setParams(sudAudioFile.getSudParams());
 	}
 
 }