SUD Processing

Extraction of SUD file clicks with SoundTrap Click Detector. Timing now
correct. Added some help pages.

src/Acquisition/AcquisitionControl.java

@@ -54,6 +54,7 @@ import asiojni.NewAsioSoundSystem;
 import nidaqdev.NIDAQProcess;
 import Acquisition.filedate.FileDate;
 import Acquisition.filedate.StandardFileDate;
+import Acquisition.filetypes.SoundFileTypes;
 import Acquisition.layoutFX.AquisitionGUIFX;
 import Acquisition.offlineFuncs.OfflineWavFileServer;
 import Acquisition.rona.RonaOfflineFileServer;
@@ -138,6 +139,8 @@ public class AcquisitionControl extends PamControlledUnit implements PamSettings
 	
 	private SUDNotificationManager sudNotificationManager;
 	
+	protected SoundFileTypes soundFileTypes;
+	
 	/**
 	 * Main control unit for audio data acquisition.
 	 * <p>
@@ -162,6 +165,8 @@ public class AcquisitionControl extends PamControlledUnit implements PamSettings
 
 		pamController = PamController.getInstance();
 		
+		soundFileTypes = new SoundFileTypes(this);
+		
 		registerDaqSystem(new SoundCardSystem(this));
 		if (PlatformInfo.calculateOS() == OSType.WINDOWS) {
 			registerDaqSystem(new ASIOSoundSystem(this));

src/Acquisition/FileInputSystem.java

@@ -16,6 +16,8 @@ import java.io.IOException;
 import java.io.Serializable;
 import java.text.DateFormat;
 import java.util.Calendar;
+import java.util.List;
+
 import javax.sound.sampled.AudioFormat;
 import javax.sound.sampled.AudioInputStream;
 import javax.sound.sampled.UnsupportedAudioFileException;
@@ -53,6 +55,7 @@ import wavFiles.ByteConverter;
 import Acquisition.filedate.FileDate;
 import Acquisition.filedate.FileDateDialogStrip;
 import Acquisition.filedate.FileDateObserver;
+import Acquisition.filetypes.SoundFileType;
 import Acquisition.pamAudio.PamAudioFileManager;
 import Acquisition.pamAudio.PamAudioFileFilter;
 import PamController.PamControlledUnitSettings;
@@ -145,6 +148,11 @@ public class FileInputSystem  extends DaqSystem implements ActionListener, PamSe
 
 	protected FileDateDialogStrip fileDateStrip;
 	
+	/**
+	 * Sound file types present in the current selections.
+	 */
+	private List<SoundFileType> selectedFileTypes;
+
 	/**
 	 * Text field for skipping initial few seconds of a file. 
 	 */
@@ -400,6 +408,9 @@ public class FileInputSystem  extends DaqSystem implements ActionListener, PamSe
 		if (newFile.length() == 0) return;
 
 		File file = new File(newFile);
+		
+		setSelectedFileTypes(acquisitionControl.soundFileTypes.getUsedTypes(file));
+		
 		if (file == null) return;
 
 		// try to work out the date of the file
@@ -1222,4 +1233,27 @@ public class FileInputSystem  extends DaqSystem implements ActionListener, PamSe
 			getDialogPanel();
 		}
 	}
+
+	/**
+	 * @return the selectedFileTypes
+	 */
+	public List<SoundFileType> getSelectedFileTypes() {
+		return selectedFileTypes;
+	}
+
+	/**
+	 * Called when the file or file list selection is changes and finds a list of all
+	 * sound file types included in the selection. this is only implemented for SUD files
+	 * at the moment, the idea being to offer some additional functionality. 
+	 * @param selectedFileTypes the selectedFileTypes to set
+	 */
+	public void setSelectedFileTypes(List<SoundFileType> selectedFileTypes) {
+		this.selectedFileTypes = selectedFileTypes;
+		if (selectedFileTypes == null) {
+			return;
+		}
+		for (SoundFileType aType : selectedFileTypes) {
+			aType.selected(this);
+		}
+	}
 }

src/Acquisition/FolderInputSystem.java

@@ -10,6 +10,8 @@ import java.awt.event.ActionListener;
 import java.io.File;
 import java.io.Serializable;
 import java.util.ArrayList;
+import java.util.List;
+
 import javax.sound.sampled.AudioFormat;
 import javax.sound.sampled.AudioInputStream;
 import javax.swing.BoxLayout;
@@ -495,6 +497,9 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings{
 //				fileListData.getFileCount(), System.currentTimeMillis() - wavListStart);
 		allFiles = fileListData.getListCopy();
 		
+		List<WavFileType> asList = allFiles;
+		setSelectedFileTypes(acquisitionControl.soundFileTypes.getUsedTypes(allFiles));
+
 		setFileDateText();
 		// also open up the first file and get the sample rate and number of channels from it
 		// and set these

src/Acquisition/filetypes/SUDFileType.java

@@ -0,0 +1,29 @@
+package Acquisition.filetypes;
+
+import Acquisition.FileInputSystem;
+import PamView.dialog.warn.WarnOnce;
+
+public class SUDFileType extends SoundFileType {
+
+	private boolean isShown = false;
+
+	private String sudInfoText = "<html>There are SoundTrap SUD files in your selection. PAMGuard can now process data from these " +
+			"directly with no need to unpack them into WAV files. " + 
+			"<p>If the SoundTrap was running with the click detector, then you should add a SoundTrap Click Detector module" +
+			" and detected clicks will automatically be extracted to binary files while processing the wav data." +
+			"<p>See the Click Detector help for further details";
+
+	public SUDFileType() {
+		super(".sud");
+	}
+
+	@Override
+	public void selected(FileInputSystem fileInputSystem) {
+		if (isShown) {
+			return;
+		}
+		WarnOnce.showWarning("SoundTrap SUD Files", sudInfoText, WarnOnce.OK_OPTION);
+		isShown = true;		
+	}
+
+}

src/Acquisition/filetypes/SoundFileType.java

@@ -0,0 +1,65 @@
+package Acquisition.filetypes;
+
+import java.io.File;
+import java.util.List;
+
+import Acquisition.FileInputSystem;
+import Acquisition.pamAudio.PamAudioFileFilter;
+import PamUtils.worker.filelist.WavFileType;
+
+/**
+ * Some functions for the File and Folder input systems to give a bit of 
+ * extra functionality / help for different file types. Primarily introduced 
+ * to give a couple of extras for sud files. 
+ * @author dg50
+ *
+ */
+public abstract class SoundFileType {
+
+	private String fileType;
+	
+	private PamAudioFileFilter fileFilter = new PamAudioFileFilter();
+
+	public SoundFileType(String fileType) {
+		this.fileType = fileType.toLowerCase();
+	}
+	
+	/**
+	 * Work out if any files of this type are included in the current selection. 
+	 * @param fileOrFolder this for a single file. 
+	 * @param includeSubfolders used with folders. 
+	 * @return true if any exist. 
+	 */
+	public boolean isFileType(File oneFile) {
+		if (oneFile == null) {
+			return false;
+		}
+		if (oneFile.isFile()) {
+			return oneFile.getName().toLowerCase().endsWith(fileType);
+		}
+		
+		return false;
+	}
+
+	/**
+	 * Work out if any files of this type are included in the current selection. 
+	 * @param fileOrFolder this for a single file. 
+	 * @param includeSubfolders used with folders. 
+	 * @return true if any exist. 
+	 */
+	public boolean hasFileType(List<WavFileType> files) {
+		if (files == null) {
+			return false;
+		}
+		for (File aFile : files) {
+			if (isFileType(aFile)) {
+				return true;
+			}
+		}
+		
+		return false;
+	}
+
+	public abstract void selected(FileInputSystem fileInputSystem);
+
+}

src/Acquisition/filetypes/SoundFileTypes.java

@@ -0,0 +1,74 @@
+package Acquisition.filetypes;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import Acquisition.AcquisitionControl;
+import PamUtils.worker.filelist.WavFileType;
+
+/**
+ * List of SoundFileType objects. 
+ * @author dg50
+ *
+ */
+public class SoundFileTypes {
+
+	private AcquisitionControl acquisitionControl;
+	
+	private ArrayList<SoundFileType> availableTypes = new ArrayList<>();
+
+	public SoundFileTypes(AcquisitionControl acquisitionControl) {
+		this.acquisitionControl = acquisitionControl;
+		availableTypes.add(new SUDFileType());
+	}
+
+	/**
+	 * Get a list of used file types. Reaslistically this 
+	 * can only return one value. 
+	 * @param aFile
+	 * @return
+	 */
+	public SoundFileType getFileType(File aFile) {
+		ArrayList<SoundFileType> usedTypes = new ArrayList<>();
+		for (SoundFileType aType : availableTypes) {
+			if (aType.isFileType(aFile)) {
+				return aType;
+			}
+		}
+		return null;
+	}
+	
+	/**
+	 * Get a list of used file types. Reaslistically this 
+	 * can only return one value but possibly it's useful to have it in the same
+	 * format as the multiple file version. . 
+	 * @param aFile
+	 * @return
+	 */
+	public List<SoundFileType> getUsedTypes(File aFile) {
+		ArrayList<SoundFileType> usedTypes = new ArrayList<>();
+		for (SoundFileType aType : availableTypes) {
+			if (aType.isFileType(aFile)) {
+				usedTypes.add(aType);
+			}
+		}
+		return usedTypes;
+	}
+
+	/**
+	 * Get a list of used file types for the folder Input System. 
+	 * @param aFile
+	 * @return
+	 */
+	public List<SoundFileType> getUsedTypes(List<WavFileType> aFile) {
+		ArrayList<SoundFileType> usedTypes = new ArrayList<>();
+		for (SoundFileType aType : availableTypes) {
+			if (aType.hasFileType(aFile)) {
+				usedTypes.add(aType);
+			}
+		}
+		return usedTypes;
+	}
+
+}

src/PamUtils/PamAudioFileFilter.java

@@ -17,7 +17,7 @@ public class PamAudioFileFilter extends PamFileFilter {
 //		addFileType(".AIFF");
 //		addFileType(".FLAC");
 		addFileType(".flac");
-//		addFileType(".sud");
+		addFileType(".sud");
 	}
 
 }

src/help/JavaHelpSearch/SCHEMA

@@ -1,2 +1,2 @@
 JavaSearch 1.0
-TMAP bs=2048 rt=1 fl=-1 id1=6679 id2=1
+TMAP bs=2048 rt=1 fl=-1 id1=6697 id2=1

src/help/Map.jhm

@@ -574,6 +574,8 @@
 
 <mapID target="utilities.SIDEModule.docs.SIDE_Overview_seq" url="utilities/SIDEModule/docs/SIDE_Overview.html#seq"/>
 
+<mapID target="detectors.clickDetectorHelp.docs.SoundTrapClickDetector" url="detectors/clickDetectorHelp/docs/SoundTrapClickDetector.html"/>
+
 <mapID target="utilities.spectrogramannotations.docs.using" url="utilities/spectrogramannotations/docs/using.html"/>
 
 <mapID target="visual_methods.loggerFormsHelp.docs.NMEAINT" url="visual_methods/loggerFormsHelp/docs/NMEAINT.html"/>
@@ -802,6 +804,8 @@
 
 <mapID target="visual_methods.loggerFormsHelp.docs.NMEACHAR" url="visual_methods/loggerFormsHelp/docs/NMEACHAR.html"/>
 
+<mapID target="sound_processing.AcquisitionHelp.docs.sudfiles" url="sound_processing/AcquisitionHelp/docs/sudfiles.html"/>
+
 <mapID target="sound_processing.LTSA.Docs.LTSADisplays" url="sound_processing/LTSA/Docs/LTSADisplays.html"/>
 
 <mapID target="localisation.difar.difarLocalisation.docs.difar_PostProcessingTutorial__Toc396467156" url="localisation/difar/difarLocalisation/docs/difar_PostProcessingTutorial.html#_Toc396467156"/>

src/help/PAMGUARD.hs

@@ -16,6 +16,11 @@
   
   
   
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src/help/PAMGUARDIndex.xml

@@ -2,6 +2,8 @@
 <!DOCTYPE index PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp Index Version 1.0//EN" "http://java.sun.com/products/javahelp/index_2_0.dtd"><!--generated by JHelpDev Version: 0.63, 14 May 2008, see jhelpdev.sourceforge.net-->
 
 <index version="1.0">
+ <indexitem text="SoundTrap " target="detectors.clickDetectorHelp.docs.SoundTrapClickDetector"/>
+
  <indexitem text="3D Localisation " target="detectors.Pam3DHelp.docs.guiOverview"/>
 
  <indexitem text="Adding or Editing a Hydrophone " target="utilities.hydrophoneArrayManagerHelp.docs.Array_NewHydrophone"/>

src/help/PAMGUARDTOC.xml

@@ -278,8 +278,10 @@
 
    <tocitem text="Asio Sound Cards " target="sound_processing.AcquisitionHelp.docs.AcquisitionAsioSoundCard" image="topic"/>
 
-   <tocitem text="Audio Files " target="sound_processing.AcquisitionHelp.docs.AcquisitionFile" image="topic"/>
+   <tocitem text="Audio Files " target="sound_processing.AcquisitionHelp.docs.AcquisitionFile" image="topic">
+    <tocitem text="SUD Files " target="sound_processing.AcquisitionHelp.docs.sudfiles" image="topic"/>
 
+   </tocitem>
    <tocitem text="Audio File Folders " target="sound_processing.AcquisitionHelp.docs.AcquisitionFileFolder" image="topic"/>
 
    <tocitem text="File Dates " target="sound_processing.AcquisitionHelp.docs.FileTimeZone" image="topic"/>
@@ -426,6 +428,8 @@
     <tocitem text="Create Binary Files Offline " target="utilities.BinaryStore.docs.CreateBinariesOffline" image="topic"/>
 
    </tocitem>
+   <tocitem text="SoundTrap Click Detector " target="detectors.clickDetectorHelp.docs.SoundTrapClickDetector" image="topic"/>
+
   </tocitem>
   <tocitem text="Whistle and Moan Detector ">
    <tocitem text="Overview " target="detectors.whistleMoanHelp.docs.whistleMoan_Overview" image="topic"/>

src/help/detectors/clickDetectorHelp/docs/SoundTrapClickDetector.html

@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html><head>
+<link href="../../../pamHelpStylesheet.css" type="text/css" rel="STYLESHEET"><title>Click Classification</title></head>
+<body><h1>
+SoundTrap Click Detector
+</h1><h2>SoundTrap Click Detector</h2>
+<br>
+
+<h3>Overview</h3>
+<p>If you are using a SountTrap recording device with built in click detection from 
+<a href="https://www.oceaninstruments.co.nz/">Ocean Instruments</a>, 
+you may need to use a modified version of the <a href="ClickDetector_clickDetector.html">Click Detector</a>. 
+</p>
+<p>The SoundTrap click detector allows you to detect and store clicks at high frequencies (say 384kHz), suitable for odontocete echolocation clicks, and 
+at the same time, record audio data files at a lower frequency (e.g. 96 or 48kHz). This optimises disk space usage and makes long deployments 
+of several months possible with moderate data storage. </p> 
+<p>Having two sample rates present within a single PAMGuard configuration is possible, using 
+<a href="../../../sound_processing/decimatorHelp/docs/decimator_decimator.html">Decimator</</a> modules, however such configurations become particularly
+complicated to configure when the sample rate of the recorded files is lower than the sample rate of the click detector.</p>
+<p>We therefore recommend that you use a modified version of the <a href="ClickDetector_clickDetector.html">Click Detector</a>which manages it's own sample rate and 
+channel information based on information extracted from the SoundTrap data.</p>
+<p>Note that the SoundTrap click detector should only be used for clicks automatically detected by the SoundTrap. If you want to detect clicks from the 
+SoundTrap recordings, then use a normal <a href="ClickDetector_clickDetector.html">Click Detector</a> in the normal way.</p>
+
+
+	<h3>Creating an instance of the SoundTrap Click Detector</h3>
+
+	<p>
+		From the <strong><em>File>Add modules>Detectors</em></strong> menu, or
+		from the pop-up menu on the data model display, select <i>'SoundTrap Click
+			Detector'</i> near the bottom of the list. Enter a descriptive name for the new detector and press Ok.
+	</p>
+	
+	<h3>Importing SoundTrap Data</h3>
+	<p>SoundTrap data are stored in proprietary files called <a href="../../../sound_processing/AcquisitionHelp/docs/sudfiles.html">SUD files</a>.</p>
+	<p> There are two ways in which you can get data from <a href="../../../sound_processing/AcquisitionHelp/docs/sudfiles.html">SUD files</a> into
+	the SoundTrap Click Detector. </p> 
+	  
+	<h4>The Old Way</h4>
+	<p>The 'standard' way of using SoundTrap data was to inflate all of the data from the compressed SUD files. For details of this process, see the 
+	SoundTrap user manuals and the SoundTrap Host software.</p>
+	<p>Normally, several inflated files are generated from each sud file:</p>
+	<ol>
+	 <li>A wav file: Audio data in standard wav file format</li>
+	 <li>An XML file: Metadata on the SoundTrap configuration, file start times in various formats, etc.</li>
+	 <li>If the click detector was running BCL and DWV files, which contain the times of clicks and click waveforms respectively.</li>
+	 </ol>
+	 <p>To convert the SUD files to the binary storage format used by PAMGuard, working in the 
+	 <a href="../../../overview/PamMasterHelp/docs/viewerMode.html">PAMGuard Viewer</a>, create a Binary Store, a 
+	 SoundTrap Click Detector and also create a  'SoundTrap Detector Import' module. Then use the import module to import the BCL and DWV 
+	 data into PAMGuard. Once imported you can run <a href="ClickDetector_clickClassification.html">Click Classifiers</a>
+	  and use other Click Detector offline functions to mark events, etc. </p>
+	 <p>If you want to run additional analysis on the WAV file data (for example to make noise measurements or to detect whistles), 
+	 create a different PAMGuard configuration to process those data.<p>
+
+	<h4>The (better) New Way</h4>
+	<p>Current versions of PAMGuard can read SUD files directly, without first unpacking them into WAV, XML, BCL and DWV files. This not 
+	only reduces the amount of disk space you need by about x4, but also saves a lot of time.</p>
+	<p>Better still, you can now set up PAMGuard in normal mode to simultaneously process the audio data in the sud file with one set of 
+	detectors, and simultaneously extract the click detector data into appropriate files for a SoundTrap Click Detector. </p>
+	
+	<p>Start PAMGuard in <a href="../../../overview/PamMasterHelp/docs/normalMode.html">Normal Mode</a> and add a 
+	<a href="../../../sound_processing/AcquisitionHelp/docs/AcquisitionOverview.html">Sound Acquisition</a> module. 
+	Add a SoundTrap Click Detector, a <a href="../../../utilities/BinaryStore/docs/binarystore_overview.html">Binary Store</a> store and a 
+	<a href="../../../utilities/generalDatabaseHelp/docs/database_database.html">Database</a> 
+	module (optional). In the <a href="../../../sound_processing/AcquisitionHelp/docs/AcquisitionConfiguration.html">Sound Acquisition dialog</a>
+	 select a single SUD file or a folder of SUD files. At this point, the SoundTrap 
+	Click Detector will be automatically configured with the correct sample rate (which won't be the sample rate displayed in the Sound Acquisition
+	module). </p>
+	<p>Configure any <a href="ClickDetector_clickClassification.html">Click Classifiers</a> you want to be run on the SoundTrap click data as it is imported.</p>
+	<p>You can then add any other detectors and measurement processes you want to run on the SoundTrap audio data, this may include 
+	instances of the normal Click Detector module if you want to detect clicks in the lower frequency audio data.</p>
+	<p>Process the data in the normal way and clicks will automatically be generated within the SoundTrap click detector</p>
+	<p>Further process you data using the <a href="../../../overview/PamMasterHelp/docs/viewerMode.html">PAMGuard Viewer</a> in the normal way.</p>  
+	
+	
+<br>
+<br>
+<br>
+</body></html>

src/help/sound_processing/AcquisitionHelp/docs/AcquisitionFile.html

@@ -7,7 +7,9 @@
 
 <h1>Audio Files</h1>
 <p>As well as analysing data from sound cards in real time, PAMGUARD can be used to analyse archived data
-from audio filed in WAV or AIF format.</p>
+from audio filed in <a href="https://en.wikipedia.org/wiki/WAV">WAV</a>,
+ <a href="https://en.wikipedia.org/wiki/Audio_Interchange_File_Format">AIF</a>, <a href="https://en.wikipedia.org/wiki/FLAC">FLAC</a>, 
+ or <a href="sudfiles.html">SUD</a> file format.</p>
 
 <br>
 <h2>Setting up an Audio File</h2>

src/help/sound_processing/AcquisitionHelp/docs/sudfiles.html

@@ -0,0 +1,27 @@
+<html>
+<head>
+<LINK href="../../../pamHelpStylesheet.css" type=text/css rel=STYLESHEET>
+<title>SUD Files</title>
+</head>
+<body>
+<h1>SoundTrap data files</h1>
+<h3>SUD Files</h3>
+<p>
+SoundTrap recorders from 
+<a href="https://www.oceaninstruments.co.nz/">Ocean Instruments</a>
+ store data in proprietary files called SUD files. See SoundTrap documentation for information on how to 
+ extract SUD files from SoundTrap recorders. </p>
+ 
+ <p>Earlier versions of PAMGuard required you to 'inflate' the SUD files into standard wav audio files using 
+ the <a href="https://www.oceaninstruments.co.nz/downloads/">SoundTrap Host software</a> before they could be processed.</p>
+ <p>The current version of PAMGuard no longer requires this since it can read data directly from the SUD files.</p>
+ <p>Inflating SUD files to WAV files generally required between 3 and 5 times as much disk space and could also take 
+ a fair amount of time, so not inflating will save both!</p>
+ 
+ <h3>SoundTrap Click Detector</h3>
+ <p>If you are using the SoundTrap build in click detector (see SoundTrap manuals) then the SUD files will also contain 
+ detected clicks.</p> <p>See the help page for the <a href="../../../detectors/clickDetectorHelp/docs/SoundTrapClickDetector.html">SoundTrap Click Detector</a> 
+ for information on how to get these clicks from the SUD files into PAMGuard. </p>
+<br><br><br>
+</body>
+</html>

src/soundtrap/sud/SudFileDWVHandler.java

@@ -216,6 +216,7 @@ public class SudFileDWVHandler implements SUDNotificationHandler {
 
 //		channelGroupDetector = clickDetector.getChannelGroupDetector(0);
 		ClickDetection click = new ClickDetection(1, elapsedSamples, nSamples, clickDetector, channelGroupDetector, 1);
+		click.setTimeMilliseconds(millis);
 		click.setWaveData(wavData);
 
 //		if (groupDetector != null) {