Merge pull request #82 from PAMGuard/main

Merge from main

.externalToolBuilders/net.sourceforge.metrics.builder.launch

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.ant.AntBuilderLaunchConfigurationType">
+    <booleanAttribute key="org.eclipse.ui.externaltools.ATTR_BUILDER_ENABLED" value="false"/>
+    <stringAttribute key="org.eclipse.ui.externaltools.ATTR_DISABLED_BUILDER" value="net.sourceforge.metrics.builder"/>
+    <mapAttribute key="org.eclipse.ui.externaltools.ATTR_TOOL_ARGUMENTS"/>
+    <booleanAttribute key="org.eclipse.ui.externaltools.ATTR_TRIGGERS_CONFIGURED" value="true"/>
+</launchConfiguration>

.project

@@ -11,8 +11,13 @@
 			</arguments>
 		</buildCommand>
 		<buildCommand>
-			<name>net.sourceforge.metrics.builder</name>
+			<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+			<triggers>full,incremental,</triggers>
 			<arguments>
+				<dictionary>
+					<key>LaunchConfigHandle</key>
+					<value>&lt;project&gt;/.externalToolBuilders/net.sourceforge.metrics.builder.launch</value>
+				</dictionary>
 			</arguments>
 		</buildCommand>
 		<buildCommand>

README.html

@@ -388,7 +388,7 @@ PamguardBeta_ViewerMode.exe):</p>
 <h1><a name="_LATEST_VERSION_2.02.03"></a><a name="_VERSION_2.02.07_January"></a><a
 name="_Latest_Version_2.02.10"></a><em><span style='font-size:12.0pt;
 font-family:"Cambria",serif;font-style:normal'><a href="#_Version_2.02.11_April">Latest
-Version 2.03.00 June 2024</a></span></em></h1>
+Version 2.02.11 May 2024</a></span></em></h1>
 
 <h1><em><span style='font-size:12.0pt;font-family:"Cambria",serif;font-style:
 normal'><a href="#_Version_2.02.10_January">Version 2.02.10 January 2024</a></span></em></h1>
@@ -465,7 +465,7 @@ Version 2.00.10 June 2017</a></span></h1>
 name="_Latest_Version_2.02.06"></a><a name="_Latest_Version_2.02.07"></a><a
 name="_Latest_Version_2.02.08"></a><a name="_Version_2.02.09_June"></a><a
 name="_Version_2.02.10_January"></a><a name="_Version_2.02.11_April"></a>Version
-2.03.00 June 2024</h1>
+2.02.11 May 2024</h1>
 
 <p class=MsoNormal>&nbsp;</p>
 
@@ -474,11 +474,22 @@ name="_Version_2.02.10_January"></a><a name="_Version_2.02.11_April"></a>Version
 <p class=MsoNormal>Deep Learning Classifier. Major upgrade to support for Deep
 Learning models in PAMGuard. See online help for details.</p>
 
-<p class=MsoNormal>Click detector: Remembers locations of displays and doesn’t
+<p class=MsoNormal>Click detector: Remembers locations of displays and doesn’t
 continually reset them. </p>
 
 <p class=MsoNormal>Help for Matched Click Classifier.</p>
 
+<p class=MsoNormal>Project information dialog. This allows capture of essential
+project information to store with your data. See menu item Settings/Project
+information.</p>
+
+<h2>Tethys Database</h2>
+
+<p class=MsoNormal>Many users will be aware that we’re integrating an interface
+to the <a href="https://tethys.sdsu.edu/">Tethys Database</a> into PAMGuard.
+Some basic features are available for testing. If interested, please contact
+the PAMGuard support team. </p>
+
 <h2>Bug Fixes</h2>
 
 <p class=MsoNormal>Linking clicks to offline clicks table. We had a database
@@ -500,14 +511,20 @@ as PAMGuard stops / restarts. </p>
 function fixed and now inserts correct times of start and ends of events into
 database. </p>
 
-<p class=MsoNormal>Acquisition “Skip initial seconds” feature, designed to
+<p class=MsoNormal>Clip generator. Changes to ensure PAMGuard keeps audio data
+long enough to make clips. In some circumstances data were being discarded too
+early so clips could not be created. </p>
+
+<p class=MsoNormal>Acquisition “Skip initial seconds” feature, designed to
 remove high sample levels e.g. from calibration tones at start of a soundtrap
 recording was not working with the click detector. This is fixed but replacing
-all data with 0’s and still sending data. Note that this may lead to
+all data with 0’s and still sending data. Note that this may lead to
 artificially low noise measures at the start of a file. </p>
 
 <p class=MsoNormal>Data reprocessing options. Updated to ensure that the option
 &quot;Start normally. Note risk of overwriting!&quot; is always available. Also
+improved code naming binary files to attempt to push them to exact times,
+rather than a couple of seconds after the hour. </p>
 improved code naming binary files to attempt to push them to exact times, rather
 than a couple of seconds after the hour. </p>
 
@@ -531,8 +548,8 @@ files) file performance</span></b><span lang=EN-US> when scrolling through
 audio data in Viewer mode. </span></p>
 
 <p class=MsoNormal><b><span lang=EN-US>Viewer Launch</span></b><span
-lang=EN-US> by right clicking on sqlite database and selecting “open with /
+lang=EN-US> by right clicking on sqlite database and selecting “open with /
-Pamguard ViewerMode” launcher menu option.</span></p>
+Pamguard ViewerMode” launcher menu option.</span></p>
 
 <h2><span lang=EN-US>Bug Fixes</span></h2>
 
@@ -580,7 +597,7 @@ clicks not being correctly reassigned to different events. </span></p>
 
 <p class=MsoNormal><b><span lang=EN-US>Screen Position</span></b><span
 lang=EN-US>: When using multiple monitors, if you move a configuration to a
-computer with a different monitor layout, the GUI should work out if it’s
+computer with a different monitor layout, the GUI should work out if it’s
 opening on a screen area which no longer exists and move itself onto the
 primary monitor. </span></p>
 
@@ -588,7 +605,7 @@ primary monitor. </span></p>
 lang=EN-US>: Previous version had a bug which caused files to not always be
 sorted into the correct order for processing. This caused some instability in
 some detectors, causing memory leaks when new data arrived with time stamps
-earlier than already processed data in memory. This is now fixed – files are ow
+earlier than already processed data in memory. This is now fixed – files are ow
 correctly sorted alphabetically </span>by file name, i.e. not including the
 name of the folder containing the files.</p>
 
@@ -610,8 +627,8 @@ were reading local time, even when set to use UTC. </span></p>
 which mostly occurred when processing large datasets of many offline files, has
 been fixed.</span></p>
 
-<p class=MsoNormal><span lang=EN-US>Data Map: “Scroll To Data” pop-up menu, which
+<p class=MsoNormal><span lang=EN-US>Data Map: “Scroll To Data” pop-up menu, which
-didn’t always scroll to the correct place, is now fixed. </span></p>
+didn’t always scroll to the correct place, is now fixed. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>Bearing Localiser offline: If reprocessing
 bearings, the localizer was not correctly loading required raw or FFT data to
@@ -634,7 +651,7 @@ files and stores them within the PAMGuard configuration. This does not affect
 processing, but is important for record keeping. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>GPS options to use any valid RMC or GGA
-string. Not all GPS receivers output their RMC data as GPRMC – e.g. some may
+string. Not all GPS receivers output their RMC data as GPRMC – e.g. some may
 output as GNRMC. A new option allows the GPS module to use any string, whatever
 the first two characters of the string name may be. </span></p>
 
@@ -643,14 +660,14 @@ the first two characters of the string name may be. </span></p>
 <h2><span lang=EN-US>Bug Fixes</span></h2>
 
 <p class=MsoNormal><span lang=EN-US>Use of localization sensor and orientation
-data for static hydrophones had a bug whereby it would continually ‘forget’
+data for static hydrophones had a bug whereby it would continually ‘forget’
 angle offsets applied to static hydrophones in viewer mode. This is now fixed. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>Click tool bar: Correctly shows event
 selection options even if no species classification options are in place. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>Fixed Landmarks: Earlier versions were
-‘losing’ these every time PAMGuard started or new data were loaded in viewer
+‘losing’ these every time PAMGuard started or new data were loaded in viewer
 mode. Now fixed. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>ROCCA: Fixed (another) memory leak which
@@ -669,11 +686,11 @@ processing.</span></p>
 
 <p class=MsoNormal><span lang=EN-US>New sound type for simulated sounds which
 generates random chirps between around 200 and 800Hz, roughly the frequency
-you’d expect sound from higher frequency baleen whales, such as humpbacks, to
+you’d expect sound from higher frequency baleen whales, such as humpbacks, to
 vocalise at. &nbsp;&nbsp;</span></p>
 
 <p class=MsoNormal><span lang=EN-US>Hiding tool tips. A menu item to
-permanently turn off all tool tips, or tap the ‘Esc’ key to turn them off for 6
+permanently turn off all tool tips, or tap the ‘Esc’ key to turn them off for 6
 seconds if they are getting in the way, particularly when trying to interact
 with displays using the mouse. </span></p>
 
@@ -694,7 +711,7 @@ whistle classification module.</span></p>
 
 <h2><span lang=EN-US>New Features</span></h2>
 
-<p class=MsoNormal><span lang=EN-US>SoundTrap SUD file reading. If you’re using
+<p class=MsoNormal><span lang=EN-US>SoundTrap SUD file reading. If you’re using
 SoundTrap autonomous recorders from Ocean Instruments, you no longer need to
 decompress the SoundTrap files prior to processing. This will save time and a
 lot of disk space. Extraction of clicks from the inbuilt SoundTrap Click
@@ -711,8 +728,8 @@ details. &nbsp;&nbsp;</span></p>
 <p class=MsoNormal><span lang=EN-US>Changes to GUI to make dialog shorter for
 low DPI screens. </span></p>
 
-<p class=MsoNormal><span lang=EN-US>Complete rewrite of the classification
+<p class=MsoNormal><span lang=EN-US>Complete rewrite of the classification system
-system to have nested classifiers which can be enabled or disabled. </span></p>
+to have nested classifiers which can be enabled or disabled. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>Changes to classification GUI to
 accommodate the new classification system.</span></p>
@@ -758,7 +775,7 @@ audio files. </span></p>
 <h2><span lang=EN-US>Bug Fixes</span></h2>
 
 <p class=MsoNormal><span lang=EN-US>Soundtrap DWV import. Will now generate
-binary files even if DWV file doesn‚’t exist (which is correct behavior in
+binary files even if DWV file doesn‚’t exist (which is correct behavior in
 quiet conditions when no clicks were detected). </span></p>
 
 <p class=MsoNormal><span lang=EN-US>Spectrogram. Changes to stop occasional
@@ -793,7 +810,7 @@ running in real time. Added template names based on file names. </p>
 <p class=MsoNormal>#13 Merging files when offline processing file folders: Had
 an error introduced in last release which caused it to fail to recognise gaps
 between files, meaning that some output data (i.e. after a gap) would have an
-incorrect time stamp. This did not affect data if the ‘merge contiguous files’
+incorrect time stamp. This did not affect data if the ‘merge contiguous files’
 option was not selected. </p>
 
 <p class=MsoNormal>#14 Logger forms data were not plotting correctly. This was
@@ -803,9 +820,9 @@ selections from drop down lists within any form.</p>
 
 <p class=MsoNormal>&nbsp;</p>
 
-<p class=MsoNormal>Note that updates have also been made to the Matlab
+<p class=MsoNormal>Note that updates have also been made to the Matlab interface
-interface to PAMGuard binary files, which has now also been migrated to GitHub
+to PAMGuard binary files, which has now also been migrated to GitHub at <a
-at <a href="https://github.com/PAMGuard/PAMGuardMatlab">https://github.com/PAMGuard/PAMGuardMatlab</a>.
+href="https://github.com/PAMGuard/PAMGuardMatlab">https://github.com/PAMGuard/PAMGuardMatlab</a>.
 </p>
 
 <h1>&nbsp;</h1>
@@ -866,7 +883,7 @@ href="http://www.pamguard.org/downloads.php?cat_id=3">here</a>.</p>
 <p class=MsoNormal><b><span lang=EN-US>Detection Group Localiser</span></b><span
 lang=EN-US> </span></p>
 
-<p class=MsoNormal>This module has been renamed “Detection Grouper”, so as to
+<p class=MsoNormal>This module has been renamed “Detection Grouper”, so as to
 avoid confusion with the Group 3D localizer. This is because the Detection
 Grouper is more for organizing data into groups to be localized than it is for
 doing localization.</p>
@@ -989,9 +1006,9 @@ included in a future release. </p>
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>17. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
 lang=EN-US> </span>An implementation of the Generalized Power Law Detector,
-developed by Tyler Helble ([Helble et al., ‘A generalized power-law detection
+developed by Tyler Helble ([Helble et al., ‘A generalized power-law detection
-algorithm for humpback whale vocalizations’, The Journal of the Acoustical
+algorithm for humpback whale vocalizations’, The Journal of the Acoustical
-Society of America, vol. 131, no. 4, pp. 2682–2699, 2012) is now available. For
+Society of America, vol. 131, no. 4, pp. 2682–2699, 2012) is now available. For
 details, see the online help </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>18. </span><span
@@ -2264,7 +2281,7 @@ file format is the addition of a Unique Data Identifier (UID) to each unit of
 data. This is intended to aid in offline analysis by making it easier for the
 user to link what they are seeing on different PAMGuard displays and also to
 link with any data post processed in Matlab or other custom analysis software.
-UID’s are also added to PAMGuard database tables. </span></p>
+UID’s are also added to PAMGuard database tables. </span></p>
 
 <h4><span lang=EN-US>Converting Old Data</span></h4>
 
@@ -2272,13 +2289,13 @@ UID
 viewer they will automatically be converted. For safety, the original binary
 files will not be overwritten and the new data will be placed in a new folder
 on your computer with the same path as the old data, but suffixed with
-‘_WithUID’, e.g. if your binary data were previously stored in the folder
+‘_WithUID’, e.g. if your binary data were previously stored in the folder
 C:\MySurvey\binarydata the new data will be written to
 C:\MySurvey\binarydata_WithUID. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>The additional UID column will be added to
 all database tables and populated with unique values. For data which are stored
-in both the binary files and in database tables, the same UID’s will be used in
+in both the binary files and in database tables, the same UID’s will be used in
 both data stores. </span></p>
 
 <h3><span lang=EN-US>New Displays</span></h3>
@@ -2342,10 +2359,10 @@ lang=EN-US>&nbsp;</span></p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>1.</span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span><span lang=EN-US>Bug 317. Rocca Module Data Purging. </span>The ROCCA
+</span><span lang=EN-US>Bug 317. Rocca Module Data Purging. </span>The ROCCA module
-module was not performing data purging when using classifiers developed for Hawaii/Temperate
+was not performing data purging when using classifiers developed for
-Pacific/North Atlantic datasets. This has been corrected.</p>
+Hawaii/Temperate Pacific/North Atlantic datasets. This has been corrected.</p>
-
+  
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2.</span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span>Bug 320. Pamguard stopped reading Click Detector Event data from database
@@ -2483,9 +2500,9 @@ dependencies)</span></p>
 
 <p class=MsoNormal><b><span lang=EN-US>Other Changes</span></b></p>
 
-<p class=MsoNormal><span lang=EN-US>The installer has been updated to handle
+<p class=MsoNormal><span lang=EN-US>The installer has been updated to handle both
-both 64 bit and 32 bit installations. PAMGuard psf files are now registered in
+64 bit and 32 bit installations. PAMGuard psf files are now registered in the
-the Windows Registry, so double-clicking on a psf file should run PAMGuard in
+Windows Registry, so double-clicking on a psf file should run PAMGuard in
 normal mode (as opposed to Viewer or Mixed modes). Note that the Windows
 Registry can only hold a single executable reference for psf files; therefore,
 for users with multiple installations of PAMGuard, double-clicking on a psf
@@ -2513,7 +2530,7 @@ November 2016</span></h1>
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>1.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 Bug 303. Some ASIO sound cards not working with either ASIO system in PAMGuard.
 For the PAMGuard ASIO system, this was due to a data format used by some sound
-cards never being properly implemented. For the “New ASIO system” which is
+cards never being properly implemented. For the “New ASIO system” which is
 based on jAsioHost, the unpacking of that format contained a bug which returned
 incorrect numbers, so data were swamped with noise. Both systems are now fixed.
 By preference, users should use the PAMGuard ASIO system since the JAsioHost
@@ -2624,8 +2641,8 @@ lang=EN-US>3.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times N
 
 <p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>4.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span><span lang=EN-US>Bug 290. Click bearings on spectrogram display plug in
+</span><span lang=EN-US>Bug 290. Click bearings on spectrogram display plug in were
-were reversed if the first hydrophone was behind the second hydrophone in the
+reversed if the first hydrophone was behind the second hydrophone in the
 configuration. This is now fixed so that it displays the same bearings as the
 main click detector display. </span></p>
 
@@ -2716,10 +2733,10 @@ since V 1.15.03:</p>
 
 <p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>1.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 272. File types: Some File Open / File Save dialogs were allowing
+</span>Bug 272. File types: Some File Open / File Save dialogs were allowing selection
-selection of all file types. e.g. Save Configuration As, Section of whistle
+of all file types. e.g. Save Configuration As, Section of whistle classifier
-classifier training file, Map file Selection, These have now been changed so
+training file, Map file Selection, These have now been changed so that only the
-that only the correct type of file can be selected.</p>
+correct type of file can be selected.</p>
 
 <p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>2.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -3111,9 +3128,9 @@ option with caution !</p>
 
 <p class=MsoListParagraph style='margin-left:47.25pt;text-indent:-29.25pt'><span
 lang=EN-US>5.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>The Open Office Database system has been removed from the list of
+</span>The Open Office Database system has been removed from the list of available
-available options since it is not reliable. If you require a free database
+options since it is not reliable. If you require a free database solution we
-solution we recommend you use the MySql Community Server <a
+recommend you use the MySql Community Server <a
 href="http://dev.mysql.com/downloads/mysql/">http://dev.mysql.com/downloads/mysql/</a></p>
 
 <p class=MsoListParagraph style='margin-left:47.25pt;text-indent:-29.25pt'><span
@@ -3305,8 +3322,8 @@ Visual Methods</p>
 <p class=MsoNormal>'<i>Multi Threading</i>' menu item moved from 'Detection'
 (now 'Settings') to 'File'</p>
 
-<p class=MsoNormal>'<i>Start</i>' and '<i>Stop</i>' menu items removed.
+<p class=MsoNormal>'<i>Start</i>' and '<i>Stop</i>' menu items removed. PAMGuard
-PAMGuard should be started and stopped using the red and black buttons.</p>
+should be started and stopped using the red and black buttons.</p>
 
 <p class=MsoNormal><b>New Modules</b></p>
 
@@ -3374,9 +3391,9 @@ help for details. </p>
 <p class=MsoNormal><i>Echo Detector and Sperm Whale IPI Computation</i> (Beta
 only, Sound Measurements Group)</p>
 
-<p class=MsoNormal>These two modules, developed by Brian Miller of the
+<p class=MsoNormal>These two modules, developed by Brian Miller of the Australian
-Australian Antarctic Division can be used to estimate the inter pulse interval
+Antarctic Division can be used to estimate the inter pulse interval of sperm
-of sperm whale clicks. (No help available)</p>
+whale clicks. (No help available)</p>
 
 <p class=MsoNormal>&nbsp;</p>
 

dependency-reduced-pom.xml

@@ -4,7 +4,7 @@
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
   <name>Pamguard</name>
-  <version>2.02.11d</version>
+  <version>2.02.11f</version>
   <description>Pamguard using Maven to control dependencies</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>2.02.11e</version>
+  <version>2.02.11f</version>
   <name>Pamguard</name>
   <description>Pamguard using Maven to control dependencies</description>
 	<url>www.pamguard.org</url>

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 = "2.02.11e";
+	static public final String version = "2.02.11f";
 	
 	/**
 	 * Release date
 	 */
-	static public final String date = "19 June 2024";
+	static public final String date = "24 June 2024";
 	
 //	/**
 //	 * Release type - Beta or Core

src/PamModel/PamModel.java

@@ -472,7 +472,7 @@ final public class PamModel implements PamSettings {
 			mi.setModulesMenuGroup(utilitiesGroup);
 			mi.setMaxNumber(1);
 			//mi.addGUICompatabilityFlag(PamGUIManager.FX); //has FX enabled GUI.
-//			mi.setHidden(SMRUEnable.isEnable() == false);
+			mi.setHidden(SMRUEnable.isEnable() == false);
 		}		
 		
 		/*

src/dataPlotsFX/rawDataPlotFX/RawSoundPlotDataFX.java

@@ -382,7 +382,7 @@ public class RawSoundPlotDataFX {
 		
 		if (soundStore.currentRawDataMillis==0){
 			if (++timeErrors < 10) {
-			System.err.println("RawSoundPlotData: Raw sound data has no associated millisecond time: "+ soundStore.currentRawDataMillis);
+//			System.err.println("RawSoundPlotData: Raw sound data has no associated millisecond time: "+ soundStore.currentRawDataMillis);
 			}
 			return;
 		}

src/help/classifiers/rawDeepLearningHelp/docs/rawDeepLearning_Bugs.html

@@ -9,8 +9,14 @@
 <body>
 	<h1 id="pamguard-s-deep-learning-module">PAMGuard&#39;s Deep
 		Learning Module</h1>
-	<h2 id="common-bugs-and-mistakes">Common Bugs and Mistakes</h2>
+
-	<br>
+	<h2 id="common-bugs-and-mistakes">Common bugs and mistakes</h2>
+	<p>The first time you use the module and/or load a different type
+		of model e.g. a tensorflow or pytorch model, you must be connected to
+		the internet.</p>
+	<p>You must install the correct version of CUDA for hardware
+		acceleration using an Nvidea GPU. See the currently supported CUDA
+		versions on the Pytorch and Tensorflow websites.</p>
 	<p>You should always have deep learning models in their own folder.
 		Do not have any additional jar files or other programming related
 		things (like .dll files) in the same or sub folders. This has been

src/help/classifiers/rawDeepLearningHelp/docs/rawDeepLearning_CreateAndConfig.html

@@ -7,20 +7,18 @@
 
 </head>
 <body>
-	<h1 id="pamguard-s-deep-learning-module">PAMGuard Deep
+	<h1 id="pamguard-s-deep-learning-module">PAMGuard Deep Learning
-		Learning Module</h1>
+		Module</h1>
-	<h2 id="creation-and-config">Creation and Configuration</h2>
+
-	<br>
+	<h2 id="creating-an-instance-of-the-module">Creating an instance
-	<h3 id="creating-an-instance-of-the-module">Creating an instance
+		of the module</h2>
-		of the module</h3>
 	<p>
 		The module can be added from the <em>File&gt; Add modules &gt;
 			Classifier &gt; Raw deep learning classifier</em> menu or by right
 		clicking in the data model. More than one instance of the module can
 		be added if multiple deep learning models are required.
 	</p>
-	<br>
+	<h2 id="module-settings">Module settings</h2>
-	<h3 id="module-settings">Module settings</h3>
 	<p>
 		The module settings are opened by selecting the <em>Settings &gt;
 			Raw deep learning classifier</em> menu. The main settings pane is shown
@@ -28,18 +26,18 @@
 		and <em>Deep Learning Model</em>
 	</p>
 	<p align="center">
-		<img width="700" height="630"
+		<img src="images/deep_leanring_module_help.png">
-			src="images/deep_leanring_module_help.png">
 	</p>
 
 	<p>
 		<em>The main settings pane for the deep learning module with
 			descriptions</em>
 	</p>
-	<br>
 	<h3 id="raw-sound-data">Raw Sound Data</h3>
 	<p>The deep learning module accepts any raw data source i.e., any
-		data source that contains raw waveform data.</p>
+		data source that contains raw waveform data e.g. clicks, clips and
+		Ishmael detections. Note that the module accepts whislte and moan
+		detections but only if a delphinID classifier has been loaded.</p>
 	<p>If the data is continuous, e.g. from the Sound Acquisition
 		module then deep learning detections are saved to PAMGuard&#39;s data
 		management system if they pass a user defined prediction threshold.
@@ -57,7 +55,6 @@
 		processes. So, for example if channels 0 and 2 are in a group, then
 		the raw waveform data from both channel 0 and 2 will be saved and can
 		be used in downstream processes, e.g., for localisation.</p>
-	<br>
 	<h3 id="segmentation">Segmentation</h3>
 	<p>
 		The segmentation section defines how the raw data is segmented. Some
@@ -72,7 +69,6 @@
 			re-merge</em> is the maximum number of segments that can form a single
 		data unit before a new data unit is automatically created.
 	</p>
-	<br>
 	<h3 id="deep-learning-model">Deep Learning Model</h3>
 	<p>The deep learning model section is used to select the deep
 		learning model. The drop down menu is used to select the framework the
@@ -92,14 +88,12 @@
 	</p>
 	<p>Once the model has loaded there some unique options depending on
 		the currently selected framework.</p>
-	<br>
 	<h4 id="generic-model">Generic Model</h4>
 	<p>
 		A generic model must be set up via the <em>Advanced</em> menu button.
 	</p>
 	<p align="center">
-		<img width="700" height="700"
+		<img src="images/advanced_settings_generic_1.png">
-			src="images/advanced_settings_generic_1.png">
 	</p>
 
 	<p>
@@ -124,8 +118,7 @@
 		including the shape of the input data e.g. a 100x50 image.
 	</p>
 	<p align="center">
-		<img width="700" height="700"
+		<img src="images/advanced_settings_generic_2.png">
-			src="images/advanced_settings_generic_2.png">
 	</p>
 
 	<p>
@@ -146,16 +139,15 @@
 		transforms and input and output data whenever settings up a new
 		PAMGuard data model and allow easier sharing of classifiers amongst
 		researchers.</p>
-	<br>
+	<h4 id="koogu-ketos-animalspot-pamguard-zip-and-delphinid-models">Koogu,
-	<h4 id="animalspot-and-ketos-models">AnimalSpot and Ketos models</h4>
+		Ketos, AnimalSpot, PAMGuard zip and delphinID models</h4>
 	<p>
-		If using an AnimalSpot or Ketos model then all transforms are
+		If using a deep learning model from a supported framework then all
-		automatically set up. The transforms can be viewed and altered via the
+		transforms are automatically set up. The transforms can be viewed and
-		Advanced menu button but in the majority of cases these settings
+		altered via the Advanced menu button but in the majority of cases
-		should not be used. It is advisable to select &quot;Use default
+		these settings should not be used. For some models, it is advisable to
-		segment length&quot; to change the <em>Window length</em> to the
+		select &quot;Use default segment length&quot; to change the <em>Window
-		default for the selected model. Note that this is often necessary for
+			length</em> to the default for the selected model.
-		Ketos models but usually not a requirement for AnimalSpot models.
 	</p>
 	<p align="center">
 		<img width="700" height="700"
@@ -163,18 +155,43 @@
 	</p>
 
 	<p>
-		<em>An AnimalSpot or Ketos model will automatically create a list
+		<em>An AnimalSpot, Ketos or other supported deep learning model
-			of transforms with the appropriate settings. These is no need to use
+			will automatically create a list of transforms with the appropriate
-			the advanced pane but it is there in case users wish to change
+			settings. These is no need to use the advanced pane but it is there
-			transform settings for some reason</em>
+			in case users wish to change transform settings for some reason</em>
 	</p>
+	<h3 id="default-models">Default Models</h3>
+	<p>Default models are selectable from the menu button in the Deep
+		Learning Pane. Default models are deep learning classifiers which are
+		open source, known to be effective and have have been published in
+		open access academic litrature; they are downloaded directly from a
+		GitHub repository and then all associated settings are automtically
+		applied. The default model selection pane also contains hyperlinks to
+		the papers descirbing each model which will take users directly to the
+		relvent website.</p>
+
+	<p align="center">
+		<img src="images/default_settings_humpback_1.png">
+	</p>
+
+	<p>
+		<em>Default models can be downloaded. Default models are models
+			which are published, open and have been known to work well amongst
+			the bioacoustics community. More will be added to PAMGaurd over time.
+			If you you would like your model to become a defualt model then drop
+			PAMGuard support an email.</em>
+	</p>
+
 	<br>
 	<br>
 	<br>
-	<p class="prevLink"><a href="rawDeepLearning_overview.html">Previous:
+	<p class="prevLink">
-	Overview</a></p>
+		<a href="rawDeepLearning_overview.html">Previous: Overview</a>
-	<p class="nextLink"><a href="rawDeepLearning_Running.html">Next:
+	</p>
-	Running the Deep Learning module</a></p>
+	<p class="nextLink">
+		<a href="rawDeepLearning_Running.html">Next: Running the Deep
+			Learning module</a>
+	</p>
 	<br>
 	<br>
 	<br>

src/help/classifiers/rawDeepLearningHelp/docs/rawDeepLearning_Results.html

@@ -9,12 +9,12 @@
 <body>
 	<h1 id="pamguard-s-deep-learning-module">PAMGuard&#39;s Deep
 		Learning Module</h1>
+
+
 	<h2 id="viewing-and-exporting-results">Viewing and exporting
 		results</h2>
-	<br>
 	<p>Output from the deep learning module can be viewed in PAMGuard
 		viewer mode, or extracted from binary files using MATLAB or R.</p>
-	<br>
 	<h3 id="pamguard-viewer-mode">PAMGuard viewer mode</h3>
 	<p>Detections form continuous raw data are shown in the datagram in
 		the same way as all data streams in PAMGuard.</p>
@@ -32,7 +32,7 @@
 		manual analyst can quickly navigate to detections with high prediction
 		values for a certain class. Hovering over or right clicking on a data
 		unit in the time display and selecting the information button, will
-		show the data unit&#39;s metadata, including the prediction values for all
+		show the data unit’s metadata, including the prediction values for all
 		output classes from the deep learning model.</p>
 	<p align="center">
 		<img src="images/bat_time_base_display.png">
@@ -50,7 +50,6 @@
 		deep learning prediction values. The spectrogram will also show deep
 		learning detections as translucent blue boxes (these must be selected
 		in the right click menu).</p>
-	<br>
 	<h3 id="matlab">MATLAB</h3>
 	<p>The easiest way to export to MATLAB is to select the desired
 		units in the time base display, right click and select the MATLAB
@@ -96,7 +95,7 @@ predicitons = dldetections(<span class="hljs-number">1</span>).annotations.dlcla
 		waveform data in each structure;</p>
 	<pre>
 		<code class="lang-matlab">
-<span class="hljs-comment">% plot all the spectrograms.</span>
+			<span class="hljs-comment">% plot all the spectrograms.</span>
 clf
 tiledlayout(<span class="hljs-number">5</span>,<span class="hljs-number">5</span>)
 <span class="hljs-keyword">for</span> <span class="hljs-built_in">i</span>=<span
@@ -155,7 +154,6 @@ tiledlayout(<span class="hljs-number">5</span>,<span class="hljs-number">5</span
 		<em>Right whale detections from a deep learning model imported
 			and then plotted in MATLAB</em>
 	</p>
-	<br>
 	<h3 id="r">R</h3>
 	<p>In the same way as MATLAB export, the PAMGuard time base display
 		and export selected data units directly to an R struct which can be
@@ -165,13 +163,17 @@ tiledlayout(<span class="hljs-number">5</span>,<span class="hljs-number">5</span
 		functions compared to the MATLAB library. The PAMBinaries R library
 		can be found <a href="https://github.com/TaikiSan21/PamBinaries">here</a>.
 	</p>
+
 	<br>
 	<br>
 	<br>
-	<p class="prevLink"><a href="rawDeepLearning_Running.html">Previous:
+	<p class="prevLink">
-	Running the Deep Learning module</a></p>
+		<a href="rawDeepLearning_Running.html">Previous: Running the Deep
-	<p class="nextLink"><a href="rawDeepLearning_Bugs.html">Next:
+			Learning module</a>
-	Common Bugs and Mistakes</a></p>
+	</p>
+	<p class="nextLink">
+		<a href="rawDeepLearning_Bugs.html">Next: Common Bugs and Mistakes</a>
+	</p>
 	<br>
 	<br>
 	<br>

src/help/classifiers/rawDeepLearningHelp/docs/rawDeepLearning_Running.html

@@ -10,12 +10,10 @@
 	<h1 id="pamguard-s-deep-learning-module">PAMGuard&#39;s Deep
 		Learning Module</h1>
 	<h2 id="running">Running</h2>
-	<br>
 	<h3 id="real-time">Real time</h3>
 	<p>In real time, the deep learning model runs automatically when
 		processing starts. A warning will appear if there are issues with the
 		model and/or it cannot cope with real time speeds.</p>
-	<br>
 	<h3 id="viewer-mode">Viewer Mode</h3>
 	<p>
 		The deep learning module can be re-run on <em>detector</em> data (e.g.
@@ -26,13 +24,18 @@
 		Detections without a deep learning annotation will have one added and
 		detections with an existing annotation will have it overwritten.
 	</p>
+
 	<br>
 	<br>
 	<br>
-	<p class="prevLink"><a href="rawDeepLearning_CreateAndConfig.html">Previous:
+	<p class="prevLink">
-	Creating and Configuring the Deep Learning module</a></p>
+		<a href="rawDeepLearning_CreateAndConfig.html">Previous: Creating
-	<p class="nextLink"><a href="rawDeepLearning_Results.html">Next:
+			and Configuring the Deep Learning module</a>
-	Viewing and Exporting Results</a></p>
+	</p>
+	<p class="nextLink">
+		<a href="rawDeepLearning_Results.html">Next: Viewing and Exporting
+			Results</a>
+	</p>
 	<br>
 	<br>
 	<br>

src/help/classifiers/rawDeepLearningHelp/docs/rawDeepLearning_overview.html

@@ -7,10 +7,11 @@
 
 </head>
 <body>
-	<h1 id="pamguard-s-deep-learning-module">PAMGuard Deep
+	<h1 id="pamguard-s-deep-learning-module">PAMGuard&#39;s deep
-		Learning Module</h1>
+		learning module</h1>
+	<p>Note: this module requires an internet connection upon first use
+		to download correct libraries.</p>
 	<h2 id="overview">Overview</h2>
-
 	<p>PAMGuard&#39;s deep learning module allows users to deploy a
 		large variety of deep learning models natively in PAMGuard. It is core
 		module, fully integrated into PAMGuard&#39;s display and data
@@ -19,9 +20,7 @@
 		signal and can integrate into multiple types of acoustic analysis
 		workflows, for example post analysis of recorder data or used as part
 		of real time localisation workflow.</p>
-		
+	<h2 id="how-it-works">How it works</h2>
-	<br>
-	<h3 id="how-it-works">How it works</h3>
 	<p>The deep learning module accepts raw data from different types
 		of data sources, e.g. from the Sound Acquisition module, clicks and
 		clips. It segments data into equal sized chunks with a specified
@@ -32,8 +31,7 @@
 		learning model, then can be automatically set up by PAMGuard.
 		Currently there are three implemented frameworks</p>
 	<p align="center">
-		<img width="900" height="370"
+		<img src="images/deep_learning_module_process.png">
-			src="images/deep_learning_module_process.png">
 	</p>
 
 	<p>
@@ -44,7 +42,6 @@
 			the model are saved and can be viewed in real time (e.g. mitigation)
 			or in post processing (e.g. data from SoundTraps).</em>
 	</p>
-	<br>
 	<h3 id="generic-model">Generic Model</h3>
 	<p>
 		A generic model allows a user to load any model compatible with the <a
@@ -54,12 +51,11 @@
 		existing framework instead of a generic model as these models will
 		automatically generate the required transforms.
 	</p>
-	<br>
 	<h3 id="animalspot">AnimalSpot</h3>
 	<p>
 		<a href="https://github.com/ChristianBergler/ANIMAL-SPOT">ANIMAL-SPOT</a>
 		is a deep learning based framework which was initially designed for <a
-			href="https://github.com/ChristianBergler/ORCA-SPOT">killer
+			href="(https://github.com/ChristianBergler/ORCA-SPOT">killer
 			whale sound detection</a>) in noise heavy underwater recordings (see <a
 			href="https://www.nature.com/articles/s41598-019-47335-w">Bergler
 			et al. (2019)</a>). It has now been expanded to a be species independent
@@ -68,21 +64,43 @@
 		AnimalSpot models will automatically set up their own data transforms
 		and output classes.
 	</p>
-	<br>
 	<h3 id="ketos">Ketos</h3>
 	<p>
 		<a href="https://meridian.cs.dal.ca/2015/04/12/ketos/">Ketos</a> is an
 		acoustic deep learning framework based on Tensorflow and developed by
 		<a href="https://meridian.cs.dal.ca/">MERIDIAN</a>. It has excellent
 		resources and tutorials and Python libraries can be installed easily
-		via pip. Imported Ketos model will automatically set up their own data
+		via pip. Imported Ketos (.ktpb) models will automatically set up their
+		own data transforms and output classes.
+	</p>
+	<h3 id="koogu">Koogu</h3>
+	<p>
+		<a href="https://shyamblast.github.io/Koogu/en/stable/">Koogu </a> is
+		a Python package which allows users to train a deep learning model.
+		Koogu helps users by integrating with some frequency used annotation
+		programs and provides tools to train and test classifiers. Imported
+		Koogu models (.kgu) will automatically set up their own data
 		transforms and output classes.
 	</p>
+	<h3 id="pamguardzip">PAMGuardZip</h3>
+	<p>
+		PAMGuard zip models consist of a deep learning model (either a
+		Tensorflow saved_model.pb or PyTorch <em>*.py model) alongside a
+			PAMGuard metdata file (</em>.pdtf*) within a zip archive. The metadata
+		file contains all the information needed for PAMGaurd to set up the
+		model. PAMGuard will import the zip file, decompress it and search for
+		the relevent deep learning model and metadata file then set up all
+		settings accordingly. This framework allows users to easily share
+		pre-tested PAMGuard compatible models.
+	</p>
+
 	<br>
 	<br>
 	<br>
-	<p class="nextLink"><a href="rawDeepLearning_CreateAndConfig.html">Next:
+	<p class="nextLink">
-	Creating and Configuring the Deep Learning module</a></p>
+		<a href="rawDeepLearning_CreateAndConfig.html">Next: Creating and
+			Configuring the Deep Learning module</a>
+	</p>
 	<br>
 	<br>
 	<br>

src/loggerForms/controls/CounterControl.java

@@ -21,6 +21,7 @@ public class CounterControl extends SimpleControl {
 	
 	Character suffix;
 	
+	public enum CounterSuffix {NOSUFFIX, CHARSUFFIX};
 	
 	public CounterControl(ControlDescription controlDescription,
 			LoggerForm loggerForm) {
@@ -36,25 +37,19 @@ public class CounterControl extends SimpleControl {
 		
 	}
 	
-	
-	
-	
-
-
-
 	private String calculateCounter() {
 		int num = FormCounterManagement.getInstance().getCounterNumber(this,controlDescription.getFormDescription().getDBTABLENAME());
 		
-		String numSt = Integer.toString(num);
+		String numSt = String.format("%03d", num);
-		int nZeros = 3-numSt.length();
+//		int nZeros = 3-numSt.length();
-		
+//		
-		String tSt = "";
+//		String tSt = "";
-		for (int i=0;i<nZeros;i++){
+//		for (int i=0;i<nZeros;i++){
-			tSt+="0";
+//			tSt+="0";
-//			System.out.println(tSt);
+////			System.out.println(tSt);
-		}
+//		}
-		
+//		
-		numSt = tSt+numSt;
+//		numSt = tSt+numSt;
 //		System.out.println(tSt);
 //		System.out.println(numSt);
 		
@@ -109,31 +104,19 @@ public class CounterControl extends SimpleControl {
 		
 	}
 	
-	
-	
-	
-
 	@Override
 	AbstractFormatter getAbstractformatter() {
 		
 		DefaultFormatter formatter = new DefaultFormatter();
 		return formatter;
 		
-		
-		
 	}
 
-
-
 	public void updateCounter() {
 		if (loggerForm.getNewOrEdit()==LoggerForm.EditDataForm) return;
 //		System.out.println("updateCounter");
 		setData(calculateCounter());
 	}
 
-	
-	
-	
-	
 }
 

src/loggerForms/formdesign/controlpropsets/CounterPropertySet.java

@@ -2,7 +2,9 @@ package loggerForms.formdesign.controlpropsets;
 
 import loggerForms.FormDescription;
 import loggerForms.UDColName;
+import loggerForms.controlDescriptions.ControlTypes;
 import loggerForms.formdesign.ControlTitle;
+import loggerForms.formdesign.itempanels.BooleanCtrlColPanel;
 import loggerForms.formdesign.itempanels.CtrlColPanel;
 
 public class CounterPropertySet extends BasePropertySet {
@@ -15,12 +17,17 @@ public class CounterPropertySet extends BasePropertySet {
 	@Override
 	public CtrlColPanel getItemPropertyPanel(ControlTitle selTitle,
 			UDColName propertyName) {
+//		if (selTitle.getType() == ControlTypes.COUNTER) {
+//			System.out.println("counter");
+//		}
 		switch (propertyName) {
 		case Plot:
 		case Autoclear:
 		case ReadOnly:
 		case AutoUpdate:
 			return null;
+//		case Topic:
+//			return new BooleanCtrlColPanel(selTitle, new );
 		}
 		return super.getItemPropertyPanel(selTitle, propertyName);
 	}