updates ready for 2.2.12

README.files/colorschememapping.xml

@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<a:clrMap xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" bg1="lt1" tx1="dk1" bg2="lt2" tx2="dk2" accent1="accent1" accent2="accent2" accent3="accent3" accent4="accent4" accent5="accent5" accent6="accent6" hlink="hlink" folHlink="folHlink"/>

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 2.02.12 June 2024</a></span></em></h1>
+Version 2.02.12 August 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>
@@ -461,11 +461,11 @@ Version 2.00.10 June 2017</a></span></h1>
 
 <h1><span style='font-size:12.0pt'><a href="#_Older_Versions">Older Versions</a></span></h1>
 
-<h1><a name="_Latest_Version_2.02.03_1"></a><a name="_Latest_Version_2.02.05"></a><a
+<h1><a name="_Hlk174698335"></a><a name="_Latest_Version_2.02.03_1"></a><a
-name="_Latest_Version_2.02.06"></a><a name="_Latest_Version_2.02.07"></a><a
+name="_Latest_Version_2.02.05"></a><a name="_Latest_Version_2.02.06"></a><a
-name="_Latest_Version_2.02.08"></a><a name="_Version_2.02.09_June"></a><a
+name="_Latest_Version_2.02.07"></a><a name="_Latest_Version_2.02.08"></a><a
-name="_Version_2.02.10_January"></a><a name="_Version_2.02.11_April"></a>Version
+name="_Version_2.02.09_June"></a><a name="_Version_2.02.10_January"></a><a
-2.02.12 June 2024</h1>
+name="_Version_2.02.11_April"></a>Version 2.02.12 August 2024</h1>
 
 <p class=MsoNormal>&nbsp;</p>
 
@@ -483,12 +483,18 @@ continually reset them. </p>
 project information to store with your data. See menu item Settings/Project
 information.</p>
 
+<p class=MsoNormal>‘Effort’ management system. New map options allow colouring
+of track line by ‘effort’ from various other modules. This is currently the
+acquisition system (so the track will change colour when PAMGuard is running),
+the binary store system (likely the same as the acquisition) or data from Logger
+forms. This system will be extended to other modules in the near future. </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.
+to the <a href="https://tethys.sdsu.edu/">Tethys Database</a> into PAMGuard. Some
-Some basic features are available for testing. If interested, please contact
+basic features are available for testing. If interested, please contact the
-the PAMGuard support team. </p>
+PAMGuard support team. </p>
 
 <h2>Bug Fixes</h2>
 
@@ -532,6 +538,9 @@ exact times, rather than a couple of seconds after the hour. </p>
 <p class=MsoNormal>Updated icons to improve display on high definition screens.
 </p>
 
+<p class=MsoNormal>SAIL Daq Card. Automatic restart when DAQ card stalls
+(happening increasingly often with latest Windows updates)</p>
+
 <h1>Version 2.02.10 January 2024</h1>
 
 <h2><span lang=EN-US>New Features</span></h2>
@@ -1026,11 +1035,10 @@ help</a>. </p>
 <h1><a name="_Latest_Beta_Version_2.01.05"></a><span lang=EN-US>Latest Version
 2.01.05 October 2020</span></h1>
 
-<p class=MsoNormal><b>If you are upgrading from a PAMGuard core release
+<p class=MsoNormal><b>If you are upgrading from a PAMGuard core release (1.15.xx),
-(1.15.xx), PAMGuard Version 2 contains major updates. You should read and
+PAMGuard Version 2 contains major updates. You should read and understand the
-understand the notes listed for <a href="#_Latest_Beta_Version_2.00.10">Beta
+notes listed for <a href="#_Latest_Beta_Version_2.00.10">Beta Version 2.00.10</a>
-Version 2.00.10</a> before proceeding with installation and use of this
+before proceeding with installation and use of this version.</b></p>
-version.</b></p>
 
 <p class=MsoNormal>This version of PAMGuard has been bundled with Java 13
 (release 13.0.1). PSFX files generated in previous beta releases (2.xx.xx)
@@ -1163,8 +1171,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>4. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>Bug
-&nbsp; 456. Under certain conditions, the Ishmael detection plugin that is shown
+&nbsp; 456. Under certain conditions, the Ishmael detection plugin that is
-at the bottom of the spectrogram can disappear about 500 msec behind the
+shown at the bottom of the spectrogram can disappear about 500 msec behind the
 current time. </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>5. </span><span
@@ -1428,8 +1436,8 @@ classify clicks. </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><span
-lang=EN-US> </span>Added option in Sound Acquisition settings dialog to override
+lang=EN-US> </span>Added option in Sound Acquisition settings dialog to
-filename time stamp and use PC local time instead. </p>
+override filename time stamp and use PC local time instead. </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>3. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@@ -2340,8 +2348,8 @@ the new version. However please note the following:</span></p>
 
 <p class=MsoListParagraph style='margin-left:54.0pt;text-indent:-36.0pt'><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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span><span lang=EN-US>New classes will be added to the configuration files, so
+</span><span lang=EN-US>New classes will be added to the configuration files,
-they will no longer work with older PAMGuard versions.</span></p>
+so they will no longer work with older PAMGuard versions.</span></p>
 
 <p class=MsoListParagraph style='margin-left:54.0pt;text-indent:-36.0pt'><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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -2464,8 +2472,8 @@ milliseconds. However, getDuration actually returns the number of samples.
 
 <p class=MsoNormal><b><span lang=EN-US>Plug-Ins</span></b></p>
 
-<p class=MsoNormal><span lang=EN-US>A major change in this version of PAMGuard is
+<p class=MsoNormal><span lang=EN-US>A major change in this version of PAMGuard
-how plug-ins are managed. PAMGuard now has the ability to dynamically load
+is how plug-ins are managed. PAMGuard now has the ability to dynamically load
 plug-in modules (saved as jar files) at runtime. This will greatly simplify the
 process of testing and distributing newly developed modules, since only a small
 jar file will be required rather than a new bespoke PAMGuard installation.</span></p>
@@ -2474,9 +2482,9 @@ jar file will be required rather than a new bespoke PAMGuard installation.</span
 unchanged, in most cases simply requiring the addition of an interface class.
 &nbsp;Instructions for the development of new modules utilizing the plug-in
 scheme can be found <a href="http://www.pamguard.org/16_HowtomakePlug-Ins.html"
-target="_blank">here</a>. &nbsp;Plug-in modules can be downloaded from the PAMGuard
+target="_blank">here</a>. &nbsp;Plug-in modules can be downloaded from the
-website here, but developers are encouraged to host and maintain their own
+PAMGuard website here, but developers are encouraged to host and maintain their
-modules.</span></p>
+own modules.</span></p>
 
 <p class=MsoNormal><span lang=EN-US>Modules of interest to the general PAM
 community will remain as part of the core PAMGuard installation. However,
@@ -2797,9 +2805,9 @@ easy to understand options have been developed in a new options dialog.</p>
 
 <p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>9.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 281. Click classification dialog has grown too big to fit on the
+</span>Bug 281. Click classification dialog has grown too big to fit on the screen.
-screen. The options have now been split across three tabbed panes which solves
+The options have now been split across three tabbed panes which solves the
-the problem.</p>
+problem.</p>
 
 <p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>10.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;
@@ -3103,10 +3111,10 @@ href="https://sourceforge.net/p/pamguard/bugs">https://sourceforge.net/p/pamguar
 
 <p class=MsoListParagraph style='margin-left:47.25pt;text-indent:-29.25pt'><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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Spectrogram annotation marks. A simple system for marking spectrograms
+</span>Spectrogram annotation marks. A simple system for marking spectrograms during
-during real time analysis has been incorporated. To use it, add the module, in
+real time analysis has been incorporated. To use it, add the module, in the
-the spectrogram settings, select the annotation marks in the 'Mark Observers'
+spectrogram settings, select the annotation marks in the 'Mark Observers' tab
-tab of the spectrogram configuration dialog, and also right click on the
+of the spectrogram configuration dialog, and also right click on the
 spectrogram and select to display the annotations. Annotations are saved to the
 database so you will also need a database module in your configuration. &nbsp;</p>
 
@@ -3376,9 +3384,9 @@ of third octave noise bands. See online help for details. </p>
 
 <p class=MsoNormal><i>Filtered Noise Measurement</i> (Sound Processing Group)</p>
 
-<p class=MsoNormal>This module, developed by Douglas Gillespie, measures noise
+<p class=MsoNormal>This module, developed by Douglas Gillespie, measures noise levels
-levels in a single frequency band using a variety of filter functions. See
+in a single frequency band using a variety of filter functions. See online help
-online help for details. </p>
+for details. </p>
 
 <p class=MsoNormal><i>Envelope Tracing</i> (Beta Only, Sound Processing Group)</p>
 
@@ -3908,11 +3916,11 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
 
 <p class=MsoNormal>2. Improved offline viewer functionality. </p>
 
-<p class=MsoNormal>The offline viewer is much improved with better data scrolling
+<p class=MsoNormal>The offline viewer is much improved with better data
-and the ability to view data either stored in the database or the binary
+scrolling and the ability to view data either stored in the database or the
-storage system. Work has stated on functions which read and use data stored in
+binary storage system. Work has stated on functions which read and use data
-audio files. This is currently limited to re-calculating and displaying
+stored in audio files. This is currently limited to re-calculating and
-displaying spectrogram data during viewer mode operation.&nbsp; </p>
+displaying displaying spectrogram data during viewer mode operation.&nbsp; </p>
 
 <p class=MsoNormal>3. Heading sensor readout</p>
 
@@ -4013,8 +4021,8 @@ channels 0 and 1. Similarly if you switched sound cards, you may have to
 reconfigure every detector and several of the displays to handle the changes in
 channel numbering. </p>
 
-<p class=MsoNormal>I have spent a considerable amount of time trying to work out
+<p class=MsoNormal>I have spent a considerable amount of time trying to work
-a better system for handling channel numbering in PAMGUARD and have decided
+out a better system for handling channel numbering in PAMGUARD and have decided
 that the only practical thing to do is to force all software channel numbering
 back to a zero indexed system. i.e. even if you read out hardware channels
 3,4,5 and 6, within PAMGUARD, everywhere apart from the Sound acquisition
@@ -4602,9 +4610,9 @@ a serial port </p>
 
 <p class=MsoNormal>New Likelihood detector. </p>
 
-<p class=MsoNormal>The likelihood detector module is an implementation of a likelihood
+<p class=MsoNormal>The likelihood detector module is an implementation of a
-ratio test with flexible algorithms and configuration to estimate likelihood.
+likelihood ratio test with flexible algorithms and configuration to estimate
-It is </p>
+likelihood. It is </p>
 
 <p class=MsoNormal>suitable for detecting both short duration Odontocete clicks
 (Sperm, Beaked, etc.) as well as moderate duration Mysticete calls (Humpback,

pom.xml

@@ -584,7 +584,7 @@ I've tried updating this to 2.11 bu tit's throwing problems at me with a missing
 		<dependency>
 			<groupId>com.fazecast</groupId>
 			<artifactId>jSerialComm</artifactId>
-			<version>2.5.3</version>
+			<version>2.11.0</version>
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/edu.emory.mathcs/JTransforms -->

src/PamController/PamguardVersionInfo.java

@@ -36,7 +36,7 @@ public class PamguardVersionInfo {
 	/**
 	 * Release date
 	 */
-	static public final String date = "2 August 2024";
+	static public final String date = "19 August 2024";
 	
 //	/**
 //	 * Release type - Beta or Core

src/ravendata/RavenDataRow.java

@@ -156,4 +156,13 @@ public class RavenDataRow {
 		return unpackOK;
 	}
 
+	@Override
+	public boolean equals(Object obj) {
+		if (obj instanceof RavenDataRow == false) {
+			return false;
+		}
+		RavenDataRow oth = (RavenDataRow) obj;
+		return this.channel == oth.channel && this.beginT == oth.beginT && this.endT == oth.endT && this.f1 == oth.f1 && this.f2 == oth.f2;
+	}
+
 }

src/ravendata/RavenProcess.java

@@ -84,20 +84,28 @@ public class RavenProcess extends PamProcess {
 		ravenDataBlock.clearAll();
 		ravenLogging.deleteData(0, System.currentTimeMillis()*2);
 		
+		RavenDataRow prevRow = null;
 		for (RavenDataRow ravenRow : ravenData) {
-			int fileInd = getTimeIndex(ravenRow.getBeginT()*1000, absTime);
+			if (ravenRow.equals(prevRow) == false) {
-			if (fileInd == absTime.length) {
+				/**
-				String msg = String.format("Data at time %6.4f is beyond the end of available sound file data", ravenRow.getBeginT());
+				 *  A lot of Raven data appear twice, with different view values. 
-				WarnOnce.showWarning("Error importing RAVEN data", msg, WarnOnce.WARNING_MESSAGE);
+				 *  No need to import both. so only doing this if they are different. 
-				break;
+				 */
+				int fileInd = getTimeIndex(ravenRow.getBeginT()*1000, absTime);
+				if (fileInd == absTime.length) {
+					String msg = String.format("Data at time %6.4f is beyond the end of available sound file data", ravenRow.getBeginT());
+					WarnOnce.showWarning("Error importing RAVEN data", msg, WarnOnce.WARNING_MESSAGE);
+					break;
+				}
+				long fileStart = fileStarts[fileInd];
+				long absStart = fileStart + (long) (ravenRow.getBeginT()*1000.)-absTime[fileInd];
+				long duration = (long) ((ravenRow.getEndT()-ravenRow.getBeginT())*1000.);
+				int chanMap = 1<<(ravenRow.getChannel()-1);
+				RavenDataUnit rdu = new RavenDataUnit(absStart, chanMap, duration, ravenRow.getF1(), ravenRow.getF2());
+				getRavenDataBlock().addPamData(rdu);
+				ravenLogging.logData(DBControlUnit.findConnection(), rdu);
 			}
-			long fileStart = fileStarts[fileInd];
+			prevRow = ravenRow;
-			long absStart = fileStart + (long) (ravenRow.getBeginT()*1000.)-absTime[fileInd];
-			long duration = (long) ((ravenRow.getEndT()-ravenRow.getBeginT())*1000.);
-			int chanMap = 1<<(ravenRow.getChannel()-1);
-			RavenDataUnit rdu = new RavenDataUnit(absStart, chanMap, duration, ravenRow.getF1(), ravenRow.getF2());
-			getRavenDataBlock().addPamData(rdu);
-			ravenLogging.logData(DBControlUnit.findConnection(), rdu);
 		}
 		
 		OfflineDataMap dataMap = ravenDataBlock.getPrimaryDataMap();

src/targetMotionOld/tethys/TMALocalizationCreator.java

@@ -146,7 +146,7 @@ public class TMALocalizationCreator implements LocalizationCreator {
 //		 now also output a perpendicular distance.
 		Double perp = groupLocResult.getPerpendicularDistance();
 		if (perp != null) {
-			loc.setPerpendicularRangeM(perp);
+			loc.setPerpendicularRangeM(AutoTethysProvider.roundDecimalPlaces(perp, 2));
 		}