Functional SUD Reader and SUD Click Extractor

All seems working. Seems to throw the odd exception at end of file, but
works OK.

README.html

@@ -15,12 +15,12 @@
 @font-face
 	{font-family:"Calibri Light";
 	panose-1:2 15 3 2 2 2 4 3 2 4;}
-@font-face
-	{font-family:Tahoma;
-	panose-1:2 11 6 4 3 5 4 4 2 4;}
 @font-face
 	{font-family:Cambria;
 	panose-1:2 4 5 3 5 4 6 3 2 4;}
+@font-face
+	{font-family:Tahoma;
+	panose-1:2 11 6 4 3 5 4 4 2 4;}
  /* Style Definitions */
  p.MsoNormal, li.MsoNormal, div.MsoNormal
 	{margin-top:0cm;
@@ -368,8 +368,8 @@ should be something like:</p>
 -Xms384m -Xmx4096m -Djava.library.path=lib64 -jar Pamguard_xxxxxx.jar</span></em></p>
 
 <p class=MsoNormal>The -Xms384m -Xmx4096m specify the initial and maximum heap
-size for the JVM being used to run Pamguard i.e. how much memory it gets to use.
+size for the JVM being used to run Pamguard i.e. how much memory it gets to
-The default max size usually being too low.</p>
+use. The default max size usually being too low.</p>
 
 <p class=MsoNormal>The -Djava.library.path=lib64 tells the JVM that it should
 look in the folder called &quot;lib64&quot; for the required shared libraries (change
@@ -381,8 +381,8 @@ a &quot;-m&quot; or &quot;-v&quot; to the list of java arguments. On Windows
 just run the appropriately named executable (e.g. PamguardBeta_MixedMode.exe or
 PamguardBeta_ViewerMode.exe):</p>
 
-<p class=MsoNormal><em><span style='font-family:"Calibri",sans-serif'>java
+<p class=MsoNormal><em><span style='font-family:"Calibri",sans-serif'>java -Xms384m
--Xms384m -Xmx4096m -Djava.library.path=lib64 -jar PamguardBeta_xxxxxx.jar -v</span></em></p>
+-Xmx4096m -Djava.library.path=lib64 -jar PamguardBeta_xxxxxx.jar -v</span></em></p>
 
 <p class=MsoNormal><em><span style='font-family:"Calibri",sans-serif'>&nbsp;</span></em></p>
 
@@ -444,7 +444,26 @@ 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><span
-lang=EN-US>Latest Version 2.02.05 October 2022</span></h1>
+lang=EN-US>Latest Version 2.02.06 November 2022</span></h1>
+
+<h2><span lang=EN-US>Bug Fix</span></h2>
+
+<p class=MsoNormal><span lang=EN-US>A memory leak has been found which seems to
+mostly occur in Viewer mode. Some data on background noise measurements are not
+being cleared from memory, so memory will eventually run out. This could happen
+after browsing a lot of data, but was most likely when reprocessing files
+offline, for example running click classifiers. This is now fixed. </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
+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 detector an also
+happen while processing SUD file data with other detectors, thereby
+streamlining the whole processing chain. Read the online Help for details.   </span></p>
+
+<h1><span lang=EN-US>Latest Version 2.02.05 October 2022</span></h1>
 
 <h2><span lang=EN-US>Click Train Detector Features and Bug Fixes</span></h2>
 
@@ -452,8 +471,9 @@ lang=EN-US>Latest Version 2.02.05 October 2022</span></h1>
 
 <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
+
-system to have nested classifiers which can be enabled or disabled. </span></p>
+<p class=MsoNormal><span lang=EN-US>Complete rewrite of the classification system
+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>
@@ -498,9 +518,9 @@ 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
+<p class=MsoNormal><span lang=EN-US>Soundtrap DWV import. Will now generate
-files even if DWV file doesn’t exist (which is correct behavior in quiet
+binary files even if DWV file doesnÂ’t exist (which is correct behavior in
-conditions when no clicks were detected). </span></p>
+quiet conditions when no clicks were detected). </span></p>
 
 <p class=MsoNormal><span lang=EN-US>Spectrogram. Changes to stop occasional
 crashing when restarting processing of wav files. </span></p>
@@ -534,8 +554,8 @@ 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
-option was not selected. </p>
+files’ option was not selected. </p>
 
 <p class=MsoNormal>#14 Logger forms data were not plotting correctly. This was
 due to the required data selection functions not being fully implemented. This
@@ -574,23 +594,23 @@ understand the notes listed for <a href="#_Latest_Beta_Version_2.00.10">Beta
 Version 2.00.10</a> before proceeding with installation and use of this
 version.</b></p>
 
-<p class=MsoNormal>This version of PAMGuard has been bundled with Java 16
+<p class=MsoNormal>This version of PAMGuard has been bundled with Java 16 (OpenJDK
-(OpenJDK release), so you will not need to install a java runtime engine
+release), so you will not need to install a java runtime engine separately.
-separately. PSFX files generated in previous beta releases (2.xx.xx) should be
+PSFX files generated in previous beta releases (2.xx.xx) should be compatible
-compatible with this version, and vice-versa. PSF files generated in core
+with this version, and vice-versa. PSF files generated in core releases
-releases (1.15.xx) can be loaded in this version, but will be converted to PSFX
+(1.15.xx) can be loaded in this version, but will be converted to PSFX files
-files when PAMGuard exits.</p>
+when PAMGuard exits.</p>
 
 <p class=MsoNormal style='margin-bottom:0cm'><span style='font-size:12.0pt;
 font-family:"Times New Roman",serif'>&nbsp;</span></p>
 
 <h2>File Format Change</h2>
 
-<p class=MsoNormal>Changes have been made to the binary file format to support
+<p class=MsoNormal>Changes have been made to the binary file format to support the
-the output of additional noise outputs for certain detectors (See below).
+output of additional noise outputs for certain detectors (See below). Binary
-Binary files created with this version will not be compatible with earlier
+files created with this version will not be compatible with earlier versions
-versions 2.01.### and below. This version will read and may convert earlier
+2.01.### and below. This version will read and may convert earlier format
-format binary files.</p>
+binary files.</p>
 
 <p class=MsoNormal style='margin-bottom:0cm'><span style='font-size:12.0pt;
 font-family:"Times New Roman",serif'>&nbsp;</span></p>
@@ -608,10 +628,10 @@ 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
-avoid confusion with the Group 3D localizer. This is because the Detection
+as to avoid confusion with the Group 3D localizer. This is because the
-Grouper is more for organizing data into groups to be localized than it is for
+Detection Grouper is more for organizing data into groups to be localized than
-doing localization.</p>
+it is for doing localization.</p>
 
 <p class=MsoNormal><b><span lang=EN-US>Minor Bug Fixes</span></b><span
 lang=EN-US> </span></p>
@@ -729,10 +749,10 @@ 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>
 An implementation of the Generalized Power Law Detector, developed by Tyler
-Helble ([Helble et al., ‘A generalized power-law detection algorithm for humpback
+Helble ([Helble et al., ‘A generalized power-law detection algorithm for
-whale vocalizations’, The Journal of the Acoustical Society of America, vol.
+humpback whale vocalizations’, The Journal of the Acoustical Society of
-131, no. 4, pp. 2682–2699, 2012) is now available. For details, see the online
+America, vol. 131, no. 4, pp. 2682–2699, 2012) is now available. For
-help </p>
+details, see the online help </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>18. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
@@ -754,10 +774,10 @@ Version 2.00.10</a> before proceeding with installation and use of this
 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) should
+(release 13.0.1). PSFX files generated in previous beta releases (2.xx.xx)
-be compatible with this version, and vice-versa. PSF files generated in core
+should be compatible with this version, and vice-versa. PSF files generated in
-releases (1.15.xx) can be loaded in this version, but will be converted to PSFX
+core releases (1.15.xx) can be loaded in this version, but will be converted to
-files when PAMGuard exits.</p>
+PSFX files when PAMGuard exits.</p>
 
 <p class=MsoNormal><b><span lang=EN-US>Bug Fixes</span></b></p>
 
@@ -840,8 +860,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
 Added logger form annotation to Spectrogram Annotation module. </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>6. </span><span
-lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Better auto-scaling in Ishmael Detector graphics window. </p>
+lang=EN-US> </span>Better auto-scaling in Ishmael Detector graphics window. </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>7. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
@@ -968,8 +988,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
 <p class=MsoNormal><b><span lang=EN-US>Upgrades</span></b></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>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Add functionality for bluetooth headsets. </p>
+lang=EN-US> </span>Add functionality for bluetooth headsets. </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
@@ -1093,9 +1113,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
 Bug 441. Plot coordinate calculations incorrect in PamAxis.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>10. </span><span
-lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Bug 442. BT Display does not change click symbol color when Colour By
+lang=EN-US> </span>Bug 442. BT Display does not change click symbol color when
-Superdetection is selected.</p>
+Colour By Superdetection is selected.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>11. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
@@ -1108,8 +1128,8 @@ files.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>13. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
-Bug 445. Overlay data in FX spectrogram display gets out of sync with underlying
+Bug 445. Overlay data in FX spectrogram display gets out of sync with
-spectrogram image.</p>
+underlying spectrogram image.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>14. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
@@ -1182,9 +1202,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
 Added a few new options to the Click Detector Sweep Classifier. </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>10. </span><span
-lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Add option to the Map module's Plot Overlay Options dialog, to show events
+lang=EN-US> </span>Add option to the Map module's Plot Overlay Options dialog,
-occuring in the future (<em><span style='font-family:"Calibri",sans-serif'>look
+to show events occuring in the future (<em><span style='font-family:"Calibri",sans-serif'>look
 ahead</span></em>) instead of the default display of events which have already
 occurred. Can make it easier to match up the map with clicks seen in the Click
 Detector display. </p>
@@ -1234,8 +1254,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
 Bug 429. Click Bearings at 180 degrees</p>
 
 <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>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Bug 430. Rocca calculates inflection point parameters incorrectly</p>
+lang=EN-US> </span>Bug 430. Rocca calculates inflection point parameters
+incorrectly</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><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;</span><span
@@ -1249,8 +1270,8 @@ Bug 432. MySQL database interface - connection problems</p>
 <p class=MsoNormal><b><span lang=EN-US>Upgrades</span></b></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>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-New display for Gebco Netcdf bathymetry maps.</p>
+lang=EN-US> </span>New display for Gebco Netcdf bathymetry maps.</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
@@ -1331,8 +1352,8 @@ files.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>12. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 425. Rocca crashing if Click Detector is used as source but the
+</span>Bug 425. Rocca crashing if Click Detector is used as source but the Click
-Click Classifier is not configured properly.</p>
+Classifier is not configured properly.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>13. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -1346,9 +1367,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
 Upgrades to the Group Localiser, including better error estimation.</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>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Click Train Detector upgrades, including ability to import time chunks from csv
+lang=EN-US> </span>Click Train Detector upgrades, including ability to import
-file for batch processing.</p>
+time chunks from csv file for batch processing.</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
@@ -1475,14 +1496,14 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
 Updates to the Ishmael module.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>9. </span><span
-lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Added option to the WarnOnce dialog to hide a warning for the current PAMGuard
+lang=EN-US> </span>Added option to the WarnOnce dialog to hide a warning for
-session, but not forever.</p>
+the current PAMGuard session, but not forever.</p>
 
 <!-- ************************************************************************************************************************** --><!-- ************************************************************************************************************************** -->
 
-<h1><a name="_Latest_Beta_Version_2.00.14c"></a><span lang=EN-US>Beta Version 2.00.14c
+<h1><a name="_Latest_Beta_Version_2.00.14c"></a><span lang=EN-US>Beta Version
-October 2018</span></h1>
+2.00.14c October 2018</span></h1>
 
 <p class=MsoNormal><span lang=EN-US>PAMGuard Version 2 contains major updates.
 You should read and understand the notes listed for <a
@@ -1518,10 +1539,10 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
 lang=EN-US> </span>Added decimal degrees option to latitude/longitude dialog.</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>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Added option in the Click Delay parameters to restrict the number of initial
+lang=EN-US> </span>Added option in the Click Delay parameters to restrict the
-samples used in the calculation. This can be useful for cleaning up delays in
+number of initial samples used in the calculation. This can be useful for
-the presence of echoes and small time delays.</p>
+cleaning up delays in the presence of echoes and small time delays.</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>
@@ -1589,7 +1610,8 @@ Annotation module which has now been given two text type annotations.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>9. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 391. Click Detector not registering change in multi-threading option.</p>
+</span>Bug 391. Click Detector not registering change in multi-threading
+option.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>10. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -1632,11 +1654,11 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
 lang=EN-US> </span>Added ability to read differential GPS data.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><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;</span>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Added check for duplicate settings in the psf file when exiting Pamguard. If
+lang=EN-US> </span>Added check for duplicate settings in the psf file when
-duplicate settings are found, user is given the option to leave them in the psf
+exiting Pamguard. If duplicate settings are found, user is given the option to
-or get rid of them. Duplicate settings are ignored by Pamguard, but can cause
+leave them in the psf or get rid of them. Duplicate settings are ignored by
-the psf file to grow large over time.</p>
+Pamguard, but can cause the psf file to grow large over time.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>6. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
@@ -1704,8 +1726,8 @@ 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>10. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 376. Error when using a serialised data map which spans a period of time
+</span>Bug 376. Error when using a serialised data map which spans a period of
-in which Pamguard modules have changed.</p>
+time in which Pamguard modules have changed.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>11. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -1744,8 +1766,9 @@ used in older versions. Older psf files can be loaded with this version, but
 will be converted.</p>
 
 <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>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Many updates to the Video Range module. Will currently only work with landmarks.</p>
+lang=EN-US> </span>Many updates to the Video Range module. Will currently only
+work with landmarks.</p>
 
 <!-- ************************************************************************************************************************** -->
 
@@ -1808,8 +1831,8 @@ Beta versions</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>11. </span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 366. Rocca manual whistle contour extraction throws error when trying
+</span>Bug 366. Rocca manual whistle contour extraction throws error when
-to classify a boxed whistle</p>
+trying to classify a boxed whistle</p>
 
 <p class=MsoNormal><b><span lang=EN-US>Upgrades</span></b></p>
 
@@ -1878,8 +1901,8 @@ 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>10.</span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 354. Whistle Classifier was crashing if user accidentally entered invalid
+</span>Bug 354. Whistle Classifier was crashing if user accidentally entered
-parameters. Have added diagnostics to prevent this.</p>
+invalid parameters. Have added diagnostics to prevent this.</p>
 
 <p class=MsoNormal><b><span lang=EN-US>Upgrades</span></b></p>
 
@@ -2009,8 +2032,8 @@ 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
-both data stores. </span></p>
+in both data stores. </span></p>
 
 <h3><span lang=EN-US>New Displays</span></h3>
 
@@ -2024,11 +2047,11 @@ Note that this display is only available if you are running Java 8 or later. </s
 
 <h3><span lang=EN-US>Event Marking and the Detection Group Localiser</span></h3>
 
-<p class=MsoNormal><span lang=EN-US>A new system of event marking which can be used
+<p class=MsoNormal><span lang=EN-US>A new system of event marking which can be
-both online and offline has been added to PAMGuard. Details are in the PAMGuard
+used both online and offline has been added to PAMGuard. Details are in the
-help file (Displays/Display Marking). Data can be selected on the Map, the
+PAMGuard help file (Displays/Display Marking). Data can be selected on the Map,
-Spectrogram Display and the new Time Display FX in a similar way and sent to
+the Spectrogram Display and the new Time Display FX in a similar way and sent
-other PAMGuard modules. The new marking and data selection system works with
+to other PAMGuard modules. The new marking and data selection system works with
 the new Detection Group Localiser. The Detection Group Localiser extends the
 functionality which always existed in the click detector to other types of data
 (e.g. Whistles) so that they can be grouped and tracked using target motion
@@ -2146,15 +2169,15 @@ working folder, and therefore is set incorrectly. This has been fixed.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><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;
-</span>Bug 314. If PAMGuard is started by double-clicking on a psf, nothing
+</span>Bug 314. If PAMGuard is started by double-clicking on a psf, nothing happens
-happens when the user selects save as new configuration. This has been fixed.</p>
+when the user selects save as new configuration. This has been fixed.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>6.</span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span>Bug 315. code searched for file in working folder, which is the
 installation folder when starting PAMGuard using a shortcut link. But when
-double-clicking on a psf, the working folder is the location of the psf. This has
+double-clicking on a psf, the working folder is the location of the psf. This
-been fixed.</p>
+has been fixed.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>7.</span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@@ -2183,8 +2206,8 @@ jar file will be required rather than a new bespoke PAMGuard installation.</span
 
 <p class=MsoNormal><span lang=EN-US>Module code development remains largely
 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
+&nbsp;Instructions for the development of new modules utilizing the plug-in
-can be found <a href="http://www.pamguard.org/16_HowtomakePlug-Ins.html"
+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 website here, but developers are encouraged to host and maintain their
 own modules.</span></p>
@@ -2192,8 +2215,8 @@ 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,
 specialized modules which are useful to only a small number of users have been
-removed and are available as a separate download. The following modules have been
+removed and are available as a separate download. The following modules have
-removed:</span></p>
+been removed:</span></p>
 
 <p class=MsoListParagraph style='margin-left:43.5pt;text-indent:-25.5pt'>1.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -2244,19 +2267,19 @@ 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
-based on jAsioHost, the unpacking of that format contained a bug which returned
+is based on jAsioHost, the unpacking of that format contained a bug which
-incorrect numbers, so data were swamped with noise. Both systems are now fixed.
+returned incorrect numbers, so data were swamped with noise. Both systems are
-By preference, users should use the PAMGuard ASIO system since the JAsioHost
+now fixed. By preference, users should use the PAMGuard ASIO system since the
-based system seems to drop samples when many channels are running at high
+JAsioHost based system seems to drop samples when many channels are running at
-sample rate. </span></p>
+high sample rate. </span></p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'>2.<span style='font-size-adjust: none;
 font-stretch: normal'><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span></span><span lang=EN-US>Bug 305. Date and Time not being correctly
 extracted from wav files created using SoundTrap recorders. Fixed by correctly
-finding and unpacking information in the accompanying xml log files that come with
+finding and unpacking information in the accompanying xml log files that come
-SoundTrap files. </span></p>
+with SoundTrap files. </span></p>
 
 <h1><a name="_Latest_Version_1.15.06"></a><span lang=EN-US>Version 1.15.06
 November 2016</span></h1>
@@ -2290,8 +2313,8 @@ data for the least square model. Both fixed. </p>
 
 <p class=MsoListParagraph style='margin-left:40.5pt;text-indent:-22.5pt'>4.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 294. Click classifier was crashing when the 'min amplitude' option
+</span>Bug 294. Click classifier was crashing when the 'min amplitude' option was
-was used. This is fixed. </p>
+used. This is fixed. </p>
 
 <p class=MsoListParagraph style='margin-left:40.5pt;text-indent:-22.5pt'>5.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -2375,9 +2398,9 @@ the database. </span></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>The number of data streams associated with the click detector
+</span><span lang=EN-US>The number of data streams associated with the click
-has been tidied up so that there are a) All Click, b) Tracked Clicks (those
+detector has been tidied up so that there are a) All Click, b) Tracked Clicks
-which are part of an event) and c) Events. </span></p>
+(those which are part of an event) and c) Events. </span></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;
@@ -2393,9 +2416,9 @@ automatic click train identification and tracking. </span></p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><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;
-</span><span lang=EN-US>The automatic click train identification is now using the
+</span><span lang=EN-US>The automatic click train identification is now using
-same internal structures as the manual tracking, so it's possible to combine
+the same internal structures as the manual tracking, so it's possible to
-automatic and manual tracking. </span></p>
+combine automatic and manual tracking. </span></p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>6.</span><span
 lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -2475,8 +2498,9 @@ today.&nbsp; </p>
 
 <p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>5.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 277. Text fields in classifier dialog were not large enough to display
+</span>Bug 277. Text fields in classifier dialog were not large enough to
-times greater than 10ms. We have increased length of text fields in the dialog.</p>
+display times greater than 10ms. We have increased length of text fields in the
+dialog.</p>
 
 <p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>6.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -2494,8 +2518,8 @@ style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&n
 </span>Bug 279. GUI Resizing: The whole PAMGuard GUI would suddenly resize to
 something very small when a dialog is opened. This has been traced to improper
 use of a common dialog component SourcePanel which tries to repack its parent
-Window. Some programmers had inadvertently set it to repack the main PAMGuard GUI
+Window. Some programmers had inadvertently set it to repack the main PAMGuard
-instead. This has been Fixed.</p>
+GUI instead. This has been Fixed.</p>
 
 <p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>8.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -2569,8 +2593,8 @@ and datagram creation.</p>
 
 <h1><a name="_Toc444450394"></a><span lang=EN-US>Version 1.15.00 February 2016</span></h1>
 
-<p class=MsoNormal><span lang=EN-US>Beta Version 1.15.00 64 bit and Core version
+<p class=MsoNormal><span lang=EN-US>Beta Version 1.15.00 64 bit and Core
-1.15.00 32 bit. Both using identical Java core software but linking to
+version 1.15.00 32 bit. Both using identical Java core software but linking to
 different libraries for control of sound input devices. </span></p>
 
 <p class=MsoNormal><span lang=EN-US>This is the first release of a 64 bit
@@ -2638,12 +2662,12 @@ boundaries when file durations are set to a maximum fixed value. </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><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;
-</span>Bug 262. Access to SQLite database conversion. This would fail when tables
+</span>Bug 262. Access to SQLite database conversion. This would fail when
-were present which were not created by PAMGuard. &nbsp;Fixes have been put in
+tables were present which were not created by PAMGuard. &nbsp;Fixes have been
-place for spaces in the table name or for not having an 'Id' column. Fixes have
+put in place for spaces in the table name or for not having an 'Id' column.
-not been implemented for spaces in a column name or use of a reserved word as a
+Fixes have not been implemented for spaces in a column name or use of a
-column name, however if either of these problems do exist it will no longer
+reserved word as a column name, however if either of these problems do exist it
-crash but issue a clear warning and carry onto the next table.</p>
+will no longer crash but issue a clear warning and carry onto the next table.</p>
 
 <p class=MsoNormal style='margin-left:18.0pt'><span lang=EN-US>&nbsp;</span></p>
 
@@ -2878,8 +2902,8 @@ minutes and seconds. Now correctly displays the number of remaining days. </p>
 
 <p class=MsoListParagraph style='margin-left:47.25pt;text-indent:-29.25pt'><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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 226. Spectrogram Mark Observer list doesn't refresh when modules added
+</span>Bug 226. Spectrogram Mark Observer list doesn't refresh when modules
-or removed. </p>
+added or removed. </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;
@@ -3049,12 +3073,11 @@ sonobuoys. See online help for details.&nbsp; </p>
 
 <p class=MsoNormal><i>MEAL Localiser</i> (Localisation Group)</p>
 
-<p class=MsoNormal>This module, developed by Jamie Macaulay of St Andrews
+<p class=MsoNormal>This module, developed by Jamie Macaulay of St Andrews University
-University estimates the 3D localisation of clicks using a variety of
+estimates the 3D localisation of clicks using a variety of algorithms. It's
-algorithms. It's primarily been developed to track harbour porpoise in three
+primarily been developed to track harbour porpoise in three dimensions over
-dimensions over scales of 10's of metres. While currently only working with
+scales of 10's of metres. While currently only working with output from the
-output from the click detector, we hope eventually to extend its use to
+click detector, we hope eventually to extend its use to whistles as well. </p>
-whistles as well. </p>
 
 <p class=MsoNormal><i>Accelerometer Readout</i> (Sensors group)</p>
 
@@ -3072,12 +3095,12 @@ marine mammal survey package. See online help for details. </p>
 
 <p class=MsoNormal><i>Alarms</i> (Utilities Group)</p>
 
-<p class=MsoNormal>This is a general system of visual and audio alarms developed
+<p class=MsoNormal>This is a general system of visual and audio alarms
-by Doug Gillespie for use on a variety of projects. The alarms can be coupled
+developed by Doug Gillespie for use on a variety of projects. The alarms can be
-to any module or detector in PAMGuard. Where appropriate, modules can control
+coupled to any module or detector in PAMGuard. Where appropriate, modules can
-which of their data will cause an alarm action (e.g. in the Click detector you
+control which of their data will cause an alarm action (e.g. in the Click
-can set which types of classified click will fire the alarm). See online help
+detector you can set which types of classified click will fire the alarm). See
-for details. &nbsp;</p>
+online help for details. &nbsp;</p>
 
 <p class=MsoNormal><i>Noise Band Monitor</i> (Sound Processing Group)</p>
 
@@ -3141,8 +3164,8 @@ Millisecond time is also now included in the output file names. </p>
 
 <p class=MsoNormal>Datagram options in Viewer have been improved so that the
 user has to verify the time binning for datagrams the first time the viewer is
-run and can also change the time bins from the File menu (See the File/BinaryStore/Datagram
+run and can also change the time bins from the File menu (See the
-options menu. </p>
+File/BinaryStore/Datagram options menu. </p>
 
 <p class=MsoNormal><i>Viewer Configuration</i></p>
 
@@ -3164,8 +3187,8 @@ horizon. </p>
 
 <p class=MsoNormal><i>Improved Filter Options</i></p>
 
-<p class=MsoNormal>Filter options (used as stand-alone filter modules and also
+<p class=MsoNormal>Filter options (used as stand-alone filter modules and also within
-within many other modules, such as the click detector and the Filtered Noise
+many other modules, such as the click detector and the Filtered Noise
 Measurement module) have been improved so that the user can specify arbitrarily
 shaped Finite Impulse Response filters (see online help for details). </p>
 
@@ -3275,9 +3298,9 @@ other data sources for the PAMGuard viewer. </p>
 
 <p class=MsoNormal style='margin-left:36.0pt'><i>Database</i></p>
 
-<p class=MsoNormal style='margin-left:36.0pt'>Can now copy data from binary storage
+<p class=MsoNormal style='margin-left:36.0pt'>Can now copy data from binary
-to the database offline for any module having both binary and database storage.
+storage to the database offline for any module having both binary and database
-</p>
+storage. </p>
 
 <p class=MsoNormal style='margin-left:36.0pt'>Can create a blank MS Access
 database (2007 and later *.accdb formats only).</p>
@@ -3376,8 +3399,8 @@ elements has been fixed. </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Database Speed: A substantial rewriting of some of the indexing methods in
+</span>Database Speed: A substantial rewriting of some of the indexing methods
-the database module has led to a significant increase in the speed at which
+in the database module has led to a significant increase in the speed at which
 data are written to the database (orders of magnitude for large databases).
 This is having a significant impact on the overall reliability of the software.
 Other changes have increased the speed (again by orders of magnitude) at which
@@ -3469,9 +3492,9 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span>Offline event marking. Offline event marking similar to functionality in
-RainbowClick is now available in the PAMGUARD viewer. Event summary data is stored
+RainbowClick is now available in the PAMGUARD viewer. Event summary data is
-in the database and can also be exported to text files (e.g. for importing into
+stored in the database and can also be exported to text files (e.g. for
-the Distance software).&nbsp; </p>
+importing into the Distance software).&nbsp; </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -3506,8 +3529,8 @@ features of the display:</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>The spectrogram will automatically generate and display spectrogram
+</span>The spectrogram will automatically generate and display spectrogram data.
-data. </p>
+</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -3578,8 +3601,8 @@ the correct data stream. This has been fixed. </p>
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span>Whistle classifier has some new features in the classifier training
-panel. It is also now possible to export training data files directly from binary
+panel. It is also now possible to export training data files directly from
-data files. </p>
+binary data files. </p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -3618,10 +3641,10 @@ 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
 displaying spectrogram data during viewer mode operation.&nbsp; </p>
 
 <p class=MsoNormal>3. Heading sensor readout</p>
@@ -3696,14 +3719,14 @@ lookup tables relating hardware channel numbers to internal channel numbers.
 0 and 1 from a normal sound card or a list of channels 0,1,2,3, etc from an
 ASIO card or National Instruments card. However, when using the ASIO sound
 acquisition system, it is possible to read out hardware channels 2,3,4,5 say
-and those numbers would propagate through PAMGUARD and be used by all the
+and those numbers would propagate through PAMGUARD and be used by all the detectors.
-detectors. While this gave some clarity to&nbsp; the displays, it also created
+While this gave some clarity to&nbsp; the displays, it also created a number of
-a number of problems since look up tables were constantly required to relate
+problems since look up tables were constantly required to relate hardware
-hardware numbers and software numbers in every PAMGUARD module. Since this type
+numbers and software numbers in every PAMGUARD module. Since this type of
-of channel numbering was only implemented several years into the PAMGUARD
+channel numbering was only implemented several years into the PAMGUARD project,
-project, it was never fully implemented or well supported by the different
+it was never fully implemented or well supported by the different modules which
-modules which resulted in a number of bugs which could cause confusion as to
+resulted in a number of bugs which could cause confusion as to which
-which hydrophones were being used during localisation or during calibrated
+hydrophones were being used during localisation or during calibrated
 measurement. The situation tended to only arise with a small number of ASIO
 sound cards such as the RME Fireface 400 on which the most useful inputs, the
 balanced line inputs, are hardware channels 4,5,6 and 7 on the back of the
@@ -3718,10 +3741,10 @@ re-label those channels 0,1,2,3. </p>
 <p class=MsoNormal>There have been other annoyances with the ASIO channel
 numbering scheme. For instance, if you had a configuration which worked in real
 time using channels 7 and 8 of a sound card, you could not use that same
-configuration to analyse wav files, which would always read their data as
+configuration to analyse wav files, which would always read their data as channels
-channels 0 and 1. Similarly if you switched sound cards, you may have to
+0 and 1. Similarly if you switched sound cards, you may have to reconfigure
-reconfigure every detector and several of the displays to handle the changes in
+every detector and several of the displays to handle the changes in channel
-channel numbering. </p>
+numbering. </p>
 
 <p class=MsoNormal>I have spent a considerable amount of time trying to work
 out a better system for handling channel numbering in PAMGUARD and have decided
@@ -3832,10 +3855,10 @@ port is closed. Might prevent a few problems when using a GPS. </p>
 <p class=MsoNormal>Crashes caused in real time or Mixed Mode if the number of
 software channels exceeds the number of hydrophones configured in the array
 manager. It is of course illogical to have software channels which are not
-assigned to a hydrophone, so rather than entirely prevent PAMGUARD from crashing
+assigned to a hydrophone, so rather than entirely prevent PAMGUARD from
-I have inserted additional checks into the hydrophone array dialog which will
+crashing I have inserted additional checks into the hydrophone array dialog
-prevent the user from closing that dialog unless all software channels are
+which will prevent the user from closing that dialog unless all software
-assigned to a hydrophone. </p>
+channels are assigned to a hydrophone. </p>
 
 <h2><span style='font-weight:normal'>Version 1.8.01 Beta February 2010</span></h2>
 
@@ -3917,10 +3940,10 @@ synchronisation.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Wigner time-frequency plot for the click detector. Clicks are NOT
+</span>Wigner time-frequency plot for the click detector. Clicks are NOT automatically
-automatically displayed in the Winger window as they are for the waveform and
+displayed in the Winger window as they are for the waveform and spectrum
-spectrum windows since the Wigner transformation is very time consuming. Clicks
+windows since the Wigner transformation is very time consuming. Clicks will be
-will be displayed if you select them with the mouse.</p>
+displayed if you select them with the mouse.</p>
 
 <p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -3932,15 +3955,15 @@ classifier is still available). </p>
 Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span>Bearing ambiguity resolution for planar and volumetric arrays. New
 features in array dialog for estimations of errors on array location. These
-feed into to a maximum likelihood estimate of angles from small 2D or 3D sub arrays
+feed into to a maximum likelihood estimate of angles from small 2D or 3D sub
-to give two polar angle coordinates. this can be used to resolve left right
+arrays to give two polar angle coordinates. this can be used to resolve left
-ambiguity and is implemented for both the click and the whistle/moan detectors.
+right ambiguity and is implemented for both the click and the whistle/moan
-As a result, the click detector bearing time display can now be set to go from
+detectors. As a result, the click detector bearing time display can now be set
--180 to 180 degrees rather than 0 - 180 degrees. In this case, clicks in the
+to go from -180 to 180 degrees rather than 0 - 180 degrees. In this case,
-upper half of the bearing display will be to port and clicks in the right half
+clicks in the upper half of the bearing display will be to port and clicks in
-will be to starboard. As you pass a whale which is to port, the clicks will
+the right half will be to starboard. As you pass a whale which is to port, the
-move UP the display. In the long term, I hope to turn this display around so
+clicks will move UP the display. In the long term, I hope to turn this display
-that time is up the screen rather than across.&nbsp; </p>
+around so that time is up the screen rather than across.&nbsp; </p>
 
 <p class=MsoNormal><b>Small features and bug fixes</b></p>
 
@@ -4135,10 +4158,10 @@ help pages</p>
 
 <p class=MsoNormal><b>Bug Fixes</b></p>
 
-<p class=MsoNormal>Memory leak caused by Night / Day colour manager now fixed. This
+<p class=MsoNormal>Memory leak caused by Night / Day colour manager now fixed.
-would cause memory leaks when multiple files were being analysed off-line and
+This would cause memory leaks when multiple files were being analysed off-line
-would eventually crash PAMGUARD. The way that colours are managed in PAMGUARD
+and would eventually crash PAMGUARD. The way that colours are managed in
-has been rewritten.&nbsp; </p>
+PAMGUARD has been rewritten.&nbsp; </p>
 
 <p class=MsoNormal>Some issues with Swing fixed that might have been causing
 hang ups on startup especially on Macs/Linux machines</p>
@@ -4151,9 +4174,9 @@ Mac/Linux machines)</p>
 
 <p class=MsoNormal>Parameters dialog shows correct channel numbers</p>
 
-<p class=MsoNormal>Click classifier mean filter option had a computational
+<p class=MsoNormal>Click classifier mean filter option had a computational error
-error which meant that classifiers using this option would not work. This has
+which meant that classifiers using this option would not work. This has now
-now been fixed. </p>
+been fixed. </p>
 
 <p class=MsoNormal><b>Sound Recorder</b></p>
 
@@ -4209,8 +4232,8 @@ file)</p>
 
 <p class=MsoNormal><b>Changes</b></p>
 
-<p class=MsoNormal>The User Input module (for text entry of information by the user)
+<p class=MsoNormal>The User Input module (for text entry of information by the
-has been moved from the Displays sub menu of the Add Modules menu, to
+user) has been moved from the Displays sub menu of the Add Modules menu, to
 Utilities. This will not affect how existing settings files are loaded. </p>
 
 <p class=MsoNormal><b>Multi-screen environments.</b></p>
@@ -4229,8 +4252,8 @@ acquisition.&nbsp; </p>
 
 <p class=MsoNormal><b>Bug fixes</b></p>
 
-<p class=MsoNormal>Speed up of graphics, particularly regarding large quantities
+<p class=MsoNormal>Speed up of graphics, particularly regarding large
-of gps track &nbsp;data</p>
+quantities of gps track &nbsp;data</p>
 
 <p class=MsoNormal>National Instruments cards with names &gt; 20 characters
 long are now correctly &nbsp;recognised. </p>
@@ -4713,12 +4736,12 @@ and Ishmael-type detectors and localisers. </p>
 <p class=MsoNormal>Information from above modules can be displayed on
 configurable user displays which support real time scrolling spectrograms and
 radar displays. Detection and localisation information can be optionally
-displayed on the map display.Map enhancements include improved scrolling whereby
+displayed on the map display.Map enhancements include improved scrolling
-the user can click and drag to pan the area. PamGuard can now interface with
+whereby the user can click and drag to pan the area. PamGuard can now interface
-MySQL database servers and users can easily select which information is logged.
+with MySQL database servers and users can easily select which information is
-(This replaces the previous 'flat-file' logging feature). A simulation module
+logged. (This replaces the previous 'flat-file' logging feature). A simulation
-allows virtual vocalising animals to be placed on the map to assist in training
+module allows virtual vocalising animals to be placed on the map to assist in
-and development. Extensive online user help has been added to PamGuard
+training and development. Extensive online user help has been added to PamGuard
 Application</p>
 
 <h2>0.03b - first version used in a real 'at sea' environment.18/08/06</h2>

pom.xml

@@ -784,7 +784,7 @@
  	<dependency>
 	    <groupId>pamguard.org</groupId>
 	    <artifactId>x3</artifactId>
-	    <version>2.1.0</version>
+	    <version>2.2.0</version>
 	</dependency>
 	
 		<!-- https://mvnrepository.com/artifact/it.sauronsoftware/jave -->

repo/pamguard/org/x3/2.2.0/_remote.repositories

@@ -0,0 +1,4 @@
+#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
+#Fri Nov 11 13:13:18 GMT 2022
+x3-2.2.0.jar>=
+x3-2.2.0.pom>=

repo/pamguard/org/x3/2.2.0/x3-2.2.0.pom

@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>pamguard.org</groupId>
+  <artifactId>x3</artifactId>
+  <version>2.2.0</version>
+  <description>POM was created from install:install-file</description>
+</project>

src/Acquisition/FileInputSystem.java

@@ -587,7 +587,7 @@ public class FileInputSystem  extends DaqSystem implements ActionListener, PamSe
 			System.out.println("The current file was null");
 			return false;
 		}
-		System.out.printf("***********************************             Opening file %s\n", currentFile.getName());
+//		System.out.printf("***********************************             Opening file %s\n", currentFile.getName());
 
 		try {
 

src/Acquisition/filetypes/SoundFileTypes.java

@@ -40,7 +40,7 @@ public class SoundFileTypes {
 	}
 	
 	/**
-	 * Get a list of used file types. Reaslistically this 
+	 * Get a list of used file types. Realistically 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

src/help/JavaHelpSearch/SCHEMA

@@ -1,2 +1,2 @@
 JavaSearch 1.0
-TMAP bs=2048 rt=1 fl=-1 id1=6697 id2=1
+TMAP bs=2048 rt=1 fl=-1 id1=6700 id2=1

src/help/PAMGUARD.hs

@@ -22,6 +22,7 @@
   
   
   
+  
   
   
   <title>Help </title>
@@ -46,6 +47,7 @@
   
   
   
+  
   
   
   <maps>
@@ -70,6 +72,7 @@
     
     
     
+    
     
     
     <homeID>
@@ -96,6 +99,7 @@ top
     
     
     
+    
     
     
     <mapref location="Map.jhm"/>
@@ -120,6 +124,7 @@ top
   
   
   
+  
   
   
   </maps>
@@ -144,6 +149,7 @@ top
   
   
   
+  
   
   
   <view mergetype="javax.help.UniteAppendMerge">
@@ -168,6 +174,7 @@ top
     
     
     
+    
     
     
     <name>
@@ -194,6 +201,7 @@ TOC
     
     
     
+    
     
     
     <label>
@@ -220,6 +228,7 @@ TOC
     
     
     
+    
     
     
     <type>
@@ -246,6 +255,7 @@ javax.help.TOCView
     
     
     
+    
     
     
     <data>
@@ -272,6 +282,7 @@ PAMGUARDTOC.xml
   
   
   
+  
   
   
   </view>
@@ -296,6 +307,7 @@ PAMGUARDTOC.xml
   
   
   
+  
   
   
   <view>
@@ -320,6 +332,7 @@ PAMGUARDTOC.xml
     
     
     
+    
     
     
     <name>
@@ -346,6 +359,7 @@ Index
     
     
     
+    
     
     
     <label>
@@ -372,6 +386,7 @@ Index
     
     
     
+    
     
     
     <type>
@@ -398,6 +413,7 @@ javax.help.IndexView
     
     
     
+    
     
     
     <data>
@@ -424,6 +440,7 @@ PAMGUARDIndex.xml
   
   
   
+  
   
   
   </view>
@@ -448,6 +465,7 @@ PAMGUARDIndex.xml
   
   
   
+  
   
   
   <view>
@@ -472,6 +490,7 @@ PAMGUARDIndex.xml
     
     
     
+    
     
     
     <name>
@@ -498,6 +517,7 @@ Search
     
     
     
+    
     
     
     <label>
@@ -524,6 +544,7 @@ Search
     
     
     
+    
     
     
     <type>
@@ -550,6 +571,7 @@ javax.help.SearchView
     
     
     
+    
     
     
     <data engine="com.sun.java.help.search.DefaultSearchEngine">
@@ -576,6 +598,7 @@ JavaHelpSearch
   
   
   
+  
   
   
   </view>
@@ -600,6 +623,7 @@ JavaHelpSearch
 
 
 
+
 
 
 </helpset>

src/help/PAMGUARDIndex.xml

@@ -2,6 +2,16 @@
 <!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="SUD Files " target="sound_processing.AcquisitionHelp.docs.sudfiles"/>
+
+ <indexitem text="SoundTrap " target="sound_processing.AcquisitionHelp.docs.sudfiles"/>
+
+ <indexitem text="Sound Trap " target="sound_processing.AcquisitionHelp.docs.sudfiles"/>
+
+ <indexitem text="Click Train " target="detectors.ClickTrainDetector.docs.ClickTrainDetector"/>
+
+ <indexitem text="SUD " target="detectors.clickDetectorHelp.docs.SoundTrapClickDetector"/>
+
  <indexitem text="SoundTrap " target="detectors.clickDetectorHelp.docs.SoundTrapClickDetector"/>
 
  <indexitem text="3D Localisation " target="detectors.Pam3DHelp.docs.guiOverview"/>

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

@@ -1,23 +1,21 @@
 <!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>
+<body><h1>Click Detector</h1>
-SoundTrap Click Detector
+<h2>SoundTrap Click Detector</h2>
-</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 
+<p>The SoundTrap click detector allows you to detect and store clicks at high frequencies (say 384kS/sec), 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 
+at the same time, record audio data files at a lower frequency (e.g. 96 or 48kS/sec). This optimises disk space usage and makes long deployments 
-of several months possible with moderate data storage. </p> 
+of several months possible without running out of data storage. </p> 
-<p>Having two sample rates present within a single PAMGuard configuration is possible, using 
+<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
+<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 
+<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>
@@ -28,7 +26,7 @@ SoundTrap recordings, then use a normal <a href="ClickDetector_clickDetector.htm
 	<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.
+			Detector'</i> near the bottom of the Detectors list. Enter a descriptive name for the new detector and press Ok.
 	</p>
 	
 	<h3>Importing SoundTrap Data</h3>
@@ -50,13 +48,17 @@ SoundTrap recordings, then use a normal <a href="ClickDetector_clickDetector.htm
 	 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), 
+	 <p>If you want to run additional analysis on the WAV file data (for example to 
+	<a href="../../../sound_processing/NoiseBands/Docs/NoiseBands.html">make noise measurements</a> or to 
+	 <a href="../../whistleMoanHelp/docs/whistleMoan_Overview.html">detect whistles</a>), 
 	 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 
+	<p>Current versions of PAMGuard can read <a href="../../../sound_processing/AcquisitionHelp/docs/sudfiles.html">SUD files</a> 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 
+	<p>Better still, you can now set up PAMGuard in normal mode to simultaneously process the audio data in the 
+	<a href="../../../sound_processing/AcquisitionHelp/docs/sudfiles.html">SUD file</a> 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 

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

@@ -18,6 +18,11 @@ SoundTrap recorders from
  <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>Mixing SUD and WAV files</h3>
+ <p>If a SUD file and a WAV file with the same name are in the same folder, then PAMGuard will ignore the SUD file
+ and process the WAV file. Note that in this case, PAMGuard will be unable to extract any metadata from the SUD file
+ and will not extract SoundTrap Click Detections (see below).</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>