Final final 2.02.06

Don't believe it until you see that tag

README.html

@@ -469,7 +469,7 @@ whistle classification module.</span></p>
 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,
+detector can also happen while processing SUD file data with other detectors,
 thereby streamlining the whole processing chain. Read the online Help for
 details. &nbsp;&nbsp;</span></p>
 
@@ -488,10 +488,10 @@ 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>
 
-<p class=MsoNormal><span lang=EN-US>Addition of data selectors to the minimum
+<p class=MsoNormal><span lang=EN-US>Addition of data selectors to the minimum number
-number of clicks accepted by the classifier. This allows the click-by-click
+of clicks accepted by the classifier. This allows the click-by-click classifier
-classifier and the click train detector to be used to together to improve
+and the click train detector to be used to together to improve classification
-classification accuracy. </span></p>
+accuracy. </span></p>
 
 <p class=MsoNormal><b><span lang=EN-US>Bug fixes</span></b></p>
 
@@ -503,8 +503,8 @@ classifier was being trimmed. </span></p>
 
 <p class=MsoNormal><b><span lang=EN-US>Documentation</span></b></p>
 
-<p class=MsoNormal><span lang=EN-US>Comprehensive help file including description
+<p class=MsoNormal><span lang=EN-US>Comprehensive help file including
-of the algorithm, screen grabs and examples.</span></p>
+description of the algorithm, screen grabs and examples.</span></p>
 
 <p class=MsoNormal><span lang=EN-US>Bug fixes</span></p>
 
@@ -639,9 +639,9 @@ href="http://www.pamguard.org/downloads.php?cat_id=3">here</a>.</p>
 lang=EN-US> </span></p>
 
 <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
+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>
@@ -1069,11 +1069,10 @@ placement, etc.</p>
 <h1><a name="_Latest_Beta_Version_2.01.03"></a><span lang=EN-US>Version 2.01.03
 February 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)
@@ -1128,8 +1127,9 @@ lang=EN-US> </span>Bug 442. BT Display does not change click symbol color when
 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>
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
-Bug 443. NI playback crashing immediately if a device is not present.</p>
+lang=EN-US> </span>Bug 443. NI playback crashing immediately if a device is not
+present.</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>
@@ -1138,8 +1138,8 @@ 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
+Bug 445. Overlay data in FX spectrogram display gets out of sync with underlying
-underlying spectrogram image.</p>
+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>
@@ -1178,9 +1178,9 @@ Added option in Sound Acquisition settings dialog to 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>
+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 Whistle &amp; Moan Detector data selector to only display
+lang=EN-US> </span>Add option to Whistle &amp; Moan Detector data selector to
-whistles that have super-detections. </p>
+only display whistles that have super-detections. </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><span
@@ -1288,8 +1288,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
 lang=EN-US> </span>Difar enhancements based on recent field testing.</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>
+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 localisation capabilities.</p>
+lang=EN-US> </span>Click Train Detector upgrades, including localisation
+capabilities.</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><span
@@ -1392,9 +1393,9 @@ lang=EN-US> </span>Added adaptive noise filter to Ishmael Detectors.</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> </span>Many upgrades to the Sound Playback module, including a
-high-pass filter, gain control, and the ability to mix wavefrom and envelope
+high-pass filter, gain control, and the ability to mix wavefrom and envelope data
-data together to listen to high-frequency clicks and dolphin whistles at the
+together to listen to high-frequency clicks and dolphin whistles at the same
-same time.</p>
+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>
@@ -1978,8 +1979,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
 Added sound playback and other useful information to bar on FX display</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
-Updates/bug fixes to the landmark module. </p>
+lang=EN-US> </span>Updates/bug fixes to the landmark module. </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
@@ -2107,8 +2108,8 @@ 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
+was not performing data purging when using classifiers developed for
 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
@@ -2140,8 +2141,8 @@ parameters to Event classifier</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>The installer now allows the user to enter command line switches/parameters
+</span>The installer now allows the user to enter command line
-to be included in *.ini files.</p>
+switches/parameters to be included in *.ini files.</p>
 
 <h1><a name="_Version_1.15.10"></a><span lang=EN-US>Version 1.15.10 March 2017</span></h1>
 
@@ -2155,8 +2156,8 @@ list grew to a ridiculous size. Code has been put in place to a) stop it
 happening again and b) to repair any configuration files which are corrupted.
 Corrupted files will be slow to load, slow to save and will be &gt; several
 megabytes in size. It may be necessary to delete the PamguardSettings table in
-any databases since these too may have become oversized which will slow down
+any databases since these too may have become oversized which will slow down viewer
-viewer mode PAMGuard start-up.</p>
+mode PAMGuard start-up.</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;
@@ -2219,9 +2220,9 @@ 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,
@@ -2313,8 +2314,8 @@ until now. It's fixed.</p>
 
 <p class=MsoListParagraph style='margin-left:40.5pt;text-indent:-22.5pt'>2.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 292. Incorrect labels on Target Motion panel in viewer - 3D algorithm
+</span>Bug 292. Incorrect labels on Target Motion panel in viewer - 3D
-was labelled as 2D.Fixed</p>
+algorithm was labelled as 2D.Fixed</p>
 
 <p class=MsoListParagraph style='margin-left:40.5pt;text-indent:-22.5pt'>3.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -2343,8 +2344,8 @@ appear when you right click on the display. </p>
 
 <p class=MsoListParagraph style='margin-left:40.5pt;text-indent:-22.5pt'>7.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-</span>Bug 297. Airgun display was not correctly showing itself at fixed locations,
+</span>Bug 297. Airgun display was not correctly showing itself at fixed
-but always following the vessel track. This is now fixed. </p>
+locations, but always following the vessel track. This is now fixed. </p>
 
 <p class=MsoListParagraph style='margin-left:40.5pt;text-indent:-22.5pt'>8.<span
 style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -2410,8 +2411,8 @@ 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 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;
@@ -2604,8 +2605,8 @@ 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
+<p class=MsoNormal><span lang=EN-US>Beta Version 1.15.00 64 bit and Core version
-version 1.15.00 32 bit. Both using identical Java core software but linking to
+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
@@ -2617,8 +2618,8 @@ problems immediately to the PAMGuard team. </span></p>
 
 <p class=MsoNormal><b><span lang=EN-US>Other Changes</span></b></p>
 
-<p class=MsoNormal><span lang=EN-US>Updated the configuration file WMM.COF for World
+<p class=MsoNormal><span lang=EN-US>Updated the configuration file WMM.COF for
-Magnetic Model to the latest 2015-2020 version. See
+World Magnetic Model to the latest 2015-2020 version. See
 https://www.ngdc.noaa.gov/geomag/WMM/soft.shtml</span></p>
 
 <p class=MsoNormal><span lang=EN-US>Small changes to the ROCCA classification
@@ -2766,8 +2767,8 @@ events. </span></p>
 
 <p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'><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;
-</span><span lang=EN-US>Bug 250. DIFAR module was crashing if it attempted to
+</span><span lang=EN-US>Bug 250. DIFAR module was crashing if it attempted to triangulate
-triangulate between more than two simultaneous bearings. Fixed. </span></p>
+between more than two simultaneous bearings. Fixed. </span></p>
 
 <p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'><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;&nbsp;
@@ -2826,8 +2827,8 @@ writing results files. Fixed. </p>
 
 <p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'><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;&nbsp;
-</span>Bug 237. Logger forms not saving data to database after sound acquisition
+</span>Bug 237. Logger forms not saving data to database after sound
-starts. Fixed. </p>
+acquisition starts. 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;
@@ -2868,17 +2869,17 @@ which is useful when using PAMGuard for demonstration purposes. </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>The sound File and Folder audio input systems now have an optional time
+</span>The sound File and Folder audio input systems now have an optional time zone
-zone setting. Note that PAMGuard analysis should still all be taking place in
+setting. Note that PAMGuard analysis should still all be taking place in UTC
-UTC and that this option is intended to allow the conversion of file times
+and that this option is intended to allow the conversion of file times which
-which were not recorded as UTC into UTC and not the other way around. Use the
+were not recorded as UTC into UTC and not the other way around. Use the option
-option with caution !</p>
+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 available
+</span>The Open Office Database system has been removed from the list of
-options since it is not reliable. If you require a free database solution we
+available options since it is not reliable. If you require a free database
-recommend you use the MySql Community Server <a
+solution we 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
@@ -2987,9 +2988,8 @@ total loss of the PAMGuard configuration in viewer mode and has been rectified.
 7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>Bug
 218. SAIL Acquisition card would hang the system. This has also been fixed. </p>
 
-<p class=MsoListParagraph style='text-indent:-18.0pt'>7.&nbsp;&nbsp;&nbsp; Bug
+<p class=MsoListParagraph style='text-indent:-18.0pt'>7.&nbsp;&nbsp;&nbsp; Bug 219.
-219. Problems displaying Offline Click Events in the Viewer map have been
+Problems displaying Offline Click Events in the Viewer map have been fixed. </p>
-fixed. </p>
 
 <p class=MsoNormal>&nbsp;</p>
 
@@ -3071,8 +3071,8 @@ 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. PAMGuard
+<p class=MsoNormal>'<i>Start</i>' and '<i>Stop</i>' menu items removed.
-should be started and stopped using the red and black buttons.</p>
+PAMGuard should be started and stopped using the red and black buttons.</p>
 
 <p class=MsoNormal><b>New Modules</b></p>
 
@@ -3087,9 +3087,9 @@ sonobuoys. See online help for details.&nbsp; </p>
 <p class=MsoNormal>This module, developed by Jamie Macaulay of St Andrews
 University estimates the 3D localisation of clicks using a variety of
 algorithms. It's primarily been developed to track harbour porpoise in three
-dimensions over scales of 10's of metres. While currently only working with
+dimensions over scales of 10's of metres. While currently only working with output
-output from the click detector, we hope eventually to extend its use to
+from the click detector, we hope eventually to extend its use to whistles as
-whistles as well. </p>
+well. </p>
 
 <p class=MsoNormal><i>Accelerometer Readout</i> (Sensors group)</p>
 
@@ -3159,25 +3159,24 @@ different. Details are available in the online help. </p>
 <p class=MsoNormal><i>FLAC File Support</i></p>
 
 <p class=MsoNormal>Can now read raw audio data direct from FLAC files. <a
-href="http://en.wikipedia.org/wiki/FLAC">FLAC</a> is a lossless compression
+href="http://en.wikipedia.org/wiki/FLAC">FLAC</a> is a lossless compression algorithm
-algorithm for audio data. Files, or folders of files are accessed in the same
+for audio data. Files, or folders of files are accessed in the same way as WAV
-way as WAV and AIFF files in the Sound Acquisition module. In a future release
+and AIFF files in the Sound Acquisition module. In a future release we also
-we also hope to provide support for writing FLAC files from the sound recorder
+hope to provide support for writing FLAC files from the sound recorder module. </p>
-module. </p>
 
 <p class=MsoNormal><i>Sound Recorder Module</i></p>
 
 <p class=MsoNormal>Now supports writing 8 and 24 bit as well as 16 bit files.
-Also writes data to dated sub folders, starting a new folder each day (UTC). Also
+Also writes data to dated sub folders, starting a new folder each day (UTC).
-provides additional information on disk space on the main display panel.
+Also provides additional information on disk space on the main display panel.
 Millisecond time is also now included in the output file names. </p>
 
 <p class=MsoNormal><i>Datagram Options</i></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
+run and can also change the time bins from the File menu (See the File/BinaryStore/Datagram
-File/BinaryStore/Datagram options menu. </p>
+options menu. </p>
 
 <p class=MsoNormal><i>Viewer Configuration</i></p>
 
@@ -3229,8 +3228,8 @@ whistle.</p>
      longer possible to change configurations once PAMGuard has been launched
      and pressing 'Cancel' on the select dialog causes PAMGuard to exit. </li>
  <li class=MsoNormal style='margin-bottom:0cm'>Airgun display. If this was
-     included in the PAMGuard model before the GPS module it would hang
+     included in the PAMGuard model before the GPS module it would hang PAMGuard.
-     PAMGuard. This has been rectified. </li>
+     This has been rectified. </li>
  <li class=MsoNormal style='margin-bottom:0cm'>Fixed occasional exceptions in
      the sound output modules when playing back from files. </li>
  <li class=MsoNormal style='margin-bottom:0cm'>Fixed exceptions in spectrogram
@@ -3411,10 +3410,10 @@ 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
+</span>Database Speed: A substantial rewriting of some of the indexing methods in
-in the database module has led to a significant increase in the speed at which
+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
+data are written to the database (orders of magnitude for large databases).
-is having a significant impact on the overall reliability of the software.
+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
 data are read back into PAMGuard when using the viewer. </p>
 
@@ -3558,9 +3557,9 @@ to 0dN</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 Binary store now saves a complete data map between runs of the PAMGUARD
+</span>The Binary store now saves a complete data map between runs of the
-viewer. This leads to significant improvements in the time the viewer takes to
+PAMGUARD viewer. This leads to significant improvements in the time the viewer
-load large data sets.</p>
+takes to load large data sets.</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;
@@ -3634,10 +3633,10 @@ source, even if that data source is loaded after the FFT module is created.</p>
 
 <p class=MsoNormal>1. Binary storage module. </p>
 
-<p class=MsoNormal>Performs a parallel role to the PAMGAURD database but uses
+<p class=MsoNormal>Performs a parallel role to the PAMGAURD database but uses binary
-binary files in a proprietary format which is considerably more efficient for
+files in a proprietary format which is considerably more efficient for data of
-data of unknown length such as whistle contours or small clips of click
+unknown length such as whistle contours or small clips of click waveform. This
-waveform. This feature is currently implemented in the following modules:</p>
+feature is currently implemented in the following modules:</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;
@@ -3653,8 +3652,8 @@ 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
+<p class=MsoNormal>The offline viewer is much improved with better data scrolling
-scrolling and the ability to view data either stored in the database or the binary
+and the ability to view data either stored in the database or the binary
 storage system. Work has stated on functions which read and use data stored in
 audio files. This is currently limited to re-calculating and displaying
 displaying spectrogram data during viewer mode operation.&nbsp; </p>
@@ -3679,8 +3678,8 @@ frequency division (i.e. previous versions would convert well from 96kHz to
 <p class=MsoNormal>1. Placement of axes on some displays (array manager and
 depth side panel). Problem in 1.9.01 Beta now fixed. </p>
 
-<p class=MsoNormal>2. Fixed problems of NMEA read out not restarting after a serial
+<p class=MsoNormal>2. Fixed problems of NMEA read out not restarting after a
-drop out. NMEA now restarts correctly. </p>
+serial drop out. NMEA now restarts correctly. </p>
 
 <p class=MsoNormal>3. Fixed a memory leak which caused occasional crashes,
 particularly when large numbers of files were processed offline. </p>
@@ -3754,22 +3753,23 @@ re-label those channels 0,1,2,3. </p>
 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
-channels 0 and 1. Similarly if you switched sound cards, you may have to
+channels 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
 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
-dialog, you will see them listed as channels 0,1,2 and 3. &nbsp;The consequences
+dialog, you will see them listed as channels 0,1,2 and 3. &nbsp;The
-of doing this are mainly very good. Most users will not notice any changes. For
+consequences of doing this are mainly very good. Most users will not notice any
-those who need for some reason to read channel numbers not starting at zero
+changes. For those who need for some reason to read channel numbers not
-things will be more stable. However, when you go to a new version with this new
+starting at zero things will be more stable. However, when you go to a new
-feature, it will be necessary to reconfigure all the modules in any existing
+version with this new feature, it will be necessary to reconfigure all the
-configurations. To do this, open the configuration dialog for each module in
+modules in any existing configurations. To do this, open the configuration
-turn and select the correct, zero indexed, channel number. </p>
+dialog for each module in turn and select the correct, zero indexed, channel
+number. </p>
 
 <p class=MsoNormal><b>Other Changes / new features</b></p>
 
@@ -3820,9 +3820,9 @@ colour from the Display menu. </p>
 
 <p class=MsoNormal>Database</p>
 
-<p class=MsoNormal>Default name for the Database module has changed from &quot;ODBC
+<p class=MsoNormal>Default name for the Database module has changed from
-Database&quot; to just &quot;Database&quot;. This will not affect existing
+&quot;ODBC Database&quot; to just &quot;Database&quot;. This will not affect
-configurations. </p>
+existing configurations. </p>
 
 <p class=MsoNormal>Sound acquisition</p>
 
@@ -3863,13 +3863,13 @@ port is closed. Might prevent a few problems when using a GPS. </p>
 
 <p class=MsoNormal><b>Bug Fixes</b></p>
 
-<p class=MsoNormal>Crashes caused in real time or Mixed Mode if the number of software
+<p class=MsoNormal>Crashes caused in real time or Mixed Mode if the number of
-channels exceeds the number of hydrophones configured in the array manager. It
+software channels exceeds the number of hydrophones configured in the array
-is of course illogical to have software channels which are not assigned to a
+manager. It is of course illogical to have software channels which are not
-hydrophone, so rather than entirely prevent PAMGUARD from crashing I have
+assigned to a hydrophone, so rather than entirely prevent PAMGUARD from
-inserted additional checks into the hydrophone array dialog which will prevent
+crashing I have inserted additional checks into the hydrophone array dialog
-the user from closing that dialog unless all software channels are assigned to
+which will prevent the user from closing that dialog unless all software
-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>
 
@@ -3880,15 +3880,15 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
 </span>Play back of high frequency wav files through National Instruments (NI)
 cards: When analysing wav files, sound can be output at high frequency
 (depending on the specification of the NI card). The primary motivation for
-this has been to develop a test bed for high frequency sound acquisition whereby
+this has been to develop a test bed for high frequency sound acquisition
-we can play 500kHz recordings of harbour porpoise out of an NI card on one
+whereby we can play 500kHz recordings of harbour porpoise out of an NI card on
-machine, into NI cards on a different machine which are testing high frequency
+one machine, into NI cards on a different machine which are testing high
-versions of the click detector.</p>
+frequency versions of the click detector.</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>Note that this does not (yet) permit simultaneous acquisition and
+</span>Note that this does not (yet) permit simultaneous acquisition and playback
-playback through</p>
+through</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;
@@ -4083,10 +4083,10 @@ 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>New menu functionality by right clicking on any of the tabs of the main
-tab control will allow the user to copy the tab contents to the system
+tab control will allow the user to copy the tab contents to the system clipboard
-clipboard from where it can be copied into other programs (e.g. Word,
+from where it can be copied into other programs (e.g. Word, Powerpoint,
-Powerpoint, etc.).Some modules, such as the map, have this implemented in other
+etc.).Some modules, such as the map, have this implemented in other menus
-menus (right click) and also allow printing.&nbsp; </p>
+(right click) and also allow printing.&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;
@@ -4191,9 +4191,9 @@ now been fixed. </p>
 
 <p class=MsoNormal><b>Sound Recorder</b></p>
 
-<p class=MsoNormal>Level meters are shown for the correct channels (after channel
+<p class=MsoNormal>Level meters are shown for the correct channels (after
-numbering has been changed). Occasional crash due to synchronisation problems
+channel numbering has been changed). Occasional crash due to synchronisation
-when &nbsp;multi-threading now fixed.</p>
+problems when &nbsp;multi-threading now fixed.</p>
 
 <p class=MsoNormal><b>Whistle Detector</b></p>
 
@@ -4467,9 +4467,9 @@ 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>Better drawing of held spectrogram when putting mark rectangles on a spectrogram
+</span>Better drawing of held spectrogram when putting mark rectangles on a
-display. All panels are now correctly frozen. The rectangle is drawn in red on
+spectrogram display. All panels are now correctly frozen. The rectangle is
-the marked panel and in green on other panels. </p>
+drawn in red on the marked panel and in green on other panels. </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;

dependency-reduced-pom.xml

@@ -4,7 +4,7 @@
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
   <name>Pamguard Java12+</name>
-  <version>2.02.05a</version>
+  <version>2.02.06</version>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
   <url>www.pamguard.org</url>
   <organization>

src/Acquisition/AcquisitionControl.java

@@ -210,14 +210,8 @@ public class AcquisitionControl extends PamControlledUnit implements PamSettings
 		else {
 			PamStatusBar statusBar = PamStatusBar.getStatusBar();
 
-			if (statusBar != null) {
+			if (statusBar != null && statusBarComponent != null) {
-				//				statusBar.getToolBar().add(statusBarText = new JLabel());
-				//				fillStatusBarText();
-				//				statusBar.getToolBar().add(levelBar = new JProgressBar(-60, 0));
-				//				levelBar.setValue(-60);
-				//				levelBar.setOrientation(JProgressBar.HORIZONTAL);
 				statusBar.add(statusBarComponent);
-//				statusBar.getToolBar().addSeparator();
 				setupStatusBar();
 			}
 		}
@@ -248,6 +242,7 @@ public class AcquisitionControl extends PamControlledUnit implements PamSettings
 	
 
 	private PamPanel systemPanel;
+	
 	protected Component getStatusBarComponent() {
 		PamPanel p = new PamPanel();
 		p.add(statusBarText = new PamLabel());

src/generalDatabase/DatabaseFetchSpeed.java

@@ -0,0 +1,33 @@
+package generalDatabase;
+
+/**
+ * Run some tests to try to work out why it's so much slower to load 
+ * data when the query is based on a non indexed column compared 
+ * to an index one, even though the actual query execution time 
+ * is a small fraction of the total time. 
+ * @author dg50
+ *
+ */
+public class DatabaseFetchSpeed {
+
+	String dbName = "C:\\ProjectData\\meyGenMayData\\Database\\MeygenTritechDetectHDD_03_24.06.2022.sqlite3";
+	long[] idRange = {9906111, 9906977};
+	long[] uidRange = {8030630, 8031496};
+	String[] utcRange = {"2022-05-24 09:27:34", "2022-05-24 09:27:52"};
+
+	public static void main(String[] args) {
+		// TODO Auto-generated method stub
+
+	}
+
+	public DatabaseFetchSpeed() {
+//
+//		qStr{1} = sprintf('SELECT Id FROM Gemini_Threshold_Detector_Targets WHERE Id BETWEEN %d and %d', ...
+//				idRange(1), idRange(2));
+//		qStr{2} = sprintf('SELECT Id FROM Gemini_Threshold_Detector_Targets WHERE UID BETWEEN %d and %d', ...
+//				uidRange(1), uidRange(2));
+//		qStr{3} = sprintf('SELECT Id FROM Gemini_Threshold_Detector_Targets WHERE UTC BETWEEN ''%s'' and ''%s''', ...
+//				utcRange{1}, utcRange{2});
+
+	}
+}

src/soundtrap/STAcquisitionControl.java

@@ -24,7 +24,10 @@
 
 package soundtrap;
 
+import java.awt.Component;
+
 import Acquisition.AcquisitionControl;
+import Acquisition.DaqSystem;
 
 /**
  * @author SCANS
@@ -34,6 +37,7 @@ public class STAcquisitionControl extends AcquisitionControl {
 
 	public static final String STUNITTYPE = "SoundTrap Data Acquisition";
 	private STAcquisitionProcess stAcquisitionProcess;
+	private STDaqSystem stDaqSystem;
 
 	/**
 	 * @param name
@@ -79,6 +83,7 @@ public class STAcquisitionControl extends AcquisitionControl {
 //		TDDataProviderRegisterFX.getInstance().registerDataInfo(new RawSoundProviderFX(this));
 
 		// add a second PAM process, for the click data
+		registerDaqSystem(stDaqSystem = new STDaqSystem());
 		addPamProcess(stAcquisitionProcess = new STAcquisitionProcess(this));
 
 	}
@@ -101,6 +106,30 @@ public class STAcquisitionControl extends AcquisitionControl {
 		return stAcquisitionProcess;
 	}
 
+//	@Override
+//	protected Component getStatusBarComponent() {
+//		// call it to create the fields, just incase, then return null;
+//		super.getStatusBarComponent();
+//		return null;
+//	}
+
+//	@Override
+//	protected void setupStatusBar() {
+////		if (systemPanel == null) return;
+////		systemPanel.removeAll();
+////		DaqSystem daqSys = findDaqSystem(null);
+////		if (daqSys == null) return;
+////		Component specialComponent = daqSys.getStatusBarComponent();
+////		if (specialComponent != null) {
+////			systemPanel.add(specialComponent);
+////		}
+//	}
+
+	@Override
+	public DaqSystem findDaqSystem(String systemType) {
+		return stDaqSystem;
+	}
+
 	
 
 }

src/soundtrap/STClickControl.java

@@ -63,7 +63,7 @@ public class STClickControl extends ClickControl {
 		super(name);
 		
 		// create a private acquisition control that only this module can see
-		rawSource = new AcquisitionControl("Private Sound Acq for Soundtrap Click Detector");
+		rawSource = new STAcquisitionControl("Private Sound Acq for Soundtrap Click Detector");
 		
 		sudFileDWVHandler = new SudFileDWVHandler(this);
 		sudFileDWVHandler.subscribeSUD();

src/soundtrap/STDaqSystem.java

@@ -0,0 +1,107 @@
+package soundtrap;
+
+import javax.swing.JComponent;
+
+import Acquisition.AcquisitionControl;
+import Acquisition.AcquisitionDialog;
+import Acquisition.DaqSystem;
+
+public class STDaqSystem extends DaqSystem {
+
+	public STDaqSystem() {
+		// TODO Auto-generated constructor stub
+	}
+
+	@Override
+	public String getSystemType() {
+		return "SoundTrap clicks";
+	}
+
+	@Override
+	public String getSystemName() {
+		return "SoundTrap clicks";
+	}
+
+	@Override
+	public JComponent getDaqSpecificDialogComponent(AcquisitionDialog acquisitionDialog) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public void dialogSetParams() {
+		// TODO Auto-generated method stub
+
+	}
+
+	@Override
+	public boolean dialogGetParams() {
+		// TODO Auto-generated method stub
+		return false;
+	}
+
+	@Override
+	public int getMaxSampleRate() {
+		return PARAMETER_UNKNOWN;
+	}
+
+	@Override
+	public int getMaxChannels() {
+		return 1;
+	}
+
+	@Override
+	public double getPeak2PeakVoltage(int swChannel) {
+		// TODO Auto-generated method stub
+		return 2;
+	}
+
+	@Override
+	public boolean prepareSystem(AcquisitionControl daqControl) {
+		// TODO Auto-generated method stub
+		return true;
+	}
+
+	@Override
+	public boolean startSystem(AcquisitionControl daqControl) {
+		// TODO Auto-generated method stub
+		return true;
+	}
+
+	@Override
+	public void stopSystem(AcquisitionControl daqControl) {
+		// TODO Auto-generated method stub
+
+	}
+
+	@Override
+	public boolean isRealTime() {
+		// TODO Auto-generated method stub
+		return true;
+	}
+
+	@Override
+	public boolean canPlayBack(float sampleRate) {
+		// TODO Auto-generated method stub
+		return false;
+	}
+
+	@Override
+	public int getDataUnitSamples() {
+		// TODO Auto-generated method stub
+		return 100;
+	}
+
+	@Override
+	public void daqHasEnded() {
+		// TODO Auto-generated method stub
+
+	}
+
+	@Override
+	public String getDeviceName() {
+		// TODO Auto-generated method stub
+		return "Sound Trap detector";
+	}
+
+}

src/soundtrap/STToolsControl.java

@@ -12,6 +12,7 @@ import PamController.PamControlledUnit;
 import PamController.PamControlledUnitSettings;
 import PamController.PamSettingManager;
 import PamController.PamSettings;
+import PamView.dialog.warn.WarnOnce;
 
 public class STToolsControl extends PamControlledUnit implements PamSettings {
 
@@ -21,9 +22,17 @@ public class STToolsControl extends PamControlledUnit implements PamSettings {
 	public static final String dwvFileEnd = ".dwv";
 	public static final String bclFileEnd = ".bcl";
 	
+	private String warn = "<html>Versions 2.02.06 of PAMGuard and later can read SoundTrap SUD files directly, removing the need " +
+	" to decompress them and then use this module to import the SoundTrap click detector data into PAMGuard.<p><br>" + 
+			"Instead you should process the SUD files in 'normal mode' and include a SoundTrap Click Detector in "
+			+ "your configuration. Click data will then be automatically unpacked into the correct binary files"
+			+ " as you process the SUD file audio data.<p><br>"
+			+ "You can remove this module which is now obsolete. See the online help for details.";
+	
 	public STToolsControl(String unitName) {
 		super("Sound Trap Tools", unitName);
 		PamSettingManager.getInstance().registerSettings(this);
+		WarnOnce.showWarning("Importing SoundTrap data", warn, WarnOnce.WARNING_MESSAGE);
 	}
 
 	/* (non-Javadoc)

src/soundtrap/sud/SudFileDWVHandler.java

@@ -77,6 +77,8 @@ public class SudFileDWVHandler implements SUDNotificationHandler {
 		stClickControl.findRawDataBlock().setChannelMap(1);
 		stClickControl.findRawDataBlock().setSampleRate((float) sampleRate, true);
 		stClickControl.getSTAcquisition().acquisitionParameters.sampleRate = (float) sampleRate;
+		stClickControl.getSTAcquisition().getAcquisitionProcess().setSampleRate((float) sampleRate, true);
+//		stClickControl.getSTAcquisition().getS().setSampleRate((float) sampleRate, true);
 //		System.out.printf("Open input stream fs = %3.1f\n", sampleRate);
 		
 	}