Merge pull request #32 from PAMGuard/main

Readme for 2.02.06
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@ -388,7 +388,10 @@ PamguardBeta_ViewerMode.exe):</p>
<h1><a name="_LATEST_VERSION_2.02.03"></a><em><span style='font-size:12.0pt;
font-family:"Cambria",serif;font-style:normal'><a
href="#_Latest_Version_2.02.05">LATEST VERSION 2.02.05 October 2022</a></span></em></h1>
href="#_Latest_Version_2.02.06">LATEST VERSION 2.02.06 November 2022</a></span></em></h1>
<h1><em><span style='font-size:12.0pt;font-family:"Cambria",serif;font-style:
normal'><a href="#_Latest_Version_2.02.05">Version 2.02.05 October 2022</a></span></em></h1>
<h1><em><span style='font-size:12.0pt;font-family:"Cambria",serif;font-style:
normal'><a href="#_Latest_Version_2.02.03_2">Version 2.02.03 February 2022</a></span></em></h1>
@ -443,8 +446,9 @@ 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 2.02.06 November 2022</span></h1>
<h1><a name="_Latest_Version_2.02.03_1"></a><a name="_Latest_Version_2.02.05"></a><a
name="_Latest_Version_2.02.06"></a><span lang=EN-US>Latest Version 2.02.06
November 2022</span></h1>
<h2><span lang=EN-US>Bug Fix</span></h2>
@ -457,13 +461,14 @@ 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 youre 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>
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. &nbsp;&nbsp;</span></p>
<h1><span lang=EN-US>Latest Version 2.02.05 October 2022</span></h1>
<h1><span lang=EN-US>Version 2.02.05 October 2022</span></h1>
<h2><span lang=EN-US>Click Train Detector Features and Bug Fixes</span></h2>
@ -472,8 +477,8 @@ streamlining the whole processing chain. Read the online Help for details.
<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>
@ -581,9 +586,8 @@ the TF FX display to crash if no data were displayed.</span></p>
<p class=MsoNormal><span lang=EN-US>See major release notes for V 2.02.01
below. </span></p>
<p class=MsoNormal><span lang=EN-US>Bug 495: TD FX display throws
NullPointerException if user has removed all data units and then moves mouse
over display area.</span></p>
<p class=MsoNormal><span lang=EN-US>Bug 495: TD FX display throws NullPointerException
if user has removed all data units and then moves mouse over display area.</span></p>
<h1><a name="_Latest_Version_2.02.01"></a><span lang=EN-US>Version 2.02.01
October 2021</span></h1>
@ -594,23 +598,23 @@ 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 (OpenJDK
release), so you will not need to install a java runtime engine separately.
PSFX files generated in previous beta releases (2.xx.xx) should be compatible
with this version, and vice-versa. PSF files generated in core releases
(1.15.xx) can be loaded in this version, but will be converted to PSFX files
when PAMGuard exits.</p>
<p class=MsoNormal>This version of PAMGuard has been bundled with Java 16
(OpenJDK release), so you will not need to install a java runtime engine
separately. PSFX files generated in previous beta releases (2.xx.xx) should be
compatible with this version, and vice-versa. PSF files generated in core
releases (1.15.xx) can be loaded in this version, but will be converted to PSFX
files 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 the
output of additional noise outputs for certain detectors (See below). Binary
files created with this version will not be compatible with earlier versions
2.01.### and below. This version will read and may convert earlier format
binary files.</p>
<p class=MsoNormal>Changes have been made to the binary file format to support
the output of additional noise outputs for certain detectors (See below).
Binary files created with this version will not be compatible with earlier
versions 2.01.### and below. This version will read and may convert earlier
format 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>
@ -629,9 +633,9 @@ 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 ÓDetection GrouperÔ, so
as to avoid confusion with the Group 3D localizer. This is because the
Detection Grouper is more for organizing data into groups to be localized than
it is for doing localization.</p>
as to avoid confusion with the Group 3D localizer. This is because the Detection
Grouper is more for organizing data into groups to be localized than it is for
doing localization.</p>
<p class=MsoNormal><b><span lang=EN-US>Minor Bug Fixes</span></b><span
lang=EN-US> </span></p>
@ -696,8 +700,8 @@ Upgrades to how PAMGuard lets the user enter custom date formats in the Sound
Acquisition dialog </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>
Extended XML-output support to all of the modules </p>
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>Extended XML-output support to all of the modules </p>
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>8. </span><span
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
@ -709,8 +713,8 @@ lang=EN-US> </span>Upgrades to the Symbol Manager framework, to give more
control over colours and symbols </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>
Added an option to hide the ship on the map </p>
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
lang=EN-US> </span>Added an option to hide the ship on the map </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>
@ -739,9 +743,9 @@ decimating/upsampling by a non-integer amount </p>
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>16. </span><span
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
Noise Level Outputs - as an aid to performance diagnosis, some detectors
(currently the GPL, Click Detector and Whistle and Moan Detector) are outputting
additional noise metrics to their binary output files. These can be read with
the <a href="https://sourceforge.net/projects/pamguard/files/Matlab/">PAMGuard
(currently the GPL, Click Detector and Whistle and Moan Detector) are
outputting additional noise metrics to their binary output files. These can be
read with the <a href="https://sourceforge.net/projects/pamguard/files/Matlab/">PAMGuard
Matlab library</a> and used to diagnose system performance in varying noise
conditions. Improved displays within PAMGuard for these noise metrics will be
included in a future release. </p>
@ -750,9 +754,9 @@ included in a future release. </p>
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., ÃÂA generalized power-law detection algorithm for
humpback whale vocalizations’, The Journal of the Acoustical Society of
America, vol. 131, no. 4, pp. 2682ÃÂ2699, 2012) is now available. For
details, see the online help </p>
humpback whale vocalizations’, The Journal of the Acoustical Society of America,
vol. 131, no. 4, pp. 2682–2699, 2012) is now available. For details, see the
online help </p>
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>18. </span><span
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
@ -1087,9 +1091,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
Bug 435. Logger forms subtabs not working.</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>
Bug 436. Bug in Serial Port interface was occassionally causing PAMGuard to
crash without error message.</p>
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>Bug 436. Bug in Serial Port interface was occassionally
causing PAMGuard to crash without error message.</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>
@ -1179,8 +1183,8 @@ Functionality to clone hydrophone streamers. </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>
Added automatic log file - all messages to the console will now be written to a
txt file as well. File is stored in user.home/Pamguard folder - look under the
Help menu item for a shortcut to open the folder. </p>
txt file as well. File is stored in user.home/Pamguard folder - look under the Help
menu item for a shortcut to open the folder. </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>
@ -1218,9 +1222,9 @@ Detector display. </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> </span>This version of PAMGuard has been upgraded to make it
compatible with Java 12. psfx files generated in previous beta releases should
be compatible with this version, and vice-versa.</p>
lang=EN-US> </span>This version of PAMGuard has been upgraded to make it compatible
with Java 12. psfx files generated in previous beta releases should be
compatible with this version, and vice-versa.</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>
@ -1282,8 +1286,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
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>
Updates to the Ishmael detectors.</p>
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>Updates to the Ishmael detectors.</p>
<!-- ************************************************************************************************************************** --><!-- ************************************************************************************************************************** -->
@ -1352,8 +1356,8 @@ 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 Click
Classifier is not configured properly.</p>
</span>Bug 425. Rocca crashing if Click Detector is used as source but the
Click 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;
@ -1580,8 +1584,8 @@ first time the spectrogram dialog is opened.</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>Bug 385. Bug in offline toolbar which will crash if the classifier
dialog is opened and then closed with no classifiers specified.</p>
</span>Bug 385. Bug in offline toolbar which will crash if the classifier dialog
is opened and then closed with no classifiers specified.</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;
@ -1862,9 +1866,9 @@ window.</p>
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2.</span><span
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>Bug 336. Files were being corrupted if the limit file size option was
set to a lower value in viewer than it has been when data were collected -
would truncate files being rewritten after change.</p>
</span>Bug 336. Files were being corrupted if the limit file size option was set
to a lower value in viewer than it has been when data were collected - would
truncate files being rewritten after change.</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;
@ -1977,8 +1981,9 @@ lang=EN-US> </span>Added a simulated white noise source which can be moved
around in the same way as other sources. </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>
Reworked annotation system, and added annotations to binary storage </p>
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>Reworked annotation system, and added annotations to binary
storage </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
@ -1999,9 +2004,9 @@ Added circular movement option to source simulation </p>
<h1><a name="_Latest_Beta_Version_2.00.10"></a><span lang=EN-US>Beta Version
2.00.10 June 2017</span></h1>
<p class=MsoNormal><span lang=EN-US>PAMGuard Version 2 contains major updates.
You should read and understand these notes before proceeding with installation
and use of this version. These changes have been funded under contract to NOAA
<p class=MsoNormal><span lang=EN-US>PAMGuard Version 2 contains major updates. You
should read and understand these notes before proceeding with installation and
use of this version. These changes have been funded under contract to NOAA
Fisheries, contract no. WE-133F-16-SE-1126.</span></p>
<h3><span lang=EN-US>Binary File Structural Changes</span></h3>
@ -2041,9 +2046,9 @@ in both data stores. </span></p>
added to PAMGuard which can display multiple types of data on the same time
axis. It can for instance be used to display bearings to whistles on a
bearing-time type display similar to that commonly used in the click detector.
Composite display graphs containing data from more than one detector are also
possible. For details, see the PAMGuard help file (Displays / Time Display FX).
Note that this display is only available if you are running Java 8 or later. </span></p>
Composite display graphs containing data from more than one detector are also possible.
For details, see the PAMGuard help file (Displays / Time Display FX). Note that
this display is only available if you are running Java 8 or later. </span></p>
<h3><span lang=EN-US>Event Marking and the Detection Group Localiser</span></h3>
@ -2113,10 +2118,10 @@ 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>1.</span><span
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>Added Copy-to-Clipboard button to Warning dialogs, to store error
messages and stack trace information on the Windows clipboard. This information
can then be easily pasted into emails, text documents, etc when contacting
Pamguard support.</p>
</span>Added Copy-to-Clipboard button to Warning dialogs, to store error messages
and stack trace information on the Windows clipboard. This information can then
be easily pasted into emails, text documents, etc when contacting Pamguard
support.</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;
@ -2144,8 +2149,8 @@ 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 viewer
mode PAMGuard start-up.</p>
any databases since these too may have become oversized which will slow down
viewer 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;
@ -2169,8 +2174,8 @@ 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 happens
when the user selects save as new configuration. This has been fixed.</p>
</span>Bug 314. If PAMGuard is started by double-clicking on a psf, nothing
happens 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;
@ -2192,9 +2197,9 @@ January 2017</span></h1>
<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'><span
lang=EN-US>1.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><span lang=EN-US>Bug 306. Certain methods have been querying
AcousticDataUnit.getDuration and expecting to receive a response in
milliseconds. However, getDuration actually returns the number of samples.
&nbsp;This has been corrected. </span></p>
AcousticDataUnit.getDuration and expecting to receive a response in milliseconds.
However, getDuration actually returns the number of samples. &nbsp;This has
been corrected. </span></p>
<p class=MsoNormal><b><span lang=EN-US>Plug-Ins</span></b></p>
@ -2237,9 +2242,9 @@ dependencies)</span></p>
<p class=MsoNormal><b><span lang=EN-US>Other Changes</span></b></p>
<p class=MsoNormal><span lang=EN-US>The installer has been updated to handle
both 64 bit and 32 bit installations. PAMGuard psf files are now registered in
the Windows Registry, so double-clicking on a psf file should run PAMGuard in
<p class=MsoNormal><span lang=EN-US>The installer has been updated to handle both
64 bit and 32 bit installations. PAMGuard psf files are now registered in the
Windows Registry, so double-clicking on a psf file should run PAMGuard in
normal mode (as opposed to Viewer or Mixed modes). Note that the Windows
Registry can only hold a single executable reference for psf files; therefore,
for users with multiple installations of PAMGuard, double-clicking on a psf
@ -2302,8 +2307,8 @@ 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 was labelled as 2D.Fixed</p>
</span>Bug 292. Incorrect labels on Target Motion panel in viewer - 3D 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;
@ -2313,8 +2318,8 @@ 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 was
used. This is fixed. </p>
</span>Bug 294. Click classifier was crashing when the 'min amplitude' option
was 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;
@ -2332,8 +2337,8 @@ 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, but always following the vessel track. This is now fixed. </p>
</span>Bug 297. Airgun display was not correctly showing itself at fixed 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;
@ -2399,8 +2404,8 @@ 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 which are part of an event) and c) Events. </span></p>
detector has been tidied up so that there are a) All Click, b) Tracked Clicks (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;
@ -2422,9 +2427,9 @@ 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;
</span><span lang=EN-US>Improved options are available to the user, via the
click detector bearing time display, to correct and relabel clicks / entire
click trains. </span></p>
</span><span lang=EN-US>Improved options are available to the user, via the click
detector bearing time display, to correct and relabel clicks / entire click
trains. </span></p>
<p class=MsoNormal><span lang=EN-US>Developers will hopefully find that the
target motion code has been improved in a way which will make it much easier to
@ -2443,16 +2448,15 @@ intuitive compared to the old method of typing directly into the database. </p>
<p class=MsoNormal><span lang=EN-US>Users have often found that PAMGuard can be
'jumpy', i.e. the spectrogram does not scroll smoothly, but pauses for a second
every few seconds. This is caused by the Java garbage collector cleaning up
unused objects in memory. With 64 bit versions, which allow for more memory,
some of these pauses were becoming quite long (due to the increased amount of
memory that needed to be cleaned up). In some circumstances, these pauses were
making data acquisition systems unstable. We have therefore entirely rewritten
the way in which PAMGuard handles arrays of spectrogram data (complex numbers)
so that instead of large numbers of small Java objects there are now fewer,
larger, simpler java objects. These reduce processing delays for garbage
collection and give an overall speed improvement, but will otherwise not be
noticed by users. </span></p>
every few seconds. This is caused by the Java garbage collector cleaning up unused
objects in memory. With 64 bit versions, which allow for more memory, some of
these pauses were becoming quite long (due to the increased amount of memory
that needed to be cleaned up). In some circumstances, these pauses were making
data acquisition systems unstable. We have therefore entirely rewritten the way
in which PAMGuard handles arrays of spectrogram data (complex numbers) so that
instead of large numbers of small Java objects there are now fewer, larger,
simpler java objects. These reduce processing delays for garbage collection and
give an overall speed improvement, but will otherwise not be noticed by users. </span></p>
<p class=MsoNormal><i><span lang=EN-US>Click Detector RainbowClick file output</span></i></p>
@ -2600,9 +2604,9 @@ 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
version of PAMGuard. As with the 32 bit version a number of C language
libraries are required to interface to external sound cards and other data
acquisition devices. These have been extensively tested on several different
computers, but may not be as stable as the 32 bit versions. Please report any
problems immediately to the PAMGuard team. </span></p>
acquisition devices. These have been extensively tested on several different computers,
but may not be as stable as the 32 bit versions. Please report any problems
immediately to the PAMGuard team. </span></p>
<p class=MsoNormal><b><span lang=EN-US>Other Changes</span></b></p>
@ -2642,9 +2646,9 @@ contains queries. Fixed.</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>Bug 254. Lookup lists failing in imported SQLite
databases. </span>This was caused by the system 'padding' topic's with blank
spaces and is now fixed. </p>
</span><span lang=EN-US>Bug 254. Lookup lists failing in imported SQLite databases.
</span>This was caused by the system 'padding' topic's with blank spaces and is
now fixed. </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;
@ -2676,8 +2680,8 @@ name="_Toc312065299"></a><a name="_Toc312063944"></a><a name="_Toc312065300"></a
name="_Toc312063945"></a>Version 1.14.00 Beta, September 2015</h1>
<p class=MsoNormal>The format of configuration files has changed for version
1.14.00. Older configurations will load with this new version, but
configurations saved with 1.14.00 may not open correctly with earlier versions.</p>
1.14.00. Older configurations will load with this new version, but configurations
saved with 1.14.00 may not open correctly with earlier versions.</p>
<p class=MsoNormal>PAMGuard Versions 1.14.00 and above will work with Java 8.
PAMGuard will continue to work with Java 7, but support for Java 7 will be
@ -2744,9 +2748,9 @@ displaying in the viewer. This is now fixed. </span></p>
<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'><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;&nbsp;
</span><span lang=EN-US>Bug 248. Crash in hydrophone array manager. Bug in
array manager would crash PAMGuard when the click detector was configured with
more channels than the sound acquisition system (almost impossible to achieve,
but someone managed it). </span></p>
array manager would crash PAMGuard when the click detector was configured with more
channels than the sound acquisition system (almost impossible to achieve, but
someone managed it). </span></p>
<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'><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;
@ -2765,8 +2769,8 @@ lang=EN-US>6.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times N
<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'><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><span lang=EN-US>Bug 252. Bug which plotted bearings to whistle and moan
detections from the front hydrophone rather than the central position between
hydrophones now fixed. </span></p>
detections from the front hydrophone rather than the central position between hydrophones
now fixed. </span></p>
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>&nbsp;</span></p>
@ -2857,11 +2861,11 @@ 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
zone setting. Note that PAMGuard analysis should still all be taking place in
UTC and that this option is intended to allow the conversion of file times
which were not recorded as UTC into UTC and not the other way around. Use the
option with caution !</p>
</span>The sound File and Folder audio input systems now have an optional time zone
setting. Note that PAMGuard analysis should still all be taking place in UTC
and that this option is intended to allow the conversion of file times which
were not recorded as UTC into UTC and not the other way around. Use the option
with caution !</p>
<p class=MsoListParagraph style='margin-left:47.25pt;text-indent:-29.25pt'><span
lang=EN-US>5.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -3068,16 +3072,17 @@ PAMGuard should be started and stopped using the red and black buttons.</p>
<p class=MsoNormal><i>DIFAR</i> (Localisation Group)</p>
<p class=MsoNormal>This module, funded by the Australian Antarctic Division
allows the de-multiplexing and calculation of angles from military style DIFAR
sonobuoys. See online help for details.&nbsp; </p>
allows the de-multiplexing and calculation of angles from military style DIFAR 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 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 output from the
click detector, we hope eventually to extend its use to whistles as well. </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
output from the click detector, we hope eventually to extend its use to
whistles as well. </p>
<p class=MsoNormal><i>Accelerometer Readout</i> (Sensors group)</p>
@ -3169,9 +3174,9 @@ File/BinaryStore/Datagram options menu. </p>
<p class=MsoNormal><i>Viewer Configuration</i></p>
<p class=MsoNormal>The Viewer configuration is now saved into a separate
database table from 'normal' settings so that Viewer can run at same time as
normal operation, but with slightly different display settings. </p>
<p class=MsoNormal>The Viewer configuration is now saved into a separate database
table from 'normal' settings so that Viewer can run at same time as normal
operation, but with slightly different display settings. </p>
<p class=MsoNormal><i>Spectrogram Display</i></p>
@ -3187,8 +3192,8 @@ horizon. </p>
<p class=MsoNormal><i>Improved Filter Options</i></p>
<p class=MsoNormal>Filter options (used as stand-alone filter modules and also within
many other modules, such as the click detector and the Filtered Noise
<p class=MsoNormal>Filter options (used as stand-alone filter modules and also
within 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>
@ -3247,11 +3252,10 @@ whistle.</p>
<li class=MsoNormal style='margin-bottom:0cm'>Storage options (<a
href="https://sourceforge.net/p/pamguard/bugs/175/">https://sourceforge.net/p/pamguard/bugs/175/</a>)
whereby clicks were stored to database is now fixed. </li>
<li class=MsoNormal style='margin-bottom:0cm'>Sound Recorder output folder is
now defaulting to the User folder (Generally
C:\Users\username\PAMRecordings) instead of C:\Program Files
(x86)\PamguardBeta which didn't work since the software doesn't have write
access to that folder. </li>
<li class=MsoNormal style='margin-bottom:0cm'>Sound Recorder output folder is now
defaulting to the User folder (Generally C:\Users\username\PAMRecordings)
instead of C:\Program Files (x86)\PamguardBeta which didn't work since the
software doesn't have write access to that folder. </li>
</ol>
<p class=MsoNormal>&nbsp;</p>
@ -3338,9 +3342,9 @@ information correctly in the binary files. </p>
<p class=MsoNormal style='margin-left:36.0pt'><i>Logger Forms</i></p>
<p class=MsoNormal style='margin-left:36.0pt'>A substantial amount of work has
been carried out on Logger forms, funded by the South West fisheries Science
Center. </p>
<p class=MsoNormal style='margin-left:36.0pt'>A substantial amount of work has been
carried out on Logger forms, funded by the South West fisheries Science Center.
</p>
<p class=MsoNormal style='margin-left:36.0pt'><i>Click Detector</i></p>
@ -3529,8 +3533,8 @@ 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 data.
</p>
</span>The spectrogram will automatically generate and display spectrogram
data. </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;
@ -3644,8 +3648,8 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
<p class=MsoNormal>The offline viewer is much improved with better data
scrolling 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>
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>
@ -3719,14 +3723,14 @@ 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 detectors.
While this gave some clarity to&nbsp; the displays, it also created a number of
problems since look up tables were constantly required to relate hardware
numbers and software numbers in every PAMGUARD module. Since this type of
channel numbering was only implemented several years into the PAMGUARD project,
it was never fully implemented or well supported by the different modules which
resulted in a number of bugs which could cause confusion as to which
hydrophones were being used during localisation or during calibrated
and those numbers would propagate through PAMGUARD and be used by all the
detectors. While this gave some clarity to&nbsp; the displays, it also created
a number of problems since look up tables were constantly required to relate
hardware numbers and software numbers in every PAMGUARD module. Since this type
of channel numbering was only implemented several years into the PAMGUARD
project, it was never fully implemented or well supported by the different
modules which resulted in a number of bugs which could cause confusion as to
which 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
@ -3741,10 +3745,10 @@ 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 channels
0 and 1. Similarly if you switched sound cards, you may have to reconfigure
every detector and several of the displays to handle the changes in channel
numbering. </p>
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
reconfigure every detector and several of the displays to handle the changes in
channel numbering. </p>
<p class=MsoNormal>I have spent a considerable amount of time trying to work
out a better system for handling channel numbering in PAMGUARD and have decided
@ -3784,8 +3788,8 @@ minute of data during real time operation. </p>
<p class=MsoNormal>PAMGUARD Viewer scrolling mechanism has changed. </p>
<p class=MsoNormal>Each display now has a small control in the right hand end
of a scroll bar or a slider which allows you to page through data. This is only
<p class=MsoNormal>Each display now has a small control in the right hand end of
a scroll bar or a slider which allows you to page through data. This is only
well implemented for the map, but will be an increasingly important feature as
more displays are set up for offline data viewing in future releases. </p>
@ -3940,10 +3944,10 @@ 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 automatically
displayed in the Winger window as they are for the waveform and spectrum
windows since the Wigner transformation is very time consuming. Clicks will be
displayed if you select them with the mouse.</p>
</span>Wigner time-frequency plot for the click detector. Clicks are NOT
automatically displayed in the Winger window as they are for the waveform and
spectrum windows since the Wigner transformation is very time consuming. Clicks
will be 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;
@ -4174,9 +4178,9 @@ 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 error
which meant that classifiers using this option would not work. This has now
been fixed. </p>
<p class=MsoNormal>Click classifier mean filter option had a computational
error which meant that classifiers using this option would not work. This has
now been fixed. </p>
<p class=MsoNormal><b>Sound Recorder</b></p>
@ -4404,8 +4408,8 @@ channels or textual content change. </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>Model viewer. Have stopped it from jumping on top of the main PAMGUARD &nbsp;display
when dialogs are closed. </p>
</span>Model viewer. Have stopped it from jumping on top of the main PAMGUARD
&nbsp;display when dialogs are closed. </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;

View File

@ -4,7 +4,7 @@
<groupId>org.pamguard</groupId>
<artifactId>Pamguard</artifactId>
<name>Pamguard Java12+</name>
<version>2.02.04ae</version>
<version>2.02.05a</version>
<description>Pamguard for Java 12+, using Maven to control dependcies</description>
<url>www.pamguard.org</url>
<organization>

View File

@ -83,8 +83,8 @@ public class SudFileDWVHandler implements SUDNotificationHandler {
@Override
public void sudStreamClosed() {
System.out.printf("SUD input stream closed, %d DWV, %d bcl Detectins and %d BCL Noise, %d chunks processed\n",
dwvCount, bclDetCount, bclNoiseCount, processedChunks);
// System.out.printf("SUD input stream closed, %d DWV, %d bcl Detectins and %d BCL Noise, %d chunks processed\n",
// dwvCount, bclDetCount, bclNoiseCount, processedChunks);
}
@Override