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.
+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. -Changes to GUI to make dialog shorter for low DPI screens.
-Complete rewrite of the classification system -to have nested classifiers which can be enabled or disabled.
+Complete rewrite of the classification +system to have nested classifiers which can be enabled or disabled.
Changes to classification GUI to accommodate the new classification system.
@@ -581,9 +586,8 @@ the TF FX display to crash if no data were displayed.See major release notes for V 2.02.01 below.
-Bug 495: TD FX display throws -NullPointerException if user has removed all data units and then moves mouse -over display area.
+Bug 495: TD FX display throws NullPointerException +if user has removed all data units and then moves mouse over display area.
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.
+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.
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.
+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.
@@ -629,9 +633,9 @@ href="http://www.pamguard.org/downloads.php?cat_id=3">here. lang=EN-US>
This module has been renamed “Detection Grouper”, so -as to avoid confusion with the Group 3D localizer. This is because the -Detection Grouper is more for organizing data into groups to be localized than -it is for doing localization.
+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.Minor Bug Fixes
@@ -696,8 +700,8 @@ Upgrades to how PAMGuard lets the user enter custom date formats in the Sound Acquisition dialog7. -Extended XML-output support to all of the modules
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Extended XML-output support to all of the modules8. @@ -709,8 +713,8 @@ lang=EN-US> Upgrades to the Symbol Manager framework, to give more control over colours and symbols
10. -Added an option to hide the ship on the map
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Added an option to hide the ship on the map11. @@ -739,9 +743,9 @@ decimating/upsampling by a non-integer amount
16. 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 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 PAMGuard Matlab library 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.
@@ -750,9 +754,9 @@ included in a future release. lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> An implementation of the Generalized Power Law Detector, developed by Tyler Helble ([Helble et al., ‘A generalized power-law detection algorithm for -humpback whale vocalizations’, The Journal of the Acoustical Society of -America, vol. 131, no. 4, pp. 2682–2699, 2012) is now available. For -details, see the online help +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 help18. @@ -1087,9 +1091,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb Bug 435. Logger forms subtabs not working.
4. -Bug 436. Bug in Serial Port interface was occassionally causing PAMGuard to -crash without error message.
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Bug 436. Bug in Serial Port interface was occassionally +causing PAMGuard to crash without error message.5. @@ -1179,8 +1183,8 @@ Functionality to clone hydrophone streamers.
5. 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.
+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.6. @@ -1218,9 +1222,9 @@ Detector display.
1. 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.
+lang=EN-US> 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.2. @@ -1282,8 +1286,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb Click Train Detector upgrades, including localisation capabilities.
4. -Updates to the Ishmael detectors.
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Updates to the Ishmael detectors. @@ -1352,8 +1356,8 @@ files.12. -Bug 425. Rocca crashing if Click Detector is used as source but the Click -Classifier is not configured properly.
+Bug 425. Rocca crashing if Click Detector is used as source but the +Click Classifier is not configured properly.13. @@ -1580,8 +1584,8 @@ first time the spectrogram dialog is opened.
4. -Bug 385. Bug in offline toolbar which will crash if the classifier -dialog is opened and then closed with no classifiers specified.
+Bug 385. Bug in offline toolbar which will crash if the classifier dialog +is opened and then closed with no classifiers specified.5. @@ -1862,9 +1866,9 @@ window.
2. -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.
+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.3. @@ -1977,8 +1981,9 @@ lang=EN-US> Added a simulated white noise source which can be moved around in the same way as other sources.
4. -Reworked annotation system, and added annotations to binary storage
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Reworked annotation system, and added annotations to binary +storage5.
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
+ 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.Beta Version
2.00.10 June 2017
-Binary File Structural Changes
@@ -2041,9 +2046,9 @@ in both data stores.
1. -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.
+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.2. @@ -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 > 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.
+any databases since these too may have become oversized which will slow down +viewer mode PAMGuard start-up.2. @@ -2169,8 +2174,8 @@ working folder, and therefore is set incorrectly. This has been fixed.
5. -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.
+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.6. @@ -2192,9 +2197,9 @@ January 2017
1. 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. - This has been corrected.
+AcousticDataUnit.getDuration and expecting to receive a response in milliseconds. +However, getDuration actually returns the number of samples. This has +been corrected.Plug-Ins
@@ -2237,9 +2242,9 @@ dependencies)Other Changes
-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
+ 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. 2.
-Bug 292. Incorrect labels on Target Motion panel in viewer - 3D
-algorithm was labelled as 2D.Fixed
3. @@ -2313,8 +2318,8 @@ data for the least square model. Both fixed.
4. -Bug 294. Click classifier was crashing when the 'min amplitude' option was -used. This is fixed.
+Bug 294. Click classifier was crashing when the 'min amplitude' option +was used. This is fixed.5. @@ -2332,8 +2337,8 @@ appear when you right click on the display.
7. -Bug 297. Airgun display was not correctly showing itself at fixed -locations, but always following the vessel track. This is now fixed.
+Bug 297. Airgun display was not correctly showing itself at fixed locations, +but always following the vessel track. This is now fixed.8. @@ -2399,8 +2404,8 @@ the database.
2. 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.
+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.3. @@ -2422,9 +2427,9 @@ combine automatic and manual tracking.
6. -Improved options are available to the user, via the -click detector bearing time display, to correct and relabel clicks / entire -click trains.
+Improved options are available to the user, via the click +detector bearing time display, to correct and relabel clicks / entire click +trains.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.
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.
+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.Click Detector RainbowClick file output
@@ -2600,9 +2604,9 @@ different libraries for control of sound input devices.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.
+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.Other Changes
@@ -2642,9 +2646,9 @@ contains queries. Fixed.2. -Bug 254. Lookup lists failing in imported SQLite -databases. This was caused by the system 'padding' topic's with blank -spaces and is now fixed.
+Bug 254. Lookup lists failing in imported SQLite databases. +This was caused by the system 'padding' topic's with blank spaces and is +now fixed.3.
@@ -2676,8 +2680,8 @@ name="_Toc312065299">Version 1.14.00 Beta, September 2015
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.
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.
3. 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).
+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).4. @@ -2765,8 +2769,8 @@ lang=EN-US>6.7. Bug 252. Bug which plotted bearings to whistle and moan -detections from the front hydrophone rather than the central position between -hydrophones now fixed.
+detections from the front hydrophone rather than the central position between hydrophones +now fixed.@@ -2857,11 +2861,11 @@ which is useful when using PAMGuard for demonstration purposes.
4. -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 !
+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 !5. @@ -3068,16 +3072,17 @@ PAMGuard should be started and stopped using the red and black buttons.
DIFAR (Localisation Group)
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.
+allows the de-multiplexing and calculation of angles from military style DIFAR sonobuoys. +See online help for details.MEAL Localiser (Localisation Group)
-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.
+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.
Accelerometer Readout (Sensors group)
@@ -3169,9 +3174,9 @@ File/BinaryStore/Datagram options menu.Viewer Configuration
-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.
+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.
Spectrogram Display
@@ -3187,8 +3192,8 @@ horizon.Improved Filter Options
-Filter options (used as stand-alone filter modules and also within -many other modules, such as the click detector and the Filtered Noise +
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).
@@ -3247,11 +3252,10 @@ whistle.@@ -3338,9 +3342,9 @@ information correctly in the binary files.
Logger Forms
-A substantial amount of work has -been carried out on Logger forms, funded by the South West fisheries Science -Center.
+A substantial amount of work has been +carried out on Logger forms, funded by the South West fisheries Science Center. +
Click Detector
@@ -3529,8 +3533,8 @@ features of the display:' -The spectrogram will automatically generate and display spectrogram data. -
+The spectrogram will automatically generate and display spectrogram +data.' @@ -3644,8 +3648,8 @@ Symbol'>'' -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.
+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.' @@ -4174,9 +4178,9 @@ Mac/Linux machines)
Parameters dialog shows correct channel numbers
-Click classifier mean filter option had a computational error -which meant that classifiers using this option would not work. This has now -been fixed.
+Click classifier mean filter option had a computational +error which meant that classifiers using this option would not work. This has +now been fixed.
Sound Recorder
@@ -4404,8 +4408,8 @@ channels or textual content change.' -Model viewer. Have stopped it from jumping on top of the main PAMGUARD display -when dialogs are closed.
+Model viewer. Have stopped it from jumping on top of the main PAMGUARD + display when dialogs are closed.'
diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml
index b88e86ad..cb5efca5 100644
--- a/dependency-reduced-pom.xml
+++ b/dependency-reduced-pom.xml
@@ -4,7 +4,7 @@