@@ -474,7 +474,7 @@ name="_Version_2.02.10_January">Version
Deep Learning Classifier. Major upgrade to support for Deep Learning models in PAMGuard. See online help for details.
-Click detector: Remembers locations of displays and doesnÂ’t +
Click detector: Remembers locations of displays and doesn’t continually reset them.
Help for Matched Click Classifier.
@@ -485,7 +485,7 @@ information.Many users will be aware that weÂ’re integrating an interface +
Many users will be aware that we’re integrating an interface to the Tethys Database into PAMGuard. Some basic features are available for testing. If interested, please contact the PAMGuard support team.
@@ -515,18 +515,19 @@ database. long enough to make clips. In some circumstances data were being discarded too early so clips could not be created. -Acquisition “Skip initial seconds” feature, designed to +
Acquisition “Skip initial seconds” feature, designed to remove high sample levels e.g. from calibration tones at start of a soundtrap recording was not working with the click detector. This is fixed but replacing -all data with 0Â’s and still sending data. Note that this may lead to +all data with 0’s and still sending data. Note that this may lead to artificially low noise measures at the start of a file.
Data reprocessing options. Updated to ensure that the option "Start normally. Note risk of overwriting!" is always available. Also improved code naming binary files to attempt to push them to exact times, rather than a couple of seconds after the hour.
-improved code naming binary files to attempt to push them to exact times, rather -than a couple of seconds after the hour. + +improved code naming binary files to attempt to push them to +exact times, rather than a couple of seconds after the hour.
Updated icons to improve display on high definition screens.
@@ -548,8 +549,8 @@ files) file performance when scrolling through audio data in Viewer mode.Viewer Launch by right clicking on sqlite database and selecting “open with / -Pamguard ViewerMode” launcher menu option.
+lang=EN-US> by right clicking on sqlite database and selecting “open with / +Pamguard ViewerMode” launcher menu option.Screen Position: When using multiple monitors, if you move a configuration to a -computer with a different monitor layout, the GUI should work out if itÂ’s +computer with a different monitor layout, the GUI should work out if it’s opening on a screen area which no longer exists and move itself onto the primary monitor.
@@ -605,7 +606,7 @@ primary monitor. lang=EN-US>: Previous version had a bug which caused files to not always be sorted into the correct order for processing. This caused some instability in some detectors, causing memory leaks when new data arrived with time stamps -earlier than already processed data in memory. This is now fixed – files are ow +earlier than already processed data in memory. This is now fixed – files are ow correctly sorted alphabetically by file name, i.e. not including the name of the folder containing the files. @@ -627,8 +628,8 @@ were reading local time, even when set to use UTC. which mostly occurred when processing large datasets of many offline files, has been fixed. -Data Map: “Scroll To Data” pop-up menu, which -didnÂ’t always scroll to the correct place, is now fixed.
+Data Map: “Scroll To Data” pop-up menu, +which didn’t always scroll to the correct place, is now fixed.
Bearing Localiser offline: If reprocessing bearings, the localizer was not correctly loading required raw or FFT data to @@ -651,7 +652,7 @@ files and stores them within the PAMGuard configuration. This does not affect processing, but is important for record keeping.
GPS options to use any valid RMC or GGA -string. Not all GPS receivers output their RMC data as GPRMC – e.g. some may +string. Not all GPS receivers output their RMC data as GPRMC – e.g. some may output as GNRMC. A new option allows the GPS module to use any string, whatever the first two characters of the string name may be.
@@ -660,14 +661,14 @@ the first two characters of the string name may be.Use of localization sensor and orientation -data for static hydrophones had a bug whereby it would continually ‘forgetÂ’ +data for static hydrophones had a bug whereby it would continually ‘forget’ angle offsets applied to static hydrophones in viewer mode. This is now fixed.
Click tool bar: Correctly shows event selection options even if no species classification options are in place.
Fixed Landmarks: Earlier versions were -‘losingÂ’ these every time PAMGuard started or new data were loaded in viewer +‘losing’ these every time PAMGuard started or new data were loaded in viewer mode. Now fixed.
ROCCA: Fixed (another) memory leak which @@ -686,11 +687,11 @@ processing.
New sound type for simulated sounds which generates random chirps between around 200 and 800Hz, roughly the frequency -youÂ’d expect sound from higher frequency baleen whales, such as humpbacks, to +you’d expect sound from higher frequency baleen whales, such as humpbacks, to vocalise at.
Hiding tool tips. A menu item to -permanently turn off all tool tips, or tap the ‘EscÂ’ key to turn them off for 6 +permanently turn off all tool tips, or tap the ‘Esc’ key to turn them off for 6 seconds if they are getting in the way, particularly when trying to interact with displays using the mouse.
@@ -711,7 +712,7 @@ whistle classification module.SoundTrap SUD file reading. If youÂ’re using
+ 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
@@ -728,8 +729,8 @@ 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.
Soundtrap DWV import. Will now generate -binary files even if DWV file doesn‚’t exist (which is correct behavior in +binary files even if DWV file doesn‚’t exist (which is correct behavior in quiet conditions when no clicks were detected).
Spectrogram. Changes to stop occasional @@ -810,7 +811,7 @@ running in real time. Added template names based on file names.
#13 Merging files when offline processing file folders: Had an error introduced in last release which caused it to fail to recognise gaps between files, meaning that some output data (i.e. after a gap) would have an -incorrect time stamp. This did not affect data if the ‘merge contiguous filesÂ’ +incorrect time stamp. This did not affect data if the ‘merge contiguous files’ option was not selected.
#14 Logger forms data were not plotting correctly. This was @@ -820,9 +821,9 @@ selections from drop down lists within any form.
-
Note that updates have also been made to the Matlab interface -to PAMGuard binary files, which has now also been migrated to GitHub at https://github.com/PAMGuard/PAMGuardMatlab. +
Note that updates have also been made to the Matlab +interface to PAMGuard binary files, which has now also been migrated to GitHub +at https://github.com/PAMGuard/PAMGuardMatlab.
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.
Detection Group Localiser
-This module has been renamed “Detection Grouper”, so as to +
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.
@@ -1006,9 +1008,9 @@ included in a future release.17. An implementation of the Generalized Power Law Detector, -developed by Tyler Helble ([Helble et al., ‘A generalized power-law detection -algorithm for humpback whale vocalizationsÂ’, The Journal of the Acoustical -Society of America, vol. 131, no. 4, pp. 2682–2699, 2012) is now available. For +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
18. .
If you are upgrading from a PAMGuard core release (1.15.xx), PAMGuard Version 2 contains major updates. You should read and -understand the notes listed for Beta Version -2.00.10 before proceeding with installation and use of this version.
+understand the notes listed for Beta +Version 2.00.10 before proceeding with installation and use of this +version.This version of PAMGuard has been bundled with Java 13 (release 13.0.1). PSFX files generated in previous beta releases (2.xx.xx) @@ -1136,11 +1139,11 @@ understand the notes listed for Beta Version 2.00.10 before proceeding with installation and use of this version.
-This version of PAMGuard has been bundled with Java 13 (release -13.0.1). PSFX files generated in previous beta releases (2.xx.xx) should 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 13 +(release 13.0.1). 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.
Bug Fixes
@@ -1160,8 +1163,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb4. Bug - 456. Under certain conditions, the Ishmael detection plugin that is -shown at the bottom of the spectrogram can disappear about 500 msec behind the + 456. Under certain conditions, the Ishmael detection plugin that is shown +at the bottom of the spectrogram can disappear about 500 msec behind the current time.
5. Added channel display to noise one band measurement display.
11. -Added Azigram module, to work in conjunction with Difar.
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Added Azigram module, to work in conjunction with Difar.12. -Added beaked whale to sim sounds
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Added beaked whale to sim sounds13. Bug 434. Pamguard Viewer mode was having problems importing settings from psfx file.
3. -Bug 435. Logger forms subtabs not working.
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Bug 435. Logger forms subtabs not working.4.
2. Added option in Sound Acquisition settings dialog to
-override filename time stamp and use PC local time instead.
3. &nb Implemented a simple UDP output for PAMGuard alarms.
7. -Changes to Spectrogram Mark Observers, to allow individual channels to be -selected instead of the spectrogram panel as a whole.
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Changes to Spectrogram Mark Observers, to allow individual +channels to be selected instead of the spectrogram panel as a whole.8.
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.
2. @@ -1561,9 +1564,9 @@ with installation and use of this version.
1. -Bug 413. Binary file crashing during load, after a system failure. Failure -could cause the file to become corrupt, which caused a crash during subsequent -load
+Bug 413. Binary file crashing during load, after a system failure. +Failure could cause the file to become corrupt, which caused a crash during +subsequent load2. @@ -1776,8 +1779,8 @@ with installation and use of this version.
1. -Bug 338. Problem displaying coastlines and bathymetric contours around the -dateline (+/- 180 longitude) in the map.
+Bug 338. Problem displaying coastlines and bathymetric contours around +the dateline (+/- 180 longitude) in the map.2. @@ -2191,7 +2194,7 @@ showing.
2. -Bug 323. Difar module. Fixed a couple of small +Bug 323. Difar module. Fixed a couple of small bugs in the DIFAR system which caused it to not work if old configuratins were used.
@@ -2281,7 +2284,7 @@ file format is the addition of a Unique Data Identifier (UID) to each unit of data. This is intended to aid in offline analysis by making it easier for the user to link what they are seeing on different PAMGuard displays and also to link with any data post processed in Matlab or other custom analysis software. -UIDÂ’s are also added to PAMGuard database tables. +UID’s are also added to PAMGuard database tables.The additional UID column will be added to all database tables and populated with unique values. For data which are stored -in both the binary files and in database tables, the same UIDÂ’s will be used in +in both the binary files and in database tables, the same UID’s will be used in both data stores.
1. -New classes will be added to the configuration files, -so they will no longer work with older PAMGuard versions.
+New classes will be added to the configuration files, so +they will no longer work with older PAMGuard versions.2. @@ -2359,14 +2362,14 @@ lang=EN-US>
1. -Bug 317. Rocca Module Data Purging. The ROCCA module -was not performing data purging when using classifiers developed for +Bug 317. Rocca Module Data Purging. The ROCCA +module was not performing data purging when using classifiers developed for Hawaii/Temperate Pacific/North Atlantic datasets. This has been corrected.
- +2. -Bug 320. Pamguard stopped reading Click Detector Event data from database -when target motion analysis information was encountered. Corrected.
+Bug 320. Pamguard stopped reading Click Detector Event data from +database when target motion analysis information was encountered. Corrected.3.
@@ -2461,8 +2464,8 @@ milliseconds. However, getDuration actually returns the number of samples.
Plug-Ins A major change in this version of PAMGuard
-is how plug-ins are managed. PAMGuard now has the ability to dynamically load
+ A major change in this version of PAMGuard is
+how plug-ins are managed. PAMGuard now has the ability to dynamically load
plug-in modules (saved as jar files) at runtime. This will greatly simplify the
process of testing and distributing newly developed modules, since only a small
jar file will be required rather than a new bespoke PAMGuard installation. 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
@@ -2530,7 +2533,7 @@ November 2016
1.
Bug 303. Some ASIO sound cards not working with either ASIO system in PAMGuard.
For the PAMGuard ASIO system, this was due to a data format used by some sound
-cards never being properly implemented. For the “New ASIO system” which is
+cards never being properly implemented. For the “New ASIO system” which is
based on jAsioHost, the unpacking of that format contained a bug which returned
incorrect numbers, so data were swamped with noise. Both systems are now fixed.
By preference, users should use the PAMGuard ASIO system since the JAsioHost
@@ -2641,8 +2644,8 @@ lang=EN-US>3.4.
-Bug 290. Click bearings on spectrogram display plug in were
-reversed if the first hydrophone was behind the second hydrophone in the
+Bug 290. Click bearings on spectrogram display plug in
+were reversed if the first hydrophone was behind the second hydrophone in the
configuration. This is now fixed so that it displays the same bearings as the
main click detector display. 1.
-Bug 272. File types: Some File Open / File Save dialogs were allowing selection
-of all file types. e.g. Save Configuration As, Section of whistle classifier
-training file, Map file Selection, These have now been changed so that only the
-correct type of file can be selected.
2. @@ -2969,9 +2972,9 @@ See the help file for details.
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Feature Request 45. Click classification settings -export / import. Click classification settings can be exported individually to files -and imported into other click detector configurations. See the help file for -details. +export / import. Click classification settings can be exported individually to +files and imported into other click detector configurations. See the help file +for details.3. @@ -3128,9 +3131,9 @@ option with caution !
5. -The Open Office Database system has been removed from the list of available -options since it is not reliable. If you require a free database solution we -recommend you use the MySql Community Server The Open Office Database system has been removed from the list of +available options since it is not reliable. If you require a free database +solution we recommend you use the MySql Community Server http://dev.mysql.com/downloads/mysql/
8. -Bug 230. Click Bearing Display. With a two hydrophone system, -clicks calculated to have a bearing of exactly 180 degrees would be displayed -at 0 degrees on the bearing time display.
+Bug 230. Click Bearing Display. With a two hydrophone +system, clicks calculated to have a bearing of exactly 180 degrees would be +displayed at 0 degrees on the bearing time display.@@ -3239,8 +3242,9 @@ total loss of the PAMGuard configuration in viewer mode and has been rectified. 7.0pt;font-family:"Times New Roman",serif'> Bug 218. SAIL Acquisition card would hang the system. This has also been fixed. -
7. Bug 219. -Problems displaying Offline Click Events in the Viewer map have been fixed.
+7. Bug +219. Problems displaying Offline Click Events in the Viewer map have been +fixed.
@@ -3322,8 +3326,8 @@ Visual Methods
'Multi Threading' menu item moved from 'Detection' (now 'Settings') to 'File'
-'Start' and 'Stop' menu items removed. PAMGuard -should be started and stopped using the red and black buttons.
+'Start' and 'Stop' menu items removed. +PAMGuard should be started and stopped using the red and black buttons.
New Modules
@@ -3391,9 +3395,9 @@ help for details.Echo Detector and Sperm Whale IPI Computation (Beta only, Sound Measurements Group)
-These two modules, developed by Brian Miller of the Australian -Antarctic Division can be used to estimate the inter pulse interval of sperm -whale clicks. (No help available)
+These two modules, developed by Brian Miller of the +Australian Antarctic Division can be used to estimate the inter pulse interval +of sperm whale clicks. (No help available)
@@ -4009,8 +4013,8 @@ channels 0 and 1. Similarly if you switched sound cards, you may have to reconfigure every detector and several of the displays to handle the changes in channel numbering. -
I have spent a considerable amount of time trying to work -out a better system for handling channel numbering in PAMGUARD and have decided +
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 @@ -4115,13 +4119,13 @@ port is closed. Might prevent a few problems when using a GPS.
Bug Fixes
-Crashes caused in real time or Mixed Mode if the number of software -channels exceeds the number of hydrophones configured in the array manager. It -is of course illogical to have software channels which are not assigned to a -hydrophone, so rather than entirely prevent PAMGUARD from crashing I have -inserted additional checks into the hydrophone array dialog which will prevent -the user from closing that dialog unless all software channels are assigned to -a hydrophone.
+Crashes caused in real time or Mixed Mode if the number of +software channels exceeds the number of hydrophones configured in the array +manager. It is of course illogical to have software channels which are not +assigned to a hydrophone, so rather than entirely prevent PAMGUARD from +crashing I have inserted additional checks into the hydrophone array dialog +which will prevent the user from closing that dialog unless all software +channels are assigned to a hydrophone.
Sound Recorder
-Level meters are shown for the correct channels (after channel -numbering has been changed). Occasional crash due to synchronisation problems -when multi-threading now fixed.
+Level meters are shown for the correct channels (after +channel numbering has been changed). Occasional crash due to synchronisation +problems when multi-threading now fixed.
Whistle Detector
@@ -4598,9 +4602,9 @@ a serial portNew Likelihood detector.
-The likelihood detector module is an implementation of a -likelihood ratio test with flexible algorithms and configuration to estimate -likelihood. It is
+The likelihood detector module is an implementation of a likelihood +ratio test with flexible algorithms and configuration to estimate likelihood. +It is
suitable for detecting both short duration Odontocete clicks (Sperm, Beaked, etc.) as well as moderate duration Mysticete calls (Humpback, @@ -4719,9 +4723,9 @@ Symbol'>'' -Better drawing of held spectrogram when putting mark rectangles on a spectrogram -display. All panels are now correctly frozen. The rectangle is drawn in red on -the marked panel and in green on other panels.
+Better drawing of held spectrogram when putting mark rectangles on a +spectrogram display. All panels are now correctly frozen. The rectangle is +drawn in red on the marked panel and in green on other panels.'
@@ -4737,9 +4741,9 @@ coming in through the ASIO card and back out through its headphone socket
'
Operation will depend on the configuration of individual sound cards and
-how they are configured to mix incoming data with data from the PC. This is sometimes
-a physical switch on the card and sometimes a software configuration utility
-specific to that sound card.
'
diff --git a/pom.xml b/pom.xml
index 2abb42ac..18b6a902 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@