The PAMGUARD project develops software to help detect, locate and classify marine mammals using Passive Acoustic Monitoring.
-See http://www.pamguard.org -and http://sourceforge.net/projects/pamguard -
+ + +Code is not on GitHub at https://github.com/PAMGuard.
Note that the interface to Microsoft Access databases is not supported in the 64 bit version or when using a 32 bit Java 8.
-It is absolutely fine to run a 32 bit PAMGuard and a 32 bit -JVM on a 64 bit computer. It is also fine to have both 32 bit and 64 bit -versions of both Java and PAMGuard installed on the same machine. The same .psf -configuration files will work with both 32 and 64 bit versions.
-On Windows, the installers will create shortcuts in the @@ -390,8 +385,12 @@ PamguardBeta_ViewerMode.exe):
-
Some minor bug fixes following our migration to GitHub. Note +that the older Bug numbers only refer to bugs reported on the SVN site. New +bugs and issues are logged on GitHub at https://github.com/PAMGuard/PAMGuard/issues. +GitHub issue number are referred to with a # symbol
+ +#6 Threading Hydrophone Locator: was not working correctly +in the latest release V2.02.02. The problem was particularly apparent in Viewer +mode but may have given false array locations in normal mode under some +circumstances. This has been fixed
+ +#11 Matched Click Classifier: fixed bug which caused crash +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 files’ +option was not selected.
+ +#14 Logger forms data were not plotting correctly. This was +due to the required data selection functions not being fully implemented. This +is now fixed and it should be possible to select what to plot based on +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. +
+ +Minor bug fix to V2.02.01 which would cause the TF FX display to crash if no data were displayed.
@@ -552,9 +588,9 @@ 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.
+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
@@ -599,8 +635,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb Upgrade database system to work with MySQL 8.03. -Improvements to datamap display, to ensure even small images will be shown
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Improvements to datamap display, to ensure even small images +will be shown4. @@ -654,8 +691,8 @@ new CPOD features
15. -Better interpolation of data by the Decimator when decimating/upsampling by a non-integer -amount
+Better interpolation of data by the Decimator when decimating/upsampling by a +non-integer amount16. @@ -671,9 +708,9 @@ 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. @@ -796,9 +833,8 @@ August 2020
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) @@ -961,8 +997,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb Added beaked whale to sim sounds
13. -Added ctrl-p hotkey to print-screen button.
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Added ctrl-p hotkey to print-screen button.14. @@ -985,11 +1021,11 @@ 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
@@ -1077,8 +1113,9 @@ process each data unit 2x doubling the output.Upgrades
1. -Added functionality to TD display to allow users to manually classify clicks.
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Added functionality to TD display to allow users to manually +classify clicks.2. @@ -1191,8 +1228,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb New display for Gebco Netcdf bathymetry maps.
2. -Difar enhancements based on recent field testing.
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Difar enhancements based on recent field testing.3. @@ -1312,10 +1349,10 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb Send Email option added to Alarm module.
7. -Added ability to scale the PAMGuard display (go to Help > Set Display Scaling Factor to -adjust the scale). This, in conjunction with the built-in Windows Display +lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Added ability to scale the PAMGuard display (go to Help > Set Display Scaling Factor +to adjust the scale). This, in conjunction with the built-in Windows Display Scaling feature, will hopefully help with issues sometimes found when using 4k/UHD/high-DPI displays. At the moment this does not fix the JavaFX components, but we're working on that.
@@ -1567,8 +1604,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb Added zoom in/out to Raw Data plugin display in spectrogram.4. -Added ability to read differential GPS data.
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Added ability to read differential GPS data.5. @@ -1664,9 +1701,10 @@ settings window was opened.
Upgrades
1. -Soundtrap module - bug fixes and more intuitive user interface when importing -Soundtrap data. Also changed the default date/time format to ISO8601 standard.
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Soundtrap module - bug fixes and more intuitive user +interface when importing Soundtrap data. Also changed the default date/time +format to ISO8601 standard.2. @@ -1761,8 +1799,8 @@ and encouraged to manually fix the database.
-PAMGuard Version 2 contains major updates.
You should read and understand the notes listed for
4.
-Bug 342. Rocca was not properly loading a previously-saved EncounterStats
-file.
5. @@ -1888,9 +1926,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb Updates/bug fixes to the landmark module.
3. -Added a simulated white noise source which can be moved around in the same way -as other sources.
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Added a simulated white noise source which can be moved +around in the same way as other sources.4. @@ -2007,10 +2045,9 @@ relatively simple through the PAMGuard GUI.
1. -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.
+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. @@ -2066,8 +2103,8 @@ after the contour was recalculated. This has been corrected.
3. -Bug 310. When exiting Viewer mode, PAMGuard queries the user whether -they are sure they want to exit without saving even though they selected Bug 310. When exiting Viewer mode, PAMGuard queries the user whether they +are sure they want to exit without saving even though they selected Save and Exit. Corrected, and added an Exit without Save option.
@@ -2230,11 +2267,11 @@ was used. This is fixed.5. -Bug 295. If a click has a total length of a single sample, the code -attempting to estimate the time delay between channels would crash. This is now -fixed. This could only occur if both pre sample and post sample were set to 0 -in the click detector, which is generally not a good idea, so this bug may have -been there for some time, it's just that no one noticed before. Fixed
+Bug 295. If a click has a total length of a single sample, the code attempting +to estimate the time delay between channels would crash. This is now fixed. +This could only occur if both pre sample and post sample were set to 0 in the +click detector, which is generally not a good idea, so this bug may have been +there for some time, it's just that no one noticed before. Fixed6. @@ -2347,9 +2384,9 @@ the future.
Logger Form Design
-A GUI driven system for designing Logger forms has been -released. Currently, this feature has no online help, but is reasonably -intuitive compared to the old method of typing directly into the database.
+A GUI driven system for designing Logger forms has been released. +Currently, this feature has no online help, but is reasonably intuitive +compared to the old method of typing directly into the database.
Improved Number handling
@@ -2421,9 +2458,9 @@ changes in future releases. New PAMGuard releases will always be able to open older binary files, however, with previous PAMGuard releases if a newer file format was opened, then PAMGuard was unable to check that the file format was newer and would attempt to read the files and might even corrupt them. Now it -will recognise that it cannot open the files, display appropriate error -messages and not attempt to read the files. NOTE that at this time there are no -planned file format changes and that this is purely a future proofing exercise. +will recognise that it cannot open the files, display appropriate error messages +and not attempt to read the files. NOTE that at this time there are no planned +file format changes and that this is purely a future proofing exercise.7. @@ -2510,11 +2547,11 @@ version 1.15.00 32 bit. Both using identical Java core software but linking to 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.
+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.Other Changes
@@ -2577,9 +2614,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb Bug 262. Access to SQLite database conversion. This would fail when tables were present which were not created by PAMGuard. Fixes have been put in place for spaces in the table name or for not having an 'Id' column. -Fixes have not been implemented for spaces in a column name or use of a reserved -word as a column name, however if either of these problems do exist it will no -longer crash but issue a clear warning and carry onto the next table. +Fixes have not been implemented for spaces in a column name or use of a +reserved word as a column name, however if either of these problems do exist it +will no longer crash but issue a clear warning and carry onto the next table.@@ -2588,8 +2625,8 @@ 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.
+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 @@ -2656,9 +2693,9 @@ 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. @@ -2752,9 +2789,9 @@ lang=EN-US>1. +tab of the spectrogram configuration dialog, and also right click on the spectrogram +and select to display the annotations. Annotations are saved to the database so +you will also need a database module in your configuration.
2. @@ -2777,9 +2814,9 @@ 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/
1. Bug
-209. Map zoom level. This was zoomed right into a range of about 1m when new
-maps were created. This is now fixed and it starts with a default range of 10km
-on the display.
2. Bug @@ -2888,8 +2925,9 @@ 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.
@@ -2987,9 +3025,9 @@ sonobuoys. See online help for details.
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.
+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)
@@ -3037,8 +3075,8 @@ audio output from high frequency data. See online help for details. long term spectral average of audio data for a spectrogram display. See online help for details. -Echo Detector and Sperm Whale IPI Computation (Beta only, -Sound Measurements Group)
+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 @@ -3059,10 +3097,11 @@ different. Details are available in the online help.
FLAC File Support
Can now read raw audio data direct from FLAC files. FLAC is a lossless compression algorithm -for audio data. Files, or folders of files are accessed in the same way as WAV -and AIFF files in the Sound Acquisition module. In a future release we also -hope to provide support for writing FLAC files from the sound recorder module.
+href="http://en.wikipedia.org/wiki/FLAC">FLAC is a lossless compression +algorithm for audio data. Files, or folders of files are accessed in the same +way as WAV and AIFF files in the Sound Acquisition module. In a future release +we also hope to provide support for writing FLAC files from the sound recorder +module.Sound Recorder Module
@@ -3075,8 +3114,8 @@ Millisecond time is also now included in the output file names.Datagram options in Viewer have been improved so that the user has to verify the time binning for datagrams the first time the viewer is -run and can also change the time bins from the File menu (See the File/BinaryStore/Datagram -options menu.
+run and can also change the time bins from the File menu (See the +File/BinaryStore/Datagram options menu.Viewer Configuration
@@ -3128,8 +3167,8 @@ whistle. longer possible to change configurations once PAMGuard has been launched and pressing 'Cancel' on the select dialog causes PAMGuard to exit.Function to import GPS data from -other data sources for the PAMGuard viewer.
+Function to import GPS data from other +data sources for the PAMGuard viewer.
Database
@@ -3306,18 +3345,18 @@ have implemented database storage for output of these modules.' -Radar Display: A bug which stopped the radar display from correctly displaying -bearings to whistles from arrays containing more than two hydrophone elements -has been fixed.
+Radar Display: A bug which stopped the radar display from correctly +displaying bearings to whistles from arrays containing more than two hydrophone +elements has been fixed.' Database Speed: A substantial rewriting of some of the indexing methods -in the database module has led to a significant increase in the speed at which -data are written to the database (orders of magnitude for large databases). -This is having a significant impact on the overall reliability of the software. -Other changes have increased the speed (again by orders of magnitude) at which -data are read back into PAMGuard when using the viewer.
+in the database module has led to a significant increase in the speed at which data +are written to the database (orders of magnitude for large databases). This is +having a significant impact on the overall reliability of the software. Other +changes have increased the speed (again by orders of magnitude) at which data +are read back into PAMGuard when using the viewer.' @@ -3420,8 +3459,8 @@ Symbol'>'' -Bearings can be calculated using the envelope of the waveform rather -than the full waveform. The waveform or envelope can also be filtered prior to +Bearings can be calculated using the envelope of the waveform rather than +the full waveform. The waveform or envelope can also be filtered prior to bearing calculation.
' -The hydrophone localisation systems have been updated to better use information -from true and magnetic heading sensors.
+The hydrophone localisation systems have been updated to better use +information from true and magnetic heading sensors.'
@@ -3577,8 +3616,8 @@ frequency division (i.e. previous versions would convert well from 96kHz to
Bug fixes 1. Placement of axes on some displays (array manager and
-depth side panel). Problem in 1.9.01 Beta now fixed. 1. Placement of axes on some displays (array manager and depth
+side panel). Problem in 1.9.01 Beta now fixed. 2. Fixed problems of NMEA read out not restarting after a
serial drop out. NMEA now restarts correctly.
There have been other annoyances with the ASIO channel numbering scheme. For instance, if you had a configuration which worked in real @@ -3984,11 +4023,11 @@ Symbol'>'' -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 clipboard -from where it can be copied into other programs (e.g. Word, Powerpoint, -etc.).Some modules, such as the map, have this implemented in other menus -(right click) and also allow printing.
+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 +clipboard from where it can be copied into other programs (e.g. Word, +Powerpoint, etc.).Some modules, such as the map, have this implemented in other +menus (right click) and also allow printing.' @@ -4020,9 +4059,9 @@ now been fixed.
Decimator was calculating incorrect filter coefficients (coefficients were based on the output sample rate, not the input sample rate, -so it's likely that actual filtering of data was minimal). This is now rectified. -Ishmael matched filter. Would crash if template file not correctly loaded. Now -issues a warning message to the terminal and does not crash.
+so it's likely that actual filtering of data was minimal). This is now +rectified. Ishmael matched filter. Would crash if template file not correctly +loaded. Now issues a warning message to the terminal and does not crash.Spelling correction on user input form (Sumbit - Submit)
@@ -4159,8 +4198,8 @@ start-up takes slightly longer than previously.Outstanding bugs
-The patch panel is known to crash if output channel numbers from -the patch panel a higher than the highest input channel number of the data +
The patch panel is known to crash if output channel numbers +from the patch panel a higher than the highest input channel number of the data acquisition.
Bug fixes
@@ -4532,7 +4571,8 @@ Symbol'>''1.0Beta 22 Jan 2008 - Pamguard -starts two releases, core and beta release, +class=Heading2Char>1.0Beta 22 Jan 2008 - +Pamguard starts two releases, core and beta release,this is the beta release
@@ -4594,8 +4634,8 @@ Symbol'>'' -Multi animal click tracking with least squares fit calculation of position -on map +Multi animal click tracking with least squares fit calculation of +position on map'
diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml
index f14e35da..3d87c487 100644
--- a/dependency-reduced-pom.xml
+++ b/dependency-reduced-pom.xml
@@ -4,7 +4,7 @@