From 6b9cf6173e0063f556240a9db44946614e6b09ec Mon Sep 17 00:00:00 2001
From: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date: Tue, 18 Mar 2025 15:17:43 +0000
Subject: [PATCH] V2.02.16 (hopefully)
Final changes for 2.02.16
---
.classpath | 3 +-
README.html | 190 +++++++++++----------
dependency-reduced-pom.xml | 4 +-
pom.xml | 2 +-
repo/tethys/org/nilus/3.2/nilus-3.2.jar | Bin 150428 -> 150491 bytes
src/PamController/PamguardVersionInfo.java | 2 +-
src/dataPlotsFX/layout/TDGraphFX.java | 4 +-
7 files changed, 110 insertions(+), 95 deletions(-)
diff --git a/.classpath b/.classpath
index 49faf461..6086187c 100644
--- a/.classpath
+++ b/.classpath
@@ -6,8 +6,9 @@
Deep Learning Classifier
+ +Better error dialogs to indicate when models are incorrect +and when the libraries have not been installed correctly.
+ +DelphinID Whistle classifier support now implemented.
+Other
Made click detector offline click event data integrity @@ -501,6 +508,11 @@ codes where the progress dialog would not close.
Project Information abstract field was not saving / reloading correctly in the configuration file. Fixed.
+Small bugs in FX Time display to improve settings pane.
+ +Fix offline file scanning in Acquisition when sub folder +button checked / unchecked.
+Fix memory issue with -RoccaContourDataBlocks not being released for garbage collection
+Fix memory issue with RoccaContourDataBlocks +not being released for garbage collection
Set RoccaContourDataBlock objects to null and stop PamObserver Timer to
@@ -796,8 +808,8 @@ mode. Now fixed. caused PAMGuard to crash when processing large data sets with the ROCCA classifier. -Ishmael Modules: Fixed bug which -occasionally caused crashes when processing many files offline.
+Ishmael Modules: Fixed bug which occasionally +caused crashes when processing many files offline.
PAMDog: Fixed bug in watchdog program which was trying to start PAMGuard before modules were fully loaded. The watchdog now @@ -888,8 +900,8 @@ click re-classification, bearing calculation, etc.)
Data selector for Whistle Classifier module
-Variable sound output level when using -National Instruments devices for sound playback.
+Variable sound output level when using National +Instruments devices for sound playback.
Speed improvement when processing flac audio files.
@@ -996,11 +1008,12 @@ font-family:"Times New Roman",serif'>Localisation Modules
-Bearing and Group 3D localization modules have been thoroughly -tested and a number of bugs rectified. Documentation has been developed and is -available in the online help. Further, a number of example configurations have -been generated, configuration files for these are available in the PAMGuard -downloads area here.
+Bearing and Group 3D localization modules have been +thoroughly tested and a number of bugs rectified. Documentation has been +developed and is available in the online help. Further, a number of example +configurations have been generated, configuration files for these are available +in the PAMGuard downloads area here.
Detection Group Localiser
@@ -1111,8 +1124,8 @@ lang=EN-US> new CPOD features15. Better interpolation of data by the Decimator when decimating/upsampling -by a non-integer amount
+lang=EN-US> Better interpolation of data by the Decimator when +decimating/upsampling by a non-integer amount16. Add functionality for bluetooth headsets.
2. Add user-facing option to adjust the startup delay for the -time-correction (Global Time module). This provides a workaround to speed up -analysis of thousands of wav files (i.e. by setting startup delay to 0 instead -of default value of 2000 ms).
+lang=EN-US> Add user-facing option to adjust the startup delay for the time-correction +(Global Time module). This provides a workaround to speed up analysis of +thousands of wav files (i.e. by setting startup delay to 0 instead of default +value of 2000 ms).3. Bug 427. Soundtrap import not closing binary files properly if BCL files do not contain off-effort 'E' line
2. -Bug 428. Decimator crashing in viewer mode
+lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> Bug 428. Decimator crashing in viewer mode3.
Upgrades 1.
-Upgrades to the Group Localiser, including better error estimation.
2.
3. Added option to export all settings and parameters as an
-XML-formatted file. Note that this required changes to the structure of the Array
-Manager, and as such any settings (psf) files created with this version of
-PAMGuard cannot be used in older versions. Older psf files can be loaded with
-this version, but will be converted.
4.
-The most significant change in the binary 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. UID's are -also added to PAMGuard database tables.
+The most significant change in the binary +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. +UID's are also added to PAMGuard database tables.
1. -Bug 308. Map Overlay Control. Storage of data saying -what get's plotted on each map and for how long became corrupted and the 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.
+Bug 308. Map Overlay Control. Storage of data +saying what get's plotted on each map and for how long became corrupted and the +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.2. @@ -2777,22 +2791,22 @@ main click detector display.
Target Motion Analysis
-A major piece of work has been undertaken -to improve the Target Motion tracking with PAMGuard. Details are available in -the online help. Users of the Click Detector will notice the following changes:
+A major piece of work has been undertaken to +improve the Target Motion tracking with PAMGuard. Details are available in the +online help. Users of the Click Detector will notice the following changes:
1. -There is now a choice of least squares and Simplex based -algorithms for real-time animal tracking. The improved algorithms also provide -better error information both for display on the map and for storage in the -database.
+There is now a choice of least squares and Simplex +based algorithms for real-time animal tracking. The improved algorithms also +provide better error information both for display on the map and for storage in +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.
+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.3. @@ -3067,9 +3081,9 @@ will no longer crash but issue a clear warning and carry onto the next table.
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.
+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 @@ -3104,13 +3118,13 @@ for details.
3. -GPS Loading into PAMGuard Viewer. This has been -modified so that the rules governing GPS data collection and storage also apply -when loading data from the database. For instance, if you've stored all GPS -data, you've probably got a record every second in the database which can -create memory overflows if you try to load a lot of data in the viewer. You can -now tell PAMGuard to only load a data point every n seconds which will reduce -the number of points loaded. Useful when making large scale overview maps of a +GPS Loading into PAMGuard Viewer. This has been modified +so that the rules governing GPS data collection and storage also apply when +loading data from the database. For instance, if you've stored all GPS data, +you've probably got a record every second in the database which can create +memory overflows if you try to load a lot of data in the viewer. You can now +tell PAMGuard to only load a data point every n seconds which will reduce the +number of points loaded. Useful when making large scale overview maps of a survey.
4.
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.@@ -3409,8 +3423,9 @@ to read on a time. Fixed
Menu Layout
-The PAMGuard menus have been rearranged into a more intuitive -grouping which we believe will help users find functionality more easily.
+The PAMGuard menus have been rearranged into a more +intuitive grouping which we believe will help users find functionality more +easily.
'Detection' menu has been renamed to 'Settings' since many menu items within this menu were not directly to do with 'Detection'.
@@ -3539,17 +3554,16 @@ 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
-Now supports writing 8 and 24 bit as well as 16 bit files. Also -writes data to dated sub folders, starting a new folder each day (UTC). Also -provides additional information on disk space on the main display panel. +
Now supports writing 8 and 24 bit as well as 16 bit files. +Also writes data to dated sub folders, starting a new folder each day (UTC). +Also provides additional information on disk space on the main display panel. Millisecond time is also now included in the output file names.
Datagram Options
@@ -3586,8 +3600,9 @@ shaped Finite Impulse Response filters (see online help for details).Radar Display
-Can now show bearings relative to true North OR the vessel heading. -Also has the option of only showing certain types of click and whistle.
+Can now show bearings relative to true North OR the vessel +heading. Also has the option of only showing certain types of click and +whistle.
Bug Fixes
@@ -3666,12 +3681,12 @@ survey software package.Core Functionality
-New storage options have been -implemented which give the user greater control of where data are stored.
+New storage options have been implemented +which give the user greater control of where data are stored.
-Modules have been arranged into different -groups in the configuration menus and tool tip texts have been added to these -menus to provide additional information to users.
+Modules have been arranged into +different groups in the configuration menus and tool tip texts have been added +to these menus to provide additional information to users.
Radar Display
@@ -3754,8 +3769,8 @@ inter-detection interval. margin-left:36.0pt'>Target Motion Analysis: Updated target motion analysis -module so that it works in three (as opposed to two) dimensions.
+margin-left:36.0pt'>Target Motion Analysis: Updated target motion analysis module +so that it works in three (as opposed to two) dimensions.@@ -3790,8 +3805,8 @@ 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 +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 @@ -4206,8 +4221,8 @@ existing configurations.
Sound acquisition
-Changes made for a previous Mac build now incorporated into -main Beta branch. This should allow for basic 2 channel sound acquisition using +
Changes made for a previous Mac build now incorporated into main +Beta branch. This should allow for basic 2 channel sound acquisition using Macs.
Bug Fixes
@@ -5010,8 +5025,7 @@ Symbol'>'