PAMGuard Release Notes
The PAMGUARD project develops software to help detect, locate and classify marine mammals using Passive Acoustic Monitoring.
All source code is on GitHub at https://github.com/PAMGuard.
PAMGUARD is free software, and you are welcome to redistribute and modify it under the terms of the GNU General Public License (either version 3 or any later version - http://www.gnu= .org/licenses/gpl-3.0-standalone.html).
The latest version of PAMGuard has been tested on 64 bit Windows 10 and Windows 11. We expect it to work without problems on 64 bit versions of Windows 8= and probably 7.
On Windows, download and run the Windows installer.
Releases since 2.01 have all been bundled with a 64 bit Java Virtual Machine (JVM). These releases will= only work on a 64 bit version of Windows. For these releases you do not need to install any Java versions yourself.
For older releases, you will need to install a Java Vi= rtual Machine (JVM) version 7 or 8 separately. Since release 1.15.00 (February 20= 16) both 32 and 64 bit JVMs are supported. Since rel= ease 1.15.08 the installer allows you to select whether to install the 64 bit version or the 32 bit version. The 64 bit JVM allows access to more memory than the 32 bit version which c= an be useful when working with many channels or at high sample rates. You may download Java from the Java website: https://java.com/en/downlo= ad/manual.jsp
Note that the interface to Microsoft Access databases = is not supported in the 64 bit version or when using a = 32 bit Java 8.
On Windows, the installers will create shortcuts in the Windows Start menu.
In a Windows operating system you may want to set the preferences for the launchers (and/or the shortcuts to them) to state that = they should always be run under Administrator privileges. These are required if = you want PAMGUARD to be able to perform actions such as using the GPS time to s= et the system clock.
If using other operating systems such as Linux or Mac OS X you should be able to launch PAMGUARD via an appropriate command line which should be something like:
j= ava -Xms384m -Xmx4096m -Djava.library.= path=3Dlib64 -jar Pamguard_xxxxxx.jar
The -Xms384m -Xmx4096m specify the initial and maximum= heap size for the JVM being used to run Pamguard i.e. how much memory it gets to use. The default max size usually being too low.
The -Djava.li= brary.path=3Dlib64 tells the JVM that it should look in the folder called "lib64" for the required shared libraries (change to lib for the 32 bit version).
For "Mixed" and "Viewer" modes jus= t add a "-m" or "-v" to the list of java arguments. On Windows just run the appropriately named executable (e.g. PamguardBeta_MixedMode.ex= e or PamguardBeta_ViewerMode.exe):
j= ava -Xms384m -Xmx4096m -Djava.library.= path=3Dlib64 -jar PamguardBeta_xxxxxx.jar -v
&= nbsp;
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 doesn’t continually reset them.
Help for Matched Click Classifier.
Project information dialog. This allows capture of ess= ential project information to store with your data. See menu item Settings/Project information.
‘Effort’ management system. New map options allow colouring of track line by ‘effort’ from various other modules. This is currently the acquisition system (so the track will change colour when PAMGuard is running), the binary store system (likely the same = as the acquisition) or data from Logger forms. This system will be extended to other modules in the near future.
“Added a new exporter which allows users to expo= rt data to .mat (MATLAB, Python), .RData (open in R) or .wav files (open in Sonic Visualiser, Audacity etc.)"
Many users will be aware that we’re integrating = an interface to the Tethys Database i= nto PAMGuard. Some basic features are available for testing. If interested, ple= ase contact the PAMGuard support team.
Linking clicks to offline clicks table. We had a datab= ase that had become corrupted so added code to relink offline clicks to their corresponding clicks from binary data.
Drawing non-acoustic data: Data that were not associat= ed with any hydrophones, e.g. visual sightings in Logger forms were not drawin= g on the map. This fixed and PAMGuard will use the vessels GPS position as reference.
Lookup tables: fix feature which was causing table ent= ries to repeat.
Click Train Detector: Add exception handlers to avoid = errors as PAMGuard stops / restarts.
Group Detection starts and ends: Check data integrity function fixed and now inserts correct times of start and ends of events in= to database.
Clip generator. Changes to ensure PAMGuard keeps audio= data 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 remove high sample levels e.g. from calibration tones at start = of a soundtrap recording was not working with the cl= ick detector. This is fixed but replacing all data with 0’s and still sen= ding data. Note that this may lead to artificially low noise measures at the sta= rt 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 aft= er the hour.
Updated icons to improve display on high definition screens.
SAIL Daq Card. Automatic restart when DAQ card stalls (happening increasingly often with latest Windows updates)
Importing modules fro= m other configurations: New options from file menu allowing import of specific modu= les, or module settings from other configurations. E.g. if you had three similar configurations and had set one of them up with a new de= tector, or got the click classifier settings set up just right in one of tho= se configurations, you can import the additional modules or the click detector settings easily into the other configurations.
Improved SUD (soundtrap compressed files) file performan= ce when scrolling through audi= o data in Viewer mode.
Viewer Launch by r= ight clicking on sqlite database and selecting ̶= 0;open with / Pamguard ViewerMode” launcher menu option.
Logger Forms
B= oolean (logical true/false, yes/no) data were not showing correctly in Viewer mode. Now fixed
D= ata selectors for plotting on map were not working, also fixed
B= earing localizer running offline was not correctly saving updated bearings to the database. Now fixed.
ROCCA Classifier fixes
A= llow Rocca to run without classifiers: Fixed bug that threw an error if no classifier files were specified in Rocca Params dialo= g
F= ix memory issue with RoccaContourDataBlocks not being rel= eased for garbage collection
S= et RoccaContourDataBlock objects to null and stop PamObserver Timer to
f= orce release
F= ix problem tracing whistles in Rocca spectrogram pop-up: Whistle and raw data were bei= ng cleared before the user had time to trace out the whistle, causing PAMGuard= to throw an exception. Both were already being cleared when the pop-up window is closed, so no need to do it here.
DIFAR Module: Bug crashing the module with null pointer errors fixed.
Whistle Detector: F= ixed bug which caused the detector to slow to almost zero speed when large complex sounds with many branches were detected.
Click Detector Offline Event Marking: Fixed problem of events not being correctly deleted and also of clicks not being correctly reassigned to different events. <= /span>
Screen Position: W= hen using multiple monitors, if you move a configuration to a 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= .
File Folder Processing: 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 detector= s, causing memory leaks when new data arrived with time stamps 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.
T= ime zone displays: Fixed some bugs associated with options to have PAMGuard display times in local time, rather than UTC. This was affecting times typed into t= he scroll bars of displays which were reading local time, even when set to use UTC.
R= OCCA Memory Leak: A memory leak in ROCCA, which mostly occurred when processing large datasets of many offline files, has been fixed.
D= ata Map: “Scroll To Data” pop-up menu, which didn’t always scroll to the correct place, is now fixed.
B= earing Localiser offline: If reprocessing bearings, the loca= lizer was not correctly loading required raw or FFT data to input to the cross correlation algorithm. This is now fixed so that= you can reprocess bearings in viewer mode.
M= ap files: Added additional exception handlers to handle corrupt map files.
R= estart Options: When you restart processing of offline files, if output data alrea= dy exist (binary data of within database tables) you will be asked if you want= to overwrite the data, cancel, or try to continue from where to left off.
U= pdated SoundTrap sud file interf= ace so that PAMGuard now extracts and stores the Click Detector settings from the = sud files and stores them within the PAMGuard configuration. This does not affect processing, but is important for record keeping.
G= PS options to use any valid RMC or GGA 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 n= ame may be.
U= se of localization sensor and orientation 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.
C= lick tool bar: Correctly shows event selection options even if no species classificat= ion options are in place.
F= ixed Landmarks: Earlier versions were ‘losing’ t= hese every time PAMGuard started or new data were loaded in viewer mode. = Now fixed.
R= OCCA: Fixed (another) memory leak which caused PAMGuard to crash when processing large data sets with the ROCCA classifier.
I= shmael Modules: Fixed bug which occasionally caused crashes when processing many f= iles offline.
PAMDog: Fixed bug in watchdog program which was trying to start PAMGuard before mod= ules were fully loaded. The watchdog now correctly waits until modules are loaded before attempting to start PAMGuard processing.
N= ew sound type for simulated sounds which generates random chirps between around 200 = and 800Hz, roughly the frequency you’d expect sound from higher frequency baleen whales, such as humpbacks, to vocalise a= t.
H= iding tool tips. A menu item to 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.
T= wo memory leaks:
A= memory leak has been found which seems to mostly occur in Viewer mode. Some data on background noise measurements are not being cleared from memory, so memory = will eventually run out. This could happen after browsing a lot of data, but was most likely when reprocessing files offline, for example running click classifiers. This is now fixed.
A= lso fixed a memory leak in the ROCCA whistle classification module.
SoundTrap
SUD file reading. If you’re using SoundTrap
autonomous recorders from Ocean Instruments, you no longer need to decompre=
ss
the SoundTrap files prior to processing. This w=
ill
save time and a lot of disk space. Extraction of clicks from the inbuilt
Features
C= hanges to GUI to make dialog shorter for low DPI screens.
C= omplete rewrite of the classification system to have nested classifiers which can be enabled or disabled.
C= hanges to classification GUI to accommodate the new classification system.
A= ddition of data selectors to the minimum number of clicks accepted by the classifier. = This allows the click-by-click classifier and the click train detector to be use= d to together to improve classification accuracy.
Bug fixes
C= lick detection bug fix in kernel which improved click fragmentation.
B= ug fix to database were JSON data from classifier was being trimmed.
Documentation
C= omprehensive help file including description of the algorithm, screen grabs and examples= .
B= ug fixes
H= elp documentation for Backup Manager
H= elp documentation for Matched Click Classifier
D= atabase logging of offline tasks (such as click re-classification, bearing calculat= ion, etc.)
D= ata selector for Whistle Classifier module
V= ariable sound output level when using National Instruments devices for sound playba= ck.
S= peed improvement when processing flac audio files. <= /span>
Soundtrap DWV import. Will now generate binary files even if DWV file doesn‚’t exist (which is correct behavior in quiet condit= ions when no clicks were detected).
S= pectrogram. Changes to stop occasional crashing when restarting processing of wav files= .
S= izing of dialogs on ultra high definition monitors so that data fields are sized correctly.
F= ixed a memory leak in ROCCA
F= ixed issues with options in Click Detector bearing time display which (when using planar and 3D arrays) allow you to plot relative to the array, the vessel, = or North.
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/PAM= Guard/PAMGuard/issues. GitHub issue number are referred to with a # symbol
#6 Threading Hydrophone Locator: was not working corre= ctly in the latest release V2.02.02. The problem was particularly apparent in Vi= ewer 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 c= rash 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 ga= ps 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 contiguo= us files’ option was not selected.
#14 Logger forms data were not plotting correctly. Thi= s was due to the required data selection functions not being fully implemented. T= his 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/PAMG= uard/PAMGuardMatlab.
M= inor bug fix to V2.02.01 which would cause the TF FX displa= y to crash if no data were displayed.
S= ee major release notes for V 2.02.01 below.
B= ug 495: TD FX display throws NullPointerException if user = has removed all data units and then moves mouse over display area.
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 B= eta Version 2.00.10 before proceeding with installation and use of this version.
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 su= pport 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.
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. Furth= er, a number of example configurations have been generated, configuration files for these are available in the PAMGuard downloads area = here.
Detection Group Localiser
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 localizati= on.
Minor Bug Fixes <= /span>
1. &n= bsp; Bug 490. Error when trying to select File in Sound Acquisition.
2. &n= bsp; Bug 491. LTSA spectrogram frequency axis does not update when changing t= he params
3. &n= bsp; Bug 492. Data Model does not update button//tooltip text when underlying data changes
4. &n= bsp; Bug 493. Click Detector does not work when using the 'skip x seconds' op= tion in Sound Acquisition dialog
5. &n= bsp; Bug 494. Detection Group Localiser data unit end time did not adjust when the last member was remove
6. &n=
bsp; Bug
495. TD FX display throws NullPointerException<=
/span>
if user has removed all data units and then moves mouse over display area <=
/p>
Upgrades 1. &n=
bsp; Added SIDE module for detector/operator analytics 2. &n=
bsp;
Upgrade database system to work with MySQL 8.0 3. &n=
bsp; Improvements to datamap display, to ensure even small images will be =
shown 4. &n=
bsp; Allow Clip Generator=
to
create both a binary record and a wav file 5. &n=
bsp; Implemented a Backup=
Manager
for backing up multiple types of data to multiple locations] 6. &n=
bsp; Upgrades to how PAMG=
uard
lets the user enter custom date formats in the Sound Acquisition dialog 7. &n=
bsp; Extended XML-output =
support
to all of the modules 8. &n=
bsp; Updates to the simul=
ated
sounds in the Sound Acquisition module 9. &n=
bsp; Upgrades to the Symb=
ol
Manager framework, to give more control over colours and symbols 10. &n=
bsp; Added an option to h=
ide the
ship on the map 11. &n=
bsp;
Update Rocca module to allow operation without a classifier (in case all you
need are the measurements) 12. &n=
bsp;
Update whistle and moan detector to better handle small stubs or spurs comi=
ng
off the side of whistles 13. &n=
bsp; Extend the Hyperbolic
Localiser to handle 2D planar arrays (previously limited to 3D volumetric
arrays) 14. &n=
bsp; new CPOD features
15. &n=
bsp; Better interpolation=
of data
by the Decimator when decimating/upsampling by a
non-integer amount 16. &n=
bsp; Noise Level Outputs =
- as an
aid to performance diagnosis, some detectors (currently the GPL, Click Dete=
ctor
and Whistle and Moan Detector) are outputting additional noise metrics to t=
heir
binary output files. These can be read with the PAMGuard <=
span
class=3DSpellE>Matlab
17. &n= bsp; 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 t= he online help
18. &n=
bsp; A Deep Learning modu=
le for
sound classification is now available. This allows users to deploy a large
variety of deep learning models natively in PAMGuard. For details, see the =
online
help.
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 B= eta 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.
Bug Fixes
1. &n= bsp; Bug 474. Click Detector Classifier fails when trying to use amplitude ra= nge for classification.
2. &n= bsp; Bug 476. Array Manager dialog throws exception if there is only 1 hydrophone.
3. &n= bsp; Bug 478. Ishmael Detector auto-scaling graphics does not work well.
4. &n= bsp; Bug 479. Increase number of characters in fixed landmark module from 50 = to 256.
5. &n= bsp; Bug 481. Depending on Windows Security settings, PAMGuard may not be abl= e to access dll library (such as NMEA).
6. &n= bsp; Bug 482. Concurrency problem when hydrophone interpolation method is not= set to "Use Latest Value".
7. &n= bsp; Bug 483. Radar display loses it's params whe= n new modules are added.
8. &n= bsp; Bug 484. Datagram Display error.
9. &n= bsp; Bug 485. 3D Group Localiser limited by millisecond times when dealing wi= th closely-spaced hydrophones.
10. &n= bsp; Bug 486. UDF tables not getting copied over to new database properly.
11. &n= bsp; Bug 487. Database module not working with newer version of MySQL
12. &n= bsp; Bug 488. Incorrect 0-peak and peak-peak calculations in Filtered Noise Measurement module.
Upgrades
1. &n= bsp; Speed up adding subdetections to superdetections= .
2. &n= bsp; Added new system of scrolling to data in Spectrogram, using CTRL+arrow keys to move to previous/next displayed data unit.
3. &n= bsp; Implemented new Effort Monitoring System to track on/off-effort information=
4. &n= bsp; Added ability to receive NMEA over UDP multicast in addition to UDP broadca= st
5. &n= bsp; Added logger form annotation to Spectrogram Annotation module.
6. &n= bsp; Better auto-scaling = in Ishmael Detector graphics window.
7. &n=
bsp; Change to Windows te=
mporary
folder location, to get around Windows Security settings that were preventi=
ng
some modules from working properly.
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 B= eta 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.
Bug Fixes
1. &n= bsp; Bug 451. Small time offset was being applied when post-processing wav fi= les.
2. &n= bsp; Bug 453. Adding a new spectrogram display causes PAMGuard to throw excep= tion
3. &n= bsp; Bug 455. Cepstrum creating data units using channels it should not be using
4. &n= bsp; 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 current time.
5. &n= bsp; Bug 457. PAMGuard throws exception in Viewer mode when trying to load a = data unit that has more than 1 annotation
6. &n= bsp; Bug 458. Contour lines on map disappear when user zooms in
7. &n= bsp; Bug 459. Rocca does not save wav clip properly when WMD is source
8. &n= bsp; Bug 460. Click Detector BT Display vertical axis shows all zeroes when zooming out
9. &n= bsp; Bug 461. Fix pam symbol drawing - bit of a mix up between width and right edge
10. &n= bsp; Bug 462. Fix time offset bug in Decimator. Was putting data times a chunk out of synch.
11. &n= bsp; Bug 463. Changed start sample in the data unit to be actual start sample= and not the end sample.
12. &n= bsp; Bug 464. Click Train Detector multiplying instead of dividing for long tracks.
13. &n= bsp; Bug 465. Matched click classifier peak search was not working.
14. &n= bsp; Bug 466. Bug in IIR filter which was not correctly handling odd numbered band pass or band stop filters.
15. &n= bsp; Bug 467. Fix bug in triggered recordings that was messing up the amount = of time.
16. &n= bsp; Bug 468. User Display tab does not disappear when the module is removed.=
17. &n= bsp; Bug 469. Mark Observers may not work properly in TD Displays
18. &n= bsp; Bug 470. Datagram not displaying colours properly, hanging while scrolli= ng.
19. &n= bsp; Bug 471. Beamformer, LTSA and Cepstrum data = not displaying data properly in Spectrogram.
20. &n= bsp; Bug 472. Viewer mode crashing when generating a Datagram from very large binary files.
21. &n= bsp; Bug 473. ReportGenerator throwing exception = when trying to generate report.
Upgrades
1. &n= bsp; Add functionality fo= r bluetooth headsets.
2. &n= bsp; Add user-facing opti= on 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. &n= bsp; Add support for RS A= qua time format.
4. &n= bsp; Add 15 minute data load option to viewer mode. <= /p>
5. &n= bsp; Add 3D map for targe= t motion module.
6. &n= bsp; Add option to alarm = module to attach screenshots of all frames to email alerts.
7. &n= bsp; Add Beamformer and B= earing Localiser modules
8. &n= bsp; Added Global Medium = Manager, to switch between air and water mediums
9. &n= bsp; Added global hotkeys to Logger module.
10. &n= bsp; Added channel displa= y to noise one band measurement display.
11. &n= bsp; Added Azigram module, to work in conjunction with Difar.
12. &n= bsp; Added beaked whale t= o sim sounds
13. &n= bsp; Added ctrl-p hotkey = to print-screen button.
14. &n=
bsp; Update simulated
14. &n=
bsp;
Changes to FX Display to make it more intuitive - menu options, button
placement, etc.
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 B= eta 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.
Bug Fixes
1. &n= bsp; Bug 433. Custom stor= age options were being lost when Pamguard restarted.
2. &n= bsp; Bug 434. Pamguard Vi= ewer mode was having problems importing settings from psfx<= /span> file.
3. &n= bsp; Bug 435. Logger forms subtabs not working.
4. &n= bsp; Bug 436. Bug in Seri= al Port interface was occassionally causing PAMGuard to= crash without error message.
5. &n= bsp; Bug 437. Right whale detector crashing if no input was set.
6. &n= bsp; Bug 438. Text not sh= owing in tabs in Night colour mode.
7. &n= bsp; Bug 439. Can no long= er access Spectrogram settings once you've selected a Click Detector as Mark Observer
8. &n= bsp; Bug 440. Measurement Computing Cards not enumerating properly.
9. &n= bsp; Bug 441. Plot coordi= nate calculations incorrect in PamAxis.
10. &n= bsp; Bug 442. BT Display = does not change click symbol color when Colour By Superdetection is selec= ted.
11. &n= bsp; Bug 443. NI playback crashing immediately if a device is not present.
12. &n= bsp; Bug 444. Bug in data selector which caused it to mess up history of recent = psf files.
13. &n= bsp; Bug 445. Overlay dat= a in FX spectrogram display gets out of sync with underlying spectrogram image.
14. &n= bsp; Bug 446. Multiple PamDataBlocks with same name = turn on/off together in Spectrogram display.
15. &n= bsp; Bug 447. Viewer mode= throws exception when trying to load beamformer localisations
16. &n= bsp; Bug 448. Detection G= roup Localiser data units not being loaded in Viewer mode.
17. &n= bsp; Bug 449. Rocca Encounter Stats output file calculating incorrect values.
18. &n= bsp; Bug 450. Ishmael Det= ectors subscribing to FFTDataBlock twice, meaning they process each data unit 2x doubling the output.
Upgrades
1. &n= bsp; Added functionality = to TD display to allow users to manually classify clicks.
2. &n= bsp; Added option in Sound Acquisition settings dialog to override filename time stamp and use PC local time instead.
3. &n= bsp; Add option to Whistl= e & Moan Detector data selector to only display whistles that have super-detections.
4. &n= bsp; Functionality to clo= ne hydrophone streamers.
5. &n= bsp; 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>
6. &n= bsp; Implemented a simple UDP output for PAMGuard alarms.
7. &n= bsp; Changes to Spectrogr= am Mark Observers, to allow individual channels to be selected instead of the spectrogram panel as a whole.
8. &n= bsp; Change to use long m= odule names in dialogs instead of short, to make it easier to know the difference between output data blocks when using the same module multiple times.
9. &n= bsp; Added a few new options to the Click Detector Sweep Classifier.
10. &n=
bsp; Add option to the Map
module's Plot Overlay Options dialog, to show events o=
ccuring
in the future (look ah=
ead)
instead of the default display of events which have already occurred. Can m=
ake
it easier to match up the map with clicks seen in the Click Detector displa=
y.
Upgrades
1. &n= bsp; This version of PAMG= uard 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. &n=
bsp;
Java 12 is better at handling Windows scaling issues on high-DPI displays.
Beyond that, users should not notice much of a difference between this vers=
ion
and previous beta releases.
P= AMGuard 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.
Bug Fixes
1. &n= bsp; Bug 427. Soundtrap import not closing binary files properly if BCL files do not contain off-ef= fort 'E' line
2. &n= bsp; Bug 428. Decimator crashing in viewer mode
3. &n= bsp; Bug 429. Click Bearings at 180 degrees
4. &n= bsp; Bug 430. Rocca calcu= lates inflection point parameters incorrectly
5. &n= bsp; Bug 431. Error when = trying to mark section of spectrogram to send to Bearing Calculator module
6. &n= bsp; Bug 432. MySQL datab= ase interface - connection problems
Upgrades
1. &n= bsp; New display for Gebco Netcdf bathymetry m= aps.
2. &n= bsp; Difar enhancements based on recent field testing.
3. &n= bsp; Click Train Detector upgrades, including localisation capabilities.
4. &n=
bsp; Updates to the Ishma=
el
detectors.
P= AMGuard 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.
Bug Fixes
1. &n= bsp; 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
2. &n=
bsp;
Bug 414. Whistle Classifier module may not classify properly when
3. &n= bsp; Bug 415. Click Detector could throw an Out Of Memory error when processing a large dataset.
4. &n=
bsp;
Bug 416. Bearing Localiser was not using the FFT information from
5. &n= bsp; Bug 418. Rocca module was not classifying clicks properly when in Vi= ewer mode.
6. &n= bsp; Bug 419. Radar display not showing correct symbol in key.
7. &n= bsp; Bug 420. The Click Classifier set was not getting updated properly in Viewer mode.
8. &n= bsp; Bug 421. Alarm module resetting the simple count too quickly
9. &n= bsp; Bug 422. Soundtrap import causing memory problems with large datasets.
10. &n= bsp; Bug 423. TD display FX scrolls extremely slowed when super detections were present.
11. &n= bsp; Bug 424. Pamguard would occasionally freeze when processing offline files.
12. &n= bsp; Bug 425. Rocca crashing if Click Detector is used as source but the Click Classifier is not configured properly.
13. &n= bsp; Bug 426. Clip Generator could cause memory issues when a large number of files were being analyzed.
Upgrades
1. &n= bsp; Upgrades to the Group Localiser, including better error estimation.
2. &n= bsp; Click Train Detector upgrades, including ability to import time chunks from csv file for batch processing.
3. &n= bsp; Better display of microseconds in dialogs.
4. &n= bsp; Added adaptive noise= filter to Ishmael Detectors.
5. &n= bsp; Many upgrades to the= Sound Playback module, including a high-pass filter, gain control, and the abilit= y to mix wavefrom and envelope data together to list= en to high-frequency clicks and dolphin whistles at the same time.
6. &n= bsp; New Analog Array Sensors module, to read data from 3-axis accelerometers.
6. &n= bsp; Send Email option ad= ded to Alarm module.
7. &n=
bsp; Added ability to sca=
le 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 hopeful=
ly
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.
P= AMGuard 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.
Bug Fixes
1. &n= bsp; Bug 401. AIS graphics in Viewer crashing.
2. &n= bsp; Bug 402. Fixed problem with data from old access database not import= ing correctly
3. &n= bsp; Bug 403. Seismic Veto throwing ClassCastExcepti= on when downstream of a Signal Amplifier and the multithreading options are changed. Fixed.
4. &n= bsp; Bug 406. Pamguard resetting UID values in binary files.
5. &n= bsp; Bug 408. Map Key icon not updated when colouring by channel. Fixed. =
6. &n= bsp; Bug 409. Fixed Click Detector not showing the correct input source in the dialog
7. &n= bsp; Bug 410. Bug in Difar module, manually e= diting sonobuoy compass corrections.
8. &n= bsp; Bug 411. Incorrect matching of GPS data sources for calibration in <= span class=3DSpellE>Difar module.
9. &n= bsp; Bug 412. Fixed problem with ship always centeri= ng on map.
Upgrades
1. &n= bsp; Improvement to Range= Rings in Map display.
2. &n= bsp; Improvement in click train detector speed.
3. &n= bsp; Added table of compa= ss calibration to the Sonobuoy Manager, and option to use magnetic variation as initial calibration.
4. &n= bsp; Matched template cla= ssifier extended to handle multiple templates.
5. &n= bsp; New methods for hand= ling and logging time offsets from the PC clock based either on GPS NMEA data or on pings of an NTP time server.
6. &n= bsp; Improvements to Difar module graphics - easier reading, better visibility at night.
7. &n= bsp; Added print screen b= utton to capture/save all PAMGuard screens to file and log the information to the database.
8. &n= bsp; Updates to the Ishmael module.
9. &n=
bsp; Added option to the =
WarnOnce dialog to hide a warning for the current PAM=
Guard
session, but not forever.
P= AMGuard 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.
Bug Fixes
1. &n= bsp; Bug 338. Problem displaying coastlines and bathymetric contours arou= nd the dateline (+/- 180 longitude) in the map.
2. &n= bsp; Bug 397. Clip Generator not able to find raw data when clips were ta= ken from many channels.
3. &n= bsp; Bugs 398 and 399. Click Detector, FFT Engine and Filter modules were losing source during startup, if the source selected was not the first raw = data source in the list.
4. &n= bsp; Bug 400. Spectrogram display running out of memory.
Upgrades
1. &n= bsp; Added decimal degree= s option to latitude/longitude dialog.
2. &n= bsp; Added option in the = Click Delay parameters to restrict the number of initial samples used in the calculation. This can be useful for cleaning up delays in the presence of echoes and small time delays.
3. &n= bsp; Increased upsampling to 2, 3 or 4 times.
4. &n=
bsp; Can now change units=
and
scale type in level meter display.
P= AMGuard 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.
Bug Fixes
1. &n= bsp; Bug 381. Logger form loses controls when the order is changed.
2. &n= bsp; Bug 382. Click species check boxes get cleared in toolbar when the C= lick Classification dialog is closed
3. &n= bsp; Bug 383. Spectrogram max frequency resetting to incorrect value the first time the spectrogram dialog is opened.
4. &n= bsp; Bug 385. Bug in offline toolbar which will crash if the classifier dialog is opened and then closed with no classifiers specified.
5. &n= bsp; Bug 386. Click Detector Sweep Classifier sometimes keeping changed settings even when user tries to cancel or discard changes
6. &n= bsp; Bug 387. Map was stopping displaying data based on the start time of data units. Have changed this to last updated time so that click events will display if they have been recently modified. Otherwise, long events get lost from the display.
7. &n= bsp; Bug 388. Spectrogram annotations not working properly in beta branch. Would make and store mark, but not store snr or notes. Both now fixed for b= oth online and offline operations. Have also added some options controlling SNR measurement period.
8. &n= bsp; Bug 389. Multiple annotations of the same class would not be stored = to the database if they had the same class. This was affecting the Spectrogram Annotation module which has now been given two text type annotations.
9. &n= bsp; Bug 391. Click Detector not registering change in multi-threading option.
10. &n= bsp; Bug 392. Click Detector throwing exception if multi-threading is tur= ned off and the Basic Sweep Classifier is testing the amplitude range.
11. &n= bsp; Bug 393. Rocca module not calculating energy, duty cycle, and windowRMS values when manually picking contour points= .
12. &n= bsp; Bug 394. Occasional divide-by-0 error in Spectrogram Display time sc= ale.
13. &n= bsp; Bug 395. Problem with hydrophone locator was resulting in an incorre= ct x position for hydrophone 0.
Upgrades
1. &n= bsp; Better way of coupli= ng scrollers in User Display panels - see new options in main menu.
2. &n= bsp; Added Matched Templa= te Click Classifier. Classifies clicks based on an ideal template to match and a template to reject. An example of this is to classify beaked whale clicks i= n an environment with dolphin clicks.
3. &n= bsp; Added zoom in/out to Raw Data plugin display in spectrogram.
4. &n= bsp; Added ability to read differential GPS data.
5. &n= bsp; Added check for dupl= icate settings in the psf file when exiting Pamguard.= If duplicate settings are found, user is given the option to leave them in the= psf or get rid of them. Duplicate settings are ignore= d by Pamguard, but can cause the psf file to grow large over time.
6. &n=
bsp;
New features in PAMGuard Beta mean that psf fil=
es
created with new versions are not compatible wth
earlier versions and all configuration data may be lost if an attempt is ma=
de
to open newly created psf files with older vers=
ions.
We have therefore changed the file extension of psf
files to .psfx in ne=
w Beta
releases. Beta releases will still load the older psf<=
/span>
files, but when the configuration is saved, the original psf
file will remain untouched and data will be written to a psfx
file with the same directory and name.
P= AMGuard 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.
Bug Fixes
1. &n= bsp; Bug 367. When adding a click to an event that already contained that click, the click was being duplicated in the subtable<= /span>.
2. &n= bsp; Bug 368. Whistles from the Whistle & Moan Detector no longer sho= w up on the FX display overlay.
3. &n= bsp; Bug 369. Map options not showing up in viewer mode when right-clicki= ng on map.
4. &n= bsp; Bug 370. Rocca crashing when receiving detections from Whistle and M= oan Detector.
5. &n= bsp; Bug 371. Rocca loses FFT channel selection when opening params dialo= g.
6. &n= bsp; Bug 372. Rocca database record incorrectly lists Whistle Classifier = file for Clicks.
7. &n= bsp; Bug 373. Incorrect GPS headings in the database are propagated throu= gh Pamguard and cause problems with mapping and TMA.
8. &n= bsp; Bug 374. Bearing Errors in Target Motion-3D Loc' calculations.
9. &n= bsp; Bug 375. Low Frequency Clicks not working.
10. &n= bsp; Bug 376. Error when using a serialised data map which spans a period of time in which Pamguard modules have change= d.
11. &n= bsp; Bug 377. changes to click events in Viewer Mode not getting saved to database.
12. &n= bsp; Bug 378. TMA dialog not displaying current Model type, and unclear w= hen event not selected.
13. &n= bsp; Bug 379. Channel boxes were being cleared whenever the Decimator settings window was opened.
Upgrades
1. &n= bsp; Soundtrap module - bug fixes and more intuitive user interface when importing Soundtrap data. Also changed the default date/time fo= rmat to ISO8601 standard.
2. &n= bsp; = A number of upgrades and fixes to the Localiser algorithms, including expandi= ng to work with whistles.
3. &n=
bsp; Added option to expo=
rt 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 (
4. &n=
bsp; Many updates to the =
Video
Range module. Will currently only work with landmarks.
P= AMGuard 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.
Bug Fixes
1. &n= bsp; Bug 355. Pamguard crashed when database module was present and Rocca tried to load classifier
2. &n= bsp; Bug 356. Ishmael Localiser losing raw audio before it had time to localise
3. &n= bsp; Bug 357. Difar storing Tracked Group lat= itude in both GroupLatitude and = GroupLongitude database columns
4. &n= bsp; Bug 358. Clip Generator not storing overlapping detections properly<= /p>
5. &n= bsp; Bug 359. Pamguard crashes when selecting auto-scale option in Noise Monitor module
6. &n= bsp; Bug 360. LTSA not loading in viewer mode
7. &n= bsp; Bug 362. Bug in maximum likelihood bearing estimator grid search
8. &n= bsp; Bug 363. Rocca throwing exception if user boxes a whistle close to t= he beginning of a file
9. &n= bsp; Bug 364. LTSA bug - get correct fft leng= th and hop into datablock and output stream
10. &n= bsp; Bug 365. Lose spectrogram settings when converting data from Core to Beta versions
11. &n= bsp; Bug 366. Rocca manual whistle contour extraction throws error when trying to classify a boxed whistle
Upgrades
1. &n=
bsp; During conversion fr=
om Core
to Beta versions, if there are any problems matching database units to bina=
ry
store units the UID values will now be set to negative numbers instead of
leaving them null. The user is warned about this and encouraged to manually=
fix
the database.
P= AMGuard 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.
Bug Fixes
1. &n= bsp; Bug 334. Fixed problem of GPS dialog occasionally resizing Pamguard window.
2. &n= bsp; 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. &n= bsp; Bug 341. Temporary objects created in the Rocca module were not bein= g discarded, and could cause memory issues in large data= sets.
4. &n= bsp; Bug 342. Rocca was not properly loading a previo= usly-saved EncounterStats file.
5. &n= bsp; Bug 343. Fixed threading issue between Rocca and Click Detector.
6. &n= bsp; Bug 346. Click Classifier not properly checking frequency ranges for invalid entries.
7. &n= bsp; Bug 347. Pamguard crashes when loading a Sound Acquisition module wh= en Java 7 is installed on computer. Caused by JFLAC library, which has been recompiled to correct issue.
8. &n= bsp; Bug 348. Map plot overlay menu not updating.
9. &n= bsp; Bug 349. Clip Generator overlay graphics sometimes crashing on map.<= /p>
10. &n= bsp; Bug 354. Whistle Classifier was crashing if user accidentally entered invalid parameters. Have added diagnostics to prevent this.
Upgrades
1. &n=
bsp; User is now able to =
specify Soundtrap date/time format
P= AMGuard 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.
Bug Fixes
1. &n= bsp; Bug 322. Fixed problem with Log event average and click templates not showing.
2. &n= bsp; Bug 323. Difar module. Fixed a couple of small bugs in = the DIFAR system which caused it to not work if old config= uratins were used.
3. &n= bsp; Bug 324. Occassional crashing in the AIS Module, as reported by user. Added warnings and more robust error handling.=
4. &n= bsp; Bug 325. Fixed bug in complex addition/subtraction methods.
5. &n= bsp; Bug 328. Fixed bug in NMEA data flow which caused a Null pointer exception.
6. &n= bsp; Bug 330. Problem with certain FLAC files not being read properly. Upgraded jFLAC library to fix.
7. &n= bsp; Bug 332. Fixed problem with secondary maps (those not in the main display) not displaying detections.
8. &n= bsp; Bug 333. Fixed problem with data end times rounding incorrectly.
Upgrades
1. &n= bsp; Added sound playback and other useful information to bar on FX display
2. &n= bsp; Updates/bug fixes to= the landmark module.
3. &n= bsp; Added a simulated wh= ite noise source which can be moved around in the same way as other sources.
4. &n= bsp; Reworked annotation = system, and added annotations to binary storage
5. &n= bsp; Added 3D rotation to= map display. Hold down the shift key while clicking and dragging on the map to = see this in action.
6. &n= bsp; Added database loggi= ng and other updates to the Click Detector trigger function
7. &n=
bsp;
Added circular movement option to source simulation
P= AMGuard 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-11= 26.
T= he Binary File structure has changed to accommodate additional information for each u= nit of data stored. This means that any data generated with PAMGuard Version 2.00.00 and above will not be compatible with older versions of PAMGuard. If you open older data sets with the PAMGuard Viewer the older data will be converted to the new format (see below for details).
T= he most significant change in the binary file format is the addition of a Unique Da= ta 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 wit= h any data post processed in Matlab or other custom analysis software. UID’s are also added to PAMGuard database tables. =
I= f old data are opened with the PAMGuard viewer they will automatically be converted. F= or safety, the original binary files will not be overwritt= en and the new data will be placed in a new folder on your computer with the s= ame path as the old data, but suffixed with ‘_WithUI= D’, e.g. if your binary data were previously stored in the folder C:\MySurvey\binarydata the new data will be written to C:\MySurvey\binarydata_WithUID.
T= he additional UID column will be added to all database tables and populated wi= th unique values. For data which are stored in both the binary files and in database tables, the same UID’s will be used in both data stores.
A= new time based scrolling display has been 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 dis= play similar to that commonly used in the click detec= tor. Composite display graphs containing data from more than one detector are al= so 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= .
A=
new
system of event marking which can be used both online and offline has been
added to PAMGuard. Details are in the PAMGuard help file (Displays/Display
Marking). Data can be selected on the Map, the Spectrogram Display and the =
new
Time Display FX in a similar way and sent to other PAMGuard modules. The new
marking and data selection system works with the new Detection Group Localiser. The Detection Group L=
ocaliser
extends the functionality which always existed in the click detector to oth=
er
types of data (e.g. Whistles) so that they can be grouped and tracked using
target motion analysis in a similar way. Details of the Detection Group
A= new system for handling display colours has been implemented across all PAMGuard displays. This gives greater flexibility to the user to control how data units are shown. For instance, = you might simply want to show clicks in blue and whistles in green. However, for clicks and whistles that have been assigned to a Detection Group, you may w= ant to colour them by the colo= ur assigned to the group.
O= ld PAMGuard configurations will work with the new version. However please note= the following:
1. &n= bsp; New classes wil= l be added to the configuration files, so they will no longer work with older PAMGuard versions.
2. &n= bsp; Display colour options will be lost and most data displayed o= n the map may default to black. This is due to the above changes to how colours are managed. Changing back to the colours of your choice is relatively simple through t= he PAMGuard GUI.
Bug Fixes
1. &n= bsp; 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. &n= bsp; Bug 320. Pamguard stopped reading Click Detector Event data from database when target motion analysis information was encountered. Corrected= .
3. &n= bsp; Bug 321. Problem reading Soundtrap 4 fil= es. Fixed.
Upgrades
1. &n= bsp; Added Copy-to-Clipboard button to Warning dialogs, to store error messages and stack trace information on the Windows clipboard. This informa= tion can then be easily pasted into emails, text documents, etc when contacting Pamguard support.
2. &n= bsp; Enhancements and bug fixes made to Difar module during 2017 ACE voyage.
3. &n= bsp; Rocca Module: added StartHr, ProportionWhists and ProportionC= licks parameters to Event classifier
4. &n= bsp; The installer now allows the user to enter command line switches/parameters to be included in *.ini fil= es.
Bug Fixes
1. &n= bsp; Bug 308. Map Ov= erlay Control. Storage of data saying what get's plotted on each map and for how long beca= me corrupted and the list grew to a ridiculous size. Code has been put in plac= e to a) stop it happening again and b) to repair any configuration files which a= re 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 t= oo may have become oversized which will slow down viewer mode PAMGuard start-up.
2. &n= bsp; Bug 309. Rocca would crash when the user would press the classify bu= tton after the contour was recalculated. This has been corrected.
3. &n=
bsp;
Bug 310. When exiting Viewer mode, PAMGuard queries the user whether
they are sure they want to exit without saving even though they selected
4. &n= bsp; Bug 311. When double-clicking on a psf f= ile to start PAMGuard, the working directory is set as the location of the psf and not as the installation folder. The library subfolder (\lib or \lib64) uses a relative path from the working folder, and therefore is set incorrectly. This has been fixed.
5. &n= bsp; 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. &n= bsp; Bug 315. code searched for file in working folder, which is the installation folder when starting PAMGuard using a shortcut link. But when double-clicking on a psf, the working folder is= the location of the psf. This has been fixed.
7. &n= bsp; Bug 316. Another error readi= ng metadata for Dtag and Soun= dTrap files has occurred due to a format change in dTag metadata. This has been fixed.
BugFixes
1. Bug 306. Certain methods have been queryi= ng AcousticDataUnit.getDuration and expecting to receive= a response in milliseconds. However, getDuration = actually returns the number of samples. This has= been corrected.
Plug-Ins
A= major change in this version of PAMGuard is how plug-ins are managed. PAMGuard no= w has the ability to dynamically load plug-in modules (s= aved 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.
M= odule code development remains largely unchanged, in most cases simply requiring the addition of an interface class. Instructions for the development of n= ew modules utilizing the plug-in scheme can be found here. Plug-in modules can be downloaded from the PAMGuard website here, but developers are encouraged to host and maintain their own modules.
M= odules of interest to the general PAM community will remain as part of the core PAMGu= ard installation. However, specialized modules which are useful to only a small number of users have been removed and are available as a separate download.= The following modules have been removed:
1. &= nbsp; Resource Monito= r
2. &= nbsp; WILD ArcGIS Int= erface
3. &= nbsp; Workshop Demo D= etector
4. &= nbsp; Echo Detector a= nd IPI Demo (bundled together, due to dependencies)
Other Changes
T= he installer has been updated to handle both 64 bit and 32= bit installations. PAMGuard psf files are now regis= tered in the Windows Registry, so double-clicking on a psf file should run PAMGuard in normal mode (as opposed to Viewer or Mixed mode= s). Note that the Windows Registry can only hold a single executable reference = for psf files; therefore, for users with multiple install= ations of PAMGuard, double-clicking on a psf will run = the most-recently installed version of PAMGuard on the system.
T= his release contains one bug fix.
Bug Fixes
1. &= nbsp; Bug 307. Unpack= er for Sound trap dwv files was not working correctly.= This is now fixed.
T= his release contains two bug fixes.
Bug Fixes
1. Bu= g 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” whi= ch is based on jAsioHost, the unpacking of that fo= rmat contained a bug which returned incorrect numbers, so data were swamped with noise. Both systems are now fixed. By preference, users should use the PAMG= uard ASIO system since the JAsioHost based system se= ems to drop samples when many channels are running at high sample rate.
2. Bug 305.= Date and Time not being correctly extracted from wav files created using SoundTrap recorders. Fixed by correctly finding and unpacking information in the accompanying xml log files that come with SoundTrap files.
T= his release contains bug fixes from release 1.15.05, mostly concerning the new target motion analysis methods. Bugs were found in several places in the system, affecting calculations using all three methods: Least Squares, 2D Simplex and 3D Simplex. To the best of our knowledge, all issues are now resolved.
Bug Fixes
1. &= nbsp; Bug 291. Click Detector Click Classifier: If this is set to "none" the click detector will freeze / crash and will put the psf file into a state where it will never load again. Incredibly, this bug seem= s to have been in place for several years and no one has come across it until no= w. It's fixed.
2. &= nbsp; Bug 292. Incorrect labels on Target Motion panel in viewer - 3D algorithm was labelled as 2D.Fixed
3. &= nbsp; Bug 293. Errors displayed in the click detector target motion panel = were wrong in the graphics for the Simplex localisers and wrong in the tabulated data for the least square model. Both fixed.
4. &= nbsp; Bug 294. Click classifier was crashing when the 'min amplitude' opti= on was used. This is fixed.
5. &= nbsp; 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
6. &= nbsp; Bug 296. Context menu popping up in click detector when marking clic= ks in Viewer mode. This has been fixed so that in viewer mode, the menu will o= nly appear when you right click on the display.
7. &= nbsp; Bug 297. Airgun display was not correctly showing itself at fixed locations, but always following the vessel track. This is now fixed.
8. &= nbsp; Bug 299. Threading Hydrophone locator. Bug found in hydrophone headi= ng calculation has been fixed.
9. &= nbsp; Bug 300. GUI Tab panel selections were not being restored correctly = when PAMGuard displays were split across multiple frames. Fixed.
10. &= nbsp; Bug 301. Multiple errors in the target motion module have been fixed= .
11. &= nbsp; Bug 302. Target motion calculations taking too long when many clicks= are included in a track. Mostly a problem when using automatic click train id. Fixed by setting an optional maximum number of clicks to use in a track.
Bug Fixes
1. &= nbsp; Bug 273. Sound = files in viewer data map. These were not being correctly catalogues in the datamap when using the PAMGuard viewer which meant th= at PAMGuard was not correctly loading sound data during offline analysis. This= is now fixed.
2. &= nbsp; Bug 287. Slow d= atabase. This has been solved by setting the default behavior of the database to have Auto Commit set to 'off'
3. Bug 288. Fixed problem of missing help fi= le image
4. &= nbsp; Bug 290. Click = bearings on spectrogram display plug in were reversed if the first hydrophone was be= hind the second hydrophone in the configuration. This is now fixed so that it displays the same bearings as the 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 Dete= ctor will notice the following changes:
1. &n= bsp; 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 disp= lay on the map and for storage in the database.
2. &n= bsp; The number of d= ata 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. &n= bsp; When tracking o= nline, all the click marking information is written to the same database tables as= are used for offline target motion analysis. This means than when reviewing data offline, the tracks created in real time are now available for review and f= urther analysis.
4. &n= bsp; A number of user options are now available for automatic click train identification and tracking.
5. &n= bsp; The automatic c= lick train identification is now using the same internal structures as the manual tracking, so it's possible to combine automatic and manual tracking.
6. &n= bsp; Improved option= s are available to the user, via the click detector bearing time display, to corr= ect and relabel clicks / entire click trains.
D= evelopers will hopefully find that the target motion code has been improved in a way which will make it much easier to provide target motion localization for ot= her detection types (e.g. whistles) in the future.
Other Features
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. =
Improved Number handling
U= sers have often found that PAMGuard can be 'jumpy', i.e. the spectrogram does not scr= oll 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 acquisiti= on systems unstable. We have therefore entirely rewritten the way in which PAMGuard handles arrays of spectrogram data (complex numbers) so that inste= ad of large numbers of small Java objects there are now fewer, larger, simpler java objects. These reduce processing delays for garbage collection and giv= e an overall speed improvement, but will otherwise no= t be noticed by users.
Click Detector RainbowClick file output
T= his feature has been removed since it has been obsolete for several years. Users should use the PAMGuard binary storage system for Click Detector data.
Bug Fixes
A number of bug fixes and c= ode improvements have been made since V 1.15.03:
1. &= nbsp; 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. &= nbsp; Bug 274. GPS Memory leak. A Memory leak associated with GPS data collection has been found which could cause PAMGuard to run out of memory a= fter a day or two's operation. This has now been fixed.
3. &= nbsp; Bug 275. Painting of thumbnail on the Map display time slider. Have fixed a small problem in the graphical display. The visibility of component= s on this slider has also been improved and a log time scale option is available= to facilitate in map data display.
4. &= nbsp; Bug 276. The default hydrophone sensitivity was -201dB re 1V/uPa. This was supposed to be used with a default prea= mp gain of 30dB. For some reason gain was no longer being added. We have there= fore set a default sensitivity of -170dB and left gain at zero. This is more typ= ical of many hydrophones in use today.
5. &= nbsp; Bug 277. Text fields in classifier dialog were not large enough to display times greater than 10ms. We have increased length of text fields in= the dialog.
6. &= nbsp; Bug 278. Have future proofed against potential binary file format changes in future releases. New PAMGuard releases will always be able to op= en 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 w= as 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 a= t this time there are no planned file format changes and that this is purel= y a future proofing exercise.
7. &= nbsp; Bug 279. GUI Resizing: The whole PAMGuard GUI would suddenly resize = to something very small when a dialog is opened. This has been traced to impro= per use of a common dialog component SourcePanel wh= ich tries to repack its parent Window. Some programmers had inadvertently set i= t to repack the main PAMGuard GUI instead. This has been Fixed.
8. &= nbsp; Bug 280. Recorder control option to automatically restart recording = were causing confusion. It was working in that the recorder would return to its previous state, but it was sometimes difficult for users to set it so that recording would always start as soon as PAMGuard started. More sensible and easy to understand options have been developed in a new options dialog.
9. &= nbsp; Bug 281. Click classification dialog has grown too big to fit on the= screen. The options have now been split across three tabbed panes which solves the problem.
10. &= nbsp; Bug 282. Quiet clicks causing too many false classifications. An additional option has been added to the click classifier to limit a class t= o a range of amplitude.
11. &= nbsp; Bug 283. The spectrogram display was not displaying data in Viewer m= ode. This has been traced to a problem in offline data mapping and has been fixe= d.
A= single bug fix concerning import from Access databases to SQLite.
1. &n= bsp; Bug 271. Proble= m 1 was that the incorrect settings were being imported into the new database. Prob= lem 2 was that indexing of imported click events in the new database was incorr= ect. Both these issues have now been fixed.
A number of small bug fixes following release of 1.15.00.
Bug Fixes
1. &n= bsp; Bug 266. Clip generator crashed in viewer when the path for output f= iles was not defined even if files were not being created. Fixed.
2. &n= bsp; Bug 267. Click detector not calculating correct bearings when multip= le hydrophone pairs with different separations were used. Fixed.
3. &n= bsp; Bug 268. ROCCA module was not saving WAV file clips. Fixed.
4. &n= bsp; Bug 269. Whistle and Moan detector paired bearing localiser was not working. This localizer searches for matching whistles on pairs of hydropho= nes. Bearings from each pair are crossed to create a localization. Fixed.
5. &n= bsp; Bug 270. Improved file names display in Pamguard Viewer offline data= map and datagram creation.
B= eta Version 1.15.00 64 bit and Core version 1.15.00 32 bit. Both using identical Java core software but linking to different libraries for control of sound input devices.
T= his is the first release of a 64 bit version of PAMGuard. A= s with the 32 bit version a number of C language librar= ies 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 vers= ions. Please report any problems immediately to the PAMGuard team.
Other Changes
U= pdated the configuration file WMM.COF for World Magnetic Model to the latest 2015-2020 version. See https://www.ngdc.noaa.gov/geomag/WMM/soft.shtml
S= mall changes to the ROCCA classification module:
1. <= /span>Remove white spaces and parenthesis characters from RoccaCont= ourStats header row
2. &n= bsp; Report 'N/A' for min time between detections, if there is only 1 detection
3. &n= bsp; Add ability to load standard notes and use in R= occaParameters dialog window
4. &n= bsp; Fixed Rocca multi-threading problem which caused Click Detector to s= end same click multiple times
Bug Fixes
1. &n= bsp; Bug 253. Databa= se import fails when Access database contains queries. Fixed.
2. &n= bsp; Bug 254. Lookup= lists failing in imported SQLite databases. This was caused by the system 'padding' topic's with blank spaces and is now f= ixed.
3. &n= bsp; Bug 256. Map not updating. Graphics updating was only happening when= new GPS data arrived and therefore didn't update when using static hydrophones. Fixed so that graphics update correctly.
4. &n= bsp; Bug Sound recorder missing a few samples between files. The sound recorder wav file output system has been rewritten in a much simpler form a= nd now won't lose samples between consecutive files when new files are started automatically. It will also start new files on integer second or minute boundaries when file durations are set to a maximum fixed value.
5. &n= bsp; Bug 262. Access to SQLite database conversion. This would fail when tables were present which were not created by PAMGuard. Fixes have be= en 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 exis= t it will no longer crash but issue a clear warning and carry onto the next tabl= e.
The format of configuration files has changed for vers= ion 1.14.00. Older configurations will load with this new version, but configurations saved with 1.14.00 may not open correctly with earlier versi= ons.
PAMGuard Versions 1.14.00 and above will work with Jav= a 8. PAMGuard will continue to work with Java 7, but support for Java 7 will be removed entirely during 2016. This means that the Microsoft Access Database interface will no longer be available. Version 1.14.00 will continue to sup= port Microsoft Access so long as you don't upgrade your Java version to Java 8. =
An alternative database interface has been provided in= the form of SQLite which has been extensively tested with all PAMGuard modules. Limited connectivity to MS Access databases using the open source UCanAccess database connection is provided in Viewer = mode which will allow users to convert old Access databases to SQLite or MySQL depending on preference. See the PAMGuard help file for further details.
Other Changes
1. &n= bsp; Feature Request= 45. Module settings import. Functions have been provided which enable us= ers to import the settings for individual modules into new configurations. See = the help file for details.
2. &n= bsp; Feature Request= 45. Click classification setting= s export / import. Click classification settings can be exported individually to fil= es and imported into other click detector configurations. See the help file for details.
3. &n= bsp; 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 po= int every n seconds which will reduce the number of = points loaded. Useful when making large scale overview maps of a survey.
4. &n= bsp; Sound Trap tools module. This is a development module for users of the Ocean Instruments Sound Trap who have it configured to run automatic click detection. = This feature is currently in its development phase and is of little relevance to most users.
Bug Fixes
1. &= nbsp; Bug 246. AIS Da= ta Unpacking. Bug in AIS data unpacker fixed.
2. &= nbsp; Bug 247. Fixed = Landmark display. Landmarks were not displaying in the viewer. This is now fixed.
3. Bug 248. Crash in hydrophone array manage= r. 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).
4. Bug 249. Corrected bugs in Rocca analysis= of click events.
5. Bug 250. DIFAR module was crashing if it attempted to triangulate between more than two simultaneous bearings. Fixed= .
6. Bug 251. Fixed error in DIFAR intensity calculation.
7. Bug 252. Bug which plotted bearings to wh= istle and moan detections from the front hydrophone rather than the central posit= ion between hydrophones now fixed.
Changes
1. &n= bsp; Improved options for plotting clicks on the map in viewer mode - can= now select clicks by the type of event they are part of (when marked as part of= an offline event).
Bug Fixes
The following bugs have been fixed for this release. <= /p>
1. Bug 231. PAMGuard freezing when starting viewer mode. (Caused by an infinite loop in the map module). Fixed.
2. Bug 232. Incorrect click length calculation in ROCCA module. Fixed.
3. Bug 233. ROCCA not analysing correct clicks in Viewer mode. Fixed.
4. Bug 234. Hydrophone import of .paf files crashing. Fixed.
5. Bug 235. Target mo= tion analyser crashes when changing default bearing line length. Fixed.
6. Bug 236. Whistle classifier crashing during batch training just prior to writing results fil= es. Fixed.
7. Bug 237. Logger fo= rms not saving data to database after sound acquisition starts. Fixed.
8. &= nbsp; Bug 238. Viewer mode out of memory error. Have adjusted memory allocation to allow more memory for the database interface. Hopefully Fixed= .
9. Bug 239. Fixed bug in the DIFAR modul= e that was incorrectly preventing cross-fixes for some calls.
Details of these bugs can be found at https://sourceforge.net/p/= pamguard/bugs
Changes
1. &n= bsp; Spectrogram annotation marks. A simple system for marking spectrogra= ms during real time analysis has been incorporated. To use it, add the module, in the spectrogram settings, select the annotation marks in the 'Mark Observers' t= ab 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 modu= le in your configuration.
2. &n= bsp; A new system for important warning messages has been implemented. Warnings such as failure to connect to the GPS or a database error will now appear at the top of the main PAMGuard display.
3. &n= bsp; File and Folder audio input systems now have an optional repeat butt= on which is useful when using PAMGuard for demonstration purposes.
4. &n= bsp; The sound File and Folder audio input systems now have an optional t= ime 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 t= he option with caution !
5. &n= bsp; 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://d= ev.mysql.com/downloads/mysql/
6. &n= bsp; Changed Rocca Measurement menu item to open a window containing click events, instead of a submenu listing click events. Using a window simplifies multiple event selections
7. &n= bsp; The DIFAR modul= e has received numerous improvements and bugfixes after 6 weeks of field testing.=
Bug Fixes
The following bugs have been fixed for this release. <= /p>
1. &n= bsp; Bug 220 Sample counts were wrapping and causing PAMGuard to report incorrect times after 2^31 samples.
2. &n= bsp; Bug 223. Click detector null clicks (This primarily only affected offline file analysis).
3. &= nbsp; Bug 225. Display of remaining recording time. Was only displaying ho= urs, minutes and seconds. Now correctly displays the number of remaining days. <= /p>
4. &n= bsp; Bug 226. Spectrogram Mark Observer list doesn't refresh when modules added or removed.
5. &n= bsp; Bug 227. Logger forms not working with MySQL. Several minor issues w= ith the MySQL interface generally and in particular with the logger forms module have been resolved.
6. &n= bsp; Bug 228. Occasional crashing when training the whistle classifier. <= /p>
7. &n= bsp; Bug 229. Fixed = bug in Viewer Mode which caused Rocca to crash when analyzing click event containi= ng unclassified clicks
8. &n= bsp; 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.
Details of these bugs can be found at https://sourceforge.net/p/= pamguard/bugs
Changes
Small changes have been made to the ROCCA whistle clas= sifier module: Added Sampling Rate, Number of Channels and Geographic Location to = the Rocca contour output file. Number of Channels and Geographic Location= can be specified by the user in the Rocca Parameters dialog Notes tab.
Bug Fixes
A number of minor bugs have= been fixed for this release.
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 star= ts with a default range of 10km on the display.
2. Bug 212. Decimator crashed. This only happened very rarely and only if a very l= arge decimation factor was used, so it's unlikely to have affected anyone.
3. Bug 215. Sound acquisition dialog crashing. Could happen if there were no sound cards installed on a system.
4. Bug 216. Whistle classifier would not work offline (in viewer mode). This is now fixed.
5. Bug 217. PAMGuard viewer fails to read a configuration at startup. This would c= ause total loss of the PAMGuard configuration in viewer mode and has been rectif= ied.
6. Bug 218. SAIL Acquisition card would hang the system. This has also been fixed.=
7. &nb= sp; Bug 219. Problems displaying Offline Click Events in the Viewer map have been fixed.
Bug Fixes
1. <= /span>Bug 208. Logger forms CHECKBOX control crashes. Fixed.
Bug Fixes
1. <= /span>Bug 207. Threading hydrophone error. Caused array location errors if GPS data s= et to read on a time. Fixed
2. <= /span>Bug 205. Crash in 3D localiser if no output CSV file set.
3. <= /span>Bug 197. Click detector reporting 'Null Click with no waveform'. Fixed
Changes
Small changes made to DIFAR module.
Configuration Changes
Menu Layout
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'.
The groupings within the File / Add Modules menu have = been rearranged so that they are now:
' = ; Maps and Mapping
' = ; Utilities
' = ; Sensors
' = ; Displays
' = ; Sound Processing
' = ; Detectors
' = ; Classifiers
' = ; Localisers
' = ; Visual Methods
The 'Hydrophone Array' menu item moved from 'Fi= le' to 'Settings'
'Multi Threading' m= enu 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.
New Modules
DIFAR (Localisation Group)
This module, funded by the Australian Antarctic Divisi= on allows the de-multiplexing and calculation of angles from military style DI= FAR 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.
Accelerometer Readout (Sensors group)
This module, funded by NOAA for the South West Fisheries Science Centre (SWFSC), measures pitch and roll from analogue accelerometer sensors in a hydrophone. Data are fed real time into= the updated hydrophone array manager in order that bearings from a tetrahedral tracking array are correctly calculated in real world coordinates.
Wild ArcGIS Interface (Maps and Mapping group)<= /p>
This module, developed by Michael Oswald / SWFSC, allo= ws PAMGuard to output data in a format suitable for display in the WILD ArcGIS marine mammal survey package. See online help for details.
Alarms (Utilities Group)
This is a general system of visual and audio alarms developed by Doug Gillespie for use on a variety of projects. The alarms ca= n be coupled to any module or detector in PAMGuard. Where appropriate, modules c= an control which of their data will cause an alarm action (e.g. in the Click detector you can set which types of classified click will fire the alarm). = See online help for details.
Noise Band Monitor (Sound Processing Group)
This module, developed by Douglas Gillespie, Measures = octave of third octave noise bands. See online help for details.
Filtered Noise Measurement (Sound Processing Gr= oup)
This module, developed by Douglas Gillespie, measures = noise levels in a single frequency band using a variety of filter functions. See online = help for details.
Envelope Tracing (Beta Only, Sound Processing G= roup)
This module, developed by Douglas Gillespie, traces the envelope of a stream of audio data. In particular, it can be used to generate audio output from high frequency data. See online h= elp for details.
Long Term Spectral Average (Sound Processing Gr= oup)
This module, developed by Douglas Gillespie, calculate= s the long term spectral average of audio data for a spectro= gram display. See online 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 inter= val of sperm whale clicks. (No help available)
New Features
Hydrophone Configuration
The hydrophone configuration system within PAMGuard ha= s been substantially rewritten, partly so that it can support multiple remote buoys (e.g. DIFAR buoys) each of which needs to be localised individually. As a consequence, the layout of the Array Manager dial= og will appear somewhat different. Details are available in the online help. <= /p>
FLAC File Support
Can now read raw audio data direct from FLAC files. FLAC is a lossless compressi= on algorithm for audio data. Files, or folders of files are accessed in the sa= me way as WAV and AIFF files in the Sound Acquisition module. In a future rele= ase we also hope to provide support for writing FLAC files from the sound recor= der 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. Millisecond time is also now included= in the output file names.
Datagram Options
Datagram options in Viewer have been improved so that = the user has to verify the time binning for datagram= s 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.
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.
Spectrogram Display
A system of sliders for setting the frequency and ampl= itude ranges of the spectrogram display has been implemented. Click the grey butt= on on the top right corner of the spectrogram display '
Video Range Module
The video range module has been modified so that it can estimate distances based on fixed objects within a picture as well as the horizon.
Improved Filter Options
Filter options (used as stand-alone filter modules
Radar Display
Can now show bearings relative to true North OR the ve= ssel heading. Also has the option of only showing certain types of click and whistle.
Bug Fixes
New Modules
Clip Generator: Saves and displays short waveform clips around detections. Can work with any detector= (or indeed any other data stream within PAMGuard).
Local time display: displays the computers local time on the main display panel.
WILD interface: provides = the user the ability to integrate Pamguard with the WILD ArcGIS-based marine mammal survey software package.
New Features
Core Functionality=
New storage options have = been implemented which give the user greater control of where data are stored. <= /p>
Modules have been arrange= d into different groups in the configuration menus and tool tip texts have been ad= ded to these menus to provide additional information to users.
Radar Display
Functionality has been ad= ded to the radar display so that bearings can be shown relative to either the vess= el or to true North.
Better control of data in= viewer mode, making is easy to scroll through and view data for short time periods= .
GPS
Function to import GPS da= ta from other data sources for the PAMGuard viewer.
Database
Can now copy data from bi= nary storage to the database offline for any module having both binary and datab= ase storage.
Can create a blank MS Acc= ess database (2007 and later *.accdb formats only).=
Can open MS Access from w= ithin PAMGuard to make it easier to view database content.
Support for open office databases.
Sound Acquisition<= /p>
National Instruments card= s: Added code in support of the new x-series devices.
ASIO sound cards: Added s= upport for a new open source ASIO driver system (jasiohost). The old system has been left in place for now while we assess users response to the newer system.
AIS
Support has been added to= the AIS module to read data from class B AIS stations (used by smaller vessels), Ba= se stations and Aids To Navigation.
Spectrogram Display
Can now scroll as well as= wrap the data.
Whistle Detector
Stores amplitude and bear= ing information correctly in the binary files.
Logger Forms
A substantial amount of w= ork has been carried out on Logger forms, funded by the South W= est fisheries Science Center.
Click Detector
Two additional displays h= ave been added to the click detector
1. <= /span>Concatenated Spectrogram which enables users to view spectra for multiple clicks within = the same event.
2. <= /span>Inter Detection Interval Display which provides a visual interpretation of the inter-detection interval.
Target Motion Analysis: Updated target motion analysis module so that it works in three (as opposed to two) dimensions.
Alarm in click detector to issue audible warning when certain click types are detected.
Display options have been improved making it easier to display only certain types of clicks.
Ishmael Detection Modules
We have implemented database storage for output of these modules.
Bug fixes
' &= nbsp; Pressing cancel will now exit PAMGuard
2. &= nbsp; Clearer when a new (blank) configuration is being created
3. &= nbsp; Can create a database for viewer mode from scratch.
'Version 1.11.=
02
Beta May 2012
New Features
'
'Version 1.11.=
01
Beta April 2012
New Modules
'Version 1.10.=
00
Beta December 2010
New features
1. Binary storage module.
Performs a parallel role to the PAMGAURD database but = uses binary files in a proprietary format which is considerably more efficient f= or data of unknown length such as whistle contours or small clips of click waveform. This feature is currently implemented in the following modules:
'Version 1.9.0=
1 Beta
May 5 2010
Bug fixes
Acquisition dialog for ASIO sound cards was resetting = all channel numbers to zero.
Degree symbols throughout PAMGUARD have been fixed so = that they work on all Win64, (Mac and Linux.)
An unnecessary channel warning from the seismic veto h= as been removed.
Contour check boxes on the map dialog have now been pl= aced in a scrolling pane so that if there are lots of contours, the dialog doesn= 't become too bit to fit on a screen.
New Feature
psf file name is now displ= ayed in the title bar of the main PAMGUARD display.
Windows Installer now sets permissions on PAMGUARD fol= der so that don't need to be an administrator in order to create new files in that directory. Prevents problems especially under Vista/Windows 7 when saving psfs and recording = sounds to the default directory.
Channel numbering
A new internal channel numbering scheme for ASIO sound= cards was released on 8 March in Alpha version 1.8.02. These changes have now been promoted to this Beta release 1.9.00. These changes were described in an em= ail to PAMGUARD User, the text of which is repeated here:
Within PAMGUARD, there have been constant problems with
lookup tables relating hardware channel numbers to internal channel numbers.
99.9% of the time, this is not a problem since people are just reading chan=
nels
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
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 change= s in channel numbering.
I have spent a considerable amount of time trying to w= ork out a better system for handling channel numbering in PAMGUARD and have dec= ided that the only practical thing to do is to force all software channel number= ing 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 dialog, you will see them listed as channels 0,1,2 and 3. The consequences of doing this are mainly very good. Most users will not notice= any changes. For those who need for some reason to read channel numbers not starting at zero things will be more stable. However, when you go to a new version with this new feature, it will be necessary to reconfigure all the modules in any existing configurations. To do this, open the configuration dialog for each module in turn and select the correct, zero indexed, channel number.
Other Changes / new features
PAMGUARD Viewer
The way in which data are loaded for each module has c= hanged in the PAMGUARD viewer. In the scroll bar for each display, at the right hand end, there are buttons for pagingforward, backward and setting page length options.
Click Detector Bearing Time display
Older versions used a vertical scroller in the right hand side of the main bearing time display to co= ntrol the display length. This has been removed and replaced by a small control consisting of an edit box and a spinner (up and down arrows) at the right hand end of the horizontal scroll bar. The scroll system now also enabled you to scroll back through up to one minute of data during real time operation.
Whistle and Moan Detector
Bearings are now written to the database.
PAMGUARD Viewer scrolling mechanism has changed.
Each display now has a small control in the right hand end of a scroll bar or a slider which allow= s you to page through data. This is only well implemented for the map, but will be an increasingly important feature as more displays are s= et up for offline data viewing in future releases.
Viewer data map
When using the PAMGUARD viewer an additional panel wil= l be displayed showing an overview of data quantity (per hour) from the various database tables connected to PAMGUARD.
Spectrogram Display overlays
The mechanism behind this has changed. Should not affe= ct operations, but if you have problems with overlays on the spectrogram, plea= se notify support@pamguard.org
All display overlays
Now pick up line colours from the Display symbol manag= er, so it's possible to set line colours by selecting a symbol with a particular l= ine colour from the Display menu.
Database
Default name for the Database module has changed from "ODBC Database" to just "Database". This will not affect 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 u= sing Macs.
Bug Fixes
Whistle and Moan Detector
Was not detecting sounds when noise reduction was perf= ormed in the Whistle Moan Detector, but was OK when no= ise reduction ran in the FFT module. This problem has been resolved.
Whistle Classifier
Bug fix in database output. The first species probabil= ity column was setting to zero. This is now fixed
Ishmael Detectors
Better rendering of detection boxes on spectrogram
Sound acquisition
When not using NI or AISO cards PAMAGUARD acquires sou= nd using javax.sound wh= ich only supports two channels. Max number of channels now specified as 2 rather than undefined.
Serial Comms
A few changes so more through tidying up of resources = when a port is closed. Might prevent a few problems when using a GPS.
Bug Fixes
Crashes caused in real time or Mixed Mode if the numbe= r 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.
New features
'Version 1.8.0=
0 Beta
January 2010
New features
'Version 1.7.0=
2 Beta
November 2009
Bug Fixes.
Airgun display occasionally crashing with a class cast exception is fixed.
FFT modules, new code in 1.7.00 for interleaving FFT b= locks from multiple channels now no longer crashes.
Bug fix. Spectrogram time and frequency scales = now display correctly and amplitude scale updates after scale parameter changes= .
Speed improvement.
PAMGAURD FFT calculations now use the JTransforms FFT library which gives a factor 2 speed improvement compared to previous F= FT methods used in PAMGUARD
New Modules
Two new modules are packaged. These are still in the f= inal stages of development. Feedback is most welcome. See online help for further details.
Whistle and Moan Detector
Whistle Classifier.
Identical to Core release 1.6.00 apart from additional modules:
'Version 1.5.0=
1 Beta
Bug fix. Channel number checking for ASIO cards changed during NI support function and will always throw an error in 1.5.00. This h= as now been fixed.
Bug Fixes
Decimator was calculating incorrect filter coefficients (coefficients were based on the output sample rate, not the input sample ra= te, so it's likely that actual filtering of data was minimal). This is now rectified. Ishmael matched filter. Would crash if template file not correct= ly loaded. Now issues a warning message to the terminal and does not crash.
Spelling correction on user input form (Sumbit - Submit)
New Features
National Instruments DAQ support (Windows 32 bit JVM Only)
The National Instruments interface has now been comprehensively rewritten and is now stable. One or more NI data acquisition devices can be used to acquire high speed data on multiple channels. See the PAMGUARD help file for details.
Performance Tests
A new menu item in the Help menu provides access to so= me system performance tests. These are still under development but have been released to Beta at the earliest opportunity since the development team req= uire feedback of test results verses performance on a variety of machines before= the tests and the corresponding help files can= be finalised.
New Features
Details of new features are documented in the PAMGUARD online help.
PAMGUARD Viewer
Reloads data from a PAMGUARD output database for viewi= ng
PAMGUARD Mixed Mode operation
Analyses data from wav or AIF file and synchronises it= with GPS data reloaded from a database so that detected sounds may be correctly localised. Multiple display frames - enables PAMGUARD GUI to be split into multiple display windows, displayed on multiple monitors if desired. Enables the operator to simultaneously view the map and the click detector for exam= ple, which is much easier than continually movi= ng between multiple tabs.
Documentation
The help file pages for the acquisition module have undergone major revision Minor additions and edits have been made to many o= ther help pages
Bug Fixes
Memory leak caused by Night / Day colour manager now f= ixed. This would cause memory leaks when multiple files were being analysed off-l= ine and would eventually crash PAMGUARD. The way that colours are managed in PAMGUARD has been rewritten.
Some issues with Swing fixed that might have been caus= ing hang ups on startup especially on Macs/Linux machines
Some tidying up of events and default ports for = serial devices to improve GPS data collection (particularly for USB-Serial GPS on Mac/Linux machines)
Click Detector
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 h= as now been fixed.
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.
Whistle Detector
Correctly triggers recordings when whistle events are detected
Sound Playback through ASIO sound cards Will no= w work with any selected channels (not just channels 0 and 1)
Bug fix. ASIO sound cards reporting errors if a channe= l list that is not 0,1,2 is used. This has been corrected so no false error messag= es are sent.
Beta release 1.3.02 is identical to Core release 1.3.00 apart from
some modules which are known to be unstable or are new= or under development.
Modules which have only been included in the Beta rele= ase are:
Utilities Group
Simulator (unstable)
Hydrophone Depth Readout (requires further testing and= help file)
Sound Processing Group
Patch Panel (unstable and requires help file)
Seismic Veto (requires help file and minor bug fixing)=
Visual Methods Group
Angle Measurement (requires further testing and help f= ile)
Video Range (requires help file)
Fixed Landmarks (requires help file)
Changes
The User Input module (for text entry of information b= y the user) has been moved from the Displays sub menu of the = Add Modules menu, to Utilities. This will not affect how existing settin= gs files are loaded.
Multi-screen environments.
In previous versions, if PAMGUARD was configured in a multiscreen environment and is then run on a single screen, it was possible that the display would not appear. PAMGUARD now checks screen dimensions at start up and ensures that the main display is visible. Consequently, program start-up takes slightly longer than previously.
Outstanding bugs
The patch panel is known to crash if output channel nu= mbers from the patch panel a higher than the highest input channel number of the = data acquisition.
Bug fixes
Speed up of graphics, particularly regarding large quantities of gps track &nb= sp;data
National Instruments cards with names > 20 characte= rs long are now correctly recognised.
Help File Updates
The help viewer has been debugged and table of content= s, search and index features now all work as they should.
The layout of the help content has been re-ordered int= o more functional groups (as laid out in the PAMGUARD add modules menu).
Improved help has been added for the following modules= :
'1.3.01 Beta.
January 27 2009
Bug Fixes
Fixed bug in serial port communication which caused cr= ash is a serial port
didn't exist.
Bug fix in whistle detector bearing calculation= .
1.3.00 Beta. January 2009
New modules
New Likelihood detector.
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 Mys= ticete calls (Humpback, Bowhead, etc.).It is not suitab= le for detecting whistles.
Note that the likelihood detector will not run with PA= MGUARD in multithreading mode.
Bug fixes
Click Detector - click train detector. Further synchronisation to deal with multithreading.
Depth Readout - Bug fix to prevent crash when dialog is opened when no input device is installed.
Localiser ' Further synchronisation of detection group localiser (affects stability of click train localiser and whistle localiser= in
multithread operation).
This release contains many bug fixes from the PAMGUARD industry field trial which took place in the Gulf of Mexico on the RV New Venture in November 2008.
Bug Fixes
'(AIS Data are a fixed data set recorded in the English Channel).
Multithreading
PAMGUARD now processes data in each module in a differ= ent processing thread. This allows PAMGUARD to use both processor cores on dual= or multi core processor machines. However, multithread= ing may still cause instability in some modules. An option is therefore accessi= ble from the main Detection menu to enable and disable multithreading.
New Modules
The following new modules have been added to the Beta Release 1.2.0
Sound Processing
1. Seismic Veto. A module for detecting and then cutti= ng out very loud sounds.
Utilities
2. Depth Readout. Readout for analogue depth sensors u= sing MeasurementComputing data acquisition devices.
Visual Methods
3. Video Range measurement. Will not capture video, bu= t can open jpeg, bitmap files, etc. or you can paste in an image for video range analysis.
4. Angle Measurement. Shaft angle encoding using Autonnic Research Ltd A3030 Absolute Rotary Encoder (= good for measuring the angle of binocular stands).
5. Fixed Landmarks. Enter and display fixed points for overlay on the map.
New Modules (not released to core)
'1.1Beta 22 Ma=
y 2008
'0.5b &nb=
sp;
31 August 2007
Requires Java 6 Update 2 (http://java.com/en/download/manual.jsp)
Major new features include:
'1.0Beta 22 Jan 2008 - Pamguard starts two releases, core and beta release,
this is the beta release
'0.4b - 29 Dec=
ember
2006, Significant enhancements
A model manager and profiler, whereby users can add/re= move modules as required.
Modules now include configurable click and whistle det= ectors and Ishmael-type detectors and localisers.
Information from above modules can be displayed on configurable user displays which support real time scrolling spectrograms a= nd radar displays. Detection and localisation information can be optionally displayed on the map display.Map enhancements include improved scrolling whereby the user can click and drag= to pan the area. PamGuard can now interface with M= ySQL database servers and users can easily select which information is logged. (= This replaces the previous 'flat-file' logging featur= e). A simulation module allows virtual vocalising animals to be placed on the map= to assist in training and development. Extensive online user help has been add= ed to PamGuard Application