Detection, Classification, and Localisation of marine mammal and other bioacoustic signals

@douggillespie I've noticed that you've put this on GitHub - this is great! just to add that it's also possible to migrate from SVN to Git and keep all past history of revisions in one repository. Since your SVN repository is public, I don't see a reason why not to do this. Instructions are e.g. at https://git-scm.com/book/en/v2/Git-and-Other-Systems-Migrating-to-Git and we can try this before many things happening here.

The new(ish) background datablocks attached to 'normal' datablocks were not getting their data cleared when the main datablock data were cleared, so were accumulating too much data and bring the system down through lack of memory.

Hi,

I don't have much time to work on Pamguard code these days, but do have enough time to file a bug-report/feature regression.

I'm no longer able to effectively process large folders of wav files using the attached psf (spectrogram, Ishmael spectrogram correlation detectors, sqlite database). In 2.02.02 Pamguard just crashes hard and all windows dissapear, and the log (attached) provides no indication of what is going on. In 2.02.05 the log includes more detail, and pamguard manages to avoid a crash, but after about 1000 files starts running extremely slowly.

The last known good version of Pamguard where I could successfully complete this task was 2.02.00 (r5437).

Cheers, Brian PamguardLogs.zip kerguelen2015_fullYear_Bm-Ant-ABZ_SpectroCorrelation_250Hz.zip

when unable to find raw data for a whistle, ROCCA would double the raw data keep time. Since it regularly can't find this data at the end of the file (e.g. when threading causes a whistle to arrive after the raw data are cleaned up) the keep time kept doubling until the memory usage of the raw datablock would kill PAMGuard. I've now hard limited this to 15 minutes, which is loads more than should ever be needed. A similar problem occurred in the Ishmael Localiser.

The datamap does not update after SoundTrap clicks have been imported. Need to add PamController.getInstance().updateDataMap() to the DWVConvertObserver at line 402 ImportBCLDialog....?

Logger forms data were not plotting correctly. This was due to the required data selection functions not being fully implemented. This is now fixed and it should be possible to select what to plot based on selections from drop down lists within any form.

Quick fix to issue #88, allow processes to setup in run nothing mode, and allow base unit data to apply for superceded versions of whistle moan detections. Error in merging caused classpath to change with same content.

Click localization never applied to superceded ClickDetector data unit (module version 1) containing TDOA data in viewer mode. Not checked on other superceded module versions.

updates to Rocca module - fix memory leak issue where RoccaContourDataBlocks being created in RoccaProcess were not being released for garbage collection

These are just a few small updates to Rocca, for the next release. I had to update the .classpath to point to my jre and thought that I had NOT committed the change back to git but... there it is. So don't bother merging that one.

• Rewrote acoustic file management in PAMGuard. Reading audio files is now accessed from one class - pamAudio.PamAudioFileManager.java. PamAudioSystem.java is now deprecated.

• Added a sud file capability to PAMGuard. Most of the changes are in a new version of the X3 library (added to Maven repo folder ). All sud file capability can be disabled by commenting out line 49 of PamAudioSystem.

Report by Brian Miller.

The behaviour of the Files and Folders Acquisition behaves very differently depending on weather I select just the folder name from the dialog, or whether I navigate into the folder and select all the files within within it. If I select all the files within the folder, then the behaviour seems to be consistent with prior versions of Pamguard, and the files are sorted by time/alphabetically and analysed in chronological order by the timestamp within the file name. If I select the just the folder, then the data appears to be analysed in random (non-chronological nor alphabetical) order. This random order happens regardless of whether I have checked the “Merge continuous files” checkbox or not. For my datasets, I’m not treating the files as continuous anyway – since for my instruments the filename timestamps use the more precise clock than the one in the A/D converter. But for someone who wants contiguous files merged this would likely be a problematic bug.

These Bugs were found during the Canada DeepAL Expedition 2022.

These small fixes were necessary to use Animal-Spot and the Bearing Calculator. @macster110 The Bearing Calculator fixes from 3 years ago are no longer necessarie on Windows. Could you kindly check it on mac?

I unfortunately cannot pinpoint the exact reason why it crashes, it doesn't log anything on the console, but instead crashed to windows with a Java(TM) Platform SE binary is unresponsive error.

if you skip a hydrophone in the configuration, it is not skipped in the bearing calculator. For example, if I have 8 hydrophones and want to localize on 0,1,2,4,5,6,7 and skip 3 using the Hardware-Software-Channels the bearing calculator uses the positions of 0,1,2,3,4,5,6

private function and an overwritten function with the same name and parameters.

@Override public void newResult(GenericPrediction modelResult, GroupedRawData groupedRawData) { modelResult.setClassNameID(getClassNameIDs(genericModelParams)); modelResult.setBinaryClassification(isBinaryResult(modelResult, genericModelParams)); newResult(modelResult, groupedRawData); }

The problem is that both functions are ambiguous, which means that in my case, newResult was calling itself endlessly. To fix this, the private function must be renamed.