Commit Graph

982 Commits

Author SHA1 Message Date
Douglas Gillespie
2fa91d69a5 Logger form plotting
Fixed logger form plotting in Viewer so that points can find their
correct GPS position (based on time)
2023-12-19 16:46:18 +00:00
Douglas Gillespie
1461808b14 Logger form plotting
Fixed logger form plotting in Viewer so that points can find their
correct GPS position (based on time)
2023-12-19 16:41:57 +00:00
Douglas Gillespie
54f5a5f0fb Logger forms viewer
Viewer display of logger forms was throwing exceptions on Boolean values
which had been stored as a String or Integer 0 or 1 in some databases.
Now fixed to turn these into a sensible boolean value for the data table
2023-12-19 16:02:28 +00:00
Douglas Gillespie
0085215eff Logger forms viewer
Viewer display of logger forms was throwing exceptions on Boolean values
which had been stored as a String or Integer 0 or 1 in some databases.
Now fixed to turn these into a sensible boolean value for the data table
2023-12-19 15:54:38 +00:00
Douglas Gillespie
ea6caecc67 Updated POM
working POM for build with Tethys. Note though that it's failing to get
rid of all signature files in the \META-INF\ folder, so the two files
META-INF\ECLIPSE_.SF and META-INF\ECLIPSE_.RSA must be removed before
the jar file can be used.
2023-12-19 12:45:56 +00:00
Douglas Gillespie
d200e5c2df Maven stuff for nilus and javaclient 2023-12-18 18:30:41 +00:00
Douglas Gillespie
bfbb58ea5a
Merge pull request #51 from PAMGuard/main
get whistle det fix
2023-12-18 18:25:29 +00:00
Douglas Gillespie
d1b40c1d86 Release V2.02.09e
fixes to WMD stub removal to make it a lot faster.
2023-12-18 16:48:36 +00:00
Douglas Gillespie
3cf0a4e1e6 Merge remote-tracking branch 'origin/main' into Tethys 2023-12-18 15:27:24 +00:00
Douglas Gillespie
291b00e1b1
Merge from DG with fixes to MatchedTemplate classifier. (#119)
* Stop command

small change so command is available as a constant

* Lots of small updates to enable opening of a secondary configuration for
batch processing control.

* Fix user input bug in viewer

which created exponential copies of user comments!

* Adding TAST trigger alarm action

To be competed when GW provide correct string for interface

* Echo offline detection

Fix up affected datablocks for offline echo detection

* fix module import

System for importing modules from other psfx files was not working.
Probably wasn't working for quite some time. Now fixed.

* Bug fixes to Match Template classifier

1) When a large template was imported only 1: fftLength of the mathc waveform was used and so clicks would be correlated with noise. The peak of the template is now used when the peak search function is selected.
2) The plus button in the tab pane had disappeared.
3) Seems like the decimators were the wrong round. So the waveforms were using an up sample function when they should have been using a decimator function. and vice versa...major bug when using different sample rates!

* Fix merge

Merged in a single commit from Jamies fork that had updates to the
template classifier. Then had to make a few changes to get it working
with other changes J had made that must have been in other commits.

---------

Co-authored-by: Jamie Mac <macster110@gmail.com>
2023-12-18 15:19:22 +00:00
Douglas Gillespie
480f55f6e9
Merge pull request #50 from PAMGuard/main
merge from main (#118)
2023-12-18 15:18:18 +00:00
Douglas Gillespie
2f41c986f4 Fix merge
Merged in a single commit from Jamies fork that had updates to the
template classifier. Then had to make a few changes to get it working
with other changes J had made that must have been in other commits.
2023-12-18 14:58:24 +00:00
Jamie Mac
1b9d80b0eb Bug fixes to Match Template classifier
1) When a large template was imported only 1: fftLength of the mathc waveform was used and so clicks would be correlated with noise. The peak of the template is now used when the peak search function is selected.
2) The plus button in the tab pane had disappeared.
3) Seems like the decimators were the wrong round. So the waveforms were using an up sample function when they should have been using a decimator function. and vice versa...major bug when using different sample rates!
2023-12-18 14:21:18 +00:00
Douglas Gillespie
667b68e231
merge from main (#118)
* Stop command

small change so command is available as a constant

* Lots of small updates to enable opening of a secondary configuration for
batch processing control.

* Fix user input bug in viewer

which created exponential copies of user comments!

* Adding TAST trigger alarm action

To be competed when GW provide correct string for interface

* Echo offline detection

Fix up affected datablocks for offline echo detection

* fix module import

System for importing modules from other psfx files was not working.
Probably wasn't working for quite some time. Now fixed.
2023-12-18 14:09:30 +00:00
Douglas Gillespie
be88f4b296 # WARNING: head commit changed in the meantime
Merge branch 'main' of https://github.com/PAMGuard/PAMGuard into main
2023-12-18 14:07:19 +00:00
Douglas Gillespie
7a321f6d95 Revert "Merge branch 'main' of https://github.com/PAMGuard/PAMGuard"
This reverts commit f52a27ccf2, reversing
changes made to 4a5c6fe52e.
2023-12-18 13:28:38 +00:00
Douglas Gillespie
f52a27ccf2 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard 2023-12-18 12:45:53 +00:00
Douglas Gillespie
4a5c6fe52e small fix in histograms
small fix in histograms to avoid null
2023-12-18 12:45:49 +00:00
Douglas Gillespie
b91105dd07 Settings import (#117)
* Stop command

small change so command is available as a constant

* Lots of small updates to enable opening of a secondary configuration for
batch processing control.

* Fix user input bug in viewer

which created exponential copies of user comments!

* Adding TAST trigger alarm action

To be competed when GW provide correct string for interface

* Echo offline detection

Fix up affected datablocks for offline echo detection

* fix module import

System for importing modules from other psfx files was not working.
Probably wasn't working for quite some time. Now fixed.
2023-12-18 09:39:25 +00:00
Douglas Gillespie
16c69ee212 Merge with main (#116)
* Stop command

small change so command is available as a constant

* Lots of small updates to enable opening of a secondary configuration for
batch processing control.
2023-12-18 09:39:25 +00:00
Douglas Gillespie
f1d6dd0c03 R2.02.09d
Fix matched template classifier import
fix azigram help file image display
2023-12-18 09:39:08 +00:00
Jamie Mac
d0030e868a Squashed commit of the following:
commit f8d2de4482
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun Dec 17 12:27:31 2023 +0000

    Settings import (#117)

    * Stop command

    small change so command is available as a constant

    * Lots of small updates to enable opening of a secondary configuration for
    batch processing control.

    * Fix user input bug in viewer

    which created exponential copies of user comments!

    * Adding TAST trigger alarm action

    To be competed when GW provide correct string for interface

    * Echo offline detection

    Fix up affected datablocks for offline echo detection

    * fix module import

    System for importing modules from other psfx files was not working.
    Probably wasn't working for quite some time. Now fixed.

commit b12ccf9c67
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 14 10:50:29 2023 +0000

    Merge with main (#116)

    * Stop command

    small change so command is available as a constant

    * Lots of small updates to enable opening of a secondary configuration for
    batch processing control.

commit 840e6c89a1
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Nov 16 20:36:14 2023 +0000

    R2.02.09d

    Fix matched template classifier import
    fix azigram help file image display

commit acc806d375
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Nov 15 13:08:02 2023 +0000

    Updated X3 library to 2.2.6

commit a4f484c76c
Merge: 8e60ad2e d7c4c278
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Nov 15 09:44:09 2023 +0000

    Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into main

commit 8e60ad2eff
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Nov 15 09:43:39 2023 +0000

    update to array diagnostics and sensor control

commit d7c4c278d8
Author: m2oswald <45486636+m2oswald@users.noreply.github.com>
Date:   Wed Nov 15 09:17:49 2023 +0000

    Added code to Rocca for training/testing classifier (#114)

    * allow Rocca to run without classifiers

    Fixed bug that threw an error if no classifier files were specified in Rocca Params dialog

    * add rocca switch to enable dev mode

    currently only shows/hides extra buttons in the Params dialog, but will
    extend to more options in the future

    * Fix memory issue with RoccaContourDataBlocks not being released for
    garbage collection

    Set RoccaContourDataBlock objects to null and stop PamObserver Timer to
    force release

    * Fix problem tracing whistles in Rocca spectrogram pop-up

    Whistle and raw data were being 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.

    * updated for training/testing classifiers

commit d5f504dcd1
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Nov 10 18:08:31 2023 +0000

    Bearing localiser offline save

    Bug stopping it correctly saving data from the offline task to the
    database fixed.

commit 7a44d49e27
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Oct 27 09:59:28 2023 +0100

    X3 Version 2.2.3

    Add maven jar files for X3/SUD version 2.2.3

commit fa5fe9943d
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Oct 26 14:44:41 2023 +0100

    update sud file management to more efficiently skip to the correct part
    of a sud file when reading data offline.

commit 60435e567a
Author: Brian S Miller <93690136+BrianSMiller@users.noreply.github.com>
Date:   Fri Sep 8 21:54:40 2023 +1000

    Fixes issues #111 and fixes #112 (DIFAR module crashes and ability to use Deep Learning Detections in DIFAR module) (#110)

    * Bugfix for OverlayMarks

    Check for a null pointer exception in OverlayMarks that was causing a crash on startup.

    * Bugfix for null pointer in symbol manager

    Fix a bug that I found where the DIFAR module was crashing the symbol manager. Seems that this was due to this subclass of clip generator having a null value for it's uniqueName. I've fixed by checking for null values and assigning a generic symbol when null.

    * DeepLearning detections canGenerateClips=true

    Set flag in DeepLearning detector so that detections are considered 'clips' by Pamguard. This allows them to be processed automatically in the DIFAR Localisation module (and maybe others).

    * DIFAR: bugfix frequency limits for auto-detections

    Fix a bug in DIFAR module where the frequency limits of automated detections were not being set properly by the DIFAR module.

    * DeepLearning - Bugfix to detection duration

    Fix bug in deep learning detector where duration (in samples) was being set to number of samples in a hop instead of the number of samples in a segment.
2023-12-18 09:34:30 +00:00
Douglas Gillespie
25d10d54b4 Start Tethys Help 2023-12-17 19:28:03 +00:00
Douglas Gillespie
a761100ba7 Merge remote-tracking branch 'origin/main' into Tethys 2023-12-17 12:52:36 +00:00
Douglas Gillespie
c3edae516b Small error handling 2023-12-17 12:52:06 +00:00
Douglas Gillespie
f8d2de4482
Settings import (#117)
* Stop command

small change so command is available as a constant

* Lots of small updates to enable opening of a secondary configuration for
batch processing control.

* Fix user input bug in viewer

which created exponential copies of user comments!

* Adding TAST trigger alarm action

To be competed when GW provide correct string for interface

* Echo offline detection

Fix up affected datablocks for offline echo detection

* fix module import

System for importing modules from other psfx files was not working.
Probably wasn't working for quite some time. Now fixed.
2023-12-17 12:27:31 +00:00
Douglas Gillespie
0039ff7422 fix module import
System for importing modules from other psfx files was not working.
Probably wasn't working for quite some time. Now fixed.
2023-12-17 12:19:18 +00:00
Jamie Mac
223b32014d Updates to Array Pane 2023-12-15 23:18:47 +00:00
Douglas Gillespie
2e29e9cd95 Deployment and Detections work
Big tidy up of Deployment and Detections output. Think it' spretty close
to a functional system now.
2023-12-15 17:49:39 +00:00
Douglas Gillespie
75d349e33c Echo offline detection
Fix up affected datablocks for offline echo detection
2023-12-14 18:52:17 +00:00
Douglas Gillespie
f55311ea36 Adding TAST trigger alarm action
To be competed when GW provide correct string for interface
2023-12-14 18:51:42 +00:00
Douglas Gillespie
760b9769d7 Merge branch 'main' of https://github.com/douggillespie/PAMGuard.git into main 2023-12-14 12:43:07 +00:00
Douglas Gillespie
4297afdc51 Fix user input bug in viewer
which created exponential copies of user comments!
2023-12-14 12:42:41 +00:00
Douglas Gillespie
3059e087ac Merge branch 'Tethys' of C:\Users\dg50\source\repos\PAMGuardTethys into
Tethys
2023-12-14 12:27:14 +00:00
Jamie Mac
ef7f8c0b99 Remove print statements 2023-12-14 12:22:22 +00:00
Douglas Gillespie
9a0005861c Merge branch 'Tethys' of C:\Users\dg50\source\repos\PAMGuardTethys into
Tethys
2023-12-14 12:14:44 +00:00
Jamie Mac
60b76fb711 Bug fixes to Match Template classifier
1) When a large template was imported only 1: fftLength of the mathc waveform was used and so clicks would be correlated with noise. The peak of the template is now used when the peak search function is selected.
2) The plus button in the tab pane had disappeared.
3) Seems like the decimators were the wrong round. So the waveforms were using an up sample function when they should have been using a decimator function. and vice versa...major bug when using different sample rates!
2023-12-14 12:06:51 +00:00
Douglas Gillespie
8781374685 Small changes to deployment table 2023-12-14 11:57:44 +00:00
Douglas Gillespie
ef92e1eea9 Merge branch 'main' of https://github.com/douggillespie/PAMGuard into main 2023-12-14 10:53:46 +00:00
Douglas Gillespie
951e3116a5
Merge pull request #48 from PAMGuard/main
Merge from main
2023-12-14 10:51:17 +00:00
Douglas Gillespie
b12ccf9c67
Merge with main (#116)
* Stop command

small change so command is available as a constant

* Lots of small updates to enable opening of a secondary configuration for
batch processing control.
2023-12-14 10:50:29 +00:00
Douglas Gillespie
02ad66db3b User input viewer bug
PAMGuard was marking multiline comments as changed and then relogging
them. Led to exponential increase in database size!
2023-12-14 10:33:46 +00:00
Douglas Gillespie
03483ded18 Deployment export
Improved deployment export interface and options.
2023-12-13 17:31:35 +00:00
Jamie Mac
25691563bf Update POM after rebase 2023-12-12 14:17:17 +00:00
Jamie Mac
54264a689b Squashed commit of the following:
commit 840e6c89a1
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Nov 16 20:36:14 2023 +0000

    R2.02.09d

    Fix matched template classifier import
    fix azigram help file image display

commit acc806d375
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Nov 15 13:08:02 2023 +0000

    Updated X3 library to 2.2.6

commit a4f484c76c
Merge: 8e60ad2e d7c4c278
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Nov 15 09:44:09 2023 +0000

    Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into main

commit 8e60ad2eff
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Nov 15 09:43:39 2023 +0000

    update to array diagnostics and sensor control

commit d7c4c278d8
Author: m2oswald <45486636+m2oswald@users.noreply.github.com>
Date:   Wed Nov 15 09:17:49 2023 +0000

    Added code to Rocca for training/testing classifier (#114)

    * allow Rocca to run without classifiers

    Fixed bug that threw an error if no classifier files were specified in Rocca Params dialog

    * add rocca switch to enable dev mode

    currently only shows/hides extra buttons in the Params dialog, but will
    extend to more options in the future

    * Fix memory issue with RoccaContourDataBlocks not being released for
    garbage collection

    Set RoccaContourDataBlock objects to null and stop PamObserver Timer to
    force release

    * Fix problem tracing whistles in Rocca spectrogram pop-up

    Whistle and raw data were being 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.

    * updated for training/testing classifiers

commit d5f504dcd1
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Nov 10 18:08:31 2023 +0000

    Bearing localiser offline save

    Bug stopping it correctly saving data from the offline task to the
    database fixed.

commit 7a44d49e27
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Oct 27 09:59:28 2023 +0100

    X3 Version 2.2.3

    Add maven jar files for X3/SUD version 2.2.3

commit fa5fe9943d
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Oct 26 14:44:41 2023 +0100

    update sud file management to more efficiently skip to the correct part
    of a sud file when reading data offline.

commit 60435e567a
Author: Brian S Miller <93690136+BrianSMiller@users.noreply.github.com>
Date:   Fri Sep 8 21:54:40 2023 +1000

    Fixes issues #111 and fixes #112 (DIFAR module crashes and ability to use Deep Learning Detections in DIFAR module) (#110)

    * Bugfix for OverlayMarks

    Check for a null pointer exception in OverlayMarks that was causing a crash on startup.

    * Bugfix for null pointer in symbol manager

    Fix a bug that I found where the DIFAR module was crashing the symbol manager. Seems that this was due to this subclass of clip generator having a null value for it's uniqueName. I've fixed by checking for null values and assigning a generic symbol when null.

    * DeepLearning detections canGenerateClips=true

    Set flag in DeepLearning detector so that detections are considered 'clips' by Pamguard. This allows them to be processed automatically in the DIFAR Localisation module (and maybe others).

    * DIFAR: bugfix frequency limits for auto-detections

    Fix a bug in DIFAR module where the frequency limits of automated detections were not being set properly by the DIFAR module.

    * DeepLearning - Bugfix to detection duration

    Fix bug in deep learning detector where duration (in samples) was being set to number of samples in a hop instead of the number of samples in a segment.
2023-12-12 12:51:13 +00:00
Jamie Mac
a235619edd Updates to FX GUI
Updates to array manager and click detector dialogs for FX GUI
2023-12-12 12:35:36 +00:00
Douglas Gillespie
860d1bec17 Update Calibration export
Stop repeating hydrophones and add two addresses to Calibrations docs
2023-12-07 20:08:17 +00:00
Douglas Gillespie
9c86b41027 Project info dialog
More wrapping of nilus objects to make a general project info tab in
PAMGuard. This is global and can share basic project informatin with the
Tethys module.
2023-12-07 15:10:45 +00:00
Douglas Gillespie
7721d7f1c0 Global metadata
Reorganised how global meta data for a PAMGuard dataset is managed by
wrapping a nilus deployment object so that PAMGuard settings can
serialise and unpack the xml version of a nilus Deployment object.
2023-12-06 17:35:57 +00:00
Douglas Gillespie
bafe93e7f5 SQLLogging revert
Revert main table definition class used by SQLLogging to
PamTableDefinition, back from EmptyTableDefinition, to maintain
compatibility with existing plugin modules.
2023-12-06 12:20:40 +00:00