Commit Graph

998 Commits

Author SHA1 Message Date
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
Douglas Gillespie
9939e8aa85 Calibrations Export
Functional Calibrations export wizard and display
2023-12-04 21:27:00 +00:00
Douglas Gillespie
275a53c042 Calibrations display
display of calibrations documents + some general tidying up of document
management and display.
2023-12-03 18:21:09 +00:00
Jamie Mac
6e5f65d35b Updates to FX Gui and Deep Learning Module 2023-11-29 08:14:56 +00:00
Douglas Gillespie
840e6c89a1 R2.02.09d
Fix matched template classifier import
fix azigram help file image display
2023-11-16 20:36:14 +00:00
Douglas Gillespie
2dd90f6a32 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard into main 2023-11-15 15:02:50 +00:00
Douglas Gillespie
58fe0d7754 Lots of small updates to enable opening of a secondary configuration for
batch processing control.
2023-11-15 15:02:18 +00:00
Douglas Gillespie
acc806d375 Updated X3 library to 2.2.6 2023-11-15 13:08:02 +00:00
Douglas Gillespie
a4f484c76c Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into main 2023-11-15 09:44:09 +00:00
Douglas Gillespie
8e60ad2eff update to array diagnostics and sensor control 2023-11-15 09:43:39 +00:00
m2oswald
d7c4c278d8
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
2023-11-15 09:17:49 +00:00
Jamie Mac
47662b5045 Squashed commit of the following:
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.
2023-11-15 06:34:55 +00:00
Jamie Mac
81907fedb8 Updates to FX display array dialog 2023-11-15 06:32:44 +00:00
Douglas Gillespie
d5f504dcd1 Bearing localiser offline save
Bug stopping it correctly saving data from the offline task to the
database fixed.
2023-11-10 18:08:31 +00:00
Douglas Gillespie
6cc01fe77a Merge branch 'main' of https://github.com/douggillespie/PAMGuard into main 2023-10-27 10:06:52 +01:00
Douglas Gillespie
9fca879c39 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into main 2023-10-27 10:02:47 +01:00
Douglas Gillespie
7a44d49e27 X3 Version 2.2.3
Add maven jar files for X3/SUD version 2.2.3
2023-10-27 09:59:28 +01:00
Douglas Gillespie
bff8eeebc5 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into main 2023-10-26 15:50:26 +01:00
Douglas Gillespie
fa5fe9943d update sud file management to more efficiently skip to the correct part
of a sud file when reading data offline.
2023-10-26 14:44:41 +01:00
Jamie Mac
137fa0e8ba Fix GPS bug in group localizer offline processing 2023-10-25 09:17:12 +01:00
Jamie Mac
fd3e8cae4b Bug fixes to group localiser.
Makes sure time dependent hydrophones positions are considered when localising
2023-10-23 10:38:06 +01:00
Jamie Mac
330dc91193 Added mimplex localisation 2023-10-11 09:41:35 +01:00
Jamie Mac
e1c70fa02e Adding mimplex to group localiser 2023-10-09 17:02:09 +01:00
Jamie Mac
46e0907cce Merge branch 'main' of https://github.com/macster110/PAMGuard 2023-10-09 14:56:14 +01:00
Jamie Mac
e8fc75dc9e Updates to FX GUI 2023-10-09 14:56:12 +01:00
Douglas Gillespie
1f8e790ae5 Collection enum
Made an enum for the different collections. More robust than passing the
names around as strings. Contains functions for converting between the
collection name and the documents names within those collections.
2023-09-29 13:43:49 +01:00
Douglas Gillespie
773f1f542b Species map i/o 2023-09-24 21:59:15 +01:00
Douglas Gillespie
8257122d14 Log Tethys output and include instrumentid in Deployment queries 2023-09-21 18:01:41 +01:00
Douglas Gillespie
4d294b56a8 Click event output 2023-09-19 16:55:33 +01:00
Douglas Gillespie
5fe0927c10 Noise logging 2023-09-18 12:49:39 +01:00
Douglas Gillespie
415ec87938 noise output 2023-09-17 21:10:23 +01:00
Douglas Gillespie
158eedce8c Detections output
more work on detections output.
2023-09-15 15:15:28 +01:00
Douglas Gillespie
db1cc75bc1 More output
More changes to Detections output.
2023-09-13 17:28:47 +01:00
Douglas Gillespie
85fd84d18a Fix binned output
couple of fixes in binned output
2023-09-11 21:52:46 +01:00
Douglas Gillespie
65dfb5688b More on granularity
Nice format of granularity in display tables.
2023-09-11 17:47:50 +01:00