Commit Graph

1182 Commits

Author SHA1 Message Date
Douglas Gillespie
abca8f5ff7
Merge from DG (#180)
* Localization output

* update localiser output

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Update LoggerFormGraphics.java

add in correct symbol managemet to forms graphics.

* Effort lines on map

Sort of working OK in real time mode.

* Working effort system

Currently only for map, but seems to work OK

* Update Tethys to latest nilus schema

* Raven importer

Start of a system for a raven importer. Not quite working yet.

* Raven import

Basic functionality working. Not nice to use though.

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* updated Nilus

A few updates around track and target motion measures.

* FX Plot for raven data

Also sorted out symbols a bit and improved symbol selector in Generic plots.

* Update spectrogram mark bearing display

Remove the 90-angle bit

* Raven extra columns

Logging of data from additional Raven table columns

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Effort lines on map

Sort of working OK in real time mode.

* Update Tethys to latest nilus schema

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* Ishmael Tethys output

Added necessaries for Tethys output from Ishmael detectors. Also found a pretty major bug in the spectrogram correlation detector, where for each block of data it was only testing the first sample of each block, not all samples, for being over threshold.

* Speed and algorithm improvements to Ish matched filter

Seems to be errors in correlation, didn't support multiple channels and
also used very old and slow FFT, so working to fix all three issues.

* Updated matched filter

Updated and working Matched filter, though still some thinking to do about how the scaling of this works, since currently scaled by the template, so whole thing is dependent on the input. Need to think of a better way to do this.

* Update match filt normalisation

Normalisation now correctly using both the template and the signal for normalisation so that it will be data amplitude independent.

* invFFT improvements

Use faster inverse FFT of real data in correlation / delay functions.

* Improve ifft's in other modules to improve TDOA speeds

* Sorting mess of spec plugin graphics

Have got the Ishmael ones scrolling, but when scrolling, there is an offset in the data due to the lag of the correlation functions. Quite hard to fix with available timing data

* Improve ish spectrogram plugin

Sorted scaling and scrollling problems.

* Improve startup checks

Rethread startup checks so that a progress bar shows when PAMGuard is checking input and output files at start up. Also include single file processing in checks.

* Apply all spectrogram overlays

Apply to all function on spectrogram overlays so changes to overlays affect all panels.

* SMall changes to OfflineTaskGroup

Copy data before processing to avoid concurrency problems

* Scroller imporvements

Better functions in scroll manager to enable jumping to somewhere interesting from other commands in PAMGuard, e.g. from data table views.

* small change to viewer scroll

Change in how it tries to miss gaps in the data
2024-11-20 08:57:39 +00:00
Douglas Gillespie
b7fffd6486
Merge from DG (#179)
* Localization output

* update localiser output

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Update LoggerFormGraphics.java

add in correct symbol managemet to forms graphics.

* Effort lines on map

Sort of working OK in real time mode.

* Working effort system

Currently only for map, but seems to work OK

* Update Tethys to latest nilus schema

* Raven importer

Start of a system for a raven importer. Not quite working yet.

* Raven import

Basic functionality working. Not nice to use though.

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* updated Nilus

A few updates around track and target motion measures.

* FX Plot for raven data

Also sorted out symbols a bit and improved symbol selector in Generic plots.

* Update spectrogram mark bearing display

Remove the 90-angle bit

* Raven extra columns

Logging of data from additional Raven table columns

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Effort lines on map

Sort of working OK in real time mode.

* Update Tethys to latest nilus schema

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* Ishmael Tethys output

Added necessaries for Tethys output from Ishmael detectors. Also found a pretty major bug in the spectrogram correlation detector, where for each block of data it was only testing the first sample of each block, not all samples, for being over threshold.

* Speed and algorithm improvements to Ish matched filter

Seems to be errors in correlation, didn't support multiple channels and
also used very old and slow FFT, so working to fix all three issues.

* Updated matched filter

Updated and working Matched filter, though still some thinking to do about how the scaling of this works, since currently scaled by the template, so whole thing is dependent on the input. Need to think of a better way to do this.

* Update match filt normalisation

Normalisation now correctly using both the template and the signal for normalisation so that it will be data amplitude independent.

* invFFT improvements

Use faster inverse FFT of real data in correlation / delay functions.

* Improve ifft's in other modules to improve TDOA speeds

* Sorting mess of spec plugin graphics

Have got the Ishmael ones scrolling, but when scrolling, there is an offset in the data due to the lag of the correlation functions. Quite hard to fix with available timing data

* Improve ish spectrogram plugin

Sorted scaling and scrollling problems.

* Improve startup checks

Rethread startup checks so that a progress bar shows when PAMGuard is checking input and output files at start up. Also include single file processing in checks.

* Apply all spectrogram overlays

Apply to all function on spectrogram overlays so changes to overlays affect all panels.

* SMall changes to OfflineTaskGroup

Copy data before processing to avoid concurrency problems

* Scroller imporvements

Better functions in scroll manager to enable jumping to somewhere interesting from other commands in PAMGuard, e.g. from data table views.

* small change to viewer scroll

Change in how it tries to miss gaps in the data
2024-11-20 08:52:52 +00:00
Douglas Gillespie
acf3169a2f
Merge from DG (#178)
* Localization output

* update localiser output

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Update LoggerFormGraphics.java

add in correct symbol managemet to forms graphics.

* Effort lines on map

Sort of working OK in real time mode.

* Working effort system

Currently only for map, but seems to work OK

* Update Tethys to latest nilus schema

* Raven importer

Start of a system for a raven importer. Not quite working yet.

* Raven import

Basic functionality working. Not nice to use though.

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* updated Nilus

A few updates around track and target motion measures.

* FX Plot for raven data

Also sorted out symbols a bit and improved symbol selector in Generic plots.

* Update spectrogram mark bearing display

Remove the 90-angle bit

* Raven extra columns

Logging of data from additional Raven table columns

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Effort lines on map

Sort of working OK in real time mode.

* Update Tethys to latest nilus schema

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* Ishmael Tethys output

Added necessaries for Tethys output from Ishmael detectors. Also found a pretty major bug in the spectrogram correlation detector, where for each block of data it was only testing the first sample of each block, not all samples, for being over threshold.

* Speed and algorithm improvements to Ish matched filter

Seems to be errors in correlation, didn't support multiple channels and
also used very old and slow FFT, so working to fix all three issues.

* Updated matched filter

Updated and working Matched filter, though still some thinking to do about how the scaling of this works, since currently scaled by the template, so whole thing is dependent on the input. Need to think of a better way to do this.

* Update match filt normalisation

Normalisation now correctly using both the template and the signal for normalisation so that it will be data amplitude independent.

* invFFT improvements

Use faster inverse FFT of real data in correlation / delay functions.

* Improve ifft's in other modules to improve TDOA speeds

* Sorting mess of spec plugin graphics

Have got the Ishmael ones scrolling, but when scrolling, there is an offset in the data due to the lag of the correlation functions. Quite hard to fix with available timing data

* Improve ish spectrogram plugin

Sorted scaling and scrollling problems.

* Improve startup checks

Rethread startup checks so that a progress bar shows when PAMGuard is checking input and output files at start up. Also include single file processing in checks.

* Apply all spectrogram overlays

Apply to all function on spectrogram overlays so changes to overlays affect all panels.

* SMall changes to OfflineTaskGroup

Copy data before processing to avoid concurrency problems

* Scroller imporvements

Better functions in scroll manager to enable jumping to somewhere interesting from other commands in PAMGuard, e.g. from data table views.

* Update PamCalendar.java

Fix issue with times in file analysis, where a time notification was being sent with incorrect file time, confusing the binary store
2024-11-08 08:59:43 +00:00
Jamie Mac
2ab8fd9444
Update readme.md 2024-11-08 08:48:31 +00:00
Jamie Mac
ba9f7a35d9
Update readme.md 2024-11-08 08:47:59 +00:00
Douglas Gillespie
4ec3b42d2b Merge branch 'main' of https://github.com/PAMGuard/PAMGuard 2024-11-02 17:31:54 +00:00
Douglas Gillespie
798f6e12a4 V14a Version info 2024-11-02 17:31:48 +00:00
Jamie Mac
4f6cda7741
Merge pull request #163 from mvdfugro/small_fixes
Few build fixes & small label improvement
2024-10-30 06:02:03 +00:00
Merlijn van Deen
6ac5877cdd Tests
- Get testing working through maven: configure junit and surefire versions
  and block resolution of conflicting surefire version through com.github.psambit9791
- Fix PamZip test (zip file was missing due to .gitignore).
  This is now the same file as blue_whale_24.kgu (but renamed to .zip)
- Fixed scaffolding of ExportTest (still doesn't test anything but at it's not longer crashing)
- Force tests to run in separate VMs to reduce the impact of the PamController singleton

Signed-off-by: Merlijn van Deen <m.vandeen@fugro.com>
2024-10-28 14:14:05 +01:00
Merlijn van Deen
e7cd4fa317 Move units to GlobalMediumManager
Signed-off-by: Merlijn van Deen <m.vandeen@fugro.com>
2024-10-28 14:14:05 +01:00
Merlijn van Deen
bb7314f453 Filtered Noise Measurement: add units to measures
Signed-off-by: Merlijn van Deen <m.vandeen@fugro.com>
2024-10-28 14:14:05 +01:00
Merlijn van Deen
a323d60361 FFT Display: add quantity and full units in axis label
Signed-off-by: Merlijn van Deen <m.vandeen@fugro.com>
2024-10-28 14:14:05 +01:00
Merlijn van Deen
0c5d1519f7 .gitignore: ignore intellij created files
Signed-off-by: Merlijn van Deen <m.vandeen@fugro.com>
2024-10-28 14:14:05 +01:00
Merlijn van Deen
9a4b8df0d1 Generics: make compiler happy about nested extends
Signed-off-by: Merlijn van Deen <m.vandeen@fugro.com>
2024-10-28 14:14:05 +01:00
Merlijn van Deen
bb794f5deb pom.xml: remove defunct talanlabs repository
Signed-off-by: Merlijn van Deen <m.vandeen@fugro.com>
2024-10-28 13:59:05 +01:00
Douglas Gillespie
95d08dd34b Fix clip generator dialog
Issue fix #177
2024-10-28 10:58:23 +00:00
Douglas Gillespie
6c7389c3fc Version 2.02.14
Released code for Version 2.02.14
2024-10-18 14:35:54 +01:00
Douglas Gillespie
6ed4ac7fcd
Merge from DG (#174)
* Localization output

* update localiser output

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Update LoggerFormGraphics.java

add in correct symbol managemet to forms graphics.

* Effort lines on map

Sort of working OK in real time mode.

* Working effort system

Currently only for map, but seems to work OK

* Update Tethys to latest nilus schema

* Raven importer

Start of a system for a raven importer. Not quite working yet.

* Raven import

Basic functionality working. Not nice to use though.

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* updated Nilus

A few updates around track and target motion measures.

* FX Plot for raven data

Also sorted out symbols a bit and improved symbol selector in Generic plots.

* Update spectrogram mark bearing display

Remove the 90-angle bit

* Raven extra columns

Logging of data from additional Raven table columns

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Effort lines on map

Sort of working OK in real time mode.

* Update Tethys to latest nilus schema

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* Ishmael Tethys output

Added necessaries for Tethys output from Ishmael detectors. Also found a pretty major bug in the spectrogram correlation detector, where for each block of data it was only testing the first sample of each block, not all samples, for being over threshold.

* Speed and algorithm improvements to Ish matched filter

Seems to be errors in correlation, didn't support multiple channels and
also used very old and slow FFT, so working to fix all three issues.

* Updated matched filter

Updated and working Matched filter, though still some thinking to do about how the scaling of this works, since currently scaled by the template, so whole thing is dependent on the input. Need to think of a better way to do this.

* Update match filt normalisation

Normalisation now correctly using both the template and the signal for normalisation so that it will be data amplitude independent.

* invFFT improvements

Use faster inverse FFT of real data in correlation / delay functions.

* Improve ifft's in other modules to improve TDOA speeds

* Sorting mess of spec plugin graphics

Have got the Ishmael ones scrolling, but when scrolling, there is an offset in the data due to the lag of the correlation functions. Quite hard to fix with available timing data

* Improve ish spectrogram plugin

Sorted scaling and scrollling problems.

* Improve startup checks

Rethread startup checks so that a progress bar shows when PAMGuard is checking input and output files at start up. Also include single file processing in checks.

* Apply all spectrogram overlays

Apply to all function on spectrogram overlays so changes to overlays affect all panels.

* SMall changes to OfflineTaskGroup

Copy data before processing to avoid concurrency problems

* Scroller imporvements

Better functions in scroll manager to enable jumping to somewhere interesting from other commands in PAMGuard, e.g. from data table views.
2024-10-14 15:59:12 +01:00
Douglas Gillespie
fc80620e74 Scroller improvements
Better jump options in scroller and fix icon problem (Resource path needs /, not \ even on windows)
2024-10-11 19:50:45 +01:00
Douglas Gillespie
a38e2262d3
Merge fromDG (#172)
* Localization output

* update localiser output

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Update LoggerFormGraphics.java

add in correct symbol managemet to forms graphics.

* Effort lines on map

Sort of working OK in real time mode.

* Working effort system

Currently only for map, but seems to work OK

* Update Tethys to latest nilus schema

* Raven importer

Start of a system for a raven importer. Not quite working yet.

* Raven import

Basic functionality working. Not nice to use though.

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* updated Nilus

A few updates around track and target motion measures.

* FX Plot for raven data

Also sorted out symbols a bit and improved symbol selector in Generic plots.

* Update spectrogram mark bearing display

Remove the 90-angle bit

* Raven extra columns

Logging of data from additional Raven table columns

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Effort lines on map

Sort of working OK in real time mode.

* Update Tethys to latest nilus schema

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* Ishmael Tethys output

Added necessaries for Tethys output from Ishmael detectors. Also found a pretty major bug in the spectrogram correlation detector, where for each block of data it was only testing the first sample of each block, not all samples, for being over threshold.

* Speed and algorithm improvements to Ish matched filter

Seems to be errors in correlation, didn't support multiple channels and
also used very old and slow FFT, so working to fix all three issues.

* Updated matched filter

Updated and working Matched filter, though still some thinking to do about how the scaling of this works, since currently scaled by the template, so whole thing is dependent on the input. Need to think of a better way to do this.

* Update match filt normalisation

Normalisation now correctly using both the template and the signal for normalisation so that it will be data amplitude independent.

* invFFT improvements

Use faster inverse FFT of real data in correlation / delay functions.

* Improve ifft's in other modules to improve TDOA speeds

* Sorting mess of spec plugin graphics

Have got the Ishmael ones scrolling, but when scrolling, there is an offset in the data due to the lag of the correlation functions. Quite hard to fix with available timing data

* Improve ish spectrogram plugin

Sorted scaling and scrollling problems.

* Improve startup checks

Rethread startup checks so that a progress bar shows when PAMGuard is checking input and output files at start up. Also include single file processing in checks.

* Apply all spectrogram overlays

Apply to all function on spectrogram overlays so changes to overlays affect all panels.

* SMall changes to OfflineTaskGroup

Copy data before processing to avoid concurrency problems

* Scroller imporvements

Better functions in scroll manager to enable jumping to somewhere interesting from other commands in PAMGuard, e.g. from data table views.
2024-10-11 16:44:45 +01:00
Douglas Gillespie
59f9dcb969 update icon loader for choice mode 2024-10-10 13:14:07 +01:00
Douglas Gillespie
653dc584ed Nearly ready for 2.02.14 release
Added CPOD help.
2024-10-09 16:58:21 +01:00
Jamie Mac
211ca7ab91
MacOS version of PAMGuard and minor UI updates (#170)
* Update exporter_help.md

Updated help for exporter

* Update .gitignore

* Bug fixes for deep learning classifier.

Updated the symbol options to make sure opacity is passed through the symbol chooser.

* Updates to the data map FX display

* Updates to DelphinID and Data ModelFX

Used a new writable image for much faster drawing in FX

* bb

* Delete C:\Users\Jamie Macaulay\MATLAB Drive\MATLAB\PAMGUARD\deep_learning\delphinID\whistle_image_example_java.mat

* Updates to DelphinID

* Updates to ReadMe and JavaFX GUI

* Update readme.md

Updates to ReadMe

* Updates to CPOD module and also delphinID classifier

* Fix colour scaling in FX data map

* Create cpod_help.md

* Update cpod_help.md

* Update cpod_help.md

* Updates to CPOD module

Added ability to export CPOD clicks
Added some extra features to data selector
Swing GUI for data selector (in progress)

* Updates to data map FX GUI

* Updates to CPOD module

* Added help files resources for CPOD

* Add CPOD resources for help

* Add CPOD resources for help

* Add CPOD resources for help

* Add CPOD resources for help

* Add CPOD resources for help

* Update cpod_help.md

* Update cpod_help.md

* Bug fixes for deep learning classifier.

Updated the symbol options to make sure opacity is passed through the symbol chooser.

* Updates to the data map FX display

* Updates to DelphinID and Data ModelFX

Used a new writable image for much faster drawing in FX

* Updates to ReadMe and JavaFX GUI

* bb

* Delete C:\Users\Jamie Macaulay\MATLAB Drive\MATLAB\PAMGUARD\deep_learning\delphinID\whistle_image_example_java.mat

* Updates to DelphinID

* Update readme.md

Updates to ReadMe

* Fix colour scaling in FX data map

* Updates to CPOD module and also delphinID classifier

* Updates to CPOD module

Added ability to export CPOD clicks
Added some extra features to data selector
Swing GUI for data selector (in progress)

* Create cpod_help.md

* Update cpod_help.md

* Update cpod_help.md

* Updates to data map FX GUI

* Updates to CPOD module

* Added help files resources for CPOD

* Add CPOD resources for help

* Add CPOD resources for help

* Add CPOD resources for help

* Add CPOD resources for help

* Add CPOD resources for help

* Update cpod_help.md

* Update cpod_help.md

* Bug fix to BT display

The BT display was not selecting clicks properly.

* Import bug fix

* Updates to data map FX GUI

* Updates to datamap FX

* Got date axis working properly.

* Added some arrows to the scroll bar for data map FX pane.

* Working on getting datagrams in FX saving

* Updates to DataMapFX and exporting annotations

* Update MLAnnotationsManager.java

* Working on adding annotations to exporter

* Bug fix for processing files and annotations for exporter

Rebase with main
Bug fix for processing files - stops only the last file processing when "Start normally" selected on data processing
R and MATLAB export of data annotation added.

* Add a ttoltip to the exporter

* Minor text change

* X3 fix and building for MACOS

* Update PAMGuard to build installer for MacOS

* Some fixes to Sound Acquisition dialog layout.

* Squashed commit of the following:

commit 1acddb4cc6
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Oct 8 15:03:32 2024 +0100

    MErge from DG (#168)

    * Localization output

    * update localiser output

    * Start effort management system

    * Start of Effort plotting

    Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

    * Logger forms update

    Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

    * Update LoggerFormGraphics.java

    add in correct symbol managemet to forms graphics.

    * Effort lines on map

    Sort of working OK in real time mode.

    * Working effort system

    Currently only for map, but seems to work OK

    * Update Tethys to latest nilus schema

    * Raven importer

    Start of a system for a raven importer. Not quite working yet.

    * Raven import

    Basic functionality working. Not nice to use though.

    * Tethys Localization work

    Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

    * updated Nilus

    A few updates around track and target motion measures.

    * FX Plot for raven data

    Also sorted out symbols a bit and improved symbol selector in Generic plots.

    * Update spectrogram mark bearing display

    Remove the 90-angle bit

    * Raven extra columns

    Logging of data from additional Raven table columns

    * Start effort management system

    * Start of Effort plotting

    Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

    * Logger forms update

    Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

    * Effort lines on map

    Sort of working OK in real time mode.

    * Update Tethys to latest nilus schema

    * Tethys Localization work

    Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

    * Ishmael Tethys output

    Added necessaries for Tethys output from Ishmael detectors. Also found a pretty major bug in the spectrogram correlation detector, where for each block of data it was only testing the first sample of each block, not all samples, for being over threshold.

    * Speed and algorithm improvements to Ish matched filter

    Seems to be errors in correlation, didn't support multiple channels and
    also used very old and slow FFT, so working to fix all three issues.

    * Updated matched filter

    Updated and working Matched filter, though still some thinking to do about how the scaling of this works, since currently scaled by the template, so whole thing is dependent on the input. Need to think of a better way to do this.

    * Update match filt normalisation

    Normalisation now correctly using both the template and the signal for normalisation so that it will be data amplitude independent.

    * invFFT improvements

    Use faster inverse FFT of real data in correlation / delay functions.

    * Improve ifft's in other modules to improve TDOA speeds

    * Sorting mess of spec plugin graphics

    Have got the Ishmael ones scrolling, but when scrolling, there is an offset in the data due to the lag of the correlation functions. Quite hard to fix with available timing data

    * Improve ish spectrogram plugin

    Sorted scaling and scrollling problems.

    * Improve startup checks

    Rethread startup checks so that a progress bar shows when PAMGuard is checking input and output files at start up. Also include single file processing in checks.

    * Apply all spectrogram overlays

    Apply to all function on spectrogram overlays so changes to overlays affect all panels.

commit f2f9870b6f
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Oct 2 15:13:12 2024 +0100

    V2.02.13c

    Release for installation on teaching lab machines.

commit 7533a7cfbe
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Oct 1 15:00:51 2024 +0100

    Tethys output of Group3DLocalisations

    Output of Group3D localiser data. Localisations only, no Detections output for this one

commit ef494c0d0e
Author: Jamie Mac <macster110@gmail.com>
Date:   Mon Sep 30 13:10:59 2024 +0100

    Sud bug fix and updates to CPOD module.  (#162)

    * Update exporter_help.md

    Updated help for exporter

    * Update .gitignore

    * Bug fixes for deep learning classifier.

    Updated the symbol options to make sure opacity is passed through the symbol chooser.

    * Updates to the data map FX display

    * Updates to DelphinID and Data ModelFX

    Used a new writable image for much faster drawing in FX

    * bb

    * Delete C:\Users\Jamie Macaulay\MATLAB Drive\MATLAB\PAMGUARD\deep_learning\delphinID\whistle_image_example_java.mat

    * Updates to DelphinID

    * Updates to ReadMe and JavaFX GUI

    * Update readme.md

    Updates to ReadMe

    * Updates to CPOD module and also delphinID classifier

    * Fix colour scaling in FX data map

    * Create cpod_help.md

    * Update cpod_help.md

    * Update cpod_help.md

    * Updates to CPOD module

    Added ability to export CPOD clicks
    Added some extra features to data selector
    Swing GUI for data selector (in progress)

    * Updates to data map FX GUI

    * Updates to CPOD module

    * Added help files resources for CPOD

    * Add CPOD resources for help

    * Add CPOD resources for help

    * Add CPOD resources for help

    * Add CPOD resources for help

    * Add CPOD resources for help

    * Update cpod_help.md

    * Update cpod_help.md

    * Bug fixes for deep learning classifier.

    Updated the symbol options to make sure opacity is passed through the symbol chooser.

    * Updates to the data map FX display

    * Updates to DelphinID and Data ModelFX

    Used a new writable image for much faster drawing in FX

    * Updates to ReadMe and JavaFX GUI

    * bb

    * Delete C:\Users\Jamie Macaulay\MATLAB Drive\MATLAB\PAMGUARD\deep_learning\delphinID\whistle_image_example_java.mat

    * Updates to DelphinID

    * Update readme.md

    Updates to ReadMe

    * Fix colour scaling in FX data map

    * Updates to CPOD module and also delphinID classifier

    * Updates to CPOD module

    Added ability to export CPOD clicks
    Added some extra features to data selector
    Swing GUI for data selector (in progress)

    * Create cpod_help.md

    * Update cpod_help.md

    * Update cpod_help.md

    * Updates to data map FX GUI

    * Updates to CPOD module

    * Added help files resources for CPOD

    * Add CPOD resources for help

    * Add CPOD resources for help

    * Add CPOD resources for help

    * Add CPOD resources for help

    * Add CPOD resources for help

    * Update cpod_help.md

    * Update cpod_help.md

    * Bug fix to BT display

    The BT display was not selecting clicks properly.

    * Import bug fix

    * Updates to data map FX GUI

    * Updates to datamap FX

    * Got date axis working properly.

    * Added some arrows to the scroll bar for data map FX pane.

    * Working on getting datagrams in FX saving

    * Updates to DataMapFX and exporting annotations

    * Update MLAnnotationsManager.java

    * Working on adding annotations to exporter

    * Bug fix for processing files and annotations for exporter

    Rebase with main
    Bug fix for processing files - stops only the last file processing when "Start normally" selected on data processing
    R and MATLAB export of data annotation added.

    * Add a ttoltip to the exporter

    * Minor text change

* Small UI improvements for Sound Acquisition and MacOS

* Bug fix to exporter

* Update to help points

Updated help points for following modules
Deep learning
CPOD
Matched click classifier
Exporter

---------

Co-authored-by: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
2024-10-09 12:39:26 +01:00
Douglas Gillespie
0bab2a01c7
Merge from Doug (#169)
* Localization output

* update localiser output

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Update LoggerFormGraphics.java

add in correct symbol managemet to forms graphics.

* Effort lines on map

Sort of working OK in real time mode.

* Working effort system

Currently only for map, but seems to work OK

* Update Tethys to latest nilus schema

* Raven importer

Start of a system for a raven importer. Not quite working yet.

* Raven import

Basic functionality working. Not nice to use though.

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* updated Nilus

A few updates around track and target motion measures.

* FX Plot for raven data

Also sorted out symbols a bit and improved symbol selector in Generic plots.

* Update spectrogram mark bearing display

Remove the 90-angle bit

* Raven extra columns

Logging of data from additional Raven table columns

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Effort lines on map

Sort of working OK in real time mode.

* Update Tethys to latest nilus schema

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* Ishmael Tethys output

Added necessaries for Tethys output from Ishmael detectors. Also found a pretty major bug in the spectrogram correlation detector, where for each block of data it was only testing the first sample of each block, not all samples, for being over threshold.

* Speed and algorithm improvements to Ish matched filter

Seems to be errors in correlation, didn't support multiple channels and
also used very old and slow FFT, so working to fix all three issues.

* Updated matched filter

Updated and working Matched filter, though still some thinking to do about how the scaling of this works, since currently scaled by the template, so whole thing is dependent on the input. Need to think of a better way to do this.

* Update match filt normalisation

Normalisation now correctly using both the template and the signal for normalisation so that it will be data amplitude independent.

* invFFT improvements

Use faster inverse FFT of real data in correlation / delay functions.

* Improve ifft's in other modules to improve TDOA speeds

* Sorting mess of spec plugin graphics

Have got the Ishmael ones scrolling, but when scrolling, there is an offset in the data due to the lag of the correlation functions. Quite hard to fix with available timing data

* Improve ish spectrogram plugin

Sorted scaling and scrollling problems.

* Improve startup checks

Rethread startup checks so that a progress bar shows when PAMGuard is checking input and output files at start up. Also include single file processing in checks.

* Apply all spectrogram overlays

Apply to all function on spectrogram overlays so changes to overlays affect all panels.

* SMall changes to OfflineTaskGroup

Copy data before processing to avoid concurrency problems
2024-10-09 11:02:25 +01:00
Douglas Gillespie
1acddb4cc6
MErge from DG (#168)
* Localization output

* update localiser output

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Update LoggerFormGraphics.java

add in correct symbol managemet to forms graphics.

* Effort lines on map

Sort of working OK in real time mode.

* Working effort system

Currently only for map, but seems to work OK

* Update Tethys to latest nilus schema

* Raven importer

Start of a system for a raven importer. Not quite working yet.

* Raven import

Basic functionality working. Not nice to use though.

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* updated Nilus

A few updates around track and target motion measures.

* FX Plot for raven data

Also sorted out symbols a bit and improved symbol selector in Generic plots.

* Update spectrogram mark bearing display

Remove the 90-angle bit

* Raven extra columns

Logging of data from additional Raven table columns

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Effort lines on map

Sort of working OK in real time mode.

* Update Tethys to latest nilus schema

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* Ishmael Tethys output

Added necessaries for Tethys output from Ishmael detectors. Also found a pretty major bug in the spectrogram correlation detector, where for each block of data it was only testing the first sample of each block, not all samples, for being over threshold.

* Speed and algorithm improvements to Ish matched filter

Seems to be errors in correlation, didn't support multiple channels and
also used very old and slow FFT, so working to fix all three issues.

* Updated matched filter

Updated and working Matched filter, though still some thinking to do about how the scaling of this works, since currently scaled by the template, so whole thing is dependent on the input. Need to think of a better way to do this.

* Update match filt normalisation

Normalisation now correctly using both the template and the signal for normalisation so that it will be data amplitude independent.

* invFFT improvements

Use faster inverse FFT of real data in correlation / delay functions.

* Improve ifft's in other modules to improve TDOA speeds

* Sorting mess of spec plugin graphics

Have got the Ishmael ones scrolling, but when scrolling, there is an offset in the data due to the lag of the correlation functions. Quite hard to fix with available timing data

* Improve ish spectrogram plugin

Sorted scaling and scrollling problems.

* Improve startup checks

Rethread startup checks so that a progress bar shows when PAMGuard is checking input and output files at start up. Also include single file processing in checks.

* Apply all spectrogram overlays

Apply to all function on spectrogram overlays so changes to overlays affect all panels.
2024-10-08 15:03:32 +01:00
Douglas Gillespie
f2f9870b6f V2.02.13c
Release for installation on teaching lab machines.
2024-10-02 15:13:12 +01:00
Douglas Gillespie
7533a7cfbe Tethys output of Group3DLocalisations
Output of Group3D localiser data. Localisations only, no Detections output for this one
2024-10-01 15:00:51 +01:00
Jamie Mac
ef494c0d0e
Sud bug fix and updates to CPOD module. (#162)
* Update exporter_help.md

Updated help for exporter

* Update .gitignore

* Bug fixes for deep learning classifier.

Updated the symbol options to make sure opacity is passed through the symbol chooser.

* Updates to the data map FX display

* Updates to DelphinID and Data ModelFX

Used a new writable image for much faster drawing in FX

* bb

* Delete C:\Users\Jamie Macaulay\MATLAB Drive\MATLAB\PAMGUARD\deep_learning\delphinID\whistle_image_example_java.mat

* Updates to DelphinID

* Updates to ReadMe and JavaFX GUI

* Update readme.md

Updates to ReadMe

* Updates to CPOD module and also delphinID classifier

* Fix colour scaling in FX data map

* Create cpod_help.md

* Update cpod_help.md

* Update cpod_help.md

* Updates to CPOD module

Added ability to export CPOD clicks
Added some extra features to data selector
Swing GUI for data selector (in progress)

* Updates to data map FX GUI

* Updates to CPOD module

* Added help files resources for CPOD

* Add CPOD resources for help

* Add CPOD resources for help

* Add CPOD resources for help

* Add CPOD resources for help

* Add CPOD resources for help

* Update cpod_help.md

* Update cpod_help.md

* Bug fixes for deep learning classifier.

Updated the symbol options to make sure opacity is passed through the symbol chooser.

* Updates to the data map FX display

* Updates to DelphinID and Data ModelFX

Used a new writable image for much faster drawing in FX

* Updates to ReadMe and JavaFX GUI

* bb

* Delete C:\Users\Jamie Macaulay\MATLAB Drive\MATLAB\PAMGUARD\deep_learning\delphinID\whistle_image_example_java.mat

* Updates to DelphinID

* Update readme.md

Updates to ReadMe

* Fix colour scaling in FX data map

* Updates to CPOD module and also delphinID classifier

* Updates to CPOD module

Added ability to export CPOD clicks
Added some extra features to data selector
Swing GUI for data selector (in progress)

* Create cpod_help.md

* Update cpod_help.md

* Update cpod_help.md

* Updates to data map FX GUI

* Updates to CPOD module

* Added help files resources for CPOD

* Add CPOD resources for help

* Add CPOD resources for help

* Add CPOD resources for help

* Add CPOD resources for help

* Add CPOD resources for help

* Update cpod_help.md

* Update cpod_help.md

* Bug fix to BT display

The BT display was not selecting clicks properly.

* Import bug fix

* Updates to data map FX GUI

* Updates to datamap FX

* Got date axis working properly.

* Added some arrows to the scroll bar for data map FX pane.

* Working on getting datagrams in FX saving

* Updates to DataMapFX and exporting annotations

* Update MLAnnotationsManager.java

* Working on adding annotations to exporter

* Bug fix for processing files and annotations for exporter

Rebase with main
Bug fix for processing files - stops only the last file processing when "Start normally" selected on data processing
R and MATLAB export of data annotation added.

* Add a ttoltip to the exporter

* Minor text change
2024-09-30 13:10:59 +01:00
m2oswald
cee21dbc3d
updates to Rocca (#161)
* 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

* added option to apply whistle classification threshold as the difference between the highest and second highest vote, instead of as an absolute value

* update Rocca help files

update help files to include description of new strong whistle options

* fix typo

Fix typo in ONR Temperate Pacific classifier reference
2024-09-19 15:52:14 +01:00
Douglas Gillespie
2d207a15c3 click selection in BT display
Cleaned up code. Hopefully fixed issue with clicks not selecting correctly on large displays.
2024-09-16 16:31:22 +01:00
Douglas Gillespie
2540fd0d32 Update README.html 2024-09-16 11:10:19 +01:00
Douglas Gillespie
42ebf67ed8
Improve startup checks (#160)
* Ishmael Tethys output

Added necessaries for Tethys output from Ishmael detectors. Also found a pretty major bug in the spectrogram correlation detector, where for each block of data it was only testing the first sample of each block, not all samples, for being over threshold.

* Speed and algorithm improvements to Ish matched filter

Seems to be errors in correlation, didn't support multiple channels and
also used very old and slow FFT, so working to fix all three issues.

* Updated matched filter

Updated and working Matched filter, though still some thinking to do about how the scaling of this works, since currently scaled by the template, so whole thing is dependent on the input. Need to think of a better way to do this.

* Update match filt normalisation

Normalisation now correctly using both the template and the signal for normalisation so that it will be data amplitude independent.

* invFFT improvements

Use faster inverse FFT of real data in correlation / delay functions.

* Improve ifft's in other modules to improve TDOA speeds

* Sorting mess of spec plugin graphics

Have got the Ishmael ones scrolling, but when scrolling, there is an offset in the data due to the lag of the correlation functions. Quite hard to fix with available timing data

* Improve ish spectrogram plugin

Sorted scaling and scrollling problems.

* Improve startup checks

Rethread startup checks so that a progress bar shows when PAMGuard is checking input and output files at start up. Also include single file processing in checks.
2024-09-15 19:01:22 +01:00
Douglas Gillespie
26475cf366 Handle no sound card
Playback when no sound cards are present: Causes problems on new PC's which won't admit to a sound card if nothing is connected, making it impossible to use sound output to slow down processing of files (e.g. during teaching). Have added delay to sort this.
2024-09-15 13:09:26 +01:00
Douglas Gillespie
3c27717479
Ishmael sort out and improve inverse FFT's (#159)
* Ishmael Tethys output

Added necessaries for Tethys output from Ishmael detectors. Also found a pretty major bug in the spectrogram correlation detector, where for each block of data it was only testing the first sample of each block, not all samples, for being over threshold.

* Speed and algorithm improvements to Ish matched filter

Seems to be errors in correlation, didn't support multiple channels and
also used very old and slow FFT, so working to fix all three issues.

* Updated matched filter

Updated and working Matched filter, though still some thinking to do about how the scaling of this works, since currently scaled by the template, so whole thing is dependent on the input. Need to think of a better way to do this.

* Update match filt normalisation

Normalisation now correctly using both the template and the signal for normalisation so that it will be data amplitude independent.

* invFFT improvements

Use faster inverse FFT of real data in correlation / delay functions.

* Improve ifft's in other modules to improve TDOA speeds

* Sorting mess of spec plugin graphics

Have got the Ishmael ones scrolling, but when scrolling, there is an offset in the data due to the lag of the correlation functions. Quite hard to fix with available timing data

* Improve ish spectrogram plugin

Sorted scaling and scrollling problems.
2024-09-15 12:12:35 +01:00
Douglas Gillespie
274997b6c4 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard 2024-08-27 12:48:20 +01:00
Douglas Gillespie
b420fd9f9d Major code cleanup
Cleanup of imports, whitespace, etc. across all of PAMGuard. No other changes to code apart from this automatic cleanup.
2024-08-27 12:48:16 +01:00
Jamie Mac
0fb5623e4b
Update readme.md
Added DOI from Zenodo
2024-08-27 12:02:39 +01:00
Douglas Gillespie
5587526399
Update CITATION.cff 2024-08-27 11:50:26 +01:00
Douglas Gillespie
38165a156e
Create CITATION.cff 2024-08-27 11:49:05 +01:00
Douglas Gillespie
b9c613ea1b Final 2.02.13
final readme and version info file for 2.02.13 release.
2024-08-27 09:13:30 +01:00
Douglas Gillespie
a98e07f576 Nearing final release 2.2.13
help for data export
fixes to fx symbol opacity
removal of too much print output
change of error message when plugins loaded (don't say there is an error when a plugin is not compatible with that run mode)
Added option for SourcePanel to have a null return value (not used in any current detectors)
2024-08-26 17:51:10 +01:00
Jamie Mac
38671987db
Bug fixes for deep leanring module (#155)
* Update exporter_help.md

Updated help for exporter

* Update .gitignore

* Bug fixes for deep learning classifier.

Updated the symbol options to make sure opacity is passed through the symbol chooser.
2024-08-26 17:15:43 +01:00
bluetintedfortress
cfd42779a1
Fix if statement for overflow (#121) 2024-08-26 11:15:11 +01:00
Douglas Gillespie
b5b9b94735
Merge from DG (#154)
* Localization output

* update localiser output

* Start effort management system

* Start of Effort plotting

Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

* Logger forms update

Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

* Update LoggerFormGraphics.java

add in correct symbol managemet to forms graphics.

* Effort lines on map

Sort of working OK in real time mode.

* Working effort system

Currently only for map, but seems to work OK

* Update Tethys to latest nilus schema

* Raven importer

Start of a system for a raven importer. Not quite working yet.

* Raven import

Basic functionality working. Not nice to use though.

* Tethys Localization work

Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

* updated Nilus

A few updates around track and target motion measures.

* FX Plot for raven data

Also sorted out symbols a bit and improved symbol selector in Generic plots.

* Update spectrogram mark bearing display

Remove the 90-angle bit

* Raven extra columns

Logging of data from additional Raven table columns
2024-08-23 16:42:39 +01:00
Douglas Gillespie
744e22d84e Merge from Jamie
Difficult merge, with many files becoming corrupted and having to be copied manually from Macster to PAMguard. hopefully all OK now.
2024-08-23 16:38:20 +01:00
Douglas Gillespie
3dfe44d383 Merge branch 'main' of https://github.com/macster110/PAMGuard into macster110-main 2024-08-23 15:23:17 +01:00
Jamie Mac
5cd0012022 Squashed commit of the following:
commit 51aa658514
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Aug 23 14:58:32 2024 +0100

    Tethys updates

    And get rid of some other files that had got into the repo by accident

commit 34ba7ebceb
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Aug 23 09:15:40 2024 +0100

    Merge from DG (#150)

    * Localization output

    * update localiser output

    * Start effort management system

    * Start of Effort plotting

    Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

    * Logger forms update

    Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

    * Update LoggerFormGraphics.java

    add in correct symbol managemet to forms graphics.

    * Effort lines on map

    Sort of working OK in real time mode.

    * Working effort system

    Currently only for map, but seems to work OK

    * Update Tethys to latest nilus schema

    * Raven importer

    Start of a system for a raven importer. Not quite working yet.

    * Raven import

    Basic functionality working. Not nice to use though.

    * Tethys Localization work

    Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

    * updated Nilus

    A few updates around track and target motion measures.

    * FX Plot for raven data

    Also sorted out symbols a bit and improved symbol selector in Generic plots.

    * Update spectrogram mark bearing display

    Remove the 90-angle bit

    * Raven extra columns

    Logging of data from additional Raven table columns

commit cb1b28423e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Aug 19 15:55:25 2024 +0100

    updates ready for 2.2.12

commit 4829b46b36
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Aug 19 11:54:24 2024 +0100

    Merge from DG (#149)

    * Localization output

    * update localiser output

    * Start effort management system

    * Start of Effort plotting

    Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

    * Logger forms update

    Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

    * Update LoggerFormGraphics.java

    add in correct symbol managemet to forms graphics.

    * Effort lines on map

    Sort of working OK in real time mode.

    * Working effort system

    Currently only for map, but seems to work OK

    * Update Tethys to latest nilus schema

    * Raven importer

    Start of a system for a raven importer. Not quite working yet.

    * Raven import

    Basic functionality working. Not nice to use though.

    * Tethys Localization work

    Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

    * updated Nilus

    A few updates around track and target motion measures.

    * FX Plot for raven data

    Also sorted out symbols a bit and improved symbol selector in Generic plots.

    * Update spectrogram mark bearing display

    Remove the 90-angle bit

commit 507ff9e28d
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sat Aug 17 14:34:54 2024 +0100

    Merge from DG (#148)

    * Localization output

    * update localiser output

    * Start effort management system

    * Start of Effort plotting

    Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

    * Logger forms update

    Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

    * Update LoggerFormGraphics.java

    add in correct symbol managemet to forms graphics.

    * Effort lines on map

    Sort of working OK in real time mode.

    * Working effort system

    Currently only for map, but seems to work OK

    * Update Tethys to latest nilus schema

    * Raven importer

    Start of a system for a raven importer. Not quite working yet.

    * Raven import

    Basic functionality working. Not nice to use though.

    * Tethys Localization work

    Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

    * updated Nilus

    A few updates around track and target motion measures.

    * FX Plot for raven data

    Also sorted out symbols a bit and improved symbol selector in Generic plots.

commit 51757499d4
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Aug 16 10:44:54 2024 +0100

    Merge from DG (#147)

    * Localization output

    * update localiser output

    * Start effort management system

    * Start of Effort plotting

    Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

    * Logger forms update

    Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

    * Update LoggerFormGraphics.java

    add in correct symbol managemet to forms graphics.

    * Effort lines on map

    Sort of working OK in real time mode.

    * Working effort system

    Currently only for map, but seems to work OK

    * Update Tethys to latest nilus schema

    * Raven importer

    Start of a system for a raven importer. Not quite working yet.

    * Raven import

    Basic functionality working. Not nice to use though.

    * Tethys Localization work

    Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

    * updated Nilus

    A few updates around track and target motion measures.

commit 46bd88c197
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Aug 16 10:40:00 2024 +0100

    Merge Tethys updates from DG (#146)

    * Localization output

    * update localiser output

    * Start effort management system

    * Start of Effort plotting

    Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output).

    * Logger forms update

    Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode.

    * Update LoggerFormGraphics.java

    add in correct symbol managemet to forms graphics.

    * Effort lines on map

    Sort of working OK in real time mode.

    * Working effort system

    Currently only for map, but seems to work OK

    * Update Tethys to latest nilus schema

    * Raven importer

    Start of a system for a raven importer. Not quite working yet.

    * Raven import

    Basic functionality working. Not nice to use though.

    * Tethys Localization work

    Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff.

    * updated Nilus

    A few updates around track and target motion measures.

commit bea4a544d0
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Aug 8 14:27:05 2024 +0100

    Merge from DG (#145)

    * Localization output

    * update localiser output

commit adf4c87781
Merge: 62121bdb 29293725
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Aug 8 09:29:24 2024 +0100

    Merge branch 'main' into main

commit 2929372533
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Aug 5 17:58:08 2024 +0100

    Tethys Localisation output

    Not all types, but getting there.

commit 62121bdbbd
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun Aug 4 11:41:08 2024 +0100

    update jserialcom to 2.11.0

commit 82adc06e3d
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Aug 2 15:26:49 2024 +0100

    Merge DG branch (#144)

    * Refactoring Tethys

    A lot of refactoring of Nilus wrappers with more useful Objects for PAMGUard to work with.

    * Improved document handling

    Abstracted wrapper around nilus documents which allows easyish calling of internal functions in Localize and Detections document without a common base class.

    * Fix doc deletion in detector output panel

commit 36455153a2
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Jul 30 16:34:35 2024 +0100

    Fix doc deletion in detector output panel

commit bc686c0fe6
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jul 26 16:12:54 2024 +0100

    Improved document handling

    Abstracted wrapper around nilus documents which allows easyish calling of internal functions in Localize and Detections document without a common base class.

commit 4f87b7b661
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jul 22 16:07:33 2024 +0100

    Refactoring Tethys

    A lot of refactoring of Nilus wrappers with more useful Objects for PAMGUard to work with.

commit 3abaff0379
Merge: a3f41e22 9eee7434
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jul 22 13:50:49 2024 +0100

    Merge pull request #86 from PAMGuard/main

    Merge from main

commit 9eee7434de
Merge: 32c7c9b2 a3f41e22
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jul 22 13:50:38 2024 +0100

    Merge branch 'main' into main

commit 32c7c9b263
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jul 22 11:55:06 2024 +0100

    Merge from Jamie (#143)

    * Working on the exporter

    * Working out on exporter

    * Working on new symbol options for deep learning and sud file options in SoundAcquisition GUI

    * Add zero pad option for sud files.

    * Updates to sud zero pad options on FX GUI

    * Implementing a data selector for the deep learning module

    * Bug fix to data transforms if the wave data and sample length are different

    * Updated POm to ignore test resources and updates to DL data selector

    * Updates to DL data selector and POM

    * Work on the data selector for the deep learning module.

    * Working on the exporter

    * Working out on exporter

    * Working on new symbol options for deep learning and sud file options in SoundAcquisition GUI

    * Add zero pad option for sud files.

    * Updates to sud zero pad options on FX GUI

    * Implementing a data selector for the deep learning module

    * Updated POm to ignore test resources and updates to DL data selector

    * Bug fix to data transforms if the wave data and sample length are different

    * Updates to DL data selector and POM

    * Work on the data selector for the deep learning module.

    * Data selectors for deep learning models now working with FX

    Still have to be implemented in Swing

    * Update deep_learning_help.md

    Updated help values to have some info on data selectors and symbol managers.

    * Updates to deep learning symbol options for swing and data selector panel for swing

    Made tooltips last longer on TD display  FX

    * Update deep_learning_help.md

    * Swing symbol modifiers for DL and peak freq

    * Squashed commit of the following:

    commit bad2255710
    Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
    Date:   Thu Jul 18 09:47:47 2024 +0100

        Better symbol options

        Add clearer options button to multi option symbol manager panel.

    * Fix bugs in detection display

    * Bug fix to hiding panes

    * Squashed commit of the following:

    commit 8b5b5b2f18
    Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
    Date:   Fri Jul 19 17:14:28 2024 +0100

        Updated data selectors for BT display

        Merging old status bar and new DataSelector options so that they work more consistently on the BT display.

    commit bad2255710
    Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
    Date:   Thu Jul 18 09:47:47 2024 +0100

        Better symbol options

        Add clearer options button to multi option symbol manager panel.

    * Deep learning bug fix

    * Ignore the class path

    * Squashed commit of the following:

    commit 577670ccd0
    Merge: 6510d226 8b5b5b2f
    Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
    Date:   Mon Jul 22 09:35:01 2024 +0100

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

    commit 6510d2260e
    Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
    Date:   Mon Jul 22 09:34:58 2024 +0100

        Remove unnecessary text output

    commit 3da8401756
    Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
    Date:   Mon Jul 22 09:29:38 2024 +0100

        updates to Daq

        New DLL, and some LED control, but hasn't fixed stalling problem.

    commit 8b5b5b2f18
    Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
    Date:   Fri Jul 19 17:14:28 2024 +0100

        Updated data selectors for BT display

        Merging old status bar and new DataSelector options so that they work more consistently on the BT display.

    commit bad2255710
    Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
    Date:   Thu Jul 18 09:47:47 2024 +0100

        Better symbol options

        Add clearer options button to multi option symbol manager panel.

    * Squashed commit of the following:

    commit 687220dad5
    Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
    Date:   Mon Jul 22 11:42:19 2024 +0100

        Change click data selector

        Change Click BT display so it can handle CompoundDataSelectors

    commit 577670ccd0
    Merge: 6510d226 8b5b5b2f
    Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
    Date:   Mon Jul 22 09:35:01 2024 +0100

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

    commit 6510d2260e
    Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
    Date:   Mon Jul 22 09:34:58 2024 +0100

        Remove unnecessary text output

    commit 3da8401756
    Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
    Date:   Mon Jul 22 09:29:38 2024 +0100

        updates to Daq

        New DLL, and some LED control, but hasn't fixed stalling problem.

    commit 8b5b5b2f18
    Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
    Date:   Fri Jul 19 17:14:28 2024 +0100

        Updated data selectors for BT display

        Merging old status bar and new DataSelector options so that they work more consistently on the BT display.

    commit bad2255710
    Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
    Date:   Thu Jul 18 09:47:47 2024 +0100

        Better symbol options

        Add clearer options button to multi option symbol manager panel.

    ---------

    Co-authored-by: Jamie Mac <macster110@gmail.com>

commit 687220dad5
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jul 22 11:42:19 2024 +0100

    Change click data selector

    Change Click BT display so it can handle CompoundDataSelectors

commit 577670ccd0
Merge: 6510d226 8b5b5b2f
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jul 22 09:35:01 2024 +0100

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

commit 6510d2260e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jul 22 09:34:58 2024 +0100

    Remove unnecessary text output

commit 3da8401756
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jul 22 09:29:38 2024 +0100

    updates to Daq

    New DLL, and some LED control, but hasn't fixed stalling problem.

commit 8b5b5b2f18
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jul 19 17:14:28 2024 +0100

    Updated data selectors for BT display

    Merging old status bar and new DataSelector options so that they work more consistently on the BT display.

commit bad2255710
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Jul 18 09:47:47 2024 +0100

    Better symbol options

    Add clearer options button to multi option symbol manager panel.

commit a3f41e22e6
Merge: 0165982a f7be084e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Jul 16 10:58:25 2024 +0100

    Merge pull request #85 from PAMGuard/main

    Fix vector error

commit 0165982a22
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jul 12 16:57:28 2024 +0100

    Work on localisation export

    Not ready to rock yet.

commit f24dd9bb91
Merge: 07f4398a 3f23474e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jul 12 16:38:11 2024 +0100

    Merge pull request #84 from PAMGuard/main

    Merge from main

commit 07f4398a1d
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Jun 25 09:25:10 2024 +0100

    Update .classpath

    Fix classpath file

commit 32ab9f7ead
Merge: 3a42eabd 7accb79f
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jun 24 15:43:47 2024 +0100

    Merge pull request #83 from PAMGuard/main

    V2.02.12

commit 3a42eabd74
Merge: 18a507b5 f7b4f44e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jun 24 13:58:16 2024 +0100

    Merge pull request #82 from PAMGuard/main

    Merge from main
2024-08-23 15:07:35 +01:00
Jamie Mac
4f233dd43e Update to the same format as PAMBinaries for exporting to R 2024-08-23 15:04:32 +01:00
Jamie Mac
a05c77b2fd
Update readme.md 2024-08-23 14:58:46 +01:00
Douglas Gillespie
51aa658514 Tethys updates
And get rid of some other files that had got into the repo by accident
2024-08-23 14:58:32 +01:00