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1 Commits

Author SHA1 Message Date
Jamie Mac
3a74152beb Squashed commit of the following: 
commit c64fa8fe9d
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Mar 7 11:24:20 2024 +0000

    opt to easily turn off restart debug output

commit 48c5387291
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Mar 7 09:22:45 2024 +0000

    binary store count (#129)

    Fix issue in binary store object count

commit 769193703a
Merge: 308442f2 23062c3f
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Mar 7 09:16:45 2024 +0000

    Merge branch 'restart' into main

commit 308442f201
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Mar 7 09:14:33 2024 +0000

    Merge from dg dev main (#128)

    * updating Tethys help

    * added help details server connection & calibration

    * Reporting outputs to user

    Use Pamguard WarnOnce system to show a message of success or failure
    after attempting to output to Tethys.

    * Removing empty fields

    Start of implementation of code that can remove empty fields from
    objects before they are written.

    * More help documentation

    Continued writing general export help.
    Added new css style
    Added image

    * Fix type in Deployment export

    * Prevent single deployment export

    For now, disable the option to export a single Deployment document for
    multiple recording periods.

    * System to search species codes

    Search the ITIS species codes in Tethys to find ITIS codes. Search can
    be on a common or scientific name.

    * Data blocks help + species codes

    More help documentation on exporting detections/localization as well as mapping detection species codes to TSNs.  Includes supporting images

    * Improved dialog for finding species codes

    Now has a progress bar to block GUI while searching database.

    * Add species codes TOC in help

    * Documented new species search in help

    * Nilus Checker

    Can check a Nilus class to see if it's missing required objects and be
    used to remove empty fields (e.g. zero length strings) from an object.

    * fixed anchor html problem

    * Messing around with checking of required fields in nilus objects.

    * split Tethys help files into smaller chunks

    * Update button enablers

    And reinstate output of a single deployment document, with non-recording
    periods stores in the QA section

    And update help TOC for latest help documents.

    ---------

    Co-authored-by: Marie <marie.roch@sdsu.edu>

commit 23062c3ff4
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Mar 4 13:59:09 2024 +0000

    Update PamController.java

    add in debug output at start and stop

commit 85b47c86af
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Mar 4 13:05:56 2024 +0000

    exception handling

    A bit more exception handling in click train detector and output of a version 10aa/other

commit e3ffd56f69
Merge: 1200b13f e6c2f325
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Mar 4 12:28:42 2024 +0000

    Merge branch 'restart' of https://github.com/douggillespie/PAMGuard into restart

commit e6c2f325b2
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sat Mar 2 10:43:41 2024 +0000

    Binary store

    Fix err in binary footer where count of objects also included the count
    of noise measurements.

commit 45b99273fa
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Feb 27 19:09:58 2024 +0000

    Restore single param call into PamParameterSet.autoGenerate

commit c36ad2a33a
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Feb 27 15:55:02 2024 +0000

    Fix settings load.

    Problems in viewer mode with long (>50char) settings names which don't
    get fully stored in the database. Fixed by only looking at the start of
    the name. Better to not use such long names.

commit 2721095a03
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Feb 27 14:08:22 2024 +0000

    Fix compound data selector V2.02.10b

    also a bug in logger forms if malformed UDF's

commit 1200b13f95
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Feb 23 15:53:00 2024 +0000

    Exception handling in CTD

commit 156952bafe
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Feb 22 17:40:45 2024 +0000

    Update MHTClickTrainAlgorithm.java

    Synchronize calls into MHT Algorithm across threads (can mess up during restarts otherwise)

commit e491028ef7
Merge: d2263bbb 21b4bc13
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Feb 15 16:52:29 2024 +0000

    Merge pull request #66 from PAMGuard/main

    merge from main

commit d2263bbba5
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Feb 15 16:48:33 2024 +0000

    Functions for better restarting after buffer overflow.

commit 21b4bc130d
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Feb 9 11:53:35 2024 +0000

    Hydrophone data loading

    Change how hydrophone data are loaded in viewer. Don't load ALL data.
    Load the loading period + some before the load period which will be one
    minute of data PLUS an extra n*2 data before that extra minute where n
    is the number of hydrophones.

commit e52701353a
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Feb 5 13:34:15 2024 +0000

    Fix data integrity bug

    Fix of bug that 'fixed' event start and end times in database for linked
    parent / child event tables. Error was caused by a mix up between
    ParentID and ParentUID fields.

commit 66b73c45e2
Merge: 0dc47fcb 9fe8e353
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Feb 2 09:08:19 2024 +0000

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

commit 0dc47fcb0b
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Feb 2 09:07:55 2024 +0000

    click display arrangement

    Added options to NOT automatically rearrange all the windows in the
    click display every time the display size changes

commit 9609546602
Merge: 82e02a21 67e58416
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Jan 30 15:01:04 2024 +0000

    Merge pull request #65 from douggillespie/Tethys

    Tethys

commit 67e5841668
Merge: 6b184529 9fe8e353
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Jan 30 15:00:00 2024 +0000

    Merge pull request #64 from PAMGuard/main

    Merge from main

commit 9fe8e35322
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Jan 30 14:58:50 2024 +0000

    MErge from dg (#127)

    * updating Tethys help

    * added help details server connection & calibration

    * Reporting outputs to user

    Use Pamguard WarnOnce system to show a message of success or failure
    after attempting to output to Tethys.

    * Removing empty fields

    Start of implementation of code that can remove empty fields from
    objects before they are written.

    * More help documentation

    Continued writing general export help.
    Added new css style
    Added image

    * Fix type in Deployment export

    * Prevent single deployment export

    For now, disable the option to export a single Deployment document for
    multiple recording periods.

    * System to search species codes

    Search the ITIS species codes in Tethys to find ITIS codes. Search can
    be on a common or scientific name.

    * Data blocks help + species codes

    More help documentation on exporting detections/localization as well as mapping detection species codes to TSNs.  Includes supporting images

    * Improved dialog for finding species codes

    Now has a progress bar to block GUI while searching database.

    * Add species codes TOC in help

    * Documented new species search in help

    * Nilus Checker

    Can check a Nilus class to see if it's missing required objects and be
    used to remove empty fields (e.g. zero length strings) from an object.

    * fixed anchor html problem

    * Messing around with checking of required fields in nilus objects.

    * split Tethys help files into smaller chunks

    * Update button enablers

    And reinstate output of a single deployment document, with non-recording
    periods stores in the QA section

    And update help TOC for latest help documents.

    ---------

    Co-authored-by: Marie <marie.roch@sdsu.edu>

commit 1c532906ca
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Jan 30 14:57:38 2024 +0000

    Merge from dg (#126)

    * updating Tethys help

    * added help details server connection & calibration

    * Reporting outputs to user

    Use Pamguard WarnOnce system to show a message of success or failure
    after attempting to output to Tethys.

    * Removing empty fields

    Start of implementation of code that can remove empty fields from
    objects before they are written.

    * More help documentation

    Continued writing general export help.
    Added new css style
    Added image

    * Fix type in Deployment export

    * Prevent single deployment export

    For now, disable the option to export a single Deployment document for
    multiple recording periods.

    * System to search species codes

    Search the ITIS species codes in Tethys to find ITIS codes. Search can
    be on a common or scientific name.

    * Data blocks help + species codes

    More help documentation on exporting detections/localization as well as mapping detection species codes to TSNs.  Includes supporting images

    * Improved dialog for finding species codes

    Now has a progress bar to block GUI while searching database.

    * Add species codes TOC in help

    * Documented new species search in help

    * Nilus Checker

    Can check a Nilus class to see if it's missing required objects and be
    used to remove empty fields (e.g. zero length strings) from an object.

    * fixed anchor html problem

    * Messing around with checking of required fields in nilus objects.

    * split Tethys help files into smaller chunks

    * Update button enablers

    And reinstate output of a single deployment document, with non-recording
    periods stores in the QA section

    And update help TOC for latest help documents.

    ---------

    Co-authored-by: Marie <marie.roch@sdsu.edu>

commit 82e02a21b3
Merge: 8b57a398 c4192a73
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Jan 30 14:56:43 2024 +0000

    Merge pull request #63 from PAMGuard/main

    MErge from main

commit c4192a7323
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Jan 30 14:51:29 2024 +0000

    Version 2.02.10

    final commit of updated version info for release

commit 5466914d4e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Jan 30 11:55:34 2024 +0000

    Merge from dev branch (#125)

    * updating Tethys help

    * added help details server connection & calibration

    * Reporting outputs to user

    Use Pamguard WarnOnce system to show a message of success or failure
    after attempting to output to Tethys.

    * Removing empty fields

    Start of implementation of code that can remove empty fields from
    objects before they are written.

    * More help documentation

    Continued writing general export help.
    Added new css style
    Added image

    * Fix type in Deployment export

    * Prevent single deployment export

    For now, disable the option to export a single Deployment document for
    multiple recording periods.

    * System to search species codes

    Search the ITIS species codes in Tethys to find ITIS codes. Search can
    be on a common or scientific name.

    * Data blocks help + species codes

    More help documentation on exporting detections/localization as well as mapping detection species codes to TSNs.  Includes supporting images

    * Improved dialog for finding species codes

    Now has a progress bar to block GUI while searching database.

    * Add species codes TOC in help

    * Documented new species search in help

    * Nilus Checker

    Can check a Nilus class to see if it's missing required objects and be
    used to remove empty fields (e.g. zero length strings) from an object.

    * fixed anchor html problem

    * Messing around with checking of required fields in nilus objects.

    * split Tethys help files into smaller chunks

    * Update button enablers

    And reinstate output of a single deployment document, with non-recording
    periods stores in the QA section

    And update help TOC for latest help documents.

    ---------

    Co-authored-by: Marie <marie.roch@sdsu.edu>

commit 8b57a3982a
Merge: f4993425 cb0d191c
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Jan 30 11:54:17 2024 +0000

    Merge pull request #62 from PAMGuard/main

    Update README.html

commit f4993425b5
Merge: dacfab07 6b184529
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Jan 30 11:52:32 2024 +0000

    Merge pull request #61 from douggillespie/Tethys

    TethysMerge in from Tetthys

commit cb0d191c08
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jan 29 20:50:07 2024 +0000

    Update README.html

    Fix problems of weird characters in readme.html

commit 6b1845293c
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jan 29 16:54:24 2024 +0000

    Update button enablers

    And reinstate output of a single deployment document, with non-recording
    periods stores in the QA section

    And update help TOC for latest help documents.

commit 810ec67077
Author: Marie <marie.roch@sdsu.edu>
Date:   Fri Jan 26 19:56:45 2024 -0800

    split Tethys help files into smaller chunks

commit dacfab07f5
Merge: a6765d72 53ca798f
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 26 10:02:00 2024 +0000

    Merge pull request #60 from PAMGuard/main

    Correct sorting of input sound files

commit 53ca798f1b
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 26 09:57:57 2024 +0000

    Correct sorting of input sound files

commit 88be6ffe2e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Jan 25 18:04:57 2024 +0000

    Messing around with checking of required fields in nilus objects.

commit fe33930ca8
Author: Marie <marie.roch@sdsu.edu>
Date:   Wed Jan 24 11:50:20 2024 -0800

    fixed anchor html problem

commit fdfa9a20d8
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Jan 24 16:32:30 2024 +0000

    Nilus Checker

    Can check a Nilus class to see if it's missing required objects and be
    used to remove empty fields (e.g. zero length strings) from an object.

commit b78bbe8b9e
Merge: c0080ae4 a6765d72
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Jan 24 14:50:22 2024 +0000

    Merge pull request #59 from douggillespie/main

    merge from main

commit a6765d72b1
Merge: efdf17f6 5fcd3607
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Jan 24 14:46:39 2024 +0000

    Merge pull request #58 from PAMGuard/main

    Remove comments in split positioner

commit 5fcd360737
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Jan 24 14:46:05 2024 +0000

    Remove comments in split positioner

commit c0080ae4f4
Merge: f1bb6e4c efdf17f6
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Jan 24 14:37:24 2024 +0000

    Merge remote-tracking branch 'origin/main' into Tethys

    Conflicts:
    	src/help/JavaHelpSearch/DOCS
    	src/help/JavaHelpSearch/DOCS.TAB
    	src/help/JavaHelpSearch/OFFSETS
    	src/help/JavaHelpSearch/POSITIONS
    	src/help/JavaHelpSearch/SCHEMA
    	src/help/JavaHelpSearch/TMAP
    	src/help/utilities/tethys/docs/tethys_quickstart.html

commit f1bb6e4c0c
Author: Marie <marie.roch@sdsu.edu>
Date:   Tue Jan 23 14:33:50 2024 -0800

    Documented new species search in help

commit 971165b72e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Jan 23 11:12:54 2024 +0000

    Add species codes TOC in help

commit 3d7224eb93
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jan 22 18:04:57 2024 +0000

    Improved dialog for finding species codes

    Now has a progress bar to block GUI while searching database.

commit 7d30b303e7
Author: Marie <marie.roch@sdsu.edu>
Date:   Sun Jan 21 15:24:13 2024 -0800

    Data blocks help + species codes

    More help documentation on exporting detections/localization as well as mapping detection species codes to TSNs.  Includes supporting images

commit baff8d140c
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun Jan 21 21:35:34 2024 +0000

    System to search species codes

    Search the ITIS species codes in Tethys to find ITIS codes. Search can
    be on a common or scientific name.

commit 54cb0d1b08
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun Jan 21 17:01:10 2024 +0000

    Prevent single deployment export

    For now, disable the option to export a single Deployment document for
    multiple recording periods.

commit 522253b489
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun Jan 21 16:25:03 2024 +0000

    Fix type in Deployment export

commit 98bc7587b5
Merge: c8bc943f e0392de9
Author: Marie <marie.roch@sdsu.edu>
Date:   Sat Jan 20 20:01:19 2024 -0800

    Merge branch 'Tethys' of https://github.com/douggillespie/PAMGuard into Tethys

commit c8bc943ff7
Author: Marie <marie.roch@sdsu.edu>
Date:   Sat Jan 20 20:01:05 2024 -0800

    More help documentation

    Continued writing general export help.
    Added new css style
    Added image

commit e0392de9c7
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 19 17:29:12 2024 +0000

    Removing empty fields

    Start of implementation of code that can remove empty fields from
    objects before they are written.

commit 65300d719a
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 19 16:29:41 2024 +0000

    Reporting outputs to user

    Use Pamguard WarnOnce system to show a message of success or failure
    after attempting to output to Tethys.

commit fa02c9826c
Merge: 3f2e4239 7efc8242
Author: Marie <marie.roch@sdsu.edu>
Date:   Thu Jan 18 19:37:29 2024 -0800

    Merge branch 'Tethys' of https://github.com/douggillespie/PAMGuard into Tethys

commit 3f2e4239b0
Author: Marie <marie.roch@sdsu.edu>
Date:   Thu Jan 18 19:37:17 2024 -0800

    added help details server connection & calibration

commit efdf17f651
Merge: 02f1889e e5fda7f7
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Jan 18 09:39:55 2024 +0000

    Merge pull request #57 from PAMGuard/main

    merge from main

commit e5fda7f72a
Merge: 3ed9be4b 02f1889e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Jan 18 09:39:45 2024 +0000

    Merge branch 'main' into main

commit 3ed9be4bfd
Merge: 42b72960 43811c1f
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Jan 18 09:36:56 2024 +0000

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

commit 42b7296075
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Jan 18 09:36:10 2024 +0000

    Hide Tethys module

    and remove text output in splitpanepositioner

commit 02f1889e39
Merge: 0bc3968d 52bbff36
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Jan 18 09:33:26 2024 +0000

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

    Conflicts:
    	src/binaryFileStorage/BinaryStore.java

commit 43811c1f9b
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Jan 18 09:31:00 2024 +0000

    Merge from DG  (#124)

    * claspath update

    * Batch processing

    Adding functionality for offline task batch processing.

commit 52bbff36e5
Merge: 0c035aa0 b373e169
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Jan 18 09:29:50 2024 +0000

    Merge pull request #56 from PAMGuard/main

    Merge from main

commit 0bc3968dc8
Merge: 52cc8c71 a3a74adb
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Jan 17 21:28:02 2024 +0000

    Fix err in binary store

commit 0c035aa0fe
Merge: 52cc8c71 a3a74adb
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Jan 17 21:28:02 2024 +0000

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

commit 52cc8c7177
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Jan 17 21:24:04 2024 +0000

    Batch processing

    Adding functionality for offline task batch processing.

commit b373e169f2
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Jan 17 21:13:14 2024 +0000

    updating Tethys help (#123)

commit 5d83af1d42
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Jan 17 21:11:31 2024 +0000

    updating Tethys help (#122)

commit 7efc824226
Merge: d05cecaf bb17d384
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Jan 17 21:11:13 2024 +0000

    Merge branch 'main' into Tethys

commit a3a74adb78
Merge: ac1a7f87 bb17d384
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Jan 17 14:37:30 2024 +0000

    Merge pull request #55 from PAMGuard/main

    MErge from main

commit d05cecaf8b
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 12 18:57:38 2024 +0000

    updating Tethys help

commit 7a1c697319
Merge: 21fa4aff ac1a7f87
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 12 15:41:54 2024 +0000

    Merge remote-tracking branch 'origin/main' into Tethys

    Conflicts:
    	pom.xml
    	src/PamController/PamguardVersionInfo.java

commit bb17d384b3
Merge: 031f4c7a 21fa4aff
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 12 15:34:05 2024 +0000

    Merge branch 'Tethys' into main

commit ac1a7f87ac
Merge: 133da119 031f4c7a
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 12 15:29:05 2024 +0000

    Merge pull request #53 from PAMGuard/main

    changes from main

commit 031f4c7ab4
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 12 15:28:23 2024 +0000

    V 2.02.09aa with click marking bug fix

commit 217283c704
Merge: 4856a827 46d01e62
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 12 11:58:31 2024 +0000

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

commit 4856a827df
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 12 11:57:11 2024 +0000

    click labelling

    fixed a couple of problems in click labelling (Viewer mode) when clics
    were reassigned to different events.

commit df178a4122
Merge: 782057c0 133da119
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 12 10:16:35 2024 +0000

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

commit 133da119e0
Merge: f097ddce 46d01e62
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 12 10:16:12 2024 +0000

    Merge pull request #52 from PAMGuard/main

    Merge from main

commit 46d01e62db
Merge: 0e5bca51 f097ddce
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 12 10:16:00 2024 +0000

    Merge branch 'main' into main

commit 0e5bca5198
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 12 10:11:21 2024 +0000

    Update X3 lib to 2.2.7

commit 21fa4aff07
Merge: 73810b85 716eb1fa
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sat Dec 30 18:50:58 2023 +0000

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

    Conflicts:
    	src/tethys/swing/TethysMainPanel.java

commit 73810b85bf
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sat Dec 30 18:48:24 2023 +0000

    use new diider location memory

commit 7a5e8f1031
Merge: e48eb002 f097ddce
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sat Dec 30 17:39:28 2023 +0000

    Merge branch 'main' into Tethys

    Conflicts:
    	pom.xml
    	src/PamController/PamguardVersionInfo.java

commit e48eb00204
Merge: 70fbeaaf 1b8bb14e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sat Dec 30 17:37:02 2023 +0000

    Merge remote-tracking branch 'upstream/main' into Tethys

    Conflicts:
    	pom.xml
    	src/loggerForms/FormsDataDisplayTable.java

commit 70fbeaafde
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sat Dec 30 17:32:57 2023 +0000

    work on deployment wizards

commit 782057c020
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sat Dec 30 17:28:23 2023 +0000

    claspath update

commit 716eb1faa7
Merge: c63fb3f3 e29f6f05
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sat Dec 30 17:26:43 2023 +0000

    Merge branch 'Tethys' of https://github.com/douggillespie/PAMGuard into Tethys

commit c63fb3f341
Merge: 56bab82b b7cbd259
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sat Dec 30 17:07:17 2023 +0000

    Merge branch 'main' into Tethys

    Conflicts:
    	src/loggerForms/FormsDataDisplayTable.java

commit f097ddce45
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sat Dec 30 17:01:46 2023 +0000

    Split pane positioner

    Handy little class for remembering and restoring the positions of
    jSplitPane's

commit f5c3ce06ce
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Dec 29 17:55:30 2023 +0000

    Database opening from Explorer

    Sorted so that a viewer database can be opened by right clicking on a
    sqlite3 file. Requires updated installer to make appropriate registry
    changes. Will be in 2.02.10

commit e29f6f0589
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Dec 22 13:38:18 2023 +0000

    Fix Effort null pointers

    Trap a coupld of null pointer exceptions which get thrown when there are
    no acoustic data.

commit 56bab82be3
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 21 18:34:58 2023 +0000

    POM Excludes signature files

    Updated POM file to correctly exclude signature files which prevented
    PAMGuard from running from the installed version (unless these were
    manually removed from the jar file).

commit 99aa3f342c
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 21 17:07:23 2023 +0000

    Update nilus and javaclient

    Updated java client and nilus jar builds for Maven.

commit f4a42d2bb2
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 21 11:22:01 2023 +0000

    update pom to groupid tethys

commit 1b8bb14e9d
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Dec 20 16:47:18 2023 +0000

    Pre release V2.02.09f

    With release notes for V2.02.10 which is coming soon ...

commit f9a0716c0f
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Dec 20 14:51:10 2023 +0000

    Updates from DG (#120)

    * 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.

    * 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

    * Logger form plotting

    Fixed logger form plotting in Viewer so that points can find their
    correct GPS position (based on time)

    * Fix small bugs

    * Fix settings import

    not all imports working. Now seems fixed.

    ---------

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

commit b7cbd2592f
Merge: ae8839e7 639f3360
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Dec 20 14:48:30 2023 +0000

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

commit ae8839e756
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Dec 20 14:48:15 2023 +0000

    Fix settings import

    not all imports working. Now seems fixed.

commit 639f33607e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Dec 20 09:05:33 2023 +0000

    Fix small bugs

commit 3e4dd77908
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Dec 19 16:41:57 2023 +0000

    Logger form plotting

    Fixed logger form plotting in Viewer so that points can find their
    correct GPS position (based on time)

commit 1d9768b8c1
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Dec 19 16:41:57 2023 +0000

    Logger form plotting

    Fixed logger form plotting in Viewer so that points can find their
    correct GPS position (based on time)

commit 2fa91d69a5
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Dec 19 16:41:57 2023 +0000

    Logger form plotting

    Fixed logger form plotting in Viewer so that points can find their
    correct GPS position (based on time)

commit 1461808b14
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Dec 19 16:41:57 2023 +0000

    Logger form plotting

    Fixed logger form plotting in Viewer so that points can find their
    correct GPS position (based on time)

commit 54f5a5f0fb
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Dec 19 15:54:38 2023 +0000

    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

commit 0085215eff
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Dec 19 15:54:38 2023 +0000

    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

commit ea6caecc67
Merge: d200e5c2 bfbb58ea
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Dec 19 12:45:56 2023 +0000

    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.

commit d200e5c2df
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Dec 18 18:30:41 2023 +0000

    Maven stuff for nilus and javaclient

commit bfbb58ea5a
Merge: 480f55f6 d1b40c1d
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Dec 18 18:25:29 2023 +0000

    Merge pull request #51 from PAMGuard/main

    get whistle det fix

commit d1b40c1d86
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Dec 18 16:48:36 2023 +0000

    Release V2.02.09e

    fixes to WMD stub removal to make it a lot faster.

commit 3cf0a4e1e6
Merge: 25d10d54 480f55f6
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Dec 18 15:27:24 2023 +0000

    Merge remote-tracking branch 'origin/main' into Tethys

commit 291b00e1b1
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Dec 18 15:19:22 2023 +0000

    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>

commit 480f55f6e9
Merge: 2f41c986 667b68e2
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Dec 18 15:18:18 2023 +0000

    Merge pull request #50 from PAMGuard/main

    merge from main (#118)

commit 2f41c986f4
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Dec 18 14:58:24 2023 +0000

    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.

commit 1b9d80b0eb
Author: Jamie Mac <macster110@gmail.com>
Date:   Thu Dec 14 12:06:51 2023 +0000

    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!

commit 667b68e231
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Dec 18 14:09:30 2023 +0000

    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.

commit be88f4b296
Merge: 0039ff74 7a321f6d
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Dec 18 14:07:19 2023 +0000

    # WARNING: head commit changed in the meantime

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

commit 7a321f6d95
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Dec 18 13:28:38 2023 +0000

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

    This reverts commit f52a27ccf2, reversing
    changes made to 4a5c6fe52e.

commit f52a27ccf2
Merge: 4a5c6fe5 f8d2de44
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Dec 18 12:45:53 2023 +0000

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

commit 4a5c6fe52e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Dec 18 12:45:49 2023 +0000

    small fix in histograms

    small fix in histograms to avoid null

commit 25d10d54b4
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun Dec 17 19:28:03 2023 +0000

    Start Tethys Help

commit a761100ba7
Merge: c3edae51 0039ff74
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun Dec 17 12:52:36 2023 +0000

    Merge remote-tracking branch 'origin/main' into Tethys

commit c3edae516b
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun Dec 17 12:52:06 2023 +0000

    Small error handling

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 0039ff7422
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun Dec 17 12:19:18 2023 +0000

    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 2e29e9cd95
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Dec 15 17:49:39 2023 +0000

    Deployment and Detections work

    Big tidy up of Deployment and Detections output. Think it' spretty close
    to a functional system now.

commit 75d349e33c
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 14 18:52:17 2023 +0000

    Echo offline detection

    Fix up affected datablocks for offline echo detection

commit f55311ea36
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 14 18:51:42 2023 +0000

    Adding TAST trigger alarm action

    To be competed when GW provide correct string for interface

commit 760b9769d7
Merge: 4297afdc 951e3116
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 14 12:43:07 2023 +0000

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

commit 4297afdc51
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 14 12:42:41 2023 +0000

    Fix user input bug in viewer

    which created exponential copies of user comments!

commit 3059e087ac
Merge: 9a000586 87813746
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 14 12:27:14 2023 +0000

    Merge branch 'Tethys' of C:\Users\dg50\source\repos\PAMGuardTethys into
    Tethys

commit 9a0005861c
Merge: 951e3116 5b649edc
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 14 12:14:44 2023 +0000

    Merge branch 'Tethys' of C:\Users\dg50\source\repos\PAMGuardTethys into
    Tethys

commit 8781374685
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 14 11:57:44 2023 +0000

    Small changes to deployment table

commit ef92e1eea9
Merge: 02ad66db 951e3116
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 14 10:53:46 2023 +0000

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

commit 951e3116a5
Merge: 2dd90f6a b12ccf9c
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 14 10:51:17 2023 +0000

    Merge pull request #48 from PAMGuard/main

    Merge from main

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 02ad66db3b
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 14 10:33:46 2023 +0000

    User input viewer bug

    PAMGuard was marking multiline comments as changed and then relogging
    them. Led to exponential increase in database size!

commit 03483ded18
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Dec 13 17:31:35 2023 +0000

    Deployment export

    Improved deployment export interface and options.

commit 860d1bec17
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 7 20:08:17 2023 +0000

    Update Calibration export

    Stop repeating hydrophones and add two addresses to Calibrations docs

commit 9c86b41027
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 7 15:10:45 2023 +0000

    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.

commit 7721d7f1c0
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Dec 6 17:35:57 2023 +0000

    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.

commit bafe93e7f5
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Dec 6 12:20:40 2023 +0000

    SQLLogging revert

    Revert main table definition class used by SQLLogging to
    PamTableDefinition, back from EmptyTableDefinition, to maintain
    compatibility with existing plugin modules.

commit 9939e8aa85
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Dec 4 21:27:00 2023 +0000

    Calibrations Export

    Functional Calibrations export wizard and display

commit 275a53c042
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun Dec 3 18:21:09 2023 +0000

    Calibrations display

    display of calibrations documents + some general tidying up of document
    management and display.

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 2dd90f6a32
Merge: 58fe0d77 acc806d3
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Nov 15 15:02:50 2023 +0000

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

commit 58fe0d7754
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Nov 15 15:02:18 2023 +0000

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

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 6cc01fe77a
Merge: 1f8e790a 9fca879c
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Oct 27 10:06:52 2023 +0100

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

commit 9fca879c39
Merge: bff8eeeb 7a44d49e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Oct 27 10:02:47 2023 +0100

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

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 bff8eeebc5
Merge: 3da3f31b fa5fe994
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Oct 26 15:50:26 2023 +0100

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

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 1f8e790ae5
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Sep 29 13:43:49 2023 +0100

    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.

commit 773f1f542b
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun Sep 24 21:59:15 2023 +0100

    Species map i/o

commit 8257122d14
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Sep 21 18:01:41 2023 +0100

    Log Tethys output and include instrumentid in Deployment queries

commit 4d294b56a8
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Sep 19 16:55:33 2023 +0100

    Click event output

commit 5fe0927c10
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Sep 18 12:49:39 2023 +0100

    Noise logging

commit 415ec87938
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun Sep 17 21:10:23 2023 +0100

    noise output

commit 158eedce8c
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Sep 15 15:15:28 2023 +0100

    Detections output

    more work on detections output.

commit db1cc75bc1
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Sep 13 17:28:47 2023 +0100

    More output

    More changes to Detections output.

commit 85fd84d18a
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Sep 11 21:52:46 2023 +0100

    Fix binned output

    couple of fixes in binned output

commit 65dfb5688b
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Sep 11 17:47:50 2023 +0100

    More on granularity

    Nice format of granularity in display tables.

commit c221d78aa2
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Sep 11 17:07:15 2023 +0100

    Added bin granularity

    binned granularity in place. TODO Encounter granularity.

commit baca001ed8
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Sep 8 16:31:00 2023 +0100

    Param output only if not display

commit 7465243169
Merge: fb00a757 3da3f31b
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Sep 8 13:32:22 2023 +0100

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

commit 3da3f31b33
Merge: dbeaa668 3385935a
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Sep 8 13:29:37 2023 +0100

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

commit dbeaa66821
Merge: 1b5454be 60435e56
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Sep 8 13:26:11 2023 +0100

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

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.

commit fb00a757cd
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Sep 7 16:58:38 2023 +0100

    Data export

    A few fixes in Detections export.

commit 3688719e25
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Aug 31 17:06:51 2023 +0100

    Working parameter output

    Only just and not complete, but working.

commit 07ced6ae6d
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Aug 29 11:53:40 2023 +0100

    Species info

    Sort out of species info which hopefully now deals with all
    eventualities.

commit 74deebe446
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Aug 8 18:29:45 2023 +0100

    Fixed queries

    Also added internal display of existing docuemtns (so they can be
    deleted)

commit 9018176899
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Jul 20 19:06:42 2023 +0100

    ITIS Codes GUI

    Basic system in place for handling ITIS species codes.

commit 5c969d8889
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Jul 19 13:56:39 2023 +0100

    work on species mapping

commit 527aeccbb8
Merge: cd70026c 3385935a
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jul 3 18:00:53 2023 +0100

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

commit cd70026cf8
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jul 3 17:53:35 2023 +0100

    Starting to map species codes

commit 3385935aec
Merge: 68b2f3bb c3c31c33
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Jul 3 17:48:41 2023 +0100

    Merge pull request #47 from PAMGuard/main

    pull from main

commit 75470b450b
Merge: f3944e35 68b2f3bb
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jun 9 13:01:35 2023 +0100

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

    Conflicts:
    	src/PamModel/PamModel.java

commit f3944e3536
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jun 9 12:56:23 2023 +0100

    Update FolderInputSystem.java

commit 68b2f3bb53
Merge: 1b5454be b0a06300
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jun 9 12:53:30 2023 +0100

    Merge pull request #46 from PAMGuard/main

    get V2.02.08 from main

commit 3df05c3ec6
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon May 29 15:27:21 2023 +0100

    Document export

commit 36da1bcbeb
Merge: 1ea20d80 1b5454be
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon May 29 09:02:48 2023 +0100

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

commit 1b5454be91
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri May 26 10:27:25 2023 +0100

    Stop command

    small change so command is available as a constant

commit d841959171
Merge: f97f967b d350d5a7
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri May 26 09:53:08 2023 +0100

    Merge pull request #45 from PAMGuard/main

    pull from main

commit f97f967b23
Merge: 508ca524 c17208d3
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue May 23 15:46:57 2023 +0100

    Merge pull request #44 from PAMGuard/main

    Map file errors

commit 508ca524e8
Merge: becb24dc db037c6d
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri May 12 15:38:04 2023 +0100

    Merge pull request #43 from PAMGuard/main

    update from main

commit 1ea20d80ed
Merge: 49843b40 becb24dc
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon May 8 15:46:04 2023 +0100

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

commit becb24dcc5
Merge: 2953d82b 29f0bf7e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon May 8 15:43:58 2023 +0100

    Merge pull request #42 from PAMGuard/main

    X3 updates

commit 49843b405f
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun May 7 20:06:59 2023 +0100

    Some query changes

    Changes in server code required update of some of the json for existing
    queries.

commit 00410d2017
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun May 7 19:00:37 2023 +0100

    Exception handling

    Exception handling and warning messages on Tethys transactions

commit 71c8415bc8
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sat May 6 19:26:04 2023 +0100

    Playing with export options

commit 38b05b13c5
Merge: 8a9719b4 2953d82b
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sat May 6 11:15:48 2023 +0100

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

commit 8a9719b425
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon May 1 18:55:35 2023 +0100

    Tethys working again

    And a bit more playing around with metadata handling for Deploymnet
    documents

commit 379cd61afa
Merge: 4f0f4a6c f74bb5eb
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Apr 24 13:35:51 2023 +0100

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

commit 4f0f4a6c36
Merge: dfb78813 795b32e4
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Apr 13 18:04:38 2023 +0100

    Merge remote-tracking branch 'PAMGuardDGOriginal/main' into main

    Conflicts:
    	src/binaryFileStorage/BinaryStoreProcess.java
    	src/clickDetector/layoutFX/clickClassifiers/SweepClassifierSetPaneFX.java

commit dfb78813ea
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Apr 13 17:41:52 2023 +0100

    Update TethysControl.java

commit dbc8f0c682
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Apr 4 21:02:09 2023 +0100

    Men items to open collections in browser

commit 35fa8270d2
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Apr 4 20:53:14 2023 +0100

    Changes to match server updates

    Deleting now working. am automatically calling a windows curl command to
    disable the cache on the server.

commit faea94205c
Merge: 573785d9 16e8184a
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Sun Apr 2 11:15:19 2023 +0100

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

    Conflicts:
    	src/Array/ArrayDialog.java
    	src/PamModel/PamModel.java
    	src/clickDetector/layoutFX/clickClassifiers/SweepClassifierSetPaneFX.java

commit 573785d98f
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Mar 31 19:07:02 2023 +0100

    GUi Play

    Export wizard for detections

commit 4be259b76b
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Mar 29 20:57:54 2023 +0100

    GUI Play

    Experimenting with GUI components

commit 642f1da873
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Mar 22 20:07:17 2023 +0000

    updated doc names

    Dog names now match their id so it's easier to delete them from Tethys

commit c7ceba1604
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Mar 21 20:05:38 2023 +0000

    GUI Work.

    working on some GUI / control options. Semi functional. Seem to have a
    problem with time zones converting from XML time to millis which need
    sorting.

commit f51a519d82
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Mar 17 21:26:13 2023 +0000

    Start Tethys GUI

commit b344b775ec
Merge: cff6f718 ecf364f9
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Mar 16 16:35:09 2023 +0000

    Merge branch 'main' of https://github.com/douggillespie/PAMGuardTethys

commit cff6f71881
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Mar 16 16:34:03 2023 +0000

    update autoprovider

commit ecf364f999
Merge: 7f680f3e 289b0659
Author: kbolaughlin <kolaughl@ucsd.edu>
Date:   Thu Mar 16 09:14:11 2023 -0700

    Merge branch 'main' of https://github.com/douggillespie/PAMGuardTethys

commit 7f680f3e20
Author: kbolaughlin <kolaughl@ucsd.edu>
Date:   Thu Mar 16 09:13:42 2023 -0700

    fixed some deploymentData defaulting

    fixed some deploymentData defaulting

commit 289b065914
Merge: 8c3c0098 140af14c
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Mar 15 23:39:33 2023 +0000

    Merge branch 'main' of https://github.com/douggillespie/PAMGuardTethys

commit 8c3c0098da
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Mar 15 23:38:51 2023 +0000

    work

commit 140af14cba
Author: kbolaughlin <kolaughl@ucsd.edu>
Date:   Wed Mar 15 16:38:13 2023 -0700

    required field update and post to tethys fxn updates

    fill in required data for deployments/detections and minor tweaks to post to tethys fxn

commit d96ace1ca2
Merge: f15a6daf 27b8456c
Author: kbolaughlin <kolaughl@ucsd.edu>
Date:   Wed Mar 15 15:05:57 2023 -0700

    Merge branch 'main' of https://github.com/douggillespie/PAMGuardTethys

commit f15a6dafa6
Author: kbolaughlin <kolaughl@ucsd.edu>
Date:   Wed Mar 15 15:05:33 2023 -0700

    TethysExportControl

    add post to tethys code in TethysExportControl

commit 27b8456c5a
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Mar 15 22:04:13 2023 +0000

    More detection work

commit e8e947b91f
Merge: ceefa618 4876899b
Author: kbolaughlin <kolaughl@ucsd.edu>
Date:   Wed Mar 15 12:38:33 2023 -0700

    Merge branch 'main' of https://github.com/douggillespie/PAMGuardTethys

commit ceefa6188c
Author: kbolaughlin <kolaughl@ucsd.edu>
Date:   Wed Mar 15 12:38:29 2023 -0700

    Update TethysExporter.java

    updated export code to add namespace to the xml produced

commit 4876899b54
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Mar 15 18:13:11 2023 +0000

    Detections Document ready to go

commit f97247f148
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Mar 15 17:21:35 2023 +0000

    Detections output

    Working towards output of Detections ...

commit 98ce0ff9d2
Merge: 68b7d08b 3991a871
Author: kbolaughlin <kolaughl@ucsd.edu>
Date:   Tue Mar 14 14:16:02 2023 -0700

    Merge branch 'main' of https://github.com/douggillespie/PAMGuardTethys

commit 68b7d08bc6
Author: kbolaughlin <kolaughl@ucsd.edu>
Date:   Tue Mar 14 14:14:22 2023 -0700

    Update TethysExporter.java

    minor tweak

commit 3991a87102
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Mar 14 21:13:48 2023 +0000

    up[dated exporter

commit 0fad7c6cfa
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Mar 14 17:34:45 2023 +0000

    Deployment doc

    Work on deployment document population

commit 103c050d0c
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Tue Mar 14 17:28:13 2023 +0000

    Trying to Merge with KB Changes

commit 2dd870956a
Author: kbolaughlin <kolaughl@ucsd.edu>
Date:   Tue Mar 14 08:40:49 2023 -0700

    Update TethysExporter.java

    small fix

commit 8842166f43
Merge: 799c7b21 501c0ec2
Author: kbolaughlin <kolaughl@ucsd.edu>
Date:   Tue Mar 14 08:38:08 2023 -0700

    Merge branch 'main' of https://github.com/douggillespie/PAMGuardTethys

commit 799c7b218e
Author: kbolaughlin <kolaughl@ucsd.edu>
Date:   Mon Mar 13 17:27:39 2023 -0700

    Update TethysExporter.java

    file importer

commit 501c0ec292
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Mar 13 21:44:19 2023 +0000

    Deployment positions

commit 98cf904830
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Mar 13 20:45:51 2023 +0000

    first very incomplete deployment doc

commit 456f9102db
Merge: 534765d1 7d69992d
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Mar 13 18:36:36 2023 +0000

    Merge branch 'main' of https://github.com/douggillespie/PAMGuardTethys

commit 534765d1cc
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Mar 13 18:35:25 2023 +0000

    notes

commit 7d69992d44
Author: kbolaughlin <kolaughl@ucsd.edu>
Date:   Mon Mar 13 11:33:46 2023 -0700

    Update TethysExporter.java

    testing

commit 24c7baab6e
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Mar 13 18:31:04 2023 +0000

    Notes

commit 43ea481c3f
Author: kbolaughlin <kolaughl@ucsd.edu>
Date:   Mon Mar 13 11:05:10 2023 -0700

    adding deployment recovery pair

commit bfed9cfa00
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Feb 23 13:37:53 2023 +0000

    Update to Nilus 3

commit 9c10af43bc
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Feb 22 10:51:04 2023 +0000

    Added code to find acquisition settings

    This is most of the data needed for TEthys

commit f12be978aa
Merge: b2e6f85f 5b649edc
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Feb 1 10:23:39 2023 +0000

    Merge pull request #2 from douggillespie/Tethys

    Merging Tethys branch into main

commit 5b649edc19
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 27 15:13:30 2023 +0000

    Comments

    Added a couple of comments to help SDSU folk get off the ground

commit b2e6f85faf
Merge: 738c9ab6 1c11e3da
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 27 14:34:12 2023 +0000

    Merge pull request #1 from douggillespie/Tethys

    Tethys

commit 1c11e3da15
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Fri Jan 27 11:11:02 2023 +0000

    DBXM Export

    A few functions to help find data.

commit f02001a6fc
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Jan 25 16:40:03 2023 +0000

    Changes for Tethys integration

commit 5e6cd42eea
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Thu Dec 15 18:21:17 2022 +0000

    Tethys Export

    A bit of fun writing some outline functions to export data to Tethys.

commit 48716cb366
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Mon Dec 12 17:04:20 2022 +0000

    XML Settings

    Added a new log of XML settings / Effort for each module to the
    database. Had to make a lot of changes so that the base table in
    SQLLogging is of type EmptyTableDefinition, not PamTableDefinition.
    Needs a lot of testing and may break plugins using logging features.

commit 29230a5c5f
Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
Date:   Wed Nov 23 14:56:25 2022 +0000

    Better XML

    Improving XML data for each detector
 2024-03-11 14:00:32 +00:00