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commit5b1cc760d8Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Nov 16 09:12:55 2022 +0000 Quick fix of calibration data for ST Click detector. Was getting a 5V input from it's bespoke acquisition, whereas needs 2. commit3f5e4e4a79Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Nov 15 21:08:40 2022 +0000 Final final 2.02.06 Don't believe it until you see that tag commit890230a6ffAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Nov 15 17:49:06 2022 +0000 Final final readme 2.02.06 commit05268d810dAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Nov 15 17:40:44 2022 +0000 Version 2.02.06 (#87) (hopefully) commit7d7ecb9545Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Nov 15 17:39:37 2022 +0000 Version 2.02.06 (#86) (hopefully) commit76e8467201Merge:d2f74f60ac280e1bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Nov 15 17:37:14 2022 +0000 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into main commitd2f74f606eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Nov 15 17:36:49 2022 +0000 readme for 2.02.06 commitac280e1b6fAuthor: m2oswald <45486636+m2oswald@users.noreply.github.com> Date: Tue Nov 15 15:41:43 2022 +0000 updates to Rocca module (#85) * 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 commit655a546764Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Nov 14 15:56:00 2022 +0000 Update X3 Jar commit96cd32034fAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Nov 14 15:55:37 2022 +0000 Delete x3-2.2.0.pom commitbf90443b1bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Nov 14 15:55:28 2022 +0000 Delete x3-2.2.0.jar commit22d32b4682Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Nov 14 15:54:15 2022 +0000 Update x3 jar file commit14c5cf5afeMerge:ccd0fc79376a9f0fAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Nov 14 15:49:36 2022 +0000 Merge branch 'main' into main commit376a9f0f0eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Nov 14 14:30:04 2022 +0000 Reinstate x3 jar commit93193638b1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Nov 14 14:29:37 2022 +0000 Last changes to x3 commitccd0fc7965Author: m2oswald <45486636+m2oswald@users.noreply.github.com> Date: Mon Nov 14 11:00:15 2022 +0000 small updates to Rocca (#84) * 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 commitea32c5cdcbAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sun Nov 13 17:41:13 2022 +0000 SUD Files (#83) * Adding comments to table definitions. Update tabledefs so tableitems can have descriptions. Useful to the coder, but can also export formal xms schema for each table. * Writing xml schema Writing xml schema for PAMGuard database with annotations as complex types * Working SUD click extractor Seems to be mostly working and can generate PAMGuard click files automatically when processing SUD files using the soundtrap click detector * Small changes to SUD in PAMGuard * Better SUD timing Using latest microsecond time extraction from SUD unpack * SUD Processing Extraction of SUD file clicks with SoundTrap Click Detector. Timing now correct. Added some help pages. * Functional SUD Reader and SUD Click Extractor All seems working. Seems to throw the odd exception at end of file, but works OK. commitf08cf4ffd7Merge:d3277be34a75afc4Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sun Nov 13 17:38:59 2022 +0000 Merge pull request #29 from PAMGuard/main Memory leak fix commitd3277be3b1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sun Nov 13 17:37:53 2022 +0000 Functional SUD Reader and SUD Click Extractor All seems working. Seems to throw the odd exception at end of file, but works OK. commitd1af000040Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat Nov 12 19:21:57 2022 +0000 SUD Processing Extraction of SUD file clicks with SoundTrap Click Detector. Timing now correct. Added some help pages. commit4a75afc414Merge:3b053ff3fe0fe11fAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Nov 11 20:59:10 2022 +0000 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into main commit3b053ff342Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Nov 11 20:58:42 2022 +0000 Memory leak Fix viewer memory leak whereby background measurements weren't being cleared between data loads, so eventually ran out of memory. commit068a8b1a27Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Nov 11 08:56:03 2022 +0000 Better SUD timing Using latest microsecond time extraction from SUD unpack commitee24c0ab6bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Nov 10 17:21:37 2022 +0000 Small changes to SUD in PAMGuard commit87cd2cd41fAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Nov 10 15:20:15 2022 +0000 Working SUD click extractor Seems to be mostly working and can generate PAMGuard click files automatically when processing SUD files using the soundtrap click detector commit61dd6ef4d1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Nov 8 16:42:57 2022 +0000 Writing xml schema Writing xml schema for PAMGuard database with annotations as complex types commitfcdb64e467Merge:a72e68c2fe0fe11fAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Nov 8 10:44:01 2022 +0000 Merge pull request #28 from PAMGuard/main Fix to issue #80 (#81) commitfe0fe11fafAuthor: stabbutt <100229685+stabbutt@users.noreply.github.com> Date: Tue Nov 8 01:02:52 2022 -0800 Fix to issue #80 (#81) * Fix network sender since it was hopelessly out of date and did not send data in the correct format. OK now, though only tested on NARW. * Fix network sender since it was hopelessly out of date and did not send data in the correct format. OK now, though only tested on NARW. * Mods to support command line and Network control of PAMGuard and to retrieve summary information from some modules. * Fix issue #80: recording path command line override * Allow RUNNOTHING bearing calculations Co-authored-by: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> commita72e68c26aAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Nov 7 17:15:04 2022 +0000 Adding comments to table definitions. Update tabledefs so tableitems can have descriptions. Useful to the coder, but can also export formal xms schema for each table. commit3e717bd207Merge:aa7f18ead2e69c50Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Nov 4 15:09:47 2022 +0000 Merge pull request #27 from PAMGuard/main Merge SUD changes from main commitd2e69c507eMerge:4f734b77aa7f18eaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Nov 4 15:09:40 2022 +0000 Merge branch 'main' into main commitaa7f18eaa2Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Nov 2 10:09:30 2022 +0000 SAIL CArd warnings Don't display in dialog when in nogui mode. Write to terminal commit4f734b7775Author: Jamie Mac <macster110@gmail.com> Date: Mon Oct 31 13:43:15 2022 +0000 Added sud file capability (#78) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. * Bug fix for click train logging The size of the string classifers field was dynamically set - this was a bug. * Bug fixes to the click train detector Bearing classifier section now updates properly when dialog reopened Fixed rare bug when garbage bot attempts to find the last data unit in a list of zero units. * Squashed commit of the following: commit5a37bfe915Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Aug 19 08:17:06 2022 +0100 Changes from DG branch (#50) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality * Java version Changes unpacker to deal with non numeric characters on Linux * Fix to getVersion() So new version of this command should now work on Linux and Windows. * Multiport test Quick tester for multiport comms * Spectrogram display Stop spectrogram display continually recreating panels since it was unsubscribing discarded ones and sometimes causing crash in observable notifications. * Backup manager bug Error if no database. Fixed. commitb08e86e330Author: Jamie Mac <macster110@gmail.com> Date: Wed Aug 17 09:16:52 2022 +0100 Bug fix for click train detector (#49) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. * Bug fix for click train logging The size of the string classifers field was dynamically set - this was a bug. Co-authored-by: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> commitef0330173bAuthor: Jamie Mac <macster110@gmail.com> Date: Mon Aug 8 10:32:19 2022 +0100 Click trian detector fixes (#48) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. Co-authored-by: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> * Update DLModelWorker.java * Create matched_click_classifer_help.md * Update help files for matched click classifier * Update matched_click_classifer_help.md * Update matched_click_classifer_help.md * New screenshots got help files * New screenshot * Update matched_click_classifer_help.md New help file for the matched click classified. * Update matched_click_classifer_help.md * Squashed commit of the following: commit6b15b3d536Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Aug 23 15:21:28 2022 +0100 Change min java version to 11 which should be ok on some embedded systems. commit4b3a37636bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Aug 23 14:30:46 2022 +0100 CTD Fixes Couple more fixes to menus and datablock selection commitc641c58e4fAuthor: Jamie Mac <macster110@gmail.com> Date: Tue Aug 23 14:19:28 2022 +0100 Bug fixes to click train detector (#51) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. * Bug fix for click train logging The size of the string classifers field was dynamically set - this was a bug. * Bug fixes to the click train detector Bearing classifier section now updates properly when dialog reopened Fixed rare bug when garbage bot attempts to find the last data unit in a list of zero units. * Squashed commit of the following: commit5a37bfe915Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Aug 19 08:17:06 2022 +0100 Changes from DG branch (#50) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality * Java version Changes unpacker to deal with non numeric characters on Linux * Fix to getVersion() So new version of this command should now work on Linux and Windows. * Multiport test Quick tester for multiport comms * Spectrogram display Stop spectrogram display continually recreating panels since it was unsubscribing discarded ones and sometimes causing crash in observable notifications. * Backup manager bug Error if no database. Fixed. commitb08e86e330Author: Jamie Mac <macster110@gmail.com> Date: Wed Aug 17 09:16:52 2022 +0100 Bug fix for click train detector (#49) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. * Bug fix for click train logging The size of the string classifers field was dynamically set - this was a bug. Co-authored-by: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> commitef0330173bAuthor: Jamie Mac <macster110@gmail.com> Date: Mon Aug 8 10:32:19 2022 +0100 Click trian detector fixes (#48) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised … * Bug fixes to the matched click classifier The matched click classifier was not working when an in built click classifier was used. This was caused by an index out of bounds exception in the alarm system. Added new features; * The Time base display now exports sample rate to .mat files. * Bug fix file separator on time base display so it works on mac and Linux * Matched click classifier imports the first click in a list of click structures as a template. * Changed default length for restricted bins to 2048. * Add picture for help file * Update matched_click_classifer_help.md * Update matched_click_classifer_help.md * Squashed commit of the following: commitb01cb4d100Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Sep 13 11:19:31 2022 +0100 Fix bug in 3DOffline task Problems with making catalogue of offline tasks. not important for now, but needs revisiting. commitae6e2f947bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Sep 13 09:12:34 2022 +0100 Merge Dougs fork (#53) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality * Java version Changes unpacker to deal with non numeric characters on Linux * Fix to getVersion() So new version of this command should now work on Linux and Windows. * Multiport test Quick tester for multiport comms * Spectrogram display Stop spectrogram display continually recreating panels since it was unsubscribing discarded ones and sometimes causing crash in observable notifications. * Backup manager bug Error if no database. Fixed. * Daylight saving problem Fix daylight saving problem in generation of timestamps in SQLTypes. See long explanation in SQLTypes.java. Only occurred in the hour after daylight saving starts. commitcd89c65d7cAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Sep 13 09:07:11 2022 +0100 Fix synchronization problem in RawDataTransfroms commit6b15b3d536Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Aug 23 15:21:28 2022 +0100 Change min java version to 11 which should be ok on some embedded systems. commit4b3a37636bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Aug 23 14:30:46 2022 +0100 CTD Fixes Couple more fixes to menus and datablock selection commitc641c58e4fAuthor: Jamie Mac <macster110@gmail.com> Date: Tue Aug 23 14:19:28 2022 +0100 Bug fixes to click train detector (#51) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. * Bug fix for click train logging The size of the string classifers field was dynamically set - this was a bug. * Bug fixes to the click train detector Bearing classifier section now updates properly when dialog reopened Fixed rare bug when garbage bot attempts to find the last data unit in a list of zero units. * Squashed commit of the following: commit5a37bfe915Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Aug 19 08:17:06 2022 +0100 Changes from DG branch (#50) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality * Java version Changes unpacker to deal with non numeric characters on Linux * Fix to getVersion() So new version of this command should now work on Linux and Windows. * Multiport test Quick tester for multiport comms * Spectrogram display Stop spectrogram display continually recreating panels since it was unsubscribing discarded ones and sometimes causing crash in observable notifications. * Backup manager bug Error if no database. Fixed. commitb08e86e330Author: Jamie Mac <macster110@gmail.com> Date: Wed Aug 17 09:16:52 2022 +0100 Bug fix for click train detector (#49) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. * Bug fix for click train logging The size of the string classifers field was dynamically set - this was a bug. Co-authored-by: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> commitef0330173bAuthor: Jamie Mac <macster110@gmail.com> Date: Mon Aug 8 10:32:19 2022 +0100 Click trian detector fixes (#48) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+… * Fixes to click train detector and deep learning * Squashed commit of the following: commit313ce0c46fAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Sep 21 15:55:12 2022 +0100 Help update (#60) * Plugin Help Small change to Help system so that plugins under development can more easily display their help * PamModel update Notes on how to add a plugin to the model during the plugin development phase. * Click Train Detector Help * Help for backup manager commit290f2fbb95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Sep 21 15:54:01 2022 +0100 Click Train Detector help (#59) * Plugin Help Small change to Help system so that plugins under development can more easily display their help * PamModel update Notes on how to add a plugin to the model during the plugin development phase. * Click Train Detector Help * Help for backup manager commit6aefbc124bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Sep 20 17:34:30 2022 +0100 Merge from DG fork (#58) * Plugin Help Small change to Help system so that plugins under development can more easily display their help * PamModel update Notes on how to add a plugin to the model during the plugin development phase. commiteb176a4568Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Sep 15 17:10:09 2022 +0100 Merge from dg (#57) commitdee7e1d52eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Sep 15 17:08:32 2022 +0100 Merge pull request #13 from PAMGuard/main (#56) commit1ed74bebe3Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Sep 15 17:06:22 2022 +0100 Merge pull request #13 from PAMGuard/main (#55) commitfbe39a7416Merge:0114c80425dd21Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Sep 15 17:05:16 2022 +0100 Merge branch 'main' into main commit425dd21d9fAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Sep 15 17:01:45 2022 +0100 Data selector for whistle classifier Added standard data selection options to whistle classifier output, and also made it a 'Detector' type for down stream data connections commit0114c80d61Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Sep 15 16:59:37 2022 +0100 Work on click train detector help commitc8e271734fAuthor: Jamie Mac <macster110@gmail.com> Date: Thu Sep 15 09:18:48 2022 +0100 Bug fixes to matched click classifier (#54) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. * Bug fix for click train logging The size of the string classifers field was dynamically set - this was a bug. * Bug fixes to the click train detector Bearing classifier section now updates properly when dialog reopened Fixed rare bug when garbage bot attempts to find the last data unit in a list of zero units. * Squashed commit of the following: commit5a37bfe915Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Aug 19 08:17:06 2022 +0100 Changes from DG branch (#50) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality * Java version Changes unpacker to deal with non numeric characters on Linux * Fix to getVersion() So new version of this command should now work on Linux and Windows. * Multiport test Quick tester for multiport comms * Spectrogram display Stop spectrogram display continually recreating panels since it was unsubscribing discarded ones and sometimes causing crash in observable notifications. * Backup manager bug Error if no database. Fixed. commitb08e86e330Author: Jamie Mac <macster110@gmail.com> Date: Wed Aug 17 09:16:52 2022 +0100 Bug fix for click train detector (#49) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. * Bug fix for click train logging The size of the string classifers field was dynamically set - this was a bug. Co-authored-by: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> commitef0330173bAuthor: Jamie Mac <macster110@gmail.com> Date: Mon Aug 8 10:32:19 2022 +0100 Click trian detector fixes (#48) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher t… * fix bug in TDOA * Squashed commit of the following: commit149dfab281Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Sep 30 09:56:13 2022 +0100 Work on bug fixes in CTD classifier (#72) commit91a704b07aAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Sep 30 09:54:33 2022 +0100 Work on bug fixes in CTD classifier (#71) commitd01576c855Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Sep 30 09:53:51 2022 +0100 Work on bug fixes in CTD classifier (#70) commit11bed6ffbaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Sep 29 14:56:29 2022 +0100 Work on bug fixes in CTD classifier (#69) commitfccc0a715dAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Sep 29 14:54:30 2022 +0100 Work on bug fixes in CTD classifier commit5983f30dedAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Sep 27 16:44:12 2022 +0100 Delete C:\temp\PamGuardTesting 2_02_04f\PAMBinary directory Get rid of a folder of pgdf files that Jamie had added to the repo commit075aceb4aaAuthor: Jamie Mac <macster110@gmail.com> Date: Tue Sep 27 16:41:05 2022 +0100 Click train detector bug fix (#68) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. * Bug fix for click train logging The size of the string classifers field was dynamically set - this was a bug. * Bug fixes to the click train detector Bearing classifier section now updates properly when dialog reopened Fixed rare bug when garbage bot attempts to find the last data unit in a list of zero units. * Squashed commit of the following: commit5a37bfe915Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Aug 19 08:17:06 2022 +0100 Changes from DG branch (#50) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality * Java version Changes unpacker to deal with non numeric characters on Linux * Fix to getVersion() So new version of this command should now work on Linux and Windows. * Multiport test Quick tester for multiport comms * Spectrogram display Stop spectrogram display continually recreating panels since it was unsubscribing discarded ones and sometimes causing crash in observable notifications. * Backup manager bug Error if no database. Fixed. commitb08e86e330Author: Jamie Mac <macster110@gmail.com> Date: Wed Aug 17 09:16:52 2022 +0100 Bug fix for click train detector (#49) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. * Bug fix for click train logging The size of the string classifers field was dynamically set - this was a bug. Co-authored-by: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> commitef0330173bAuthor: Jamie Mac <macster110@gmail.com> Date: Mon Aug 8 10:32:19 2022 +0100 Click trian detector fixes (#48) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) … * Click train fixes * Fixes to click train detector * Squashed commit of the following: commit3a452936c0Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Sep 30 14:50:33 2022 +0100 Fixes from DG (#74) * Work on bug fixes in CTD classifier * couple of final neatenings up of CTD commit4015461fbcAuthor: Jamie Mac <macster110@gmail.com> Date: Fri Sep 30 14:23:17 2022 +0100 Fixes to click train detector (#73) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. * Bug fix for click train logging The size of the string classifers field was dynamically set - this was a bug. * Bug fixes to the click train detector Bearing classifier section now updates properly when dialog reopened Fixed rare bug when garbage bot attempts to find the last data unit in a list of zero units. * Squashed commit of the following: commit5a37bfe915Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Aug 19 08:17:06 2022 +0100 Changes from DG branch (#50) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality * Java version Changes unpacker to deal with non numeric characters on Linux * Fix to getVersion() So new version of this command should now work on Linux and Windows. * Multiport test Quick tester for multiport comms * Spectrogram display Stop spectrogram display continually recreating panels since it was unsubscribing discarded ones and sometimes causing crash in observable notifications. * Backup manager bug Error if no database. Fixed. commitb08e86e330Author: Jamie Mac <macster110@gmail.com> Date: Wed Aug 17 09:16:52 2022 +0100 Bug fix for click train detector (#49) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. * Bug fix for click train logging The size of the string classifers field was dynamically set - this was a bug. Co-authored-by: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> commitef0330173bAuthor: Jamie Mac <macster110@gmail.com> Date: Mon Aug 8 10:32:19 2022 +0100 Click trian detector fixes (#48) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks … * Fix to click train detector NO_SPECIES flag was not being in standard classifier so beaked whales were being classified. * Getting sud files working * .sud decompression implemented Sud decompression implemented in real time and viewer mode. .sudx files hold a file map which is reloaded allowing rapid scrolling of sud files in viewer mode. * Rewrite how PAMGuard manages Audio Files PAMGuard audio file management is a mess (sorry Doug) requiring changes to code in at least 3 separate classes to make a new type of audio file work in real time and viewer mode. Have consolidated all audio file stuff into a PamAudioFileManager class which has a static getInstance() function. Any new type of audio file added in future (e.g. next is probably AudioMoth triggered recordings) then all that is needed is the Interface PamAudioFileloader to be satisfied and added to PamAudioFileManager list of audio file loaders. * Bug fix for sud in viewer mode and FX updates Fixed bug in sud file where IO exception occurred at the end of a file in viewer mode. Updates to click detector dialog in FX GUI. Updates to example sound factory. * Some more work on FX GUI * Added some validators in FX GUI ValidatorFX is awesome * Updates to FX GUI * Squashed commit of the following: commit67060016c2Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Oct 21 12:26:42 2022 +0100 REsolve issues in binayUIDFunctions commit61c3d80f30Merge:1de5ec64473d1bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Oct 21 12:23:08 2022 +0100 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into main commit1de5ec6e11Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Oct 21 12:22:09 2022 +0100 Change error reporting in Binary UID functions Message on screen rather than stack trace since it's normal when a psfx moves to a different pc commit4473d1b1bfAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Oct 21 11:12:04 2022 +0100 Merge from DG (#77) * Work on bug fixes in CTD classifier * couple of final neatenings up of CTD * DWV Import Fixed DWV importer so that a binary file is still created if a DWV file doesn't exist. this is totally normal in quiet conditions, so the correct thing to do is to generate a binary file with no data so that effort is correctly recorded. * Error reporting in -nogui A lot of warnings were being issued and trying to use the default window which caused a null pointer when running -nogui. This is fixed by a) not trying to access frames which are null and b) changing the PAMWarning system to write messages to terminal rather than open a dialog. commit63cc66a4b1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Oct 18 17:04:16 2022 +0100 Merge from DG (#76) * Work on bug fixes in CTD classifier * couple of final neatenings up of CTD * DWV Import Fixed DWV importer so that a binary file is still created if a DWV file doesn't exist. this is totally normal in quiet conditions, so the correct thing to do is to generate a binary file with no data so that effort is correctly recorded. commite4faed5cfcAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Oct 4 11:18:37 2022 +0100 Add exitnosave command Add command for UDP or terminal control which will exit PAMGuard without first saving the settings commitf4f7cc59b6Author: Jamie Mac <macster110@gmail.com> Date: Mon Oct 3 14:30:22 2022 +0100 Fix to click trian detector (#75) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. * Bug fix for click train logging The size of the string classifers field was dynamically set - this was a bug. * Bug fixes to the click train detector Bearing classifier section now updates properly when dialog reopened Fixed rare bug when garbage bot attempts to find the last data unit in a list of zero units. * Squashed commit of the following: commit5a37bfe915Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Aug 19 08:17:06 2022 +0100 Changes from DG branch (#50) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality * Java version Changes unpacker to deal with non numeric characters on Linux * Fix to getVersion() So new version of this command should now work on Linux and Windows. * Multiport test Quick tester for multiport comms * Spectrogram display Stop spectrogram display continually recreating panels since it was unsubscribing discarded ones and sometimes causing crash in observable notifications. * Backup manager bug Error if no database. Fixed. commitb08e86e330Author: Jamie Mac <macster110@gmail.com> Date: Wed Aug 17 09:16:52 2022 +0100 Bug fix for click train detector (#49) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit9a9f542d95Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:42:45 2022 +0100 Merge DG to Main (#46) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit49cd547aeeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:40:29 2022 +0100 Merge DG branch (#45) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors * UDP Control Added multiport functionality commit016cfd0da5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:35:06 2022 +0100 Dialog positioning New functions to better positions dialogs on screen commitc9f2ab3e97Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 11:13:24 2022 +0100 puch to main (#44) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors * Work on batch processing, after testing of options to autostart, autoexit and set wav file folder, database and binary store. * Update MHTClickTrainAlgorithm.java Fix unsynchronised access to a datablock in click train detector which was causing index errors. * Revamp of offline process messaging and control Includes some databsae logging of completed tasks * Offline task logging Bit more work, including notes and database storage of task reprocessing. Guess this could all become 'proper' PAMGuard data and be shown in a table on the display but that not priority enough. * Dialog packing Fix a couple of dialogs which don't back well on HDPI monitors commit55f5a3fcf1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 1 10:59:36 2022 +0100 Group detections menu Small changes to limit the number of menu items in "Add to existing group" to a maximum of 25 entries. commitb3f6c0e665Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 29 10:50:45 2022 +0100 Handle -nogui option in PamWorker PamWorker used to catalog files at startup (if a file folder input system is used). This creates a progress dialog. Stop it appearing in -nogui operations. commit8569b6b579Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 22 08:30:47 2022 +0100 Click display fixes (#41) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly 2. Component sizes in display dialog on hres monitors commit128a512ff6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 16:37:57 2022 +0100 Another attempt at stopping it crashing on a headless system Dealing with displays that get created for clickangle vetos and a call to the gui in the click train detector. commit6eaa6e4978Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 19 08:20:07 2022 +0100 nogoi fix for headless systems. (#40) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. commit9fdd30556bAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 12 15:53:07 2022 +0100 Variable sound output level (#39) Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Bug fixes to click train detector Fixed bug with number of coasts in the MHT Kernel Added an option for amplitude to have a maximum Removed print statements. * Bug fix for click train logging The size of the string classifers field was dynamically set - this was a bug. Co-authored-by: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> commitef0330173bAuthor: Jamie Mac <macster110@gmail.com> Date: Mon Aug 8 10:32:19 2022 +0100 Click trian detector fixes (#48) * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * More screenshots * Add screenshots * Update click_train_help.md * Add classifier screenshot * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update POM with latest jdl4pam * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Update pom.xml * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Update click_train_help.md * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Screenshots * Update click_train_help.md * More screenshots * Update click_train_help.md * Update click_train_help.md * Add screenshots * Add classifier screenshot * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Update click_train_help.md * Add screenshots for click train detector help * Screenshots * Update click_train_help.md * Defult option for CPOD and porpoise to click train detector. Also a minor * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Create click_train_help.md * Update click_train_help.md * Update click_train_help.md * Updates and bug fixes to click train detector and CPOD importer * Bug fix for raw spectrogram in TDDisplayFX * Update KetosClassifier.java * Fix standard classifier JSON logging * Fixed bug in sweep classifier when using SoundTrap click detections * Added some colour averaging in the TFDisplayFX spectrgoram * Bug fix for rainbow click bearings Bug fix when rainbow clicks are imported mean bearings cannot be calculated - was an array size issue in DelayGroup * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Updated the prediction plots on time display Deep learning prediciton plots on the time display have now been updated to have some colour options and also act as a legend. * Updates to TDisplayFX yFIshmael now owrks with TDisplayFX TDisplayFX UI changes to make simpler. Some abstraction for drawing lines on TDisplayFX * Merge fixes to click train detector * Bug fix to UI * Updates to FX GUI * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Merge fixes to click train detector * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Updates to click train detector New GUI for click train classification - more intuitive and allows users to build more powerful classifiers. CPOD data can now build average waveforms. CPOD click trains can be viewed in TDisplayFX pop up menu displays Fixed Peak Frequency symbol chooser so it saves the colour box settings * Screenshots * Updates and bug fixes to click train detector and CPOD importer * Fix standard classifier JSON logging * Google humpback whale deep learning classifier Google's humpback whale deep learning classifier can now be imported. Updated TDisplayFX to make the data selection panes cleaner and clearer. Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour. * Bug fix to UI * Bug fixes to FX GUI * Updates to click train detector * Squashed commit of the following: commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updates to click train detector * Squashed commit of the following: commit62b020b320Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat May 14 06:52:20 2022 +0100 Add a new offlinefileslist function commit3a9a5311aaAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Apr 27 09:43:31 2022 +0100 Update .gitignore commit9f998165eeAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon May 2 19:40:24 2022 +0100 Updates to support ContactCollator plugin (#33) * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * fix problem in SummaryComand * Update command line options * Change synchronization on RawDataTransforms soit uses the owner data holder, not itself for synchronization. Otherwise you get thread locks. * Update command line options * Update DecimatorParams.java * couple of updates to support new contact collator plugin * Sorting out sample rate info in clip display to support Contact Collator plugin * FLAC Speed Improve flac speed * Update .gitignore * Update .gitignore * Updates to support new features in Contact Collator * Small update to RawDatautils to handle null data * Updated data selector for click train detector * Click train detector updates and bug fixes Fixed very annoying bug which meant templates did not show properly when the dialog was first opened in swing. Added feature to simple classifier were % of clicks of one click classification (or other data selector paramter) can be used to classify. * Bug fix and improvements for Ketos Ketos models now automatically set the correct sample length when loaded. Bug fix for the TDisplayFX - null pointer exception if no class names loaded and sorted recently introduced bug in drawing predictions. * Updates to deep learning and FX GUI Added some more example sounds to deep learning UI. Updated click detector in the FX GUI. * PAMGuard FX sound output update * Updates to FX GUI * Updates to FX GUI * Update RawDataTransforms.java * Fixes to FX UI * Squashed commit of the following: commit11ba8bf91eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 4 11:45:47 2022 +0100 MErge from DG Branch (#47) * Variable sound output level Mods to SoundPlayback module to allow additional parameters. Implemented system for NI cards to allow changes to selected output voltage range meaning output can be boosted to level higher than current default. * Code to support nogui operations when no screens present on headless system * Fix problem of nogui headless operation trying to access screen size. * Click detector display fixes 1. ICI not displaying correctly … Co-authored-by: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> commit30793b55b0Merge:abc33adb63cc66a4Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Oct 21 11:11:03 2022 +0100 Merge pull request #26 from PAMGuard/main Merge from DG (#76) commitabc33adbfdAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Oct 21 11:09:35 2022 +0100 Error reporting in -nogui A lot of warnings were being issued and trying to use the default window which caused a null pointer when running -nogui. This is fixed by a) not trying to access frames which are null and b) changing the PAMWarning system to write messages to terminal rather than open a dialog. commit0029fbb1c1Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Oct 18 17:02:49 2022 +0100 DWV Import Fixed DWV importer so that a binary file is still created if a DWV file doesn't exist. this is totally normal in quiet conditions, so the correct thing to do is to generate a binary file with no data so that effort is correctly recorded. commit15d4468a0eMerge:68271501e4faed5cAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Oct 4 11:19:37 2022 +0100 Merge pull request #25 from PAMGuard/main Merge changes from main commit682715018fAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Sep 30 14:49:33 2022 +0100 couple of final neatenings up of CTD commitde809b6572Merge:cc003c164015461fAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Sep 30 14:24:34 2022 +0100 Merge pull request #24 from PAMGuard/main Fixes to click train detector (#73) commitcc003c167aMerge:55cd735e149dfab2Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Sep 30 14:10:59 2022 +0100 Merge pull request #23 from PAMGuard/main Work on bug fixes in CTD classifier (#72) commit55cd735ec3Merge:f899d01a91a704b0Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Sep 30 09:55:32 2022 +0100 Merge pull request #22 from PAMGuard/main merge main commitf899d01a41Merge:83f1343bfccc0a71Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Sep 29 14:55:24 2022 +0100 Merge pull request #21 from PAMGuard/main Work on bug fixes in CTD classifier commit83f1343b02Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Sep 29 14:54:52 2022 +0100 Work on bug fixes in CTD classifier commit481315187fMerge:570479ef5983f30dAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Sep 27 16:57:54 2022 +0100 Merge pull request #20 from PAMGuard/main Get CTD bug fix commit570479efcfMerge:ec4082ebcf4c97a2Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Sep 23 11:47:13 2022 +0100 Merge pull request #19 from PAMGuard/main CTD Data Selector fixes (#66)
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# Log file
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*.log
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# BlueJ files
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*.ctxt
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# Mobile Tools for Java (J2ME)
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.mtj.tmp/
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#ignore target directory
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/target/
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# Package Files remove jar from this since there is one we want. Most are in target which is excluded anyway.#
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*.notjar
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*.war
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*.nar
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*.ear
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*.zip
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*.tar.gz
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*.rar
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*.dll
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# eclipse project file
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.project
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.hprof
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# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
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hs_err_pid*
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bin/
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.classpath
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.DS_Store
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.classpath
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target/WMM.COF
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settings.xml
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.classpath
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.classpath
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.classpath
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