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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>
This commit is contained in:
Jamie Mac
GitHub
parent
7d62dfa542
commit
4f734b7775
@ -6,8 +6,9 @@
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/Java 17">
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<attributes>
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<attribute name="module" value="true"/>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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@ -16,6 +17,5 @@
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="lib" path="/X3/src/org"/>
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<classpathentry kind="output" path="target/classes"/>
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</classpath>
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117
README.html
117
README.html
@ -499,8 +499,8 @@ audio files. </span></p>
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<h2><span lang=EN-US>Bug Fixes</span></h2>
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<p class=MsoNormal><span lang=EN-US>Soundtrap DWV import. Will now generate
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binary files even if DWV file doesn’t exist (which is correct behavior in quiet
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<p class=MsoNormal><span lang=EN-US>Soundtrap DWV import. Will now generate binary
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files even if DWV file doesnt exist (which is correct behavior in quiet
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conditions when no clicks were detected). </span></p>
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<p class=MsoNormal><span lang=EN-US>Spectrogram. Changes to stop occasional
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@ -535,7 +535,7 @@ running in real time. Added template names based on file names. </p>
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<p class=MsoNormal>#13 Merging files when offline processing file folders: Had
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an error introduced in last release which caused it to fail to recognise gaps
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between files, meaning that some output data (i.e. after a gap) would have an
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incorrect time stamp. This did not affect data if the ‘merge contiguous files’
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incorrect time stamp. This did not affect data if the merge contiguous files
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option was not selected. </p>
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<p class=MsoNormal>#14 Logger forms data were not plotting correctly. This was
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@ -609,7 +609,7 @@ href="http://www.pamguard.org/downloads.php?cat_id=3">here</a>.</p>
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<p class=MsoNormal><b><span lang=EN-US>Detection Group Localiser</span></b><span
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lang=EN-US> </span></p>
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<p class=MsoNormal>This module has been renamed “Detection Grouper”, so as to
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<p class=MsoNormal>This module has been renamed Detection Grouper, so as to
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avoid confusion with the Group 3D localizer. This is because the Detection
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Grouper is more for organizing data into groups to be localized than it is for
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doing localization.</p>
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@ -730,9 +730,9 @@ included in a future release. </p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>17. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
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An implementation of the Generalized Power Law Detector, developed by Tyler
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Helble ([Helble et al., ‘A generalized power-law detection algorithm for humpback
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whale vocalizations’, The Journal of the Acoustical Society of America, vol.
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131, no. 4, pp. 2682–2699, 2012) is now available. For details, see the online
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Helble ([Helble et al., A generalized power-law detection algorithm for humpback
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whale vocalizations, The Journal of the Acoustical Society of America, vol.
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131, no. 4, pp. 26822699, 2012) is now available. For details, see the online
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help </p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>18. </span><span
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@ -755,10 +755,10 @@ Version 2.00.10</a> before proceeding with installation and use of this
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version.</b></p>
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<p class=MsoNormal>This version of PAMGuard has been bundled with Java 13
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(release 13.0.1). PSFX files generated in previous beta releases (2.xx.xx)
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should be compatible with this version, and vice-versa. PSF files generated in
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core releases (1.15.xx) can be loaded in this version, but will be converted to
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PSFX files when PAMGuard exits.</p>
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(release 13.0.1). PSFX files generated in previous beta releases (2.xx.xx) should
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be compatible with this version, and vice-versa. PSF files generated in core
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releases (1.15.xx) can be loaded in this version, but will be converted to PSFX
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files when PAMGuard exits.</p>
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<p class=MsoNormal><b><span lang=EN-US>Bug Fixes</span></b></p>
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@ -1705,8 +1705,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>10. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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</span>Bug 376. Error when using a serialised data map which spans a period of
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time in which Pamguard modules have changed.</p>
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</span>Bug 376. Error when using a serialised data map which spans a period of time
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in which Pamguard modules have changed.</p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>11. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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@ -1996,7 +1996,7 @@ file format is the addition of a Unique Data Identifier (UID) to each unit of
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data. This is intended to aid in offline analysis by making it easier for the
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user to link what they are seeing on different PAMGuard displays and also to
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link with any data post processed in Matlab or other custom analysis software.
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UID’s are also added to PAMGuard database tables. </span></p>
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UIDs are also added to PAMGuard database tables. </span></p>
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<h4><span lang=EN-US>Converting Old Data</span></h4>
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@ -2004,13 +2004,13 @@ UID
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viewer they will automatically be converted. For safety, the original binary
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files will not be overwritten and the new data will be placed in a new folder
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on your computer with the same path as the old data, but suffixed with
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‘_WithUID’, e.g. if your binary data were previously stored in the folder
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_WithUID, e.g. if your binary data were previously stored in the folder
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C:\MySurvey\binarydata the new data will be written to
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C:\MySurvey\binarydata_WithUID. </span></p>
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<p class=MsoNormal><span lang=EN-US>The additional UID column will be added to
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all database tables and populated with unique values. For data which are stored
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in both the binary files and in database tables, the same UID’s will be used in
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in both the binary files and in database tables, the same UIDs will be used in
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both data stores. </span></p>
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<h3><span lang=EN-US>New Displays</span></h3>
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@ -2116,14 +2116,14 @@ switches/parameters to be included in *.ini files.</p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>1.</span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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</span><span lang=EN-US>Bug 308. Map Overlay Control. </span>Storage of data saying
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what get's plotted on each map and for how long became corrupted and the list
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grew to a ridiculous size. Code has been put in place to a) stop it happening
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again and b) to repair any configuration files which are corrupted. Corrupted
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files will be slow to load, slow to save and will be > several megabytes in
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size. It may be necessary to delete the PamguardSettings table in any databases
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since these too may have become oversized which will slow down viewer mode
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PAMGuard start-up.</p>
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</span><span lang=EN-US>Bug 308. Map Overlay Control. </span>Storage of data
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saying what get's plotted on each map and for how long became corrupted and the
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list grew to a ridiculous size. Code has been put in place to a) stop it
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||||
happening again and b) to repair any configuration files which are corrupted.
|
||||
Corrupted files will be slow to load, slow to save and will be > several
|
||||
megabytes in size. It may be necessary to delete the PamguardSettings table in
|
||||
any databases since these too may have become oversized which will slow down viewer
|
||||
mode PAMGuard start-up.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2.</span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -2245,7 +2245,7 @@ November 2016</span></h1>
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>1.
|
||||
Bug 303. Some ASIO sound cards not working with either ASIO system in PAMGuard.
|
||||
For the PAMGuard ASIO system, this was due to a data format used by some sound
|
||||
cards never being properly implemented. For the “New ASIO system” which is
|
||||
cards never being properly implemented. For the New ASIO system which is
|
||||
based on jAsioHost, the unpacking of that format contained a bug which returned
|
||||
incorrect numbers, so data were swamped with noise. Both systems are now fixed.
|
||||
By preference, users should use the PAMGuard ASIO system since the JAsioHost
|
||||
@ -2394,9 +2394,9 @@ automatic click train identification and tracking. </span></p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>5.</span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span><span lang=EN-US>The automatic click train identification is now using
|
||||
the same internal structures as the manual tracking, so it's possible to
|
||||
combine automatic and manual tracking. </span></p>
|
||||
</span><span lang=EN-US>The automatic click train identification is now using the
|
||||
same internal structures as the manual tracking, so it's possible to combine
|
||||
automatic and manual tracking. </span></p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>6.</span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -2476,9 +2476,8 @@ today. </p>
|
||||
|
||||
<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>5.<span
|
||||
style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Bug 277. Text fields in classifier dialog were not large enough to
|
||||
display times greater than 10ms. We have increased length of text fields in the
|
||||
dialog.</p>
|
||||
</span>Bug 277. Text fields in classifier dialog were not large enough to display
|
||||
times greater than 10ms. We have increased length of text fields in the dialog.</p>
|
||||
|
||||
<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>6.<span
|
||||
style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -2496,8 +2495,8 @@ style='font-size:7.0pt;font-family:"Times New Roman",serif'> &n
|
||||
</span>Bug 279. GUI Resizing: The whole PAMGuard GUI would suddenly resize to
|
||||
something very small when a dialog is opened. This has been traced to improper
|
||||
use of a common dialog component SourcePanel which tries to repack its parent
|
||||
Window. Some programmers had inadvertently set it to repack the main PAMGuard
|
||||
GUI instead. This has been Fixed.</p>
|
||||
Window. Some programmers had inadvertently set it to repack the main PAMGuard GUI
|
||||
instead. This has been Fixed.</p>
|
||||
|
||||
<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>8.<span
|
||||
style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -2571,8 +2570,8 @@ and datagram creation.</p>
|
||||
|
||||
<h1><a name="_Toc444450394"></a><span lang=EN-US>Version 1.15.00 February 2016</span></h1>
|
||||
|
||||
<p class=MsoNormal><span lang=EN-US>Beta Version 1.15.00 64 bit and Core
|
||||
version 1.15.00 32 bit. Both using identical Java core software but linking to
|
||||
<p class=MsoNormal><span lang=EN-US>Beta Version 1.15.00 64 bit and Core version
|
||||
1.15.00 32 bit. Both using identical Java core software but linking to
|
||||
different libraries for control of sound input devices. </span></p>
|
||||
|
||||
<p class=MsoNormal><span lang=EN-US>This is the first release of a 64 bit
|
||||
@ -2818,9 +2817,9 @@ lang=EN-US>1.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times N
|
||||
</span>Spectrogram annotation marks. A simple system for marking spectrograms
|
||||
during real time analysis has been incorporated. To use it, add the module, in
|
||||
the spectrogram settings, select the annotation marks in the 'Mark Observers'
|
||||
tab of the spectrogram configuration dialog, and also right click on the spectrogram
|
||||
and select to display the annotations. Annotations are saved to the database so
|
||||
you will also need a database module in your configuration. </p>
|
||||
tab of the spectrogram configuration dialog, and also right click on the
|
||||
spectrogram and select to display the annotations. Annotations are saved to the
|
||||
database so you will also need a database module in your configuration. </p>
|
||||
|
||||
<p class=MsoListParagraph style='margin-left:47.25pt;text-indent:-29.25pt'><span
|
||||
lang=EN-US>2.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -2880,8 +2879,8 @@ minutes and seconds. Now correctly displays the number of remaining days. </p>
|
||||
|
||||
<p class=MsoListParagraph style='margin-left:47.25pt;text-indent:-29.25pt'><span
|
||||
lang=EN-US>4.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Bug 226. Spectrogram Mark Observer list doesn't refresh when modules
|
||||
added or removed. </p>
|
||||
</span>Bug 226. Spectrogram Mark Observer list doesn't refresh when modules added
|
||||
or removed. </p>
|
||||
|
||||
<p class=MsoListParagraph style='margin-left:47.25pt;text-indent:-29.25pt'><span
|
||||
lang=EN-US>5.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -3277,9 +3276,9 @@ other data sources for the PAMGuard viewer. </p>
|
||||
|
||||
<p class=MsoNormal style='margin-left:36.0pt'><i>Database</i></p>
|
||||
|
||||
<p class=MsoNormal style='margin-left:36.0pt'>Can now copy data from binary
|
||||
storage to the database offline for any module having both binary and database
|
||||
storage. </p>
|
||||
<p class=MsoNormal style='margin-left:36.0pt'>Can now copy data from binary storage
|
||||
to the database offline for any module having both binary and database storage.
|
||||
</p>
|
||||
|
||||
<p class=MsoNormal style='margin-left:36.0pt'>Can create a blank MS Access
|
||||
database (2007 and later *.accdb formats only).</p>
|
||||
@ -3471,9 +3470,9 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
|
||||
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Offline event marking. Offline event marking similar to functionality in
|
||||
RainbowClick is now available in the PAMGUARD viewer. Event summary data is
|
||||
stored in the database and can also be exported to text files (e.g. for
|
||||
importing into the Distance software). </p>
|
||||
RainbowClick is now available in the PAMGUARD viewer. Event summary data is stored
|
||||
in the database and can also be exported to text files (e.g. for importing into
|
||||
the Distance software). </p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
|
||||
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -3620,11 +3619,11 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
|
||||
|
||||
<p class=MsoNormal>2. Improved offline viewer functionality. </p>
|
||||
|
||||
<p class=MsoNormal>The offline viewer is much improved with better data
|
||||
scrolling and the ability to view data either stored in the database or the
|
||||
binary storage system. Work has stated on functions which read and use data
|
||||
stored in audio files. This is currently limited to re-calculating and
|
||||
displaying displaying spectrogram data during viewer mode operation. </p>
|
||||
<p class=MsoNormal>The offline viewer is much improved with better data scrolling
|
||||
and the ability to view data either stored in the database or the binary
|
||||
storage system. Work has stated on functions which read and use data stored in
|
||||
audio files. This is currently limited to re-calculating and displaying
|
||||
displaying spectrogram data during viewer mode operation. </p>
|
||||
|
||||
<p class=MsoNormal>3. Heading sensor readout</p>
|
||||
|
||||
@ -4137,10 +4136,10 @@ help pages</p>
|
||||
|
||||
<p class=MsoNormal><b>Bug Fixes</b></p>
|
||||
|
||||
<p class=MsoNormal>Memory leak caused by Night / Day colour manager now fixed.
|
||||
This would cause memory leaks when multiple files were being analysed off-line
|
||||
and would eventually crash PAMGUARD. The way that colours are managed in
|
||||
PAMGUARD has been rewritten. </p>
|
||||
<p class=MsoNormal>Memory leak caused by Night / Day colour manager now fixed. This
|
||||
would cause memory leaks when multiple files were being analysed off-line and
|
||||
would eventually crash PAMGUARD. The way that colours are managed in PAMGUARD
|
||||
has been rewritten. </p>
|
||||
|
||||
<p class=MsoNormal>Some issues with Swing fixed that might have been causing
|
||||
hang ups on startup especially on Macs/Linux machines</p>
|
||||
@ -4211,8 +4210,8 @@ file)</p>
|
||||
|
||||
<p class=MsoNormal><b>Changes</b></p>
|
||||
|
||||
<p class=MsoNormal>The User Input module (for text entry of information by the
|
||||
user) has been moved from the Displays sub menu of the Add Modules menu, to
|
||||
<p class=MsoNormal>The User Input module (for text entry of information by the user)
|
||||
has been moved from the Displays sub menu of the Add Modules menu, to
|
||||
Utilities. This will not affect how existing settings files are loaded. </p>
|
||||
|
||||
<p class=MsoNormal><b>Multi-screen environments.</b></p>
|
||||
@ -4383,8 +4382,8 @@ channels or textual content change. </p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
|
||||
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Model viewer. Have stopped it from jumping on top of the main PAMGUARD
|
||||
display when dialogs are closed. </p>
|
||||
</span>Model viewer. Have stopped it from jumping on top of the main PAMGUARD display
|
||||
when dialogs are closed. </p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
|
||||
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
|
||||
@ -1,21 +0,0 @@
|
||||
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
||||
<launchConfiguration type="org.eclipse.m2e.Maven2LaunchConfigurationType">
|
||||
<booleanAttribute key="M2_DEBUG_OUTPUT" value="false"/>
|
||||
<stringAttribute key="M2_GOALS" value="package shade:shade"/>
|
||||
<booleanAttribute key="M2_NON_RECURSIVE" value="false"/>
|
||||
<booleanAttribute key="M2_OFFLINE" value="false"/>
|
||||
<stringAttribute key="M2_PROFILES" value=""/>
|
||||
<listAttribute key="M2_PROPERTIES"/>
|
||||
<stringAttribute key="M2_RUNTIME" value="EMBEDDED"/>
|
||||
<booleanAttribute key="M2_SKIP_TESTS" value="true"/>
|
||||
<intAttribute key="M2_THREADS" value="1"/>
|
||||
<booleanAttribute key="M2_UPDATE_SNAPSHOTS" value="false"/>
|
||||
<stringAttribute key="M2_USER_SETTINGS" value=""/>
|
||||
<booleanAttribute key="M2_WORKSPACE_RESOLUTION" value="false"/>
|
||||
<booleanAttribute key="org.eclipse.jdt.launching.ATTR_ATTR_USE_ARGFILE" value="false"/>
|
||||
<booleanAttribute key="org.eclipse.jdt.launching.ATTR_SHOW_CODEDETAILS_IN_EXCEPTION_MESSAGES" value="true"/>
|
||||
<booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_CLASSPATH_ONLY_JAR" value="false"/>
|
||||
<stringAttribute key="org.eclipse.jdt.launching.JRE_CONTAINER" value="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-13/"/>
|
||||
<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-mx6000m -Djava.library.path=lib64"/>
|
||||
<stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${workspace_loc:/PamGuard Main DG}"/>
|
||||
</launchConfiguration>
|
||||
@ -74,9 +74,9 @@
|
||||
<artifactId>javafx-maven-plugin</artifactId>
|
||||
<version>0.0.6</version>
|
||||
<configuration>
|
||||
<source>16</source>
|
||||
<target>16</target>
|
||||
<release>16</release>
|
||||
<source>17</source>
|
||||
<target>17</target>
|
||||
<release>17</release>
|
||||
</configuration>
|
||||
</plugin>
|
||||
<plugin>
|
||||
|
||||
22
pom.xml
22
pom.xml
@ -76,9 +76,9 @@
|
||||
<artifactId>javafx-maven-plugin</artifactId>
|
||||
<version>0.0.6</version>
|
||||
<configuration>
|
||||
<source>16</source>
|
||||
<target>16</target>
|
||||
<release>16</release>
|
||||
<source>17</source>
|
||||
<target>17</target>
|
||||
<release>17</release>
|
||||
</configuration>
|
||||
</plugin>
|
||||
|
||||
@ -391,6 +391,13 @@
|
||||
<version>${javafx.version}</version>
|
||||
</dependency>
|
||||
|
||||
<!-- Decorates JavaFX components-->
|
||||
<dependency>
|
||||
<groupId>net.synedra</groupId>
|
||||
<artifactId>validatorfx</artifactId>
|
||||
<version>0.4.0</version>
|
||||
</dependency>
|
||||
|
||||
<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-compress -->
|
||||
<dependency>
|
||||
<groupId>org.apache.commons</groupId>
|
||||
@ -777,7 +784,7 @@
|
||||
<dependency>
|
||||
<groupId>pamguard.org</groupId>
|
||||
<artifactId>x3</artifactId>
|
||||
<version>2.0.0</version>
|
||||
<version>2.1.0</version>
|
||||
</dependency>
|
||||
|
||||
<!-- https://mvnrepository.com/artifact/it.sauronsoftware/jave -->
|
||||
@ -826,6 +833,13 @@
|
||||
<version>1.6.5-1</version>
|
||||
</dependency>
|
||||
|
||||
<!-- Theme for JavaFX -->
|
||||
<dependency>
|
||||
<groupId>io.github.mkpaz</groupId>
|
||||
<artifactId>atlantafx-base</artifactId>
|
||||
<version>1.0.0</version>
|
||||
</dependency>
|
||||
|
||||
|
||||
</dependencies>
|
||||
</project>
|
||||
4
repo/pamguard/org/x3/1.0.0/_remote.repositories
Normal file
4
repo/pamguard/org/x3/1.0.0/_remote.repositories
Normal file
@ -0,0 +1,4 @@
|
||||
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
|
||||
#Fri Aug 14 15:49:24 CEST 2020
|
||||
x3-1.0.0.pom>=
|
||||
x3-1.0.0.jar>=
|
||||
BIN
repo/pamguard/org/x3/1.0.0/x3-1.0.0.jar
Normal file
BIN
repo/pamguard/org/x3/1.0.0/x3-1.0.0.jar
Normal file
Binary file not shown.
9
repo/pamguard/org/x3/1.0.0/x3-1.0.0.pom
Normal file
9
repo/pamguard/org/x3/1.0.0/x3-1.0.0.pom
Normal file
@ -0,0 +1,9 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
<groupId>pamguard.org</groupId>
|
||||
<artifactId>x3</artifactId>
|
||||
<version>1.0.0</version>
|
||||
<description>POM was created from install:install-file</description>
|
||||
</project>
|
||||
4
repo/pamguard/org/x3/2.0.0/_remote.repositories
Normal file
4
repo/pamguard/org/x3/2.0.0/_remote.repositories
Normal file
@ -0,0 +1,4 @@
|
||||
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
|
||||
#Fri Sep 25 10:46:11 CEST 2020
|
||||
x3-2.0.0.pom>=
|
||||
x3-2.0.0.jar>=
|
||||
39
repo/pamguard/org/x3/2.0.0/m2e-lastUpdated.properties
Normal file
39
repo/pamguard/org/x3/2.0.0/m2e-lastUpdated.properties
Normal file
@ -0,0 +1,39 @@
|
||||
#Fri Jan 14 08:14:25 GMT 2022
|
||||
repo|file\:///Users/au671271/pamguard/PAMGuard/repo|sources=1632311094649
|
||||
central|https\://jmachund.jfrog.io/artifactory/jpam2|javadoc=1641807924466
|
||||
repo|file\:///Users/au671271/git/PAMGuard/repo|javadoc=1642148065400
|
||||
github|https\://maven.pkg.github.com/macster110/jpam|sources=1642147913185
|
||||
repo|file\:///Users/au671271/pamguard/PAMGuard_16_mvn/repo|sources=1625576160247
|
||||
icm|http\://maven.icm.edu.pl/artifactory/repo|javadoc=1600971368390
|
||||
talan|https\://nexus.talanlabs.com/content/repositories/releases/|sources=1642147913185
|
||||
geomajas|http\://maven.geomajas.org/|javadoc=1642148065400
|
||||
central|https\://repo.maven.apache.org/maven2|javadoc=1642065819015
|
||||
bedatadriven|https\://nexus.bedatadriven.com/content/groups/public/|sources=1642147913185
|
||||
repo|file\:///Users/au671271/pamguard/PAMGuard_12_mvn/repo|sources=1602589977893
|
||||
jpamutils|https\://raw.github.com/macster110/jpam/mvn-repo/|javadoc=1642065819015
|
||||
icm|http\://maven.icm.edu.pl/artifactory/repo|sources=1600971300139
|
||||
geomajas|http\://maven.geomajas.org/|sources=1642147913185
|
||||
central|https\://repo1.maven.org/maven2|sources=1642147913185
|
||||
central|https\://repo.maven.apache.org/maven2|sources=1642065813019
|
||||
github|https\://maven.pkg.github.com/macster110/jpam|javadoc=1642148065400
|
||||
bintray-jerady-maven|https\://dl.bintray.com/jerady/maven|sources=1602589977893
|
||||
bedatadriven|https\://nexus.bedatadriven.com/content/groups/public/|javadoc=1642148065400
|
||||
jpamutils|https\://raw.github.com/macster110/jpam/mvn-repo/|sources=1642065813019
|
||||
my-local-repo|file\:///Users/au671271/pamguard/PAMGuard_12_mvn/src/jars|sources=1600949483388
|
||||
repo|file\:///Users/au671271/git/PAMGuard/repo|sources=1642147913185
|
||||
bintray-macster110-jtorch4pam|macster110|https\://dl.bintray.com/macster110/jtorch4pam|javadoc=1642148065400
|
||||
jdl4pam|https\://raw.github.com/macster110/jpam/mvn-repo/|javadoc=1642065819015
|
||||
unidata-all|https\://artifacts.unidata.ucar.edu/repository/unidata-all/|sources=1642147913185
|
||||
icm|https\://maven.averbis.com/m2/|sources=1601026887474
|
||||
bintray-jerady-maven|https\://dl.bintray.com/jerady/maven|javadoc=1602590126606
|
||||
talan|https\://nexus.talanlabs.com/content/repositories/releases/|javadoc=1642148065400
|
||||
central|https\://jmachund.jfrog.io/artifactory/jpam2|sources=1641807658592
|
||||
my-local-repo|file\:///Users/au671271/pamguard/PAMGuard_12_mvn/src/jars|javadoc=1600949605299
|
||||
unidata-all|https\://artifacts.unidata.ucar.edu/repository/unidata-all/|javadoc=1642148065400
|
||||
icm|https\://maven.averbis.com/m2/|javadoc=1601027283465
|
||||
repo|file\:///Users/au671271/pamguard/PAMGuard_12_mvn/repo|javadoc=1602590126606
|
||||
jdl4pam|https\://raw.github.com/macster110/jpam/mvn-repo/|sources=1642065813019
|
||||
bintray-macster110-jtorch4pam|macster110|https\://dl.bintray.com/macster110/jtorch4pam|sources=1642147913185
|
||||
repo|file\:///Users/au671271/pamguard/PAMGuard_16_mvn/repo|javadoc=1625576167973
|
||||
repo|file\:///Users/au671271/pamguard/PAMGuard/repo|javadoc=1632313121603
|
||||
central|https\://repo1.maven.org/maven2|javadoc=1642148065400
|
||||
38
repo/pamguard/org/x3/2.0.0/x3-2.0.0-javadoc.jar.lastUpdated
Normal file
38
repo/pamguard/org/x3/2.0.0/x3-2.0.0-javadoc.jar.lastUpdated
Normal file
@ -0,0 +1,38 @@
|
||||
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
|
||||
#Fri Jan 14 08:14:25 GMT 2022
|
||||
https\://dl.bintray.com/macster110/jtorch4pam/.error=
|
||||
file\:///Users/au671271/pamguard/PAMGuard_12_mvn/src/jars/.error=
|
||||
https\://jmachund.jfrog.io/artifactory/jpam2/.lastUpdated=1625576167971
|
||||
file\:///Users/au671271/pamguard/PAMGuard/repo/.error=
|
||||
file\:///Users/au671271/pamguard/PAMGuard_16_mvn/repo/.lastUpdated=1622023729745
|
||||
https\://dl.bintray.com/macster110/jtorch4pam/.lastUpdated=1600949601867
|
||||
file\:///Users/au671271/git/PAMGuard/repo/.error=
|
||||
https\://nexus.bedatadriven.com/content/groups/public/.error=
|
||||
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.error=
|
||||
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.lastUpdated=1600949603273
|
||||
https\://maven.averbis.com/m2/.lastUpdated=1601027283464
|
||||
file\:///Users/au671271/git/PAMGuard/repo/.lastUpdated=1641807924465
|
||||
https\://raw.github.com/macster110/jpam/mvn-repo/.lastUpdated=1642065819012
|
||||
file\:///Users/au671271/pamguard/PAMGuard_16_mvn/repo/.error=
|
||||
http\://maven.icm.edu.pl/artifactory/repo/.lastUpdated=1600971368389
|
||||
https\://nexus.bedatadriven.com/content/groups/public/.lastUpdated=1600949604396
|
||||
http\://maven.icm.edu.pl/artifactory/repo/.error=
|
||||
https\://repo1.maven.org/maven2/.error=
|
||||
@default-github-https\://maven.pkg.github.com/macster110/jpam/.lastUpdated=1642148065399
|
||||
file\:///Users/au671271/pamguard/PAMGuard/repo/.lastUpdated=1632313121601
|
||||
https\://repo1.maven.org/maven2/.lastUpdated=1642148065192
|
||||
https\://dl.bintray.com/jerady/maven/.lastUpdated=1600949602327
|
||||
http\://maven.geomajas.org/.lastUpdated=1600949604068
|
||||
https\://nexus.talanlabs.com/content/repositories/releases/.error=
|
||||
file\:///Users/au671271/pamguard/PAMGuard_12_mvn/repo/.error=
|
||||
file\:///Users/au671271/pamguard/PAMGuard_12_mvn/src/jars/.lastUpdated=1600949601869
|
||||
https\://repo.maven.apache.org/maven2/.lastUpdated=1600949605299
|
||||
http\://maven.geomajas.org/.error=
|
||||
https\://jmachund.jfrog.io/artifactory/jpam2/.error=
|
||||
https\://nexus.talanlabs.com/content/repositories/releases/.lastUpdated=1600949604877
|
||||
https\://maven.averbis.com/m2/.error=
|
||||
https\://repo.maven.apache.org/maven2/.error=
|
||||
file\:///Users/au671271/pamguard/PAMGuard_12_mvn/repo/.lastUpdated=1602590126603
|
||||
https\://maven.pkg.github.com/macster110/jpam/.error=Could not transfer artifact pamguard.org\:x3\:jar\:javadoc\:2.0.0 from/to github (https\://maven.pkg.github.com/macster110/jpam)\: Access denied to https\://maven.pkg.github.com/macster110/jpam/pamguard/org/x3/2.0.0/x3-2.0.0-javadoc.jar. Error code 401,
|
||||
https\://dl.bintray.com/jerady/maven/.error=
|
||||
https\://raw.github.com/macster110/jpam/mvn-repo/.error=
|
||||
38
repo/pamguard/org/x3/2.0.0/x3-2.0.0-sources.jar.lastUpdated
Normal file
38
repo/pamguard/org/x3/2.0.0/x3-2.0.0-sources.jar.lastUpdated
Normal file
@ -0,0 +1,38 @@
|
||||
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
|
||||
#Fri Jan 14 08:11:53 GMT 2022
|
||||
https\://dl.bintray.com/macster110/jtorch4pam/.error=
|
||||
file\:///Users/au671271/pamguard/PAMGuard_12_mvn/src/jars/.error=
|
||||
https\://jmachund.jfrog.io/artifactory/jpam2/.lastUpdated=1625576160246
|
||||
file\:///Users/au671271/pamguard/PAMGuard/repo/.error=
|
||||
file\:///Users/au671271/pamguard/PAMGuard_16_mvn/repo/.lastUpdated=1622023729649
|
||||
https\://dl.bintray.com/macster110/jtorch4pam/.lastUpdated=1600949479758
|
||||
file\:///Users/au671271/git/PAMGuard/repo/.error=
|
||||
https\://nexus.bedatadriven.com/content/groups/public/.error=
|
||||
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.error=
|
||||
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.lastUpdated=1600949481209
|
||||
https\://maven.averbis.com/m2/.lastUpdated=1601026887474
|
||||
file\:///Users/au671271/git/PAMGuard/repo/.lastUpdated=1641807658590
|
||||
https\://raw.github.com/macster110/jpam/mvn-repo/.lastUpdated=1642065813017
|
||||
file\:///Users/au671271/pamguard/PAMGuard_16_mvn/repo/.error=
|
||||
http\://maven.icm.edu.pl/artifactory/repo/.lastUpdated=1600971300137
|
||||
https\://nexus.bedatadriven.com/content/groups/public/.lastUpdated=1600949482388
|
||||
http\://maven.icm.edu.pl/artifactory/repo/.error=
|
||||
https\://repo1.maven.org/maven2/.error=
|
||||
@default-github-https\://maven.pkg.github.com/macster110/jpam/.lastUpdated=1642147913184
|
||||
file\:///Users/au671271/pamguard/PAMGuard/repo/.lastUpdated=1632311094646
|
||||
https\://repo1.maven.org/maven2/.lastUpdated=1642147912977
|
||||
https\://dl.bintray.com/jerady/maven/.lastUpdated=1600949480238
|
||||
http\://maven.geomajas.org/.lastUpdated=1600949482017
|
||||
https\://nexus.talanlabs.com/content/repositories/releases/.error=
|
||||
file\:///Users/au671271/pamguard/PAMGuard_12_mvn/repo/.error=
|
||||
file\:///Users/au671271/pamguard/PAMGuard_12_mvn/src/jars/.lastUpdated=1600949479759
|
||||
https\://repo.maven.apache.org/maven2/.lastUpdated=1600949483387
|
||||
http\://maven.geomajas.org/.error=
|
||||
https\://jmachund.jfrog.io/artifactory/jpam2/.error=
|
||||
https\://nexus.talanlabs.com/content/repositories/releases/.lastUpdated=1600949482866
|
||||
https\://maven.averbis.com/m2/.error=
|
||||
https\://repo.maven.apache.org/maven2/.error=
|
||||
file\:///Users/au671271/pamguard/PAMGuard_12_mvn/repo/.lastUpdated=1602589977891
|
||||
https\://maven.pkg.github.com/macster110/jpam/.error=Could not transfer artifact pamguard.org\:x3\:jar\:sources\:2.0.0 from/to github (https\://maven.pkg.github.com/macster110/jpam)\: Access denied to https\://maven.pkg.github.com/macster110/jpam/pamguard/org/x3/2.0.0/x3-2.0.0-sources.jar. Error code 401,
|
||||
https\://dl.bintray.com/jerady/maven/.error=
|
||||
https\://raw.github.com/macster110/jpam/mvn-repo/.error=
|
||||
18
repo/pamguard/org/x3/2.0.0/x3-2.0.0.jar.lastUpdated
Normal file
18
repo/pamguard/org/x3/2.0.0/x3-2.0.0.jar.lastUpdated
Normal file
@ -0,0 +1,18 @@
|
||||
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
|
||||
#Thu Sep 24 13:58:55 CEST 2020
|
||||
https\://dl.bintray.com/macster110/jtorch4pam/.error=
|
||||
file\:///Users/au671271/pamguard/PAMGuard_12_mvn/src/jars/.error=
|
||||
https\://dl.bintray.com/macster110/jtorch4pam/.lastUpdated=1600948677455
|
||||
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.error=
|
||||
https\://nexus.bedatadriven.com/content/groups/public/.error=
|
||||
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.lastUpdated=1600948714963
|
||||
https\://dl.bintray.com/jerady/maven/.lastUpdated=1600948680041
|
||||
http\://maven.geomajas.org/.lastUpdated=1600948729479
|
||||
https\://nexus.talanlabs.com/content/repositories/releases/.error=
|
||||
file\:///Users/au671271/pamguard/PAMGuard_12_mvn/src/jars/.lastUpdated=1600948677498
|
||||
https\://repo.maven.apache.org/maven2/.lastUpdated=1600948686447
|
||||
http\://maven.geomajas.org/.error=
|
||||
https\://nexus.talanlabs.com/content/repositories/releases/.lastUpdated=1600948735430
|
||||
https\://repo.maven.apache.org/maven2/.error=
|
||||
https\://dl.bintray.com/jerady/maven/.error=
|
||||
https\://nexus.bedatadriven.com/content/groups/public/.lastUpdated=1600948734692
|
||||
@ -1 +0,0 @@
|
||||
851e2c9b153f1686858523e69d78da20
|
||||
@ -1 +0,0 @@
|
||||
4d89dd98cf0188bb3bfe4afd74dc427ce23d3a41
|
||||
18
repo/pamguard/org/x3/2.0.0/x3-2.0.0.pom.lastUpdated
Normal file
18
repo/pamguard/org/x3/2.0.0/x3-2.0.0.pom.lastUpdated
Normal file
@ -0,0 +1,18 @@
|
||||
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
|
||||
#Thu Sep 24 13:57:29 CEST 2020
|
||||
https\://dl.bintray.com/macster110/jtorch4pam/.error=
|
||||
file\:///Users/au671271/pamguard/PAMGuard_12_mvn/src/jars/.error=
|
||||
https\://dl.bintray.com/macster110/jtorch4pam/.lastUpdated=1600948647604
|
||||
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.error=
|
||||
https\://nexus.bedatadriven.com/content/groups/public/.error=
|
||||
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.lastUpdated=1600948648002
|
||||
https\://dl.bintray.com/jerady/maven/.lastUpdated=1600948647670
|
||||
http\://maven.geomajas.org/.lastUpdated=1600948648672
|
||||
https\://nexus.talanlabs.com/content/repositories/releases/.error=
|
||||
file\:///Users/au671271/pamguard/PAMGuard_12_mvn/src/jars/.lastUpdated=1600948647606
|
||||
https\://repo.maven.apache.org/maven2/.lastUpdated=1600948649503
|
||||
http\://maven.geomajas.org/.error=
|
||||
https\://nexus.talanlabs.com/content/repositories/releases/.lastUpdated=1600948649324
|
||||
https\://repo.maven.apache.org/maven2/.error=
|
||||
https\://dl.bintray.com/jerady/maven/.error=
|
||||
https\://nexus.bedatadriven.com/content/groups/public/.lastUpdated=1600948648816
|
||||
@ -1 +0,0 @@
|
||||
e09a0e45701b683f485aedf1349cab24
|
||||
@ -1 +0,0 @@
|
||||
45129eae7b4f9c502cceffe8358fdc7e19ceaa39
|
||||
4
repo/pamguard/org/x3/2.1.0/_remote.repositories
Normal file
4
repo/pamguard/org/x3/2.1.0/_remote.repositories
Normal file
@ -0,0 +1,4 @@
|
||||
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
|
||||
#Tue Oct 11 15:59:57 BST 2022
|
||||
x3-2.1.0.jar>=
|
||||
x3-2.1.0.pom>=
|
||||
13
repo/pamguard/org/x3/2.1.0/m2e-lastUpdated.properties
Normal file
13
repo/pamguard/org/x3/2.1.0/m2e-lastUpdated.properties
Normal file
@ -0,0 +1,13 @@
|
||||
#Thu Oct 06 15:38:43 BST 2022
|
||||
bedatadriven|https\://nexus.bedatadriven.com/content/groups/public/|javadoc=1665067123455
|
||||
repo|file\:///Users/au671271/git/PAMGuard/repo|javadoc=1665067123455
|
||||
repo|file\:///Users/au671271/git/PAMGuard/repo|sources=1665067040129
|
||||
talan|https\://nexus.talanlabs.com/content/repositories/releases/|sources=1665067040129
|
||||
bintray-macster110-jtorch4pam|macster110|https\://dl.bintray.com/macster110/jtorch4pam|javadoc=1665067123455
|
||||
bedatadriven|https\://nexus.bedatadriven.com/content/groups/public/|sources=1665067040129
|
||||
unidata-all|https\://artifacts.unidata.ucar.edu/repository/unidata-all/|sources=1665067040129
|
||||
talan|https\://nexus.talanlabs.com/content/repositories/releases/|javadoc=1665067123455
|
||||
central|https\://repo1.maven.org/maven2|sources=1665067040129
|
||||
unidata-all|https\://artifacts.unidata.ucar.edu/repository/unidata-all/|javadoc=1665067123455
|
||||
bintray-macster110-jtorch4pam|macster110|https\://dl.bintray.com/macster110/jtorch4pam|sources=1665067040129
|
||||
central|https\://repo1.maven.org/maven2|javadoc=1665067123455
|
||||
14
repo/pamguard/org/x3/2.1.0/x3-2.1.0-javadoc.jar.lastUpdated
Normal file
14
repo/pamguard/org/x3/2.1.0/x3-2.1.0-javadoc.jar.lastUpdated
Normal file
@ -0,0 +1,14 @@
|
||||
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
|
||||
#Thu Oct 06 15:38:43 BST 2022
|
||||
@default-talan-https\://nexus.talanlabs.com/content/repositories/releases/.lastUpdated=1665067122194
|
||||
https\://dl.bintray.com/macster110/jtorch4pam/.error=Could not transfer artifact pamguard.org\:x3\:jar\:javadoc\:2.1.0 from/to bintray-macster110-jtorch4pam (https\://dl.bintray.com/macster110/jtorch4pam)\: Remote host terminated the handshake
|
||||
https\://repo1.maven.org/maven2/.error=
|
||||
file\:///Users/au671271/git/PAMGuard/repo/.error=
|
||||
https\://nexus.bedatadriven.com/content/groups/public/.error=
|
||||
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.error=
|
||||
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.lastUpdated=1665067121806
|
||||
https\://repo1.maven.org/maven2/.lastUpdated=1665067123455
|
||||
https\://nexus.talanlabs.com/content/repositories/releases/.error=Could not transfer artifact pamguard.org\:x3\:jar\:javadoc\:2.1.0 from/to talan (https\://nexus.talanlabs.com/content/repositories/releases/)\: Access denied to https\://nexus.talanlabs.com/content/repositories/releases/pamguard/org/x3/2.1.0/x3-2.1.0-javadoc.jar. Error code 401, Unauthorized
|
||||
file\:///Users/au671271/git/PAMGuard/repo/.lastUpdated=1665067120886
|
||||
4d1f727a0c17e3b21ef2f6654eed0b3113a4db97@default-bintray-macster110-jtorch4pam-https\://dl.bintray.com/macster110/jtorch4pam/.lastUpdated=1665067120883
|
||||
https\://nexus.bedatadriven.com/content/groups/public/.lastUpdated=1665067122025
|
||||
14
repo/pamguard/org/x3/2.1.0/x3-2.1.0-sources.jar.lastUpdated
Normal file
14
repo/pamguard/org/x3/2.1.0/x3-2.1.0-sources.jar.lastUpdated
Normal file
@ -0,0 +1,14 @@
|
||||
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
|
||||
#Thu Oct 06 15:37:20 BST 2022
|
||||
@default-talan-https\://nexus.talanlabs.com/content/repositories/releases/.lastUpdated=1665067039941
|
||||
https\://dl.bintray.com/macster110/jtorch4pam/.error=Could not transfer artifact pamguard.org\:x3\:jar\:sources\:2.1.0 from/to bintray-macster110-jtorch4pam (https\://dl.bintray.com/macster110/jtorch4pam)\: Remote host terminated the handshake
|
||||
https\://repo1.maven.org/maven2/.error=
|
||||
file\:///Users/au671271/git/PAMGuard/repo/.error=
|
||||
https\://nexus.bedatadriven.com/content/groups/public/.error=
|
||||
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.error=
|
||||
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.lastUpdated=1665067039627
|
||||
https\://repo1.maven.org/maven2/.lastUpdated=1665067040128
|
||||
https\://nexus.talanlabs.com/content/repositories/releases/.error=Could not transfer artifact pamguard.org\:x3\:jar\:sources\:2.1.0 from/to talan (https\://nexus.talanlabs.com/content/repositories/releases/)\: Access denied to https\://nexus.talanlabs.com/content/repositories/releases/pamguard/org/x3/2.1.0/x3-2.1.0-sources.jar. Error code 401, Unauthorized
|
||||
file\:///Users/au671271/git/PAMGuard/repo/.lastUpdated=1665067038933
|
||||
4d1f727a0c17e3b21ef2f6654eed0b3113a4db97@default-bintray-macster110-jtorch4pam-https\://dl.bintray.com/macster110/jtorch4pam/.lastUpdated=1665067038929
|
||||
https\://nexus.bedatadriven.com/content/groups/public/.lastUpdated=1665067039782
|
||||
BIN
repo/pamguard/org/x3/2.1.0/x3-2.1.0.jar
Normal file
BIN
repo/pamguard/org/x3/2.1.0/x3-2.1.0.jar
Normal file
Binary file not shown.
9
repo/pamguard/org/x3/2.1.0/x3-2.1.0.pom
Normal file
9
repo/pamguard/org/x3/2.1.0/x3-2.1.0.pom
Normal file
@ -0,0 +1,9 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
<groupId>pamguard.org</groupId>
|
||||
<artifactId>x3</artifactId>
|
||||
<version>2.1.0</version>
|
||||
<description>POM was created from install:install-file</description>
|
||||
</project>
|
||||
16
repo/pamguard/org/x3/2.1.0/x3-2.1.0.pom.lastUpdated
Normal file
16
repo/pamguard/org/x3/2.1.0/x3-2.1.0.pom.lastUpdated
Normal file
@ -0,0 +1,16 @@
|
||||
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
|
||||
#Thu Oct 06 15:51:34 BST 2022
|
||||
@default-talan-https\://nexus.talanlabs.com/content/repositories/releases/.lastUpdated=1665067894494
|
||||
https\://dl.bintray.com/macster110/jtorch4pam/.error=Could not transfer artifact pamguard.org\:x3\:pom\:2.1.0 from/to bintray-macster110-jtorch4pam (https\://dl.bintray.com/macster110/jtorch4pam)\: Remote host terminated the handshake
|
||||
@default-repo-file\://${project.basedir}/repo/.lastUpdated=1665067029837
|
||||
https\://repo1.maven.org/maven2/.error=
|
||||
file\:///Users/au671271/git/PAMGuard/repo/.error=
|
||||
https\://nexus.bedatadriven.com/content/groups/public/.error=
|
||||
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.error=
|
||||
https\://artifacts.unidata.ucar.edu/repository/unidata-all/.lastUpdated=1665067032579
|
||||
https\://repo1.maven.org/maven2/.lastUpdated=1665067036872
|
||||
https\://nexus.talanlabs.com/content/repositories/releases/.error=Could not transfer artifact pamguard.org\:x3\:pom\:2.1.0 from/to talan (https\://nexus.talanlabs.com/content/repositories/releases/)\: Access denied to https\://nexus.talanlabs.com/content/repositories/releases/pamguard/org/x3/2.1.0/x3-2.1.0.pom. Error code 401, Unauthorized
|
||||
file\://${project.basedir}/repo/.error=Could not transfer artifact pamguard.org\:x3\:pom\:2.1.0 from/to repo (file\://${project.basedir}/repo)\: Repository path /repo does not exist, and cannot be created.
|
||||
file\:///Users/au671271/git/PAMGuard/repo/.lastUpdated=1665067033714
|
||||
4d1f727a0c17e3b21ef2f6654eed0b3113a4db97@default-bintray-macster110-jtorch4pam-https\://dl.bintray.com/macster110/jtorch4pam/.lastUpdated=1665067894257
|
||||
https\://nexus.bedatadriven.com/content/groups/public/.lastUpdated=1665067034011
|
||||
@ -1,12 +0,0 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<metadata>
|
||||
<groupId>pamguard.org</groupId>
|
||||
<artifactId>x3</artifactId>
|
||||
<versioning>
|
||||
<release>2.0.0</release>
|
||||
<versions>
|
||||
<version>2.0.0</version>
|
||||
</versions>
|
||||
<lastUpdated>20200929205724</lastUpdated>
|
||||
</versioning>
|
||||
</metadata>
|
||||
@ -1 +0,0 @@
|
||||
47ffb77b88155d037480604e508371ff
|
||||
@ -1 +0,0 @@
|
||||
9c238e70383b552aaaf3161eaeee8ed238d90ff8
|
||||
@ -15,7 +15,7 @@ import javax.swing.JTextArea;
|
||||
import javax.swing.SwingWorker;
|
||||
import javax.swing.border.TitledBorder;
|
||||
|
||||
import PamUtils.PamAudioFileFilter;
|
||||
import Acquisition.pamAudio.PamAudioFileFilter;
|
||||
import PamView.dialog.PamDialog;
|
||||
|
||||
public class CheckWavFileHeaders extends PamDialog {
|
||||
|
||||
@ -47,6 +47,8 @@ import wavFiles.ByteConverter;
|
||||
import Acquisition.filedate.FileDate;
|
||||
import Acquisition.filedate.FileDateDialogStrip;
|
||||
import Acquisition.filedate.FileDateObserver;
|
||||
import Acquisition.pamAudio.PamAudioFileManager;
|
||||
import Acquisition.pamAudio.PamAudioFileFilter;
|
||||
import Acquisition.pamAudio.PamAudioSystem;
|
||||
import PamController.PamControlledUnitSettings;
|
||||
import PamController.PamController;
|
||||
@ -54,7 +56,6 @@ import PamController.PamSettingManager;
|
||||
import PamController.PamSettings;
|
||||
import PamDetection.RawDataUnit;
|
||||
import PamModel.SMRUEnable;
|
||||
import PamUtils.PamAudioFileFilter;
|
||||
import PamUtils.PamCalendar;
|
||||
import PamUtils.PamFileChooser;
|
||||
import PamView.dialog.PamLabel;
|
||||
@ -408,7 +409,7 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
// acquisitionDialog.NotifyChange();
|
||||
if (file.isFile() && !file.isHidden() && acquisitionDialog != null) {
|
||||
try {
|
||||
AudioInputStream audioStream = PamAudioSystem.getAudioInputStream(file);
|
||||
AudioInputStream audioStream = PamAudioFileManager.getInstance().getAudioInputStream(file);
|
||||
|
||||
// // Get additional information from the header if it's a wav file.
|
||||
// if (WavFileInputStream.class.isAssignableFrom(audioStream.getClass())) {
|
||||
@ -537,6 +538,7 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
}
|
||||
|
||||
public File getCurrentFile() {
|
||||
System.out.println("fileInputParameters: " + fileInputParameters);
|
||||
if (fileInputParameters.recentFiles == null) return null;
|
||||
if (fileInputParameters.recentFiles.size() < 1) return null;
|
||||
String fileName = fileInputParameters.recentFiles.get(0);
|
||||
@ -559,8 +561,11 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
public boolean prepareInputFile() {
|
||||
|
||||
File currentFile = getCurrentFile();
|
||||
// System.out.printf("*********************************** Opening file %s\n", currentFile.getName());
|
||||
if (currentFile == null) return false;
|
||||
if (currentFile == null) {
|
||||
System.out.println("The current file was null");
|
||||
return false;
|
||||
}
|
||||
System.out.printf("*********************************** Opening file %s\n", currentFile.getName());
|
||||
|
||||
try {
|
||||
|
||||
@ -568,7 +573,7 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
audioStream.close();
|
||||
}
|
||||
|
||||
audioStream = PamAudioSystem.getAudioInputStream(currentFile);
|
||||
audioStream = PamAudioFileManager.getInstance().getAudioInputStream(currentFile);
|
||||
|
||||
if (audioStream == null) {
|
||||
return false;
|
||||
@ -645,7 +650,8 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
|
||||
String audioFileStr = getCurrentFile()==null? "Null File": getCurrentFile().getAbsolutePath();
|
||||
|
||||
System.err.println("FileInputSystem: runFileAnalysis: AudioFilr format is null: " + audioFileStr);
|
||||
System.err.println("FileInputSystem: runFileAnalysis: AudioFile format is null: " + audioFileStr);
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
|
||||
@ -28,11 +28,12 @@ import Acquisition.layoutFX.DAQSettingsPane;
|
||||
import Acquisition.layoutFX.FolderInputPane;
|
||||
import javafx.application.Platform;
|
||||
import pamguard.GlobalArguments;
|
||||
import Acquisition.pamAudio.PamAudioFileManager;
|
||||
import Acquisition.pamAudio.PamAudioFileFilter;
|
||||
import Acquisition.pamAudio.PamAudioSystem;
|
||||
import PamController.PamControlledUnitSettings;
|
||||
import PamController.PamController;
|
||||
import PamController.PamSettings;
|
||||
import PamUtils.PamAudioFileFilter;
|
||||
import PamUtils.PamCalendar;
|
||||
import PamUtils.PamFileChooser;
|
||||
import PamUtils.PamFileFilter;
|
||||
@ -429,6 +430,8 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings{
|
||||
File aFile = files[0];
|
||||
setNewFile(aFile.getAbsolutePath());
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
* The file chooser is returning sub classes of File which are not
|
||||
* serialisable, so we can't use them. We need to convert their
|
||||
@ -505,7 +508,7 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings{
|
||||
if (file.isFile() && !file.isHidden() && acquisitionDialog != null) {
|
||||
//Hidden files should not be used in analysis...
|
||||
try {
|
||||
audioStream = PamAudioSystem.getAudioInputStream(file);
|
||||
audioStream = PamAudioFileManager.getInstance().getAudioInputStream(file);
|
||||
AudioFormat audioFormat = audioStream.getFormat();
|
||||
fileSamples = audioStream.getFrameLength();
|
||||
acquisitionDialog.setSampleRate(audioFormat.getSampleRate());
|
||||
@ -568,6 +571,7 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings{
|
||||
|
||||
@Override
|
||||
public File getCurrentFile() {
|
||||
//System.out.println("All files: " + allFiles);
|
||||
if (allFiles != null && allFiles.size() > currentFile) {
|
||||
return allFiles.get(currentFile);
|
||||
}
|
||||
|
||||
@ -10,6 +10,7 @@ import java.util.Arrays;
|
||||
import java.util.Calendar;
|
||||
import java.util.Date;
|
||||
|
||||
import javax.sound.sampled.AudioFormat;
|
||||
import javax.sound.sampled.AudioInputStream;
|
||||
import javax.sound.sampled.UnsupportedAudioFileException;
|
||||
import javax.sound.sampled.AudioFormat.Encoding;
|
||||
@ -25,10 +26,11 @@ import org.jflac.metadata.StreamInfo;
|
||||
import org.jflac.util.ByteData;
|
||||
|
||||
import wavFiles.ByteConverter;
|
||||
import Acquisition.pamAudio.PamAudioFileManager;
|
||||
import Acquisition.pamAudio.PamAudioFileFilter;
|
||||
import Acquisition.pamAudio.PamAudioSystem;
|
||||
import PamDetection.RawDataUnit;
|
||||
import PamUtils.FileParts;
|
||||
import PamUtils.PamAudioFileFilter;
|
||||
import PamUtils.PamCalendar;
|
||||
import PamUtils.PamFileFilter;
|
||||
import PamUtils.PamUtils;
|
||||
@ -150,7 +152,7 @@ public class RonaInputSystem extends FolderInputSystem {
|
||||
audioStreams[i].close();
|
||||
}
|
||||
|
||||
audioStreams[i] = PamAudioSystem.getAudioInputStream(findChannelFile(currentFile, i, 2));
|
||||
audioStreams[i] = PamAudioFileManager.getInstance().getAudioInputStream(findChannelFile(currentFile, i, 2));
|
||||
|
||||
audioFormat = audioStreams[i].getFormat();
|
||||
|
||||
|
||||
@ -5,7 +5,7 @@ import java.util.ArrayList;
|
||||
import Acquisition.AudioFileFuncs;
|
||||
import Acquisition.FolderInputSystem;
|
||||
import Acquisition.WavFileFuncs;
|
||||
import PamUtils.PamAudioFileFilter;
|
||||
import Acquisition.pamAudio.PamAudioFileFilter;
|
||||
import javafx.geometry.Insets;
|
||||
import javafx.application.Platform;
|
||||
import javafx.beans.property.SimpleDoubleProperty;
|
||||
|
||||
@ -11,10 +11,9 @@ import org.controlsfx.glyphfont.Glyph;
|
||||
import Acquisition.FileInputParameters;
|
||||
import Acquisition.FolderInputParameters;
|
||||
import Acquisition.FolderInputSystem;
|
||||
import Acquisition.pamAudio.PamAudioFileFilter;
|
||||
import PamController.PamController;
|
||||
import PamController.PamFolders;
|
||||
import PamController.SettingsPane;
|
||||
import PamUtils.PamAudioFileFilter;
|
||||
import PamUtils.PamCalendar;
|
||||
import PamUtils.worker.PamWorker;
|
||||
import PamUtils.worker.filelist.FileListData;
|
||||
@ -24,7 +23,6 @@ import javafx.beans.property.SimpleIntegerProperty;
|
||||
import javafx.beans.property.SimpleStringProperty;
|
||||
import javafx.collections.FXCollections;
|
||||
import javafx.collections.ObservableList;
|
||||
import javafx.geometry.Insets;
|
||||
import javafx.geometry.Pos;
|
||||
import javafx.scene.Node;
|
||||
import javafx.scene.control.CheckBox;
|
||||
@ -48,7 +46,6 @@ import pamViewFX.fxNodes.PamComboBox;
|
||||
import pamViewFX.fxNodes.PamHBox;
|
||||
import pamViewFX.fxNodes.PamProgressBar;
|
||||
import pamViewFX.fxNodes.PamVBox;
|
||||
import pamViewFX.fxNodes.utilityPanes.PamToggleSwitch;
|
||||
|
||||
/**
|
||||
* Pane for the folder input of the sound acquisition.
|
||||
@ -626,7 +623,7 @@ public class FolderInputPane extends DAQSettingsPane<FolderInputParameters>{
|
||||
return;
|
||||
}
|
||||
|
||||
System.out.println("File list worker: " + worker );
|
||||
//System.out.println("File list worker: " + worker );
|
||||
//must ensure this is on the FX thread
|
||||
//Platform.runLater(()->{
|
||||
this.progressBar.progressProperty().bind(worker.getPamWorkProgress().getProgressProperty());
|
||||
|
||||
@ -2,31 +2,22 @@ package Acquisition.offlineFuncs;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileFilter;
|
||||
import java.io.FileInputStream;
|
||||
import java.io.FileNotFoundException;
|
||||
import java.io.IOException;
|
||||
import java.util.Iterator;
|
||||
|
||||
import javax.sound.sampled.AudioFormat;
|
||||
import javax.sound.sampled.AudioInputStream;
|
||||
import javax.sound.sampled.UnsupportedAudioFileException;
|
||||
import javax.sound.sampled.AudioFormat.Encoding;
|
||||
|
||||
import org.jflac.FLACDecoder;
|
||||
import org.jflac.PCMProcessor;
|
||||
import org.jflac.metadata.Metadata;
|
||||
import org.jflac.metadata.StreamInfo;
|
||||
import org.jflac.sound.spi.FlacAudioFileReader;
|
||||
import org.jflac.util.ByteData;
|
||||
|
||||
import Acquisition.filedate.FileDate;
|
||||
import Acquisition.pamAudio.PamAudioSystem;
|
||||
import Acquisition.pamAudio.PamAudioFileManager;
|
||||
import Acquisition.pamAudio.PamAudioFileLoader;
|
||||
import Acquisition.pamAudio.PamAudioFileFilter;
|
||||
import PamController.OfflineFileDataStore;
|
||||
import PamDetection.RawDataUnit;
|
||||
import PamUtils.PamAudioFileFilter;
|
||||
import PamUtils.PamCalendar;
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import PamguardMVC.PamRawDataBlock;
|
||||
import PamguardMVC.dataOffline.OfflineDataLoadInfo;
|
||||
import dataMap.OfflineDataMap;
|
||||
import dataMap.filemaps.FileDataMapPoint;
|
||||
@ -37,18 +28,13 @@ import wavFiles.ByteConverter;
|
||||
/**
|
||||
* This has been split off from OfflineFileServer so that OfflineFileServer can be used with
|
||||
* other file types.
|
||||
* @author dg50
|
||||
* @author Doug Gillespie
|
||||
*
|
||||
*/
|
||||
public class OfflineWavFileServer extends OfflineFileServer<FileDataMapPoint> {
|
||||
|
||||
private FileDate fileDate;
|
||||
|
||||
private ByteConverter byteConverter;
|
||||
|
||||
private AudioInputStream audioInputStream;
|
||||
private AudioFormat audioFormat;
|
||||
|
||||
public OfflineWavFileServer(OfflineFileDataStore offlineRawDataStore, FileDate fileDate) {
|
||||
super(offlineRawDataStore);
|
||||
this.fileDate = fileDate;
|
||||
@ -109,7 +95,10 @@ public class OfflineWavFileServer extends OfflineFileServer<FileDataMapPoint> {
|
||||
continue;
|
||||
}
|
||||
}
|
||||
file = mapPoint.getSoundFile();/*
|
||||
file = mapPoint.getSoundFile();
|
||||
|
||||
//TODO - this should be integrated into the PamAudioFileManager.
|
||||
/*
|
||||
* Now need to open file file as an input stream (what a bore !)
|
||||
*/
|
||||
AudioInputStream audioStream;
|
||||
@ -139,7 +128,7 @@ public class OfflineWavFileServer extends OfflineFileServer<FileDataMapPoint> {
|
||||
}
|
||||
else {
|
||||
try {
|
||||
audioStream = PamAudioSystem.getAudioInputStream(file);
|
||||
audioStream = PamAudioFileManager.getInstance().getAudioInputStream(file);
|
||||
if (audioStream == null) {
|
||||
it.remove();
|
||||
continue;
|
||||
@ -166,302 +155,7 @@ public class OfflineWavFileServer extends OfflineFileServer<FileDataMapPoint> {
|
||||
|
||||
}
|
||||
|
||||
private boolean loadWavData(PamDataBlock dataBlock, OfflineDataLoadInfo offlineDataLoadInfo,
|
||||
ViewLoadObserver loadObserver) {
|
||||
|
||||
// Debug.out.println("OfflineFileServer: Load Wav Data: " + offlineDataLoadInfo.getCurrentObserver().getObserverName() );
|
||||
OfflineDataMap<FileDataMapPoint> dataMap = getDataMap();
|
||||
Iterator<FileDataMapPoint> mapIt = dataMap.getListIterator();
|
||||
FileDataMapPoint mapPoint = findFirstMapPoint(mapIt, offlineDataLoadInfo.getStartMillis(), offlineDataLoadInfo.getEndMillis());
|
||||
if (openSoundFile(mapPoint.getSoundFile()) == false) {
|
||||
System.out.println("Could not open .wav sound file " + mapPoint.getSoundFile().getAbsolutePath());
|
||||
return false;
|
||||
}
|
||||
File soundFile;
|
||||
|
||||
byteConverter = ByteConverter.createByteConverter(audioFormat);
|
||||
long currentTime = mapPoint.getStartTime();
|
||||
long prevFileEnd = mapPoint.getEndTime();
|
||||
boolean fileGap = false;
|
||||
int newSamples;
|
||||
double[][] doubleData;
|
||||
int nChannels = audioFormat.getChannels();
|
||||
int blockSamples = Math.max((int) audioFormat.getSampleRate() / 10, 1000);
|
||||
int frameSize = audioFormat.getFrameSize();
|
||||
if (frameSize < 0) {
|
||||
frameSize = audioFormat.getChannels()*audioFormat.getSampleSizeInBits()/8;
|
||||
}
|
||||
if (frameSize <= 0) {
|
||||
System.out.println("The frame size is less than zero " + mapPoint.getSoundFile().getAbsolutePath());
|
||||
return false;
|
||||
}
|
||||
byte[] inputBuffer = new byte[blockSamples * frameSize];
|
||||
int bytesRead = 0;
|
||||
long totalSamples = 0;
|
||||
// long fileSamples = 0;
|
||||
long millisecondsGaps = 0;
|
||||
long ms;
|
||||
|
||||
RawDataUnit newDataUnit;
|
||||
long skipped = 0;
|
||||
if (currentTime < offlineDataLoadInfo.getStartMillis()) {
|
||||
// need to fast forward in current file.
|
||||
long skipBytes = (long) (((offlineDataLoadInfo.getStartMillis()-currentTime)*audioFormat.getSampleRate()*audioFormat.getFrameSize())/1000.);
|
||||
try {
|
||||
skipped = audioInputStream.skip(skipBytes);
|
||||
// Debug.out.println("Skipped " + skipped);
|
||||
} catch (IOException e) {
|
||||
/**
|
||||
* The datamap point may be longer than the actual file here ? In any case, with the
|
||||
* NEMO data which is 5 mins per hour, this get's hit for the file before the
|
||||
* file we want every time !
|
||||
*/
|
||||
// System.out.println("End of audio file " + mapPoint.getSoundFile().getName());
|
||||
e.printStackTrace();
|
||||
}
|
||||
currentTime = offlineDataLoadInfo.getStartMillis();
|
||||
}
|
||||
ms = currentTime;
|
||||
while (ms < offlineDataLoadInfo.getEndMillis() && currentTime < offlineDataLoadInfo.getEndMillis()) {
|
||||
if (offlineDataLoadInfo.cancel) {
|
||||
//add the position we got to
|
||||
offlineDataLoadInfo.setLastLoadInfo(new AquisitionLoadPoint(ms, bytesRead));
|
||||
|
||||
|
||||
break;
|
||||
}
|
||||
try {
|
||||
bytesRead = audioInputStream.read(inputBuffer);
|
||||
} catch (IOException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
if (bytesRead <= 0) {
|
||||
skipped = 0 ; //reset ot zero because were not skipping anyu bytes here.
|
||||
/*
|
||||
* that's the end of that file, so get the next one if there
|
||||
* is one, if not then break.
|
||||
*/
|
||||
if (mapIt.hasNext() == false) {
|
||||
break;
|
||||
}
|
||||
mapPoint = mapIt.next();
|
||||
fileGap = (mapPoint.getStartTime() - prevFileEnd) > 1000;
|
||||
// if (fileGap) {
|
||||
// System.out.println(String.format("Sound file gap %3.3fs from %s to %s",
|
||||
// (double) (mapPoint.getStartTime()-prevFileEnd) / 1000.,
|
||||
// PamCalendar.formatTime(prevFileEnd), PamCalendar.formatTime(mapPoint.getStartTime())));
|
||||
// }
|
||||
prevFileEnd = mapPoint.getEndTime();
|
||||
if (!fileGap) { // don't carry on if there is a file gap
|
||||
if (openSoundFile(mapPoint.getSoundFile()) == false) {
|
||||
break;
|
||||
}
|
||||
// try again to read data.
|
||||
try {
|
||||
bytesRead = audioInputStream.read(inputBuffer);
|
||||
} catch (IOException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
if (bytesRead <= 0) {
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
newSamples = bytesRead / frameSize;
|
||||
doubleData = new double[nChannels][newSamples];
|
||||
int convertedSamples = byteConverter.bytesToDouble(inputBuffer, doubleData, bytesRead);
|
||||
ms = getOfflineRawDataStore().getParentProcess().absSamplesToMilliseconds(totalSamples);
|
||||
ms = currentTime + (long)(totalSamples * 1000 / (double) audioFormat.getSampleRate());
|
||||
|
||||
for (int ichan = 0; ichan < nChannels; ichan++) {
|
||||
|
||||
newDataUnit = new RawDataUnit(ms, 1 << ichan, totalSamples, newSamples);
|
||||
newDataUnit.setFileSamples(totalSamples + skipped / frameSize); //set the number samples into the wav file.
|
||||
newDataUnit.setRawData(doubleData[ichan], true);
|
||||
|
||||
//System.out.println("New wav data: " + PamCalendar.formatDateTime(newDataUnit.getTimeMilliseconds()));
|
||||
getRawDataBlock().addPamData(newDataUnit);
|
||||
}
|
||||
if (fileGap) {
|
||||
currentTime = mapPoint.getStartTime();
|
||||
totalSamples = 0;
|
||||
// fileSamples = 0;
|
||||
}
|
||||
|
||||
totalSamples += newSamples;
|
||||
// fileSamples += newSamples;
|
||||
}
|
||||
|
||||
// System.out.println("Finished loading wav: " + offlineDataLoadInfo.getCurrentObserver().getObserverName() );
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
private boolean loadFlacData(PamDataBlock dataBlock, OfflineDataLoadInfo offlineDataLoadInfo,
|
||||
ViewLoadObserver loadObserver) {
|
||||
// System.out.println(String.format("Load flac data from "));
|
||||
/*
|
||||
* Only seem able to read whole flac files - so read the whole file
|
||||
* and just output samples of interest to data units. A bit crude,
|
||||
* but will probably not be too slow.
|
||||
*/
|
||||
OfflineDataMap<FileDataMapPoint> dataMap = this.getDataMap();
|
||||
Iterator<FileDataMapPoint> mapIt = dataMap.getListIterator();
|
||||
FileDataMapPoint mapPoint;
|
||||
File soundFile;
|
||||
mapPoint = findFirstMapPoint(mapIt, offlineDataLoadInfo.getStartMillis(), offlineDataLoadInfo.getEndMillis());
|
||||
if (mapPoint == null) {
|
||||
return false;
|
||||
}
|
||||
while (mapPoint != null) {
|
||||
|
||||
// AudioInputStream inputStream;
|
||||
// try {
|
||||
// inputStream = new FlacAudioFileReader().getAudioInputStream(mapPoint.getSoundFile());
|
||||
// } catch (UnsupportedAudioFileException | IOException e1) {
|
||||
// // TODO Auto-generated catch block
|
||||
// e1.printStackTrace();
|
||||
// }
|
||||
FileInputStream fileStream;
|
||||
try {
|
||||
fileStream = new FileInputStream(mapPoint.getSoundFile());
|
||||
} catch (FileNotFoundException e) {
|
||||
e.printStackTrace();
|
||||
return false;
|
||||
}
|
||||
FLACDecoder flacDecoder = new FLACDecoder(fileStream);
|
||||
// Metadata metaData[] = null;
|
||||
// try {
|
||||
// metaData = flacDecoder.readMetadata();
|
||||
// } catch (IOException e) {
|
||||
// // TODO Auto-generated catch block
|
||||
// e.printStackTrace();
|
||||
// }
|
||||
flacDecoder.addPCMProcessor(new FlacPCM(mapPoint, dataBlock, fileStream,
|
||||
offlineDataLoadInfo, loadObserver));
|
||||
// StreamInfo streamInfo = flacDecoder.getStreamInfo(); // returns null !
|
||||
try {
|
||||
flacDecoder.decode();
|
||||
} catch (IOException e) {
|
||||
// TODO Auto-generated catch block
|
||||
// e.printStackTrace();
|
||||
return false;
|
||||
}
|
||||
if (mapIt.hasNext() == false) {
|
||||
break;
|
||||
}
|
||||
mapPoint = mapIt.next();
|
||||
if (mapPoint.getStartTime() > offlineDataLoadInfo.getEndMillis()) {
|
||||
break;
|
||||
}
|
||||
}
|
||||
return true;
|
||||
}
|
||||
|
||||
/**
|
||||
* Only seem to be able to
|
||||
* @author doug
|
||||
*
|
||||
*/
|
||||
private class FlacPCM implements PCMProcessor {
|
||||
|
||||
private FileInputStream fileStream;
|
||||
private int frameSize;
|
||||
private long fileSamples;
|
||||
private int nChannels;
|
||||
private FileDataMapPoint mapPoint;
|
||||
private int totalSamples;
|
||||
private int sampleRate;
|
||||
private ViewLoadObserver loadObserver;
|
||||
private PamRawDataBlock dataBlock;
|
||||
private OfflineDataLoadInfo offlineDataLoadInfo;
|
||||
|
||||
|
||||
long ms=-1;
|
||||
|
||||
public FlacPCM(FileDataMapPoint mapPoint, PamDataBlock dataBlock, FileInputStream fileStream, OfflineDataLoadInfo offlineDataLoadInfo, ViewLoadObserver loadObserver) {
|
||||
this.mapPoint = mapPoint;
|
||||
this.dataBlock = (PamRawDataBlock) dataBlock;
|
||||
this.fileStream = fileStream;
|
||||
this.loadObserver = loadObserver;
|
||||
this.offlineDataLoadInfo=offlineDataLoadInfo;
|
||||
// System.out.printf("New FLAC decoder %s working from %s to %s\n", offlineDataLoadInfo.toString(),
|
||||
// PamCalendar.formatDBDateTime(offlineDataLoadInfo.getStartMillis()),
|
||||
// PamCalendar.formatDBDateTime(offlineDataLoadInfo.getEndMillis()));
|
||||
}
|
||||
|
||||
@Override
|
||||
public void processPCM(ByteData byteData) {
|
||||
if (offlineDataLoadInfo.cancel) {
|
||||
|
||||
try {
|
||||
fileStream.close();
|
||||
ms = Math.max(offlineDataLoadInfo.getStartMillis(), ms);
|
||||
offlineDataLoadInfo.setLastLoadInfo(new AquisitionLoadPoint(ms, -1));
|
||||
} catch (IOException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
ms = mapPoint.getStartTime() + (long)totalSamples * 1000L / (long)sampleRate;
|
||||
// System.out.println(String.format("PCM data at %s samps %d (load %s - %s)", PamCalendar.formatTime2(ms, 3), totalSamples,
|
||||
// PamCalendar.formatTime2(dataStart, 3), PamCalendar.formatTime2(dataEnd, 3)));
|
||||
if (ms > offlineDataLoadInfo.getEndMillis()) {
|
||||
try {
|
||||
fileStream.close();
|
||||
} catch (IOException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
return;
|
||||
}
|
||||
int newSamples = byteData.getLen() / frameSize;
|
||||
if (ms >= offlineDataLoadInfo.getStartMillis()) {
|
||||
double[][] doubleData = new double[nChannels][newSamples];
|
||||
byteConverter.bytesToDouble(byteData.getData(), doubleData, byteData.getLen());
|
||||
RawDataUnit newDataUnit = null;
|
||||
for (int ichan = 0; ichan < nChannels; ichan++) {
|
||||
|
||||
newDataUnit = new RawDataUnit(ms, 1 << ichan, totalSamples, newSamples);
|
||||
newDataUnit.setRawData(doubleData[ichan]);
|
||||
|
||||
dataBlock.addPamData(newDataUnit);
|
||||
|
||||
// GetOutputDataBlock().addPamData(pamDataUnit);
|
||||
}
|
||||
}
|
||||
// System.out.println(String.format("new samps %d at %s", newSamples, PamCalendar.formatTime(ms, 3)));
|
||||
|
||||
totalSamples += newSamples;
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void processStreamInfo(StreamInfo streamInfo) {
|
||||
frameSize = streamInfo.getChannels() * streamInfo.getBitsPerSample() / 8;
|
||||
byteConverter = ByteConverter.createByteConverter(streamInfo.getBitsPerSample() / 8, false, Encoding.PCM_SIGNED);
|
||||
fileSamples = streamInfo.getTotalSamples();
|
||||
nChannels = streamInfo.getChannels();
|
||||
sampleRate = streamInfo.getSampleRate();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private boolean openSoundFile(File soundFile) {
|
||||
|
||||
try {
|
||||
audioInputStream = PamAudioSystem.getAudioInputStream(soundFile);
|
||||
if (audioInputStream == null) return false;
|
||||
audioFormat = audioInputStream.getFormat();
|
||||
} catch (UnsupportedAudioFileException e) {
|
||||
e.printStackTrace();
|
||||
} catch (IOException e) {
|
||||
e.printStackTrace();
|
||||
return false;
|
||||
}
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean loadData(PamDataBlock dataBlock, OfflineDataLoadInfo offlineLoadDataInfo, ViewLoadObserver loadObserver) {
|
||||
@ -482,34 +176,17 @@ public class OfflineWavFileServer extends OfflineFileServer<FileDataMapPoint> {
|
||||
if (mapPoint == null) {
|
||||
return false;
|
||||
}
|
||||
if (mapPoint.getSoundFile().getName().toLowerCase().endsWith(".flac")) {
|
||||
return loadFlacData(dataBlock, offlineLoadDataInfo, loadObserver);
|
||||
}
|
||||
// if (mapPoint.getSoundFile().getName().toLowerCase().endsWith(".wav")) {
|
||||
if (isStandardAudio(mapPoint.getSoundFile().getName())) {
|
||||
return loadWavData(dataBlock, offlineLoadDataInfo, loadObserver);
|
||||
}
|
||||
|
||||
return true;
|
||||
}
|
||||
PamAudioFileLoader audioFile = PamAudioFileManager.getInstance().getAudioLoader(mapPoint.getSoundFile());
|
||||
|
||||
private String[] standardAudioTypes = {".wav", ".aif", ".aiff"};
|
||||
|
||||
/**
|
||||
* Is it a standard aif or wav audio file which can be opened with the standard reader ?
|
||||
* @param fileName
|
||||
* @return
|
||||
*/
|
||||
private boolean isStandardAudio(String fileName) {
|
||||
if (fileName == null) {
|
||||
if (audioFile==null) {
|
||||
System.err.println("OfflineWavFileServer: could not find audio loader for mapped sound file: " + mapPoint.getSoundFile());
|
||||
return false;
|
||||
}
|
||||
fileName = fileName.toLowerCase();
|
||||
for (int i = 0; i < standardAudioTypes.length; i++) {
|
||||
if (fileName.endsWith(standardAudioTypes[i])) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
|
||||
return audioFile.loadAudioData(this, dataBlock, offlineLoadDataInfo, loadObserver);
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
236
src/Acquisition/pamAudio/FlacAudioFile.java
Normal file
236
src/Acquisition/pamAudio/FlacAudioFile.java
Normal file
@ -0,0 +1,236 @@
|
||||
package Acquisition.pamAudio;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileInputStream;
|
||||
import java.io.FileNotFoundException;
|
||||
import java.io.IOException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.Iterator;
|
||||
|
||||
import javax.sound.sampled.AudioInputStream;
|
||||
import javax.sound.sampled.UnsupportedAudioFileException;
|
||||
import javax.sound.sampled.AudioFormat.Encoding;
|
||||
|
||||
import org.jflac.FLACDecoder;
|
||||
import org.jflac.PCMProcessor;
|
||||
import org.jflac.metadata.StreamInfo;
|
||||
import org.jflac.sound.spi.FlacAudioFileReader;
|
||||
import org.jflac.util.ByteData;
|
||||
|
||||
import Acquisition.offlineFuncs.AquisitionLoadPoint;
|
||||
import PamDetection.RawDataUnit;
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import PamguardMVC.PamRawDataBlock;
|
||||
import PamguardMVC.dataOffline.OfflineDataLoadInfo;
|
||||
import dataMap.OfflineDataMap;
|
||||
import dataMap.filemaps.FileDataMapPoint;
|
||||
import dataMap.filemaps.OfflineFileServer;
|
||||
import pamScrollSystem.ViewLoadObserver;
|
||||
import wavFiles.ByteConverter;
|
||||
|
||||
|
||||
/**
|
||||
* Opens a Flac compressed audio files.
|
||||
*
|
||||
* @author Jamie Macaulay, Doug Gillespie
|
||||
*
|
||||
*/
|
||||
public class FlacAudioFile implements PamAudioFileLoader {
|
||||
|
||||
|
||||
/**
|
||||
* Get the file extensions associated with loading these data.
|
||||
*/
|
||||
private ArrayList<String> fileExtensions;
|
||||
|
||||
public FlacAudioFile() {
|
||||
fileExtensions = new ArrayList<String>(Arrays.asList(new String[]{".flac"}));
|
||||
}
|
||||
|
||||
@Override
|
||||
public ArrayList<String> getFileExtensions() {
|
||||
return fileExtensions;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getName() {
|
||||
return "FLAC";
|
||||
}
|
||||
|
||||
@Override
|
||||
public AudioInputStream getAudioStream(File soundFile) {
|
||||
if (soundFile != null && isFlacFile(soundFile)) {
|
||||
try {
|
||||
return new FlacAudioFileReader().getAudioInputStream(soundFile);
|
||||
}
|
||||
catch (UnsupportedAudioFileException | IOException e) {
|
||||
System.err.println("Could not open flac file: " + soundFile.getName());
|
||||
return null;
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean loadAudioData(OfflineFileServer offlineFileServer, PamDataBlock dataBlock, OfflineDataLoadInfo offlineDataLoadInfo,
|
||||
ViewLoadObserver loadObserver) {
|
||||
// System.out.println(String.format("Load flac data from "));
|
||||
/*
|
||||
* Only seem able to read whole flac files - so read the whole file
|
||||
* and just output samples of interest to data units. A bit crude,
|
||||
* but will probably not be too slow.
|
||||
*/
|
||||
OfflineDataMap<FileDataMapPoint> dataMap = offlineFileServer.getDataMap();
|
||||
Iterator<FileDataMapPoint> mapIt = dataMap.getListIterator();
|
||||
FileDataMapPoint mapPoint;
|
||||
File soundFile;
|
||||
mapPoint = offlineFileServer.findFirstMapPoint(mapIt, offlineDataLoadInfo.getStartMillis(), offlineDataLoadInfo.getEndMillis());
|
||||
if (mapPoint == null) {
|
||||
return false;
|
||||
}
|
||||
while (mapPoint != null) {
|
||||
|
||||
// AudioInputStream inputStream;
|
||||
// try {
|
||||
// inputStream = new FlacAudioFileReader().getAudioInputStream(mapPoint.getSoundFile());
|
||||
// } catch (UnsupportedAudioFileException | IOException e1) {
|
||||
// // TODO Auto-generated catch block
|
||||
// e1.printStackTrace();
|
||||
// }
|
||||
FileInputStream fileStream;
|
||||
try {
|
||||
fileStream = new FileInputStream(mapPoint.getSoundFile());
|
||||
} catch (FileNotFoundException e) {
|
||||
e.printStackTrace();
|
||||
return false;
|
||||
}
|
||||
FLACDecoder flacDecoder = new FLACDecoder(fileStream);
|
||||
// Metadata metaData[] = null;
|
||||
// try {
|
||||
// metaData = flacDecoder.readMetadata();
|
||||
// } catch (IOException e) {
|
||||
// // TODO Auto-generated catch block
|
||||
// e.printStackTrace();
|
||||
// }
|
||||
flacDecoder.addPCMProcessor(new FlacPCM(mapPoint, dataBlock, fileStream,
|
||||
offlineDataLoadInfo, loadObserver));
|
||||
// StreamInfo streamInfo = flacDecoder.getStreamInfo(); // returns null !
|
||||
try {
|
||||
flacDecoder.decode();
|
||||
} catch (IOException e) {
|
||||
// TODO Auto-generated catch block
|
||||
// e.printStackTrace();
|
||||
return false;
|
||||
}
|
||||
if (mapIt.hasNext() == false) {
|
||||
break;
|
||||
}
|
||||
mapPoint = mapIt.next();
|
||||
if (mapPoint.getStartTime() > offlineDataLoadInfo.getEndMillis()) {
|
||||
break;
|
||||
}
|
||||
}
|
||||
return true;
|
||||
}
|
||||
|
||||
/**
|
||||
* Only seem to be able to
|
||||
* @author doug
|
||||
*
|
||||
*/
|
||||
private class FlacPCM implements PCMProcessor {
|
||||
|
||||
private FileInputStream fileStream;
|
||||
private int frameSize;
|
||||
private long fileSamples;
|
||||
private int nChannels;
|
||||
private FileDataMapPoint mapPoint;
|
||||
private int totalSamples;
|
||||
private int sampleRate;
|
||||
private ViewLoadObserver loadObserver;
|
||||
private PamRawDataBlock dataBlock;
|
||||
private OfflineDataLoadInfo offlineDataLoadInfo;
|
||||
|
||||
|
||||
long ms=-1;
|
||||
private ByteConverter byteConverter;
|
||||
|
||||
public FlacPCM(FileDataMapPoint mapPoint, PamDataBlock dataBlock, FileInputStream fileStream, OfflineDataLoadInfo offlineDataLoadInfo, ViewLoadObserver loadObserver) {
|
||||
this.mapPoint = mapPoint;
|
||||
this.dataBlock = (PamRawDataBlock) dataBlock;
|
||||
this.fileStream = fileStream;
|
||||
this.loadObserver = loadObserver;
|
||||
this.offlineDataLoadInfo=offlineDataLoadInfo;
|
||||
// System.out.printf("New FLAC decoder %s working from %s to %s\n", offlineDataLoadInfo.toString(),
|
||||
// PamCalendar.formatDBDateTime(offlineDataLoadInfo.getStartMillis()),
|
||||
// PamCalendar.formatDBDateTime(offlineDataLoadInfo.getEndMillis()));
|
||||
}
|
||||
|
||||
@Override
|
||||
public void processPCM(ByteData byteData) {
|
||||
if (offlineDataLoadInfo.cancel) {
|
||||
|
||||
try {
|
||||
fileStream.close();
|
||||
ms = Math.max(offlineDataLoadInfo.getStartMillis(), ms);
|
||||
offlineDataLoadInfo.setLastLoadInfo(new AquisitionLoadPoint(ms, -1));
|
||||
} catch (IOException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
ms = mapPoint.getStartTime() + (long)totalSamples * 1000L / (long)sampleRate;
|
||||
// System.out.println(String.format("PCM data at %s samps %d (load %s - %s)", PamCalendar.formatTime2(ms, 3), totalSamples,
|
||||
// PamCalendar.formatTime2(dataStart, 3), PamCalendar.formatTime2(dataEnd, 3)));
|
||||
if (ms > offlineDataLoadInfo.getEndMillis()) {
|
||||
try {
|
||||
fileStream.close();
|
||||
} catch (IOException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
return;
|
||||
}
|
||||
int newSamples = byteData.getLen() / frameSize;
|
||||
if (ms >= offlineDataLoadInfo.getStartMillis()) {
|
||||
double[][] doubleData = new double[nChannels][newSamples];
|
||||
byteConverter.bytesToDouble(byteData.getData(), doubleData, byteData.getLen());
|
||||
RawDataUnit newDataUnit = null;
|
||||
for (int ichan = 0; ichan < nChannels; ichan++) {
|
||||
|
||||
newDataUnit = new RawDataUnit(ms, 1 << ichan, totalSamples, newSamples);
|
||||
newDataUnit.setRawData(doubleData[ichan]);
|
||||
|
||||
dataBlock.addPamData(newDataUnit);
|
||||
|
||||
// GetOutputDataBlock().addPamData(pamDataUnit);
|
||||
}
|
||||
}
|
||||
// System.out.println(String.format("new samps %d at %s", newSamples, PamCalendar.formatTime(ms, 3)));
|
||||
|
||||
totalSamples += newSamples;
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void processStreamInfo(StreamInfo streamInfo) {
|
||||
frameSize = streamInfo.getChannels() * streamInfo.getBitsPerSample() / 8;
|
||||
byteConverter = ByteConverter.createByteConverter(streamInfo.getBitsPerSample() / 8, false, Encoding.PCM_SIGNED);
|
||||
fileSamples = streamInfo.getTotalSamples();
|
||||
nChannels = streamInfo.getChannels();
|
||||
sampleRate = streamInfo.getSampleRate();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private static boolean isFlacFile(File file) {
|
||||
String name = file.getName();
|
||||
if (name.length() < 5) {
|
||||
return false;
|
||||
}
|
||||
String end = name.substring(name.length()-5).toLowerCase();
|
||||
return (end.equals(".flac"));
|
||||
}
|
||||
|
||||
}
|
||||
52
src/Acquisition/pamAudio/PamAudioFile.java
Normal file
52
src/Acquisition/pamAudio/PamAudioFile.java
Normal file
@ -0,0 +1,52 @@
|
||||
package Acquisition.pamAudio;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.ArrayList;
|
||||
|
||||
import javax.sound.sampled.AudioInputStream;
|
||||
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import PamguardMVC.dataOffline.OfflineDataLoadInfo;
|
||||
import dataMap.filemaps.OfflineFileServer;
|
||||
import pamScrollSystem.ViewLoadObserver;
|
||||
|
||||
/**
|
||||
* Interface for PAMGuard opening a sound file.
|
||||
*
|
||||
* @author Jamie Macaulay
|
||||
*
|
||||
*/
|
||||
public interface PamAudioFile {
|
||||
|
||||
/**
|
||||
* Get file extensions associated with the file type
|
||||
* @return a list of the file extensions (e.g.".wav")
|
||||
*/
|
||||
public ArrayList<String> getFileExtensions();
|
||||
|
||||
|
||||
/**
|
||||
* Get the name of the file.
|
||||
* @return the name of the file
|
||||
*/
|
||||
public String getName();
|
||||
|
||||
|
||||
/**
|
||||
* Get the audio stream for the file
|
||||
* @return the audio input stream.
|
||||
*/
|
||||
public AudioInputStream getAudioStream(File soundFile);
|
||||
|
||||
/**
|
||||
* Load a section of audio data.
|
||||
* @param dataBlock - the data block.
|
||||
* @param offlineFileServer - the offline file server.
|
||||
* @param offlineDataLoadInfo - the offline data load info.
|
||||
* @return true if the file has been loaded
|
||||
*/
|
||||
boolean loadAudioData(OfflineFileServer offlineFileServer, PamDataBlock dataBlock,
|
||||
OfflineDataLoadInfo offlineDataLoadInfo, ViewLoadObserver loadObserver);
|
||||
|
||||
|
||||
}
|
||||
87
src/Acquisition/pamAudio/PamAudioFileFilter.java
Normal file
87
src/Acquisition/pamAudio/PamAudioFileFilter.java
Normal file
@ -0,0 +1,87 @@
|
||||
package Acquisition.pamAudio;
|
||||
|
||||
import java.io.File;
|
||||
|
||||
import org.apache.commons.io.FilenameUtils;
|
||||
|
||||
import PamUtils.PamFileFilter;
|
||||
|
||||
/**
|
||||
* The file filter for audio files compatible with PAMGuard.
|
||||
* <p>
|
||||
* All file extensions from all PamAudioFileLoaders in PamAudioManager are
|
||||
* accepted by the file filter. The file filter will aslo discard compressed
|
||||
* audio files if there exists a raw audio file of the same name.
|
||||
*
|
||||
* @author Jamie Macaulay
|
||||
*
|
||||
*/
|
||||
public class PamAudioFileFilter extends PamFileFilter {
|
||||
|
||||
private PamAudioFileManager pamAudioFileManager;
|
||||
|
||||
public PamAudioFileFilter(PamAudioFileManager pamAudioFileManager) {
|
||||
|
||||
/**
|
||||
* PamfileFilter converts everything to lower case, so no need to have upper and lower versions of
|
||||
* each ending.
|
||||
*/
|
||||
super("Audio Files", ".wav");
|
||||
|
||||
this.pamAudioFileManager = pamAudioFileManager;
|
||||
|
||||
//add all the file types.
|
||||
for (int i=0; i<pamAudioFileManager.getAudioFileLoaders().size(); i++) {
|
||||
for (int j=0; j<pamAudioFileManager.getAudioFileLoaders().get(i).getFileExtensions().size(); j++) {
|
||||
if (!pamAudioFileManager.getAudioFileLoaders().get(i).getFileExtensions().get(j).equals(".wav")){
|
||||
// already added .wav but add all other file extensions.
|
||||
addFileType(pamAudioFileManager.getAudioFileLoaders().get(i).getFileExtensions().get(j));
|
||||
}
|
||||
|
||||
};
|
||||
}
|
||||
}
|
||||
|
||||
public PamAudioFileFilter() {
|
||||
this(PamAudioFileManager.getInstance());
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean accept(File f) {
|
||||
//System.out.println("Accept?: " + super.accept(f) + " " + f.getName() );
|
||||
if (super.accept(f)) {
|
||||
//need to do an extra check here. Is there a .wav file or other raw wav file
|
||||
//that has the same name as another file type? If so we do not want both a compressed
|
||||
//and uncompressed file to be read - instead ignore the compressed file and only accept
|
||||
//the wav file.
|
||||
|
||||
if (pamAudioFileManager.isExtension(f, pamAudioFileManager.getRawFileLoader()) || f.isDirectory()) {
|
||||
//if a raw file then all OK.
|
||||
//System.out.println("Accepted file 1: " + f.getName());
|
||||
return true;
|
||||
}
|
||||
|
||||
String blankFileName = FilenameUtils.removeExtension(f.getAbsolutePath());
|
||||
//System.out.println("Blank file 1: " + blankFileName);
|
||||
|
||||
|
||||
File rawfile;
|
||||
for (int i=0; i<pamAudioFileManager.getRawFileLoader().getFileExtensions().size(); i++) {
|
||||
rawfile = new File(blankFileName + pamAudioFileManager.getRawFileLoader().getFileExtensions().get(i));
|
||||
//System.out.println("Raw file 1: " + blankFileName);
|
||||
|
||||
if (rawfile.exists()) {
|
||||
//the raw file will have been picked up by the file filter already or subsequently. So do not
|
||||
//use the other file.
|
||||
return false;
|
||||
}
|
||||
}
|
||||
//System.out.println("Accepted file 2: " + f.getName());
|
||||
return true;
|
||||
|
||||
}
|
||||
else return false;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
52
src/Acquisition/pamAudio/PamAudioFileLoader.java
Normal file
52
src/Acquisition/pamAudio/PamAudioFileLoader.java
Normal file
@ -0,0 +1,52 @@
|
||||
package Acquisition.pamAudio;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.ArrayList;
|
||||
|
||||
import javax.sound.sampled.AudioInputStream;
|
||||
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import PamguardMVC.dataOffline.OfflineDataLoadInfo;
|
||||
import dataMap.filemaps.OfflineFileServer;
|
||||
import pamScrollSystem.ViewLoadObserver;
|
||||
|
||||
/**
|
||||
* Interface for PAMGuard opening a sound file.
|
||||
*
|
||||
* @author Jamie Macaulay
|
||||
*
|
||||
*/
|
||||
public interface PamAudioFileLoader {
|
||||
|
||||
/**
|
||||
* Get file extensions associated with the file type
|
||||
* @return a list of the file extensions (e.g.".wav")
|
||||
*/
|
||||
public ArrayList<String> getFileExtensions();
|
||||
|
||||
|
||||
/**
|
||||
* Get the name of the file.
|
||||
* @return the name of the file
|
||||
*/
|
||||
public String getName();
|
||||
|
||||
|
||||
/**
|
||||
* Get the audio stream for the file
|
||||
* @return the audio input stream.
|
||||
*/
|
||||
public AudioInputStream getAudioStream(File soundFile);
|
||||
|
||||
/**
|
||||
* Load a section of audio data.
|
||||
* @param dataBlock - the data block.
|
||||
* @param offlineFileServer - the offline file server.
|
||||
* @param offlineDataLoadInfo - the offline data load info.
|
||||
* @return true if the file has been loaded
|
||||
*/
|
||||
public boolean loadAudioData(OfflineFileServer offlineFileServer, PamDataBlock dataBlock,
|
||||
OfflineDataLoadInfo offlineDataLoadInfo, ViewLoadObserver loadObserver);
|
||||
|
||||
|
||||
}
|
||||
173
src/Acquisition/pamAudio/PamAudioFileManager.java
Normal file
173
src/Acquisition/pamAudio/PamAudioFileManager.java
Normal file
@ -0,0 +1,173 @@
|
||||
package Acquisition.pamAudio;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.IOException;
|
||||
import java.util.ArrayList;
|
||||
|
||||
import javax.sound.sampled.AudioInputStream;
|
||||
import javax.sound.sampled.UnsupportedAudioFileException;
|
||||
|
||||
import org.codehaus.plexus.util.FileUtils;
|
||||
|
||||
/**
|
||||
* Central class for opening sound files.
|
||||
* <p>
|
||||
* PamAudioFieManager holds a list of PamAudioFile classes. Each PamAudioFile
|
||||
* can open a certain type of sound file e.g. flac or raw wav files.
|
||||
* PamAudioFieManager provides fucntions around the list to open files, provide
|
||||
* file filters etc.
|
||||
*
|
||||
* @author Jamie Macaulay
|
||||
*
|
||||
*/
|
||||
public class PamAudioFileManager {
|
||||
|
||||
/**
|
||||
* Instance of the PamAudioFieManager.
|
||||
*/
|
||||
private static PamAudioFileManager pamAudioFileManager;
|
||||
|
||||
/**
|
||||
* The pam audio file types.
|
||||
*/
|
||||
private ArrayList<PamAudioFileLoader> pamAudioFileTypes;
|
||||
|
||||
/**
|
||||
* The default file loader for raw files. A reference to this is kept so that
|
||||
* file loaders can preferentially select raw files over compressed file if they
|
||||
* have the same name e.g. if using a folder of uncompressed SoundTrap data that
|
||||
* contains both .sud and .wav files then only .wav files should be read.
|
||||
*/
|
||||
private WavAudioFile rawFileLoader;
|
||||
|
||||
public PamAudioFileManager() {
|
||||
pamAudioFileTypes = new ArrayList<PamAudioFileLoader>();
|
||||
|
||||
/***** Add new audio file types here *****/
|
||||
pamAudioFileTypes.add(rawFileLoader = new WavAudioFile());
|
||||
pamAudioFileTypes.add(new FlacAudioFile());
|
||||
pamAudioFileTypes.add(new SudAudioFile());
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the audio file loader for a file.
|
||||
*
|
||||
* @param soundFile - the sound file
|
||||
* @return the audio file loader.
|
||||
*/
|
||||
public PamAudioFileLoader getAudioLoader(File soundFile) {
|
||||
for (int i = 0; i < pamAudioFileTypes.size(); i++) {
|
||||
if (isExtension(soundFile, pamAudioFileTypes.get(i))) {
|
||||
return pamAudioFileTypes.get(i);
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
/**
|
||||
* Check if a file has an extension supported by a PamAudioFile.
|
||||
*
|
||||
* @param file
|
||||
* @param pamAudioFile
|
||||
*/
|
||||
public boolean isExtension(File file, PamAudioFileLoader pamAudioFile) {
|
||||
for (int i = 0; i < pamAudioFile.getFileExtensions().size(); i++) {
|
||||
if (isSoundFile(file, pamAudioFile.getFileExtensions().get(i))) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
public boolean isSoundFile(File soundFile, String soundExtension) {
|
||||
String extension = FileUtils.getExtension(soundFile.getName());
|
||||
|
||||
//System.out.println("Sound Extension: " + soundExtension + " File extension: " + extension);
|
||||
return (soundExtension.equals(extension) || soundExtension.equals("." + extension));
|
||||
}
|
||||
|
||||
/**
|
||||
* Open an audio input stream. If the file is a Wav file, then it will attempt
|
||||
* to read the file with PAMGuards bespoke audio stream reader. This includes
|
||||
* support for wav files which are > 2GByte in size and also works for floating
|
||||
* point 32 bit files (which the Java one doesn't). If that fails, or if its not
|
||||
* a wav file, then the standard java AudioInputStream is used.
|
||||
*
|
||||
* @param file file to open
|
||||
* @return a new audio input stream
|
||||
* @throws UnsupportedAudioFileException thrown if it can't understand the audio
|
||||
* format.
|
||||
* @throws IOException
|
||||
*/
|
||||
public AudioInputStream getAudioInputStream(File file) throws UnsupportedAudioFileException, IOException {
|
||||
// if (file != null && isWavFile(file) && file.length() > largeFileSize) {
|
||||
if (file.exists() == false) {
|
||||
System.err.println("PamAudioFileManager: the input file was null");
|
||||
return null;
|
||||
}
|
||||
|
||||
AudioInputStream stream = null;
|
||||
for (int i = 0; i < pamAudioFileTypes.size(); i++) {
|
||||
System.out.println(file.getName() + " " + pamAudioFileTypes.get(i).getName());
|
||||
if (isExtension(file, pamAudioFileTypes.get(i))) {
|
||||
//System.out.println("Get stream for: " +pamAudioFileTypes.get(i).getName());
|
||||
stream = pamAudioFileTypes.get(i).getAudioStream(file);
|
||||
if (pamAudioFileTypes != null) {
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (stream == null) {
|
||||
// have a punt at opening as a default audiostream
|
||||
//System.out.println("Try default stream for: " +file.getName() );
|
||||
|
||||
stream = new WavAudioFile().getAudioStream(file);
|
||||
}
|
||||
|
||||
if (stream == null) {
|
||||
System.err.println("PamAudioFileManager: unable to open an AudioStream for " + file.getName());
|
||||
}
|
||||
|
||||
return stream;
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the instance of the PamAudioManager
|
||||
*/
|
||||
public static PamAudioFileManager getInstance() {
|
||||
if (pamAudioFileManager == null) {
|
||||
pamAudioFileManager = new PamAudioFileManager();
|
||||
}
|
||||
return pamAudioFileManager;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the audio file filter
|
||||
*
|
||||
* @return the audio file filter.
|
||||
*/
|
||||
public PamAudioFileFilter getAudioFileFilter() {
|
||||
return new PamAudioFileFilter(this);
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the current audio file
|
||||
*
|
||||
* @return a list oif the current audio loaders.
|
||||
*/
|
||||
public ArrayList<PamAudioFileLoader> getAudioFileLoaders() {
|
||||
return this.pamAudioFileTypes;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the default file loader for raw files.
|
||||
* @return the default file loader for raw files.
|
||||
*/
|
||||
public WavAudioFile getRawFileLoader() {
|
||||
return rawFileLoader;
|
||||
}
|
||||
|
||||
}
|
||||
@ -10,7 +10,13 @@ import javax.sound.sampled.UnsupportedAudioFileException;
|
||||
//import org.kc7bfi.jflac.sound.spi.FlacAudioFileReader;
|
||||
import org.jflac.sound.spi.FlacAudioFileReader;
|
||||
|
||||
|
||||
/**
|
||||
* Now replaced with PamAudioFileManager.
|
||||
*
|
||||
* @author Jamie Macaulay
|
||||
*
|
||||
*/
|
||||
@Deprecated
|
||||
public class PamAudioSystem {
|
||||
|
||||
private static final long largeFileSize = 01L<<31;
|
||||
@ -50,7 +56,7 @@ public class PamAudioSystem {
|
||||
return new SudAudioFileReader().getAudioInputStream(file);
|
||||
}
|
||||
catch (UnsupportedAudioFileException e) {
|
||||
|
||||
//e.printStackTrace();
|
||||
}
|
||||
}
|
||||
try {
|
||||
@ -58,6 +64,7 @@ public class PamAudioSystem {
|
||||
}
|
||||
catch (Exception e) {
|
||||
System.out.println("Error in audio file " + file.getName() + ": " + e.getMessage());
|
||||
e.printStackTrace();
|
||||
return null;
|
||||
}
|
||||
}
|
||||
@ -93,10 +100,10 @@ public class PamAudioSystem {
|
||||
*/
|
||||
private static boolean isSudFile(File file) {
|
||||
String name = file.getName();
|
||||
if (name.length() < 5) {
|
||||
if (name.length() < 4) {
|
||||
return false;
|
||||
}
|
||||
String end = name.substring(name.length()-5).toLowerCase();
|
||||
String end = name.substring(name.length()-4).toLowerCase();
|
||||
return (end.equals(".sud"));
|
||||
}
|
||||
|
||||
|
||||
63
src/Acquisition/pamAudio/SudAudioFile.java
Normal file
63
src/Acquisition/pamAudio/SudAudioFile.java
Normal file
@ -0,0 +1,63 @@
|
||||
package Acquisition.pamAudio;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.IOException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
|
||||
import javax.sound.sampled.AudioInputStream;
|
||||
import javax.sound.sampled.UnsupportedAudioFileException;
|
||||
|
||||
/**
|
||||
* Opens a .sud audio file.
|
||||
* <p>
|
||||
* Sud files contain X3 compressed audio data. The sud
|
||||
* file reader opens files, creating a map of the file and saving
|
||||
* the map as a.sudx file so it can be read more rapidly when the file
|
||||
* is next accessed.
|
||||
* <p>
|
||||
* The SudioAudioInput stream fully implements AudioInputStream and so
|
||||
* sud files can be accessed using much of the same code as .wav files.
|
||||
*
|
||||
* @author Jamie Macaulay
|
||||
*
|
||||
*/
|
||||
public class SudAudioFile extends WavAudioFile {
|
||||
|
||||
|
||||
public SudAudioFile() {
|
||||
super();
|
||||
fileExtensions = new ArrayList<String>(Arrays.asList(new String[]{".sud"}));
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getName() {
|
||||
return "SUD";
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public AudioInputStream getAudioStream(File soundFile) {
|
||||
if (soundFile.exists() == false) {
|
||||
System.err.println("The sud file does not exist: " + soundFile);
|
||||
return null;
|
||||
}
|
||||
if (soundFile != null) {
|
||||
try {
|
||||
return new SudAudioFileReader().getAudioInputStream(soundFile);
|
||||
}
|
||||
// don't do anything and it will try the built in Audiosystem
|
||||
catch (UnsupportedAudioFileException e) {
|
||||
System.err.println("Could not open sud file: not a supported file " + soundFile.getName());
|
||||
|
||||
e.printStackTrace();
|
||||
} catch (IOException e) {
|
||||
System.err.println("Could not open sud file: IO Exception: " + soundFile.getName());
|
||||
|
||||
e.printStackTrace();
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
}
|
||||
@ -2,6 +2,7 @@ package Acquisition.pamAudio;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.IOException;
|
||||
import org.pamguard.x3.sud.*;
|
||||
|
||||
import javax.sound.sampled.AudioInputStream;
|
||||
import javax.sound.sampled.UnsupportedAudioFileException;
|
||||
@ -14,10 +15,40 @@ import javax.sound.sampled.UnsupportedAudioFileException;
|
||||
*/
|
||||
public class SudAudioFileReader {
|
||||
|
||||
/**
|
||||
* The current sud audio input stream
|
||||
*/
|
||||
SudAudioInputStream sudAudioInputStream;
|
||||
|
||||
/**
|
||||
* Parameters for opening .sud files.
|
||||
*/
|
||||
SudParams sudParams;
|
||||
|
||||
|
||||
public SudAudioFileReader() {
|
||||
sudParams = new SudParams();
|
||||
//set up the sud params for default. i.e. just read files and
|
||||
//don't save any decompressed or meta data.
|
||||
sudParams.saveWav = false;
|
||||
sudParams.saveMeta = false;
|
||||
sudParams.zeroPad = true;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the audio input streamn.
|
||||
* @param file - the .sud file to open.
|
||||
* @return the sud AudioStream.
|
||||
* @throws UnsupportedAudioFileException
|
||||
* @throws IOException
|
||||
*/
|
||||
public AudioInputStream getAudioInputStream(File file) throws UnsupportedAudioFileException, IOException {
|
||||
// TODO Auto-generated method stub
|
||||
return null;
|
||||
try {
|
||||
sudAudioInputStream = SudAudioInputStream.openInputStream(file, sudParams, false);
|
||||
} catch (Exception e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
return sudAudioInputStream;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
250
src/Acquisition/pamAudio/WavAudioFile.java
Normal file
250
src/Acquisition/pamAudio/WavAudioFile.java
Normal file
@ -0,0 +1,250 @@
|
||||
package Acquisition.pamAudio;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.IOException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.Iterator;
|
||||
|
||||
import javax.sound.sampled.AudioFormat;
|
||||
import javax.sound.sampled.AudioInputStream;
|
||||
import javax.sound.sampled.AudioSystem;
|
||||
import javax.sound.sampled.UnsupportedAudioFileException;
|
||||
|
||||
import org.codehaus.plexus.util.FileUtils;
|
||||
import Acquisition.offlineFuncs.AquisitionLoadPoint;
|
||||
import PamDetection.RawDataUnit;
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import PamguardMVC.dataOffline.OfflineDataLoadInfo;
|
||||
import dataMap.OfflineDataMap;
|
||||
import dataMap.filemaps.FileDataMapPoint;
|
||||
import dataMap.filemaps.OfflineFileServer;
|
||||
import pamScrollSystem.ViewLoadObserver;
|
||||
import wavFiles.ByteConverter;
|
||||
|
||||
/**
|
||||
* Wav audio file - opens any raw audio file.
|
||||
* <p>
|
||||
* This should be used a standard class for opening audio files
|
||||
*
|
||||
* @author Jamie Macaulay, Doug Gillepsie
|
||||
*
|
||||
*/
|
||||
public class WavAudioFile implements PamAudioFileLoader {
|
||||
|
||||
/**
|
||||
* The audio input stream of the last loaded file.
|
||||
*/
|
||||
private AudioInputStream audioInputStream;
|
||||
|
||||
/**
|
||||
* The audioformat of the last laoded file.
|
||||
*/
|
||||
private AudioFormat audioFormat;
|
||||
|
||||
/**
|
||||
* Get the file extensions associated with loading these data.
|
||||
*/
|
||||
protected ArrayList<String> fileExtensions;
|
||||
|
||||
public WavAudioFile() {
|
||||
fileExtensions = new ArrayList<String>(Arrays.asList(new String[]{".wav", ".aif", ".aiff"}));
|
||||
}
|
||||
|
||||
@Override
|
||||
public ArrayList<String> getFileExtensions() {
|
||||
return fileExtensions;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getName() {
|
||||
return "WAV";
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean loadAudioData(OfflineFileServer offlineFileServer, PamDataBlock dataBlock, OfflineDataLoadInfo offlineDataLoadInfo, ViewLoadObserver loadObserver) {
|
||||
|
||||
// Debug.out.println("OfflineFileServer: Load Wav Data: " + offlineDataLoadInfo.getCurrentObserver().getObserverName() );
|
||||
OfflineDataMap<FileDataMapPoint> dataMap = offlineFileServer.getDataMap();
|
||||
Iterator<FileDataMapPoint> mapIt = dataMap.getListIterator();
|
||||
FileDataMapPoint mapPoint = offlineFileServer.findFirstMapPoint(mapIt, offlineDataLoadInfo.getStartMillis(), offlineDataLoadInfo.getEndMillis());
|
||||
|
||||
if (openSoundFile(mapPoint.getSoundFile()) == false) {
|
||||
System.out.println("Could not open .wav sound file " + mapPoint.getSoundFile().getAbsolutePath());
|
||||
return false;
|
||||
}
|
||||
File soundFile;
|
||||
|
||||
ByteConverter byteConverter = ByteConverter.createByteConverter(audioFormat);
|
||||
long currentTime = mapPoint.getStartTime();
|
||||
long prevFileEnd = mapPoint.getEndTime();
|
||||
boolean fileGap = false;
|
||||
int newSamples;
|
||||
double[][] doubleData;
|
||||
int nChannels = audioFormat.getChannels();
|
||||
int blockSamples = Math.max((int) audioFormat.getSampleRate() / 10, 1000);
|
||||
int frameSize = audioFormat.getFrameSize();
|
||||
if (frameSize < 0) {
|
||||
frameSize = audioFormat.getChannels()*audioFormat.getSampleSizeInBits()/8;
|
||||
}
|
||||
if (frameSize <= 0) {
|
||||
System.out.println("The frame size is less than zero " + mapPoint.getSoundFile().getAbsolutePath());
|
||||
return false;
|
||||
}
|
||||
byte[] inputBuffer = new byte[blockSamples * frameSize];
|
||||
int bytesRead = 0;
|
||||
long totalSamples = 0;
|
||||
// long fileSamples = 0;
|
||||
long millisecondsGaps = 0;
|
||||
long ms;
|
||||
|
||||
RawDataUnit newDataUnit;
|
||||
long skipped = 0;
|
||||
if (currentTime < offlineDataLoadInfo.getStartMillis()) {
|
||||
// need to fast forward in current file.
|
||||
long skipBytes = (long) (((offlineDataLoadInfo.getStartMillis()-currentTime)*audioFormat.getSampleRate()*audioFormat.getFrameSize())/1000.);
|
||||
try {
|
||||
|
||||
//System.out.println("Skipped " + skipped+ " " + skipBytes + " " + audioInputStream.available());
|
||||
skipped = audioInputStream.skip(skipBytes);
|
||||
//System.out.println("Offline " + (offlineDataLoadInfo.getStartMillis()-currentTime) + " ms : frame size: " + audioFormat.getFrameSize());
|
||||
|
||||
} catch (IOException e) {
|
||||
/**
|
||||
* The datamap point may be longer than the actual file here ? In any case, with the
|
||||
* NEMO data which is 5 mins per hour, this get's hit for the file before the
|
||||
* file we want every time !
|
||||
*/
|
||||
// System.out.println("End of audio file " + mapPoint.getSoundFile().getName());
|
||||
e.printStackTrace();
|
||||
}
|
||||
currentTime = offlineDataLoadInfo.getStartMillis();
|
||||
}
|
||||
ms = currentTime;
|
||||
while (ms < offlineDataLoadInfo.getEndMillis() && currentTime < offlineDataLoadInfo.getEndMillis()) {
|
||||
if (offlineDataLoadInfo.cancel) {
|
||||
//add the position we got to
|
||||
offlineDataLoadInfo.setLastLoadInfo(new AquisitionLoadPoint(ms, bytesRead));
|
||||
|
||||
|
||||
break;
|
||||
}
|
||||
try {
|
||||
if (inputBuffer.length<audioInputStream.available()) {
|
||||
bytesRead = audioInputStream.read(inputBuffer);
|
||||
}
|
||||
else {
|
||||
bytesRead = 0; //force new file to load.
|
||||
}
|
||||
} catch (IOException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
if (bytesRead <= 0) {
|
||||
skipped = 0 ; //reset ot zero because were not skipping anyu bytes here.
|
||||
/*
|
||||
* that's the end of that file, so get the next one if there
|
||||
* is one, if not then break.
|
||||
*/
|
||||
if (mapIt.hasNext() == false) {
|
||||
break;
|
||||
}
|
||||
mapPoint = mapIt.next();
|
||||
fileGap = (mapPoint.getStartTime() - prevFileEnd) > 1000;
|
||||
// if (fileGap) {
|
||||
// System.out.println(String.format("Sound file gap %3.3fs from %s to %s",
|
||||
// (double) (mapPoint.getStartTime()-prevFileEnd) / 1000.,
|
||||
// PamCalendar.formatTime(prevFileEnd), PamCalendar.formatTime(mapPoint.getStartTime())));
|
||||
// }
|
||||
prevFileEnd = mapPoint.getEndTime();
|
||||
if (!fileGap) { // don't carry on if there is a file gap
|
||||
if (openSoundFile(mapPoint.getSoundFile()) == false) {
|
||||
break;
|
||||
}
|
||||
// try again to read data.
|
||||
try {
|
||||
bytesRead = audioInputStream.read(inputBuffer);
|
||||
} catch (IOException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
if (bytesRead <= 0) {
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
newSamples = bytesRead / frameSize;
|
||||
doubleData = new double[nChannels][newSamples];
|
||||
int convertedSamples = byteConverter.bytesToDouble(inputBuffer, doubleData, bytesRead);
|
||||
ms = offlineFileServer.getOfflineRawDataStore().getParentProcess().absSamplesToMilliseconds(totalSamples);
|
||||
ms = currentTime + (long)(totalSamples * 1000 / (double) audioFormat.getSampleRate());
|
||||
|
||||
for (int ichan = 0; ichan < nChannels; ichan++) {
|
||||
|
||||
newDataUnit = new RawDataUnit(ms, 1 << ichan, totalSamples, newSamples);
|
||||
newDataUnit.setFileSamples(totalSamples + skipped / frameSize); //set the number samples into the wav file.
|
||||
newDataUnit.setRawData(doubleData[ichan], true);
|
||||
|
||||
//System.out.println("New wav data: " + PamCalendar.formatDateTime(newDataUnit.getTimeMilliseconds()));
|
||||
offlineFileServer.getRawDataBlock().addPamData(newDataUnit);
|
||||
}
|
||||
if (fileGap) {
|
||||
currentTime = mapPoint.getStartTime();
|
||||
totalSamples = 0;
|
||||
// fileSamples = 0;
|
||||
}
|
||||
|
||||
totalSamples += newSamples;
|
||||
// fileSamples += newSamples;
|
||||
}
|
||||
|
||||
// System.out.println("Finished loading wav: " + offlineDataLoadInfo.getCurrentObserver().getObserverName() );
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Open a sound file.
|
||||
* @param soundFile
|
||||
* @return
|
||||
*/
|
||||
private boolean openSoundFile(File soundFile) {
|
||||
|
||||
audioInputStream = getAudioStream(soundFile);
|
||||
if (audioInputStream == null) return false;
|
||||
audioFormat = audioInputStream.getFormat();
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public AudioInputStream getAudioStream(File soundFile) {
|
||||
if (soundFile.exists() == false) return null;
|
||||
if (soundFile != null && isSoundFile(soundFile)) {
|
||||
try {
|
||||
return WavFileInputStream.openInputStream(soundFile);
|
||||
}
|
||||
catch (UnsupportedAudioFileException | IOException e) {
|
||||
e.printStackTrace();
|
||||
// don't do anything and it will try the built in Audiosystem
|
||||
System.err.println("Could not open wav file: trying default audio stream: " + soundFile.getName());
|
||||
}
|
||||
}
|
||||
try {
|
||||
return AudioSystem.getAudioInputStream(soundFile);
|
||||
}
|
||||
catch (Exception e) {
|
||||
System.out.println("Error in audio file " + soundFile.getName() + ": " + e.getMessage());
|
||||
e.printStackTrace();
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
public boolean isSoundFile(File soundFile) {
|
||||
String extension = FileUtils.getExtension(soundFile.getName());
|
||||
return (extension.equals(".wav"));
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
@ -33,8 +33,8 @@ import javax.swing.JFileChooser;
|
||||
import javax.swing.JLabel;
|
||||
import javax.swing.JPanel;
|
||||
|
||||
import Acquisition.pamAudio.PamAudioFileFilter;
|
||||
import PamDetection.RawDataUnit;
|
||||
import PamUtils.PamAudioFileFilter;
|
||||
import PamUtils.PamFileChooser;
|
||||
|
||||
|
||||
|
||||
@ -0,0 +1,221 @@
|
||||
package Localiser.algorithms.timeDelayLocalisers.bearingLoc;
|
||||
|
||||
|
||||
import Localiser.DelayMeasurementParams;
|
||||
import PamController.SettingsPane;
|
||||
import fftFilter.FFTFilterParams;
|
||||
import javafx.scene.Node;
|
||||
import javafx.scene.control.CheckBox;
|
||||
import javafx.scene.control.Label;
|
||||
import javafx.scene.control.TextField;
|
||||
import javafx.scene.control.Tooltip;
|
||||
import javafx.scene.layout.BorderPane;
|
||||
import javafx.scene.layout.Pane;
|
||||
import pamViewFX.fxNodes.PamButton;
|
||||
import pamViewFX.fxNodes.PamGridPane;
|
||||
import pamViewFX.fxNodes.PamSpinner;
|
||||
import pamViewFX.fxNodes.pamDialogFX.PamDialogFX;
|
||||
import pamViewFX.fxNodes.utilityPanes.SimpleFilterPaneFX;
|
||||
|
||||
public class DelayOptionsPaneFX extends SettingsPane<DelayMeasurementParams> {
|
||||
|
||||
|
||||
private CheckBox filterBearings, envelopeBearings, useLeadingEdge, upSample;
|
||||
private PamButton filterSettings;
|
||||
private Label filterDescription;
|
||||
|
||||
/**
|
||||
* The current delay measurement parameters.
|
||||
*/
|
||||
private DelayMeasurementParams delayMeasurementParams;
|
||||
|
||||
|
||||
/**
|
||||
* Check box for restricting samples.
|
||||
*/
|
||||
private CheckBox restrictSamples;
|
||||
|
||||
/**
|
||||
* Restrict the number of samples.
|
||||
*/
|
||||
private TextField restrictSamplesField;
|
||||
|
||||
private PamSpinner<Integer> upSampleSpinner;
|
||||
|
||||
|
||||
private SimpleFilterPaneFX simpleFilterPane = new SimpleFilterPaneFX();
|
||||
|
||||
public DelayOptionsPaneFX() {
|
||||
super(null);
|
||||
// TODO Auto-generated constructor stub
|
||||
}
|
||||
|
||||
|
||||
public Pane createDelayOptionsPane() {
|
||||
int gridy=0;
|
||||
|
||||
PamGridPane mainPanel = new PamGridPane();
|
||||
// mainPanel.setBorder(new TitledBorder("Delay measurement options"));
|
||||
mainPanel.add(filterBearings = new CheckBox("Filter data before measurement"), 0,gridy);
|
||||
PamGridPane.setColumnSpan(filterBearings, 2);
|
||||
filterBearings.setOnAction((action)->{
|
||||
enableControls();
|
||||
});
|
||||
gridy++;
|
||||
|
||||
mainPanel.add(filterSettings = new PamButton("Settings"), 0,gridy);
|
||||
filterSettings.setOnAction((action)->{
|
||||
FFTFilterParams newParams = simpleFilterPane.getParams(delayMeasurementParams.delayFilterParams);
|
||||
if (newParams != null) {
|
||||
delayMeasurementParams.delayFilterParams = newParams.clone();
|
||||
describeFilter();
|
||||
}
|
||||
});
|
||||
gridy++;
|
||||
|
||||
mainPanel.add(filterDescription = new Label(" "), 0,gridy);
|
||||
gridy++;
|
||||
mainPanel.add(upSample = new CheckBox("Up sample data x2"), 0,gridy);
|
||||
upSample.setTooltip(new Tooltip("Up sampling data to a higher frequency can improve timing accuracy for narrow band clicks (i.e. harbour porpoise)"));
|
||||
gridy++;
|
||||
|
||||
|
||||
//SpinnerListModel spinnerModel = new SpinnerListModel(Arrays.asList(new Integer[] {2,3,4})); //restrict the spinenr options.
|
||||
|
||||
mainPanel.add(upSampleSpinner = new PamSpinner<Integer>(2,4,2,1), 0,gridy);
|
||||
upSampleSpinner.valueProperty().addListener((obsval, oldVa, newVal)->{
|
||||
upSample.setText("Up sample data x" + this.upSampleSpinner.getValue());
|
||||
});
|
||||
gridy++;
|
||||
|
||||
mainPanel.add(envelopeBearings = new CheckBox("Use waveform envelope"), 0, gridy);
|
||||
gridy++;
|
||||
|
||||
|
||||
mainPanel.add(new Label(" "), 0, gridy);
|
||||
gridy++;
|
||||
|
||||
mainPanel.add(new Label(" "), 0, gridy);
|
||||
gridy++;
|
||||
|
||||
|
||||
mainPanel.add(useLeadingEdge = new CheckBox("Use envelope leading edge only"), 0, gridy);
|
||||
gridy++;
|
||||
PamGridPane.setColumnSpan(useLeadingEdge, 2);
|
||||
envelopeBearings.setOnAction((action)->{
|
||||
enableControls();
|
||||
});
|
||||
envelopeBearings.setOnAction((action)->{
|
||||
enableControls();
|
||||
});
|
||||
PamGridPane.setColumnSpan(envelopeBearings, 2);
|
||||
|
||||
|
||||
//restrict
|
||||
mainPanel.add(restrictSamples = new CheckBox("Restrict length"), 0, gridy);
|
||||
gridy++;
|
||||
PamGridPane.setColumnSpan(restrictSamples, 2);
|
||||
restrictSamples.setOnAction((action)->{
|
||||
enableControls();
|
||||
});
|
||||
mainPanel.add(restrictSamplesField = new TextField(), 2, gridy);
|
||||
|
||||
|
||||
restrictSamples.setTooltip(new Tooltip("In environments where echoes are an issue restricting inital samples of detections "
|
||||
+ "(e.g. click snippets) is a simple but effective way to increase the accuracy of time delay calculations. "
|
||||
+ "WARNING: Remember that this must cover the potential time delay in grouped detections "));
|
||||
filterBearings.setTooltip(new Tooltip("Filter data prior to bearing measurement to imporve accuracy"));
|
||||
filterSettings.setTooltip(new Tooltip("Setup filter options"));
|
||||
envelopeBearings.setTooltip(new Tooltip("Using the envelope can provide more accurate bearings for some narrowband pulses"));
|
||||
filterDescription.setTooltip(new Tooltip("Current filter settings"));
|
||||
useLeadingEdge.setTooltip(new Tooltip("For long pulses, or where there are echoes, restrict the calculation to the leading edge of the envelope"));
|
||||
|
||||
BorderPane pane = new BorderPane();
|
||||
pane.setCenter(mainPanel);
|
||||
|
||||
return pane;
|
||||
}
|
||||
|
||||
|
||||
private void enableControls() {
|
||||
filterSettings.setDisable(!filterBearings.isSelected());
|
||||
filterDescription.setDisable(!filterBearings.isSelected());
|
||||
useLeadingEdge.setDisable(!envelopeBearings.isSelected());
|
||||
restrictSamplesField.setDisable(!restrictSamples.isSelected());
|
||||
if (!envelopeBearings.isSelected()) {
|
||||
// useLeadingEdge.setSelected(false);
|
||||
}
|
||||
}
|
||||
|
||||
private void describeFilter() {
|
||||
if (delayMeasurementParams == null || delayMeasurementParams.delayFilterParams == null) {
|
||||
filterDescription.setText("No filter");
|
||||
return;
|
||||
}
|
||||
filterDescription.setText(delayMeasurementParams.delayFilterParams.toString());
|
||||
}
|
||||
|
||||
@Override
|
||||
public void setParams(DelayMeasurementParams delayMeasurementParams) {
|
||||
this.delayMeasurementParams = delayMeasurementParams;
|
||||
filterBearings.setSelected(delayMeasurementParams.filterBearings);
|
||||
upSample.setSelected(delayMeasurementParams.getUpSample() > 1);
|
||||
envelopeBearings.setSelected(delayMeasurementParams.envelopeBearings);
|
||||
useLeadingEdge.setSelected(delayMeasurementParams.useLeadingEdge);
|
||||
restrictSamples.setSelected(delayMeasurementParams.useRestrictedBins);
|
||||
restrictSamplesField.setText(String.format("%d", delayMeasurementParams.restrictedBins));
|
||||
|
||||
upSample.setText("Up sample data x" + this.upSampleSpinner.getValue());
|
||||
|
||||
enableControls();
|
||||
describeFilter();
|
||||
}
|
||||
|
||||
@Override
|
||||
public DelayMeasurementParams getParams(DelayMeasurementParams delayMeasurementParams) {
|
||||
delayMeasurementParams.delayFilterParams = this.delayMeasurementParams.delayFilterParams;
|
||||
delayMeasurementParams.filterBearings = filterBearings.isSelected();
|
||||
delayMeasurementParams.setUpSample(upSample.isSelected() ? ((Integer) this.upSampleSpinner.getValue()).intValue() : 1);
|
||||
delayMeasurementParams.envelopeBearings = envelopeBearings.isSelected();
|
||||
delayMeasurementParams.useLeadingEdge = useLeadingEdge.isSelected() && delayMeasurementParams.envelopeBearings;
|
||||
|
||||
delayMeasurementParams.useRestrictedBins=this.restrictSamples.isSelected();
|
||||
|
||||
try {
|
||||
delayMeasurementParams.restrictedBins=Integer.valueOf(this.restrictSamplesField.getText());
|
||||
}
|
||||
catch(Exception e) {
|
||||
PamDialogFX.showWarning(null, "Delay measurement settings", "The entry in the samples text field is invalid.");
|
||||
return null;
|
||||
}
|
||||
|
||||
if (delayMeasurementParams.useRestrictedBins && delayMeasurementParams.restrictedBins<10) {
|
||||
PamDialogFX.showWarning(null, "Delay measurement settings", "The entry in the samples text field is invalid. It must be >= 10");
|
||||
return null;
|
||||
}
|
||||
|
||||
if (delayMeasurementParams.filterBearings && delayMeasurementParams.delayFilterParams == null) {
|
||||
PamDialogFX.showWarning(null, "Delay measurement settings", "Filter parameters have not been set");
|
||||
return null;
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getName() {
|
||||
return "Delay Measurment Params";
|
||||
}
|
||||
|
||||
@Override
|
||||
public Node getContentNode() {
|
||||
// TODO Auto-generated method stub
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void paneInitialized() {
|
||||
// TODO Auto-generated method stub
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
@ -765,6 +765,7 @@ final public class PamModel implements PamModelInterface, PamSettings {
|
||||
mi.addDependency(new PamDependency(ClickDetection.class, "clickDetector.ClickControl"));
|
||||
mi.setToolTipText("Classifies clicks based on an ideal template to match and a template to reject. "
|
||||
+ "An example of this is to classify beaked whale clicks in an environment with dolphin clicks");
|
||||
mi.addGUICompatabilityFlag(PamGUIManager.FX);
|
||||
mi.setModulesMenuGroup(classifierGroup);
|
||||
|
||||
|
||||
|
||||
@ -1,5 +1,7 @@
|
||||
package PamUtils;
|
||||
|
||||
import PamUtils.PamFileFilter;
|
||||
|
||||
public class PamAudioFileFilter extends PamFileFilter {
|
||||
|
||||
public PamAudioFileFilter() {
|
||||
|
||||
@ -33,7 +33,7 @@ public class PamFileFilter extends javax.swing.filechooser.FileFilter implements
|
||||
|
||||
private String prefix = null;
|
||||
|
||||
private boolean acceptFolders = true;
|
||||
protected boolean acceptFolders = true;
|
||||
|
||||
|
||||
public PamFileFilter(String description, String defExtension) {
|
||||
|
||||
@ -6,6 +6,7 @@ import javax.sound.sampled.AudioFileFormat;
|
||||
import javax.sound.sampled.AudioFormat;
|
||||
import javax.sound.sampled.AudioInputStream;
|
||||
|
||||
import Acquisition.pamAudio.PamAudioFileManager;
|
||||
import Acquisition.pamAudio.PamAudioSystem;
|
||||
import PamController.PamGUIManager;
|
||||
import javafx.beans.property.BooleanProperty;
|
||||
@ -64,7 +65,7 @@ public class WavFileType extends File {
|
||||
*/
|
||||
private AudioFormat getAudioFormat(File file) {
|
||||
try {
|
||||
AudioInputStream audioStream = PamAudioSystem.getAudioInputStream(file);
|
||||
AudioInputStream audioStream = PamAudioFileManager.getInstance().getAudioInputStream(file);
|
||||
|
||||
AudioFormat audioFormat = audioStream.getFormat();
|
||||
|
||||
|
||||
@ -2,7 +2,7 @@ package PamUtils.worker.filelist;
|
||||
|
||||
import java.io.File;
|
||||
|
||||
import PamUtils.PamAudioFileFilter;
|
||||
import Acquisition.pamAudio.PamAudioFileFilter;
|
||||
|
||||
/**
|
||||
* Worker which extracts acoustic files from a folder.
|
||||
|
||||
3664
src/Resources/css/nord-dark.css
Normal file
3664
src/Resources/css/nord-dark.css
Normal file
File diff suppressed because one or more lines are too long
3664
src/Resources/css/nord-light.css
Normal file
3664
src/Resources/css/nord-light.css
Normal file
File diff suppressed because one or more lines are too long
@ -561,3 +561,15 @@
|
||||
-fx-icon-color: black;
|
||||
}
|
||||
|
||||
|
||||
/********************************************
|
||||
* *
|
||||
* Spinner *
|
||||
* *
|
||||
*********************************************/
|
||||
|
||||
|
||||
.spinner {
|
||||
-fx-pref-width: 100px;
|
||||
}
|
||||
|
||||
|
||||
@ -977,4 +977,13 @@
|
||||
-fx-icon-color: black;
|
||||
}
|
||||
|
||||
/********************************************
|
||||
* *
|
||||
* Spinner *
|
||||
* *
|
||||
*********************************************/
|
||||
|
||||
|
||||
.spinner {
|
||||
-fx-pref-width: 100px;
|
||||
}
|
||||
|
||||
3706
src/Resources/css/primer-dark.css
Normal file
3706
src/Resources/css/primer-dark.css
Normal file
File diff suppressed because one or more lines are too long
3664
src/Resources/css/primer-light.css
Normal file
3664
src/Resources/css/primer-light.css
Normal file
File diff suppressed because one or more lines are too long
779
src/Resources/css/primer-pamguard.css
Normal file
779
src/Resources/css/primer-pamguard.css
Normal file
@ -0,0 +1,779 @@
|
||||
|
||||
|
||||
{
|
||||
-color-dark: #010409;
|
||||
-color-light: #ffffff;
|
||||
-color-base-0: #f0f6fc;
|
||||
-color-base-1: #c9d1d9;
|
||||
-color-base-2: #b1bac4;
|
||||
-color-base-3: #8b949e;
|
||||
-color-base-4: #6e7681;
|
||||
-color-base-5: #484f58;
|
||||
-color-base-6: #30363d;
|
||||
-color-base-7: #21262d;
|
||||
-color-base-8: #161b22;
|
||||
-color-base-9: #0d1117;
|
||||
-color-accent-0: #cae8ff;
|
||||
-color-accent-1: #a5d6ff;
|
||||
-color-accent-2: #79c0ff;
|
||||
-color-accent-3: #58a6ff;
|
||||
-color-accent-4: #388bfd;
|
||||
-color-accent-5: #1f6feb;
|
||||
-color-accent-6: #1158c7;
|
||||
-color-accent-7: #0d419d;
|
||||
-color-accent-8: #0c2d6b;
|
||||
-color-accent-9: #051d4d;
|
||||
-color-success-0: #aff5b4;
|
||||
-color-success-1: #7ee787;
|
||||
-color-success-2: #56d364;
|
||||
-color-success-3: #3fb950;
|
||||
-color-success-4: #2ea043;
|
||||
-color-success-5: #238636;
|
||||
-color-success-6: #196c2e;
|
||||
-color-success-7: #0f5323;
|
||||
-color-success-8: #033a16;
|
||||
-color-success-9: #04260f;
|
||||
-color-warning-0: #f8e3a1;
|
||||
-color-warning-1: #f2cc60;
|
||||
-color-warning-2: #e3b341;
|
||||
-color-warning-3: #d29922;
|
||||
-color-warning-4: #bb8009;
|
||||
-color-warning-5: #9e6a03;
|
||||
-color-warning-6: #845306;
|
||||
-color-warning-7: #693e00;
|
||||
-color-warning-8: #4b2900;
|
||||
-color-warning-9: #341a00;
|
||||
-color-danger-0: #ffdcd7;
|
||||
-color-danger-1: #ffc1ba;
|
||||
-color-danger-2: #ffa198;
|
||||
-color-danger-3: #ff7b72;
|
||||
-color-danger-4: #f85149;
|
||||
-color-danger-5: #da3633;
|
||||
-color-danger-6: #b62324;
|
||||
-color-danger-7: #8e1519;
|
||||
-color-danger-8: #67060c;
|
||||
-color-danger-9: #490202;
|
||||
-color-fg-default: #c9d1d9;
|
||||
-color-fg-muted: #8b949e;
|
||||
-color-fg-subtle: #6e7681;
|
||||
-color-fg-emphasis: #ffffff;
|
||||
-color-bg-default: #0d1117;
|
||||
-color-bg-overlay: #0d1117;
|
||||
-color-bg-subtle: #161b22;
|
||||
-color-bg-inset: #010409;
|
||||
-color-border-default: #30363d;
|
||||
-color-border-muted: #21262d;
|
||||
-color-border-subtle: rgba(240, 246, 252, 0.1);
|
||||
-color-shadow-default: #010409;
|
||||
-color-neutral-emphasis-plus: #6e7681;
|
||||
-color-neutral-emphasis: #6e7681;
|
||||
-color-neutral-muted: rgba(110, 118, 129, 0.4);
|
||||
-color-neutral-subtle: rgba(110, 118, 129, 0.1);
|
||||
-color-accent-fg: #58a6ff;
|
||||
-color-accent-emphasis: #1f6feb;
|
||||
-color-accent-muted: rgba(56, 139, 253, 0.4);
|
||||
-color-accent-subtle: rgba(56, 139, 253, 0.15);
|
||||
-color-warning-fg: #d29922;
|
||||
-color-warning-emphasis: #9e6a03;
|
||||
-color-warning-muted: rgba(187, 128, 9, 0.4);
|
||||
-color-warning-subtle: rgba(187, 128, 9, 0.15);
|
||||
-color-success-fg: #3fb950;
|
||||
-color-success-emphasis: #238636;
|
||||
-color-success-muted: rgba(46, 160, 67, 0.4);
|
||||
-color-success-subtle: rgba(46, 160, 67, 0.15);
|
||||
-color-danger-fg: #f85149;
|
||||
-color-danger-emphasis: #da3633;
|
||||
-color-danger-muted: rgba(248, 81, 73, 0.4);
|
||||
-color-danger-subtle: rgba(248, 81, 73, 0.15);
|
||||
-color-chart-1: #f3622d;
|
||||
-color-chart-2: #fba71b;
|
||||
-color-chart-3: #57b757;
|
||||
-color-chart-4: #41a9c9;
|
||||
-color-chart-5: #4258c9;
|
||||
-color-chart-6: #9a42c8;
|
||||
-color-chart-7: #c84164;
|
||||
-color-chart-8: #888888;
|
||||
-color-chart-1-alpha70: rgba(243, 98, 45, 0.7);
|
||||
-color-chart-2-alpha70: rgba(251, 167, 27, 0.7);
|
||||
-color-chart-3-alpha70: rgba(87, 183, 87, 0.7);
|
||||
-color-chart-4-alpha70: rgba(65, 169, 201, 0.7);
|
||||
-color-chart-5-alpha70: rgba(66, 88, 201, 0.7);
|
||||
-color-chart-6-alpha70: rgba(154, 66, 200, 0.7);
|
||||
-color-chart-7-alpha70: rgba(200, 65, 100, 0.7);
|
||||
-color-chart-8-alpha70: rgba(136, 136, 136, 0.7);
|
||||
-color-chart-1-alpha20: rgba(243, 98, 45, 0.2);
|
||||
-color-chart-2-alpha20: rgba(251, 167, 27, 0.2);
|
||||
-color-chart-3-alpha20: rgba(87, 183, 87, 0.2);
|
||||
-color-chart-4-alpha20: rgba(65, 169, 201, 0.2);
|
||||
-color-chart-5-alpha20: rgba(66, 88, 201, 0.2);
|
||||
-color-chart-6-alpha20: rgba(154, 66, 200, 0.2);
|
||||
-color-chart-7-alpha20: rgba(200, 65, 100, 0.2);
|
||||
-color-chart-8-alpha20: rgba(136, 136, 136, 0.2);
|
||||
|
||||
-fx-pambackground: rgba(238,238,238);
|
||||
-fx-darkbackground: -color-bg-default;
|
||||
-fx-darkbackground-trans: rgba(13, 17, 23,0.90);
|
||||
-fx-highlight: -color-base-6;
|
||||
-fx-highlight_border: -color-button-fg;
|
||||
-fx-text: -color-fg-default;
|
||||
-fx-border_col: -color-border-default;
|
||||
-fx-icon_col: -color-fg-default;
|
||||
}
|
||||
|
||||
.root {
|
||||
-fx-background-color:-fx-darkbackground;
|
||||
-fx-font-size: 12px;
|
||||
-fx-background-radius: inherit;
|
||||
-fx-background-insets: inherit;
|
||||
-fx-padding: 5px 5px 5px 5px;
|
||||
}
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* Panes *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
.pane {
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
}
|
||||
|
||||
.pane-trans{
|
||||
-fx-background-color: -fx-darkbackground-trans;
|
||||
}
|
||||
|
||||
.pane-opaque {
|
||||
-fx-background-color: -fx-pambackground;
|
||||
}
|
||||
|
||||
/*for plot panes*/
|
||||
.pane-plot {
|
||||
-fx-background-color: -fx-plotbackground;
|
||||
}
|
||||
|
||||
|
||||
.button {
|
||||
-color-button-bg: -color-bg-subtle;
|
||||
-color-button-fg: -color-fg-default;
|
||||
-color-button-border: -color-border-default;
|
||||
-color-button-bg-hover: -color-base-6;
|
||||
-color-button-fg-hover: -color-button-fg;
|
||||
-color-button-border-hover: -color-button-border;
|
||||
-color-button-bg-focused: -color-button-bg;
|
||||
-color-button-fg-focused: -color-button-fg;
|
||||
-color-button-border-focused: -color-accent-emphasis;
|
||||
-color-button-bg-pressed: -color-bg-subtle;
|
||||
-color-button-fg-pressed: -color-button-fg;
|
||||
-color-button-border-pressed: transparent;
|
||||
-fx-background-color: -color-button-border, -color-button-bg;
|
||||
-fx-background-insets: 0, 1px;
|
||||
-fx-background-radius: 4px;
|
||||
-fx-graphic-text-gap: 6px;
|
||||
-fx-text-fill: -color-button-fg;
|
||||
-fx-alignment: CENTER;
|
||||
-fx-padding: 8px 12px 8px 12px;
|
||||
}
|
||||
|
||||
.menu-button,
|
||||
.split-menu-button {
|
||||
-color-button-bg: -color-bg-subtle;
|
||||
-color-button-fg: -color-fg-default;
|
||||
-color-button-border: -color-border-default;
|
||||
-color-button-bg-hover: -color-base-6;
|
||||
-color-button-fg-hover: -color-button-fg;
|
||||
-color-button-border-hover: -color-button-border;
|
||||
-color-button-bg-focused: -color-button-bg;
|
||||
-color-button-fg-focused: -color-button-fg;
|
||||
-color-button-border-focused: -color-accent-emphasis;
|
||||
-color-button-bg-pressed: -color-bg-subtle;
|
||||
-color-button-fg-pressed: -color-button-fg;
|
||||
-color-button-border-pressed: transparent;
|
||||
-fx-background-color: -color-button-border, -color-button-bg;
|
||||
-fx-background-insets: 0, 1px;
|
||||
-fx-background-radius: 4px;
|
||||
-fx-graphic-text-gap: 6px;
|
||||
-fx-text-fill: -color-button-fg;
|
||||
-fx-alignment: CENTER;
|
||||
-fx-padding: 0;
|
||||
-fx-alignment: CENTER_LEFT;
|
||||
}
|
||||
|
||||
.menu-button.accent,
|
||||
.split-menu-button.accent {
|
||||
-color-button-bg: -color-accent-emphasis;
|
||||
-color-button-fg: -color-fg-emphasis;
|
||||
-color-button-border: -color-accent-emphasis;
|
||||
-color-button-bg-hover: -color-accent-emphasis;
|
||||
-color-button-fg-hover: -color-fg-emphasis;
|
||||
-color-button-border-hover: -color-accent-emphasis;
|
||||
-color-button-bg-focused: -color-accent-6;
|
||||
-color-button-fg-focused: -color-fg-emphasis;
|
||||
-color-button-border-focused: -color-accent-emphasis;
|
||||
-color-button-bg-pressed: -color-accent-emphasis;
|
||||
-color-button-fg-pressed: -color-fg-emphasis;
|
||||
-color-button-border-pressed: transparent;
|
||||
}
|
||||
.menu-button.accent.button-outlined,
|
||||
.split-menu-button.accent.button-outlined {
|
||||
-color-button-bg: -color-bg-default;
|
||||
-color-button-fg: -color-accent-fg;
|
||||
-color-button-bg-hover: -color-accent-emphasis;
|
||||
-color-button-fg-hover: -color-fg-emphasis;
|
||||
}
|
||||
.menu-button.accent.flat,
|
||||
.split-menu-button.accent.flat {
|
||||
-color-button-fg: -color-accent-fg;
|
||||
-color-button-bg-hover: -color-accent-subtle;
|
||||
}
|
||||
.menu-button.success,
|
||||
.split-menu-button.success {
|
||||
-color-button-bg: -color-success-emphasis;
|
||||
-color-button-fg: -color-fg-emphasis;
|
||||
-color-button-border: -color-success-emphasis;
|
||||
-color-button-bg-hover: -color-success-emphasis;
|
||||
-color-button-fg-hover: -color-fg-emphasis;
|
||||
-color-button-border-hover: -color-success-emphasis;
|
||||
-color-button-bg-focused: -color-success-6;
|
||||
-color-button-fg-focused: -color-fg-emphasis;
|
||||
-color-button-border-focused: -color-success-emphasis;
|
||||
-color-button-bg-pressed: -color-success-emphasis;
|
||||
-color-button-fg-pressed: -color-fg-emphasis;
|
||||
-color-button-border-pressed: transparent;
|
||||
}
|
||||
.menu-button.success.button-outlined,
|
||||
.split-menu-button.success.button-outlined {
|
||||
-color-button-bg: -color-bg-default;
|
||||
-color-button-fg: -color-success-fg;
|
||||
-color-button-bg-hover: -color-success-emphasis;
|
||||
-color-button-fg-hover: -color-fg-emphasis;
|
||||
}
|
||||
.menu-button.success.flat,
|
||||
.split-menu-button.success.flat {
|
||||
-color-button-fg: -color-success-fg;
|
||||
-color-button-bg-hover: -color-success-subtle;
|
||||
}
|
||||
.menu-button.danger,
|
||||
.split-menu-button.danger {
|
||||
-color-button-bg: -color-danger-emphasis;
|
||||
-color-button-fg: -color-fg-emphasis;
|
||||
-color-button-border: -color-danger-emphasis;
|
||||
-color-button-bg-hover: -color-danger-emphasis;
|
||||
-color-button-fg-hover: -color-fg-emphasis;
|
||||
-color-button-border-hover: -color-danger-emphasis;
|
||||
-color-button-bg-focused: -color-danger-6;
|
||||
-color-button-fg-focused: -color-fg-emphasis;
|
||||
-color-button-border-focused: -color-danger-emphasis;
|
||||
-color-button-bg-pressed: -color-danger-emphasis;
|
||||
-color-button-fg-pressed: -color-fg-emphasis;
|
||||
-color-button-border-pressed: transparent;
|
||||
}
|
||||
.menu-button.danger.button-outlined,
|
||||
.split-menu-button.danger.button-outlined {
|
||||
-color-button-bg: -color-bg-default;
|
||||
-color-button-fg: -color-danger-fg;
|
||||
-color-button-bg-hover: -color-danger-emphasis;
|
||||
-color-button-fg-hover: -color-fg-emphasis;
|
||||
}
|
||||
.menu-button.danger.flat,
|
||||
.split-menu-button.danger.flat {
|
||||
-color-button-fg: -color-danger-fg;
|
||||
-color-button-bg-hover: -color-danger-subtle;
|
||||
}
|
||||
.menu-button.flat,
|
||||
.split-menu-button.flat {
|
||||
-color-button-bg: transparent;
|
||||
-color-button-fg: -color-fg-default;
|
||||
-color-button-border: transparent;
|
||||
-color-button-bg-hover: -color-bg-subtle;
|
||||
-color-button-fg-hover: -color-button-fg;
|
||||
-color-button-border-hover: -color-bg-subtle;
|
||||
-color-button-bg-focused: -color-button-bg;
|
||||
-color-button-fg-focused: -color-button-fg;
|
||||
-color-button-border-focused: -color-button-bg;
|
||||
-color-button-bg-pressed: -color-button-bg;
|
||||
-color-button-fg-pressed: -color-button-fg;
|
||||
-color-button-border-pressed: transparent;
|
||||
}
|
||||
|
||||
|
||||
.toggle-button {
|
||||
-color-button-bg: -color-bg-subtle;
|
||||
-color-button-fg: -color-fg-default;
|
||||
-color-button-border: -color-border-default;
|
||||
-color-button-bg-hover: -color-base-6;
|
||||
-color-button-fg-hover: -color-button-fg;
|
||||
-color-button-border-hover: -color-button-border;
|
||||
-color-button-bg-focused: -color-button-bg;
|
||||
-color-button-fg-focused: -color-button-fg;
|
||||
-color-button-border-focused: -color-accent-emphasis;
|
||||
-color-button-bg-pressed: -color-bg-subtle;
|
||||
-color-button-fg-pressed: -color-button-fg;
|
||||
-color-button-border-pressed: transparent;
|
||||
-fx-background-color: -color-button-border, -color-button-bg;
|
||||
-fx-background-insets: 0, 1px;
|
||||
-fx-background-radius: 4px;
|
||||
-fx-graphic-text-gap: 6px;
|
||||
-fx-text-fill: -color-button-fg;
|
||||
-fx-alignment: CENTER;
|
||||
-color-button-bg-selected: -color-accent-emphasis;
|
||||
-color-button-fg-selected: -color-fg-emphasis;
|
||||
-fx-padding: 8px 12px 8px 12px;
|
||||
}
|
||||
|
||||
|
||||
.list-view {
|
||||
-color-cell-bg: -color-bg-default;
|
||||
-color-cell-fg: -color-fg-default;
|
||||
-color-cell-bg-selected: -color-base-6;
|
||||
-color-cell-fg-selected: -color-fg-default;
|
||||
-color-cell-bg-odd: -color-bg-subtle;
|
||||
-color-cell-border: -color-border-default;
|
||||
-fx-border-color: -color-cell-border;
|
||||
-fx-border-width: 1px;
|
||||
-fx-border-radius: 0;
|
||||
}
|
||||
|
||||
.table-view {
|
||||
-color-cell-bg: -color-bg-default;
|
||||
-color-cell-fg: -color-fg-default;
|
||||
-color-cell-bg-selected: -color-base-6;
|
||||
-color-cell-fg-selected: -color-fg-default;
|
||||
-color-cell-bg-odd: -color-bg-subtle;
|
||||
-color-cell-border: -color-border-default;
|
||||
-fx-border-color: -color-cell-border;
|
||||
-fx-border-width: 1px;
|
||||
-fx-border-radius: 0;
|
||||
-color-header-bg: -color-bg-subtle;
|
||||
-color-header-fg: -color-fg-default;
|
||||
}
|
||||
|
||||
.titled-pane > .title > .text {
|
||||
-fx-font-size: 1em;
|
||||
}
|
||||
|
||||
.tree-view {
|
||||
-color-cell-bg: -color-bg-default;
|
||||
-color-cell-fg: -color-fg-default;
|
||||
-color-cell-bg-selected: -color-base-6;
|
||||
-color-cell-fg-selected: -color-fg-default;
|
||||
-color-cell-bg-odd: -color-bg-subtle;
|
||||
-color-cell-border: -color-border-default;
|
||||
-fx-border-color: -color-cell-border;
|
||||
-fx-border-width: 1px;
|
||||
-fx-border-radius: 0;
|
||||
}
|
||||
|
||||
.tree-table-view {
|
||||
-color-cell-bg: -color-bg-default;
|
||||
-color-cell-fg: -color-fg-default;
|
||||
-color-cell-bg-selected: -color-base-6;
|
||||
-color-cell-fg-selected: -color-fg-default;
|
||||
-color-cell-bg-odd: -color-bg-subtle;
|
||||
-color-cell-border: -color-border-default;
|
||||
-fx-border-color: -color-cell-border;
|
||||
-fx-border-width: 1px;
|
||||
-fx-border-radius: 0;
|
||||
-color-header-bg: -color-bg-subtle;
|
||||
-color-header-fg: -color-fg-default;
|
||||
}
|
||||
|
||||
.list-view:focused > .virtual-flow > .clipped-container > .sheet > .list-cell:filled:selected,
|
||||
.tree-view:focused > .virtual-flow > .clipped-container > .sheet > .tree-cell:filled:selected,
|
||||
.table-view:focused > .virtual-flow > .clipped-container > .sheet > .table-row-cell:filled:selected,
|
||||
.tree-table-view:focused > .virtual-flow > .clipped-container > .sheet > .tree-table-row-cell:filled:selected {
|
||||
-color-cell-fg: -color-cell-fg-selected;
|
||||
-fx-background-color: -color-cell-border, -color-cell-bg-selected;
|
||||
}
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* ikonli icons *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
#module-pane .ikonli-font-icon {
|
||||
-fx-icon-color: black;
|
||||
}
|
||||
|
||||
|
||||
.titled-pane {
|
||||
-fx-background-color: -color-bg-default;
|
||||
-fx-text-fill: -color-fg-default;
|
||||
-fx-effect: none;
|
||||
}
|
||||
|
||||
|
||||
/****************************************************************
|
||||
|
||||
ScrollPane
|
||||
|
||||
****************************************************************/
|
||||
.scroll-pane {
|
||||
-fx-background: #0d1117;
|
||||
-fx-background-color: transparent;
|
||||
}
|
||||
|
||||
.scroll-pane > .viewport {
|
||||
-fx-background-color: transparent;
|
||||
}
|
||||
|
||||
.scroll-pane-dark {
|
||||
-fx-background: -fx-darkbackground;
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
}
|
||||
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* Hiding Tab *
|
||||
* *
|
||||
******************************************************************************/
|
||||
#hide-tab {
|
||||
-fx-background-color: transparent;
|
||||
-fx-border-radius: 5 5 0 0;
|
||||
-fx-background-radius: 5 5 0 0;
|
||||
-fx-border-color: -fx-border_col;
|
||||
}
|
||||
|
||||
#show-tab {
|
||||
-fx-background-color: transparent;
|
||||
-fx-border-radius: 5 5 0 0;
|
||||
-fx-background-radius: 5 5 0 0;
|
||||
-fx-border-color: -fx-border_col;
|
||||
}
|
||||
|
||||
#hide-tab-highlight {
|
||||
-fx-background-color: -fx-highlight;
|
||||
-fx-border-radius: 5 5 0 0;
|
||||
-fx-background-radius: 5 5 0 0;
|
||||
-fx-border-color: -fx-highlight_border;
|
||||
}
|
||||
|
||||
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* Button *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
/*.button{
|
||||
-fx-text-fill: white;
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-border-color: -fx-border_col;
|
||||
-fx-border-radius: 5;
|
||||
-fx-background-radius:6;
|
||||
-fx-padding: 3 6 6 6;
|
||||
}*/
|
||||
|
||||
/*.button:hover{
|
||||
-fx-background-color: -fx-highlight;
|
||||
-fx-border-color: -fx-highlight_border;
|
||||
}
|
||||
|
||||
.button:selected{
|
||||
-fx-border-color: -fx-highlight;
|
||||
}
|
||||
*/
|
||||
/**
|
||||
* Button for closing a hiding panel. Right indicates bottoms points towards the right, closing a hiding panel
|
||||
* on the right hand side of the screen. These buttons have a transparent background and rounded corners.
|
||||
*/
|
||||
/** top-left, top-right, bottom-right, and bottom-left corners, in that order. */
|
||||
.close-button-right{
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 0 10 10 0;
|
||||
-fx-border-color: transparent;
|
||||
-fx-border-radius: 0 10 10 0;
|
||||
}
|
||||
|
||||
|
||||
.close-button-left{
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 10 0 0 10;
|
||||
-fx-border-color: transparent;
|
||||
-fx-border-radius: 10 0 0 10;
|
||||
}
|
||||
|
||||
|
||||
.close-button-top{
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 10 10 0 0;
|
||||
-fx-border-color: transparent;
|
||||
-fx-border-radius: 10 10 0 0;
|
||||
}
|
||||
|
||||
|
||||
.close-button-bottom{
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 0 0 10 10;
|
||||
-fx-border-color: transparent;
|
||||
-fx-border-radius: 0 0 10 10;
|
||||
}
|
||||
|
||||
|
||||
.close-button-bottom-trans{
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 0 0 10 10;
|
||||
-fx-border-radius: 0 0 10 10;
|
||||
}
|
||||
|
||||
.close-button-left-trans{
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 10 0 0 10;
|
||||
-fx-border-radius: 10 0 0 10;
|
||||
}
|
||||
|
||||
.close-button-right-trans{
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 0 10 10 0;
|
||||
-fx-border-radius: 0 10 10 0;
|
||||
}
|
||||
|
||||
.square-button{
|
||||
-fx-background-radius: 0 0 0 0;
|
||||
-fx-border-radius: 0 0 0 0;
|
||||
}
|
||||
|
||||
.square-button-trans{
|
||||
-fx-background-color: transparent;
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-radius: 0 0 0 0;
|
||||
-fx-border-radius: 0 0 0 0;
|
||||
}
|
||||
|
||||
.module-hide-top{
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-radius: 5 5 0 0;
|
||||
-fx-border-radius: 5 5 0 0;
|
||||
}
|
||||
|
||||
.module-hide-bottom{
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-radius: 0 0 5 5;
|
||||
-fx-border-radius: 0 0 5 5;
|
||||
}
|
||||
|
||||
.delete-button:hover{
|
||||
-fx-background-color: rgba(1,0,0,0.7);
|
||||
}
|
||||
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* Pop over *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
.popover {
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-background-radius: 5;
|
||||
-fx-border-radius: 5;
|
||||
}
|
||||
|
||||
.popover > .content {
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-background-radius: 5;
|
||||
-fx-border-radius: 5;
|
||||
}
|
||||
|
||||
.popover > .arrow {
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-background-radius: 5;
|
||||
-fx-border-radius: 5;
|
||||
}
|
||||
|
||||
/*weird way to do it but need this to colour the arrow*/
|
||||
.popover > .border {
|
||||
/*-fx-stroke: linear-gradient(to bottom, rgba(0,0,0, .3), rgba(0, 0, 0, .7)) ;*/
|
||||
-fx-stroke-width: 0.5;
|
||||
-fx-fill: -fx-darkbackground; /* instead -fx-background-color */
|
||||
}
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* SplitMenuButton *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
.split-menu-button{
|
||||
-fx-text-fill: -fx-text;
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-border-color: -fx-border_col;
|
||||
-fx-border-radius: 5;
|
||||
}
|
||||
|
||||
|
||||
.split-menu-button:hover{
|
||||
/*-fx-border-color: -fx-highlight_border;*/
|
||||
}
|
||||
|
||||
|
||||
.split-menu-button .label {
|
||||
-fx-text-fill: white;
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-border-radius: 5;
|
||||
}
|
||||
|
||||
|
||||
.split-menu-button .label:hover {
|
||||
-fx-background-color: -fx-highlight;
|
||||
}
|
||||
|
||||
|
||||
.split-menu-button .arrow-button {
|
||||
-fx-text-fill: -fx-text;
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-border-radius: 5;
|
||||
}
|
||||
|
||||
|
||||
.split-menu-button .arrow-button:hover {
|
||||
-fx-background-color: -fx-highlight;
|
||||
}
|
||||
|
||||
|
||||
/**********/
|
||||
|
||||
|
||||
.menu-item {
|
||||
-fx-background-color: -color-bg-default;
|
||||
-fx-padding: 8px 12px 8px 12px;
|
||||
}
|
||||
.menu-item > .graphic-container {
|
||||
-fx-padding: 0 6px 0 0;
|
||||
}
|
||||
.menu-item > .label {
|
||||
-fx-padding: 0 1em 0 0;
|
||||
-fx-text-fill: -color-fg-default;
|
||||
}
|
||||
.menu-item > .left-container {
|
||||
-fx-padding: 0 1em 0 0;
|
||||
}
|
||||
.menu-item > .right-container {
|
||||
-fx-padding: 0 0 0 0.5em;
|
||||
}
|
||||
.menu-item:focused {
|
||||
-fx-background-color: -color-base-7, -color-base-7;
|
||||
}
|
||||
.menu-item:disabled {
|
||||
-fx-opacity: 0.4;
|
||||
-fx-background-color: -color-bg-default;
|
||||
}
|
||||
|
||||
|
||||
|
||||
/********************************************
|
||||
* *
|
||||
* Spinner *
|
||||
* *
|
||||
*********************************************/
|
||||
|
||||
|
||||
.spinner {
|
||||
-fx-pref-width: 120px;
|
||||
}
|
||||
|
||||
.dialog-pane > .content {
|
||||
-fx-padding: 1em 1em 1em 1em;
|
||||
}
|
||||
|
||||
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* Hiding Pane *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
|
||||
/**
|
||||
* Button for closing a hiding panel. Right indicates bottoms points towards the right, closing a hiding panel
|
||||
* on the right hand side of the screen. These buttons have a transparent background and rounded corners.
|
||||
*/
|
||||
/** top-left, top-right, bottom-right, and bottom-left corners, in that order. */
|
||||
.close-button-right{
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 0 10 10 0;
|
||||
-fx-border-radius: 0 10 10 0;
|
||||
}
|
||||
|
||||
.close-button-right:hover {
|
||||
-fx-background-color: -fx-highlight;
|
||||
}
|
||||
|
||||
|
||||
.close-button-left{
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 10 0 0 10;
|
||||
-fx-border-radius: 10 0 0 10;
|
||||
}
|
||||
|
||||
.close-button-left:hover {
|
||||
-fx-background-color: -fx-highlight;
|
||||
}
|
||||
|
||||
|
||||
.close-button-top{
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 10 10 0 0;
|
||||
-fx-border-radius: 10 10 0 0;
|
||||
}
|
||||
|
||||
|
||||
.close-button-bottom {
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 0 0 10 10;
|
||||
-fx-border-radius: 0 0 10 10;
|
||||
}
|
||||
|
||||
.close-button-bottom:hover {
|
||||
-fx-background-color: -fx-highlight;
|
||||
}
|
||||
|
||||
|
||||
.close-button-bottom-grey{
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-radius: 0 0 10 10;
|
||||
-fx-border-radius: 0 0 10 10;
|
||||
}
|
||||
|
||||
.close-button-left-trans{
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 10 0 0 10;
|
||||
-fx-border-radius: 10 0 0 10;
|
||||
}
|
||||
|
||||
.close-button-left-trans:focused {
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 10 0 0 10;
|
||||
-fx-border-radius: 10 0 0 10;
|
||||
}
|
||||
|
||||
.close-button-right-trans{
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 0 10 10 0;
|
||||
-fx-border-radius: 0 10 10 0;
|
||||
}
|
||||
|
||||
.close-button-right-trans:focused {
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 0 10 10 0;
|
||||
-fx-border-radius: 0 10 10 0;
|
||||
}
|
||||
|
||||
|
||||
.menu-square-button {
|
||||
-fx-border-color: -fx_border_col;
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 0 0 0 0;
|
||||
-fx-border-radius: 0 0 0 0;
|
||||
}
|
||||
|
||||
12
src/audioMoth/AudioMothControl.java
Normal file
12
src/audioMoth/AudioMothControl.java
Normal file
@ -0,0 +1,12 @@
|
||||
package audioMoth;
|
||||
|
||||
import PamController.PamControlledUnit;
|
||||
|
||||
public class AudioMothControl extends PamControlledUnit {
|
||||
|
||||
public AudioMothControl(String unitType, String unitName) {
|
||||
super(unitType, unitName);
|
||||
// TODO Auto-generated constructor stub
|
||||
}
|
||||
|
||||
}
|
||||
@ -6,7 +6,7 @@ import java.io.IOException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.attribute.BasicFileAttributes;
|
||||
|
||||
import PamUtils.PamAudioFileFilter;
|
||||
import Acquisition.pamAudio.PamAudioFileFilter;
|
||||
import PamUtils.PamCalendar;
|
||||
|
||||
public class TestFileDates {
|
||||
|
||||
@ -226,7 +226,7 @@ public class SweepClassifier implements ClickIdentifier , PamSettings {
|
||||
return clickDetector;
|
||||
}
|
||||
|
||||
protected int getNextFreeCode(int currCode) {
|
||||
public int getNextFreeCode(int currCode) {
|
||||
int newCode = currCode;
|
||||
while (codeTaken(++newCode));
|
||||
return newCode;
|
||||
@ -277,7 +277,7 @@ public class SweepClassifier implements ClickIdentifier , PamSettings {
|
||||
* Set the params for the sweep classifier.
|
||||
* @params the sweep classifier params to set.
|
||||
*/
|
||||
public void setSeepClassifierParams(SweepClassifierParameters sweepClassifierParameters) {
|
||||
public void setSweepClassifierParams(SweepClassifierParameters sweepClassifierParameters) {
|
||||
this.sweepClassifierParameters=sweepClassifierParameters;
|
||||
}
|
||||
|
||||
|
||||
@ -106,7 +106,10 @@ public class ClickParameters implements Serializable, Cloneable, ManagedParamete
|
||||
*/
|
||||
public int backgroundIntervalMillis = 5000;
|
||||
|
||||
public int clickClassifierType = ClickClassifierManager.CLASSIFY_BASIC;
|
||||
/**
|
||||
* The type of classifier to use - CLASSIFY_SWEEP is the default.
|
||||
*/
|
||||
public int clickClassifierType = ClickClassifierManager.CLASSIFY_BETTER;
|
||||
|
||||
public boolean runEchoOnline = false;
|
||||
|
||||
|
||||
@ -6,6 +6,7 @@ import java.text.ParseException;
|
||||
import clickDetector.ClickControl;
|
||||
import clickDetector.ClickParameters;
|
||||
import clickDetector.layoutFX.clickClassifiers.ClickClassifyPaneFX;
|
||||
import javafx.geometry.HPos;
|
||||
import javafx.geometry.Orientation;
|
||||
import javafx.geometry.Pos;
|
||||
import javafx.scene.Node;
|
||||
@ -14,12 +15,14 @@ import javafx.scene.control.Label;
|
||||
import javafx.scene.control.Spinner;
|
||||
import javafx.scene.control.Tab;
|
||||
import javafx.scene.control.TabPane;
|
||||
import javafx.scene.layout.ColumnConstraints;
|
||||
import javafx.scene.layout.GridPane;
|
||||
import javafx.scene.layout.Pane;
|
||||
import javafx.scene.layout.Priority;
|
||||
import javafx.scene.paint.Color;
|
||||
import javafx.scene.shape.Line;
|
||||
import javafx.util.StringConverter;
|
||||
import net.synedra.validatorfx.Validator;
|
||||
import PamController.PamController;
|
||||
import PamController.SettingsPane;
|
||||
import PamDetection.RawDataUnit;
|
||||
@ -44,7 +47,7 @@ import pamViewFX.fxNodes.utilityPanes.GroupedSourcePaneFX;
|
||||
*/
|
||||
public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
|
||||
public static double PREF_SPINNER_WIDTH = 100;
|
||||
public static double PREF_SPINNER_WIDTH = 140;
|
||||
|
||||
/**
|
||||
* Group source pane for the click settings pane.
|
||||
@ -160,25 +163,35 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
private Tab tdoaTab;
|
||||
|
||||
/**
|
||||
* The default pane width
|
||||
* The main holder pane.
|
||||
*/
|
||||
public static double paneWidth=500;
|
||||
private PamBorderPane mainPane;
|
||||
|
||||
/**
|
||||
* The default pane height.
|
||||
*/
|
||||
public static double paneHeigt=800;
|
||||
public static double PREF_PANE_HEIGHT=850;
|
||||
|
||||
/**
|
||||
* The main holder pane.
|
||||
* The default pane width
|
||||
*/
|
||||
private PamBorderPane mainPane;
|
||||
public static double PREF_PANE_WIDTH=550;
|
||||
|
||||
|
||||
/**
|
||||
* Validator which checks for errors
|
||||
*/
|
||||
private Validator clickValidator;
|
||||
|
||||
|
||||
|
||||
public ClickSettingsPane(ClickControl clickControl){
|
||||
super(null);
|
||||
this.clickControl=clickControl;
|
||||
mainPane= new PamBorderPane();
|
||||
|
||||
clickValidator = new Validator();
|
||||
|
||||
pamTabbedPane=new PamTabPane();
|
||||
pamTabbedPane.setAddTabButton(false);
|
||||
pamTabbedPane.setTabClosingPolicy(TabPane.TabClosingPolicy.UNAVAILABLE);
|
||||
@ -199,10 +212,10 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
//add everything to tabs.
|
||||
pamTabbedPane.getTabs().add(new Tab("Click Detection", detectionPane));
|
||||
clickDelayPane=createDelayPane();
|
||||
pamTabbedPane.getTabs().add(tdoaTab=new Tab("Click TDOA", clickDelayPane.getContentNode()));
|
||||
pamTabbedPane.getTabs().add(tdoaTab=new Tab("TDOA and Echoes", clickDelayPane.getContentNode()));
|
||||
tdoaTab.setOnSelectionChanged((event)->{
|
||||
if (pamTabbedPane.getSelectionModel().getSelectedItem()==tdoaTab){
|
||||
System.out.println("clickDelayPane: "+clickDelayPane);
|
||||
//System.out.println("clickDelayPane: "+clickDelayPane);
|
||||
//need to update the tab with a copy of the current click params.
|
||||
clickDelayPane.setParams(clickClassificationPane.getParams(clickParameters.clone()));
|
||||
}
|
||||
@ -217,19 +230,19 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
triggerFilter=new FilterPaneFX(Orientation.VERTICAL);
|
||||
pamTabbedPane.getTabs().add(new Tab("Trigger Filter", triggerFilter.getContentNode()));
|
||||
|
||||
//echo detection pane.
|
||||
echoDetection= new ClickEchoPane(clickControl);
|
||||
pamTabbedPane.getTabs().add(new Tab("Echo Detection", echoDetection.getContentNode()));
|
||||
// //echo detection pane.
|
||||
// echoDetection= new ClickEchoPane(clickControl);
|
||||
// pamTabbedPane.getTabs().add(new Tab("Echo Detection", echoDetection.getContentNode()));
|
||||
|
||||
/***Note: FX does not implment click train detection in click detector****/
|
||||
|
||||
//classifiaction pane.
|
||||
pamTabbedPane.getTabs().add(new Tab("Click Classification", clickClassificationPane=new ClickClassifyPaneFX(clickControl)));
|
||||
pamTabbedPane.getTabs().add(new Tab("Classification", clickClassificationPane=new ClickClassifyPaneFX(clickControl)));
|
||||
|
||||
//want a slightly bigger pane as a lot going on in this dialog.
|
||||
//Note JavaFX 8u61 + has auto DPI scaling so this is really the size of a dialog on a standard HD monitor of
|
||||
//reasonable size, rather than actual pixels
|
||||
mainPane.setPrefSize(paneWidth, paneHeigt);
|
||||
mainPane.setPrefSize(PREF_PANE_WIDTH, PREF_PANE_HEIGHT);
|
||||
|
||||
//addTabListeners();
|
||||
mainPane.setCenter(new PamBorderPane(pamTabbedPane));
|
||||
@ -269,7 +282,7 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
sourcePane=createClickSourcePane(); //create the source pane.
|
||||
|
||||
|
||||
GridPane.setColumnSpan(sourcePane.getDataBlockBox(), 4);
|
||||
GridPane.setColumnSpan(sourcePane.getDataBlockBox(), 2);
|
||||
//now create trigger pane. The trigger pane is added to the source pane.
|
||||
Label triggerLabel = new Label("Trigger Channels");
|
||||
PamGuiManagerFX.titleFont2style(triggerLabel);
|
||||
@ -277,6 +290,7 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
|
||||
triggerChannels=new Pane();
|
||||
sourcePane.getSourcePane().add(triggerChannels,1,3);
|
||||
GridPane.setHalignment(triggerChannels, HPos.RIGHT);
|
||||
createTriggerChannels();
|
||||
//sourcePane.getSourcePane().add(createClickTriggerPane(), 2, 3);
|
||||
|
||||
@ -285,7 +299,18 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
// pamTabbedPane.getTabs().add(new Tab("Click Echoes", createEchoPane()));
|
||||
// pamTabbedPane.getTabs().add(new Tab("Click Delays", createDelayPane()));
|
||||
|
||||
sourcePane.setPrefWidth(paneWidth);
|
||||
ColumnConstraints col1 = new ColumnConstraints();
|
||||
col1.setHgrow(Priority.ALWAYS);
|
||||
|
||||
ColumnConstraints col2 = new ColumnConstraints();
|
||||
col2.setHgrow(Priority.SOMETIMES);
|
||||
col2.setHalignment(HPos.RIGHT);
|
||||
sourcePane.getSourcePane().getColumnConstraints().addAll(col1, col2);
|
||||
|
||||
PamHBox.setHgrow(sourcePane.getChannelPane(), Priority.NEVER);
|
||||
|
||||
//sourcePane.setMinWidth(PREF_PANE_WIDTH);
|
||||
sourcePane.getSourcePane().setPrefWidth(PREF_PANE_WIDTH);
|
||||
|
||||
return sourcePane;
|
||||
}
|
||||
@ -326,7 +351,7 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
preSampleSpinner=new PamSpinner<Integer>(0, 10000000, 100, 20);
|
||||
preSampleSpinner.setEditable(true);
|
||||
preSampleSpinner.getStyleClass().add(Spinner.STYLE_CLASS_SPLIT_ARROWS_HORIZONTAL);
|
||||
preSampleSpinner.setPrefWidth(PREF_SPINNER_WIDTH);
|
||||
//preSampleSpinner.setPrefWidth(PREF_SPINNER_WIDTH);
|
||||
|
||||
lengthPane.add(preSampleSpinner,1,2);
|
||||
lengthPane.add(new Label("samples"),2,2);
|
||||
@ -336,7 +361,8 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
postSampleSpinner=new PamSpinner<Integer>(0, 10000000, 100, 20);
|
||||
postSampleSpinner.setEditable(true);
|
||||
postSampleSpinner.getStyleClass().add(Spinner.STYLE_CLASS_SPLIT_ARROWS_HORIZONTAL);
|
||||
postSampleSpinner.setPrefWidth(PREF_SPINNER_WIDTH);
|
||||
//postSampleSpinner.setPrefWidth(PREF_SPINNER_WIDTH);
|
||||
|
||||
|
||||
lengthPane.add(postSampleSpinner,1,3);
|
||||
lengthPane.add(new Label("samples"),2,3);
|
||||
@ -360,13 +386,24 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
else selectNoChannels();
|
||||
});
|
||||
|
||||
//create a list of trigger boxes
|
||||
//create a list of trigger boxesc
|
||||
for (int i=0; i<triggerBoxes.length; i++){
|
||||
triggerBoxes[i]=new CheckBox(("Channel "+i));
|
||||
final int n=i;
|
||||
triggerBoxes[i].setOnAction((action)->{
|
||||
selectionChanged(n);
|
||||
clickValidator.validate(); //make sure all nodes are resrt when one channel is ticked.
|
||||
});
|
||||
clickValidator.createCheck()
|
||||
.dependsOn(("trigger " + n), triggerBoxes[i].selectedProperty())
|
||||
.withMethod(c -> {
|
||||
if (!isATriggerSelected() ) {
|
||||
c.error("At least one trigger channel needs to be selected for the module to work");
|
||||
}
|
||||
})
|
||||
.decorates(triggerBoxes[n])
|
||||
.immediate();
|
||||
|
||||
}
|
||||
|
||||
populateTriggerPane();
|
||||
@ -406,7 +443,7 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
threshold.getStyleClass().add(Spinner.STYLE_CLASS_SPLIT_ARROWS_HORIZONTAL);
|
||||
threshold.getValueFactory().valueProperty().addListener((obs, before, after)->{
|
||||
clickParameters.dbThreshold=after;
|
||||
clickTriggerGraph.updateWaveformGraph(this.clickParameters);
|
||||
clickTriggerGraph.updateGraphFilter();
|
||||
});
|
||||
triggerBox.add(threshold,1,0);
|
||||
triggerBox.add(new Label("dB"),2,0);
|
||||
@ -420,7 +457,7 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
longFilter.getValueFactory().valueProperty().addListener((obs, before, after)->{
|
||||
clickParameters.longFilter=after;
|
||||
clickTriggerGraph.setLongFilter(clickParameters.longFilter);
|
||||
clickTriggerGraph.updateWaveformGraph(this.clickParameters);
|
||||
clickTriggerGraph.updateGraphFilter();
|
||||
});
|
||||
triggerBox.add(longFilter,1,1);
|
||||
longFilter.setPrefWidth(PREF_SPINNER_WIDTH);
|
||||
@ -444,11 +481,14 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
shortFilter.getValueFactory().valueProperty().addListener((obs, before, after)->{
|
||||
clickParameters.shortFilter=after;
|
||||
clickTriggerGraph.setShortFilter(clickParameters.shortFilter);
|
||||
clickTriggerGraph.updateWaveformGraph(this.clickParameters);
|
||||
clickTriggerGraph.updateGraphFilter();
|
||||
});
|
||||
shortFilter.setPrefWidth(PREF_SPINNER_WIDTH);
|
||||
triggerBox.add(shortFilter,1,3);
|
||||
|
||||
//forces the grid pane to be larger - grid panes can be a little funny.
|
||||
shortFilter.setMinWidth(PREF_SPINNER_WIDTH);
|
||||
|
||||
triggerPane.add(triggerBox,0,1);
|
||||
|
||||
//triggerPane.setGridLinesVisible(true);
|
||||
@ -525,7 +565,7 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the current channle bitmap.
|
||||
* Get the current channels bitmap.
|
||||
* @return integer channel bitmap
|
||||
*/
|
||||
private int getChannels(){
|
||||
@ -539,6 +579,32 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
return channels;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Get the number of selected trigger channels.
|
||||
* @return the number of selected trigger channels.
|
||||
*/
|
||||
private int getNSelectedTrigger() {
|
||||
int channels=getChannels();
|
||||
int n=0;
|
||||
//now add correct trigger children again
|
||||
for (int i = 0; i < Math.min(PamConstants.MAX_CHANNELS, triggerBoxes.length); i++) {
|
||||
if ((channels & 1<<i) != 0 && triggerBoxes[i].isSelected()){
|
||||
n++;
|
||||
};
|
||||
}
|
||||
return n;
|
||||
}
|
||||
|
||||
/**
|
||||
* Check whether at least one trigger channel is selected.
|
||||
* @return true of a trigger channel is selected.
|
||||
*/
|
||||
private boolean isATriggerSelected() {
|
||||
return getNSelectedTrigger()>0;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Create trigger channels
|
||||
*/
|
||||
@ -555,6 +621,8 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
triggerChannels.getChildren().add(selectAll);
|
||||
for (int i = 0; i < Math.min(PamConstants.MAX_CHANNELS, triggerBoxes.length); i++) {
|
||||
if ((channels & 1<<i) != 0){
|
||||
|
||||
//triggerBoxes[i] = new CheckBox("Channel " + i);
|
||||
triggerChannels.getChildren().add(triggerBoxes[i]);
|
||||
triggerBoxes[i].layoutYProperty().unbind();
|
||||
triggerBoxes[i].layoutYProperty().bind(sourcePane.getChannelBoxes()[i].layoutYProperty());
|
||||
@ -670,6 +738,8 @@ public class ClickSettingsPane extends SettingsPane<ClickParameters>{
|
||||
}
|
||||
}
|
||||
|
||||
clickParameters = clickClassificationPane.getParams(clickParameters);
|
||||
|
||||
}
|
||||
catch (Exception e){
|
||||
e.printStackTrace();
|
||||
|
||||
@ -1,15 +1,25 @@
|
||||
package clickDetector.layoutFX;
|
||||
|
||||
import clickDetector.ClickParameters;
|
||||
import java.util.ArrayList;
|
||||
|
||||
import PamUtils.PamArrayUtils;
|
||||
import javafx.concurrent.Task;
|
||||
import javafx.geometry.Pos;
|
||||
import javafx.scene.chart.LineChart;
|
||||
import javafx.scene.chart.NumberAxis;
|
||||
import javafx.scene.chart.XYChart.Data;
|
||||
import javafx.scene.chart.XYChart.Series;
|
||||
import javafx.scene.control.ChoiceBox;
|
||||
import javafx.scene.layout.Pane;
|
||||
import javafx.scene.layout.StackPane;
|
||||
import pamViewFX.fxNodes.PamBorderPane;
|
||||
import pamViewFX.fxNodes.PamStackPane;
|
||||
import pamViewFX.fxNodes.pamChart.PamLineChart;
|
||||
import simulatedAcquisition.sounds.ClickSound;
|
||||
import simulatedAcquisition.sounds.ClickSound.WINDOWTYPE;
|
||||
import simulatedAcquisition.sounds.SimSignal;
|
||||
import rawDeepLearningClassifier.layoutFX.exampleSounds.ExampleSound;
|
||||
import rawDeepLearningClassifier.layoutFX.exampleSounds.ExampleSoundFactory;
|
||||
import rawDeepLearningClassifier.layoutFX.exampleSounds.ExampleSoundFactory.ExampleSoundCategory;
|
||||
import rawDeepLearningClassifier.layoutFX.exampleSounds.ExampleSoundFactory.ExampleSoundType;
|
||||
import javafx.application.Platform;
|
||||
|
||||
/**
|
||||
* Graph which shows a click and associated trigger functions
|
||||
@ -18,12 +28,6 @@ import simulatedAcquisition.sounds.SimSignal;
|
||||
*/
|
||||
public class ClickTriggerGraph extends PamBorderPane {
|
||||
|
||||
public final static int PORPOISE_CLICK=0;
|
||||
|
||||
public final static int SPERM_WHALE=1;
|
||||
|
||||
|
||||
private int currentClick=PORPOISE_CLICK;
|
||||
|
||||
private NumberAxis xAxis;
|
||||
|
||||
@ -48,46 +52,31 @@ public class ClickTriggerGraph extends PamBorderPane {
|
||||
|
||||
private int freq2;
|
||||
|
||||
public static final int PREF_GRAPH_WIDTH = 400;
|
||||
|
||||
/**
|
||||
* The example sound factory.
|
||||
*/
|
||||
private ExampleSoundFactory exampleSoundFactory;
|
||||
|
||||
private Series<Number, Number> signalLevelSeries;
|
||||
|
||||
private Series<Number, Number> noiseLevelSeries;
|
||||
|
||||
Task<Integer> task;
|
||||
|
||||
private double[] waveform;
|
||||
|
||||
|
||||
public ClickTriggerGraph(){
|
||||
this.exampleSoundFactory = new ExampleSoundFactory();
|
||||
this.setCenter(createWaveformGraph());
|
||||
this.setPrefWidth(400);
|
||||
//FIXME - seems to a resize bug in high DPI displays. Seems fixed in 8u60.
|
||||
this.waveform=generateClickWaveform(currentClick, noise);
|
||||
generateClickWaveform(ExampleSoundType.PORPOISE_CLICK, noise);
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Update graph. Delete current data series and create new one.
|
||||
*/
|
||||
public void updateWaveformGraph(ClickParameters clickParameters){
|
||||
|
||||
// System.out.println(" Graph width: xAxis: "+xAxis.widthProperty().get());
|
||||
// System.out.println(" Graph width: this: "+this.widthProperty().get());
|
||||
// System.out.println(" Graph width: plotChart: "+plotChart.widthProperty().get());
|
||||
// System.out.println(" xAxisLayout:: "+xAxis.layoutXProperty().get());
|
||||
// System.out.println(" plotLayout:: "+plotChart.layoutXProperty().get());
|
||||
|
||||
Series<Number, Number> waveformSeries = new Series<Number, Number>();
|
||||
Series<Number, Number> signalLevelSeries = new Series<Number, Number>();
|
||||
Series<Number, Number> noiseLevelSeries = new Series<Number, Number>();
|
||||
|
||||
|
||||
double[] signalLevel=calcFilter(waveform, shortFilter);
|
||||
double[] noiseLevel=calcFilter(waveform, longFilter);
|
||||
|
||||
|
||||
for (int i=0; i<waveform.length; i++){
|
||||
waveformSeries.getData().add(new Data<Number, Number>(i, waveform[i]));
|
||||
signalLevelSeries.getData().add(new Data<Number, Number>(i, signalLevel[i]));
|
||||
noiseLevelSeries.getData().add(new Data<Number, Number>(i, noiseLevel[i]));
|
||||
|
||||
}
|
||||
|
||||
plotChart.getData().removeAll(plotChart.getData());
|
||||
plotChart.getData().addAll(waveformSeries,signalLevelSeries,noiseLevelSeries);
|
||||
}
|
||||
|
||||
|
||||
public double[] calcFilter(double[] waveform, double alpha){
|
||||
@ -100,51 +89,11 @@ public class ClickTriggerGraph extends PamBorderPane {
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Generate a click waveform with some added noise.
|
||||
* @param type - the type of click e.g. ClickTriggerGraph.PORPOISE_CLICK.
|
||||
* @param noise. 0 to 1. 1 means max noise amplitude will be same as maximum click amplitude.
|
||||
* @return click and noise waveform.
|
||||
*/
|
||||
private double[] generateClickWaveform(int type, double noise){
|
||||
SimSignal clickSound;
|
||||
int sR;
|
||||
double length;
|
||||
double freq;
|
||||
switch (type){
|
||||
//TODO - add more types of clicks.
|
||||
case PORPOISE_CLICK:
|
||||
clickSound=new ClickSound("Porpoise", freq=140000, freq2=140000, length=0.00015, WINDOWTYPE.HANN);
|
||||
sR=500000;
|
||||
break;
|
||||
case SPERM_WHALE:
|
||||
clickSound=(new ClickSound("Beaked Whale", 30000, 60000, length = 0.3e-3, WINDOWTYPE.HANN));
|
||||
sR=192000;
|
||||
break;
|
||||
default:
|
||||
clickSound=new ClickSound("Porpoise", freq=140000, freq2=140000, length=0.00015, WINDOWTYPE.HANN);
|
||||
sR=500000;
|
||||
break;
|
||||
}
|
||||
|
||||
//now need to work out how many noise samples to add. Use the length of the click
|
||||
int nNoiseSamples=(int) (2*length*sR);
|
||||
double[] waveform=new double[3*nNoiseSamples];
|
||||
int n=0;
|
||||
for (int i=0; i<3*nNoiseSamples; i++){
|
||||
double noiseSample=noise*(Math.random()-0.5);
|
||||
double[] signal=clickSound.getSignal(0,sR,0);
|
||||
if (i>nNoiseSamples && n <signal.length){
|
||||
waveform[i]=signal[n]+noiseSample;
|
||||
n=n+1;
|
||||
}
|
||||
else waveform[i]=noiseSample;
|
||||
}
|
||||
public Pane createWaveformGraph(){
|
||||
|
||||
return waveform;
|
||||
}
|
||||
StackPane stackPane = new PamStackPane();
|
||||
|
||||
public LineChart<Number, Number> createWaveformGraph(){
|
||||
|
||||
xAxis=new NumberAxis();
|
||||
xAxis.setMaxWidth(Double.MAX_VALUE);
|
||||
@ -162,10 +111,29 @@ public class ClickTriggerGraph extends PamBorderPane {
|
||||
plotChart.setLegendVisible(false);
|
||||
plotChart.setCreateSymbols(false);
|
||||
|
||||
|
||||
plotChart.getStyleClass().add("thin-chart");
|
||||
//plotChart.getXAxis().setSide(Side.BOTTOM);
|
||||
return plotChart;
|
||||
|
||||
ChoiceBox<ExampleSoundType> waveformChoice = new ChoiceBox<ExampleSoundType>();
|
||||
ArrayList<ExampleSoundType> exampleSounds = exampleSoundFactory.getExampleSoundTypes(ExampleSoundCategory.ODONTOCETES_CLICKS, ExampleSoundCategory.BAT);
|
||||
|
||||
for (int i=0; i<exampleSounds.size(); i++) {
|
||||
waveformChoice.getItems().add(exampleSounds.get(i));
|
||||
}
|
||||
waveformChoice.setOnAction((action)->{
|
||||
generateClickWaveform(waveformChoice.getSelectionModel().getSelectedItem(), noise);
|
||||
updateGraphWaveform() ;
|
||||
updateGraphFilter();
|
||||
});
|
||||
waveformChoice.getSelectionModel().select(ExampleSoundType.PORPOISE_CLICK);
|
||||
waveformChoice.setPrefWidth(180);
|
||||
|
||||
StackPane.setAlignment(waveformChoice, Pos.TOP_RIGHT);
|
||||
|
||||
|
||||
stackPane.getChildren().addAll(plotChart, waveformChoice);
|
||||
|
||||
return stackPane;
|
||||
}
|
||||
|
||||
public double getLongFilter() {
|
||||
@ -176,6 +144,131 @@ public class ClickTriggerGraph extends PamBorderPane {
|
||||
this.longFilter = longFilter;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Update the waveform of the species.
|
||||
*/
|
||||
public synchronized void updateGraphWaveform() {
|
||||
plotChart.getData().clear();
|
||||
|
||||
|
||||
Series<Number, Number> waveformSeries = new Series<Number, Number>();
|
||||
for (int i=0; i<waveform.length; i++){
|
||||
waveformSeries.getData().add(new Data<Number, Number>(i, waveform[i]));
|
||||
}
|
||||
|
||||
plotChart.getData().add(waveformSeries);
|
||||
}
|
||||
/**
|
||||
* Update graph. Delete current data series and create new one.
|
||||
*/
|
||||
public synchronized void updateGraphFilter(){
|
||||
|
||||
if (waveform.length<500) {
|
||||
if (task!=null) {
|
||||
task.cancel(true);
|
||||
}
|
||||
|
||||
//no need to do on separate thread.
|
||||
plotChart.getData().remove(signalLevelSeries);
|
||||
plotChart.getData().remove(noiseLevelSeries);
|
||||
|
||||
plotChart.getData().add(signalLevelSeries = calcSeries(waveform, shortFilter));
|
||||
plotChart.getData().add(noiseLevelSeries = calcSeries(waveform, longFilter));
|
||||
}
|
||||
else {
|
||||
if (task!=null) {
|
||||
if (task.isRunning()) {
|
||||
return;
|
||||
}
|
||||
}
|
||||
|
||||
/***
|
||||
* FIXME
|
||||
* This is a little ridiculous but there are two bugs in JavaFX
|
||||
* 1) The line chart is super slow
|
||||
* 2) If you get a freeze in the FX application thread then your trigger the spinner button multiple times.
|
||||
*
|
||||
* Doing this on a thread gets rid of the issue but is not a particular nice solution.
|
||||
*/
|
||||
|
||||
task = new Task<Integer>() {
|
||||
@Override protected Integer call() throws Exception {
|
||||
|
||||
Series<Number, Number> signalLevelSeries1 = calcSeries(waveform, shortFilter);
|
||||
Series<Number, Number> noiseLevelSeries2 = calcSeries(waveform, longFilter);
|
||||
|
||||
Platform.runLater(()->{
|
||||
// if (shortFilter!=shortFilter1 || forceChange) {
|
||||
plotChart.getData().remove(signalLevelSeries);
|
||||
plotChart.getData().add(signalLevelSeries1);
|
||||
signalLevelSeries = signalLevelSeries1;
|
||||
// }
|
||||
|
||||
// if (shortFilter!=shortFilter1 || forceChange) {
|
||||
plotChart.getData().remove(noiseLevelSeries);
|
||||
plotChart.getData().add(noiseLevelSeries2);
|
||||
noiseLevelSeries = noiseLevelSeries2;
|
||||
// }
|
||||
|
||||
});
|
||||
|
||||
return 0;
|
||||
}
|
||||
};
|
||||
|
||||
Thread th = new Thread(task);
|
||||
th.setDaemon(true);
|
||||
th.start();
|
||||
}
|
||||
}
|
||||
|
||||
private Series<Number, Number> calcSeries(double[] waveform, double alpha){
|
||||
Series<Number, Number> signalLevelSeries1 = new Series<Number, Number>();
|
||||
double[] signalLevel=calcFilter(waveform, alpha);
|
||||
|
||||
for (int i=0; i<waveform.length; i++){
|
||||
signalLevelSeries1.getData().add(new Data<Number, Number>(i, signalLevel[i]));
|
||||
}
|
||||
|
||||
return signalLevelSeries1;
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Generate a click waveform with some added noise.
|
||||
* @param type - the type of click e.g. ClickTriggerGraph.PORPOISE_CLICK.
|
||||
* @param noise. 0 to 1. 1 means max noise amplitude will be same as maximum click amplitude.
|
||||
* @return click and noise waveform.
|
||||
*/
|
||||
private void generateClickWaveform(ExampleSoundType selectedItem, double noise) {
|
||||
|
||||
ExampleSound sound = this.exampleSoundFactory.getExampleSound(selectedItem);
|
||||
|
||||
double sR = sound.getSampleRate();
|
||||
|
||||
//System.out.println("Waveform: " + sound.getWave().length + " " + selectedItem);
|
||||
|
||||
double[] clickWave = PamArrayUtils.divide( sound.getWave(), PamArrayUtils.max( sound.getWave()));
|
||||
//now need to work out how many noise samples to add. Use the length of the click
|
||||
int nNoiseSamples=Math.min((int) (clickWave.length), sound.getWave().length >2000? 0 : 100);
|
||||
double[] waveform=new double[2*nNoiseSamples + clickWave.length];
|
||||
int n=0;
|
||||
double[] signal=clickWave;
|
||||
for (int i=0; i<waveform.length; i++){
|
||||
double noiseSample=noise*(Math.random()-0.5);
|
||||
if (i>nNoiseSamples && n<clickWave.length){
|
||||
waveform[i]=signal[n]+noiseSample;
|
||||
n=n+1;
|
||||
}
|
||||
else waveform[i]=noiseSample;
|
||||
}
|
||||
|
||||
this.waveform=waveform;
|
||||
//System.out.println("Waveform: " + waveform.length);
|
||||
}
|
||||
|
||||
|
||||
public double getShortFilter() {
|
||||
return shortFilter;
|
||||
}
|
||||
|
||||
@ -18,6 +18,7 @@ import clickDetector.ClickClassifiers.basic.BasicClickIdentifier;
|
||||
|
||||
/**
|
||||
* Pane for the basic click classifier.
|
||||
*
|
||||
* @author Jamie Macaulay
|
||||
*
|
||||
*/
|
||||
@ -319,4 +320,13 @@ public class BasicIdentifierPaneFX implements ClassifyPaneFX {
|
||||
return clickClassifiers;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Get the flip pane. One side shows the table, the other shows the currently selected classifier settings.
|
||||
* @return the flip pane.
|
||||
*/
|
||||
public PamFlipPane getFlipPane() {
|
||||
return flipPane;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@ -23,10 +23,13 @@ import pamViewFX.fxNodes.PamHBox;
|
||||
import pamViewFX.fxNodes.PamStackPane;
|
||||
import pamViewFX.fxNodes.PamVBox;
|
||||
import pamViewFX.fxNodes.hidingPane.HidingPane;
|
||||
import pamViewFX.fxNodes.utilityPanes.PamToggleSwitch;
|
||||
|
||||
/**
|
||||
* Pane which allows users to select click classifiers. Rather than opening endless dialogs click settings are
|
||||
* handled by sliding panes.
|
||||
* <p>
|
||||
* Note that this is a copy...ish of the swing frameowrk - wouldn't od things this way usually.
|
||||
* @author Jamie Macaulay
|
||||
*
|
||||
*/
|
||||
@ -43,7 +46,7 @@ public class ClickClassifyPaneFX extends PamStackPane {
|
||||
private ClickControl clickControl;
|
||||
|
||||
|
||||
private CheckBox runOnlineCheckBox;
|
||||
private PamToggleSwitch runOnlineCheckBox;
|
||||
|
||||
private CheckBox discardClicksCheckBox;
|
||||
|
||||
@ -120,7 +123,7 @@ public class ClickClassifyPaneFX extends PamStackPane {
|
||||
classifierComboBox.getItems().add(clickControl.getClassifierManager().getClassifierName(i));
|
||||
classifierComboBox.setOnAction((action)->{
|
||||
//get the current click identifier.
|
||||
System.out.println("ClickClassifyPaneFX:setOnAction: " +classifierComboBox.getSelectionModel().getSelectedIndex());
|
||||
//System.out.println("ClickClassifyPaneFX:setOnAction: " +classifierComboBox.getSelectionModel().getSelectedIndex());
|
||||
currentClickIdentifier=clickControl.getClassifierManager().
|
||||
getClassifier(classifierComboBox.getSelectionModel().getSelectedIndex());
|
||||
//change the centre pane to classifier specific pane
|
||||
@ -128,8 +131,8 @@ public class ClickClassifyPaneFX extends PamStackPane {
|
||||
});
|
||||
}
|
||||
|
||||
runOnlineCheckBox=new CheckBox("Run Classifier");
|
||||
discardClicksCheckBox=new CheckBox("Discdard Classified Clicks");
|
||||
runOnlineCheckBox=new PamToggleSwitch("Run Classifier");
|
||||
//discardClicksCheckBox=new CheckBox("Discdard Classified Clicks");
|
||||
|
||||
PamHBox pamHBox=new PamHBox();
|
||||
pamHBox.setAlignment(Pos.CENTER);
|
||||
@ -168,6 +171,9 @@ public class ClickClassifyPaneFX extends PamStackPane {
|
||||
|
||||
//System.out.println("ClickClassifyPaneFX:setParams(): " +classifierComboBox.getSelectionModel().getSelectedIndex());
|
||||
classifierComboBox.getSelectionModel().select(clickParameters.clickClassifierType);
|
||||
|
||||
//System.out.println("ClickClassifyPaneFX: setParams: get selected classifier is: " + clickParameters.clickClassifierType);
|
||||
|
||||
//set classifier parameters
|
||||
if (currentClickIdentifier!=null && currentClickIdentifier.getClassifierPane()!=null) {
|
||||
this.currentClickIdentifier.getClassifierPane().setParams();
|
||||
@ -180,6 +186,8 @@ public class ClickClassifyPaneFX extends PamStackPane {
|
||||
//System.out.println("ClickClassifyPaneFX:getParams(): " +classifierComboBox.getSelectionModel().getSelectedIndex());
|
||||
|
||||
clickParameters.clickClassifierType=classifierComboBox.getSelectionModel().getSelectedIndex();
|
||||
|
||||
//System.out.println("ClickClassifyPaneFX: getParams: get selected classifier is: " + clickParameters.clickClassifierType);
|
||||
if (currentClickIdentifier != null && currentClickIdentifier.getClassifierPane() != null) {
|
||||
currentClickIdentifier.getClassifierPane().getParams();
|
||||
}
|
||||
|
||||
@ -38,6 +38,14 @@ public class SweepClassifierPaneFX extends BasicIdentifierPaneFX {
|
||||
@Override
|
||||
public void setClassifierPane(ClickTypeProperty clickTypeProperty){
|
||||
SweepClassifierSetPaneFX sweepPane=new SweepClassifierSetPaneFX(sweepClickClassifier);
|
||||
|
||||
|
||||
//make it so the title of the pane is the same as the name as the classifier
|
||||
getFlipPane().getAdvLabel().textProperty().unbind();
|
||||
getFlipPane().getAdvLabel().textProperty().bind( sweepPane.getNameTextProperty());
|
||||
|
||||
sweepPane.classifierItemRow = sweepClickClassifier.getSweepClassifierParams().getSetRow((SweepClassifierSet) clickTypeProperty.getClickType());
|
||||
|
||||
sweepPane.setParams(clickTypeProperty);
|
||||
super.getClickTypeHolder().setCenter(sweepPane.getContentNode());
|
||||
|
||||
@ -52,14 +60,20 @@ public class SweepClassifierPaneFX extends BasicIdentifierPaneFX {
|
||||
|
||||
@Override
|
||||
public void setParams() {
|
||||
|
||||
sweepIdParameters = sweepClickClassifier.getSweepClassifierParams().clone();
|
||||
|
||||
|
||||
//change the table
|
||||
tableDataChanged();
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean getParams() {
|
||||
sweepClickClassifier.setSeepClassifierParams(sweepIdParameters);
|
||||
// System.out.println("Sweep classifier getParams: " + sweepIdParameters);
|
||||
if (sweepIdParameters==null) sweepIdParameters = new SweepClassifierParameters();
|
||||
|
||||
sweepClickClassifier.setSweepClassifierParams(sweepIdParameters);
|
||||
|
||||
//remove all classifiers and add whatever is in the table.
|
||||
sweepClickClassifier.getSweepClassifierParams().removeAll();
|
||||
|
||||
@ -3,6 +3,7 @@ package clickDetector.layoutFX.clickClassifiers;
|
||||
|
||||
import fftFilter.FFTFilterParams;
|
||||
import fftManager.FFTLengthModeled;
|
||||
import javafx.beans.property.StringProperty;
|
||||
import javafx.geometry.HPos;
|
||||
import javafx.geometry.Insets;
|
||||
import javafx.geometry.Orientation;
|
||||
@ -30,9 +31,13 @@ import pamViewFX.fxNodes.picker.SymbolPicker;
|
||||
import pamViewFX.fxNodes.utilityPanes.FreqBandPane;
|
||||
import pamViewFX.fxNodes.utilityPanes.PamToggleSwitch;
|
||||
import pamViewFX.fxNodes.utilityPanes.SimpleFilterPaneFX;
|
||||
import pamViewFX.fxNodes.utilsFX.PamUtilsFX;
|
||||
import pamViewFX.PamGuiManagerFX;
|
||||
import net.synedra.validatorfx.Validator;
|
||||
|
||||
import PamController.SettingsPane;
|
||||
import PamView.PamSymbol;
|
||||
import PamView.symbol.SymbolData;
|
||||
import clickDetector.ClickClassifiers.basicSweep.CodeHost;
|
||||
import clickDetector.ClickClassifiers.basicSweep.SweepClassifier;
|
||||
import clickDetector.ClickClassifiers.basicSweep.SweepClassifierSet;
|
||||
@ -95,7 +100,11 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
|
||||
*/
|
||||
private AmplitudeBlock amplitudeBlock;
|
||||
|
||||
PamBorderPane mainPane = new PamBorderPane();
|
||||
private PamBorderPane mainPane = new PamBorderPane();
|
||||
|
||||
private Validator validator = new Validator();
|
||||
|
||||
public int classifierItemRow;
|
||||
|
||||
public SweepClassifierSetPaneFX(SweepClassifier sweepClassifier){
|
||||
super(null);
|
||||
@ -325,6 +334,14 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
|
||||
*/
|
||||
private Label lengthMS;
|
||||
|
||||
private ComboBox<String> lengthTypeBox;
|
||||
|
||||
private CheckBox restrictLength;
|
||||
|
||||
private ColorPicker lineColourPicker;
|
||||
|
||||
private ColorPicker fillColourPicker;
|
||||
|
||||
OptionsBox() {
|
||||
super("General Options", false);
|
||||
this.getHolderPane().setCenter(createOptionsPane());
|
||||
@ -334,6 +351,7 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
|
||||
//create the general options
|
||||
private Node createOptionsPane(){
|
||||
|
||||
|
||||
PamGridPane pamGridPane=new PamGridPane();
|
||||
pamGridPane.setHgap(5);
|
||||
pamGridPane.setVgap(5);
|
||||
@ -343,25 +361,54 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
|
||||
|
||||
nameField=new TextField();
|
||||
nameField.setPrefColumnCount(10);
|
||||
pamGridPane.add(nameField, 0, 0);
|
||||
PamGridPane.setColumnSpan(nameField, 2);
|
||||
pamGridPane.add(nameField, 1, 0);
|
||||
PamGridPane.setColumnSpan(nameField, 8);
|
||||
PamGridPane.setHgrow(nameField, Priority.ALWAYS);
|
||||
|
||||
validator.createCheck()
|
||||
.dependsOn("speciesname", nameField.textProperty())
|
||||
.withMethod(c -> {
|
||||
String userName = c.get("speciesname");
|
||||
if (userName == null || userName.length()<=0) {
|
||||
c.error("The classifier must have a name");
|
||||
}
|
||||
})
|
||||
.decorates(nameField)
|
||||
.immediate();
|
||||
;
|
||||
|
||||
|
||||
pamGridPane.add(new Label("Code"), 3, 0);
|
||||
pamGridPane.add(new Label("Code"), 0, 1);
|
||||
|
||||
codeSpinner=new PamSpinner<Integer> (0, 500, 0, 1);
|
||||
codeSpinner=new PamSpinner<Integer> (1, 500, 0, 1);
|
||||
codeSpinner.setEditable(true);
|
||||
//codeSpinner.setPrefWidth(150);
|
||||
codeSpinner.getStyleClass().add(Spinner.STYLE_CLASS_SPLIT_ARROWS_HORIZONTAL);
|
||||
pamGridPane.add(codeSpinner, 1, 0);
|
||||
pamGridPane.add(codeSpinner, 1, 1);
|
||||
|
||||
// pamGridPane.add(new Label("Symbol"), 0,1);
|
||||
|
||||
//create colour picker to allow users to change symbol colour.
|
||||
symbolPicker=new SymbolPicker();
|
||||
pamGridPane.add(symbolPicker, 2, 0);
|
||||
pamGridPane.add(symbolPicker, 3,1);
|
||||
|
||||
pamGridPane.add(new Label("Symbol"), 2,1);
|
||||
|
||||
lineColourPicker = new ColorPicker();
|
||||
lineColourPicker.setStyle("-fx-color-label-visible: false ;");
|
||||
lineColourPicker.setOnAction((action)->{
|
||||
symbolPicker.setLineColour(lineColourPicker.getValue());
|
||||
});
|
||||
pamGridPane.add(lineColourPicker, 4, 1);
|
||||
|
||||
|
||||
fillColourPicker = new ColorPicker();
|
||||
fillColourPicker.setStyle("-fx-color-label-visible: false ;");
|
||||
fillColourPicker.setOnAction((action)->{
|
||||
symbolPicker.setFillColour(fillColourPicker.getValue());
|
||||
});
|
||||
pamGridPane.add(fillColourPicker, 5, 1);
|
||||
|
||||
pamGridPane.add(new Label("Symbol"), 3,0);
|
||||
|
||||
// //create a button to allow users to change symbol shape.
|
||||
// symbolColour=new ColorPicker();
|
||||
@ -371,35 +418,46 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
|
||||
// });
|
||||
|
||||
//channel options
|
||||
pamGridPane.add(new Label("Channels"), 0,1);
|
||||
pamGridPane.add(new Label("Channels"), 0,2);
|
||||
|
||||
channelsBox = new ComboBox<String>();
|
||||
for (int i = 0; i < 3; i++) {
|
||||
channelsBox.getItems().add(SweepClassifierSet.getChannelOptionsName(i));
|
||||
}
|
||||
pamGridPane.add(channelsBox, 1,1);
|
||||
pamGridPane.add(channelsBox, 1,2);
|
||||
|
||||
PamGridPane.setColumnSpan(channelsBox, 7);
|
||||
PamGridPane.setColumnSpan(channelsBox,8 );
|
||||
|
||||
//restrict parameter to click centre
|
||||
PamHBox clickCenterBox=new PamHBox();
|
||||
clickCenterBox.setSpacing(5);
|
||||
|
||||
clickCenterBox.getChildren().add(new CheckBox("Analyse click "));
|
||||
clickCenterBox.getChildren().add(restrictLength = new CheckBox("Trim click"));
|
||||
|
||||
clickLengthSpinner=new PamSpinner<Integer>(4,102400,128,32);
|
||||
clickLengthSpinner.setEditable(true);
|
||||
//clickLengthSpinner.setPrefWidth(150);
|
||||
clickLengthSpinner.getStyleClass().add(Spinner.STYLE_CLASS_SPLIT_ARROWS_HORIZONTAL);
|
||||
clickLengthSpinner.valueProperty().addListener((obsVal, oldVal, newVal)->{
|
||||
setLengthLabel();
|
||||
});
|
||||
|
||||
clickCenterBox.getChildren().add(clickLengthSpinner);
|
||||
clickCenterBox.getChildren().add(new Label("samples"));
|
||||
Label samplesLabel =new Label("samples");
|
||||
clickCenterBox.getChildren().add(samplesLabel);
|
||||
clickCenterBox.getChildren().add(lengthMS=new Label("()"));
|
||||
clickCenterBox.getChildren().add(new Label("around click center."));
|
||||
clickCenterBox.getChildren().add(lengthTypeBox = new ComboBox<String>());
|
||||
lengthTypeBox.getItems().add("around click center");
|
||||
lengthTypeBox.getItems().add("from start of click");
|
||||
clickCenterBox.setAlignment(Pos.CENTER_LEFT);
|
||||
PamGridPane.setColumnSpan(clickCenterBox, 4);
|
||||
PamGridPane.setHgrow(clickCenterBox, Priority.ALWAYS);
|
||||
pamGridPane.add(clickCenterBox, 0,2);
|
||||
|
||||
restrictLength.setOnAction((action)->{
|
||||
lengthTypeBox.setDisable(!restrictLength.isSelected());
|
||||
clickLengthSpinner.setDisable(!restrictLength.isSelected());
|
||||
samplesLabel.setDisable(!restrictLength.isSelected());
|
||||
lengthMS.setDisable(!restrictLength.isSelected());
|
||||
});
|
||||
|
||||
|
||||
// //column constraints
|
||||
// ColumnConstraints col1 = new ColumnConstraints();
|
||||
@ -415,13 +473,15 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
|
||||
//
|
||||
// pamGridPane.getColumnConstraints().addAll(col1, col2, col3,col4);
|
||||
|
||||
return pamGridPane;
|
||||
PamVBox holder = new PamVBox();
|
||||
holder.setSpacing(5);
|
||||
holder.getChildren().addAll(pamGridPane,clickCenterBox);
|
||||
|
||||
return holder;
|
||||
}
|
||||
|
||||
@Override
|
||||
public int getCode() {
|
||||
// TODO Auto-generated method stub
|
||||
return codeSpinner.getValue();
|
||||
}
|
||||
|
||||
@ -442,22 +502,88 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
|
||||
lengthMS.setText(String.format("(%.2f ms)", fftLength * 1000 / sr));
|
||||
}
|
||||
|
||||
/**
|
||||
* Set the length in seconds.
|
||||
*/
|
||||
private void setLengthLabel() {
|
||||
float sr = sweepClassifier.getClickDetector().getSampleRate();
|
||||
lengthMS.setText(String.format("(%.2f ms)", clickLengthSpinner.getValue() * 1000 / sr));
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void setParams() {
|
||||
|
||||
if (sweepClassifierSet == null) {
|
||||
//symbolViewer.setSymbol(null);
|
||||
symbolPicker.getSelectionModel().select(0);
|
||||
nameField.setText("");
|
||||
setCode(sweepClassifier.getNextFreeCode(0));
|
||||
}
|
||||
else {
|
||||
symbolPicker.setSymbol(sweepClassifierSet.symbol == null? null : sweepClassifierSet.symbol.getSymbol());
|
||||
nameField.setText(sweepClassifierSet.getName());
|
||||
codeSpinner.getValueFactory().setValue(sweepClassifierSet.getSpeciesCode());
|
||||
setCode(sweepClassifierSet.getSpeciesCode());
|
||||
}
|
||||
|
||||
if (sweepClassifierSet == null) {
|
||||
return;
|
||||
}
|
||||
|
||||
lengthTypeBox.getSelectionModel().select(sweepClassifierSet.restrictedBinstype);
|
||||
|
||||
channelsBox.getSelectionModel().select(sweepClassifierSet.channelChoices);
|
||||
clickLengthSpinner.getValueFactory().setValue(sweepClassifierSet.restrictedBins);
|
||||
restrictLength.setSelected(sweepClassifierSet.restrictLength);
|
||||
setFFTLength(sweepClassifierSet.restrictedBins);
|
||||
|
||||
|
||||
// nameField.setText(sweepClassifierSet.getName());
|
||||
// codeSpinner.getValueFactory().setValue(sweepClassifierSet.getSpeciesCode());
|
||||
// channelsBox.getSelectionModel().select(sweepClassifierSet.channelChoices);
|
||||
//
|
||||
// //length stuff
|
||||
// clickLengthSpinner.getValueFactory().setValue(sweepClassifierSet.restrictedBins);
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
protected boolean getParams() {
|
||||
sweepClassifierSet.setName(nameField.getText());
|
||||
sweepClassifierSet.setSpeciesCode(codeSpinner.getValue());
|
||||
|
||||
if (this.symbolPicker.getValue()==null) {
|
||||
return showWarning("You must pick a symbol");
|
||||
}
|
||||
|
||||
SymbolData symbolData = new SymbolData(this.symbolPicker.getValue().getSymbol(), 10,10,true,
|
||||
PamUtilsFX.fxToAWTColor(this.lineColourPicker.getValue()), PamUtilsFX.fxToAWTColor(this.fillColourPicker.getValue()));
|
||||
sweepClassifierSet.symbol= new PamSymbol(symbolData);
|
||||
if (sweepClassifierSet.getName().length() <= 0) {
|
||||
return showWarning("You must enter a name for this type of click");
|
||||
}
|
||||
sweepClassifierSet.setSpeciesCode(getCode());
|
||||
if (sweepClassifier.codeDuplicated(sweepClassifierSet, classifierItemRow) ||
|
||||
sweepClassifierSet.getSpeciesCode() <= 0){
|
||||
return showWarning("You must enter a unique positive integer species code");
|
||||
}
|
||||
if (sweepClassifierSet.symbol == null) {
|
||||
return showWarning("You must select a symbol");
|
||||
}
|
||||
sweepClassifierSet.channelChoices = channelsBox.getSelectionModel().getSelectedIndex();
|
||||
sweepClassifierSet.restrictLength = restrictLength.isSelected();
|
||||
|
||||
sweepClassifierSet.restrictedBinstype = lengthTypeBox.getSelectionModel().getSelectedIndex();
|
||||
|
||||
try {
|
||||
sweepClassifierSet.restrictedBins = clickLengthSpinner.getValue();
|
||||
}
|
||||
catch (NumberFormatException e) {
|
||||
return showWarning("Invalid Restricted length value");
|
||||
}
|
||||
return true;
|
||||
// sweepClassifierSet.setName(nameField.getText());
|
||||
// sweepClassifierSet.setSpeciesCode(codeSpinner.getValue());
|
||||
// sweepClassifierSet.channelChoices=channelsBox.getSelectionModel().getSelectedIndex();
|
||||
// sweepClassifierSet.restrictedBins=clickLengthSpinner.getValue();
|
||||
}
|
||||
|
||||
@Override
|
||||
@ -465,6 +591,10 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
|
||||
// TODO Auto-generated method stub
|
||||
}
|
||||
|
||||
public TextField getNameLabel() {
|
||||
return this.nameField;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
@ -1111,4 +1241,15 @@ public class SweepClassifierSetPaneFX extends SettingsPane<ClickTypeProperty> {
|
||||
|
||||
}
|
||||
|
||||
|
||||
public StringProperty getNameTextProperty() {
|
||||
return optionBox.getNameLabel().textProperty();
|
||||
}
|
||||
|
||||
private boolean showWarning(String string) {
|
||||
PamDialogFX.showWarning(string);
|
||||
return false;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
@ -9,10 +9,7 @@ import clickTrainDetector.classification.CTClassifier;
|
||||
import clickTrainDetector.classification.CTClassifierParams;
|
||||
import clickTrainDetector.classification.CTClassifierType;
|
||||
import clickTrainDetector.classification.bearingClassifier.BearingClassifier;
|
||||
import clickTrainDetector.classification.bearingClassifier.BearingClassifierParams;
|
||||
import clickTrainDetector.classification.idiClassifier.IDIClassification;
|
||||
import clickTrainDetector.classification.idiClassifier.IDIClassifier;
|
||||
import clickTrainDetector.classification.simplechi2classifier.Chi2CTClassification;
|
||||
import clickTrainDetector.classification.simplechi2classifier.Chi2ThresholdClassifier;
|
||||
import clickTrainDetector.classification.templateClassifier.CTTemplateClassifier;
|
||||
import clickTrainDetector.layout.classification.CTClassifierGraphics;
|
||||
|
||||
@ -342,7 +342,7 @@ public abstract class OfflineFileServer<TmapPoint extends FileDataMapPoint> impl
|
||||
return "Sound Files";
|
||||
}
|
||||
|
||||
protected TmapPoint findFirstMapPoint(Iterator<TmapPoint> mapIterator, long startMillis, long endMillis) {
|
||||
public TmapPoint findFirstMapPoint(Iterator<TmapPoint> mapIterator, long startMillis, long endMillis) {
|
||||
TmapPoint mapPoint, prevMapPoint = null;
|
||||
while (mapIterator.hasNext()) {
|
||||
mapPoint = mapIterator.next();
|
||||
|
||||
@ -4,6 +4,7 @@ import java.util.ArrayList;
|
||||
|
||||
import PamController.PamController;
|
||||
import PamModel.PamModuleInfo;
|
||||
import atlantafx.base.theme.PrimerDark;
|
||||
import dataModelFX.ConnectionNodeParams.PAMConnectionNodeType;
|
||||
import dataModelFX.connectionNodes.ModuleIconFactory;
|
||||
import javafx.beans.property.ObjectProperty;
|
||||
@ -12,6 +13,7 @@ import javafx.event.EventHandler;
|
||||
import javafx.geometry.Insets;
|
||||
import javafx.scene.Node;
|
||||
import javafx.scene.SnapshotParameters;
|
||||
import javafx.scene.control.Button;
|
||||
import javafx.scene.control.Tooltip;
|
||||
import javafx.scene.image.ImageView;
|
||||
import javafx.scene.input.ClipboardContent;
|
||||
@ -72,7 +74,9 @@ public class DataModelModulePane extends PamBorderPane {
|
||||
|
||||
private PamScrollPane createPane(){
|
||||
moduleSelectPane=new PamScrollPane();
|
||||
|
||||
moduleSelectPane.getStylesheets().add(PamStylesManagerFX.getPamStylesManagerFX().getCurStyle().getSlidingDialogCSS());
|
||||
|
||||
moduleSelectPane.setPrefWidth(250);
|
||||
moduleSelectPane.getStyleClass().add("scroll-pane-dark");
|
||||
|
||||
|
||||
@ -16,6 +16,7 @@ import pamViewFX.fxNodes.connectionPane.StandardConnectionNode;
|
||||
import pamViewFX.fxNodes.connectionPane.StandardConnectionPlug;
|
||||
import pamViewFX.fxNodes.connectionPane.structures.ConnectionGroupStructure;
|
||||
import pamViewFX.fxNodes.connectionPane.structures.ConnectionStructure;
|
||||
import pamViewFX.fxStyles.PamStylesManagerFX;
|
||||
import javafx.beans.property.ObjectProperty;
|
||||
import javafx.geometry.Orientation;
|
||||
import javafx.scene.control.SplitPane;
|
||||
|
||||
@ -71,7 +71,7 @@ public class ModuleProcessDiagram extends PamBorderPane {
|
||||
|
||||
|
||||
public ModuleProcessDiagram (PamControlledUnit pamControlledUnit){
|
||||
this.getStylesheets().add(PamController.getInstance().getGuiManagerFX().getPamSettingsCSS());
|
||||
//this.getStylesheets().add(PamController.getInstance().getGuiManagerFX().getPamSettingsCSS());
|
||||
this.pamControlledUnit=pamControlledUnit;
|
||||
createUpdateTimer();
|
||||
createControlDataModel();
|
||||
@ -81,7 +81,7 @@ public class ModuleProcessDiagram extends PamBorderPane {
|
||||
private void createControlDataModel(){
|
||||
this.setMinWidth(100);
|
||||
this.setPrefWidth(USE_COMPUTED_SIZE);
|
||||
this.setStyle("-fx-background-color: -fx-darkbackground");
|
||||
//this.setStyle("-fx-background-color: -fx-darkbackground");
|
||||
this.populateDataModel();
|
||||
}
|
||||
|
||||
|
||||
@ -158,7 +158,7 @@ public class TDDisplayFX extends PamBorderPane {
|
||||
/**
|
||||
* The height of the control pane.
|
||||
*/
|
||||
final static double controlPaneHeight=63;
|
||||
final static double CONTROL_PANE_HEIGHT=80;
|
||||
|
||||
|
||||
/**
|
||||
@ -238,7 +238,7 @@ public class TDDisplayFX extends PamBorderPane {
|
||||
//create top hiding panel.
|
||||
controlPane=new TDControlPaneFX(tdControl,this);
|
||||
controlPane.setParams(tdParametersFX);
|
||||
controlPane.setPrefHeight(controlPaneHeight);
|
||||
controlPane.setPrefHeight(CONTROL_PANE_HEIGHT);
|
||||
|
||||
hidingControlPane=new HidingPane(Side.TOP, controlPane, this, false );
|
||||
hidingControlPane.showHidePane(tdParametersFX.showControl);
|
||||
|
||||
@ -272,7 +272,7 @@ public class TDGraphFX extends PamBorderPane {
|
||||
* blocks.
|
||||
*/
|
||||
tdAxisSelPane = new TDDataSelPaneFX(this);
|
||||
tdAxisSelPane.setPrefWidth(250);
|
||||
tdAxisSelPane.setPrefWidth(280);
|
||||
// put pane inside a scroll pane for graph resizing
|
||||
PamScrollPane scrollPane = new PamScrollPane(tdAxisSelPane);
|
||||
// scrollPane.setFitToWidth(true);
|
||||
|
||||
@ -7,11 +7,14 @@ import java.util.ArrayList;
|
||||
import javax.swing.JMenu;
|
||||
import javax.swing.JMenuItem;
|
||||
import PamController.PamControlledUnit;
|
||||
import PamController.PamControlledUnitGUI;
|
||||
import PamController.PamControlledUnitSettings;
|
||||
import PamController.PamControllerInterface;
|
||||
import PamController.PamGUIManager;
|
||||
import PamController.PamSettingManager;
|
||||
import PamController.PamSettings;
|
||||
import PamController.SettingsPane;
|
||||
import PamView.WrapperControlledGUISwing;
|
||||
import PamView.symbol.SymbolData;
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import clickDetector.ClickClassifiers.ClickTypeProvider;
|
||||
@ -67,6 +70,17 @@ public class MTClassifierControl extends PamControlledUnit implements PamSetting
|
||||
*/
|
||||
private MTOfflineProcess mtOfflineProcess;
|
||||
|
||||
/**
|
||||
* The JavaFX graphics
|
||||
*/
|
||||
private MTControlGUI matchedClickGUIFX;
|
||||
|
||||
/**
|
||||
* The swing graphics - in this case the graphics are JavaFX so this calls a swing wrapper
|
||||
* to hold the JavaFX graphics.
|
||||
*/
|
||||
private PamControlledUnitGUI matchedClickGUIGUISwing;
|
||||
|
||||
|
||||
public MTClassifierControl(String unitName) {
|
||||
super("Matched Template Classifier", unitName);
|
||||
@ -379,6 +393,33 @@ public class MTClassifierControl extends PamControlledUnit implements PamSetting
|
||||
return mtOfflineProcess;
|
||||
}
|
||||
|
||||
public void setMTParams(MatchedTemplateParams newParams) {
|
||||
this.matchedTemplateParams = newParams;
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the GUI for the PAMControlled unit. This has multiple GUI options which
|
||||
* are instantiated depending on the view type.
|
||||
*
|
||||
* @param flag. The GUI type flag defined in PAMGuiManager.
|
||||
* @return the GUI for the PamControlledUnit unit.
|
||||
*/
|
||||
public PamControlledUnitGUI getGUI(int flag) {
|
||||
if (flag == PamGUIManager.FX) {
|
||||
if (matchedClickGUIFX == null) {
|
||||
matchedClickGUIFX = new MTControlGUI(this);
|
||||
}
|
||||
return matchedClickGUIFX;
|
||||
}
|
||||
if (flag == PamGUIManager.SWING) {
|
||||
if (matchedClickGUIGUISwing == null) {
|
||||
matchedClickGUIGUISwing = new WrapperControlledGUISwing(this);
|
||||
}
|
||||
return matchedClickGUIGUISwing;
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
74
src/matchedTemplateClassifer/MTControlGUI.java
Normal file
74
src/matchedTemplateClassifer/MTControlGUI.java
Normal file
@ -0,0 +1,74 @@
|
||||
package matchedTemplateClassifer;
|
||||
|
||||
import PamController.PamControlledUnitGUI;
|
||||
import PamController.PamController;
|
||||
import PamController.PamControllerInterface;
|
||||
import PamController.PamGUIManager;
|
||||
import PamController.SettingsPane;
|
||||
import PamView.WrapperControlledGUISwing;
|
||||
import pamViewFX.PamControlledGUIFX;
|
||||
import rawDeepLearningClassifier.DLControl;
|
||||
import rawDeepLearningClassifier.DLControlGUI;
|
||||
import rawDeepLearningClassifier.RawDLParams;
|
||||
|
||||
/**
|
||||
* The JavaFX GUI for the Matched click classifier control...
|
||||
* @author Jamie Macaulay
|
||||
*
|
||||
*/
|
||||
public class MTControlGUI extends PamControlledGUIFX {
|
||||
|
||||
/**
|
||||
* The dl control.
|
||||
*/
|
||||
private MTClassifierControl mtControl;
|
||||
|
||||
|
||||
public MTControlGUI(MTClassifierControl dlcontrol) {
|
||||
this.mtControl = dlcontrol;
|
||||
}
|
||||
|
||||
/**
|
||||
* The settings pane contains ALL possible setting for the module in one placed.
|
||||
* Settings panes can be divided into tabs for more space etc.
|
||||
*
|
||||
* @param <T>
|
||||
* @return a Pane containing controls to change settings for module.
|
||||
*/
|
||||
public SettingsPane<?> getSettingsPane(){
|
||||
mtControl.getSettingsPane().setParams(mtControl.getMTParams());
|
||||
return mtControl.getSettingsPane();
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public void updateParams() {
|
||||
MatchedTemplateParams newParams=mtControl.getSettingsPane().getParams(mtControl.getMTParams());
|
||||
if (newParams!=null) {
|
||||
mtControl.setMTParams(newParams);
|
||||
}
|
||||
//setup the controlled unit.
|
||||
mtControl.setupControlledUnit();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void notifyGUIChange(int changeType) {
|
||||
switch (changeType) {
|
||||
case PamController.INITIALIZATION_COMPLETE:
|
||||
break;
|
||||
case PamControllerInterface.CHANGED_PROCESS_SETTINGS:
|
||||
//data source may have potentially changed. e.g. by a datamodelfx Need to set in params.
|
||||
//System.out.println("FFTControl: CHANGED_PROCESS_SETTINGS : " +fftProcess.getParentDataBlock());
|
||||
if (mtControl.getParentDataBlock()!=null){
|
||||
mtControl.getMTParams().dataSourceName = mtControl.getParentDataBlock().getDataName();
|
||||
}
|
||||
else mtControl.getMTParams().dataSourceName = "";
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
@ -4,6 +4,7 @@ import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
|
||||
import PamController.PamController;
|
||||
import PamDetection.RawDataUnit;
|
||||
import PamUtils.complex.ComplexArray;
|
||||
import PamView.symbol.PamSymbolManager;
|
||||
import PamguardMVC.PamDataBlock;
|
||||
@ -12,8 +13,10 @@ import PamguardMVC.PamInstantProcess;
|
||||
import PamguardMVC.PamObservable;
|
||||
import PamguardMVC.RawDataHolder;
|
||||
import Spectrogram.WindowFunction;
|
||||
import clickDetector.ClickDetection;
|
||||
import clickDetector.ClickLength;
|
||||
import clickDetector.ClickClassifiers.basicSweep.SweepClassifierSet;
|
||||
import clipgenerator.ClipDataUnit;
|
||||
import fftManager.FastFFT;
|
||||
import matchedTemplateClassifer.annotation.MatchedClickAnnotation;
|
||||
import matchedTemplateClassifer.annotation.MatchedClickAnnotationType;
|
||||
@ -486,6 +489,21 @@ public class MTProcess extends PamInstantProcess {
|
||||
return bespokeClassifierManager;
|
||||
}
|
||||
|
||||
/**
|
||||
* A list of data block class types which are compatible as parent data blocks
|
||||
* for the PamProcess. This can return null, e.g. in the case of Acquisition
|
||||
* process.
|
||||
*
|
||||
* @return a list of PamDataBlock sub class types which can be used as parent
|
||||
* data blocks for the process.
|
||||
*/
|
||||
@Override
|
||||
public ArrayList getCompatibleDataUnits(){
|
||||
return new ArrayList<Class<? extends PamDataUnit>>(Arrays.asList(ClickDetection.class));
|
||||
}
|
||||
|
||||
|
||||
|
||||
// /**
|
||||
// * Get the parent click data block.
|
||||
// * @return the click data block which is the parent of the process.
|
||||
|
||||
@ -9,9 +9,10 @@ import java.net.Socket;
|
||||
import javax.swing.JComponent;
|
||||
import javax.swing.Timer;
|
||||
|
||||
import x3.CRC16;
|
||||
import x3.X3FrameDecode;
|
||||
import x3.X3FrameHeader;
|
||||
import org.pamguard.x3.x3.CRC16;
|
||||
import org.pamguard.x3.x3.X3FrameDecode;
|
||||
import org.pamguard.x3.x3.X3FrameHeader;
|
||||
|
||||
import networkTransfer.NetworkObject;
|
||||
import networkTransfer.receive.BuoyStatusDataUnit;
|
||||
import networkTransfer.receive.NetworkDataUser;
|
||||
|
||||
@ -13,12 +13,15 @@ import pamViewFX.fxNodes.PamVBox;
|
||||
import pamViewFX.fxNodes.internalNode.PamInternalPane;
|
||||
import pamViewFX.fxNodes.pamDialogFX.PamDialogFX;
|
||||
import pamViewFX.fxNodes.pamDialogFX.PamSettingsDialogFX;
|
||||
import pamViewFX.fxStyles.PamAtlantaStyle;
|
||||
import pamViewFX.fxStyles.PamStylesManagerFX;
|
||||
import pamViewFX.pamTask.PamTaskUpdate;
|
||||
import userDisplayFX.UserDisplayNodeFX;
|
||||
import PamModel.PamModel;
|
||||
import PamModel.PamModuleInfo;
|
||||
import PamView.PamViewInterface;
|
||||
import atlantafx.base.theme.PrimerDark;
|
||||
import atlantafx.base.theme.PrimerLight;
|
||||
import dataMap.layoutFX.DataMapPaneFX;
|
||||
import PamController.PAMControllerGUI;
|
||||
import PamController.PamControlledUnit;
|
||||
@ -28,6 +31,7 @@ import PamController.PamGUIManager;
|
||||
import PamController.PamSettingManager;
|
||||
import PamController.PamSettings;
|
||||
import dataModelFX.DataModelPaneFX;
|
||||
import javafx.application.Application;
|
||||
import javafx.application.Platform;
|
||||
import javafx.event.ActionEvent;
|
||||
import javafx.geometry.Insets;
|
||||
@ -159,19 +163,22 @@ public class PamGuiManagerFX implements PAMControllerGUI, PamSettings {
|
||||
*/
|
||||
private void start(Stage primaryStage) {
|
||||
|
||||
PamStylesManagerFX.getPamStylesManagerFX().setCurStyle(new PamAtlantaStyle());
|
||||
|
||||
//add stage
|
||||
stages.add(primaryView = new PamGuiFX(primaryStage, this));
|
||||
//create new data model.
|
||||
dataModelFX=stages.get(0).addDataModelTab();
|
||||
|
||||
scene = new Scene(stages.get(0));
|
||||
scene.getStylesheets().add(getPamCSS());
|
||||
|
||||
|
||||
// Application.setUserAgentStylesheet(new PrimerDark().getUserAgentStylesheet());
|
||||
// stages.get(0).prefWidthProperty().bind(scene.widthProperty());
|
||||
// stages.get(0).prefHeightProperty().bind(scene.heightProperty());
|
||||
|
||||
primaryStage.setScene(scene);
|
||||
// scene.getStylesheets().add(pamCSS);
|
||||
scene.getStylesheets().add(getPamCSS());
|
||||
//need to add this for material design icons and fontawesome icons
|
||||
// scene.getStylesheets().addAll(GlyphsStyle.DEFAULT.getStylePath());
|
||||
|
||||
@ -458,7 +465,7 @@ public class PamGuiManagerFX implements PAMControllerGUI, PamSettings {
|
||||
TabSelectionPane tabSelectionPane=new TabSelectionPane(stages.get(0));
|
||||
|
||||
PamSettingsDialogFX<?> settingsDialog=new PamSettingsDialogFX(tabSelectionPane);
|
||||
settingsDialog.getDialogPane().getStylesheets().add(PamController.getInstance().getGuiManagerFX().getPamSettingsCSS());
|
||||
settingsDialog.getDialogPane().getStylesheets().add(PamStylesManagerFX.getPamStylesManagerFX().getCurStyle().getDialogCSS());
|
||||
settingsDialog.initStyle(StageStyle.UNDECORATED);
|
||||
|
||||
// ChoiceDialog<String> dialog = new ChoiceDialog<>(tabStrings.get(1), tabStrings);
|
||||
@ -485,7 +492,7 @@ public class PamGuiManagerFX implements PAMControllerGUI, PamSettings {
|
||||
* Get CSS for PAMGUARD setting 'look and feel' for sliding dialogs
|
||||
* @return the CSS for settings feels.
|
||||
*/
|
||||
public String getPamSettingsCSS() {
|
||||
public String getPamSettingsCSS() {//return new PrimerDark().getUserAgentStylesheet();
|
||||
// return getClass().getResource("/Resources/css/pamSettingsCSS.css").toExternalForm();
|
||||
return PamStylesManagerFX.getPamStylesManagerFX().getCurStyle().getSlidingDialogCSS();
|
||||
}
|
||||
@ -495,6 +502,7 @@ public class PamGuiManagerFX implements PAMControllerGUI, PamSettings {
|
||||
* @return the standard CSS fro PAMGUARD.
|
||||
*/
|
||||
public String getPamCSS() {
|
||||
//return new PrimerLight().getUserAgentStylesheet();
|
||||
// return getClass().getResource("/Resources/css/pamCSS.css").toExternalForm();
|
||||
return PamStylesManagerFX.getPamStylesManagerFX().getCurStyle().getGUICSS();
|
||||
}
|
||||
@ -503,8 +511,9 @@ public class PamGuiManagerFX implements PAMControllerGUI, PamSettings {
|
||||
* Get CSS for PAMGUARD GUI standard 'look and feel' for regular dialogs
|
||||
* @return the standard CSS fro PAMGUARD.
|
||||
*/
|
||||
public String getPamDialogCSS() {
|
||||
return PamStylesManagerFX.getPamStylesManagerFX().getCurStyle().getSlidingDialogCSS();
|
||||
public String getPamDialogCSS() {//return new PrimerDark().getUserAgentStylesheet();
|
||||
|
||||
return PamStylesManagerFX.getPamStylesManagerFX().getCurStyle().getDialogCSS();
|
||||
}
|
||||
|
||||
|
||||
@ -644,7 +653,7 @@ public class PamGuiManagerFX implements PAMControllerGUI, PamSettings {
|
||||
mainPane.getChildren().addAll(title, namePane);
|
||||
|
||||
dialog.getDialogPane().setContent(mainPane);
|
||||
dialog.getDialogPane().getStylesheets().add(PamController.getInstance().getGuiManagerFX().getPamSettingsCSS());
|
||||
dialog.getDialogPane().getStylesheets().add(this.getPamDialogCSS());
|
||||
|
||||
//add listener to prevent close request if the dialog
|
||||
final Button btOk = (Button) dialog.getDialogPane().lookupButton(ButtonType.OK);
|
||||
|
||||
@ -166,6 +166,8 @@ public class PamGuiTabFX extends PamTabFX {
|
||||
//create a new GUI frame.
|
||||
PamGuiFX pamGUIFX=new PamGuiFX(tabPane, newStage, pamGui.getPamGuiManagerFX());
|
||||
pamGUIFX.getStylesheets().add(pamGui.getPamGuiManagerFX().getPamCSS());
|
||||
|
||||
|
||||
//need to add PamGUIFX to list in PamGUIManagerFX.
|
||||
pamGui.getPamGuiManagerFX().getPamGuiFXList().add(pamGUIFX);
|
||||
newStage.setOnCloseRequest(e->{
|
||||
|
||||
@ -18,50 +18,50 @@ public class PamSpinner<T> extends Spinner<T>{
|
||||
* Default widths are way off in JavaFX for spinners.
|
||||
*/
|
||||
// private static final double PAMSPINNER_PREF_WIDTH = USE_COMPUTED_SIZE;
|
||||
private static final double PAMSPINNER_PREF_WIDTH = 100;
|
||||
//private static final double PAMSPINNER_PREF_WIDTH = 100;
|
||||
|
||||
public PamSpinner() {
|
||||
super();
|
||||
this.setPrefWidth(PAMSPINNER_PREF_WIDTH);
|
||||
//this.setPrefWidth(PAMSPINNER_PREF_WIDTH);
|
||||
// TODO Auto-generated constructor stub
|
||||
}
|
||||
|
||||
|
||||
public PamSpinner(double min, double max, double initialValue, double amountToStepBy) {
|
||||
super(min, max, initialValue, amountToStepBy);
|
||||
this.setPrefWidth(PAMSPINNER_PREF_WIDTH);
|
||||
//this.setPrefWidth(PAMSPINNER_PREF_WIDTH);
|
||||
addDefocusConverter();
|
||||
}
|
||||
|
||||
|
||||
public PamSpinner(double min, double max, double initialValue) {
|
||||
super(min, max, initialValue);
|
||||
this.setPrefWidth(PAMSPINNER_PREF_WIDTH);
|
||||
//this.setPrefWidth(PAMSPINNER_PREF_WIDTH);
|
||||
addDefocusConverter();
|
||||
}
|
||||
|
||||
public PamSpinner(int min, int max, int initialValue, int amountToStepBy) {
|
||||
super(min, max, initialValue, amountToStepBy);
|
||||
this.setPrefWidth(PAMSPINNER_PREF_WIDTH);
|
||||
//this.setPrefWidth(PAMSPINNER_PREF_WIDTH);
|
||||
addDefocusConverter();
|
||||
}
|
||||
|
||||
public PamSpinner(int min, int max, int initialValue) {
|
||||
super(min, max, initialValue);
|
||||
this.setPrefWidth(PAMSPINNER_PREF_WIDTH);
|
||||
//this.setPrefWidth(PAMSPINNER_PREF_WIDTH);
|
||||
addDefocusConverter();
|
||||
}
|
||||
|
||||
public PamSpinner(ObservableList<T> arg0) {
|
||||
super(arg0);
|
||||
this.setPrefWidth(PAMSPINNER_PREF_WIDTH);
|
||||
//this.setPrefWidth(PAMSPINNER_PREF_WIDTH);
|
||||
addDefocusConverter();
|
||||
}
|
||||
|
||||
public PamSpinner(SpinnerValueFactory<T> arg0) {
|
||||
super(arg0);
|
||||
addDefocusConverter();
|
||||
this.setPrefWidth(PAMSPINNER_PREF_WIDTH);
|
||||
//this.setPrefWidth(PAMSPINNER_PREF_WIDTH);
|
||||
}
|
||||
|
||||
/**
|
||||
|
||||
@ -1,492 +0,0 @@
|
||||
/**
|
||||
* CSS for PAMGUARD settings panels. These are dark with clean white buttons and a cyan highlight them.
|
||||
*
|
||||
* Author: Jamie Macaulay;
|
||||
**/
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* Declare colour variables *
|
||||
* *
|
||||
******************************************************************************/
|
||||
* {
|
||||
-fx-darkbackground: rgba(60,60,60,.90);
|
||||
-fx-highlight: rgba(0,204,204,.75);
|
||||
-fx-highlight_border: rgba(0,204,204,1);
|
||||
-fx-text: white;
|
||||
-fx-border_col: white;
|
||||
}
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* Panes *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
.root {
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-padding: 10;
|
||||
}
|
||||
|
||||
.pane {
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
}
|
||||
|
||||
.border{
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
}
|
||||
|
||||
.grid {
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
}
|
||||
|
||||
.hBox {
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
}
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* Hiding Tab *
|
||||
* *
|
||||
******************************************************************************/
|
||||
#hide-tab {
|
||||
-fx-background-color: transparent;
|
||||
-fx-border-radius: 5 5 0 0;
|
||||
-fx-background-radius: 5 5 0 0;
|
||||
-fx-border-color: -fx-border_col;
|
||||
}
|
||||
|
||||
#show-tab {
|
||||
-fx-background-color: transparent;
|
||||
-fx-border-radius: 5 5 0 0;
|
||||
-fx-background-radius: 5 5 0 0;
|
||||
-fx-border-color: -fx-border_col;
|
||||
}
|
||||
|
||||
#hide-tab-highlight {
|
||||
-fx-background-color: -fx-highlight;
|
||||
-fx-border-radius: 5 5 0 0;
|
||||
-fx-background-radius: 5 5 0 0;
|
||||
-fx-border-color: -fx-highlight_border;
|
||||
}
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* Label *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
.label{
|
||||
-fx-text-fill: -fx-text;
|
||||
}
|
||||
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* Slider *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
|
||||
.slider .axis {
|
||||
-fx-fill: -fx-text;
|
||||
-fx-stroke: -fx-text;
|
||||
-fx-tick-label-fill: -fx-text;
|
||||
-fx-text-fill: -fx-text;
|
||||
-fx-tick-mark-stroke: -fx-text;
|
||||
}
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* Dialog Pane *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
.dialog-pane {
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
}
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* Button *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
.button{
|
||||
-fx-text-fill: white;
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-border-color: -fx-border_col;
|
||||
-fx-border-radius: 5;
|
||||
-fx-background-radius:6;
|
||||
-fx-padding: 3 6 6 6;
|
||||
}
|
||||
|
||||
.button:hover{
|
||||
-fx-background-color: -fx-highlight;
|
||||
-fx-border-color: -fx-highlight_border;
|
||||
}
|
||||
|
||||
.button:selected{
|
||||
-fx-border-color: -fx-highlight;
|
||||
}
|
||||
|
||||
/**
|
||||
* Button for closing a hiding panel. Right indicates bottoms points towards the right, closing a hiding panel
|
||||
* on the right hand side of the screen. These buttons have a transparent background and rounded corners.
|
||||
*/
|
||||
/** top-left, top-right, bottom-right, and bottom-left corners, in that order. */
|
||||
.close-button-right{
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 0 10 10 0;
|
||||
-fx-border-radius: 0 10 10 0;
|
||||
}
|
||||
|
||||
|
||||
.close-button-left{
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 10 0 0 10;
|
||||
-fx-border-radius: 10 0 0 10;
|
||||
}
|
||||
|
||||
|
||||
.close-button-top{
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 10 10 0 0;
|
||||
-fx-border-radius: 10 10 0 0;
|
||||
}
|
||||
|
||||
|
||||
.close-button-bottom{
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 0 0 10 10;
|
||||
-fx-border-radius: 0 0 10 10;
|
||||
}
|
||||
|
||||
|
||||
.close-button-bottom-grey{
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-radius: 0 0 10 10;
|
||||
-fx-border-radius: 0 0 10 10;
|
||||
}
|
||||
|
||||
.close-button-left-trans{
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 10 0 0 10;
|
||||
-fx-border-radius: 10 0 0 10;
|
||||
}
|
||||
|
||||
.close-button-right-trans{
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-radius: 0 10 10 0;
|
||||
-fx-border-radius: 0 10 10 0;
|
||||
}
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* TextField *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
.text-field {
|
||||
-fx-border-color: transparent;
|
||||
-fx-background-color: transparent;
|
||||
-fx-border-color: -fx-border_col;
|
||||
-fx-border-radius: 5;
|
||||
-fx-text-fill: -fx-text;
|
||||
}
|
||||
|
||||
.text-field:selected{
|
||||
-fx-border-color: -fx-highlight;
|
||||
}
|
||||
|
||||
.text-field:focused{
|
||||
-fx-border-color: -fx-highlight;
|
||||
}
|
||||
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* MenuButton *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
.menu-button{
|
||||
-fx-text-fill: -fx-text;
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-border-color: rgb(255, 255, 255);
|
||||
-fx-border-radius: 5;
|
||||
-fx-padding: 3 6 6 6;
|
||||
}
|
||||
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* SplitMenuButton *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
.split-menu-button{
|
||||
-fx-text-fill: -fx-text;
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-border-color: -fx-border_col;
|
||||
-fx-border-radius: 5;
|
||||
}
|
||||
|
||||
|
||||
.split-menu-button:hover{
|
||||
-fx-border-color: -fx-highlight_border;
|
||||
}
|
||||
|
||||
|
||||
.split-menu-button .label {
|
||||
-fx-text-fill: white;
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-border-radius: 5;
|
||||
}
|
||||
|
||||
|
||||
.split-menu-button .label:hover {
|
||||
-fx-background-color: -fx-highlight;
|
||||
}
|
||||
|
||||
|
||||
.split-menu-button .arrow-button {
|
||||
-fx-text-fill: -fx-text;
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-border-radius: 5;
|
||||
}
|
||||
|
||||
|
||||
.split-menu-button .arrow-button:hover {
|
||||
-fx-background-color: -fx-highlight;
|
||||
}
|
||||
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* Radio Button *
|
||||
* *
|
||||
******************************************************************************/
|
||||
.radio-button {
|
||||
/* -fx-text-fill: rgb(255, 255, 255, 0.4);*/
|
||||
-fx-text-fill: -fx-text;
|
||||
/* -fx-effect: dropshadow(one-pass-box , rgba(0, 0, 0, 0.6), 0, 0.0 , 0 , 1 );*/
|
||||
-fx-border-width: 0px;
|
||||
}
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* Check Box *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
.check-box {
|
||||
/* -fx-text-fill: rgb(255, 255, 255, 0.4);*/
|
||||
-fx-text-fill: -fx-text;
|
||||
/* -fx-effect: dropshadow(one-pass-box , rgba(0, 0, 0, 0.6), 0, 0.0 , 0 , 1 );*/
|
||||
-fx-border-width: 0px;
|
||||
}
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* ComboBox *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
|
||||
.combo-box-base{
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-border-color: -fx-border_col;
|
||||
-fx-border-radius: 5;
|
||||
-fx-padding: 3 6 6 6;
|
||||
}
|
||||
|
||||
.choice-box{
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-border-color: -fx-border_col;
|
||||
-fx-border-radius: 5;
|
||||
-fx-padding: 3 6 6 6;
|
||||
}
|
||||
|
||||
|
||||
/*******************************************************************************
|
||||
* *
|
||||
* MenuItem *
|
||||
* *
|
||||
******************************************************************************/
|
||||
|
||||
|
||||
.menu-item .label {
|
||||
-fx-text-fill: -fx-text;
|
||||
/*Must be transpernt so that semi transparent colour is not added to smei transparent*/
|
||||
-fx-background-color: transparent;
|
||||
}
|
||||
|
||||
|
||||
.menu-item:focused {
|
||||
-fx-background-color: -fx-highlight;
|
||||
}
|
||||
|
||||
.menu-item:focused .label {
|
||||
-fx-text-fill: -fx-text;
|
||||
/*Weird fix-must make transparent for correct colour to show*/
|
||||
-fx-background-color: rgba(0,204,204,0);
|
||||
}
|
||||
|
||||
.context-menu {
|
||||
-fx-skin: "com.sun.javafx.scene.control.skin.ContextMenuSkin";
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-background-insets: 0, 1, 2;
|
||||
-fx-background-radius: 0 6 6 6, 0 5 5 5, 0 4 4 4;
|
||||
/* -fx-padding: 0.666667em 0.083333em 0.666667em 0.083333em; 8 1 8 1 */
|
||||
-fx-padding: 0.333333em 0.083333em 0.666667em 0.083333em; /* 4 1 8 1 */
|
||||
}
|
||||
|
||||
/****************************************************************
|
||||
|
||||
ScrollPane
|
||||
|
||||
****************************************************************/
|
||||
.scroll-pane {
|
||||
-fx-background: transparent;
|
||||
-fx-background-color: transparent;
|
||||
}
|
||||
|
||||
|
||||
/****************************************************************
|
||||
|
||||
ScrollBar
|
||||
|
||||
****************************************************************/
|
||||
.scroll-bar {
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-background-radius: 2em;
|
||||
}
|
||||
.scroll-bar:horizontal .track,
|
||||
.scroll-bar:vertical .track {
|
||||
-fx-background-color: transparent;
|
||||
-fx-border-color:transparent;
|
||||
-fx-background-radius: 2em;
|
||||
}
|
||||
.scroll-bar:vertical .track-background,
|
||||
.scroll-bar:horizontal .track-background {
|
||||
-fx-background-color: transparent;
|
||||
-fx-background-insets: 0;
|
||||
-fx-background-radius: 2em;
|
||||
}
|
||||
.scroll-bar:horizontal .thumb {
|
||||
-fx-background-color: rgb(211,211,211);
|
||||
-fx-background-insets: 4 0 4 0;
|
||||
-fx-background-radius: 2em;
|
||||
}
|
||||
.scroll-bar:vertical .thumb {
|
||||
-fx-background-color: rgb(211,211,211);
|
||||
-fx-background-insets: 0 4 0 4;
|
||||
-fx-background-radius: 2em;
|
||||
}
|
||||
.scroll-bar:horizontal .thumb:hover,
|
||||
.scroll-bar:vertical .thumb:hover {
|
||||
-fx-background-color: rgb(231,231,231);
|
||||
}
|
||||
.scroll-bar:horizontal .thumb:pressed,
|
||||
.scroll-bar:vertical .thumb:pressed {
|
||||
-fx-background-color: rgb(255,255,255);
|
||||
}
|
||||
.scroll-bar:vertical .increment-button, .scroll-bar:vertical .decrement-button {
|
||||
-fx-background-color:transparent;
|
||||
-fx-background-radius: 2em;
|
||||
-fx-padding: 5;
|
||||
}
|
||||
.scroll-bar:horizontal .increment-button, .scroll-bar:horizontal .decrement-button {
|
||||
-fx-background-color:transparent;
|
||||
-fx-background-radius: 2em;
|
||||
-fx-padding: 5;
|
||||
}
|
||||
.scroll-bar:horizontal .increment-arrow {
|
||||
-fx-shape: "M 0 0 L 4 8 L 8 0 Z";
|
||||
-fx-background-color: rgb(211,211,211);
|
||||
-fx-padding: 0.25em;
|
||||
-fx-rotate: -90;
|
||||
}
|
||||
.scroll-bar:vertical .increment-arrow {
|
||||
-fx-background-color: rgb(211,211,211);
|
||||
-fx-shape: "M 0 0 L 4 8 L 8 0 Z";
|
||||
-fx-padding: 0.25em;
|
||||
-fx-rotate: 0;
|
||||
}
|
||||
.scroll-bar:horizontal .decrement-arrow {
|
||||
-fx-background-color: rgb(211,211,211);
|
||||
-fx-shape: "M 0 0 L 4 8 L 8 0 Z";
|
||||
-fx-padding: 0.25em;
|
||||
-fx-rotate: 90;
|
||||
}
|
||||
.scroll-bar:vertical .decrement-arrow {
|
||||
-fx-background-color: rgb(211,211,211);
|
||||
-fx-shape: "M 0 0 L 4 8 L 8 0 Z";
|
||||
-fx-padding: 0.25em;
|
||||
-fx-rotate: -180;
|
||||
}
|
||||
.scroll-bar:vertical:focused,
|
||||
.scroll-bar:horizontal:focused {
|
||||
-fx-background-color: transparent,rgb(96,96,96),rgb(96,96,96);
|
||||
}
|
||||
|
||||
/****************************************************************
|
||||
|
||||
Spinner
|
||||
|
||||
****************************************************************/
|
||||
|
||||
.spinner {
|
||||
-fx-background: -fx-darkbackground;
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-background-radius: 10;
|
||||
-fx-border-radius: 10;
|
||||
-fx-border-color: transparent;
|
||||
}
|
||||
|
||||
.spinner .text-field {
|
||||
-fx-background: -fx-darkbackground;
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-border-radius: 0 0 0 0;
|
||||
-fx-padding: 7 0 7 0;
|
||||
-fx-border-color: transparent;
|
||||
}
|
||||
|
||||
.spinner .increment-arrow-button {
|
||||
-fx-text-fill: white;
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-border-color: -fx-border_col;
|
||||
-fx-border-radius: 5 5 0 0;
|
||||
-fx-padding: 7 0 7 0;
|
||||
}
|
||||
|
||||
.spinner .increment-arrow {
|
||||
-fx-background-color: white;
|
||||
}
|
||||
|
||||
.spinner .increment-arrow-button:hover {
|
||||
-fx-background-color: -fx-highlight;
|
||||
-fx-border-color: -fx-highlight_border;
|
||||
-fx-background-radius: 6 6 0 0;
|
||||
-fx-border-radius: 6 6 0 0;
|
||||
}
|
||||
|
||||
.spinner .decrement-arrow-button {
|
||||
-fx-text-fill: white;
|
||||
-fx-background-color: -fx-darkbackground;
|
||||
-fx-border-color: -fx-border_col;
|
||||
-fx-border-radius: 0 0 6 6
|
||||
}
|
||||
|
||||
.spinner .decrement-arrow {
|
||||
-fx-background-color: white;
|
||||
}
|
||||
|
||||
.spinner .decrement-arrow-button:hover {
|
||||
-fx-background-color: -fx-highlight;
|
||||
-fx-border-color: -fx-highlight_border;
|
||||
-fx-background-radius: 0 0 6 6;
|
||||
-fx-border-radius: 0 0 6 6;
|
||||
}
|
||||
@ -2,6 +2,7 @@ package pamViewFX.fxNodes.pamDialogFX;
|
||||
|
||||
import java.util.Optional;
|
||||
|
||||
import javafx.geometry.Insets;
|
||||
import javafx.stage.Stage;
|
||||
import javafx.stage.StageStyle;
|
||||
import pamViewFX.fxStyles.PamStylesManagerFX;
|
||||
@ -25,11 +26,13 @@ public class PamSettingsDialogFX<T> extends PamDialogFX<T> {
|
||||
this.settingsPane=settingsPane;
|
||||
this.setTitle(settingsPane.getName());
|
||||
this.setContent(settingsPane.getContentNode());
|
||||
|
||||
|
||||
// if (PamController.getInstance().getGuiManagerFX()!=null){
|
||||
// this.getDialogPane().getStylesheets().add(PamController.getInstance().getGuiManagerFX().getPamSettingsCSS());
|
||||
// }
|
||||
PamStylesManagerFX stylesManager = PamStylesManagerFX.getPamStylesManagerFX();
|
||||
this.getDialogPane().getStylesheets().add(stylesManager.getCurStyle().getSlidingDialogCSS());
|
||||
this.getDialogPane().getStylesheets().add(stylesManager.getCurStyle().getDialogCSS());
|
||||
this.setOnShown((value)->{
|
||||
settingsPane.paneInitialized();
|
||||
});
|
||||
|
||||
@ -1,5 +1,6 @@
|
||||
package pamViewFX.fxNodes.picker;
|
||||
|
||||
import PamView.PamSymbol;
|
||||
import PamView.PamSymbolType;
|
||||
import javafx.geometry.Point2D;
|
||||
import javafx.scene.canvas.Canvas;
|
||||
@ -127,7 +128,7 @@ public class SymbolPicker extends ComboBox<PamSymbolFX> {
|
||||
|
||||
/**
|
||||
* Set the symbol with a symbol type.
|
||||
* @param symbol
|
||||
* @param symbol - the symbol type.
|
||||
*/
|
||||
public void setValue(PamSymbolType symbol) {
|
||||
for (int i=0; i<getItems().size(); i++){
|
||||
@ -137,5 +138,16 @@ public class SymbolPicker extends ComboBox<PamSymbolFX> {
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Set the symbol with a symbol type. Note, replicates setValue for convenience.
|
||||
* @param symbol - the symbol type.
|
||||
*/
|
||||
public void setSymbol(PamSymbolType symbol) {
|
||||
setValue(symbol);
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
@ -3,13 +3,16 @@ package pamViewFX.fxNodes.utilityPanes;
|
||||
|
||||
import javafx.event.ActionEvent;
|
||||
import javafx.event.EventHandler;
|
||||
import javafx.geometry.Pos;
|
||||
import javafx.scene.control.CheckBox;
|
||||
import javafx.scene.control.ComboBox;
|
||||
import javafx.scene.control.Label;
|
||||
import javafx.scene.control.RadioButton;
|
||||
import javafx.scene.control.ToggleGroup;
|
||||
import javafx.scene.layout.GridPane;
|
||||
import javafx.scene.layout.Pane;
|
||||
import javafx.scene.layout.Priority;
|
||||
import net.synedra.validatorfx.Validator;
|
||||
import pamViewFX.PamGuiManagerFX;
|
||||
import pamViewFX.fxNodes.PamGridPane;
|
||||
import pamViewFX.fxNodes.PamHBox;
|
||||
@ -50,6 +53,15 @@ public class GroupedSourcePaneFX extends SourcePaneFX {
|
||||
*/
|
||||
private PamGridPane sourcePane;
|
||||
|
||||
/**
|
||||
* Holds channels and group settings.
|
||||
*/
|
||||
private PamVBox channelPanel;
|
||||
|
||||
/**
|
||||
* Validator for channels
|
||||
*/
|
||||
private Validator channelValidator;
|
||||
|
||||
|
||||
public GroupedSourcePaneFX(Class sourceType, boolean hasChannels, boolean includeSubClasses, boolean autoGrouping) {
|
||||
@ -64,6 +76,8 @@ public class GroupedSourcePaneFX extends SourcePaneFX {
|
||||
@Override
|
||||
protected void createPanel() {
|
||||
|
||||
channelValidator = new Validator();
|
||||
|
||||
sourcePane=new PamGridPane();
|
||||
sourcePane.setVgap(5);
|
||||
sourcePane.setHgap(5);
|
||||
@ -90,7 +104,7 @@ public class GroupedSourcePaneFX extends SourcePaneFX {
|
||||
sourcePane.setMaxWidth(Double.MAX_VALUE);
|
||||
|
||||
//create pane to hold channels.
|
||||
PamVBox channelPanel=new PamVBox();
|
||||
channelPanel=new PamVBox();
|
||||
channelPanel.setSpacing(5);
|
||||
|
||||
Label channelLabel = new Label("Channels");
|
||||
@ -124,15 +138,39 @@ public class GroupedSourcePaneFX extends SourcePaneFX {
|
||||
selectAll.setOnAction((action)->{
|
||||
if (selectAll.isSelected()) selectAllChannels();
|
||||
else selectNoChannels();
|
||||
channelValidator.validate(); //makes sure any error signs are removed
|
||||
});
|
||||
|
||||
//create check to show at least some check boxes need to be selected.
|
||||
channelValidator.createCheck()
|
||||
.dependsOn(("select all"), selectAll.selectedProperty())
|
||||
.withMethod(c -> {
|
||||
if (!isAChannelSelected() ) {
|
||||
c.error("At least one channel needs to be selected for the module to work");
|
||||
}
|
||||
})
|
||||
.decorates(selectAll)
|
||||
.immediate();
|
||||
;
|
||||
//create a list of channels and combo boxes for groups.
|
||||
if (isHasChannels()){
|
||||
for (int i = 0; i < PamConstants.MAX_CHANNELS; i++){
|
||||
channelBoxes[i] = new CheckBox("Channel " + i);
|
||||
channelValidator.createCheck()
|
||||
.dependsOn(("channel " + i), channelBoxes[i].selectedProperty())
|
||||
.withMethod(c -> {
|
||||
if (!isAChannelSelected() ) {
|
||||
c.error("At least one channel needs to be selected for the module to work");
|
||||
}
|
||||
})
|
||||
.decorates(channelBoxes[i])
|
||||
.immediate();
|
||||
;
|
||||
//channelPanel.getChildren().add(channelBoxes[i]);
|
||||
final int n=i;
|
||||
channelBoxes[i].setOnAction((action)->{
|
||||
selectionChanged(n);
|
||||
channelValidator.validate(); //makes sure any error signs are removed.
|
||||
});
|
||||
groupList[i]=new ComboBox<Integer>();
|
||||
//System.out.println("SourcePanel.java creatPanel"+i);
|
||||
@ -149,82 +187,43 @@ public class GroupedSourcePaneFX extends SourcePaneFX {
|
||||
PamHBox channelGroupPane=new PamHBox();
|
||||
channelGroupPane.setSpacing(15);
|
||||
channelGroupPane.getChildren().addAll(channelPanel, autoGroupPane);
|
||||
channelGroupPane.setAlignment(Pos.TOP_LEFT);
|
||||
|
||||
sourcePane.add(channelGroupPane,0,3);
|
||||
|
||||
//create source comboBox.
|
||||
this.setCenter(sourcePane);
|
||||
|
||||
|
||||
// //old swing layout panels
|
||||
// panel = new JPanel();
|
||||
// JPanel sourcePanel = new JPanel();
|
||||
// sourcePanel.setLayout(new BorderLayout());
|
||||
// // add stuff to the panel.
|
||||
// if (borderTitle != null) {
|
||||
// sourcePanel.setBorder(new TitledBorder(borderTitle));
|
||||
// }
|
||||
// panel.setLayout(new BorderLayout());
|
||||
//// panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
|
||||
// sourcePanel.add(BorderLayout.CENTER, sourceList = new JComboBox());
|
||||
// panel.add(BorderLayout.NORTH, sourcePanel);
|
||||
// sourceList.addActionListener(this);
|
||||
// if (hasChannels) {
|
||||
// JPanel channelGroupPanel = new JPanel();
|
||||
// channelGroupPanel.setLayout(new BorderLayout());
|
||||
// channelGroupPanel.setBorder(new TitledBorder("Channel list and grouping"));
|
||||
// JPanel channelPanel = new JPanel();
|
||||
// JPanel autoGroupPanel = new JPanel();
|
||||
// autoGroupPanel.setLayout(new BoxLayout(autoGroupPanel, BoxLayout.Y_AXIS));
|
||||
// autoGroupPanel.add(new JLabel("Auto Grouping"));
|
||||
// autoGroupPanel.add(allSingles = new JRadioButton("No grouping"));
|
||||
// autoGroupPanel.add(allTogether = new JRadioButton("One group"));
|
||||
// autoGroupPanel.add(userGrouped = new JRadioButton("User groups"));
|
||||
// allSingles.addActionListener(new GroupAction(GROUP_SINGLES));
|
||||
// allTogether.addActionListener(new GroupAction(GROUP_ALL));
|
||||
// userGrouped.addActionListener(new GroupAction(GROUP_USER));
|
||||
// ButtonGroup bg = new ButtonGroup();
|
||||
// bg.add(allSingles);
|
||||
// bg.add(allTogether);
|
||||
// bg.add(userGrouped);
|
||||
//// channelPanel.setLayout(new BoxLayout(channelPanel, BoxLayout.Y_AXIS));
|
||||
// GridBagLayout layout;
|
||||
//// channelPanel.setBorder(new TitledBorder("Channel list and grouping"));
|
||||
// channelPanel.setLayout(layout = new GridBagLayout());
|
||||
// GridBagConstraints c = new GridBagConstraints();
|
||||
// c.gridwidth = 2;
|
||||
// c.anchor = GridBagConstraints.WEST;
|
||||
// c.gridx = c.gridy = 0;
|
||||
// addComponent(channelPanel, autoGroupPanel, c);
|
||||
//// addComponent(channelPanel, new JLabel("Channel list ..."), c);
|
||||
// c.gridwidth = 1;
|
||||
// c.insets = new Insets(0,5,0,5);
|
||||
// c.gridy++;
|
||||
// c.gridx = 0;
|
||||
// addComponent(channelPanel, new JLabel("Channel"), c);
|
||||
// c.gridx++;
|
||||
// addComponent(channelPanel, new JLabel("Group"), c);
|
||||
// groupList = new JComboBox[PamConstants.MAX_CHANNELS];
|
||||
// channelBoxes = new JCheckBox[PamConstants.MAX_CHANNELS];
|
||||
// for (int i = 0; i < PamConstants.MAX_CHANNELS; i++){
|
||||
// channelBoxes[i] = new JCheckBox("Channel " + i);
|
||||
// groupList[i] = new JComboBox();
|
||||
// c.gridy ++;
|
||||
// c.gridx = 0;
|
||||
// addComponent(channelPanel, channelBoxes[i], c);
|
||||
// c.gridx ++;
|
||||
// addComponent(channelPanel, groupList[i], c);
|
||||
//// channelPanel.add(channelBoxes[i]);
|
||||
// channelBoxes[i].setVisible(false);
|
||||
// groupList[i].setVisible(false);
|
||||
// channelBoxes[i].addActionListener(new SelectionListener(i));
|
||||
// }
|
||||
// channelGroupPanel.add(BorderLayout.WEST, autoGroupPanel);
|
||||
// channelGroupPanel.add(BorderLayout.CENTER, channelPanel);
|
||||
// panel.add(BorderLayout.CENTER, channelGroupPanel);
|
||||
// }
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the validator for the channel. This can identify errors
|
||||
* in
|
||||
* @return
|
||||
*/
|
||||
public Validator getChannelValidator() {
|
||||
return channelValidator;
|
||||
}
|
||||
|
||||
/**
|
||||
* Check if
|
||||
* @return
|
||||
*/
|
||||
private boolean isAChannelSelected() {
|
||||
int channels = 0;
|
||||
PamDataBlock sb = getSource();
|
||||
if (sb != null) {
|
||||
// channels = sb.getChannelMap();
|
||||
channels = sb.getSequenceMap();
|
||||
}
|
||||
int n=0;
|
||||
//remove all channels from vertical box pane.
|
||||
for (int i = 0; i < Math.min(PamConstants.MAX_CHANNELS, channelBoxes.length); i++) {
|
||||
if ((channels & 1<<i) != 0 && this.channelBoxes[i].isSelected()) n++;
|
||||
}
|
||||
if (n==0) return false;
|
||||
else return true;
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void showChannels() {
|
||||
@ -459,4 +458,12 @@ public class GroupedSourcePaneFX extends SourcePaneFX {
|
||||
return channelListPane;
|
||||
}
|
||||
|
||||
/**
|
||||
* The pane that holds the channels and the group settings.
|
||||
* @return the channel pane.
|
||||
*/
|
||||
public Pane getChannelPane() {
|
||||
return channelPanel;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@ -270,6 +270,7 @@ public class SourcePaneFX extends PamBorderPane {
|
||||
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Tell the pane the source has changed.
|
||||
*/
|
||||
|
||||
@ -39,7 +39,7 @@ public class SettingsFileDialogFX {
|
||||
singleInstance = new SettingsFileDialogFX();
|
||||
singleInstance.settingsDialog=new PamSettingsDialogFX(singleInstance.settingsFilePane);
|
||||
// singleInstance.settingsDialog.getDialogPane().getStylesheets().add(singleInstance.getClass().getResource("/Resources/css/pamSettingsCSS.css").toExternalForm());
|
||||
singleInstance.settingsDialog.getDialogPane().getStylesheets().add(PamStylesManagerFX.getPamStylesManagerFX().getCurStyle().getSlidingDialogCSS());
|
||||
singleInstance.settingsDialog.getDialogPane().getStylesheets().add(PamStylesManagerFX.getPamStylesManagerFX().getCurStyle().getDialogCSS());
|
||||
}
|
||||
|
||||
singleInstance.settingsFilePane.setParams(settingsFileData);
|
||||
|
||||
@ -72,6 +72,9 @@ public class SettingsFilePane extends SettingsPane<SettingsFileData> {
|
||||
browseButton.setOnAction((action)->{
|
||||
browseFile(false);
|
||||
});
|
||||
browseButton.prefHeightProperty().bind(fileBox.heightProperty());
|
||||
|
||||
|
||||
PamButton browseSaveButton = new PamButton();
|
||||
// browseSaveButton.setGraphic(PamGlyphDude.createPamGlyph(MaterialDesignIcon.PLUS, Color.WHITE, PamGuiManagerFX.iconSize));
|
||||
browseSaveButton.setGraphic(PamGlyphDude.createPamIcon("mdi2p-plus", Color.WHITE, PamGuiManagerFX.iconSize));
|
||||
@ -82,6 +85,9 @@ public class SettingsFilePane extends SettingsPane<SettingsFileData> {
|
||||
folderSelectPane.getChildren().addAll(fileBox, browseSaveButton, browseButton);
|
||||
vBox.getChildren().add(folderSelectPane);
|
||||
|
||||
browseSaveButton.prefHeightProperty().bind(fileBox.heightProperty());
|
||||
|
||||
|
||||
fileBox.prefHeightProperty().bind(browseButton.heightProperty());
|
||||
|
||||
// //option to show on start up.
|
||||
|
||||
@ -10,6 +10,7 @@ import binaryFileStorage.BinaryStore;
|
||||
import pamViewFX.fxNodes.PamBorderPane;
|
||||
import pamViewFX.fxNodes.PamGridPane;
|
||||
import pamViewFX.fxNodes.pamDialogFX.PamDialogFX;
|
||||
import pamViewFX.fxStyles.PamStylesManagerFX;
|
||||
import javafx.geometry.HPos;
|
||||
import javafx.geometry.Pos;
|
||||
import javafx.scene.Node;
|
||||
@ -57,6 +58,8 @@ public class StorageOptionsPane extends SettingsPane<StorageParameters>{
|
||||
PamGridPane gridPane=new PamGridPane();
|
||||
|
||||
|
||||
|
||||
|
||||
Label l = new Label(" Binary Store ");
|
||||
l.setTextAlignment(TextAlignment.CENTER);
|
||||
if (binaryStore == null) {
|
||||
|
||||
68
src/pamViewFX/fxStyles/PamAtlantaStyle.java
Normal file
68
src/pamViewFX/fxStyles/PamAtlantaStyle.java
Normal file
@ -0,0 +1,68 @@
|
||||
package pamViewFX.fxStyles;
|
||||
|
||||
/*
|
||||
* PAMGUARD - Passive Acoustic Monitoring GUARDianship.
|
||||
* To assist in the Detection Classification and Localisation
|
||||
* of marine mammals (cetaceans).
|
||||
*
|
||||
* Copyright (C) 2006
|
||||
*
|
||||
* This program is free software; you can redistribute it and/or
|
||||
* modify it under the terms of the GNU General Public License
|
||||
* as published by the Free Software Foundation; either version 2
|
||||
* of the License, or (at your option) any later version.
|
||||
*
|
||||
* This program is distributed in the hope that it will be useful,
|
||||
* but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
* GNU General Public License for more details.
|
||||
*
|
||||
* You should have received a copy of the GNU General Public License
|
||||
* along with this program; if not, write to the Free Software
|
||||
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
|
||||
*/
|
||||
|
||||
/**
|
||||
* Class defining the default CSS Style sheets to use for JavaFX displays. This class can be extended and one or more methods overridden to
|
||||
* specify new CSS styles. Style sheets can be specified for 3 different categories: sliding dialogs, regular dialogs, and all other components
|
||||
* (incl. displays, etc). In addition, each category can have a style sheet to use for daytime mode and one to use for nighttime mode. The
|
||||
* relative URI paths to the individual style sheets are specified as private fields, and accessed through public methods. The day/night switch
|
||||
* is based on the name of the current PamColors colour scheme being used.
|
||||
*
|
||||
* @author Jamie Macaulay
|
||||
*
|
||||
*/
|
||||
public class PamAtlantaStyle extends PamDefaultStyle {
|
||||
|
||||
/**
|
||||
* Relative location of the CSS style sheet to be used for the Pamguard GUI (but not dialogs)
|
||||
*/
|
||||
//private String guiCSS = "/Resources/css/pamCSS.css";
|
||||
//private String guiCSS = new NordDark().getUserAgentStylesheet();
|
||||
protected String primerGuiCSS = "/Resources/css/primer-light.css";
|
||||
|
||||
|
||||
/**
|
||||
* Relative location of the CSS style sheet to be used for the Pamguard standard dialogs
|
||||
*/
|
||||
//private String dialogCSS = "/Resources/css/pamSettingsCSS.css";
|
||||
//private String dialogCSS = new PrimerDark().getUserAgentStylesheet();
|
||||
protected String primerDialogCSS = "/Resources/css/primer-dark.css";
|
||||
|
||||
|
||||
/**
|
||||
* Relative location of the CSS style sheet to be used for the Pamguard sliding dialogs
|
||||
*/
|
||||
//private String slidingDialogCSS = "/Resources/css/pamCSS.css";
|
||||
//private String slidingDialogCSS = new PrimerDark().getUserAgentStylesheet();
|
||||
protected String primerSlidingDialogCSS = "/Resources/css/primer-pamguard.css";
|
||||
|
||||
public PamAtlantaStyle() {
|
||||
super.guiCSS = primerGuiCSS;
|
||||
super.dialogCSS = primerDialogCSS;
|
||||
super.slidingDialogCSS = primerSlidingDialogCSS;
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
@ -42,35 +42,35 @@ public class PamDefaultStyle {
|
||||
/**
|
||||
* Relative location of the CSS style sheet to be used for the Pamguard GUI (but not dialogs)
|
||||
*/
|
||||
private String guiCSS = "/Resources/css/pamCSS.css";
|
||||
protected String guiCSS = "/Resources/css/pamCSS.css";
|
||||
|
||||
/**
|
||||
* Relative location of the CSS style sheet to be used for the Pamguard GUI when in night mode. If there
|
||||
* is not a style sheet specific to night mode, set it to null or point back to the guiCSS field.
|
||||
*/
|
||||
private String guiCSSNightMode = guiCSS;
|
||||
protected String guiCSSNightMode = guiCSS;
|
||||
|
||||
/**
|
||||
* Relative location of the CSS style sheet to be used for the Pamguard standard dialogs
|
||||
*/
|
||||
private String dialogCSS = "/Resources/css/pamDefaultDialogCSS.css";
|
||||
protected String dialogCSS = "/Resources/css/pamDefaultDialogCSS.css";
|
||||
|
||||
/**
|
||||
* Relative location of the CSS style sheet to be used for the Pamguard std dialogs when in night mode. If there
|
||||
* is not a style sheet specific to night mode, set it to null or point back to the dialogCSS field.
|
||||
*/
|
||||
private String dialogCSSNightMode = dialogCSS;
|
||||
protected String dialogCSSNightMode = dialogCSS;
|
||||
|
||||
/**
|
||||
* Relative location of the CSS style sheet to be used for the Pamguard sliding dialogs
|
||||
*/
|
||||
private String slidingDialogCSS = "/Resources/css/pamSettingsCSS.css";
|
||||
protected String slidingDialogCSS = "/Resources/css/pamSettingsCSS.css";
|
||||
|
||||
/**
|
||||
* Relative location of the CSS style sheet to be used for the Pamguard sliding dialogs when in night mode. If there
|
||||
* is not a style sheet specific to night mode, set it to null or point back to the slidingDialogCSS field.
|
||||
*/
|
||||
private String slidingDialogCSSNightMode = slidingDialogCSS;
|
||||
protected String slidingDialogCSSNightMode = slidingDialogCSS;
|
||||
|
||||
/**
|
||||
* <p>Return the CSS Style sheet to be used for the Pamguard GUI (displays and such) but not the dialogs.</p>
|
||||
|
||||
@ -50,7 +50,7 @@ import warnings.PamWarning;
|
||||
public class RawDLSettingsPane extends SettingsPane<RawDLParams>{
|
||||
|
||||
|
||||
public static double MAX_WIDTH = 250;
|
||||
public static double MAX_WIDTH = 270;
|
||||
|
||||
/**
|
||||
* The source for the FFT data source.
|
||||
@ -181,7 +181,6 @@ public class RawDLSettingsPane extends SettingsPane<RawDLParams>{
|
||||
vBox.getChildren().add(label);
|
||||
|
||||
windowLength = new PamSpinner<Integer>(0, Integer.MAX_VALUE, 10, 10000);
|
||||
windowLength.setPrefWidth(100);
|
||||
windowLength.getStyleClass().add(Spinner.STYLE_CLASS_SPLIT_ARROWS_HORIZONTAL);
|
||||
windowLength.setEditable(true);
|
||||
windowLength.valueProperty().addListener((obsVal, oldVal, newVal)->{
|
||||
@ -189,7 +188,6 @@ public class RawDLSettingsPane extends SettingsPane<RawDLParams>{
|
||||
});
|
||||
|
||||
hopLength = new PamSpinner<Integer>(0, Integer.MAX_VALUE, 10, 10000);
|
||||
hopLength.setPrefWidth(100);
|
||||
hopLength.getStyleClass().add(Spinner.STYLE_CLASS_SPLIT_ARROWS_HORIZONTAL);
|
||||
hopLength.setEditable(true);
|
||||
hopLength.valueProperty().addListener((obsVal, oldVal, newVal)->{
|
||||
@ -197,7 +195,6 @@ public class RawDLSettingsPane extends SettingsPane<RawDLParams>{
|
||||
});
|
||||
|
||||
reMergeSeg = new PamSpinner<Integer>(0, Integer.MAX_VALUE, 1, 1);
|
||||
reMergeSeg.setPrefWidth(100);
|
||||
reMergeSeg.getStyleClass().add(Spinner.STYLE_CLASS_SPLIT_ARROWS_HORIZONTAL);
|
||||
reMergeSeg.setEditable(true);
|
||||
|
||||
|
||||
@ -1,6 +1,12 @@
|
||||
package rawDeepLearningClassifier.layoutFX.exampleSounds;
|
||||
|
||||
import java.net.URL;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import simulatedAcquisition.sounds.SimSignal;
|
||||
|
||||
/**
|
||||
* The example sound factory
|
||||
@ -9,6 +15,8 @@ import java.net.URL;
|
||||
*/
|
||||
public class ExampleSoundFactory {
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* An example sound type.
|
||||
* @author Jamie macaulay
|
||||
@ -16,21 +24,32 @@ public class ExampleSoundFactory {
|
||||
*/
|
||||
public enum ExampleSoundType {
|
||||
|
||||
BAT_CALL("Bat Call (Myotis daubentonii)"),
|
||||
PORPOISE_CLICK("Harbour Porpoise (Phocoena phocoena)", ExampleSoundCategory.ODONTOCETES_CLICKS),
|
||||
|
||||
RIGHT_WHALE("Southern Right Whale (Eubalaena australis)"),
|
||||
SPERM_WHALE("Sperm Whale (Physeter macrocephalus)", ExampleSoundCategory.ODONTOCETES_CLICKS),
|
||||
|
||||
MINKE_WHALE("Minke Whale (Balaenoptera spp.)"),
|
||||
DOLPHIN("Dolphin (Delphinid)", ExampleSoundCategory.ODONTOCETES_CLICKS),
|
||||
|
||||
HUMPBACK_WHALE("Humpback whale (Megaptera novaeangliae) ");
|
||||
BEAKED_WHALE("Beaked Whale (Ziphiidae)", ExampleSoundCategory.ODONTOCETES_CLICKS),
|
||||
|
||||
BAT_CALL("Bat Call (Myotis daubentonii)", ExampleSoundCategory.BAT),
|
||||
|
||||
RIGHT_WHALE("Southern Right Whale (Eubalaena australis)", ExampleSoundCategory.MYSTICETES),
|
||||
|
||||
MINKE_WHALE("Minke Whale (Balaenoptera spp.)", ExampleSoundCategory.MYSTICETES),
|
||||
|
||||
HUMPBACK_WHALE("Humpback whale (Megaptera novaeangliae) ", ExampleSoundCategory.MYSTICETES);
|
||||
|
||||
private final String text;
|
||||
|
||||
private final ExampleSoundCategory soundCategory;
|
||||
|
||||
/**
|
||||
* @param text
|
||||
*/
|
||||
ExampleSoundType(final String text) {
|
||||
ExampleSoundType(final String text, final ExampleSoundCategory soundCategory) {
|
||||
this.text = text;
|
||||
this.soundCategory = soundCategory;
|
||||
}
|
||||
|
||||
/* (non-Javadoc)
|
||||
@ -40,7 +59,172 @@ public class ExampleSoundFactory {
|
||||
public String toString() {
|
||||
return text;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get category of the example sound.
|
||||
* @return the example sound category.
|
||||
*/
|
||||
public ExampleSoundCategory getCategory() {
|
||||
return soundCategory;
|
||||
}
|
||||
}
|
||||
|
||||
public enum ExampleSoundCategory {MYSTICETES, ODONTOCETES_CLICKS, OCONTOCETES_TONAL, BAT}
|
||||
|
||||
/**
|
||||
* Get all the example sounds for a particular category.
|
||||
* @param - the category of sund to extract.
|
||||
* @return the example sounds for a category.
|
||||
*/
|
||||
private List<ExampleSoundType> getAnExampleSoundTypes(ExampleSoundCategory category) {
|
||||
|
||||
List<ExampleSoundType> exampleSounds = Arrays.asList(ExampleSoundType.values());
|
||||
|
||||
List<ExampleSoundType> resultSet =
|
||||
exampleSounds.stream()
|
||||
.filter(c -> c.getCategory().equals(category))
|
||||
.collect(Collectors.toList());
|
||||
|
||||
return resultSet;
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Get all the example sounds for a set of categories.
|
||||
* @param - the categories to use.
|
||||
* @return the example sounds for a category.
|
||||
*/
|
||||
public ArrayList<ExampleSoundType> getExampleSoundTypes(ExampleSoundCategory... cateogry) {
|
||||
|
||||
|
||||
ArrayList<ExampleSoundType> resultSet = new ArrayList<ExampleSoundType>();
|
||||
|
||||
for (int i=0; i<cateogry.length; i++) {
|
||||
|
||||
resultSet.addAll(getAnExampleSoundTypes(cateogry[i]));
|
||||
}
|
||||
|
||||
return resultSet;
|
||||
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
*Beaked whale click template, sR is 192000;
|
||||
*/
|
||||
public static final double[] beakedWhale1 = {2.47E-04,4.17E-04,-2.08E-04,-4.96E-04,2.10E-04,1.77E-04,-1.94E-04,4.12E-04,
|
||||
-3.52E-04,-4.06E-04,5.34E-04,1.78E-04,-1.57E-04,-3.78E-04,6.04E-04,2.92E-04,-1.11E-03,-9.88E-05,4.69E-04,4.78E-04,-2.56E-04,
|
||||
-6.52E-04,9.52E-04,7.76E-04,-1.24E-03,-2.34E-03,-7.72E-04,5.15E-03,9.90E-03,-7.51E-03,-2.34E-02,1.01E-02,2.53E-02,-1.19E-02,-1.14E-02,
|
||||
8.45E-03,4.52E-04,-7.41E-03,-3.62E-03,1.55E-02,7.40E-03,-1.44E-02,-2.38E-04,7.15E-04,-1.20E-02,3.95E-04,1.57E-02,4.98E-03,1.92E-03,
|
||||
1.54E-02,-2.55E-02,-5.13E-02,2.06E-02,4.93E-02,4.04E-03,1.07E-02,-4.28E-03,-6.29E-02,-2.66E-02,3.46E-02,3.53E-02,3.77E-02,2.10E-02,
|
||||
-5.72E-02,-8.11E-02,-2.50E-03,4.14E-02,7.01E-02,7.57E-02,-4.29E-02,-1.31E-01,-7.97E-02,4.48E-02,1.41E-01,1.17E-01,-3.82E-02,-1.92E-01,
|
||||
-1.16E-01,6.49E-02,1.70E-01,1.65E-01,-1.03E-01,-2.66E-01,-4.51E-02,1.66E-01,2.08E-01,9.35E-03,-2.98E-01,-1.26E-01,2.83E-01,1.67E-01,
|
||||
-1.97E-01,-2.05E-01,9.55E-02,2.64E-01,-3.56E-02,-2.88E-01,2.30E-02,2.49E-01,-2.65E-02,-1.77E-01,1.71E-02,1.22E-01,6.03E-03,-1.18E-01,
|
||||
1.24E-02,1.12E-01,-6.87E-02,-3.49E-02,6.68E-02,-3.83E-02,-1.76E-02,4.04E-02,4.81E-03,-4.35E-02,3.24E-03,5.49E-02,-3.68E-02,-1.93E-02,
|
||||
3.83E-02,-2.45E-02,-6.69E-03,3.95E-02,-1.97E-02,-3.61E-02,4.18E-02,3.72E-03,-3.75E-02,3.54E-02,-4.81E-03,-3.30E-02,3.52E-02,2.50E-03,
|
||||
-3.08E-02,1.80E-02,1.40E-02,-2.37E-02,4.51E-03,1.71E-02,-1.81E-02,-6.25E-04,1.83E-02,-1.33E-02,-9.61E-03,1.96E-02,-2.14E-03,
|
||||
-1.97E-02,1.43E-02,9.88E-03,-1.85E-02,5.62E-03,1.13E-02,-1.41E-02,-6.57E-04,1.33E-02,-6.73E-03,-7.21E-03,1.07E-02,-2.59E-03,
|
||||
-1.03E-02,1.08E-02,5.15E-03,-1.25E-02,7.48E-04,9.56E-03,-5.28E-03,-5.46E-03,7.89E-03,1.54E-04,-8.15E-03,5.09E-03,6.07E-03,-7.92E-03,
|
||||
-7.59E-04,8.78E-03,-5.57E-03,-5.39E-03,8.47E-03,-1.48E-03,-7.02E-03,5.20E-03,3.33E-03,-6.12E-03,8.16E-04,6.54E-03,-4.25E-03,-3.56E-03,
|
||||
4.57E-03,-6.18E-04,-1.87E-03,1.52E-03,3.46E-04};
|
||||
|
||||
|
||||
/**
|
||||
* Dolphin click template. sR is 500000;
|
||||
*/
|
||||
public static final double[] porp1 = {-3.05E-05,-0.002563477,-0.004974365,0.011444092,-0.009521484,-0.025115967,0.043365479,0.006896973,-0.090332031,0.045959473,
|
||||
0.112335205,-0.129669189,-0.099395752,0.208465576,0.036865234,-0.25994873,0.040771484,0.273834229,-0.121124268,-0.264709473,0.18447876,0.235626221,-0.241851807,
|
||||
-0.194458008,0.281036377,0.129699707,-0.306427002,-0.048278809,0.293182373,-0.043273926,-0.243774414,0.110229492,0.162536621,-0.144958496,-0.078491211,0.136444092,
|
||||
0.004547119,-0.105926514,0.037628174,0.058898926,-0.05682373,-0.018371582,0.047973633,-0.018737793,-0.024383545,0.03302002,-0.014404297,-0.030517578,0.045227051,
|
||||
0.002532959,-0.063751221,0.027191162,0.057067871,-0.054901123,-0.042449951,0.065246582,0.016448975,-0.06741333,0.002319336,0.055664063,-0.023345947,-0.040496826,
|
||||
0.030548096,0.015625,-0.033569336,0.002441406,0.022857666,-0.019042969,-0.013702393,0.020965576,0.001831055,-0.023101807,0.001068115,0.01739502,-0.005401611,
|
||||
-0.017944336,0.004394531,0.013427734,-0.008880615,-0.013122559,0.007781982,0.006561279,-0.010650635,-0.004150391,0.005310059};
|
||||
/**
|
||||
* Dolphin click template. sR is 192000;
|
||||
*/
|
||||
public static final double[] dolphin1 = {3.56E-05,1.13E-03,-1.28E-03,4.39E-05,1.17E-04,4.11E-04,-3.05E-04,1.57E-04,-3.45E-04,5.21E-04,-5.18E-04,
|
||||
1.93E-03,-8.44E-04,-1.62E-04,-8.80E-04,2.74E-04,-4.06E-04,1.32E-03,-7.23E-04,5.70E-04,-6.91E-04,6.78E-04,-7.04E-04,-1.36E-03,-4.10E-04,
|
||||
1.41E-03,-1.11E-03,1.36E-03,-9.02E-04,-2.69E-04,-1.49E-04,2.05E-04,-1.53E-04,6.97E-05,-7.78E-04,9.78E-04,-1.04E-03,-9.00E-05,-8.66E-04,
|
||||
6.78E-05,-1.06E-03,1.39E-03,-6.03E-04,3.49E-04,2.80E-04,9.42E-04,-3.65E-04,-5.98E-04,-1.91E-04,4.00E-04,-1.22E-03,4.52E-04,-1.35E-03,8.43E-04,
|
||||
-1.20E-03,5.83E-04,-3.36E-04,1.26E-03,-2.39E-04,1.63E-04,-1.31E-03,1.15E-03,9.60E-04,1.58E-03,-5.09E-04,1.16E-03,-1.15E-03,-2.38E-04,-3.77E-04,
|
||||
1.37E-04,-1.57E-03,1.30E-03,-9.01E-04,1.00E-03,-9.13E-06,8.95E-04,-9.26E-04,3.68E-04,-6.05E-05,5.16E-04,-2.56E-04,2.45E-03,-1.46E-03,1.80E-03,
|
||||
-5.76E-04,4.27E-03,4.60E-03,1.62E-02,2.77E-02,4.65E-02,-2.96E-02,-1.70E-01,-3.27E-01,1.98E-01,7.30E-01,-1.69E-01,-4.94E-01,3.59E-02,1.08E-01,
|
||||
2.70E-02,-9.51E-03,-2.52E-02,-1.19E-02,5.12E-03,3.54E-03,9.35E-03,6.57E-03,5.81E-03,-1.82E-03,-3.81E-03,-1.73E-02,-3.26E-03,1.66E-02,1.47E-02,
|
||||
-1.78E-04,-1.35E-02,-5.18E-03,5.96E-03,1.20E-03,-2.03E-03,8.27E-04,3.08E-03,7.34E-03,2.49E-03,-8.53E-03,-3.58E-03,-4.46E-03,2.39E-03,6.70E-03,
|
||||
2.08E-03,-1.54E-03,3.96E-05,-3.75E-04,4.47E-05,9.08E-04,1.13E-03,-4.51E-04,-1.16E-03,-2.38E-03,1.33E-03,4.09E-03,-4.09E-05,-2.57E-03,-7.47E-05,
|
||||
-4.94E-04,-1.12E-04,-2.10E-04,3.48E-04,-1.33E-04,-8.04E-04,-1.28E-04,2.31E-04,1.63E-03,4.06E-03,-1.90E-03,-4.81E-03,-3.43E-03,2.05E-03,2.64E-03,
|
||||
1.05E-03,-1.25E-03,-1.52E-03,-2.15E-04,5.58E-04,1.09E-03,-2.92E-04,-7.16E-05,-1.62E-04,-7.08E-04,1.37E-03,-3.63E-04,-1.01E-04,-9.10E-04,4.76E-04,
|
||||
-4.89E-04,6.00E-04,-1.97E-03,-3.72E-04,-1.23E-03,-2.13E-03,1.80E-03,1.72E-03,-4.45E-04,8.07E-04,2.73E-03,1.87E-03,-3.51E-04,-1.79E-03,
|
||||
-4.25E-05,-3.60E-04,-6.36E-03,-3.80E-03};
|
||||
/**
|
||||
* Sperm whale click that contains P0 , P1 and P2 pulses. sR is 192000/4
|
||||
*/
|
||||
public static final double[] sperm1 = {6.25E-05,-2.17E-05,4.27E-05,-0.00020994,-0.000214738,4.15E-05,-4.20E-06,-1.19E-05,1.43E-05,-6.63E-06,-0.000131916,7.46E-05,7.74E-05,
|
||||
-3.48E-05,0.000112665,7.23E-05,0.000124127,-0.000327633,-0.000504408,-0.0001821,-9.08E-06,-0.000303635,-0.00091038,-0.000737628,-0.002809006,-0.002485561,0.002436103,
|
||||
0.001387111,-0.000240529,0.008338125,0.01556416,0.003837149,-0.012601288,-0.010037818,0.001317383,0.006350685,0.003097904,-0.003146625,-0.005176637,-0.005103367,
|
||||
-0.003033016,0.000264741,0.000979974,0.001417843,0.001295476,0.000270959,-0.000941692,-0.002497482,-0.001093983,0.001588331,0.001606697,0.000428882,0.000342588,
|
||||
0.000576856,0.000175455,0.000351797,0.000535963,6.16E-05,-2.81E-05,3.01E-05,-4.62E-05,6.29E-05,-0.00032481,-0.000627716,0.000541881,0.000930361,6.94E-05,-8.11E-05,
|
||||
-0.001084492,-0.001999887,-0.000853651,-0.000455461,-0.0009841,-0.000148444,0.000505996,0.000659125,0.002106154,0.00305439,0.002859567,0.002226094,-0.001580242,
|
||||
-0.005047821,-0.003593811,-0.002505516,-0.00239728,0.000993556,0.004712824,0.005116607,0.002759289,-0.000433693,-0.00259594,-0.002059373,6.38E-05,0.00080239,0.001226022,
|
||||
0.000524362,-5.97E-05,0.000218345,0.002725451,0.013643442,0.007104888,-0.013153579,-0.000327077,0.008434641,-0.034580464,-0.058165279,0.001699742,0.050940528,0.016095566,
|
||||
-0.019505718,-0.014421101,0.00069818,0.012322224,0.015961877,0.019905987,0.012646343,-0.003135543,-0.003774804,-0.002494694,-0.004462543,-2.78E-05,0.006201286,0.007524738,
|
||||
-0.000122701,-0.00686273,-0.003151422,0.000472041,-0.004336464,-0.006828523,-0.0036367,-0.004451807,-0.00476565,-0.00059454,0.001060291,0.000210872,0.000292835,0.001312147,
|
||||
0.00354525,0.003836739,-0.001563894,-0.003728106,0.000589295,0.002063008,0.005110769,0.008073922,0.002351888,0.000991397,0.004482293,0.001852083,-0.001210519,-0.003916204,
|
||||
-0.009643673,-0.011895388,-0.011094342,-0.009496773,0.007035453,0.021768597,0.012407682,0.007770304,0.009816115,-0.004929878,-0.02191959,-0.021845953,-0.009616377,0.003728446,
|
||||
0.011398892,0.007160923,-0.001221613,-0.003364027,-0.001979512,-0.00161046,-0.000138627,0.00464312,0.004116845,0.001597662,0.003842689,0.002166315,-0.001378553,-0.005946158,
|
||||
-0.011386535,-0.004845226,0.002418087,-0.003915996,-0.001246813,0.028316573,0.039767874,-0.002601435,-0.030996041,-0.012193441,0.000524819,-0.003479641,-0.001961131,0.005014191,
|
||||
0.000109726,-0.008264739,-0.003328171,-0.003266307,-0.005688887,0.002147438,0.005314515,0.003113408,0.000906803,-0.00362076,-0.004367909,0.001707293,0.004516978,0.002670098,
|
||||
0.005179915,0.005209394,0.000157009,-0.001113109,0.000351461,-0.00070744,-0.002641287,-0.000378381,0.000650114,-0.000699954,0.001493645,0.002380219,0.001847398,0.000957028,
|
||||
-0.00020906,-0.001138818,-0.005258351,-0.004390589,-0.000750034,0.001350919,0.005041997,0.004159317,0.00380484,0.006116095,0.004054061,-0.007240427,-0.015931238,-0.008497872,
|
||||
-0.004869947,-0.005248341,0.005820257,0.017324379,0.015179912,0.001501706,-0.004758621,-0.004807403,-0.004766533,0.000532342,0.001876597,0.002421249,0.002974527,-0.003363805,
|
||||
-0.006394844,-0.004090489,-0.000551194,0.000815621,0.002722833,0.006326427,0.002422239,1.71E-05,0.001718135,0.000155882,-9.98E-06,0.000374249,0.000685689,-0.00060601,
|
||||
-0.002945803,-0.001182812,0.000705219,0.000131511,-0.001627181,-0.004276435,-0.004121385,-0.001013222,-0.000580473,-0.001749975,-0.000810329,0.001049795,0.002380673,
|
||||
0.00092144,-0.001721435,-0.001959407,0.001039882,0.003527076,0.001077526,0.001321712,0.003990982,0.00159095,-6.99E-05,0.000197319,0.000611932,0.000414778,-0.000977586,
|
||||
0.000546997,-0.00015996,-0.003209788,-0.002958488,-0.001050216,0.000691699,-0.002462978,-0.00411392,-0.001070453,-0.002638013};
|
||||
|
||||
// /**
|
||||
// * Generate a click waveform with some added noise.
|
||||
// * @param type - the type of click e.g. ClickTriggerGraph.PORPOISE_CLICK.
|
||||
// * @param noise. 0 to 1. 1 means max noise amplitude will be same as maximum click amplitude.
|
||||
// * @return click and noise waveform.
|
||||
// */
|
||||
// private double[] generateClickWaveform(ExampleSoundType type, double noise){
|
||||
// SimSignal clickSound;
|
||||
// int sR;
|
||||
// double length;
|
||||
// double freq;
|
||||
// switch (type){
|
||||
// //TODO - add more types of clicks.
|
||||
// case PORPOISE_CLICK:
|
||||
// clickSound=new ClickSound("Porpoise", freq=140000, freq2=140000, length=0.00015, WINDOWTYPE.HANN);
|
||||
// sR=500000;
|
||||
// break;
|
||||
// case SPERM_WHALE:
|
||||
// clickSound=(new ClickSound("Beaked Whale", 30000, 60000, length = 0.3e-3, WINDOWTYPE.HANN));
|
||||
// sR=192000;
|
||||
// break;
|
||||
// default:
|
||||
// clickSound=new ClickSound("Porpoise", freq=140000, freq2=140000, length=0.00015, WINDOWTYPE.HANN);
|
||||
// sR=500000;
|
||||
// break;
|
||||
// }
|
||||
//
|
||||
// //now need to work out how many noise samples to add. Use the length of the click
|
||||
// int nNoiseSamples=(int) (2*length*sR);
|
||||
// double[] waveform=new double[3*nNoiseSamples];
|
||||
// int n=0;
|
||||
// for (int i=0; i<3*nNoiseSamples; i++){
|
||||
// double noiseSample=noise*(Math.random()-0.5);
|
||||
// double[] signal=clickSound.getSignal(0,sR,0);
|
||||
// if (i>nNoiseSamples && n <signal.length){
|
||||
// waveform[i]=signal[n]+noiseSample;
|
||||
// n=n+1;
|
||||
// }
|
||||
// else waveform[i]=noiseSample;
|
||||
// }
|
||||
//
|
||||
// return waveform;
|
||||
// }
|
||||
|
||||
/**
|
||||
* Get the example sound type.
|
||||
@ -54,7 +238,7 @@ public class ExampleSoundFactory {
|
||||
switch (exampleSoundType) {
|
||||
case BAT_CALL:
|
||||
path = getClass().getResource("/Resources/exampleSounds/DUB_20200623_000152_885.wav");
|
||||
exampleSound = new SimpleExampleSound(path);
|
||||
exampleSound = new SimpleExampleSound(path, 2500, 5000);
|
||||
break;
|
||||
case RIGHT_WHALE:
|
||||
//file = new File("src/rawDeepLearningClassifier/layoutFX/exampleSounds/southern_right_whale_clip2.wav");
|
||||
@ -71,11 +255,44 @@ public class ExampleSoundFactory {
|
||||
path = getClass().getResource("/Resources/exampleSounds/Humpback_whale.wav");
|
||||
exampleSound = new SimpleExampleSound(path);
|
||||
break;
|
||||
case PORPOISE_CLICK:
|
||||
exampleSound = new SimpleExampleSound(porp1, 500000);
|
||||
break;
|
||||
case SPERM_WHALE:
|
||||
exampleSound = new SimpleExampleSound(sperm1, 48000);
|
||||
break;
|
||||
case BEAKED_WHALE:
|
||||
exampleSound = new SimpleExampleSound(beakedWhale1, 192000);
|
||||
break;
|
||||
case DOLPHIN:
|
||||
exampleSound = new SimpleExampleSound(dolphin1, 192000);
|
||||
break;
|
||||
default:
|
||||
break;
|
||||
|
||||
|
||||
}
|
||||
return exampleSound;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get all the example sounds for a particular category.
|
||||
* @param - the category of sund to extract.
|
||||
* @return the example sounds for a category.
|
||||
*/
|
||||
public ExampleSoundType[] getExampleSoundTypes(ExampleSoundCategory category) {
|
||||
|
||||
|
||||
List<ExampleSoundType> exampleSounds = Arrays.asList(ExampleSoundType.values());
|
||||
|
||||
List<ExampleSoundType> resultSet =
|
||||
exampleSounds.stream()
|
||||
.filter(c -> c.getCategory().equals(category))
|
||||
.collect(Collectors.toList());
|
||||
|
||||
return (ExampleSoundType[]) resultSet.toArray();
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
@ -40,6 +40,21 @@ public class SimpleExampleSound implements ExampleSound{
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
public SimpleExampleSound(URL path, int start, int end) {
|
||||
try {
|
||||
data = DLUtils.loadWavFile(path);
|
||||
} catch (IOException | UnsupportedAudioFileException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
data = data.trim(start, end);
|
||||
}
|
||||
|
||||
public SimpleExampleSound(double[] wave, float sampleRate) {
|
||||
this.data = new AudioData(wave, sampleRate);
|
||||
}
|
||||
|
||||
@Override
|
||||
public double[] getWave() {
|
||||
return data.getScaledSampleAmpliudes();
|
||||
@ -50,4 +65,5 @@ public class SimpleExampleSound implements ExampleSound{
|
||||
return data.getSampleRate();
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
@ -16,8 +16,8 @@ import org.apache.commons.compress.archivers.ArchiveStreamFactory;
|
||||
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
|
||||
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
|
||||
import org.apache.commons.compress.utils.IOUtils;
|
||||
import org.pamguard.x3.x3.X3JNIEncoder;
|
||||
|
||||
import x3.X3JNIEncoder;
|
||||
import PamController.PamControlledUnitSettings;
|
||||
import PamController.PamController;
|
||||
import PamController.PamSettingManager;
|
||||
@ -37,7 +37,7 @@ public class ZipUnpacker implements PamSettings {
|
||||
|
||||
private ZipSettings zipSettings = new ZipSettings();
|
||||
|
||||
private x3.X3JNIEncoder x3Encoder;
|
||||
private X3JNIEncoder x3Encoder;
|
||||
|
||||
public ZipUnpacker(PamController pamController) {
|
||||
super();
|
||||
|
||||
Loading…
Reference in New Issue
Block a user