PAMGuard/dependency-reduced-pom.xml

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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.pamguard</groupId>
<artifactId>Pamguard</artifactId>
2024-02-14 14:27:11 +00:00
<name>Pamguard</name>
MacOS version of PAMGuard and minor UI updates (#170) * Update exporter_help.md Updated help for exporter * Update .gitignore * Bug fixes for deep learning classifier. Updated the symbol options to make sure opacity is passed through the symbol chooser. * Updates to the data map FX display * Updates to DelphinID and Data ModelFX Used a new writable image for much faster drawing in FX * bb * Delete C:\Users\Jamie Macaulay\MATLAB Drive\MATLAB\PAMGUARD\deep_learning\delphinID\whistle_image_example_java.mat * Updates to DelphinID * Updates to ReadMe and JavaFX GUI * Update readme.md Updates to ReadMe * Updates to CPOD module and also delphinID classifier * Fix colour scaling in FX data map * Create cpod_help.md * Update cpod_help.md * Update cpod_help.md * Updates to CPOD module Added ability to export CPOD clicks Added some extra features to data selector Swing GUI for data selector (in progress) * Updates to data map FX GUI * Updates to CPOD module * Added help files resources for CPOD * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Update cpod_help.md * Update cpod_help.md * Bug fixes for deep learning classifier. Updated the symbol options to make sure opacity is passed through the symbol chooser. * Updates to the data map FX display * Updates to DelphinID and Data ModelFX Used a new writable image for much faster drawing in FX * Updates to ReadMe and JavaFX GUI * bb * Delete C:\Users\Jamie Macaulay\MATLAB Drive\MATLAB\PAMGUARD\deep_learning\delphinID\whistle_image_example_java.mat * Updates to DelphinID * Update readme.md Updates to ReadMe * Fix colour scaling in FX data map * Updates to CPOD module and also delphinID classifier * Updates to CPOD module Added ability to export CPOD clicks Added some extra features to data selector Swing GUI for data selector (in progress) * Create cpod_help.md * Update cpod_help.md * Update cpod_help.md * Updates to data map FX GUI * Updates to CPOD module * Added help files resources for CPOD * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Update cpod_help.md * Update cpod_help.md * Bug fix to BT display The BT display was not selecting clicks properly. * Import bug fix * Updates to data map FX GUI * Updates to datamap FX * Got date axis working properly. * Added some arrows to the scroll bar for data map FX pane. * Working on getting datagrams in FX saving * Updates to DataMapFX and exporting annotations * Update MLAnnotationsManager.java * Working on adding annotations to exporter * Bug fix for processing files and annotations for exporter Rebase with main Bug fix for processing files - stops only the last file processing when "Start normally" selected on data processing R and MATLAB export of data annotation added. * Add a ttoltip to the exporter * Minor text change * X3 fix and building for MACOS * Update PAMGuard to build installer for MacOS * Some fixes to Sound Acquisition dialog layout. * Squashed commit of the following: commit 1acddb4cc6045ae9c9f654e680931b6907aad321 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Oct 8 15:03:32 2024 +0100 MErge from DG (#168) * Localization output * update localiser output * Start effort management system * Start of Effort plotting Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output). * Logger forms update Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode. * Update LoggerFormGraphics.java add in correct symbol managemet to forms graphics. * Effort lines on map Sort of working OK in real time mode. * Working effort system Currently only for map, but seems to work OK * Update Tethys to latest nilus schema * Raven importer Start of a system for a raven importer. Not quite working yet. * Raven import Basic functionality working. Not nice to use though. * Tethys Localization work Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff. * updated Nilus A few updates around track and target motion measures. * FX Plot for raven data Also sorted out symbols a bit and improved symbol selector in Generic plots. * Update spectrogram mark bearing display Remove the 90-angle bit * Raven extra columns Logging of data from additional Raven table columns * Start effort management system * Start of Effort plotting Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output). * Logger forms update Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode. * Effort lines on map Sort of working OK in real time mode. * Update Tethys to latest nilus schema * Tethys Localization work Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff. * Ishmael Tethys output Added necessaries for Tethys output from Ishmael detectors. Also found a pretty major bug in the spectrogram correlation detector, where for each block of data it was only testing the first sample of each block, not all samples, for being over threshold. * Speed and algorithm improvements to Ish matched filter Seems to be errors in correlation, didn't support multiple channels and also used very old and slow FFT, so working to fix all three issues. * Updated matched filter Updated and working Matched filter, though still some thinking to do about how the scaling of this works, since currently scaled by the template, so whole thing is dependent on the input. Need to think of a better way to do this. * Update match filt normalisation Normalisation now correctly using both the template and the signal for normalisation so that it will be data amplitude independent. * invFFT improvements Use faster inverse FFT of real data in correlation / delay functions. * Improve ifft's in other modules to improve TDOA speeds * Sorting mess of spec plugin graphics Have got the Ishmael ones scrolling, but when scrolling, there is an offset in the data due to the lag of the correlation functions. Quite hard to fix with available timing data * Improve ish spectrogram plugin Sorted scaling and scrollling problems. * Improve startup checks Rethread startup checks so that a progress bar shows when PAMGuard is checking input and output files at start up. Also include single file processing in checks. * Apply all spectrogram overlays Apply to all function on spectrogram overlays so changes to overlays affect all panels. commit f2f9870b6fbd84164d391af7324ffdfb8d1f65ba Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Oct 2 15:13:12 2024 +0100 V2.02.13c Release for installation on teaching lab machines. commit 7533a7cfbe9119bd8365c5b42ebd9e9960526861 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Oct 1 15:00:51 2024 +0100 Tethys output of Group3DLocalisations Output of Group3D localiser data. Localisations only, no Detections output for this one commit ef494c0d0e986e6cac76f5d02559f2204416a984 Author: Jamie Mac <macster110@gmail.com> Date: Mon Sep 30 13:10:59 2024 +0100 Sud bug fix and updates to CPOD module. (#162) * Update exporter_help.md Updated help for exporter * Update .gitignore * Bug fixes for deep learning classifier. Updated the symbol options to make sure opacity is passed through the symbol chooser. * Updates to the data map FX display * Updates to DelphinID and Data ModelFX Used a new writable image for much faster drawing in FX * bb * Delete C:\Users\Jamie Macaulay\MATLAB Drive\MATLAB\PAMGUARD\deep_learning\delphinID\whistle_image_example_java.mat * Updates to DelphinID * Updates to ReadMe and JavaFX GUI * Update readme.md Updates to ReadMe * Updates to CPOD module and also delphinID classifier * Fix colour scaling in FX data map * Create cpod_help.md * Update cpod_help.md * Update cpod_help.md * Updates to CPOD module Added ability to export CPOD clicks Added some extra features to data selector Swing GUI for data selector (in progress) * Updates to data map FX GUI * Updates to CPOD module * Added help files resources for CPOD * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Update cpod_help.md * Update cpod_help.md * Bug fixes for deep learning classifier. Updated the symbol options to make sure opacity is passed through the symbol chooser. * Updates to the data map FX display * Updates to DelphinID and Data ModelFX Used a new writable image for much faster drawing in FX * Updates to ReadMe and JavaFX GUI * bb * Delete C:\Users\Jamie Macaulay\MATLAB Drive\MATLAB\PAMGUARD\deep_learning\delphinID\whistle_image_example_java.mat * Updates to DelphinID * Update readme.md Updates to ReadMe * Fix colour scaling in FX data map * Updates to CPOD module and also delphinID classifier * Updates to CPOD module Added ability to export CPOD clicks Added some extra features to data selector Swing GUI for data selector (in progress) * Create cpod_help.md * Update cpod_help.md * Update cpod_help.md * Updates to data map FX GUI * Updates to CPOD module * Added help files resources for CPOD * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Update cpod_help.md * Update cpod_help.md * Bug fix to BT display The BT display was not selecting clicks properly. * Import bug fix * Updates to data map FX GUI * Updates to datamap FX * Got date axis working properly. * Added some arrows to the scroll bar for data map FX pane. * Working on getting datagrams in FX saving * Updates to DataMapFX and exporting annotations * Update MLAnnotationsManager.java * Working on adding annotations to exporter * Bug fix for processing files and annotations for exporter Rebase with main Bug fix for processing files - stops only the last file processing when "Start normally" selected on data processing R and MATLAB export of data annotation added. * Add a ttoltip to the exporter * Minor text change * Small UI improvements for Sound Acquisition and MacOS * Bug fix to exporter * Update to help points Updated help points for following modules Deep learning CPOD Matched click classifier Exporter --------- Co-authored-by: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
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<version>2.02.13c</version>
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<description>Pamguard using Maven to control dependencies</description>
<url>www.pamguard.org</url>
<organization>
<name>Sea Mammal Research Unit, University of St. Andrews</name>
<url>http://www.smru.st-andrews.ac.uk</url>
</organization>
<build>
<sourceDirectory>${basedir}/src</sourceDirectory>
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<testSourceDirectory>${basedir}/src/test</testSourceDirectory>
<resources>
<resource>
<directory>src</directory>
<excludes>
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<exclude>META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA</exclude>
<exclude>**/*.java</exclude>
<exclude>jars/*.*</exclude>
</excludes>
</resource>
</resources>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version>
<configuration>
<lifecycleMappingMetadata>
<pluginExecutions>
<pluginExecution>
<pluginExecutionFilter>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<versionRange>[3.1.1,)</versionRange>
<goals>
<goal>purge-local-repository</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore />
</action>
</pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.12.1</version>
<dependencies>
<dependency>
<groupId>org.eclipse.tycho</groupId>
<artifactId>tycho-compiler-jdt</artifactId>
Squashed commit of the following: commit 840e6c89a1fe2a1029b1b8c5c1d5419e7baec581 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Nov 16 20:36:14 2023 +0000 R2.02.09d Fix matched template classifier import fix azigram help file image display commit acc806d375b484323e23ccfd02435a3b667ff7b3 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Nov 15 13:08:02 2023 +0000 Updated X3 library to 2.2.6 commit a4f484c76c17c761d779f52c1a8dddafdc03dcd5 Merge: 8e60ad2e d7c4c278 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Nov 15 09:44:09 2023 +0000 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into main commit 8e60ad2eff108c29bcb024a5f9ca3b2ef4fe20ae Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Nov 15 09:43:39 2023 +0000 update to array diagnostics and sensor control commit d7c4c278d806b3ab4effe45153079fc4792ce764 Author: m2oswald <45486636+m2oswald@users.noreply.github.com> Date: Wed Nov 15 09:17:49 2023 +0000 Added code to Rocca for training/testing classifier (#114) * allow Rocca to run without classifiers Fixed bug that threw an error if no classifier files were specified in Rocca Params dialog * add rocca switch to enable dev mode currently only shows/hides extra buttons in the Params dialog, but will extend to more options in the future * Fix memory issue with RoccaContourDataBlocks not being released for garbage collection Set RoccaContourDataBlock objects to null and stop PamObserver Timer to force release * Fix problem tracing whistles in Rocca spectrogram pop-up Whistle and raw data were being cleared before the user had time to trace out the whistle, causing PAMGuard to throw an exception. Both were already being cleared when the pop-up window is closed, so no need to do it here. * updated for training/testing classifiers commit d5f504dcd1a28fcf88d18b7624826e0e1d325ab9 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Nov 10 18:08:31 2023 +0000 Bearing localiser offline save Bug stopping it correctly saving data from the offline task to the database fixed. commit 7a44d49e27189d2a1049662ae9f6e1dce81a098f Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Oct 27 09:59:28 2023 +0100 X3 Version 2.2.3 Add maven jar files for X3/SUD version 2.2.3 commit fa5fe9943db6b10a64f563b8a05917f12341182c Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Oct 26 14:44:41 2023 +0100 update sud file management to more efficiently skip to the correct part of a sud file when reading data offline. commit 60435e567a9e38a7c47c2f0df21f3147e15d5e74 Author: Brian S Miller <93690136+BrianSMiller@users.noreply.github.com> Date: Fri Sep 8 21:54:40 2023 +1000 Fixes issues #111 and fixes #112 (DIFAR module crashes and ability to use Deep Learning Detections in DIFAR module) (#110) * Bugfix for OverlayMarks Check for a null pointer exception in OverlayMarks that was causing a crash on startup. * Bugfix for null pointer in symbol manager Fix a bug that I found where the DIFAR module was crashing the symbol manager. Seems that this was due to this subclass of clip generator having a null value for it's uniqueName. I've fixed by checking for null values and assigning a generic symbol when null. * DeepLearning detections canGenerateClips=true Set flag in DeepLearning detector so that detections are considered 'clips' by Pamguard. This allows them to be processed automatically in the DIFAR Localisation module (and maybe others). * DIFAR: bugfix frequency limits for auto-detections Fix a bug in DIFAR module where the frequency limits of automated detections were not being set properly by the DIFAR module. * DeepLearning - Bugfix to detection duration Fix bug in deep learning detector where duration (in samples) was being set to number of samples in a hop instead of the number of samples in a segment.
2023-12-12 12:51:13 +00:00
<version>1.5.1</version>
</dependency>
</dependencies>
<configuration>
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<release>21</release>
<compilerId>jdt</compilerId>
</configuration>
</plugin>
<plugin>
<groupId>org.openjfx</groupId>
<artifactId>javafx-maven-plugin</artifactId>
<version>0.0.8</version>
</plugin>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
Squashed commit of the following: commit 840e6c89a1fe2a1029b1b8c5c1d5419e7baec581 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Nov 16 20:36:14 2023 +0000 R2.02.09d Fix matched template classifier import fix azigram help file image display commit acc806d375b484323e23ccfd02435a3b667ff7b3 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Nov 15 13:08:02 2023 +0000 Updated X3 library to 2.2.6 commit a4f484c76c17c761d779f52c1a8dddafdc03dcd5 Merge: 8e60ad2e d7c4c278 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Nov 15 09:44:09 2023 +0000 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into main commit 8e60ad2eff108c29bcb024a5f9ca3b2ef4fe20ae Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Nov 15 09:43:39 2023 +0000 update to array diagnostics and sensor control commit d7c4c278d806b3ab4effe45153079fc4792ce764 Author: m2oswald <45486636+m2oswald@users.noreply.github.com> Date: Wed Nov 15 09:17:49 2023 +0000 Added code to Rocca for training/testing classifier (#114) * allow Rocca to run without classifiers Fixed bug that threw an error if no classifier files were specified in Rocca Params dialog * add rocca switch to enable dev mode currently only shows/hides extra buttons in the Params dialog, but will extend to more options in the future * Fix memory issue with RoccaContourDataBlocks not being released for garbage collection Set RoccaContourDataBlock objects to null and stop PamObserver Timer to force release * Fix problem tracing whistles in Rocca spectrogram pop-up Whistle and raw data were being cleared before the user had time to trace out the whistle, causing PAMGuard to throw an exception. Both were already being cleared when the pop-up window is closed, so no need to do it here. * updated for training/testing classifiers commit d5f504dcd1a28fcf88d18b7624826e0e1d325ab9 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Nov 10 18:08:31 2023 +0000 Bearing localiser offline save Bug stopping it correctly saving data from the offline task to the database fixed. commit 7a44d49e27189d2a1049662ae9f6e1dce81a098f Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Oct 27 09:59:28 2023 +0100 X3 Version 2.2.3 Add maven jar files for X3/SUD version 2.2.3 commit fa5fe9943db6b10a64f563b8a05917f12341182c Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Oct 26 14:44:41 2023 +0100 update sud file management to more efficiently skip to the correct part of a sud file when reading data offline. commit 60435e567a9e38a7c47c2f0df21f3147e15d5e74 Author: Brian S Miller <93690136+BrianSMiller@users.noreply.github.com> Date: Fri Sep 8 21:54:40 2023 +1000 Fixes issues #111 and fixes #112 (DIFAR module crashes and ability to use Deep Learning Detections in DIFAR module) (#110) * Bugfix for OverlayMarks Check for a null pointer exception in OverlayMarks that was causing a crash on startup. * Bugfix for null pointer in symbol manager Fix a bug that I found where the DIFAR module was crashing the symbol manager. Seems that this was due to this subclass of clip generator having a null value for it's uniqueName. I've fixed by checking for null values and assigning a generic symbol when null. * DeepLearning detections canGenerateClips=true Set flag in DeepLearning detector so that detections are considered 'clips' by Pamguard. This allows them to be processed automatically in the DIFAR Localisation module (and maybe others). * DIFAR: bugfix frequency limits for auto-detections Fix a bug in DIFAR module where the frequency limits of automated detections were not being set properly by the DIFAR module. * DeepLearning - Bugfix to detection duration Fix bug in deep learning detector where duration (in samples) was being set to number of samples in a hop instead of the number of samples in a segment.
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<version>3.2.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer>
<manifestEntries>
<Main-Class>pamguard.Pamguard</Main-Class>
<Class-Path>.</Class-Path>
<SplashScreen-Image>Resources/pgBlankSplash.png</SplashScreen-Image>
</manifestEntries>
</transformer>
<transformer />
</transformers>
</configuration>
</execution>
</executions>
<configuration>
<transformers>
<transformer />
</transformers>
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<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
<exclude>test/resources/**</exclude>
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</excludes>
</filter>
</filters>
</configuration>
</plugin>
<plugin>
<groupId>com.github.marschall</groupId>
<artifactId>jdeps-maven-plugin</artifactId>
<version>0.5.1</version>
</plugin>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.1.1</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/tempDependencies</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
</configuration>
</execution>
</executions>
</plugin>
MacOS version of PAMGuard and minor UI updates (#170) * Update exporter_help.md Updated help for exporter * Update .gitignore * Bug fixes for deep learning classifier. Updated the symbol options to make sure opacity is passed through the symbol chooser. * Updates to the data map FX display * Updates to DelphinID and Data ModelFX Used a new writable image for much faster drawing in FX * bb * Delete C:\Users\Jamie Macaulay\MATLAB Drive\MATLAB\PAMGUARD\deep_learning\delphinID\whistle_image_example_java.mat * Updates to DelphinID * Updates to ReadMe and JavaFX GUI * Update readme.md Updates to ReadMe * Updates to CPOD module and also delphinID classifier * Fix colour scaling in FX data map * Create cpod_help.md * Update cpod_help.md * Update cpod_help.md * Updates to CPOD module Added ability to export CPOD clicks Added some extra features to data selector Swing GUI for data selector (in progress) * Updates to data map FX GUI * Updates to CPOD module * Added help files resources for CPOD * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Update cpod_help.md * Update cpod_help.md * Bug fixes for deep learning classifier. Updated the symbol options to make sure opacity is passed through the symbol chooser. * Updates to the data map FX display * Updates to DelphinID and Data ModelFX Used a new writable image for much faster drawing in FX * Updates to ReadMe and JavaFX GUI * bb * Delete C:\Users\Jamie Macaulay\MATLAB Drive\MATLAB\PAMGUARD\deep_learning\delphinID\whistle_image_example_java.mat * Updates to DelphinID * Update readme.md Updates to ReadMe * Fix colour scaling in FX data map * Updates to CPOD module and also delphinID classifier * Updates to CPOD module Added ability to export CPOD clicks Added some extra features to data selector Swing GUI for data selector (in progress) * Create cpod_help.md * Update cpod_help.md * Update cpod_help.md * Updates to data map FX GUI * Updates to CPOD module * Added help files resources for CPOD * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Update cpod_help.md * Update cpod_help.md * Bug fix to BT display The BT display was not selecting clicks properly. * Import bug fix * Updates to data map FX GUI * Updates to datamap FX * Got date axis working properly. * Added some arrows to the scroll bar for data map FX pane. * Working on getting datagrams in FX saving * Updates to DataMapFX and exporting annotations * Update MLAnnotationsManager.java * Working on adding annotations to exporter * Bug fix for processing files and annotations for exporter Rebase with main Bug fix for processing files - stops only the last file processing when "Start normally" selected on data processing R and MATLAB export of data annotation added. * Add a ttoltip to the exporter * Minor text change * X3 fix and building for MACOS * Update PAMGuard to build installer for MacOS * Some fixes to Sound Acquisition dialog layout. * Squashed commit of the following: commit 1acddb4cc6045ae9c9f654e680931b6907aad321 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Oct 8 15:03:32 2024 +0100 MErge from DG (#168) * Localization output * update localiser output * Start effort management system * Start of Effort plotting Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output). * Logger forms update Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode. * Update LoggerFormGraphics.java add in correct symbol managemet to forms graphics. * Effort lines on map Sort of working OK in real time mode. * Working effort system Currently only for map, but seems to work OK * Update Tethys to latest nilus schema * Raven importer Start of a system for a raven importer. Not quite working yet. * Raven import Basic functionality working. Not nice to use though. * Tethys Localization work Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff. * updated Nilus A few updates around track and target motion measures. * FX Plot for raven data Also sorted out symbols a bit and improved symbol selector in Generic plots. * Update spectrogram mark bearing display Remove the 90-angle bit * Raven extra columns Logging of data from additional Raven table columns * Start effort management system * Start of Effort plotting Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output). * Logger forms update Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode. * Effort lines on map Sort of working OK in real time mode. * Update Tethys to latest nilus schema * Tethys Localization work Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff. * Ishmael Tethys output Added necessaries for Tethys output from Ishmael detectors. Also found a pretty major bug in the spectrogram correlation detector, where for each block of data it was only testing the first sample of each block, not all samples, for being over threshold. * Speed and algorithm improvements to Ish matched filter Seems to be errors in correlation, didn't support multiple channels and also used very old and slow FFT, so working to fix all three issues. * Updated matched filter Updated and working Matched filter, though still some thinking to do about how the scaling of this works, since currently scaled by the template, so whole thing is dependent on the input. Need to think of a better way to do this. * Update match filt normalisation Normalisation now correctly using both the template and the signal for normalisation so that it will be data amplitude independent. * invFFT improvements Use faster inverse FFT of real data in correlation / delay functions. * Improve ifft's in other modules to improve TDOA speeds * Sorting mess of spec plugin graphics Have got the Ishmael ones scrolling, but when scrolling, there is an offset in the data due to the lag of the correlation functions. Quite hard to fix with available timing data * Improve ish spectrogram plugin Sorted scaling and scrollling problems. * Improve startup checks Rethread startup checks so that a progress bar shows when PAMGuard is checking input and output files at start up. Also include single file processing in checks. * Apply all spectrogram overlays Apply to all function on spectrogram overlays so changes to overlays affect all panels. commit f2f9870b6fbd84164d391af7324ffdfb8d1f65ba Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Oct 2 15:13:12 2024 +0100 V2.02.13c Release for installation on teaching lab machines. commit 7533a7cfbe9119bd8365c5b42ebd9e9960526861 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Oct 1 15:00:51 2024 +0100 Tethys output of Group3DLocalisations Output of Group3D localiser data. Localisations only, no Detections output for this one commit ef494c0d0e986e6cac76f5d02559f2204416a984 Author: Jamie Mac <macster110@gmail.com> Date: Mon Sep 30 13:10:59 2024 +0100 Sud bug fix and updates to CPOD module. (#162) * Update exporter_help.md Updated help for exporter * Update .gitignore * Bug fixes for deep learning classifier. Updated the symbol options to make sure opacity is passed through the symbol chooser. * Updates to the data map FX display * Updates to DelphinID and Data ModelFX Used a new writable image for much faster drawing in FX * bb * Delete C:\Users\Jamie Macaulay\MATLAB Drive\MATLAB\PAMGUARD\deep_learning\delphinID\whistle_image_example_java.mat * Updates to DelphinID * Updates to ReadMe and JavaFX GUI * Update readme.md Updates to ReadMe * Updates to CPOD module and also delphinID classifier * Fix colour scaling in FX data map * Create cpod_help.md * Update cpod_help.md * Update cpod_help.md * Updates to CPOD module Added ability to export CPOD clicks Added some extra features to data selector Swing GUI for data selector (in progress) * Updates to data map FX GUI * Updates to CPOD module * Added help files resources for CPOD * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Update cpod_help.md * Update cpod_help.md * Bug fixes for deep learning classifier. Updated the symbol options to make sure opacity is passed through the symbol chooser. * Updates to the data map FX display * Updates to DelphinID and Data ModelFX Used a new writable image for much faster drawing in FX * Updates to ReadMe and JavaFX GUI * bb * Delete C:\Users\Jamie Macaulay\MATLAB Drive\MATLAB\PAMGUARD\deep_learning\delphinID\whistle_image_example_java.mat * Updates to DelphinID * Update readme.md Updates to ReadMe * Fix colour scaling in FX data map * Updates to CPOD module and also delphinID classifier * Updates to CPOD module Added ability to export CPOD clicks Added some extra features to data selector Swing GUI for data selector (in progress) * Create cpod_help.md * Update cpod_help.md * Update cpod_help.md * Updates to data map FX GUI * Updates to CPOD module * Added help files resources for CPOD * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Add CPOD resources for help * Update cpod_help.md * Update cpod_help.md * Bug fix to BT display The BT display was not selecting clicks properly. * Import bug fix * Updates to data map FX GUI * Updates to datamap FX * Got date axis working properly. * Added some arrows to the scroll bar for data map FX pane. * Working on getting datagrams in FX saving * Updates to DataMapFX and exporting annotations * Update MLAnnotationsManager.java * Working on adding annotations to exporter * Bug fix for processing files and annotations for exporter Rebase with main Bug fix for processing files - stops only the last file processing when "Start normally" selected on data processing R and MATLAB export of data annotation added. * Add a ttoltip to the exporter * Minor text change * Small UI improvements for Sound Acquisition and MacOS * Bug fix to exporter * Update to help points Updated help points for following modules Deep learning CPOD Matched click classifier Exporter --------- Co-authored-by: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com>
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Squashed commit of the following: commit 840e6c89a1fe2a1029b1b8c5c1d5419e7baec581 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Nov 16 20:36:14 2023 +0000 R2.02.09d Fix matched template classifier import fix azigram help file image display commit acc806d375b484323e23ccfd02435a3b667ff7b3 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Nov 15 13:08:02 2023 +0000 Updated X3 library to 2.2.6 commit a4f484c76c17c761d779f52c1a8dddafdc03dcd5 Merge: 8e60ad2e d7c4c278 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Nov 15 09:44:09 2023 +0000 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into main commit 8e60ad2eff108c29bcb024a5f9ca3b2ef4fe20ae Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Wed Nov 15 09:43:39 2023 +0000 update to array diagnostics and sensor control commit d7c4c278d806b3ab4effe45153079fc4792ce764 Author: m2oswald <45486636+m2oswald@users.noreply.github.com> Date: Wed Nov 15 09:17:49 2023 +0000 Added code to Rocca for training/testing classifier (#114) * allow Rocca to run without classifiers Fixed bug that threw an error if no classifier files were specified in Rocca Params dialog * add rocca switch to enable dev mode currently only shows/hides extra buttons in the Params dialog, but will extend to more options in the future * Fix memory issue with RoccaContourDataBlocks not being released for garbage collection Set RoccaContourDataBlock objects to null and stop PamObserver Timer to force release * Fix problem tracing whistles in Rocca spectrogram pop-up Whistle and raw data were being cleared before the user had time to trace out the whistle, causing PAMGuard to throw an exception. Both were already being cleared when the pop-up window is closed, so no need to do it here. * updated for training/testing classifiers commit d5f504dcd1a28fcf88d18b7624826e0e1d325ab9 Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Nov 10 18:08:31 2023 +0000 Bearing localiser offline save Bug stopping it correctly saving data from the offline task to the database fixed. commit 7a44d49e27189d2a1049662ae9f6e1dce81a098f Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Oct 27 09:59:28 2023 +0100 X3 Version 2.2.3 Add maven jar files for X3/SUD version 2.2.3 commit fa5fe9943db6b10a64f563b8a05917f12341182c Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Oct 26 14:44:41 2023 +0100 update sud file management to more efficiently skip to the correct part of a sud file when reading data offline. commit 60435e567a9e38a7c47c2f0df21f3147e15d5e74 Author: Brian S Miller <93690136+BrianSMiller@users.noreply.github.com> Date: Fri Sep 8 21:54:40 2023 +1000 Fixes issues #111 and fixes #112 (DIFAR module crashes and ability to use Deep Learning Detections in DIFAR module) (#110) * Bugfix for OverlayMarks Check for a null pointer exception in OverlayMarks that was causing a crash on startup. * Bugfix for null pointer in symbol manager Fix a bug that I found where the DIFAR module was crashing the symbol manager. Seems that this was due to this subclass of clip generator having a null value for it's uniqueName. I've fixed by checking for null values and assigning a generic symbol when null. * DeepLearning detections canGenerateClips=true Set flag in DeepLearning detector so that detections are considered 'clips' by Pamguard. This allows them to be processed automatically in the DIFAR Localisation module (and maybe others). * DIFAR: bugfix frequency limits for auto-detections Fix a bug in DIFAR module where the frequency limits of automated detections were not being set properly by the DIFAR module. * DeepLearning - Bugfix to detection duration Fix bug in deep learning detector where duration (in samples) was being set to number of samples in a hop instead of the number of samples in a segment.
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2024-04-25 16:00:29 +00:00
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