mirror of
https://github.com/PAMGuard/PAMGuard.git
synced 2024-11-21 14:42:27 +00:00
Squashed commit of the following:
commit51aa658514Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Aug 23 14:58:32 2024 +0100 Tethys updates And get rid of some other files that had got into the repo by accident commit34ba7ebcebAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Aug 23 09:15:40 2024 +0100 Merge from DG (#150) * Localization output * update localiser output * Start effort management system * Start of Effort plotting Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output). * Logger forms update Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode. * Update LoggerFormGraphics.java add in correct symbol managemet to forms graphics. * Effort lines on map Sort of working OK in real time mode. * Working effort system Currently only for map, but seems to work OK * Update Tethys to latest nilus schema * Raven importer Start of a system for a raven importer. Not quite working yet. * Raven import Basic functionality working. Not nice to use though. * Tethys Localization work Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff. * updated Nilus A few updates around track and target motion measures. * FX Plot for raven data Also sorted out symbols a bit and improved symbol selector in Generic plots. * Update spectrogram mark bearing display Remove the 90-angle bit * Raven extra columns Logging of data from additional Raven table columns commitcb1b28423eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 19 15:55:25 2024 +0100 updates ready for 2.2.12 commit4829b46b36Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 19 11:54:24 2024 +0100 Merge from DG (#149) * Localization output * update localiser output * Start effort management system * Start of Effort plotting Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output). * Logger forms update Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode. * Update LoggerFormGraphics.java add in correct symbol managemet to forms graphics. * Effort lines on map Sort of working OK in real time mode. * Working effort system Currently only for map, but seems to work OK * Update Tethys to latest nilus schema * Raven importer Start of a system for a raven importer. Not quite working yet. * Raven import Basic functionality working. Not nice to use though. * Tethys Localization work Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff. * updated Nilus A few updates around track and target motion measures. * FX Plot for raven data Also sorted out symbols a bit and improved symbol selector in Generic plots. * Update spectrogram mark bearing display Remove the 90-angle bit commit507ff9e28dAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sat Aug 17 14:34:54 2024 +0100 Merge from DG (#148) * Localization output * update localiser output * Start effort management system * Start of Effort plotting Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output). * Logger forms update Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode. * Update LoggerFormGraphics.java add in correct symbol managemet to forms graphics. * Effort lines on map Sort of working OK in real time mode. * Working effort system Currently only for map, but seems to work OK * Update Tethys to latest nilus schema * Raven importer Start of a system for a raven importer. Not quite working yet. * Raven import Basic functionality working. Not nice to use though. * Tethys Localization work Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff. * updated Nilus A few updates around track and target motion measures. * FX Plot for raven data Also sorted out symbols a bit and improved symbol selector in Generic plots. commit51757499d4Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Aug 16 10:44:54 2024 +0100 Merge from DG (#147) * Localization output * update localiser output * Start effort management system * Start of Effort plotting Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output). * Logger forms update Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode. * Update LoggerFormGraphics.java add in correct symbol managemet to forms graphics. * Effort lines on map Sort of working OK in real time mode. * Working effort system Currently only for map, but seems to work OK * Update Tethys to latest nilus schema * Raven importer Start of a system for a raven importer. Not quite working yet. * Raven import Basic functionality working. Not nice to use though. * Tethys Localization work Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff. * updated Nilus A few updates around track and target motion measures. commit46bd88c197Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Aug 16 10:40:00 2024 +0100 Merge Tethys updates from DG (#146) * Localization output * update localiser output * Start effort management system * Start of Effort plotting Strat of effort plotting on map. Framework for using Effort data in other areas (such as Tethys output). * Logger forms update Effort and Symbol selectors working with Logger forms. Also functions to add, edit and delete form rows in Viewer mode. * Update LoggerFormGraphics.java add in correct symbol managemet to forms graphics. * Effort lines on map Sort of working OK in real time mode. * Working effort system Currently only for map, but seems to work OK * Update Tethys to latest nilus schema * Raven importer Start of a system for a raven importer. Not quite working yet. * Raven import Basic functionality working. Not nice to use though. * Tethys Localization work Abstracting out writing of localization objects and document header information so that individual localisers can give fine scale control of this stuff. * updated Nilus A few updates around track and target motion measures. commitbea4a544d0Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 8 14:27:05 2024 +0100 Merge from DG (#145) * Localization output * update localiser output commitadf4c87781Merge:62121bdb29293725Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Aug 8 09:29:24 2024 +0100 Merge branch 'main' into main commit2929372533Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Aug 5 17:58:08 2024 +0100 Tethys Localisation output Not all types, but getting there. commit62121bdbbdAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Sun Aug 4 11:41:08 2024 +0100 update jserialcom to 2.11.0 commit82adc06e3dAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Aug 2 15:26:49 2024 +0100 Merge DG branch (#144) * Refactoring Tethys A lot of refactoring of Nilus wrappers with more useful Objects for PAMGUard to work with. * Improved document handling Abstracted wrapper around nilus documents which allows easyish calling of internal functions in Localize and Detections document without a common base class. * Fix doc deletion in detector output panel commit36455153a2Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 30 16:34:35 2024 +0100 Fix doc deletion in detector output panel commitbc686c0fe6Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 26 16:12:54 2024 +0100 Improved document handling Abstracted wrapper around nilus documents which allows easyish calling of internal functions in Localize and Detections document without a common base class. commit4f87b7b661Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 16:07:33 2024 +0100 Refactoring Tethys A lot of refactoring of Nilus wrappers with more useful Objects for PAMGUard to work with. commit3abaff0379Merge:a3f41e229eee7434Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 13:50:49 2024 +0100 Merge pull request #86 from PAMGuard/main Merge from main commit9eee7434deMerge:32c7c9b2a3f41e22Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 13:50:38 2024 +0100 Merge branch 'main' into main commit32c7c9b263Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 11:55:06 2024 +0100 Merge from Jamie (#143) * Working on the exporter * Working out on exporter * Working on new symbol options for deep learning and sud file options in SoundAcquisition GUI * Add zero pad option for sud files. * Updates to sud zero pad options on FX GUI * Implementing a data selector for the deep learning module * Bug fix to data transforms if the wave data and sample length are different * Updated POm to ignore test resources and updates to DL data selector * Updates to DL data selector and POM * Work on the data selector for the deep learning module. * Working on the exporter * Working out on exporter * Working on new symbol options for deep learning and sud file options in SoundAcquisition GUI * Add zero pad option for sud files. * Updates to sud zero pad options on FX GUI * Implementing a data selector for the deep learning module * Updated POm to ignore test resources and updates to DL data selector * Bug fix to data transforms if the wave data and sample length are different * Updates to DL data selector and POM * Work on the data selector for the deep learning module. * Data selectors for deep learning models now working with FX Still have to be implemented in Swing * Update deep_learning_help.md Updated help values to have some info on data selectors and symbol managers. * Updates to deep learning symbol options for swing and data selector panel for swing Made tooltips last longer on TD display FX * Update deep_learning_help.md * Swing symbol modifiers for DL and peak freq * Squashed commit of the following: commitbad2255710Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Jul 18 09:47:47 2024 +0100 Better symbol options Add clearer options button to multi option symbol manager panel. * Fix bugs in detection display * Bug fix to hiding panes * Squashed commit of the following: commit8b5b5b2f18Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 19 17:14:28 2024 +0100 Updated data selectors for BT display Merging old status bar and new DataSelector options so that they work more consistently on the BT display. commitbad2255710Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Jul 18 09:47:47 2024 +0100 Better symbol options Add clearer options button to multi option symbol manager panel. * Deep learning bug fix * Ignore the class path * Squashed commit of the following: commit577670ccd0Merge:6510d2268b5b5b2fAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 09:35:01 2024 +0100 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard commit6510d2260eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 09:34:58 2024 +0100 Remove unnecessary text output commit3da8401756Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 09:29:38 2024 +0100 updates to Daq New DLL, and some LED control, but hasn't fixed stalling problem. commit8b5b5b2f18Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 19 17:14:28 2024 +0100 Updated data selectors for BT display Merging old status bar and new DataSelector options so that they work more consistently on the BT display. commitbad2255710Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Jul 18 09:47:47 2024 +0100 Better symbol options Add clearer options button to multi option symbol manager panel. * Squashed commit of the following: commit687220dad5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 11:42:19 2024 +0100 Change click data selector Change Click BT display so it can handle CompoundDataSelectors commit577670ccd0Merge:6510d2268b5b5b2fAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 09:35:01 2024 +0100 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard commit6510d2260eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 09:34:58 2024 +0100 Remove unnecessary text output commit3da8401756Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 09:29:38 2024 +0100 updates to Daq New DLL, and some LED control, but hasn't fixed stalling problem. commit8b5b5b2f18Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 19 17:14:28 2024 +0100 Updated data selectors for BT display Merging old status bar and new DataSelector options so that they work more consistently on the BT display. commitbad2255710Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Jul 18 09:47:47 2024 +0100 Better symbol options Add clearer options button to multi option symbol manager panel. --------- Co-authored-by: Jamie Mac <macster110@gmail.com> commit687220dad5Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 11:42:19 2024 +0100 Change click data selector Change Click BT display so it can handle CompoundDataSelectors commit577670ccd0Merge:6510d2268b5b5b2fAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 09:35:01 2024 +0100 Merge branch 'main' of https://github.com/PAMGuard/PAMGuard commit6510d2260eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 09:34:58 2024 +0100 Remove unnecessary text output commit3da8401756Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jul 22 09:29:38 2024 +0100 updates to Daq New DLL, and some LED control, but hasn't fixed stalling problem. commit8b5b5b2f18Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 19 17:14:28 2024 +0100 Updated data selectors for BT display Merging old status bar and new DataSelector options so that they work more consistently on the BT display. commitbad2255710Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Thu Jul 18 09:47:47 2024 +0100 Better symbol options Add clearer options button to multi option symbol manager panel. commita3f41e22e6Merge:0165982af7be084eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jul 16 10:58:25 2024 +0100 Merge pull request #85 from PAMGuard/main Fix vector error commit0165982a22Author: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 12 16:57:28 2024 +0100 Work on localisation export Not ready to rock yet. commitf24dd9bb91Merge:07f4398a3f23474eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Fri Jul 12 16:38:11 2024 +0100 Merge pull request #84 from PAMGuard/main Merge from main commit07f4398a1dAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Tue Jun 25 09:25:10 2024 +0100 Update .classpath Fix classpath file commit32ab9f7eadMerge:3a42eabd7accb79fAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jun 24 15:43:47 2024 +0100 Merge pull request #83 from PAMGuard/main V2.02.12 commit3a42eabd74Merge:18a507b5f7b4f44eAuthor: Douglas Gillespie <50671166+douggillespie@users.noreply.github.com> Date: Mon Jun 24 13:58:16 2024 +0100 Merge pull request #82 from PAMGuard/main Merge from main
This commit is contained in:
Jamie Mac
parent
4f233dd43e
commit
5cd0012022
8
.gitignore
vendored
8
.gitignore
vendored
@ -25,7 +25,9 @@
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# eclipse project file
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.project
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.hprof
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# hprof memory analyser files.
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*.hprof
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java_pid*.*
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# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
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hs_err_pid*
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@ -112,7 +114,3 @@ settings.xml
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.classpath
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.settings/org.eclipse.jdt.core.prefs
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.classpath
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.classpath
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.settings/org.eclipse.core.resources.prefs
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.settings/org.eclipse.jdt.core.prefs
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dependency-reduced-pom.xml
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@ -1,9 +1,19 @@
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eclipse.preferences.version=1
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org.eclipse.jdt.core.codeComplete.argumentPrefixes=
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org.eclipse.jdt.core.codeComplete.argumentSuffixes=
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org.eclipse.jdt.core.codeComplete.fieldPrefixes=
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org.eclipse.jdt.core.codeComplete.fieldSuffixes=
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org.eclipse.jdt.core.codeComplete.localPrefixes=
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org.eclipse.jdt.core.codeComplete.localSuffixes=
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org.eclipse.jdt.core.codeComplete.staticFieldPrefixes=
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org.eclipse.jdt.core.codeComplete.staticFieldSuffixes=
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org.eclipse.jdt.core.codeComplete.staticFinalFieldPrefixes=
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org.eclipse.jdt.core.codeComplete.staticFinalFieldSuffixes=
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org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
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org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
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org.eclipse.jdt.core.compiler.codegen.targetPlatform=21
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org.eclipse.jdt.core.compiler.codegen.targetPlatform=19
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org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
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org.eclipse.jdt.core.compiler.compliance=21
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org.eclipse.jdt.core.compiler.compliance=19
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org.eclipse.jdt.core.compiler.debug.lineNumber=generate
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org.eclipse.jdt.core.compiler.debug.localVariable=generate
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org.eclipse.jdt.core.compiler.debug.sourceFile=generate
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@ -13,4 +23,4 @@ org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
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org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
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org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=warning
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org.eclipse.jdt.core.compiler.release=enabled
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org.eclipse.jdt.core.compiler.source=21
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org.eclipse.jdt.core.compiler.source=19
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5033
README.html
5033
README.html
File diff suppressed because it is too large
Load Diff
@ -1,16 +0,0 @@
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To build an executable jar file from the PAMGuard source using Eclipse, you need to use this build configuration
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'Build PAMGuard.launch'
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You cannot simply export the project as a runnable jar file, or you will not get the required Maven dependencies.
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To use this with Eclipse, from your workspace, select File, then import, then in the list of things to be imported select
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Run/Debug Launch Configurations, hit Next
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Then in the Import Launch Configurations panel, browse to this folder. Select the folder (not a specific file)
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then in the left panel, select the folder, then in the right panel the configuration you wish to import
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(i.e. Build PAMGuard.launch) and hit Finish
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Then go to 'Run Configurations' and find the launch in the 'Maven Builds' section. You'll probably have to change the
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Base directory at the top of the panel to select the right project within your workspace.
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Once that's done, you can Run the configuration. It will take a while to get all the Maven dependencies and will output
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a runnable jar file into the 'targets' folder in your workspace.
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The name and version number of the created files are taken from the POM.xml file, so edit that if you want a different name.
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For unknown reasons, it makes three files. They are all the same, you can delete the ones starting with 'original-' and
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ending with '-shared'
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@ -14,6 +14,7 @@ public class RWTethysDataProvider extends AutoTethysProvider {
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public RWTethysDataProvider(TethysControl tethysControl, PamDataBlock pamDataBlock) {
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super(tethysControl, pamDataBlock);
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setAddFrequencyInfo(true);
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}
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@Override
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@ -15,8 +15,8 @@ public class ClickBlockSpeciesManager extends DataBlockSpeciesManager<ClickDetec
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public ClickBlockSpeciesManager(ClickControl clickControl, ClickDataBlock clickDataBlock) {
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super(clickDataBlock);
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this.clickControl = clickControl;
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setDefaultDefaultSpecies(new SpeciesMapItem(ITISTypes.OTHER, "Unknown", "Unknown"));
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setDefaultSpeciesCode("Unknown");
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setDefaultDefaultSpecies(new SpeciesMapItem(ITISTypes.CETACEAN, "Click", "Click"));
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setDefaultSpeciesCode("Click");
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}
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@Override
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@ -12,25 +12,25 @@ import PamDetection.LocContents;
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import PamUtils.LatLong;
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import PamguardMVC.PamDataBlock;
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import PamguardMVC.PamDataUnit;
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import nilus.AngularCoordinateType;
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import nilus.Helper;
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import nilus.LocalizationType;
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import nilus.Localize;
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import nilus.WGS84CoordinateType;
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import nilus.LocalizationType.Angular;
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import nilus.LocalizationType.Parameters;
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import nilus.LocalizationType.WGS84;
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import nilus.LocalizationType.Parameters.TargetMotionAnalysis;
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import nilus.Localize.Effort;
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import nilus.Localize.Effort.CoordinateReferenceSystem;
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import nilus.Localize.Effort.CoordinateReferenceSystem.ReferenceFrame;
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import pamMaths.PamVector;
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import targetMotionOld.TargetMotionLocaliser;
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import tethys.TethysTimeFuncs;
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import tethys.localization.Anchor;
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import tethys.localization.CoordinateName;
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import tethys.localization.LocalizationBuilder;
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import tethys.localization.LocalizationCreator;
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import tethys.localization.LocalizationSubTypes;
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import tethys.localization.LocalizationTypes;
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import tethys.localization.ReferenceFrame;
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import tethys.localization.TimeReference;
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import tethys.pamdata.AutoTethysProvider;
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@ -38,7 +38,7 @@ public class TMALocalizationCreator implements LocalizationCreator {
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int maxDimension = 2;
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public TMALocalizationCreator(TargetMotionLocaliser targetMotionLocaliser) {
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// TODO Auto-generated constructor stub
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}
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@ -53,12 +53,36 @@ public class TMALocalizationCreator implements LocalizationCreator {
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locTypes.add(LocalizationTypes.Point.toString());
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locTypes.add(LocalizationTypes.PerpendicularRange.toString());
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/**
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* Currently, TMA is only outputing as WGS84. Future release will have
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* options to put out local xyz coordinates instead, in which case this
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* will be Engineering and the referenceFrame will become instrument.
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*/
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CoordinateReferenceSystem coordRefs = locEffort.getCoordinateReferenceSystem();
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coordRefs.setName(CoordinateName.WGS84.toString());
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coordRefs.setSubtype(LocalizationSubTypes.Geographic.toString());
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ReferenceFrame refFrame = localizationBuilder.getDefaultReferenceFrame(CoordinateName.WGS84, LocalizationSubTypes.Geographic);
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if (refFrame != null) {
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coordRefs.setReferenceFrame(refFrame);
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}
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// /**
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// * TMA is always references to the earth.
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// */
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// ReferenceFrame refFrame = coordRefs.getReferenceFrame();
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// if (refFrame == null) {
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// refFrame = new ReferenceFrame();
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// try {
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// Helper.createRequiredElements(refFrame);
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// } catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
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// e.printStackTrace();
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// }
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// coordRefs.setReferenceFrame(refFrame);
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// }
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// refFrame.setAnchor(Anchor.WGS84.toString());
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locEffort.setDimension(2);
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return true;
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}
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@ -115,19 +139,19 @@ public class TMALocalizationCreator implements LocalizationCreator {
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* Needs a bit of work to get errors in correct direction (needs import
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* of track data for this value ?) and conversion to latlong units.
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*/
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// if (errorVec != null && errorVec.length >= 2) {
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// wgsErr = new WGS84CoordinateType();
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// wgsErr.setLongitude(errorVec[0]);
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// wgsErr.setLatitude(errorVec[1]);
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// if (hasDepth && errorVec.length >= 3) {
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// wgsErr.setElevationM(errorVec[2]);
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// }
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// wgs84.setCoordinateError(wgsErr);
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||||
// }
|
||||
|
||||
|
||||
// if (errorVec != null && errorVec.length >= 2) {
|
||||
// wgsErr = new WGS84CoordinateType();
|
||||
// wgsErr.setLongitude(errorVec[0]);
|
||||
// wgsErr.setLatitude(errorVec[1]);
|
||||
// if (hasDepth && errorVec.length >= 3) {
|
||||
// wgsErr.setElevationM(errorVec[2]);
|
||||
// }
|
||||
// wgs84.setCoordinateError(wgsErr);
|
||||
// }
|
||||
|
||||
|
||||
loc.setWGS84(wgs84);
|
||||
|
||||
|
||||
// set the TMA information
|
||||
Parameters params = loc.getParameters();
|
||||
if (params == null) {
|
||||
@ -142,31 +166,31 @@ public class TMALocalizationCreator implements LocalizationCreator {
|
||||
if (timeAbeam != null) {
|
||||
loc.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(timeAbeam));
|
||||
}
|
||||
|
||||
// now also output a perpendicular distance.
|
||||
|
||||
// now also output a perpendicular distance.
|
||||
Double perp = groupLocResult.getPerpendicularDistance();
|
||||
if (perp != null) {
|
||||
loc.setPerpendicularRangeM(AutoTethysProvider.roundDecimalPlaces(perp, 2));
|
||||
}
|
||||
|
||||
|
||||
// con only output one type.
|
||||
// if (perp != null) {
|
||||
// AngularCoordinateType acType = new AngularCoordinateType();
|
||||
// acType.setAngle1(90);
|
||||
// acType.setDistanceM(AutoTethysProvider.roundDecimalPlaces(perp,1));
|
||||
// Angular angular = new Angular();
|
||||
// angular.setCoordinate(acType);
|
||||
// if (errors != null) {
|
||||
// AngularCoordinateType angErr = new AngularCoordinateType();
|
||||
// angErr.setDistanceM(errors.norm());
|
||||
// angular.setCoordinateError(angErr);
|
||||
// }
|
||||
// loc.setAngular(angular);
|
||||
// }
|
||||
|
||||
|
||||
|
||||
|
||||
// con only output one type.
|
||||
// if (perp != null) {
|
||||
// AngularCoordinateType acType = new AngularCoordinateType();
|
||||
// acType.setAngle1(90);
|
||||
// acType.setDistanceM(AutoTethysProvider.roundDecimalPlaces(perp,1));
|
||||
// Angular angular = new Angular();
|
||||
// angular.setCoordinate(acType);
|
||||
// if (errors != null) {
|
||||
// AngularCoordinateType angErr = new AngularCoordinateType();
|
||||
// angErr.setDistanceM(errors.norm());
|
||||
// angular.setCoordinateError(angErr);
|
||||
// }
|
||||
// loc.setAngular(angular);
|
||||
// }
|
||||
|
||||
|
||||
|
||||
return loc;
|
||||
}
|
||||
|
||||
|
||||
@ -87,6 +87,7 @@ import tethys.dbxml.TethysException;
|
||||
import tethys.deployment.swing.DeploymentWizard;
|
||||
import tethys.deployment.swing.EffortProblemDialog;
|
||||
import tethys.deployment.swing.RecordingGapDialog;
|
||||
import tethys.localization.TethysLatLong;
|
||||
import tethys.niluswraps.PDeployment;
|
||||
import tethys.output.TethysExportParams;
|
||||
import tethys.pamdata.AutoTethysProvider;
|
||||
@ -909,8 +910,8 @@ public class DeploymentHandler extends CollectionHandler implements TethysStateO
|
||||
GpsData gpsData = gpsDataUnit.getGpsData();
|
||||
Point gpsPoint = new Point();
|
||||
gpsPoint.setTimeStamp(TethysTimeFuncs.xmlGregCalFromMillis(gpsDataUnit.getTimeMilliseconds()));
|
||||
gpsPoint.setLatitude(gpsData.getLatitude());
|
||||
gpsPoint.setLongitude(PamUtils.constrainedAngle(gpsData.getLongitude()));
|
||||
gpsPoint.setLatitude(TethysLatLong.formatLatitude(gpsData.getLatitude()));
|
||||
gpsPoint.setLongitude(TethysLatLong.formatLongitude(gpsData.getLongitude()));
|
||||
CourseOverGroundDegN cog = gpsPoint.getCourseOverGroundDegN();
|
||||
if (cog == null) {
|
||||
cog = new CourseOverGroundDegN();
|
||||
@ -1080,8 +1081,8 @@ public class DeploymentHandler extends CollectionHandler implements TethysStateO
|
||||
double recLat = deploymentData.getRecoveryDetails().getLatitude();
|
||||
double recLong = deploymentData.getRecoveryDetails().getLongitude();
|
||||
if (recLat != 0 & recLong != 0.) {
|
||||
deployment.getRecoveryDetails().setLatitude(recLat);
|
||||
deployment.getRecoveryDetails().setLongitude(PamUtils.constrainedAngle(recLong));
|
||||
deployment.getRecoveryDetails().setLatitude(TethysLatLong.formatLatitude(recLat));
|
||||
deployment.getRecoveryDetails().setLongitude(TethysLatLong.formatLongitude(recLong));
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -620,7 +620,7 @@ public class DetectionsHandler extends CollectionHandler {
|
||||
* Check the document name isn't already used and increment id as necessary.
|
||||
*/
|
||||
while (true) {
|
||||
fullId = String.format("%s_%d", prefix, uniqueDetectionsId++);
|
||||
fullId = String.format("%s_D_%d", prefix, uniqueDetectionsId++);
|
||||
if (!tethysControl.getDbxmlQueries().documentExists(Collection.Detections.toString(), fullId)) {
|
||||
break;
|
||||
}
|
||||
|
||||
10
src/tethys/localization/Anchor.java
Normal file
10
src/tethys/localization/Anchor.java
Normal file
@ -0,0 +1,10 @@
|
||||
package tethys.localization;
|
||||
|
||||
/**
|
||||
* Anchors for localization effort coordinate system.
|
||||
* @author dg50
|
||||
*
|
||||
*/
|
||||
public enum Anchor {
|
||||
UTMZone, WGS84, instrument;
|
||||
}
|
||||
@ -3,6 +3,18 @@ package tethys.localization;
|
||||
import java.math.BigInteger;
|
||||
import java.util.List;
|
||||
|
||||
import javax.xml.bind.JAXBException;
|
||||
import javax.xml.parsers.ParserConfigurationException;
|
||||
|
||||
import org.w3c.dom.Element;
|
||||
|
||||
import Array.ArrayManager;
|
||||
import Array.PamArray;
|
||||
import Array.Streamer;
|
||||
import Array.streamerOrigin.OriginSettings;
|
||||
import Array.streamerOrigin.StaticOriginSettings;
|
||||
import GPS.GpsData;
|
||||
import GPS.GpsDataUnit;
|
||||
import Localiser.LocalisationAlgorithm;
|
||||
import Localiser.LocalisationAlgorithmInfo;
|
||||
import Localiser.detectionGroupLocaliser.GroupLocResult;
|
||||
@ -14,6 +26,7 @@ import PamUtils.LatLong;
|
||||
import PamUtils.PamUtils;
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import PamguardMVC.PamDataUnit;
|
||||
import binaryFileStorage.DataUnitFileInformation;
|
||||
import nilus.AlgorithmType;
|
||||
import nilus.AngularCoordinateType;
|
||||
import nilus.BearingType;
|
||||
@ -31,10 +44,12 @@ import nilus.LocalizationType.Parameters;
|
||||
import nilus.LocalizationType.References;
|
||||
import nilus.LocalizationType.WGS84;
|
||||
import nilus.LocalizationType.Parameters.TargetMotionAnalysis;
|
||||
import nilus.LocalizationType.Parameters.UserDefined;
|
||||
import nilus.LocalizationType.References.Reference;
|
||||
import nilus.Localize.Effort;
|
||||
import nilus.Localize.Effort.CoordinateReferenceSystem;
|
||||
import nilus.Localize.Effort.ReferencedDocuments;
|
||||
import nilus.Localize.Effort.CoordinateReferenceSystem.ReferenceFrame;
|
||||
import nilus.Localize.Effort.ReferencedDocuments.Document;
|
||||
import pamMaths.PamVector;
|
||||
import tethys.Collection;
|
||||
@ -68,6 +83,8 @@ public class LocalizationBuilder {
|
||||
private Localize currentDocument;
|
||||
private LocalizationCreator localisationCreator;
|
||||
private TethysDataProvider dataProvider;
|
||||
|
||||
private Helper helper;
|
||||
|
||||
public LocalizationBuilder(TethysControl tethysControl, PDeployment deployment, Detections detectionsDocument, PamDataBlock dataBlock,
|
||||
StreamExportParams exportParams) {
|
||||
@ -76,6 +93,11 @@ public class LocalizationBuilder {
|
||||
this.dataBlock = dataBlock;
|
||||
this.streamExportParams = exportParams;
|
||||
this.tethysControl = tethysControl;
|
||||
try {
|
||||
helper = new Helper();
|
||||
} catch (JAXBException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
dataProvider = dataBlock.getTethysDataProvider(tethysControl);
|
||||
localisationHandler = tethysControl.getLocalizationHandler();
|
||||
localisationAlgorithm = dataBlock.getLocalisationAlgorithm();
|
||||
@ -123,13 +145,13 @@ public class LocalizationBuilder {
|
||||
}
|
||||
Document detectsDoc = new Document();
|
||||
detectsDoc.setId(detectionsDocument.getId());
|
||||
detectsDoc.setType(Collection.Localizations.collectionName());
|
||||
detectsDoc.setType(Collection.Detections.collectionName());
|
||||
detectsDoc.setIndex(BigInteger.ZERO);
|
||||
eff.getReferencedDocuments().getDocument().add(detectsDoc);
|
||||
}
|
||||
|
||||
|
||||
String prefix = deployment.nilusObject.getId() + "_" + dataProvider.getDetectionsName();
|
||||
String prefix = deployment.nilusObject.getId() + "_" + dataProvider.getDetectionsName() + "_L";
|
||||
String fullId = localisationHandler.getLocalisationdocId(prefix);
|
||||
currentDocument.setId(fullId);
|
||||
// detections.setDescription(dataProvider.getDescription(deployment, tethysExportParams));
|
||||
@ -185,6 +207,54 @@ public class LocalizationBuilder {
|
||||
return done;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get a default reference frame for the header of a localization document. This is very dependent
|
||||
* on the localization subtype. Also on whether the array is fixed or moving. It it's fixed, then
|
||||
* we also need to add the instrument lat long.
|
||||
* @param coordinateName
|
||||
* @param subType
|
||||
* @return
|
||||
*/
|
||||
public ReferenceFrame getDefaultReferenceFrame(CoordinateName coordinateName, LocalizationSubTypes subType) {
|
||||
ReferenceFrame referenceFrame = new ReferenceFrame();
|
||||
switch (subType) {
|
||||
case Derived:
|
||||
referenceFrame.setAnchor(Anchor.UTMZone.toString()); // i never use this on. If I do, this will need work !
|
||||
break;
|
||||
case Engineering:
|
||||
referenceFrame.setAnchor(Anchor.instrument.toString());
|
||||
break;
|
||||
case Geographic:
|
||||
referenceFrame.setAnchor(Anchor.WGS84.toString());
|
||||
break;
|
||||
default:
|
||||
break;
|
||||
}
|
||||
/*
|
||||
* And see if it's a fixed or moving array. Will just have to look at the
|
||||
* first streamer here. Hard to copy with multiples !
|
||||
*/
|
||||
PamArray array = ArrayManager.getArrayManager().getCurrentArray();
|
||||
Streamer streamer = array.getStreamer(0);
|
||||
if (streamer != null) {
|
||||
OriginSettings origin = streamer.getOriginSettings();
|
||||
if (origin instanceof StaticOriginSettings) {
|
||||
StaticOriginSettings staticOrigin = (StaticOriginSettings) origin;
|
||||
GpsDataUnit ll = staticOrigin.getStaticPosition();
|
||||
if (ll != null) {
|
||||
GpsData pos = ll.getGpsData();
|
||||
if (pos != null) {
|
||||
referenceFrame.setLatitude(TethysLatLong.formatLatitude(pos.getLatitude()));
|
||||
referenceFrame.setLongitude(TethysLatLong.formatLongitude(pos.getLongitude()));
|
||||
referenceFrame.setDatum(String.format("Altitude %3.2fm", pos.getHeight()));
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return referenceFrame;
|
||||
}
|
||||
|
||||
public boolean sortStandardCoordinates(PamDataBlock dataBlock) {
|
||||
LocalisationInfo locInfo = dataBlock.getLocalisationContents();
|
||||
Effort locEffort = currentDocument.getEffort();
|
||||
@ -202,6 +272,7 @@ public class LocalizationBuilder {
|
||||
// List<String> locTypes = locEffort.getLocalizationType();
|
||||
boolean ambiguity = locInfo.hasLocContent(LocContents.HAS_AMBIGUITY);
|
||||
CoordinateReferenceSystem coordRefs = locEffort.getCoordinateReferenceSystem();
|
||||
ReferenceFrame referenceFrame = null;
|
||||
List<String> locTypes = locEffort.getLocalizationType();
|
||||
if (locInfo.getLocContent() == 0) {
|
||||
return false;
|
||||
@ -217,6 +288,7 @@ public class LocalizationBuilder {
|
||||
else {
|
||||
locEffort.setDimension(2);
|
||||
}
|
||||
referenceFrame = getDefaultReferenceFrame(CoordinateName.WGS84, LocalizationSubTypes.Geographic);
|
||||
// locEffort.set
|
||||
}
|
||||
else if (locInfo.hasLocContent(LocContents.HAS_XYZ)) {
|
||||
@ -224,12 +296,14 @@ public class LocalizationBuilder {
|
||||
coordRefs.setSubtype(LocalizationSubTypes.Engineering.toString());
|
||||
locTypes.add(LocalizationTypes.Point.toString());
|
||||
locEffort.setDimension(3);
|
||||
referenceFrame = getDefaultReferenceFrame(CoordinateName.Cartesian, LocalizationSubTypes.Engineering);
|
||||
}
|
||||
else if (locInfo.hasLocContent(LocContents.HAS_XY)) {
|
||||
coordRefs.setName(CoordinateName.Cartesian.toString());
|
||||
coordRefs.setSubtype(LocalizationSubTypes.Engineering.toString());
|
||||
locTypes.add(LocalizationTypes.Point.toString());
|
||||
locEffort.setDimension(2);
|
||||
referenceFrame = getDefaultReferenceFrame(CoordinateName.Cartesian, LocalizationSubTypes.Engineering);
|
||||
}
|
||||
else if (locInfo.hasLocContent(LocContents.HAS_BEARING)) {
|
||||
coordRefs.setName(CoordinateName.Polar.toString());
|
||||
@ -241,10 +315,12 @@ public class LocalizationBuilder {
|
||||
else {
|
||||
locEffort.setDimension(2);
|
||||
}
|
||||
referenceFrame = getDefaultReferenceFrame(CoordinateName.Polar, LocalizationSubTypes.Engineering);
|
||||
}
|
||||
else {
|
||||
return false;
|
||||
}
|
||||
coordRefs.setReferenceFrame(referenceFrame);
|
||||
|
||||
return true;
|
||||
}
|
||||
@ -329,21 +405,41 @@ public class LocalizationBuilder {
|
||||
locType.setSpeciesId(species);
|
||||
}
|
||||
}
|
||||
|
||||
References references = locType.getReferences();
|
||||
if (references == null) {
|
||||
references = new References();
|
||||
try {
|
||||
Helper.createRequiredElements(references);
|
||||
} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
locType.setReferences(references);
|
||||
|
||||
/*
|
||||
* Add references back to PAMGuard data as for Detections.
|
||||
* Same code as in Detections, but classes are different (though with the same fields).
|
||||
*/
|
||||
Parameters params = getParameters(locType);
|
||||
String uid = BigInteger.valueOf(dataUnit.getUID()).toString();
|
||||
Element el = addUserDefined(params,"PAMGuardUID", uid);
|
||||
DataUnitFileInformation fileInf = dataUnit.getDataUnitFileInformation();
|
||||
if (fileInf != null) {
|
||||
el.setAttribute("BinaryFile", fileInf.getShortFileName(2048));
|
||||
el.setAttribute("FileIndex", Long.valueOf(fileInf.getIndexInFile()).toString());
|
||||
}
|
||||
Reference reference = new Reference();
|
||||
reference.setIndex(BigInteger.valueOf(dataUnit.getUID()));
|
||||
reference.setEventRef("UID");
|
||||
locType.getReferences().getReference().add(reference);
|
||||
if (dataUnit.getDatabaseIndex() > 0) {
|
||||
// only write the database index if it's > 0, i.e. is used.
|
||||
addUserDefined(params, "DatabaseId", String.format("%d", dataUnit.getDatabaseIndex()));
|
||||
}
|
||||
|
||||
/*
|
||||
* Not needed. something to do with references to Detection docs.
|
||||
*/
|
||||
// References references = locType.getReferences();
|
||||
// if (references == null) {
|
||||
// references = new References();
|
||||
// try {
|
||||
// Helper.createRequiredElements(references);
|
||||
// } catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
|
||||
// e.printStackTrace();
|
||||
// }
|
||||
// locType.setReferences(references);
|
||||
// }
|
||||
// Reference reference = new Reference();
|
||||
// reference.setIndex(BigInteger.valueOf(dataUnit.getUID()));
|
||||
// reference.setEventRef("UID");
|
||||
// locType.getReferences().getReference().add(reference);
|
||||
|
||||
return locType;
|
||||
}
|
||||
@ -405,11 +501,7 @@ public class LocalizationBuilder {
|
||||
locType.setWGS84(wgs84);
|
||||
|
||||
// locType.setParameters(null);
|
||||
Parameters params = locType.getParameters();
|
||||
if (params == null) {
|
||||
params = new Parameters();
|
||||
locType.setParameters(params);
|
||||
}
|
||||
Parameters params = getParameters(locType);
|
||||
TargetMotionAnalysis tma = new TargetMotionAnalysis();
|
||||
tma.setStart(TethysTimeFuncs.xmlGregCalFromMillis(dataUnit.getTimeMilliseconds()));
|
||||
tma.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(dataUnit.getEndTimeInMilliseconds()));
|
||||
@ -442,6 +534,40 @@ public class LocalizationBuilder {
|
||||
|
||||
return locType;
|
||||
}
|
||||
|
||||
/**
|
||||
* Convenience method to get the Parameters object for a localisation and
|
||||
* to automatically create it if it doesn't exist.
|
||||
* @param localization
|
||||
* @return
|
||||
*/
|
||||
public Parameters getParameters(LocalizationType localization) {
|
||||
Parameters params = localization.getParameters();
|
||||
if (params == null) {
|
||||
params = new Parameters();
|
||||
localization.setParameters(params);
|
||||
}
|
||||
return params;
|
||||
}
|
||||
|
||||
public Element addUserDefined(Parameters parameters, String parameterName, String parameterValue) {
|
||||
UserDefined userDefined = parameters.getUserDefined();
|
||||
if (userDefined == null) {
|
||||
userDefined = new UserDefined();
|
||||
parameters.setUserDefined(userDefined);
|
||||
}
|
||||
Element el = null;
|
||||
try {
|
||||
el = helper.AddAnyElement(userDefined.getAny(), parameterName, parameterValue);
|
||||
} catch (JAXBException e) {
|
||||
e.printStackTrace();
|
||||
return null;
|
||||
} catch (ParserConfigurationException e) {
|
||||
e.printStackTrace();
|
||||
return null;
|
||||
}
|
||||
return el;
|
||||
}
|
||||
|
||||
public LocalizationType createSphericalLoc(PamDataUnit dataUnit) {
|
||||
// TODO Auto-generated method stub
|
||||
|
||||
@ -2,17 +2,8 @@ package tethys.localization;
|
||||
|
||||
import java.util.ArrayList;
|
||||
|
||||
import Localiser.detectionGroupLocaliser.GroupLocResult;
|
||||
import Localiser.detectionGroupLocaliser.GroupLocalisation;
|
||||
import PamDetection.AbstractLocalisation;
|
||||
import PamDetection.LocContents;
|
||||
import PamUtils.LatLong;
|
||||
import PamUtils.PamUtils;
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import nilus.Localize;
|
||||
import nilus.SpeciesIDType;
|
||||
import pamMaths.PamVector;
|
||||
import nilus.Localize.Effort.CoordinateReferenceSystem;
|
||||
import tethys.Collection;
|
||||
import tethys.CollectionHandler;
|
||||
import tethys.TethysControl;
|
||||
|
||||
122
src/tethys/localization/TethysLatLong.java
Normal file
122
src/tethys/localization/TethysLatLong.java
Normal file
@ -0,0 +1,122 @@
|
||||
package tethys.localization;
|
||||
|
||||
import PamUtils.PamUtils;
|
||||
import tethys.pamdata.AutoTethysProvider;
|
||||
|
||||
/**
|
||||
* Static formatting (rounding and range checking) functions for latlong values.
|
||||
* @author dg50
|
||||
*
|
||||
*/
|
||||
public class TethysLatLong {
|
||||
|
||||
/*
|
||||
* A degree is 60 minutes and a minute is one mile = 1852m.
|
||||
* Therefore one metre of latitude is 9e-6 degrees.
|
||||
* One mm of latitude is therefore 9e-9 degrees.
|
||||
* GPS Accuracy is generally <3m, so 6dp generally OK for track data. however,
|
||||
* localisations around a small static array may want mm accuracy, so need 8dp.
|
||||
* For a double precision number, resolution at 360 degrees is 14dp
|
||||
*
|
||||
*/
|
||||
|
||||
/**
|
||||
* Number of decimal places for metre accuracy
|
||||
*/
|
||||
public static int metreDecimalPlaces = 6;
|
||||
|
||||
/**
|
||||
* Number of decimal places for mm accuracy.
|
||||
*/
|
||||
public static int mmDecimalPlaces = 9;
|
||||
|
||||
/**
|
||||
* Check range of a latitude value.
|
||||
* This function does absolutely nothing, but is here for completeness.
|
||||
* @param latitude
|
||||
* @return
|
||||
*/
|
||||
public static Double formatLatitude(Double latitude) {
|
||||
if (latitude == null) {
|
||||
return null;
|
||||
}
|
||||
return latitude;
|
||||
}
|
||||
|
||||
/**
|
||||
* Check range and round a latitude value to a set number of decimal places.
|
||||
* @param latitude
|
||||
* @param decimalPlaces
|
||||
* @return
|
||||
*/
|
||||
public static Double formatLatitude(Double latitude, int decimalPlaces) {
|
||||
if (latitude == null) {
|
||||
return null;
|
||||
}
|
||||
return AutoTethysProvider.roundDecimalPlaces(latitude, decimalPlaces);
|
||||
}
|
||||
|
||||
/**
|
||||
* format a latitude to metre accuracy
|
||||
* @param latitude
|
||||
* @return
|
||||
*/
|
||||
public static Double formatLatitude_m(Double latitude) {
|
||||
return formatLatitude(latitude, metreDecimalPlaces);
|
||||
}
|
||||
|
||||
/**
|
||||
* format a latitude to mm accuracy
|
||||
* @param latitude
|
||||
* @return
|
||||
*/
|
||||
public static Double formatLatitude_mm(Double latitude) {
|
||||
return formatLatitude(latitude, mmDecimalPlaces);
|
||||
}
|
||||
|
||||
/**
|
||||
* Check range of a longitude value which must be between 0 and 360.
|
||||
* This function does absolutely nothing, but is here for completeness.
|
||||
* @param latitude
|
||||
* @return
|
||||
*/
|
||||
public static Double formatLongitude(Double longitude) {
|
||||
if (longitude == null) {
|
||||
return null;
|
||||
}
|
||||
return PamUtils.constrainedAngle(longitude);
|
||||
}
|
||||
|
||||
/**
|
||||
* Check range and round a longitude value to a set number of decimal places.
|
||||
* @param latitude
|
||||
* @param decimalPlaces
|
||||
* @return
|
||||
*/
|
||||
public static Double formatLongitude(Double longitude, int decimalPlaces) {
|
||||
if (longitude == null) {
|
||||
return null;
|
||||
}
|
||||
longitude = formatLongitude(longitude); // constrain first.
|
||||
return AutoTethysProvider.roundDecimalPlaces(longitude, decimalPlaces);
|
||||
}
|
||||
|
||||
/**
|
||||
* format a longitude value to m accuracy.
|
||||
* @param latitude
|
||||
* @return
|
||||
*/
|
||||
public static Double formatLongitude_m(Double longitude) {
|
||||
return formatLongitude(longitude, metreDecimalPlaces);
|
||||
}
|
||||
|
||||
/**
|
||||
* format a longitude value to mm accuracy.
|
||||
* @param latitude
|
||||
* @return
|
||||
*/
|
||||
public static Double formatLongitude_mm(Double longitude) {
|
||||
return formatLongitude(longitude, mmDecimalPlaces);
|
||||
}
|
||||
|
||||
}
|
||||
@ -1,32 +1,34 @@
|
||||
package tethys.pamdata;
|
||||
|
||||
import java.io.StringReader;
|
||||
import java.math.BigInteger;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import javax.xml.bind.JAXBException;
|
||||
import javax.xml.parsers.ParserConfigurationException;
|
||||
import javax.xml.transform.Source;
|
||||
import javax.xml.transform.Transformer;
|
||||
import javax.xml.transform.TransformerFactory;
|
||||
import javax.xml.transform.dom.DOMResult;
|
||||
import javax.xml.transform.dom.DOMSource;
|
||||
import javax.xml.transform.stream.StreamSource;
|
||||
|
||||
import org.w3c.dom.Document;
|
||||
import org.w3c.dom.Element;
|
||||
import org.w3c.dom.Node;
|
||||
import org.w3c.dom.NodeList;
|
||||
|
||||
import Localiser.LocalisationAlgorithm;
|
||||
import Localiser.LocalisationAlgorithmInfo;
|
||||
import PamController.PamControlledUnit;
|
||||
import PamController.PamSettings;
|
||||
import PamController.PamguardVersionInfo;
|
||||
import PamController.settings.output.xml.PamguardXMLWriter;
|
||||
import PamDetection.LocalisationInfo;
|
||||
import PamUtils.XMLUtils;
|
||||
import PamguardMVC.DataAutomationInfo;
|
||||
import PamguardMVC.DataUnitBaseData;
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import PamguardMVC.PamDataUnit;
|
||||
import PamguardMVC.PamProcess;
|
||||
import PamguardMVC.TFContourData;
|
||||
import PamguardMVC.TFContourProvider;
|
||||
import binaryFileStorage.DataUnitFileInformation;
|
||||
import generalDatabase.DBSchemaWriter;
|
||||
import generalDatabase.SQLLogging;
|
||||
import nilus.AlgorithmType;
|
||||
import nilus.Deployment;
|
||||
import nilus.DescriptionType;
|
||||
@ -52,23 +54,11 @@ import tethys.species.SpeciesMapItem;
|
||||
import tethys.swing.export.ExportWizardCard;
|
||||
import whistleClassifier.WhistleContour;
|
||||
|
||||
import javax.xml.bind.JAXBException;
|
||||
import javax.xml.parsers.ParserConfigurationException;
|
||||
import javax.xml.transform.*;
|
||||
import javax.xml.transform.dom.DOMResult;
|
||||
import javax.xml.transform.dom.DOMSource;
|
||||
import javax.xml.transform.stream.StreamResult;
|
||||
import javax.xml.transform.stream.StreamSource;
|
||||
import java.io.File;
|
||||
import java.io.IOException;
|
||||
import java.io.StringReader;
|
||||
import java.net.URISyntaxException;
|
||||
|
||||
/**
|
||||
* Automatically provides Tethys data for a PAMGuard datablock.
|
||||
* Automatically provides Tethys data for a PAMGuard datablock.
|
||||
* Does most of what needs to be done, though individual modules
|
||||
* will want to override this, call the base createDetection function and then add a
|
||||
* few more bespoke elements.
|
||||
* will want to override this, call the base createDetection function and then add a
|
||||
* few more bespoke elements.
|
||||
* @author dg50
|
||||
*
|
||||
*/
|
||||
@ -79,6 +69,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
private PamControlledUnit pamControlledUnit;
|
||||
private TethysControl tethysControl;
|
||||
private Helper helper;
|
||||
private boolean addFrequencyInfo = false;
|
||||
|
||||
public AutoTethysProvider(TethysControl tethysControl, PamDataBlock pamDataBlock) {
|
||||
this.tethysControl = tethysControl;
|
||||
@ -91,7 +82,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
e.printStackTrace();
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public DescriptionType getDescription(Deployment deployment, TethysExportParams tethysExportParams) {
|
||||
DescriptionType description = new DescriptionType();
|
||||
@ -106,9 +97,9 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
@Override
|
||||
public AlgorithmType getAlgorithm(Collection collection) {
|
||||
/**
|
||||
* Probably need to split this to provide detection algorithm parameters and
|
||||
* localisation algorithm parameters, or pass in the document type as a function
|
||||
* argument.
|
||||
* Probably need to split this to provide detection algorithm parameters and
|
||||
* localisation algorithm parameters, or pass in the document type as a function
|
||||
* argument.
|
||||
*/
|
||||
AlgorithmType algorithm = new AlgorithmType();
|
||||
try {
|
||||
@ -116,7 +107,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
} catch (IllegalArgumentException | IllegalAccessException | InstantiationException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
// do the parameters as normal whether it's dets or locs.
|
||||
// do the parameters as normal whether it's dets or locs.
|
||||
nilus.AlgorithmType.Parameters algoParameters = this.getAlgorithmParameters();
|
||||
if (algoParameters != null) {
|
||||
algorithm.setParameters(algoParameters);
|
||||
@ -125,7 +116,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
nilus.AlgorithmType.Parameters locParameters = this.getLocalisationParameters();
|
||||
if (locParameters == null) {
|
||||
/*
|
||||
* It seems Tethys MUST have parameters, so make an empty one if needed.
|
||||
* It seems Tethys MUST have parameters, so make an empty one if needed.
|
||||
*/
|
||||
locParameters = new nilus.AlgorithmType.Parameters();
|
||||
}
|
||||
@ -133,7 +124,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
algorithm.setParameters(locParameters);
|
||||
}
|
||||
else if (locParameters != null) {
|
||||
// merge the two sets, putting the localisation information first.
|
||||
// merge the two sets, putting the localisation information first.
|
||||
List<Element> mainList = algoParameters.getAny();
|
||||
List<Element> locList = locParameters.getAny();
|
||||
if (mainList != null && locList != null) {
|
||||
@ -150,7 +141,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
}
|
||||
|
||||
/**
|
||||
* Localisation parameters. Some localisers don't actually have any parameters,
|
||||
* Localisation parameters. Some localisers don't actually have any parameters,
|
||||
* but Tethys requires a parameters element, so if there aren't any, set a dummy
|
||||
* @return
|
||||
*/
|
||||
@ -181,13 +172,13 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
nilus.AlgorithmType.Parameters parameters = new nilus.AlgorithmType.Parameters();
|
||||
List<Element> paramList = parameters.getAny();
|
||||
paramList.add(paramEl);
|
||||
|
||||
|
||||
return parameters;
|
||||
}
|
||||
|
||||
@Override
|
||||
public nilus.AlgorithmType.Parameters getAlgorithmParameters() {
|
||||
if (pamControlledUnit instanceof PamSettings == false) {
|
||||
if (!(pamControlledUnit instanceof PamSettings)) {
|
||||
return null;
|
||||
}
|
||||
PamSettings pamSettings = (PamSettings) pamControlledUnit;
|
||||
@ -211,7 +202,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
|
||||
/**
|
||||
* Not used. Was an attempt to automatically add name spaces to the PAMGuard settings
|
||||
* XML I generate, but we found a better way.
|
||||
* XML I generate, but we found a better way.
|
||||
* @param doc
|
||||
* @param settingsEl
|
||||
* @param xmlNameSpace
|
||||
@ -270,7 +261,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
|
||||
DOMSource source = new DOMSource(doc);
|
||||
|
||||
// Result
|
||||
// Result
|
||||
// Source text = new StreamSource(new File("input.xml"));
|
||||
DOMResult result = new DOMResult();
|
||||
transformer.transform(source, result);
|
||||
@ -294,8 +285,8 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
}
|
||||
|
||||
/**
|
||||
* Algorithm method. Default is the module name. Can change to a paper citation
|
||||
* by overriding this
|
||||
* Algorithm method. Default is the module name. Can change to a paper citation
|
||||
* by overriding this
|
||||
* @return
|
||||
*/
|
||||
private String getAlgorithmMethod() {
|
||||
@ -335,16 +326,21 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
}
|
||||
detection.setSpeciesId(species);
|
||||
/*
|
||||
* NOTE: I use channel bitmaps throughout since detections are often made on multiple channels.
|
||||
* NOTE: I use channel bitmaps throughout since detections are often made on multiple channels.
|
||||
*/
|
||||
detection.setChannel(BigInteger.valueOf(dataUnit.getChannelBitmap()));
|
||||
|
||||
nilus.Detection.Parameters detParams = new nilus.Detection.Parameters();
|
||||
detection.setParameters(detParams);
|
||||
double[] freqs = dataUnit.getFrequency();
|
||||
if (freqs != null && freqs[1] != 0) {
|
||||
detParams.setMinFreqHz(freqs[0]);
|
||||
detParams.setMaxFreqHz(freqs[1]);
|
||||
if (addFrequencyInfo) {
|
||||
/**
|
||||
* Don't add by default.
|
||||
*/
|
||||
double[] freqs = dataUnit.getFrequency();
|
||||
if (freqs != null && freqs[1] != 0) {
|
||||
detParams.setMinFreqHz(freqs[0]);
|
||||
detParams.setMaxFreqHz(freqs[1]);
|
||||
}
|
||||
}
|
||||
double ampli = dataUnit.getAmplitudeDB();
|
||||
ampli = roundDecimalPlaces(ampli, 1);
|
||||
@ -359,7 +355,8 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
el.setAttribute("BinaryFile", fileInf.getShortFileName(2048));
|
||||
el.setAttribute("FileIndex", Long.valueOf(fileInf.getIndexInFile()).toString());
|
||||
}
|
||||
if (dataUnit.getDatabaseIndex() >= 0) {
|
||||
if (dataUnit.getDatabaseIndex() > 0) {
|
||||
// only write the database index if it's > 0, i.e. is used.
|
||||
addUserDefined(detParams, "DatabaseId", String.format("%d", dataUnit.getDatabaseIndex()));
|
||||
}
|
||||
|
||||
@ -387,7 +384,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
|
||||
/**
|
||||
* Get tonal sounds contour. Sadly there are two slightly different interfaces in use
|
||||
* in PAMGuard, so try them both.
|
||||
* in PAMGuard, so try them both.
|
||||
* @param detParams
|
||||
* @return true if a contour was added
|
||||
*/
|
||||
@ -402,7 +399,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
List<Double> offsetS = tonal.getOffsetS();
|
||||
List<Double> hz = tonal.getHz();
|
||||
for (int i = 0; i < tMillis.length; i++) {
|
||||
offsetS.add(roundSignificantFigures((double) (tMillis[i]-tMillis[0]) / 1000., 4));
|
||||
offsetS.add(roundSignificantFigures((tMillis[i]-tMillis[0]) / 1000., 4));
|
||||
hz.add(roundSignificantFigures(fHz[i], 4));
|
||||
}
|
||||
detParams.setTonal(tonal);
|
||||
@ -485,7 +482,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
kind.setCall(mapItem.getCallType());
|
||||
|
||||
|
||||
effortKinds.add(kind);
|
||||
effortKinds.add(kind);
|
||||
|
||||
}
|
||||
|
||||
@ -495,7 +492,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
public String getDetectionsMethod() {
|
||||
/*
|
||||
* could really do with knowing what type of detector we're dealing with, i.e. if it's
|
||||
* automatic or manual. For most blocks this is fixed, though some may have a mixture of both !
|
||||
* automatic or manual. For most blocks this is fixed, though some may have a mixture of both !
|
||||
*/
|
||||
DataAutomationInfo dataAutomation = pamDataBlock.getDataAutomationInfo();
|
||||
String method;
|
||||
@ -524,7 +521,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
String blockName = pamDataBlock.getDataName();
|
||||
String documentName;
|
||||
/**
|
||||
* If the datablock name is the same as the unit name, no need to repeat onesself.
|
||||
* If the datablock name is the same as the unit name, no need to repeat onesself.
|
||||
*/
|
||||
if (pcuName.equals(blockName)) {
|
||||
documentName = new String(pcuName); // copy it, since we're about to modify it!
|
||||
@ -539,7 +536,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
public static double roundDecimalPlaces(double value, int decPlaces) {
|
||||
double scale = Math.pow(10, decPlaces);
|
||||
long longVal = Math.round(value*scale);
|
||||
return (double) longVal/scale;
|
||||
return longVal/scale;
|
||||
}
|
||||
|
||||
public static double roundSignificantFigures(double value, int sigFigs) {
|
||||
@ -551,7 +548,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
double scale = sigFigs-Math.floor(Math.log10(value));
|
||||
scale = Math.pow(10, scale);
|
||||
long longVal = Math.round(value*scale);
|
||||
return sign*(double) longVal/scale;
|
||||
return sign*longVal/scale;
|
||||
}
|
||||
|
||||
@Override
|
||||
@ -571,7 +568,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
return true;
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
public boolean canExportLocalisations(GranularityEnumType granularityType) {
|
||||
LocalisationInfo locCont = pamDataBlock.getLocalisationContents();
|
||||
@ -582,7 +579,7 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
}
|
||||
|
||||
/**
|
||||
* Granularity is OK for export.
|
||||
* Granularity is OK for export.
|
||||
* @param granularityType
|
||||
* @return
|
||||
*/
|
||||
@ -607,7 +604,21 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
|
||||
protected PamDataBlock getPamDataBlock() {
|
||||
return pamDataBlock;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @return the addFrequencyInfo
|
||||
*/
|
||||
public boolean isAddFrequencyInfo() {
|
||||
return addFrequencyInfo;
|
||||
}
|
||||
|
||||
/**
|
||||
* @param addFrequencyInfo the addFrequencyInfo to set
|
||||
*/
|
||||
public void setAddFrequencyInfo(boolean addFrequencyInfo) {
|
||||
this.addFrequencyInfo = addFrequencyInfo;
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
@ -7,8 +7,14 @@ package tethys.species;
|
||||
*/
|
||||
public class ITISTypes {
|
||||
|
||||
/*
|
||||
* A few that get used in defaults copied from itis.gov for convenience.
|
||||
*/
|
||||
public static final int OTHER = -10;
|
||||
public static final int ANTHROPOGENIC = 1758;
|
||||
public static final int CETACEAN = 180403;
|
||||
public static final int ODONTOCETE = 180404;
|
||||
public static final int MYSTICETE = 552298;
|
||||
|
||||
public static final String getName(int code) {
|
||||
switch (code) {
|
||||
|
||||
@ -8,6 +8,7 @@ public class WhistleMoanTethysProvider extends AutoTethysProvider {
|
||||
|
||||
public WhistleMoanTethysProvider(TethysControl tethysControl, PamDataBlock pamDataBlock) {
|
||||
super(tethysControl, pamDataBlock);
|
||||
setAddFrequencyInfo(true);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user