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Small changes to support batch process module
A couple of small changes to add functionality for batch processor
This commit is contained in:
Douglas Gillespie
parent
42efd2b765
commit
543779bbf1
100
README.html
100
README.html
@ -499,6 +499,9 @@ to first available input source. </p>
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<p class=MsoNormal>Fixed units on spectrogram displays for air based
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measurements.</p>
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<p class=MsoNormal>Fixed bug in whistle and moan detector graphics that caused
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whistles with branches to not draw.</p>
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<h1>Version 2.02.14 October 2024</h1>
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<h2>New Features</h2>
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@ -571,14 +574,14 @@ Visualiser, Audacity etc.)</p>
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<h2>Tethys Database</h2>
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<p class=MsoNormal>Many users will be aware that we’re integrating an interface
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to the <a href="https://tethys.sdsu.edu/">Tethys Database</a> into PAMGuard. Some
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basic features are available for testing. If interested, please contact the
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PAMGuard support team. </p>
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to the <a href="https://tethys.sdsu.edu/">Tethys Database</a> into PAMGuard.
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Some basic features are available for testing. If interested, please contact
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the PAMGuard support team. </p>
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<h2>Bug Fixes</h2>
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<p class=MsoNormal>Linking clicks to offline clicks table. We had a database that
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had become corrupted so added code to relink offline clicks to their
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<p class=MsoNormal>Linking clicks to offline clicks table. We had a database
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that had become corrupted so added code to relink offline clicks to their
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corresponding clicks from binary data. </p>
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<p class=MsoNormal>Drawing non-acoustic data: Data that were not associated
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@ -677,8 +680,8 @@ do it here.</span></p>
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Bug crashing the module with null pointer errors fixed.</span></p>
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<p class=MsoNormal><b><span lang=EN-US>Whistle Detector</span></b><span
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lang=EN-US>: Fixed bug which caused the detector to slow to almost zero speed when
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large complex sounds with many branches were detected. </span></p>
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lang=EN-US>: Fixed bug which caused the detector to slow to almost zero speed
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when large complex sounds with many branches were detected. </span></p>
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<p class=MsoNormal><b><span lang=EN-US>Click Detector Offline Event Marking</span></b><span
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lang=EN-US>: Fixed problem of events not being correctly deleted and also of
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@ -1223,8 +1226,9 @@ August 2020</span></h1>
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<p class=MsoNormal><b>If you are upgrading from a PAMGuard core release
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(1.15.xx), PAMGuard Version 2 contains major updates. You should read and
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understand the notes listed for <a href="#_Latest_Beta_Version_2.00.10">Beta Version
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2.00.10</a> before proceeding with installation and use of this version.</b></p>
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understand the notes listed for <a href="#_Latest_Beta_Version_2.00.10">Beta
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Version 2.00.10</a> before proceeding with installation and use of this
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version.</b></p>
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<p class=MsoNormal>This version of PAMGuard has been bundled with Java 13
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(release 13.0.1). PSFX files generated in previous beta releases (2.xx.xx)
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@ -1340,10 +1344,10 @@ lang=EN-US> </span>Add functionality for bluetooth headsets. </p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
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lang=EN-US> </span>Add user-facing option to adjust the startup delay for the
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time-correction (Global Time module). This provides a workaround to speed up analysis
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of thousands of wav files (i.e. by setting startup delay to 0 instead of
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default value of 2000 ms). </p>
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lang=EN-US> </span>Add user-facing option to adjust the startup delay for the time-correction
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(Global Time module). This provides a workaround to speed up analysis of
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thousands of wav files (i.e. by setting startup delay to 0 instead of default
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value of 2000 ms). </p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>3. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
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@ -1515,8 +1519,8 @@ classify clicks. </p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
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lang=EN-US> </span>Added option in Sound Acquisition settings dialog to
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override filename time stamp and use PC local time instead. </p>
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lang=EN-US> </span>Added option in Sound Acquisition settings dialog to override
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filename time stamp and use PC local time instead. </p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>3. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
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@ -1751,8 +1755,8 @@ lang=EN-US> </span>Send Email option added to Alarm module.</p>
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
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lang=EN-US> </span>Added ability to scale the PAMGuard display (go to <em><span
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style='font-family:"Calibri",sans-serif'>Help > Set Display Scaling Factor</span></em>
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to adjust the scale). This, in conjunction with the built-in Windows Display
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Scaling feature, will hopefully help with issues sometimes found when using
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to adjust the scale). This, in conjunction with the built-in Windows Display Scaling
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feature, will hopefully help with issues sometimes found when using
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4k/UHD/high-DPI displays. At the moment this does not fix the JavaFX
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components, but we're working on that.</p>
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@ -2430,8 +2434,8 @@ the new version. However please note the following:</span></p>
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<p class=MsoListParagraph style='margin-left:54.0pt;text-indent:-36.0pt'><span
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lang=EN-US>1.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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</span><span lang=EN-US>New classes will be added to the configuration files, so
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they will no longer work with older PAMGuard versions.</span></p>
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</span><span lang=EN-US>New classes will be added to the configuration files,
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so they will no longer work with older PAMGuard versions.</span></p>
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<p class=MsoListParagraph style='margin-left:54.0pt;text-indent:-36.0pt'><span
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lang=EN-US>2.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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@ -2554,19 +2558,19 @@ milliseconds. However, getDuration actually returns the number of samples.
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<p class=MsoNormal><b><span lang=EN-US>Plug-Ins</span></b></p>
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<p class=MsoNormal><span lang=EN-US>A major change in this version of PAMGuard is
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how plug-ins are managed. PAMGuard now has the ability to dynamically load
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<p class=MsoNormal><span lang=EN-US>A major change in this version of PAMGuard
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is how plug-ins are managed. PAMGuard now has the ability to dynamically load
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plug-in modules (saved as jar files) at runtime. This will greatly simplify the
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process of testing and distributing newly developed modules, since only a small
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jar file will be required rather than a new bespoke PAMGuard installation.</span></p>
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<p class=MsoNormal><span lang=EN-US>Module code development remains largely
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unchanged, in most cases simply requiring the addition of an interface class.
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<p class=MsoNormal><span lang=EN-US>Module code development remains largely unchanged,
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in most cases simply requiring the addition of an interface class.
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Instructions for the development of new modules utilizing the plug-in
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system can be found <a href="http://www.PAMGuard.org/16_HowtomakePlug-Ins.html"
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scheme can be found>here</a>. Plug-in modules can be downloaded from the PAMGuard
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website here, but developers are encouraged to host and maintain their own
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modules.</span></p>
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scheme can be found>here</a>. Plug-in modules can be downloaded from the
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PAMGuard website here, but developers are encouraged to host and maintain their
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own modules.</span></p>
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<p class=MsoNormal><span lang=EN-US>Modules of interest to the general PAM
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community will remain as part of the core PAMGuard installation. However,
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@ -2887,9 +2891,9 @@ easy to understand options have been developed in a new options dialog.</p>
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<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>9.<span
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style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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</span>Bug 281. Click classification dialog has grown too big to fit on the screen.
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The options have now been split across three tabbed panes which solves the
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problem.</p>
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</span>Bug 281. Click classification dialog has grown too big to fit on the
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screen. The options have now been split across three tabbed panes which solves
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the problem.</p>
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<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>10.<span
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style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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@ -3193,10 +3197,10 @@ href="https://sourceforge.net/p/PAMGuard/bugs">https://sourceforge.net/p/PAMGuar
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<p class=MsoListParagraph style='margin-left:47.25pt;text-indent:-29.25pt'><span
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lang=EN-US>1.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
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</span>Spectrogram annotation marks. A simple system for marking spectrograms
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during real time analysis has been incorporated. To use it, add the module, in
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the spectrogram settings, select the annotation marks in the 'Mark Observers'
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tab of the spectrogram configuration dialog, and also right click on the
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</span>Spectrogram annotation marks. A simple system for marking spectrograms during
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real time analysis has been incorporated. To use it, add the module, in the
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spectrogram settings, select the annotation marks in the 'Mark Observers' tab
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of the spectrogram configuration dialog, and also right click on the
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spectrogram and select to display the annotations. Annotations are saved to the
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database so you will also need a database module in your configuration. </p>
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@ -3466,9 +3470,9 @@ of third octave noise bands. See online help for details. </p>
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<p class=MsoNormal><i>Filtered Noise Measurement</i> (Sound Processing Group)</p>
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<p class=MsoNormal>This module, developed by Douglas Gillespie, measures noise levels
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in a single frequency band using a variety of filter functions. See online help
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for details. </p>
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<p class=MsoNormal>This module, developed by Douglas Gillespie, measures noise
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levels in a single frequency band using a variety of filter functions. See
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online help for details. </p>
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<p class=MsoNormal><i>Envelope Tracing</i> (Beta Only, Sound Processing Group)</p>
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@ -3998,11 +4002,11 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
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<p class=MsoNormal>2. Improved offline viewer functionality. </p>
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<p class=MsoNormal>The offline viewer is much improved with better data scrolling
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and the ability to view data either stored in the database or the binary
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storage system. Work has stated on functions which read and use data stored in
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audio files. This is currently limited to re-calculating and displaying
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displaying spectrogram data during viewer mode operation. </p>
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<p class=MsoNormal>The offline viewer is much improved with better data
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scrolling and the ability to view data either stored in the database or the
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binary storage system. Work has stated on functions which read and use data
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stored in audio files. This is currently limited to re-calculating and
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displaying displaying spectrogram data during viewer mode operation. </p>
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<p class=MsoNormal>3. Heading sensor readout</p>
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@ -4103,8 +4107,8 @@ channels 0 and 1. Similarly if you switched sound cards, you may have to
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reconfigure every detector and several of the displays to handle the changes in
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channel numbering. </p>
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<p class=MsoNormal>I have spent a considerable amount of time trying to work out
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a better system for handling channel numbering in PAMGuard and have decided
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<p class=MsoNormal>I have spent a considerable amount of time trying to work
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out a better system for handling channel numbering in PAMGuard and have decided
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that the only practical thing to do is to force all software channel numbering
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back to a zero indexed system. i.e. even if you read out hardware channels
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3,4,5 and 6, within PAMGuard, everywhere apart from the Sound acquisition
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@ -4692,9 +4696,9 @@ a serial port </p>
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<p class=MsoNormal>New Likelihood detector. </p>
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<p class=MsoNormal>The likelihood detector module is an implementation of a likelihood
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ratio test with flexible algorithms and configuration to estimate likelihood.
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It is </p>
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<p class=MsoNormal>The likelihood detector module is an implementation of a
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likelihood ratio test with flexible algorithms and configuration to estimate
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likelihood. It is </p>
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<p class=MsoNormal>suitable for detecting both short duration Odontocete clicks
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(Sperm, Beaked, etc.) as well as moderate duration Mysticete calls (Humpback,
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@ -5020,8 +5024,8 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
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<p class=MsoNormal> </p>
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<p class=MsoNormal><a name="_Toc312065304"></a><a name="_Toc312063949"></a><span
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class=Heading2Char><span style='font-size:13.0pt'>1.0Beta 22 Jan 2008 -
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PAMGuard starts two releases, core and beta release</span></span>, </p>
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class=Heading2Char><span style='font-size:13.0pt'>1.0Beta 22 Jan 2008 - PAMGuard
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starts two releases, core and beta release</span></span>, </p>
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<p class=MsoNormal>this is the beta release</p>
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@ -1,5 +1,6 @@
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package PamController;
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import java.awt.Window;
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import java.io.DataInputStream;
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import java.io.DataOutputStream;
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import java.io.EOFException;
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@ -10,7 +11,11 @@ import java.io.FileOutputStream;
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import java.io.IOException;
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import java.util.ArrayList;
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import javax.swing.JFileChooser;
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import PamUtils.PamCalendar;
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import PamUtils.PamFileChooser;
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import PamUtils.PamFileFilter;
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import PamView.dialog.warn.WarnOnce;
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import binaryFileStorage.BinaryFooter;
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import binaryFileStorage.BinaryHeader;
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@ -81,15 +86,32 @@ public class PSFXReadWriter {
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* Initially write to a temp file, then rename the temp file.
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* @param fileName the name to use for the save file (full name, including path)
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* @param timeStamp time stamp in milliseconds
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* @return
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* @return true on success
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*/
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public synchronized boolean writePSFX(String fileName, long timeStamp) {
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// get an object containing everything we'll need to know.
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PamSettingsGroup psg = PamSettingManager.getInstance().getCurrentSettingsGroup();
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// force the time stamp to be that given - might need to be exact !
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psg.setSettingsTime(timeStamp);
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return writePSFX(fileName, psg);
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}
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/**
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* Write settings to the given file<br>
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* Initially write to a temp file, then rename the temp file.
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* @param fileName the name to use for the save file (full name, including path)
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* @param psg PAMGuard settings group
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* @return true on success
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*/
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public synchronized boolean writePSFX(String fileName, PamSettingsGroup psg) {
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BinaryHeader header = new BinaryHeader(SETTINGSSTORE, SETTINGSSTORE, SETTINGSSTORE, 0);
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long timeStamp = psg.getSettingsTime();
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header.setAnalysisDate(timeStamp);
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header.setDataDate(timeStamp);
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@ -133,6 +155,33 @@ public class PSFXReadWriter {
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return true;
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}
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/**
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* Select a psfx file.
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* @param toRead if true, only selects existing files with the open dialog.
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* @return File or null.
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*/
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public File selectSettingsFile(Window frame, boolean toRead) {
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File start = new File(PamFolders.getDefaultProjectFolder());
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JFileChooser jFileChooser = new PamFileChooser(start);
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// jFileChooser.setFileFilter(new SettingsFileFilter());
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jFileChooser.setApproveButtonText("Select");
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PamFileFilter fileFilter = new PamFileFilter("PAMGUARD Settings files", PamSettingManager.getCurrentSettingsFileEnd());
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jFileChooser.setFileFilter(fileFilter);
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jFileChooser.setAcceptAllFileFilterUsed(false);
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// jFileChooser.setFileFilter(new FileNameExtensionFilter("PAMGUARD Settings files", defaultFile));
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int state = 0;
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if (toRead) {
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jFileChooser.showOpenDialog(frame);
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}
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else {
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jFileChooser.showSaveDialog(frame);
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}
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if (state != JFileChooser.APPROVE_OPTION) return null;
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File newFile = jFileChooser.getSelectedFile();
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newFile = PamFileFilter.checkFileEnd(newFile, PamSettingManager.getCurrentSettingsFileEnd(), true);
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return newFile;
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}
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private boolean writeData(DataOutputStream dos, int objectId, byte[] data) {
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int totalLen = data.length + 16;
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int dataLen = data.length;
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@ -244,7 +244,7 @@ public abstract class DataBlockTableView<T extends PamDataUnit> {
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if (dataUnitCopy == null) {
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return null;
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}
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return dataUnitCopy.get(tableRow);
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return dataUnitCopy.get(rowIndex);
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// return pamDataBlock.getDataUnit(rowIndex, PamDataBlock.REFERENCE_CURRENT);
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}
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}
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@ -286,6 +286,9 @@ public abstract class DataBlockTableView<T extends PamDataUnit> {
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* @return
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*/
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public int getDataIndexForRow(int tableRow) {
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if (tableRow == -1) {
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return -1;
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}
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if (dataUnitCopy == null) {
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return tableRow;
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}
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