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SUD Files (#83)
* Adding comments to table definitions. Update tabledefs so tableitems can have descriptions. Useful to the coder, but can also export formal xms schema for each table. * Writing xml schema Writing xml schema for PAMGuard database with annotations as complex types * Working SUD click extractor Seems to be mostly working and can generate PAMGuard click files automatically when processing SUD files using the soundtrap click detector * Small changes to SUD in PAMGuard * Better SUD timing Using latest microsecond time extraction from SUD unpack * SUD Processing Extraction of SUD file clicks with SoundTrap Click Detector. Timing now correct. Added some help pages. * Functional SUD Reader and SUD Click Extractor All seems working. Seems to throw the odd exception at end of file, but works OK.
This commit is contained in:
Douglas Gillespie
GitHub
parent
4a75afc414
commit
ea32c5cdcb
433
README.html
433
README.html
@ -15,12 +15,12 @@
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@font-face
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{font-family:"Calibri Light";
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panose-1:2 15 3 2 2 2 4 3 2 4;}
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@font-face
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{font-family:Tahoma;
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panose-1:2 11 6 4 3 5 4 4 2 4;}
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@font-face
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{font-family:Cambria;
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panose-1:2 4 5 3 5 4 6 3 2 4;}
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@font-face
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{font-family:Tahoma;
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panose-1:2 11 6 4 3 5 4 4 2 4;}
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/* Style Definitions */
|
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p.MsoNormal, li.MsoNormal, div.MsoNormal
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{margin-top:0cm;
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@ -368,8 +368,8 @@ should be something like:</p>
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-Xms384m -Xmx4096m -Djava.library.path=lib64 -jar Pamguard_xxxxxx.jar</span></em></p>
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<p class=MsoNormal>The -Xms384m -Xmx4096m specify the initial and maximum heap
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size for the JVM being used to run Pamguard i.e. how much memory it gets to use.
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The default max size usually being too low.</p>
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size for the JVM being used to run Pamguard i.e. how much memory it gets to
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use. The default max size usually being too low.</p>
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<p class=MsoNormal>The -Djava.library.path=lib64 tells the JVM that it should
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look in the folder called "lib64" for the required shared libraries (change
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@ -381,8 +381,8 @@ a "-m" or "-v" to the list of java arguments. On Windows
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just run the appropriately named executable (e.g. PamguardBeta_MixedMode.exe or
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PamguardBeta_ViewerMode.exe):</p>
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<p class=MsoNormal><em><span style='font-family:"Calibri",sans-serif'>java
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-Xms384m -Xmx4096m -Djava.library.path=lib64 -jar PamguardBeta_xxxxxx.jar -v</span></em></p>
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<p class=MsoNormal><em><span style='font-family:"Calibri",sans-serif'>java -Xms384m
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-Xmx4096m -Djava.library.path=lib64 -jar PamguardBeta_xxxxxx.jar -v</span></em></p>
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<p class=MsoNormal><em><span style='font-family:"Calibri",sans-serif'> </span></em></p>
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@ -444,7 +444,26 @@ Version 2.00.10 June 2017</a></span></h1>
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<h1><span style='font-size:12.0pt'><a href="#_Older_Versions">Older Versions</a></span></h1>
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<h1><a name="_Latest_Version_2.02.03_1"></a><a name="_Latest_Version_2.02.05"></a><span
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lang=EN-US>Latest Version 2.02.05 October 2022</span></h1>
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lang=EN-US>Latest Version 2.02.06 November 2022</span></h1>
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<h2><span lang=EN-US>Bug Fix</span></h2>
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<p class=MsoNormal><span lang=EN-US>A memory leak has been found which seems to
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mostly occur in Viewer mode. Some data on background noise measurements are not
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being cleared from memory, so memory will eventually run out. This could happen
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after browsing a lot of data, but was most likely when reprocessing files
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offline, for example running click classifiers. This is now fixed. </span></p>
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<h2><span lang=EN-US>New Features</span></h2>
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<p class=MsoNormal><span lang=EN-US>SoundTrap SUD file reading. If you’re using
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SoundTrap autonomous recorders from Ocean Instruments, you no longer need to decompress
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the SoundTrap files prior to processing. This will save time and a lot of disk
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space. Extraction of clicks from the inbuilt SoundTrap Click detector an also
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happen while processing SUD file data with other detectors, thereby
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streamlining the whole processing chain. Read the online Help for details. </span></p>
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<h1><span lang=EN-US>Latest Version 2.02.05 October 2022</span></h1>
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<h2><span lang=EN-US>Click Train Detector Features and Bug Fixes</span></h2>
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@ -452,8 +471,9 @@ lang=EN-US>Latest Version 2.02.05 October 2022</span></h1>
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<p class=MsoNormal><span lang=EN-US>Changes to GUI to make dialog shorter for
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low DPI screens. </span></p>
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<p class=MsoNormal><span lang=EN-US>Complete rewrite of the classification
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system to have nested classifiers which can be enabled or disabled. </span></p>
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<p class=MsoNormal><span lang=EN-US>Complete rewrite of the classification system
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to have nested classifiers which can be enabled or disabled. </span></p>
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<p class=MsoNormal><span lang=EN-US>Changes to classification GUI to
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accommodate the new classification system.</span></p>
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@ -498,9 +518,9 @@ audio files. </span></p>
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<h2><span lang=EN-US>Bug Fixes</span></h2>
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<p class=MsoNormal><span lang=EN-US>Soundtrap DWV import. Will now generate binary
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files even if DWV file doesnt exist (which is correct behavior in quiet
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conditions when no clicks were detected). </span></p>
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<p class=MsoNormal><span lang=EN-US>Soundtrap DWV import. Will now generate
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binary files even if DWV file doesnÂ’t exist (which is correct behavior in
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quiet conditions when no clicks were detected). </span></p>
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<p class=MsoNormal><span lang=EN-US>Spectrogram. Changes to stop occasional
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crashing when restarting processing of wav files. </span></p>
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@ -534,8 +554,8 @@ running in real time. Added template names based on file names. </p>
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<p class=MsoNormal>#13 Merging files when offline processing file folders: Had
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an error introduced in last release which caused it to fail to recognise gaps
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between files, meaning that some output data (i.e. after a gap) would have an
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incorrect time stamp. This did not affect data if the Âmerge contiguous filesÂ
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option was not selected. </p>
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incorrect time stamp. This did not affect data if the ‘merge contiguous
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files’ option was not selected. </p>
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<p class=MsoNormal>#14 Logger forms data were not plotting correctly. This was
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due to the required data selection functions not being fully implemented. This
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@ -574,23 +594,23 @@ 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 16
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(OpenJDK release), so you will not need to install a java runtime engine
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separately. PSFX files generated in previous beta releases (2.xx.xx) should be
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compatible with this version, and vice-versa. PSF files generated in core
|
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releases (1.15.xx) can be loaded in this version, but will be converted to PSFX
|
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files when PAMGuard exits.</p>
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<p class=MsoNormal>This version of PAMGuard has been bundled with Java 16 (OpenJDK
|
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release), so you will not need to install a java runtime engine separately.
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PSFX files generated in previous beta releases (2.xx.xx) should be compatible
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with this version, and vice-versa. PSF files generated in core releases
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(1.15.xx) can be loaded in this version, but will be converted to PSFX files
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when PAMGuard exits.</p>
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<p class=MsoNormal style='margin-bottom:0cm'><span style='font-size:12.0pt;
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font-family:"Times New Roman",serif'> </span></p>
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<h2>File Format Change</h2>
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<p class=MsoNormal>Changes have been made to the binary file format to support
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the output of additional noise outputs for certain detectors (See below).
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Binary files created with this version will not be compatible with earlier
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versions 2.01.### and below. This version will read and may convert earlier
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format binary files.</p>
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<p class=MsoNormal>Changes have been made to the binary file format to support the
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output of additional noise outputs for certain detectors (See below). Binary
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files created with this version will not be compatible with earlier versions
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2.01.### and below. This version will read and may convert earlier format
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binary files.</p>
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<p class=MsoNormal style='margin-bottom:0cm'><span style='font-size:12.0pt;
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font-family:"Times New Roman",serif'> </span></p>
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@ -608,10 +628,10 @@ href="http://www.pamguard.org/downloads.php?cat_id=3">here</a>.</p>
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<p class=MsoNormal><b><span lang=EN-US>Detection Group Localiser</span></b><span
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lang=EN-US> </span></p>
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<p class=MsoNormal>This module has been renamed ÂDetection GrouperÂ, so as to
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avoid confusion with the Group 3D localizer. This is because the Detection
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Grouper is more for organizing data into groups to be localized than it is for
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doing localization.</p>
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<p class=MsoNormal>This module has been renamed “Detection Grouper”, so
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as to avoid confusion with the Group 3D localizer. This is because the
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Detection Grouper is more for organizing data into groups to be localized than
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it is for doing localization.</p>
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<p class=MsoNormal><b><span lang=EN-US>Minor Bug Fixes</span></b><span
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lang=EN-US> </span></p>
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@ -729,10 +749,10 @@ included in a future release. </p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>17. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
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An implementation of the Generalized Power Law Detector, developed by Tyler
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Helble ([Helble et al., ÂA generalized power-law detection algorithm for humpback
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whale vocalizationsÂ, The Journal of the Acoustical Society of America, vol.
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131, no. 4, pp. 2682Â2699, 2012) is now available. For details, see the online
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help </p>
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Helble ([Helble et al., ‘A generalized power-law detection algorithm for
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humpback whale vocalizations’, The Journal of the Acoustical Society of
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America, vol. 131, no. 4, pp. 2682–2699, 2012) is now available. For
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||||
details, see the online help </p>
|
||||
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||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>18. </span><span
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||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
||||
@ -754,10 +774,10 @@ Version 2.00.10</a> before proceeding with installation and use of this
|
||||
version.</b></p>
|
||||
|
||||
<p class=MsoNormal>This version of PAMGuard has been bundled with Java 13
|
||||
(release 13.0.1). PSFX files generated in previous beta releases (2.xx.xx) should
|
||||
be compatible with this version, and vice-versa. PSF files generated in core
|
||||
releases (1.15.xx) can be loaded in this version, but will be converted to PSFX
|
||||
files when PAMGuard exits.</p>
|
||||
(release 13.0.1). PSFX files generated in previous beta releases (2.xx.xx)
|
||||
should be compatible with this version, and vice-versa. PSF files generated in
|
||||
core releases (1.15.xx) can be loaded in this version, but will be converted to
|
||||
PSFX files when PAMGuard exits.</p>
|
||||
|
||||
<p class=MsoNormal><b><span lang=EN-US>Bug Fixes</span></b></p>
|
||||
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||||
@ -840,8 +860,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb
|
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Added logger form annotation to Spectrogram Annotation module. </p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>6. </span><span
|
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
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Better auto-scaling in Ishmael Detector graphics window. </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>Better auto-scaling in Ishmael Detector graphics window. </p>
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>7. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
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@ -968,8 +988,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb
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<p class=MsoNormal><b><span lang=EN-US>Upgrades</span></b></p>
|
||||
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>1. </span><span
|
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
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Add functionality for bluetooth headsets. </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>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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@ -1093,9 +1113,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb
|
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Bug 441. Plot coordinate calculations incorrect in PamAxis.</p>
|
||||
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>10. </span><span
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
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Bug 442. BT Display does not change click symbol color when Colour By
|
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Superdetection is selected.</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>Bug 442. BT Display does not change click symbol color when
|
||||
Colour By Superdetection is selected.</p>
|
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|
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<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>11. </span><span
|
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
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@ -1108,8 +1128,8 @@ files.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>13. </span><span
|
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
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Bug 445. Overlay data in FX spectrogram display gets out of sync with underlying
|
||||
spectrogram image.</p>
|
||||
Bug 445. Overlay data in FX spectrogram display gets out of sync with
|
||||
underlying spectrogram image.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>14. </span><span
|
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
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@ -1182,9 +1202,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb
|
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Added a few new options to the Click Detector Sweep Classifier. </p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>10. </span><span
|
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lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
||||
Add option to the Map module's Plot Overlay Options dialog, to show events
|
||||
occuring in the future (<em><span style='font-family:"Calibri",sans-serif'>look
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
|
||||
lang=EN-US> </span>Add option to the Map module's Plot Overlay Options dialog,
|
||||
to show events occuring in the future (<em><span style='font-family:"Calibri",sans-serif'>look
|
||||
ahead</span></em>) instead of the default display of events which have already
|
||||
occurred. Can make it easier to match up the map with clicks seen in the Click
|
||||
Detector display. </p>
|
||||
@ -1234,8 +1254,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb
|
||||
Bug 429. Click Bearings at 180 degrees</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>4. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
||||
Bug 430. Rocca calculates inflection point parameters incorrectly</p>
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
|
||||
lang=EN-US> </span>Bug 430. Rocca calculates inflection point parameters
|
||||
incorrectly</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>5. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
|
||||
@ -1249,8 +1270,8 @@ Bug 432. MySQL database interface - connection problems</p>
|
||||
<p class=MsoNormal><b><span lang=EN-US>Upgrades</span></b></p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>1. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
||||
New display for Gebco Netcdf bathymetry maps.</p>
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
|
||||
lang=EN-US> </span>New display for Gebco Netcdf bathymetry maps.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
|
||||
@ -1331,8 +1352,8 @@ files.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>12. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Bug 425. Rocca crashing if Click Detector is used as source but the
|
||||
Click Classifier is not configured properly.</p>
|
||||
</span>Bug 425. Rocca crashing if Click Detector is used as source but the Click
|
||||
Classifier is not configured properly.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>13. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -1346,9 +1367,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb
|
||||
Upgrades to the Group Localiser, including better error estimation.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
||||
Click Train Detector upgrades, including ability to import time chunks from csv
|
||||
file for batch processing.</p>
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
|
||||
lang=EN-US> </span>Click Train Detector upgrades, including ability to import
|
||||
time chunks from csv file for batch processing.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>3. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
|
||||
@ -1475,14 +1496,14 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb
|
||||
Updates to the Ishmael module.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>9. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
||||
Added option to the WarnOnce dialog to hide a warning for the current PAMGuard
|
||||
session, but not forever.</p>
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
|
||||
lang=EN-US> </span>Added option to the WarnOnce dialog to hide a warning for
|
||||
the current PAMGuard session, but not forever.</p>
|
||||
|
||||
<!-- ************************************************************************************************************************** --><!-- ************************************************************************************************************************** -->
|
||||
|
||||
<h1><a name="_Latest_Beta_Version_2.00.14c"></a><span lang=EN-US>Beta Version 2.00.14c
|
||||
October 2018</span></h1>
|
||||
<h1><a name="_Latest_Beta_Version_2.00.14c"></a><span lang=EN-US>Beta Version
|
||||
2.00.14c October 2018</span></h1>
|
||||
|
||||
<p class=MsoNormal><span lang=EN-US>PAMGuard Version 2 contains major updates.
|
||||
You should read and understand the notes listed for <a
|
||||
@ -1518,10 +1539,10 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb
|
||||
lang=EN-US> </span>Added decimal degrees option to latitude/longitude dialog.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
||||
Added option in the Click Delay parameters to restrict the number of initial
|
||||
samples used in the calculation. This can be useful for cleaning up delays in
|
||||
the presence of echoes and small time delays.</p>
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
|
||||
lang=EN-US> </span>Added option in the Click Delay parameters to restrict the
|
||||
number of initial samples used in the calculation. This can be useful for
|
||||
cleaning up delays in the presence of echoes and small time delays.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>3. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
||||
@ -1589,7 +1610,8 @@ Annotation module which has now been given two text type annotations.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>9. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Bug 391. Click Detector not registering change in multi-threading option.</p>
|
||||
</span>Bug 391. Click Detector not registering change in multi-threading
|
||||
option.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>10. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -1632,11 +1654,11 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb
|
||||
lang=EN-US> </span>Added ability to read differential GPS data.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>5. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
||||
Added check for duplicate settings in the psf file when exiting Pamguard. If
|
||||
duplicate settings are found, user is given the option to leave them in the psf
|
||||
or get rid of them. Duplicate settings are ignored by Pamguard, but can cause
|
||||
the psf file to grow large over time.</p>
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
|
||||
lang=EN-US> </span>Added check for duplicate settings in the psf file when
|
||||
exiting Pamguard. If duplicate settings are found, user is given the option to
|
||||
leave them in the psf or get rid of them. Duplicate settings are ignored by
|
||||
Pamguard, but can cause the psf file to grow large over time.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>6. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
||||
@ -1704,8 +1726,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>10. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Bug 376. Error when using a serialised data map which spans a period of time
|
||||
in which Pamguard modules have changed.</p>
|
||||
</span>Bug 376. Error when using a serialised data map which spans a period of
|
||||
time in which Pamguard modules have changed.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>11. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -1744,8 +1766,9 @@ used in older versions. Older psf files can be loaded with this version, but
|
||||
will be converted.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>4. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span>
|
||||
Many updates to the Video Range module. Will currently only work with landmarks.</p>
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
|
||||
lang=EN-US> </span>Many updates to the Video Range module. Will currently only
|
||||
work with landmarks.</p>
|
||||
|
||||
<!-- ************************************************************************************************************************** -->
|
||||
|
||||
@ -1808,8 +1831,8 @@ Beta versions</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>11. </span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Bug 366. Rocca manual whistle contour extraction throws error when trying
|
||||
to classify a boxed whistle</p>
|
||||
</span>Bug 366. Rocca manual whistle contour extraction throws error when
|
||||
trying to classify a boxed whistle</p>
|
||||
|
||||
<p class=MsoNormal><b><span lang=EN-US>Upgrades</span></b></p>
|
||||
|
||||
@ -1878,8 +1901,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> &nb
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>10.</span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Bug 354. Whistle Classifier was crashing if user accidentally entered invalid
|
||||
parameters. Have added diagnostics to prevent this.</p>
|
||||
</span>Bug 354. Whistle Classifier was crashing if user accidentally entered
|
||||
invalid parameters. Have added diagnostics to prevent this.</p>
|
||||
|
||||
<p class=MsoNormal><b><span lang=EN-US>Upgrades</span></b></p>
|
||||
|
||||
@ -2009,8 +2032,8 @@ C:\MySurvey\binarydata_WithUID. </span></p>
|
||||
|
||||
<p class=MsoNormal><span lang=EN-US>The additional UID column will be added to
|
||||
all database tables and populated with unique values. For data which are stored
|
||||
in both the binary files and in database tables, the same UIDÂs will be used in
|
||||
both data stores. </span></p>
|
||||
in both the binary files and in database tables, the same UID’s will be used
|
||||
in both data stores. </span></p>
|
||||
|
||||
<h3><span lang=EN-US>New Displays</span></h3>
|
||||
|
||||
@ -2024,11 +2047,11 @@ Note that this display is only available if you are running Java 8 or later. </s
|
||||
|
||||
<h3><span lang=EN-US>Event Marking and the Detection Group Localiser</span></h3>
|
||||
|
||||
<p class=MsoNormal><span lang=EN-US>A new system of event marking which can be used
|
||||
both online and offline has been added to PAMGuard. Details are in the PAMGuard
|
||||
help file (Displays/Display Marking). Data can be selected on the Map, the
|
||||
Spectrogram Display and the new Time Display FX in a similar way and sent to
|
||||
other PAMGuard modules. The new marking and data selection system works with
|
||||
<p class=MsoNormal><span lang=EN-US>A new system of event marking which can be
|
||||
used both online and offline has been added to PAMGuard. Details are in the
|
||||
PAMGuard help file (Displays/Display Marking). Data can be selected on the Map,
|
||||
the Spectrogram Display and the new Time Display FX in a similar way and sent
|
||||
to other PAMGuard modules. The new marking and data selection system works with
|
||||
the new Detection Group Localiser. The Detection Group Localiser extends the
|
||||
functionality which always existed in the click detector to other types of data
|
||||
(e.g. Whistles) so that they can be grouped and tracked using target motion
|
||||
@ -2146,15 +2169,15 @@ working folder, and therefore is set incorrectly. This has been fixed.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>5.</span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Bug 314. If PAMGuard is started by double-clicking on a psf, nothing
|
||||
happens when the user selects save as new configuration. This has been fixed.</p>
|
||||
</span>Bug 314. If PAMGuard is started by double-clicking on a psf, nothing happens
|
||||
when the user selects save as new configuration. This has been fixed.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>6.</span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Bug 315. code searched for file in working folder, which is the
|
||||
installation folder when starting PAMGuard using a shortcut link. But when
|
||||
double-clicking on a psf, the working folder is the location of the psf. This has
|
||||
been fixed.</p>
|
||||
double-clicking on a psf, the working folder is the location of the psf. This
|
||||
has been fixed.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>7.</span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span
|
||||
@ -2183,8 +2206,8 @@ jar file will be required rather than a new bespoke PAMGuard installation.</span
|
||||
|
||||
<p class=MsoNormal><span lang=EN-US>Module code development remains largely
|
||||
unchanged, in most cases simply requiring the addition of an interface class.
|
||||
Instructions for the development of new modules utilizing the plug-in scheme
|
||||
can be found <a href="http://www.pamguard.org/16_HowtomakePlug-Ins.html"
|
||||
Instructions for the development of new modules utilizing the plug-in
|
||||
scheme can be found <a href="http://www.pamguard.org/16_HowtomakePlug-Ins.html"
|
||||
target="_blank">here</a>. Plug-in modules can be downloaded from the
|
||||
PAMGuard website here, but developers are encouraged to host and maintain their
|
||||
own modules.</span></p>
|
||||
@ -2192,8 +2215,8 @@ own modules.</span></p>
|
||||
<p class=MsoNormal><span lang=EN-US>Modules of interest to the general PAM
|
||||
community will remain as part of the core PAMGuard installation. However,
|
||||
specialized modules which are useful to only a small number of users have been
|
||||
removed and are available as a separate download. The following modules have been
|
||||
removed:</span></p>
|
||||
removed and are available as a separate download. The following modules have
|
||||
been removed:</span></p>
|
||||
|
||||
<p class=MsoListParagraph style='margin-left:43.5pt;text-indent:-25.5pt'>1.<span
|
||||
style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -2244,19 +2267,19 @@ November 2016</span></h1>
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>1.
|
||||
Bug 303. Some ASIO sound cards not working with either ASIO system in PAMGuard.
|
||||
For the PAMGuard ASIO system, this was due to a data format used by some sound
|
||||
cards never being properly implemented. For the ÂNew ASIO system which is
|
||||
based on jAsioHost, the unpacking of that format contained a bug which returned
|
||||
incorrect numbers, so data were swamped with noise. Both systems are now fixed.
|
||||
By preference, users should use the PAMGuard ASIO system since the JAsioHost
|
||||
based system seems to drop samples when many channels are running at high
|
||||
sample rate. </span></p>
|
||||
cards never being properly implemented. For the “New ASIO system” which
|
||||
is based on jAsioHost, the unpacking of that format contained a bug which
|
||||
returned incorrect numbers, so data were swamped with noise. Both systems are
|
||||
now fixed. By preference, users should use the PAMGuard ASIO system since the
|
||||
JAsioHost based system seems to drop samples when many channels are running at
|
||||
high sample rate. </span></p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'>2.<span style='font-size-adjust: none;
|
||||
font-stretch: normal'><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span></span><span lang=EN-US>Bug 305. Date and Time not being correctly
|
||||
extracted from wav files created using SoundTrap recorders. Fixed by correctly
|
||||
finding and unpacking information in the accompanying xml log files that come with
|
||||
SoundTrap files. </span></p>
|
||||
finding and unpacking information in the accompanying xml log files that come
|
||||
with SoundTrap files. </span></p>
|
||||
|
||||
<h1><a name="_Latest_Version_1.15.06"></a><span lang=EN-US>Version 1.15.06
|
||||
November 2016</span></h1>
|
||||
@ -2290,8 +2313,8 @@ data for the least square model. Both fixed. </p>
|
||||
|
||||
<p class=MsoListParagraph style='margin-left:40.5pt;text-indent:-22.5pt'>4.<span
|
||||
style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Bug 294. Click classifier was crashing when the 'min amplitude' option
|
||||
was used. This is fixed. </p>
|
||||
</span>Bug 294. Click classifier was crashing when the 'min amplitude' option was
|
||||
used. This is fixed. </p>
|
||||
|
||||
<p class=MsoListParagraph style='margin-left:40.5pt;text-indent:-22.5pt'>5.<span
|
||||
style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -2375,9 +2398,9 @@ the database. </span></p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>2.</span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span><span lang=EN-US>The number of data streams associated with the click detector
|
||||
has been tidied up so that there are a) All Click, b) Tracked Clicks (those
|
||||
which are part of an event) and c) Events. </span></p>
|
||||
</span><span lang=EN-US>The number of data streams associated with the click
|
||||
detector has been tidied up so that there are a) All Click, b) Tracked Clicks
|
||||
(those which are part of an event) and c) Events. </span></p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>3.</span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -2393,9 +2416,9 @@ automatic click train identification and tracking. </span></p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>5.</span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span><span lang=EN-US>The automatic click train identification is now using the
|
||||
same internal structures as the manual tracking, so it's possible to combine
|
||||
automatic and manual tracking. </span></p>
|
||||
</span><span lang=EN-US>The automatic click train identification is now using
|
||||
the same internal structures as the manual tracking, so it's possible to
|
||||
combine automatic and manual tracking. </span></p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>6.</span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -2475,8 +2498,9 @@ today. </p>
|
||||
|
||||
<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>5.<span
|
||||
style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Bug 277. Text fields in classifier dialog were not large enough to display
|
||||
times greater than 10ms. We have increased length of text fields in the dialog.</p>
|
||||
</span>Bug 277. Text fields in classifier dialog were not large enough to
|
||||
display times greater than 10ms. We have increased length of text fields in the
|
||||
dialog.</p>
|
||||
|
||||
<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>6.<span
|
||||
style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -2494,8 +2518,8 @@ style='font-size:7.0pt;font-family:"Times New Roman",serif'> &n
|
||||
</span>Bug 279. GUI Resizing: The whole PAMGuard GUI would suddenly resize to
|
||||
something very small when a dialog is opened. This has been traced to improper
|
||||
use of a common dialog component SourcePanel which tries to repack its parent
|
||||
Window. Some programmers had inadvertently set it to repack the main PAMGuard GUI
|
||||
instead. This has been Fixed.</p>
|
||||
Window. Some programmers had inadvertently set it to repack the main PAMGuard
|
||||
GUI instead. This has been Fixed.</p>
|
||||
|
||||
<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>8.<span
|
||||
style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -2569,8 +2593,8 @@ and datagram creation.</p>
|
||||
|
||||
<h1><a name="_Toc444450394"></a><span lang=EN-US>Version 1.15.00 February 2016</span></h1>
|
||||
|
||||
<p class=MsoNormal><span lang=EN-US>Beta Version 1.15.00 64 bit and Core version
|
||||
1.15.00 32 bit. Both using identical Java core software but linking to
|
||||
<p class=MsoNormal><span lang=EN-US>Beta Version 1.15.00 64 bit and Core
|
||||
version 1.15.00 32 bit. Both using identical Java core software but linking to
|
||||
different libraries for control of sound input devices. </span></p>
|
||||
|
||||
<p class=MsoNormal><span lang=EN-US>This is the first release of a 64 bit
|
||||
@ -2638,12 +2662,12 @@ boundaries when file durations are set to a maximum fixed value. </p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>5.</span><span
|
||||
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Bug 262. Access to SQLite database conversion. This would fail when tables
|
||||
were present which were not created by PAMGuard. Fixes have been put in
|
||||
place for spaces in the table name or for not having an 'Id' column. Fixes have
|
||||
not been implemented for spaces in a column name or use of a reserved word as a
|
||||
column name, however if either of these problems do exist it will no longer
|
||||
crash but issue a clear warning and carry onto the next table.</p>
|
||||
</span>Bug 262. Access to SQLite database conversion. This would fail when
|
||||
tables were present which were not created by PAMGuard. Fixes have been
|
||||
put in place for spaces in the table name or for not having an 'Id' column.
|
||||
Fixes have not been implemented for spaces in a column name or use of a
|
||||
reserved word as a column name, however if either of these problems do exist it
|
||||
will no longer crash but issue a clear warning and carry onto the next table.</p>
|
||||
|
||||
<p class=MsoNormal style='margin-left:18.0pt'><span lang=EN-US> </span></p>
|
||||
|
||||
@ -2878,8 +2902,8 @@ minutes and seconds. Now correctly displays the number of remaining days. </p>
|
||||
|
||||
<p class=MsoListParagraph style='margin-left:47.25pt;text-indent:-29.25pt'><span
|
||||
lang=EN-US>4.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Bug 226. Spectrogram Mark Observer list doesn't refresh when modules added
|
||||
or removed. </p>
|
||||
</span>Bug 226. Spectrogram Mark Observer list doesn't refresh when modules
|
||||
added or removed. </p>
|
||||
|
||||
<p class=MsoListParagraph style='margin-left:47.25pt;text-indent:-29.25pt'><span
|
||||
lang=EN-US>5.</span><span lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -3049,12 +3073,11 @@ sonobuoys. See online help for details. </p>
|
||||
|
||||
<p class=MsoNormal><i>MEAL Localiser</i> (Localisation Group)</p>
|
||||
|
||||
<p class=MsoNormal>This module, developed by Jamie Macaulay of St Andrews
|
||||
University estimates the 3D localisation of clicks using a variety of
|
||||
algorithms. It's primarily been developed to track harbour porpoise in three
|
||||
dimensions over scales of 10's of metres. While currently only working with
|
||||
output from the click detector, we hope eventually to extend its use to
|
||||
whistles as well. </p>
|
||||
<p class=MsoNormal>This module, developed by Jamie Macaulay of St Andrews University
|
||||
estimates the 3D localisation of clicks using a variety of algorithms. It's
|
||||
primarily been developed to track harbour porpoise in three dimensions over
|
||||
scales of 10's of metres. While currently only working with output from the
|
||||
click detector, we hope eventually to extend its use to whistles as well. </p>
|
||||
|
||||
<p class=MsoNormal><i>Accelerometer Readout</i> (Sensors group)</p>
|
||||
|
||||
@ -3072,12 +3095,12 @@ marine mammal survey package. See online help for details. </p>
|
||||
|
||||
<p class=MsoNormal><i>Alarms</i> (Utilities Group)</p>
|
||||
|
||||
<p class=MsoNormal>This is a general system of visual and audio alarms developed
|
||||
by Doug Gillespie for use on a variety of projects. The alarms can be coupled
|
||||
to any module or detector in PAMGuard. Where appropriate, modules can control
|
||||
which of their data will cause an alarm action (e.g. in the Click detector you
|
||||
can set which types of classified click will fire the alarm). See online help
|
||||
for details. </p>
|
||||
<p class=MsoNormal>This is a general system of visual and audio alarms
|
||||
developed by Doug Gillespie for use on a variety of projects. The alarms can be
|
||||
coupled to any module or detector in PAMGuard. Where appropriate, modules can
|
||||
control which of their data will cause an alarm action (e.g. in the Click
|
||||
detector you can set which types of classified click will fire the alarm). See
|
||||
online help for details. </p>
|
||||
|
||||
<p class=MsoNormal><i>Noise Band Monitor</i> (Sound Processing Group)</p>
|
||||
|
||||
@ -3141,8 +3164,8 @@ Millisecond time is also now included in the output file names. </p>
|
||||
|
||||
<p class=MsoNormal>Datagram options in Viewer have been improved so that the
|
||||
user has to verify the time binning for datagrams the first time the viewer is
|
||||
run and can also change the time bins from the File menu (See the File/BinaryStore/Datagram
|
||||
options menu. </p>
|
||||
run and can also change the time bins from the File menu (See the
|
||||
File/BinaryStore/Datagram options menu. </p>
|
||||
|
||||
<p class=MsoNormal><i>Viewer Configuration</i></p>
|
||||
|
||||
@ -3164,8 +3187,8 @@ horizon. </p>
|
||||
|
||||
<p class=MsoNormal><i>Improved Filter Options</i></p>
|
||||
|
||||
<p class=MsoNormal>Filter options (used as stand-alone filter modules and also
|
||||
within many other modules, such as the click detector and the Filtered Noise
|
||||
<p class=MsoNormal>Filter options (used as stand-alone filter modules and also within
|
||||
many other modules, such as the click detector and the Filtered Noise
|
||||
Measurement module) have been improved so that the user can specify arbitrarily
|
||||
shaped Finite Impulse Response filters (see online help for details). </p>
|
||||
|
||||
@ -3275,9 +3298,9 @@ other data sources for the PAMGuard viewer. </p>
|
||||
|
||||
<p class=MsoNormal style='margin-left:36.0pt'><i>Database</i></p>
|
||||
|
||||
<p class=MsoNormal style='margin-left:36.0pt'>Can now copy data from binary storage
|
||||
to the database offline for any module having both binary and database storage.
|
||||
</p>
|
||||
<p class=MsoNormal style='margin-left:36.0pt'>Can now copy data from binary
|
||||
storage to the database offline for any module having both binary and database
|
||||
storage. </p>
|
||||
|
||||
<p class=MsoNormal style='margin-left:36.0pt'>Can create a blank MS Access
|
||||
database (2007 and later *.accdb formats only).</p>
|
||||
@ -3376,8 +3399,8 @@ elements has been fixed. </p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
|
||||
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Database Speed: A substantial rewriting of some of the indexing methods in
|
||||
the database module has led to a significant increase in the speed at which
|
||||
</span>Database Speed: A substantial rewriting of some of the indexing methods
|
||||
in the database module has led to a significant increase in the speed at which
|
||||
data are written to the database (orders of magnitude for large databases).
|
||||
This is having a significant impact on the overall reliability of the software.
|
||||
Other changes have increased the speed (again by orders of magnitude) at which
|
||||
@ -3469,9 +3492,9 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
|
||||
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Offline event marking. Offline event marking similar to functionality in
|
||||
RainbowClick is now available in the PAMGUARD viewer. Event summary data is stored
|
||||
in the database and can also be exported to text files (e.g. for importing into
|
||||
the Distance software). </p>
|
||||
RainbowClick is now available in the PAMGUARD viewer. Event summary data is
|
||||
stored in the database and can also be exported to text files (e.g. for
|
||||
importing into the Distance software). </p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
|
||||
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -3506,8 +3529,8 @@ features of the display:</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
|
||||
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>The spectrogram will automatically generate and display spectrogram
|
||||
data. </p>
|
||||
</span>The spectrogram will automatically generate and display spectrogram data.
|
||||
</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
|
||||
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -3578,8 +3601,8 @@ the correct data stream. This has been fixed. </p>
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
|
||||
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Whistle classifier has some new features in the classifier training
|
||||
panel. It is also now possible to export training data files directly from binary
|
||||
data files. </p>
|
||||
panel. It is also now possible to export training data files directly from
|
||||
binary data files. </p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
|
||||
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -3618,10 +3641,10 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
|
||||
|
||||
<p class=MsoNormal>2. Improved offline viewer functionality. </p>
|
||||
|
||||
<p class=MsoNormal>The offline viewer is much improved with better data scrolling
|
||||
and the ability to view data either stored in the database or the binary
|
||||
storage system. Work has stated on functions which read and use data stored in
|
||||
audio files. This is currently limited to re-calculating and displaying
|
||||
<p class=MsoNormal>The offline viewer is much improved with better data
|
||||
scrolling and the ability to view data either stored in the database or the
|
||||
binary storage system. Work has stated on functions which read and use data
|
||||
stored in audio files. This is currently limited to re-calculating and displaying
|
||||
displaying spectrogram data during viewer mode operation. </p>
|
||||
|
||||
<p class=MsoNormal>3. Heading sensor readout</p>
|
||||
@ -3696,14 +3719,14 @@ lookup tables relating hardware channel numbers to internal channel numbers.
|
||||
0 and 1 from a normal sound card or a list of channels 0,1,2,3, etc from an
|
||||
ASIO card or National Instruments card. However, when using the ASIO sound
|
||||
acquisition system, it is possible to read out hardware channels 2,3,4,5 say
|
||||
and those numbers would propagate through PAMGUARD and be used by all the
|
||||
detectors. While this gave some clarity to the displays, it also created
|
||||
a number of problems since look up tables were constantly required to relate
|
||||
hardware numbers and software numbers in every PAMGUARD module. Since this type
|
||||
of channel numbering was only implemented several years into the PAMGUARD
|
||||
project, it was never fully implemented or well supported by the different
|
||||
modules which resulted in a number of bugs which could cause confusion as to
|
||||
which hydrophones were being used during localisation or during calibrated
|
||||
and those numbers would propagate through PAMGUARD and be used by all the detectors.
|
||||
While this gave some clarity to the displays, it also created a number of
|
||||
problems since look up tables were constantly required to relate hardware
|
||||
numbers and software numbers in every PAMGUARD module. Since this type of
|
||||
channel numbering was only implemented several years into the PAMGUARD project,
|
||||
it was never fully implemented or well supported by the different modules which
|
||||
resulted in a number of bugs which could cause confusion as to which
|
||||
hydrophones were being used during localisation or during calibrated
|
||||
measurement. The situation tended to only arise with a small number of ASIO
|
||||
sound cards such as the RME Fireface 400 on which the most useful inputs, the
|
||||
balanced line inputs, are hardware channels 4,5,6 and 7 on the back of the
|
||||
@ -3718,10 +3741,10 @@ re-label those channels 0,1,2,3. </p>
|
||||
<p class=MsoNormal>There have been other annoyances with the ASIO channel
|
||||
numbering scheme. For instance, if you had a configuration which worked in real
|
||||
time using channels 7 and 8 of a sound card, you could not use that same
|
||||
configuration to analyse wav files, which would always read their data as
|
||||
channels 0 and 1. Similarly if you switched sound cards, you may have to
|
||||
reconfigure every detector and several of the displays to handle the changes in
|
||||
channel numbering. </p>
|
||||
configuration to analyse wav files, which would always read their data as channels
|
||||
0 and 1. Similarly if you switched sound cards, you may have to reconfigure
|
||||
every detector and several of the displays to handle the changes in channel
|
||||
numbering. </p>
|
||||
|
||||
<p class=MsoNormal>I have spent a considerable amount of time trying to work
|
||||
out a better system for handling channel numbering in PAMGUARD and have decided
|
||||
@ -3832,10 +3855,10 @@ port is closed. Might prevent a few problems when using a GPS. </p>
|
||||
<p class=MsoNormal>Crashes caused in real time or Mixed Mode if the number of
|
||||
software channels exceeds the number of hydrophones configured in the array
|
||||
manager. It is of course illogical to have software channels which are not
|
||||
assigned to a hydrophone, so rather than entirely prevent PAMGUARD from crashing
|
||||
I have inserted additional checks into the hydrophone array dialog which will
|
||||
prevent the user from closing that dialog unless all software channels are
|
||||
assigned to a hydrophone. </p>
|
||||
assigned to a hydrophone, so rather than entirely prevent PAMGUARD from
|
||||
crashing I have inserted additional checks into the hydrophone array dialog
|
||||
which will prevent the user from closing that dialog unless all software
|
||||
channels are assigned to a hydrophone. </p>
|
||||
|
||||
<h2><span style='font-weight:normal'>Version 1.8.01 Beta February 2010</span></h2>
|
||||
|
||||
@ -3917,10 +3940,10 @@ synchronisation.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
|
||||
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Wigner time-frequency plot for the click detector. Clicks are NOT
|
||||
automatically displayed in the Winger window as they are for the waveform and
|
||||
spectrum windows since the Wigner transformation is very time consuming. Clicks
|
||||
will be displayed if you select them with the mouse.</p>
|
||||
</span>Wigner time-frequency plot for the click detector. Clicks are NOT automatically
|
||||
displayed in the Winger window as they are for the waveform and spectrum
|
||||
windows since the Wigner transformation is very time consuming. Clicks will be
|
||||
displayed if you select them with the mouse.</p>
|
||||
|
||||
<p class=MsoListParagraph style='text-indent:-18.0pt'><span style='font-family:
|
||||
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
@ -3932,15 +3955,15 @@ classifier is still available). </p>
|
||||
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>
|
||||
</span>Bearing ambiguity resolution for planar and volumetric arrays. New
|
||||
features in array dialog for estimations of errors on array location. These
|
||||
feed into to a maximum likelihood estimate of angles from small 2D or 3D sub arrays
|
||||
to give two polar angle coordinates. this can be used to resolve left right
|
||||
ambiguity and is implemented for both the click and the whistle/moan detectors.
|
||||
As a result, the click detector bearing time display can now be set to go from
|
||||
-180 to 180 degrees rather than 0 - 180 degrees. In this case, clicks in the
|
||||
upper half of the bearing display will be to port and clicks in the right half
|
||||
will be to starboard. As you pass a whale which is to port, the clicks will
|
||||
move UP the display. In the long term, I hope to turn this display around so
|
||||
that time is up the screen rather than across. </p>
|
||||
feed into to a maximum likelihood estimate of angles from small 2D or 3D sub
|
||||
arrays to give two polar angle coordinates. this can be used to resolve left
|
||||
right ambiguity and is implemented for both the click and the whistle/moan
|
||||
detectors. As a result, the click detector bearing time display can now be set
|
||||
to go from -180 to 180 degrees rather than 0 - 180 degrees. In this case,
|
||||
clicks in the upper half of the bearing display will be to port and clicks in
|
||||
the right half will be to starboard. As you pass a whale which is to port, the
|
||||
clicks will move UP the display. In the long term, I hope to turn this display
|
||||
around so that time is up the screen rather than across. </p>
|
||||
|
||||
<p class=MsoNormal><b>Small features and bug fixes</b></p>
|
||||
|
||||
@ -4135,10 +4158,10 @@ help pages</p>
|
||||
|
||||
<p class=MsoNormal><b>Bug Fixes</b></p>
|
||||
|
||||
<p class=MsoNormal>Memory leak caused by Night / Day colour manager now fixed. This
|
||||
would cause memory leaks when multiple files were being analysed off-line and
|
||||
would eventually crash PAMGUARD. The way that colours are managed in PAMGUARD
|
||||
has been rewritten. </p>
|
||||
<p class=MsoNormal>Memory leak caused by Night / Day colour manager now fixed.
|
||||
This would cause memory leaks when multiple files were being analysed off-line
|
||||
and would eventually crash PAMGUARD. The way that colours are managed in
|
||||
PAMGUARD has been rewritten. </p>
|
||||
|
||||
<p class=MsoNormal>Some issues with Swing fixed that might have been causing
|
||||
hang ups on startup especially on Macs/Linux machines</p>
|
||||
@ -4151,9 +4174,9 @@ Mac/Linux machines)</p>
|
||||
|
||||
<p class=MsoNormal>Parameters dialog shows correct channel numbers</p>
|
||||
|
||||
<p class=MsoNormal>Click classifier mean filter option had a computational
|
||||
error which meant that classifiers using this option would not work. This has
|
||||
now been fixed. </p>
|
||||
<p class=MsoNormal>Click classifier mean filter option had a computational error
|
||||
which meant that classifiers using this option would not work. This has now
|
||||
been fixed. </p>
|
||||
|
||||
<p class=MsoNormal><b>Sound Recorder</b></p>
|
||||
|
||||
@ -4209,8 +4232,8 @@ file)</p>
|
||||
|
||||
<p class=MsoNormal><b>Changes</b></p>
|
||||
|
||||
<p class=MsoNormal>The User Input module (for text entry of information by the user)
|
||||
has been moved from the Displays sub menu of the Add Modules menu, to
|
||||
<p class=MsoNormal>The User Input module (for text entry of information by the
|
||||
user) has been moved from the Displays sub menu of the Add Modules menu, to
|
||||
Utilities. This will not affect how existing settings files are loaded. </p>
|
||||
|
||||
<p class=MsoNormal><b>Multi-screen environments.</b></p>
|
||||
@ -4229,8 +4252,8 @@ acquisition. </p>
|
||||
|
||||
<p class=MsoNormal><b>Bug fixes</b></p>
|
||||
|
||||
<p class=MsoNormal>Speed up of graphics, particularly regarding large quantities
|
||||
of gps track data</p>
|
||||
<p class=MsoNormal>Speed up of graphics, particularly regarding large
|
||||
quantities of gps track data</p>
|
||||
|
||||
<p class=MsoNormal>National Instruments cards with names > 20 characters
|
||||
long are now correctly recognised. </p>
|
||||
@ -4713,12 +4736,12 @@ and Ishmael-type detectors and localisers. </p>
|
||||
<p class=MsoNormal>Information from above modules can be displayed on
|
||||
configurable user displays which support real time scrolling spectrograms and
|
||||
radar displays. Detection and localisation information can be optionally
|
||||
displayed on the map display.Map enhancements include improved scrolling whereby
|
||||
the user can click and drag to pan the area. PamGuard can now interface with
|
||||
MySQL database servers and users can easily select which information is logged.
|
||||
(This replaces the previous 'flat-file' logging feature). A simulation module
|
||||
allows virtual vocalising animals to be placed on the map to assist in training
|
||||
and development. Extensive online user help has been added to PamGuard
|
||||
displayed on the map display.Map enhancements include improved scrolling
|
||||
whereby the user can click and drag to pan the area. PamGuard can now interface
|
||||
with MySQL database servers and users can easily select which information is
|
||||
logged. (This replaces the previous 'flat-file' logging feature). A simulation
|
||||
module allows virtual vocalising animals to be placed on the map to assist in
|
||||
training and development. Extensive online user help has been added to PamGuard
|
||||
Application</p>
|
||||
|
||||
<h2>0.03b - first version used in a real 'at sea' environment.18/08/06</h2>
|
||||
|
||||
6
pom.xml
6
pom.xml
@ -780,12 +780,12 @@
|
||||
</dependency>
|
||||
-->
|
||||
|
||||
<!-- not in Maven repository -->
|
||||
<!-- not in Maven repository -->
|
||||
<dependency>
|
||||
<groupId>pamguard.org</groupId>
|
||||
<artifactId>x3</artifactId>
|
||||
<version>2.1.0</version>
|
||||
</dependency>
|
||||
<version>2.2.0</version>
|
||||
</dependency>
|
||||
|
||||
<!-- https://mvnrepository.com/artifact/it.sauronsoftware/jave -->
|
||||
<dependency>
|
||||
|
||||
4
repo/pamguard/org/x3/2.2.0/_remote.repositories
Normal file
4
repo/pamguard/org/x3/2.2.0/_remote.repositories
Normal file
@ -0,0 +1,4 @@
|
||||
#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
|
||||
#Fri Nov 11 13:13:18 GMT 2022
|
||||
x3-2.2.0.jar>=
|
||||
x3-2.2.0.pom>=
|
||||
BIN
repo/pamguard/org/x3/2.2.0/x3-2.2.0.jar
Normal file
BIN
repo/pamguard/org/x3/2.2.0/x3-2.2.0.jar
Normal file
Binary file not shown.
9
repo/pamguard/org/x3/2.2.0/x3-2.2.0.pom
Normal file
9
repo/pamguard/org/x3/2.2.0/x3-2.2.0.pom
Normal file
@ -0,0 +1,9 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
<groupId>pamguard.org</groupId>
|
||||
<artifactId>x3</artifactId>
|
||||
<version>2.2.0</version>
|
||||
<description>POM was created from install:install-file</description>
|
||||
</project>
|
||||
@ -38,6 +38,9 @@ import javax.swing.JMenuItem;
|
||||
import javax.swing.JOptionPane;
|
||||
import javax.swing.SwingConstants;
|
||||
|
||||
import org.pamguard.x3.sud.Chunk;
|
||||
import org.pamguard.x3.sud.SudFileListener;
|
||||
|
||||
import dataGram.DatagramManager;
|
||||
import dataMap.OfflineDataMapPoint;
|
||||
import dataMap.filemaps.OfflineFileServer;
|
||||
@ -49,12 +52,13 @@ import simulatedAcquisition.SimProcess;
|
||||
import asiojni.ASIOSoundSystem;
|
||||
import asiojni.NewAsioSoundSystem;
|
||||
import nidaqdev.NIDAQProcess;
|
||||
import nidaqdev.networkdaq.NINetworkDaq;
|
||||
import Acquisition.filedate.FileDate;
|
||||
import Acquisition.filedate.StandardFileDate;
|
||||
import Acquisition.filetypes.SoundFileTypes;
|
||||
import Acquisition.layoutFX.AquisitionGUIFX;
|
||||
import Acquisition.offlineFuncs.OfflineWavFileServer;
|
||||
import Acquisition.rona.RonaOfflineFileServer;
|
||||
import Acquisition.sud.SUDNotificationManager;
|
||||
import Array.ArrayManager;
|
||||
import Array.PamArray;
|
||||
import Array.Preamplifier;
|
||||
@ -132,7 +136,10 @@ public class AcquisitionControl extends PamControlledUnit implements PamSettings
|
||||
* The JavaFX GUI for the sound acquisition module.
|
||||
*/
|
||||
private AquisitionGUIFX aquisitionGUIFX;
|
||||
|
||||
|
||||
private SUDNotificationManager sudNotificationManager;
|
||||
|
||||
protected SoundFileTypes soundFileTypes;
|
||||
|
||||
/**
|
||||
* Main control unit for audio data acquisition.
|
||||
@ -158,6 +165,8 @@ public class AcquisitionControl extends PamControlledUnit implements PamSettings
|
||||
|
||||
pamController = PamController.getInstance();
|
||||
|
||||
soundFileTypes = new SoundFileTypes(this);
|
||||
|
||||
registerDaqSystem(new SoundCardSystem(this));
|
||||
if (PlatformInfo.calculateOS() == OSType.WINDOWS) {
|
||||
registerDaqSystem(new ASIOSoundSystem(this));
|
||||
@ -833,5 +842,16 @@ public class AcquisitionControl extends PamControlledUnit implements PamSettings
|
||||
public String getModuleSummary(boolean clear) {
|
||||
return getDaqProcess().getRawDataBlock().getSummaryString(clear);
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Get the SUD processing notification manager.
|
||||
* @return SUD processing notification manager.
|
||||
*/
|
||||
public SUDNotificationManager getSUDNotificationManager() {
|
||||
if (sudNotificationManager == null) {
|
||||
sudNotificationManager = new SUDNotificationManager();
|
||||
}
|
||||
return sudNotificationManager;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@ -33,23 +33,23 @@ public class AcquisitionLogging extends SQLLogging {
|
||||
this.acquisitionControl = acquisitionControl;
|
||||
|
||||
tableDef = new PamTableDefinition(pamDataBlock.getDataName(), UPDATE_POLICY_OVERWRITE);
|
||||
tableDef.addTableItem(adcClockTime = new PamTableItem("ADC Clock", Types.TIMESTAMP));
|
||||
tableDef.addTableItem(adcClockMillis = new PamTableItem("ADC Clock millis", Types.INTEGER));
|
||||
tableDef.addTableItem(rawADCTime = new PamTableItem("RAW ADC Clock", Types.TIMESTAMP));
|
||||
tableDef.addTableItem(gSamples = new PamTableItem("GigaSamples", Types.INTEGER));
|
||||
tableDef.addTableItem(samples = new PamTableItem("Samples", Types.INTEGER));
|
||||
tableDef.addTableItem(GPSPPSTime = new PamTableItem("GPSPPSTime", Types.TIMESTAMP));
|
||||
tableDef.addTableItem(status = new PamTableItem("Status", Types.CHAR, 20));
|
||||
tableDef.addTableItem(reason = new PamTableItem("Reason", Types.CHAR, 50));
|
||||
tableDef.addTableItem(daqSystemType = new PamTableItem("SystemType", Types.CHAR, 50));
|
||||
tableDef.addTableItem(daqSystemName = new PamTableItem("SystemName", Types.CHAR, 50));
|
||||
tableDef.addTableItem(sampleRate = new PamTableItem("sampleRate", Types.INTEGER));
|
||||
tableDef.addTableItem(nChannels = new PamTableItem("nChannels", Types.INTEGER));
|
||||
tableDef.addTableItem(voltsPeak2Peak = new PamTableItem("voltsPeak2Peak", Types.DOUBLE));
|
||||
tableDef.addTableItem(gain = new PamTableItem("gain", Types.REAL));
|
||||
tableDef.addTableItem(duration = new PamTableItem("duration", Types.DOUBLE));
|
||||
tableDef.addTableItem(clockError = new PamTableItem("clockError", Types.DOUBLE));
|
||||
tableDef.addTableItem(serverTime = new PamTableItem("Server Time", Types.TIMESTAMP));
|
||||
tableDef.addTableItem(adcClockTime = new PamTableItem("ADC Clock", Types.TIMESTAMP, "Time based on PC clock and samples since last PC clock read"));
|
||||
tableDef.addTableItem(adcClockMillis = new PamTableItem("ADC Clock millis", Types.INTEGER, "Millis for adcClockTime if not supported by database"));
|
||||
tableDef.addTableItem(rawADCTime = new PamTableItem("RAW ADC Clock", Types.TIMESTAMP, "Time based on start time and number of samples acquired"));
|
||||
tableDef.addTableItem(gSamples = new PamTableItem("GigaSamples", Types.INTEGER, "Billions of samples. Add this*1e9 to samples"));
|
||||
tableDef.addTableItem(samples = new PamTableItem("Samples", Types.INTEGER, "Samples. Add this to GigaSamples*1e9"));
|
||||
tableDef.addTableItem(GPSPPSTime = new PamTableItem("GPSPPSTime", Types.TIMESTAMP, "Time derived from a GPS with PPS output"));
|
||||
tableDef.addTableItem(status = new PamTableItem("Status", Types.CHAR, 20, "Acquisition Status: 'Start', 'Stop', 'Continue'"));
|
||||
tableDef.addTableItem(reason = new PamTableItem("Reason", Types.CHAR, 50, "Reason for status change"));
|
||||
tableDef.addTableItem(daqSystemType = new PamTableItem("SystemType", Types.CHAR, 50, "Type of acquisition system"));
|
||||
tableDef.addTableItem(daqSystemName = new PamTableItem("SystemName", Types.CHAR, 50, "Specific acquistision system"));
|
||||
tableDef.addTableItem(sampleRate = new PamTableItem("sampleRate", Types.INTEGER, "Sample rate (samples per second)"));
|
||||
tableDef.addTableItem(nChannels = new PamTableItem("nChannels", Types.INTEGER, "Total number of channels"));
|
||||
tableDef.addTableItem(voltsPeak2Peak = new PamTableItem("voltsPeak2Peak", Types.DOUBLE, "Peak to peak input voltage of ADC"));
|
||||
tableDef.addTableItem(gain = new PamTableItem("gain", Types.REAL, "Additional amplifier gain"));
|
||||
tableDef.addTableItem(duration = new PamTableItem("duration", Types.DOUBLE, "Time since start in seconds"));
|
||||
tableDef.addTableItem(clockError = new PamTableItem("clockError", Types.DOUBLE, "Clock error in milliseconds"));
|
||||
tableDef.addTableItem(serverTime = new PamTableItem("Server Time", Types.TIMESTAMP, "Time taken from an Internet time server"));
|
||||
|
||||
setTableDefinition(tableDef);
|
||||
}
|
||||
|
||||
@ -254,9 +254,11 @@ public class AcquisitionProcess extends PamProcess {
|
||||
|
||||
bufferOverflow = false;
|
||||
// daqCheckTime = PamCalendar.getTimeInMillis();
|
||||
Timer t = new Timer(1, new ReallyStart());
|
||||
t.setRepeats(false);
|
||||
t.start();
|
||||
if (!netRX) {
|
||||
Timer t = new Timer(1, new ReallyStart());
|
||||
t.setRepeats(false);
|
||||
t.start();
|
||||
}
|
||||
}
|
||||
|
||||
private boolean addServerTime(DaqStatusDataUnit daqStatusDataUnit) {
|
||||
|
||||
@ -7,6 +7,8 @@ import java.awt.GridBagLayout;
|
||||
import java.awt.Insets;
|
||||
import java.awt.event.ActionEvent;
|
||||
import java.awt.event.ActionListener;
|
||||
import java.io.ByteArrayInputStream;
|
||||
import java.io.DataInputStream;
|
||||
import java.io.File;
|
||||
import java.io.FileInputStream;
|
||||
import java.io.FileNotFoundException;
|
||||
@ -14,6 +16,8 @@ import java.io.IOException;
|
||||
import java.io.Serializable;
|
||||
import java.text.DateFormat;
|
||||
import java.util.Calendar;
|
||||
import java.util.List;
|
||||
|
||||
import javax.sound.sampled.AudioFormat;
|
||||
import javax.sound.sampled.AudioInputStream;
|
||||
import javax.sound.sampled.UnsupportedAudioFileException;
|
||||
@ -31,6 +35,10 @@ import javax.swing.border.TitledBorder;
|
||||
import org.jflac.FLACDecoder;
|
||||
import org.jflac.frame.Frame;
|
||||
import org.jflac.util.ByteData;
|
||||
import org.pamguard.x3.sud.Chunk;
|
||||
import org.pamguard.x3.sud.SudAudioInputStream;
|
||||
import org.pamguard.x3.sud.SudFileListener;
|
||||
import org.pamguard.x3.sud.SudParams;
|
||||
import org.jflac.PCMProcessor;
|
||||
import org.jflac.metadata.StreamInfo;
|
||||
import org.jflac.sound.spi.FlacEncoding;
|
||||
@ -47,15 +55,14 @@ import wavFiles.ByteConverter;
|
||||
import Acquisition.filedate.FileDate;
|
||||
import Acquisition.filedate.FileDateDialogStrip;
|
||||
import Acquisition.filedate.FileDateObserver;
|
||||
import Acquisition.filetypes.SoundFileType;
|
||||
import Acquisition.pamAudio.PamAudioFileManager;
|
||||
import Acquisition.pamAudio.PamAudioFileFilter;
|
||||
import Acquisition.pamAudio.PamAudioSystem;
|
||||
import PamController.PamControlledUnitSettings;
|
||||
import PamController.PamController;
|
||||
import PamController.PamSettingManager;
|
||||
import PamController.PamSettings;
|
||||
import PamDetection.RawDataUnit;
|
||||
import PamModel.SMRUEnable;
|
||||
import PamUtils.PamCalendar;
|
||||
import PamUtils.PamFileChooser;
|
||||
import PamView.dialog.PamLabel;
|
||||
@ -140,6 +147,11 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
protected ByteConverter byteConverter;
|
||||
|
||||
protected FileDateDialogStrip fileDateStrip;
|
||||
|
||||
/**
|
||||
* Sound file types present in the current selections.
|
||||
*/
|
||||
private List<SoundFileType> selectedFileTypes;
|
||||
|
||||
/**
|
||||
* Text field for skipping initial few seconds of a file.
|
||||
@ -151,6 +163,9 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
*/
|
||||
private PamWarning fileWarning;
|
||||
|
||||
private SudAudioInputStream sudAudioInputStream;
|
||||
|
||||
private SudListener sudListener;
|
||||
|
||||
public FileInputSystem(AcquisitionControl acquisitionControl) {
|
||||
this.acquisitionControl = acquisitionControl;
|
||||
@ -177,7 +192,7 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
}
|
||||
return daqDialog;
|
||||
}
|
||||
|
||||
|
||||
protected JPanel createDaqDialogPanel() {
|
||||
|
||||
JPanel p = new JPanel();
|
||||
@ -216,18 +231,18 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
fileDateStrip.addObserver(this);
|
||||
p.add(fileDateStrip.getDialogComponent(), constraints);
|
||||
|
||||
// if (SMRUEnable.isEnable()) {
|
||||
// if (SMRUEnable.isEnable()) {
|
||||
// no reason to hide this option from users.
|
||||
constraints.gridy++;
|
||||
constraints.gridx = 0;
|
||||
constraints.gridwidth = 1;
|
||||
addComponent(p, new JLabel("Skip initial"), constraints);
|
||||
constraints.gridx++;
|
||||
addComponent(p, skipSecondsField = new JTextField(4), constraints);
|
||||
constraints.gridx++;
|
||||
addComponent(p, new JLabel("seconds"), constraints);
|
||||
constraints.anchor = GridBagConstraints.EAST;
|
||||
// }
|
||||
constraints.gridy++;
|
||||
constraints.gridx = 0;
|
||||
constraints.gridwidth = 1;
|
||||
addComponent(p, new JLabel("Skip initial"), constraints);
|
||||
constraints.gridx++;
|
||||
addComponent(p, skipSecondsField = new JTextField(4), constraints);
|
||||
constraints.gridx++;
|
||||
addComponent(p, new JLabel("seconds"), constraints);
|
||||
constraints.anchor = GridBagConstraints.EAST;
|
||||
// }
|
||||
|
||||
// addComponent(p, new JLabel("File date :"), constraints);
|
||||
// constraints.gridx++;
|
||||
@ -251,7 +266,7 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
// would hold a null. The system type is used by the getParameterSet method to decide
|
||||
// whether or not to include the parameters in the XML output
|
||||
if (fileInputParameters.systemType==null) fileInputParameters.systemType=getSystemType();
|
||||
|
||||
|
||||
fillFileList();
|
||||
|
||||
if (repeat != null) {
|
||||
@ -289,7 +304,7 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
fileInputParameters.recentFiles.trimToSize();
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
if (repeat == null) {
|
||||
fileInputParameters.repeatLoop = false;
|
||||
}
|
||||
@ -306,7 +321,7 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
return false;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
@ -337,7 +352,7 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
protected void selectFile() {
|
||||
//IshmaelDetector.MatchFiltParamsDialog copies a bunch of this. If you
|
||||
//modifiy this, please check that too.
|
||||
|
||||
|
||||
String currFile = (String) fileNameCombo.getSelectedItem();
|
||||
// seems to just support aif and wav files at the moment
|
||||
// Type[] audioTypes = AudioSystem.getAudioFileTypes();
|
||||
@ -393,6 +408,9 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
if (newFile.length() == 0) return;
|
||||
|
||||
File file = new File(newFile);
|
||||
|
||||
setSelectedFileTypes(acquisitionControl.soundFileTypes.getUsedTypes(file));
|
||||
|
||||
if (file == null) return;
|
||||
|
||||
// try to work out the date of the file
|
||||
@ -421,6 +439,10 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
// }
|
||||
// }
|
||||
|
||||
if (audioStream instanceof SudAudioInputStream) {
|
||||
acquisitionControl.getSUDNotificationManager().interpretNewFile(newFile, (SudAudioInputStream) audioStream);
|
||||
}
|
||||
|
||||
AudioFormat audioFormat = audioStream.getFormat();
|
||||
// fileLength = file.length();
|
||||
fileSamples = audioStream.getFrameLength();
|
||||
@ -477,7 +499,7 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
public long getSkipStartFileTime() {
|
||||
return fileInputParameters.skipStartFileTime;
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public boolean canPlayBack(float sampleRate) {
|
||||
// TODO Auto-generated method stub
|
||||
@ -538,7 +560,7 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
}
|
||||
|
||||
public File getCurrentFile() {
|
||||
System.out.println("fileInputParameters: " + fileInputParameters);
|
||||
// System.out.println("fileInputParameters: " + fileInputParameters);
|
||||
if (fileInputParameters.recentFiles == null) return null;
|
||||
if (fileInputParameters.recentFiles.size() < 1) return null;
|
||||
String fileName = fileInputParameters.recentFiles.get(0);
|
||||
@ -565,7 +587,7 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
System.out.println("The current file was null");
|
||||
return false;
|
||||
}
|
||||
System.out.printf("*********************************** Opening file %s\n", currentFile.getName());
|
||||
// System.out.printf("*********************************** Opening file %s\n", currentFile.getName());
|
||||
|
||||
try {
|
||||
|
||||
@ -575,12 +597,25 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
|
||||
audioStream = PamAudioFileManager.getInstance().getAudioInputStream(currentFile);
|
||||
|
||||
if (audioStream instanceof SudAudioInputStream) {
|
||||
sudAudioInputStream = (SudAudioInputStream) audioStream;
|
||||
if (sudListener == null) {
|
||||
sudListener = new SudListener();
|
||||
}
|
||||
sudAudioInputStream.addSudFileListener(sudListener);
|
||||
// sudAudioInputStream.ad
|
||||
acquisitionControl.getSUDNotificationManager().newSudInputStream(sudAudioInputStream);
|
||||
}
|
||||
else {
|
||||
sudAudioInputStream = null;
|
||||
}
|
||||
|
||||
if (audioStream == null) {
|
||||
return false;
|
||||
}
|
||||
|
||||
audioFormat = audioStream.getFormat();
|
||||
|
||||
|
||||
if (audioFormat==null) {
|
||||
System.err.println("AudioFormat was null: " + currentFile.getAbsolutePath());
|
||||
return false;
|
||||
@ -592,7 +627,7 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
|
||||
acquisitionControl.getAcquisitionProcess().setSampleRate(audioFormat.getSampleRate(), true);
|
||||
fileInputParameters.bitDepth = audioFormat.getSampleSizeInBits();
|
||||
|
||||
|
||||
loadByteConverter(audioFormat);
|
||||
|
||||
} catch (UnsupportedAudioFileException ex) {
|
||||
@ -608,18 +643,27 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
return true;
|
||||
}
|
||||
|
||||
private class SudListener implements SudFileListener {
|
||||
|
||||
@Override
|
||||
public void chunkProcessed(int chunkID, Chunk sudChunk) {
|
||||
acquisitionControl.getSUDNotificationManager().chunkProcessed(chunkID, sudChunk);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
public boolean runFileAnalysis() {
|
||||
// keep a reference to where data will be put.
|
||||
this.newDataUnits = acquisitionControl.getDaqProcess().getNewDataQueue();
|
||||
|
||||
// if (this.newDataUnits == null) {
|
||||
// System.err.println("newDataUnits: == null: ");
|
||||
// return false;
|
||||
// }
|
||||
|
||||
// if (this.newDataUnits == null) {
|
||||
// System.err.println("newDataUnits: == null: ");
|
||||
// return false;
|
||||
// }
|
||||
|
||||
if (!prepareInputFile() && getCurrentFile()!=null) {
|
||||
|
||||
|
||||
String audioFileStr = getCurrentFile()==null? "Null File": getCurrentFile().getAbsolutePath();
|
||||
String title = "Error loading audio file";
|
||||
String msg = "<html><p>There was an error trying to access the audio file </p><b> " +
|
||||
@ -647,14 +691,14 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
this.startTimeMS = PamCalendar.getTimeInMillis();
|
||||
|
||||
if (audioFormat==null) {
|
||||
|
||||
|
||||
String audioFileStr = getCurrentFile()==null? "Null File": getCurrentFile().getAbsolutePath();
|
||||
|
||||
System.err.println("FileInputSystem: runFileAnalysis: AudioFile format is null: " + audioFileStr);
|
||||
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
|
||||
nChannels = audioFormat.getChannels();
|
||||
|
||||
acquisitionControl.getDaqProcess().setSampleRate(sampleRate = audioFormat.getSampleRate(), true);
|
||||
@ -997,6 +1041,9 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
}
|
||||
}
|
||||
if (audioStream != null) {
|
||||
if (audioStream instanceof SudAudioInputStream) {
|
||||
acquisitionControl.getSUDNotificationManager().sudStreamClosed();
|
||||
}
|
||||
try {
|
||||
audioStream.close();
|
||||
audioStream = null;
|
||||
@ -1124,7 +1171,7 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
}
|
||||
|
||||
public void sayEta(long timeMs) {
|
||||
|
||||
|
||||
if (etaLabel==null) return;
|
||||
|
||||
if (timeMs < 0) {
|
||||
@ -1186,4 +1233,27 @@ public class FileInputSystem extends DaqSystem implements ActionListener, PamSe
|
||||
getDialogPanel();
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* @return the selectedFileTypes
|
||||
*/
|
||||
public List<SoundFileType> getSelectedFileTypes() {
|
||||
return selectedFileTypes;
|
||||
}
|
||||
|
||||
/**
|
||||
* Called when the file or file list selection is changes and finds a list of all
|
||||
* sound file types included in the selection. this is only implemented for SUD files
|
||||
* at the moment, the idea being to offer some additional functionality.
|
||||
* @param selectedFileTypes the selectedFileTypes to set
|
||||
*/
|
||||
public void setSelectedFileTypes(List<SoundFileType> selectedFileTypes) {
|
||||
this.selectedFileTypes = selectedFileTypes;
|
||||
if (selectedFileTypes == null) {
|
||||
return;
|
||||
}
|
||||
for (SoundFileType aType : selectedFileTypes) {
|
||||
aType.selected(this);
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -10,6 +10,8 @@ import java.awt.event.ActionListener;
|
||||
import java.io.File;
|
||||
import java.io.Serializable;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import javax.sound.sampled.AudioFormat;
|
||||
import javax.sound.sampled.AudioInputStream;
|
||||
import javax.swing.BoxLayout;
|
||||
@ -494,6 +496,9 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings{
|
||||
// System.out.printf("Wav list recieved with %d files after %d millis\n",
|
||||
// fileListData.getFileCount(), System.currentTimeMillis() - wavListStart);
|
||||
allFiles = fileListData.getListCopy();
|
||||
|
||||
List<WavFileType> asList = allFiles;
|
||||
setSelectedFileTypes(acquisitionControl.soundFileTypes.getUsedTypes(allFiles));
|
||||
|
||||
setFileDateText();
|
||||
// also open up the first file and get the sample rate and number of channels from it
|
||||
|
||||
@ -13,6 +13,7 @@ import java.util.TimeZone;
|
||||
import Acquisition.KETime;
|
||||
import Acquisition.layoutFX.FileDatePane;
|
||||
import Acquisition.layoutFX.StandardFileDatePane;
|
||||
import Acquisition.sud.SUDFileTime;
|
||||
import PamController.PamControlledUnitSettings;
|
||||
import PamController.PamSettingManager;
|
||||
import PamController.PamSettings;
|
||||
@ -157,6 +158,11 @@ public class StandardFileDate implements FileDate, PamSettings {
|
||||
if (settings.isUseBespokeFormat() && settings.getForcedDateFormat() != null) {
|
||||
return forcedDataFormat(file, settings.getForcedDateFormat());
|
||||
}
|
||||
|
||||
long sudTime = SUDFileTime.getSUDFileTime(file);
|
||||
if (sudTime != Long.MIN_VALUE) {
|
||||
return sudTime;
|
||||
}
|
||||
|
||||
/*
|
||||
* Dtag files have an accompanying XML file which
|
||||
@ -168,6 +174,7 @@ public class StandardFileDate implements FileDate, PamSettings {
|
||||
setLastFormat("D3 time from xml file");
|
||||
return dTagTime;
|
||||
}
|
||||
|
||||
|
||||
long stTime = SoundTrapTime.getSoundTrapTime(file, settings.getDateTimeFormatToUse());
|
||||
if (stTime != Long.MIN_VALUE) {
|
||||
|
||||
29
src/Acquisition/filetypes/SUDFileType.java
Normal file
29
src/Acquisition/filetypes/SUDFileType.java
Normal file
@ -0,0 +1,29 @@
|
||||
package Acquisition.filetypes;
|
||||
|
||||
import Acquisition.FileInputSystem;
|
||||
import PamView.dialog.warn.WarnOnce;
|
||||
|
||||
public class SUDFileType extends SoundFileType {
|
||||
|
||||
private boolean isShown = false;
|
||||
|
||||
private String sudInfoText = "<html>There are SoundTrap SUD files in your selection. PAMGuard can now process data from these " +
|
||||
"directly with no need to unpack them into WAV files. " +
|
||||
"<p>If the SoundTrap was running with the click detector, then you should add a SoundTrap Click Detector module" +
|
||||
" and detected clicks will automatically be extracted to binary files while processing the wav data." +
|
||||
"<p>See the Click Detector help for further details";
|
||||
|
||||
public SUDFileType() {
|
||||
super(".sud");
|
||||
}
|
||||
|
||||
@Override
|
||||
public void selected(FileInputSystem fileInputSystem) {
|
||||
if (isShown) {
|
||||
return;
|
||||
}
|
||||
WarnOnce.showWarning("SoundTrap SUD Files", sudInfoText, WarnOnce.OK_OPTION);
|
||||
isShown = true;
|
||||
}
|
||||
|
||||
}
|
||||
65
src/Acquisition/filetypes/SoundFileType.java
Normal file
65
src/Acquisition/filetypes/SoundFileType.java
Normal file
@ -0,0 +1,65 @@
|
||||
package Acquisition.filetypes;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.List;
|
||||
|
||||
import Acquisition.FileInputSystem;
|
||||
import Acquisition.pamAudio.PamAudioFileFilter;
|
||||
import PamUtils.worker.filelist.WavFileType;
|
||||
|
||||
/**
|
||||
* Some functions for the File and Folder input systems to give a bit of
|
||||
* extra functionality / help for different file types. Primarily introduced
|
||||
* to give a couple of extras for sud files.
|
||||
* @author dg50
|
||||
*
|
||||
*/
|
||||
public abstract class SoundFileType {
|
||||
|
||||
private String fileType;
|
||||
|
||||
private PamAudioFileFilter fileFilter = new PamAudioFileFilter();
|
||||
|
||||
public SoundFileType(String fileType) {
|
||||
this.fileType = fileType.toLowerCase();
|
||||
}
|
||||
|
||||
/**
|
||||
* Work out if any files of this type are included in the current selection.
|
||||
* @param fileOrFolder this for a single file.
|
||||
* @param includeSubfolders used with folders.
|
||||
* @return true if any exist.
|
||||
*/
|
||||
public boolean isFileType(File oneFile) {
|
||||
if (oneFile == null) {
|
||||
return false;
|
||||
}
|
||||
if (oneFile.isFile()) {
|
||||
return oneFile.getName().toLowerCase().endsWith(fileType);
|
||||
}
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
/**
|
||||
* Work out if any files of this type are included in the current selection.
|
||||
* @param fileOrFolder this for a single file.
|
||||
* @param includeSubfolders used with folders.
|
||||
* @return true if any exist.
|
||||
*/
|
||||
public boolean hasFileType(List<WavFileType> files) {
|
||||
if (files == null) {
|
||||
return false;
|
||||
}
|
||||
for (File aFile : files) {
|
||||
if (isFileType(aFile)) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
public abstract void selected(FileInputSystem fileInputSystem);
|
||||
|
||||
}
|
||||
74
src/Acquisition/filetypes/SoundFileTypes.java
Normal file
74
src/Acquisition/filetypes/SoundFileTypes.java
Normal file
@ -0,0 +1,74 @@
|
||||
package Acquisition.filetypes;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import Acquisition.AcquisitionControl;
|
||||
import PamUtils.worker.filelist.WavFileType;
|
||||
|
||||
/**
|
||||
* List of SoundFileType objects.
|
||||
* @author dg50
|
||||
*
|
||||
*/
|
||||
public class SoundFileTypes {
|
||||
|
||||
private AcquisitionControl acquisitionControl;
|
||||
|
||||
private ArrayList<SoundFileType> availableTypes = new ArrayList<>();
|
||||
|
||||
public SoundFileTypes(AcquisitionControl acquisitionControl) {
|
||||
this.acquisitionControl = acquisitionControl;
|
||||
availableTypes.add(new SUDFileType());
|
||||
}
|
||||
|
||||
/**
|
||||
* Get a list of used file types. Reaslistically this
|
||||
* can only return one value.
|
||||
* @param aFile
|
||||
* @return
|
||||
*/
|
||||
public SoundFileType getFileType(File aFile) {
|
||||
ArrayList<SoundFileType> usedTypes = new ArrayList<>();
|
||||
for (SoundFileType aType : availableTypes) {
|
||||
if (aType.isFileType(aFile)) {
|
||||
return aType;
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get a list of used file types. Realistically this
|
||||
* can only return one value but possibly it's useful to have it in the same
|
||||
* format as the multiple file version. .
|
||||
* @param aFile
|
||||
* @return
|
||||
*/
|
||||
public List<SoundFileType> getUsedTypes(File aFile) {
|
||||
ArrayList<SoundFileType> usedTypes = new ArrayList<>();
|
||||
for (SoundFileType aType : availableTypes) {
|
||||
if (aType.isFileType(aFile)) {
|
||||
usedTypes.add(aType);
|
||||
}
|
||||
}
|
||||
return usedTypes;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get a list of used file types for the folder Input System.
|
||||
* @param aFile
|
||||
* @return
|
||||
*/
|
||||
public List<SoundFileType> getUsedTypes(List<WavFileType> aFile) {
|
||||
ArrayList<SoundFileType> usedTypes = new ArrayList<>();
|
||||
for (SoundFileType aType : availableTypes) {
|
||||
if (aType.hasFileType(aFile)) {
|
||||
usedTypes.add(aType);
|
||||
}
|
||||
}
|
||||
return usedTypes;
|
||||
}
|
||||
|
||||
}
|
||||
@ -109,7 +109,7 @@ public class PamAudioFileManager {
|
||||
|
||||
AudioInputStream stream = null;
|
||||
for (int i = 0; i < pamAudioFileTypes.size(); i++) {
|
||||
System.out.println(file.getName() + " " + pamAudioFileTypes.get(i).getName());
|
||||
// System.out.println(file.getName() + " " + pamAudioFileTypes.get(i).getName());
|
||||
if (isExtension(file, pamAudioFileTypes.get(i))) {
|
||||
//System.out.println("Get stream for: " +pamAudioFileTypes.get(i).getName());
|
||||
stream = pamAudioFileTypes.get(i).getAudioStream(file);
|
||||
|
||||
86
src/Acquisition/sud/SUDFileTime.java
Normal file
86
src/Acquisition/sud/SUDFileTime.java
Normal file
@ -0,0 +1,86 @@
|
||||
package Acquisition.sud;
|
||||
|
||||
import java.io.File;
|
||||
|
||||
import org.pamguard.x3.sud.ChunkHeader;
|
||||
import org.pamguard.x3.sud.SudAudioInputStream;
|
||||
import org.pamguard.x3.sud.SudFileMap;
|
||||
import org.pamguard.x3.sud.SudParams;
|
||||
|
||||
import PamUtils.PamCalendar;
|
||||
|
||||
public class SUDFileTime {
|
||||
|
||||
private static long sudTime;
|
||||
|
||||
private static String lastFilePath = "";
|
||||
/**
|
||||
* Temp measure to get the time from the first available sud record.
|
||||
* @param file
|
||||
* @return
|
||||
*/
|
||||
public static long getSUDFileTime(File file) {
|
||||
if (file == null || file.exists() == false) {
|
||||
return Long.MIN_VALUE;
|
||||
}
|
||||
if (file.getName().toLowerCase().endsWith(".sud") == false) {
|
||||
return Long.MIN_VALUE;
|
||||
}
|
||||
String filePath = file.getAbsolutePath();
|
||||
if (filePath.equals(lastFilePath)) {
|
||||
return sudTime;
|
||||
}
|
||||
/**
|
||||
* Open the sud file and read it until the first chunk arrive, get the time
|
||||
* from there and close it again. I don't really see another way.
|
||||
*/
|
||||
// long t1 = System.currentTimeMillis();
|
||||
sudTime = Long.MIN_VALUE;
|
||||
SudParams sudParams = new SudParams();
|
||||
sudParams.saveMeta = false;
|
||||
sudParams.saveWav = false;
|
||||
try {
|
||||
SudAudioInputStream sudAudioInputStream = SudAudioInputStream.openInputStream(file, sudParams, false);
|
||||
if (sudAudioInputStream == null) {
|
||||
return Long.MIN_VALUE;
|
||||
}
|
||||
SudFileMap sudMap = sudAudioInputStream.getSudMap();
|
||||
if (sudMap == null) {
|
||||
return Long.MIN_VALUE;
|
||||
}
|
||||
long t = sudMap.getFirstChunkTimeMillis();
|
||||
if (t != 0) {
|
||||
sudTime = t;
|
||||
}
|
||||
// sudAudioInputStream.addSudFileListener((chunkID, sudChunk)->{
|
||||
// ChunkHeader chunkHead = sudChunk.chunkHeader;
|
||||
// if (chunkHead == null || sudTime != Long.MIN_VALUE) {
|
||||
// return;
|
||||
// }
|
||||
// long millis = (long) chunkHead.TimeS*1000 + (long) chunkHead.TimeOffsetUs/1000;
|
||||
// if (millis > 0) {
|
||||
// sudTime = millis;
|
||||
// lastFilePath = filePath;
|
||||
// }
|
||||
// });
|
||||
//
|
||||
// while (sudAudioInputStream.available() > 0 && sudTime == Long.MIN_VALUE) {
|
||||
//
|
||||
// //note this is reading bytes of uncompressed continuous recordings only.
|
||||
// sudAudioInputStream.read();
|
||||
// }
|
||||
//
|
||||
sudAudioInputStream.close();
|
||||
// long t2 = System.currentTimeMillis();
|
||||
// System.out.printf("SUD file time %s extracted in %d milliseconds\n", PamCalendar.formatDBDateTime(sudTime), t2-t1);
|
||||
|
||||
} catch (Exception e) {
|
||||
System.err.println("Error getting time from SUD file: " + e.getMessage());
|
||||
}
|
||||
|
||||
return sudTime;
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
36
src/Acquisition/sud/SUDNotificationHandler.java
Normal file
36
src/Acquisition/sud/SUDNotificationHandler.java
Normal file
@ -0,0 +1,36 @@
|
||||
package Acquisition.sud;
|
||||
|
||||
import org.pamguard.x3.sud.Chunk;
|
||||
import org.pamguard.x3.sud.SudAudioInputStream;
|
||||
import org.pamguard.x3.sud.SudFileListener;
|
||||
import org.pamguard.x3.sud.SudProgressListener;
|
||||
|
||||
public interface SUDNotificationHandler extends SudFileListener, SudProgressListener {
|
||||
|
||||
/**
|
||||
* A new SUD file input stream has been opened.
|
||||
* @param sudAudioInputStream
|
||||
*/
|
||||
public void newSudInputStream(SudAudioInputStream sudAudioInputStream);
|
||||
|
||||
/**
|
||||
* SUD stream has closed.
|
||||
*/
|
||||
public void sudStreamClosed();
|
||||
|
||||
@Override
|
||||
public void progress(double arg0, int arg1, int arg2);
|
||||
|
||||
@Override
|
||||
public void chunkProcessed(int chunkId, Chunk sudChunk);
|
||||
|
||||
/**
|
||||
* Notification that a new file or folder is selected. This is called when a file
|
||||
* or folder is selected in the dialog, NOT when acquisition starts, so is a good
|
||||
* opportunity for the SUD Click Detector to work out channel maps and sample rates.
|
||||
* @param newFile
|
||||
* @param sudAudioStream
|
||||
*/
|
||||
public void interpretNewFile(String newFile, SudAudioInputStream sudAudioStream);
|
||||
|
||||
}
|
||||
66
src/Acquisition/sud/SUDNotificationManager.java
Normal file
66
src/Acquisition/sud/SUDNotificationManager.java
Normal file
@ -0,0 +1,66 @@
|
||||
package Acquisition.sud;
|
||||
|
||||
import java.util.ArrayList;
|
||||
|
||||
import org.pamguard.x3.sud.Chunk;
|
||||
import org.pamguard.x3.sud.SudAudioInputStream;
|
||||
import org.pamguard.x3.sud.SudFileListener;
|
||||
import org.pamguard.x3.sud.SudProgressListener;
|
||||
|
||||
/**
|
||||
* Class to handle appropriate notifications for SUD files, which go a bit
|
||||
* beyond what's handled in the chunk notifications.
|
||||
* @author dg50
|
||||
*
|
||||
*/
|
||||
public class SUDNotificationManager implements SUDNotificationHandler {
|
||||
|
||||
private ArrayList<SUDNotificationHandler> handlers = new ArrayList();
|
||||
|
||||
public void addNotificationHandler(SUDNotificationHandler sudNotificationHandler) {
|
||||
if (handlers.contains(sudNotificationHandler)) {
|
||||
return;
|
||||
}
|
||||
handlers.add(sudNotificationHandler);
|
||||
}
|
||||
|
||||
public boolean removeNotificationHandler(SUDNotificationHandler sudNotificationHandler) {
|
||||
return handlers.remove(sudNotificationHandler);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void newSudInputStream(SudAudioInputStream sudAudioInputStream) {
|
||||
for (SUDNotificationHandler handler : handlers) {
|
||||
handler.newSudInputStream(sudAudioInputStream);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void sudStreamClosed() {
|
||||
for (SUDNotificationHandler handler : handlers) {
|
||||
handler.sudStreamClosed();
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void progress(double arg0, int arg1, int arg2) {
|
||||
for (SUDNotificationHandler handler : handlers) {
|
||||
handler.progress(arg0, arg1, arg2);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void chunkProcessed(int chunkId, Chunk sudChunk) {
|
||||
for (SUDNotificationHandler handler : handlers) {
|
||||
handler.chunkProcessed(chunkId, sudChunk);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void interpretNewFile(String newFile, SudAudioInputStream sudAudioStream) {
|
||||
for (SUDNotificationHandler handler : handlers) {
|
||||
handler.interpretNewFile(newFile, sudAudioStream);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
@ -77,6 +77,9 @@ public class ThreadingHydrophoneLocator extends StraightHydrophoneLocator implem
|
||||
*/
|
||||
while (gpsIt.hasPrevious()) {
|
||||
gpsUnit = gpsIt.previous();
|
||||
if (gpsUnit == null) {
|
||||
continue;
|
||||
}
|
||||
gpsData = gpsUnit;
|
||||
if (gpsUnit.getTimeInMillis() < timeMilliseconds) {
|
||||
break;
|
||||
|
||||
@ -1,6 +1,5 @@
|
||||
package PamController.command;
|
||||
|
||||
import Map.GetMapFile;
|
||||
import PamController.PamControlledUnit;
|
||||
import PamController.PamController;
|
||||
import PamUtils.PamCalendar;
|
||||
@ -56,6 +55,9 @@ public class SummaryCommand extends ExtCommand {
|
||||
totalString += String.format("\n<%s>%s:%s<\\%s>", aModule.getShortUnitType(),
|
||||
aModule.getUnitName(), aString, aModule.getShortUnitType());
|
||||
}
|
||||
if (clear) {
|
||||
lastCallTime = nowTime;
|
||||
}
|
||||
return totalString;
|
||||
}
|
||||
|
||||
|
||||
@ -673,11 +673,6 @@ final public class PamModel implements PamModelInterface, PamSettings {
|
||||
+ "bearings to source, group into click trains, etc.");
|
||||
mi.setModulesMenuGroup(detectorsGroup);
|
||||
mi.addGUICompatabilityFlag(PamGUIManager.FX);
|
||||
|
||||
mi = PamModuleInfo.registerControlledUnit("soundtrap.STClickControl", "SoundTrap Click Detector");
|
||||
mi.setModulesMenuGroup(detectorsGroup);
|
||||
mi.setToolTipText("Click Detector module for Soundtrap detector data");
|
||||
mi.setHidden(isViewer == false);
|
||||
|
||||
mi = PamModuleInfo.registerControlledUnit("clickTrainDetector.ClickTrainControl", "Click Train Detector");
|
||||
mi.addDependency(new PamDependency(RawDataUnit.class, "clickDetector.ClickControl"));
|
||||
@ -729,6 +724,11 @@ final public class PamModel implements PamModelInterface, PamSettings {
|
||||
mi.setToolTipText("Generalised Power Law Detector for tonal sounds");
|
||||
mi.setModulesMenuGroup(detectorsGroup);
|
||||
|
||||
mi = PamModuleInfo.registerControlledUnit("soundtrap.STClickControl", "SoundTrap Click Detector");
|
||||
mi.setModulesMenuGroup(detectorsGroup);
|
||||
mi.setToolTipText("Click Detector module for Soundtrap detector data only");
|
||||
// mi.setHidden(isViewer == false);
|
||||
|
||||
// mi = PamModuleInfo.registerControlledUnit("WorkshopDemo.WorkshopController", "Workshop Demo Detector");
|
||||
// mi.addDependency(new PamDependency(FFTDataUnit.class, "fftManager.PamFFTControl"));
|
||||
// mi.setToolTipText("Simple demo detector for programmers");
|
||||
|
||||
@ -17,7 +17,7 @@ public class PamAudioFileFilter extends PamFileFilter {
|
||||
// addFileType(".AIFF");
|
||||
// addFileType(".FLAC");
|
||||
addFileType(".flac");
|
||||
// addFileType(".sud");
|
||||
addFileType(".sud");
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@ -1,7 +1,9 @@
|
||||
package PamUtils;
|
||||
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.ByteArrayInputStream;
|
||||
import java.io.File;
|
||||
import java.io.FileWriter;
|
||||
import java.io.IOException;
|
||||
import java.io.InputStream;
|
||||
import java.io.StringWriter;
|
||||
@ -9,6 +11,7 @@ import java.io.StringWriter;
|
||||
import javax.xml.parsers.DocumentBuilder;
|
||||
import javax.xml.parsers.DocumentBuilderFactory;
|
||||
import javax.xml.parsers.ParserConfigurationException;
|
||||
import javax.xml.transform.OutputKeys;
|
||||
import javax.xml.transform.Transformer;
|
||||
import javax.xml.transform.TransformerException;
|
||||
import javax.xml.transform.TransformerFactory;
|
||||
@ -183,4 +186,47 @@ public class XMLUtils {
|
||||
}
|
||||
return doc;
|
||||
}
|
||||
/**
|
||||
* Write to the given file.
|
||||
* @param doc xml document
|
||||
* @param outFile file
|
||||
* @throws IOException
|
||||
*/
|
||||
public static void writeToFile(Document doc, File outFile) throws IOException {
|
||||
String asString = getAsString(doc);
|
||||
if (asString!=null) {
|
||||
try {
|
||||
BufferedWriter out = new BufferedWriter(new FileWriter(outFile, false));
|
||||
out.write(asString);
|
||||
out.close();
|
||||
} catch (IOException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the xml document as a String.
|
||||
* @param doc xml document
|
||||
* @return xml content as a a string.
|
||||
*/
|
||||
public static String getAsString(Document doc) {
|
||||
try {
|
||||
DOMSource domSource = new DOMSource(doc);
|
||||
StringWriter writer = new StringWriter();
|
||||
StreamResult result = new StreamResult(writer);
|
||||
TransformerFactory tf = TransformerFactory.newInstance();
|
||||
Transformer transformer = tf.newTransformer();
|
||||
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
|
||||
transformer.setOutputProperty(OutputKeys.ENCODING, "ISO-8859-1");
|
||||
// transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
|
||||
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
|
||||
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
|
||||
transformer.transform(domSource, result);
|
||||
return writer.toString();
|
||||
} catch (TransformerException e) {
|
||||
e.printStackTrace();
|
||||
return null;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -17,7 +17,7 @@ public class SnrSqlAddon implements SQLLoggingAddon {
|
||||
public SnrSqlAddon(SNRAnnotationType snrAnnotationType) {
|
||||
super();
|
||||
this.snrAnnotationType = snrAnnotationType;
|
||||
snr = new PamTableItem("snr", Types.DOUBLE);
|
||||
snr = new PamTableItem("snr", Types.DOUBLE, "Signal to Noise ratio");
|
||||
}
|
||||
|
||||
@Override
|
||||
|
||||
@ -18,10 +18,10 @@ public class SPLSqlAddon implements SQLLoggingAddon {
|
||||
public SPLSqlAddon(SPLAnnotationType splAnnotationType) {
|
||||
super();
|
||||
this.splAnnotationType = splAnnotationType;
|
||||
rms = new PamTableItem("RMS", Types.DOUBLE);
|
||||
zeroPeak = new PamTableItem("ZeroPeak", Types.DOUBLE);
|
||||
peakPeak = new PamTableItem("PeakPeak", Types.DOUBLE);
|
||||
sel = new PamTableItem("SEL", Types.DOUBLE);
|
||||
rms = new PamTableItem("RMS", Types.DOUBLE, "RMS Level");
|
||||
zeroPeak = new PamTableItem("ZeroPeak", Types.DOUBLE, "Zero to Peak Level");
|
||||
peakPeak = new PamTableItem("PeakPeak", Types.DOUBLE, "Peak to Peak Level");
|
||||
sel = new PamTableItem("SEL", Types.DOUBLE, "Sound Exposure Level");
|
||||
}
|
||||
|
||||
@Override
|
||||
|
||||
@ -20,7 +20,7 @@ public class StringSQLLogging implements SQLLoggingAddon {
|
||||
super();
|
||||
this.stringAnnotationType = stringAnnotationType;
|
||||
notes = new PamTableItem(stringAnnotationType.getAnnotationName(),
|
||||
Types.CHAR, stringAnnotationType.getMaxLength());
|
||||
Types.CHAR, stringAnnotationType.getMaxLength(), "Notes");
|
||||
}
|
||||
|
||||
@Override
|
||||
|
||||
@ -21,16 +21,16 @@ public class BearingAnnotationSQL implements SQLLoggingAddon {
|
||||
public BearingAnnotationSQL(BearingAnnotationType bearingAnnotationType) {
|
||||
super();
|
||||
this.bearingAnnotationType = bearingAnnotationType;
|
||||
algoName = new PamTableItem("BearingAlgorithm", Types.CHAR, 30);
|
||||
angle[0] = new PamTableItem("BearingAngle1", Types.REAL);
|
||||
angle[1] = new PamTableItem("BearingAngle2", Types.REAL);
|
||||
angleError[0] = new PamTableItem("BearingError1", Types.REAL);
|
||||
angleError[1] = new PamTableItem("BearingError2", Types.REAL);
|
||||
refAngles[0] = new PamTableItem("ReferenceAngle1", Types.REAL);
|
||||
refAngles[1] = new PamTableItem("ReferenceAngle2", Types.REAL);
|
||||
bfPhones = new PamTableItem("BearingPhones", Types.INTEGER);
|
||||
bfArrayType = new PamTableItem("BearingArrayType", Types.SMALLINT);
|
||||
bfContents = new PamTableItem("BearingLocContents", Types.INTEGER);
|
||||
algoName = new PamTableItem("BearingAlgorithm", Types.CHAR, 30, "Algorithm Name");
|
||||
angle[0] = new PamTableItem("BearingAngle1", Types.REAL, "Horizontal angle (radians)");
|
||||
angle[1] = new PamTableItem("BearingAngle2", Types.REAL, "Vertical angle (radians)");
|
||||
angleError[0] = new PamTableItem("BearingError1", Types.REAL, "Horizontal angle error (radians)");
|
||||
angleError[1] = new PamTableItem("BearingError2", Types.REAL, "Vertical angle error (radians)");
|
||||
refAngles[0] = new PamTableItem("ReferenceAngle1", Types.REAL, "Horizontal angle reference");
|
||||
refAngles[1] = new PamTableItem("ReferenceAngle2", Types.REAL, "Vertical angle reference");
|
||||
bfPhones = new PamTableItem("BearingPhones", Types.INTEGER, "Used hydrophones bitmap");
|
||||
bfArrayType = new PamTableItem("BearingArrayType", Types.SMALLINT, "Array Type 1=point;2=line;3=plane;4=volume");
|
||||
bfContents = new PamTableItem("BearingLocContents", Types.INTEGER, "Bitmap of localisation information types");
|
||||
}
|
||||
|
||||
@Override
|
||||
|
||||
@ -130,7 +130,18 @@ public class BinaryStorageDialogPanel {
|
||||
binaryStoreSettings.autoNewFiles = autoNewFiles.isSelected();
|
||||
binaryStoreSettings.datedSubFolders = dateSubFolders.isSelected();
|
||||
binaryStoreSettings.limitFileSize = limitfileSize.isSelected();
|
||||
|
||||
|
||||
if (allowChannelOffsets) {
|
||||
try {
|
||||
binaryStoreSettings.channelShift = Integer.valueOf(channelOffset.getText());
|
||||
}
|
||||
catch (NumberFormatException e) {
|
||||
return PamDialog.showWarning(owner, errorTitle, "Invalid channel offset number format");
|
||||
}
|
||||
if (binaryStoreSettings.channelShift < 0 || binaryStoreSettings.channelShift > 31) {
|
||||
return PamDialog.showWarning(owner, errorTitle, "Channel offset bust be between 0 and 31");
|
||||
}
|
||||
}
|
||||
if (PamController.getInstance().getRunMode() == PamController.RUN_PAMVIEW) {
|
||||
return true;
|
||||
}
|
||||
@ -157,17 +168,6 @@ public class BinaryStorageDialogPanel {
|
||||
return PamDialog.showWarning(owner, errorTitle, "Invalid file size data");
|
||||
}
|
||||
}
|
||||
if (allowChannelOffsets) {
|
||||
try {
|
||||
binaryStoreSettings.channelShift = Integer.valueOf(channelOffset.getText());
|
||||
}
|
||||
catch (NumberFormatException e) {
|
||||
return PamDialog.showWarning(owner, errorTitle, "Invalid channel offset number format");
|
||||
}
|
||||
if (binaryStoreSettings.channelShift < 0 || binaryStoreSettings.channelShift > 31) {
|
||||
return PamDialog.showWarning(owner, errorTitle, "Channel offset bust be between 0 and 31");
|
||||
}
|
||||
}
|
||||
NoiseStoreType nst = (NoiseStoreType) noiseStoreType.getSelectedItem();
|
||||
if (nst == null) {
|
||||
return PamDialog.showWarning(owner, errorTitle, "You must select a noise storage type");
|
||||
|
||||
@ -1096,7 +1096,7 @@ public class ClickDetector extends PamProcess {
|
||||
* @return true if the tasks complete successfully and the click is to be kept.
|
||||
* false otherwise.
|
||||
*/
|
||||
private boolean completeClick(ClickDetection newClick) {
|
||||
public boolean completeClick(ClickDetection newClick) {
|
||||
|
||||
if (newClick.dataType == ClickDetection.CLICK_CLICK) {
|
||||
int nChannels = PamUtils.getNumChannels(newClick.getChannelBitmap());
|
||||
|
||||
@ -428,11 +428,26 @@ PamSettingsSource {
|
||||
JMenuItem speedMenu = new JMenuItem("Test database speed");
|
||||
speedMenu.addActionListener(new SpeedMenu(parentFrame));
|
||||
menu.add(speedMenu);
|
||||
|
||||
JMenuItem exSchema = new JMenuItem("Export database schema");
|
||||
exSchema.addActionListener(new ActionListener() {
|
||||
|
||||
@Override
|
||||
public void actionPerformed(ActionEvent e) {
|
||||
exportDatabaseSchema(parentFrame);
|
||||
}
|
||||
});
|
||||
menu.add(exSchema);
|
||||
}
|
||||
return menu;
|
||||
}
|
||||
|
||||
|
||||
protected void exportDatabaseSchema(JFrame parentFrame) {
|
||||
dbProcess.exportDatabaseSchema(parentFrame);
|
||||
}
|
||||
|
||||
|
||||
class DatabaseFileMenuAction implements ActionListener {
|
||||
|
||||
private Frame frame;
|
||||
|
||||
@ -22,6 +22,8 @@ import java.sql.Statement;
|
||||
import java.sql.Types;
|
||||
import java.util.ArrayList;
|
||||
|
||||
import javax.swing.JFileChooser;
|
||||
import javax.swing.JFrame;
|
||||
import javax.swing.JOptionPane;
|
||||
import javax.swing.SwingUtilities;
|
||||
import javax.swing.Timer;
|
||||
@ -36,7 +38,9 @@ import loggerForms.UDFTableDefinition;
|
||||
import loggerForms.formdesign.FormEditor;
|
||||
import PamController.PamControlledUnit;
|
||||
import PamController.PamController;
|
||||
import PamController.PamFolders;
|
||||
import PamUtils.PamCalendar;
|
||||
import PamUtils.PamFileChooser;
|
||||
import PamView.dialog.warn.WarnOnce;
|
||||
import PamguardMVC.PamDataBlock;
|
||||
import PamguardMVC.PamDataUnit;
|
||||
@ -1393,4 +1397,42 @@ public class DBProcess extends PamProcess {
|
||||
return logViewerSettings;
|
||||
}
|
||||
|
||||
/**
|
||||
* Export all available database schema, converting PamTableDefinitions into
|
||||
* valid xsd documents.
|
||||
* @param parentFrame
|
||||
*/
|
||||
public void exportDatabaseSchema(JFrame parentFrame) {
|
||||
File startLoc = PamFolders.getFileChooserPath(PamFolders.getDefaultProjectFolder());
|
||||
PamFileChooser fc = new PamFileChooser();
|
||||
fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
|
||||
startLoc = PamFolders.getFileChooserPath(startLoc);
|
||||
fc.setCurrentDirectory(startLoc);
|
||||
|
||||
int ans = fc.showDialog(parentFrame, "Select storage folder");
|
||||
|
||||
if (ans == JFileChooser.APPROVE_OPTION) {
|
||||
startLoc = fc.getSelectedFile();
|
||||
exportDatabaseSchema(parentFrame, startLoc);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Export all table definitions to xsd files in given folder.
|
||||
* @param parentFrame
|
||||
* @param folder
|
||||
*/
|
||||
private void exportDatabaseSchema(JFrame parentFrame, File folder) {
|
||||
ArrayList<PamDataBlock> allDataBlocks = PamController.getInstance().getDataBlocks();
|
||||
DBSchemaWriter schemaWriter = new DBSchemaWriter();
|
||||
for (PamDataBlock aBlock : allDataBlocks) {
|
||||
SQLLogging logging = aBlock.getLogging();
|
||||
if (logging == null) {
|
||||
continue;
|
||||
}
|
||||
schemaWriter.writeSchema(folder, aBlock);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
263
src/generalDatabase/DBSchemaWriter.java
Normal file
263
src/generalDatabase/DBSchemaWriter.java
Normal file
@ -0,0 +1,263 @@
|
||||
package generalDatabase;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.IOException;
|
||||
import java.sql.Types;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import javax.xml.parsers.DocumentBuilderFactory;
|
||||
|
||||
import org.w3c.dom.Document;
|
||||
import org.w3c.dom.Element;
|
||||
|
||||
import PamUtils.XMLUtils;
|
||||
import PamguardMVC.PamDataBlock;
|
||||
|
||||
/**
|
||||
* Functions for writing database table schema in a format
|
||||
* compatible with the Tethys schemas.
|
||||
* @author dg50
|
||||
*
|
||||
*/
|
||||
public class DBSchemaWriter {
|
||||
|
||||
private PamTableDefinition baseTableDefinition = new PamTableDefinition("PamTableDefinition");
|
||||
|
||||
private PamTableDefinition parentTable;
|
||||
|
||||
public DBSchemaWriter() {
|
||||
// TODO Auto-generated constructor stub
|
||||
}
|
||||
|
||||
|
||||
public boolean writeStandardTableDef(File outputFolder, PamDataBlock dataBlock) {
|
||||
PamTableDefinition aTable = new PamTableDefinition("PamStandardTable");
|
||||
parentTable = null;
|
||||
exportDatabaseSchema(outputFolder, dataBlock, null, aTable);
|
||||
parentTable = aTable;
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
public boolean writeSchema(File outputFolder, PamDataBlock dataBlock) {
|
||||
if (dataBlock == null) {
|
||||
return false;
|
||||
}
|
||||
SQLLogging logging = dataBlock.getLogging();
|
||||
if (logging == null) {
|
||||
return false;
|
||||
}
|
||||
|
||||
|
||||
PamTableDefinition tableDef = logging.getTableDefinition();
|
||||
tableDef = logging.getBaseTableDefinition();
|
||||
|
||||
if (tableDef instanceof PamTableDefinition) {
|
||||
writeStandardTableDef(outputFolder, dataBlock);
|
||||
}
|
||||
else {
|
||||
parentTable = null;
|
||||
}
|
||||
|
||||
exportDatabaseSchema(outputFolder, dataBlock, logging, tableDef);
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
private void exportDatabaseSchema(File outputFolder, PamDataBlock dataBlock, SQLLogging logging, PamTableDefinition tableDef) {
|
||||
|
||||
/**
|
||||
* write a parent item, e.g. if tableDef is a sub class of PamTableDefinition
|
||||
*/
|
||||
// String parentName = writeParentTableSchema(outputFolder, dataBlock, tableDef);
|
||||
|
||||
String tableName = tableDef.getTableName();
|
||||
Document doc = PamUtils.XMLUtils.createBlankDoc();
|
||||
Element schemaEl = doc.createElement("xs:schema");
|
||||
schemaEl.setAttribute("xmlns:xs","http://www.w3.org/2001/XMLSchema");
|
||||
schemaEl.setAttribute("targetNamespace", "http://tethys.sdsu.edu/schema/1.0");
|
||||
doc.appendChild(schemaEl);
|
||||
if (parentTable != null) {
|
||||
Element parentEl = doc.createElement("xs:include");
|
||||
parentEl.setAttribute("schemaLocation", parentTable.getTableName()+".xsd");
|
||||
schemaEl.appendChild(parentEl);
|
||||
}
|
||||
|
||||
fillItemElement(doc, schemaEl, tableDef.pamTableItems);
|
||||
|
||||
if (logging != null) {
|
||||
ArrayList<SQLLoggingAddon> annots = logging.getLoggingAddOns();
|
||||
if (annots != null) {
|
||||
for (SQLLoggingAddon addon : annots) {
|
||||
Element compEl = addAddonElement(doc, schemaEl, addon);
|
||||
if (compEl != null) {
|
||||
schemaEl.appendChild(compEl);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
try {
|
||||
File outputFile = new File(outputFolder, tableName+".xsd");
|
||||
XMLUtils.writeToFile(doc, outputFile);
|
||||
} catch (IOException e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Add a complex element for a SQLLogging addon.
|
||||
* @param doc
|
||||
* @param schemaEl
|
||||
* @param addon
|
||||
*/
|
||||
private Element addAddonElement(Document doc, Element schemaEl, SQLLoggingAddon addon) {
|
||||
Element compEl = doc.createElement("xs:complexType");
|
||||
|
||||
Element oEl = doc.createElement("xs:element");
|
||||
oEl.setAttribute("name", addon.getName());
|
||||
|
||||
Element seqEl = doc.createElement("xs:sequence");
|
||||
|
||||
|
||||
PamTableDefinition mtTable = new PamTableDefinition(addon.getName());
|
||||
addon.addTableItems(mtTable);
|
||||
// this is a mess ! must avoid the standard items.
|
||||
fillItemElement(doc, seqEl, mtTable.pamTableItems);
|
||||
|
||||
|
||||
compEl.appendChild(seqEl);
|
||||
|
||||
oEl.appendChild(compEl);
|
||||
return oEl;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Fills information on items in a list into the given element
|
||||
* This may be the schema element or may be a complex element.
|
||||
* @param doc
|
||||
* @param schemaEl
|
||||
* @param tableItems
|
||||
*/
|
||||
private void fillItemElement(Document doc, Element schemaEl, List<PamTableItem> tableItems) {
|
||||
for (PamTableItem tableItem : tableItems) {
|
||||
if (shouldSkip(tableItem, parentTable)) {
|
||||
// element is included in parent table, so skip it.
|
||||
continue;
|
||||
}
|
||||
|
||||
Element itemEl = doc.createElement("xs:element");
|
||||
itemEl.setAttribute("name", tableItem.getName());
|
||||
itemEl.setAttribute("type", sqlTypeToString(tableItem.getSqlType(), tableItem.getLength()));
|
||||
String documentation = tableItem.getDescription();
|
||||
if (documentation != null) {
|
||||
Element annotation = doc.createElement("xs:annotation");
|
||||
itemEl.appendChild(annotation);
|
||||
Element docEl = doc.createElement("xs:documentation");
|
||||
docEl.setTextContent(documentation);
|
||||
annotation.appendChild(docEl);
|
||||
}
|
||||
schemaEl.appendChild(itemEl);
|
||||
}
|
||||
}
|
||||
|
||||
private boolean shouldSkip(PamTableItem tableItem, PamTableDefinition parentTable) {
|
||||
if (parentTable == null) {
|
||||
return false;
|
||||
}
|
||||
if (parentTable.findTableItem(tableItem.getName()) != null) {
|
||||
return true;
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
|
||||
// private String writeParentTableSchema(File outputFolder, PamDataBlock dataBlock, PamTableDefinition tableDef) {
|
||||
// /**
|
||||
// * Write a schema of everything that is in the parent table, then include a reference to that
|
||||
// * schema. To do this, we need to a) establish if there is a table def parent, then go through
|
||||
// * all the fields in THIS tableDef, see if the field exists in the parent. IF it exists in the
|
||||
// * parent, write it in the parent doc, if it's only in this, write it in this doc. So far so good, but
|
||||
// * we need to also make this recursive so it can build layer on layer ?
|
||||
// * Reaslistically, this is all too complicated ! Just write out the schema for the PamTableDefinition
|
||||
// * at the start of everything, and skip those fields in everything else. This will be a bit ad-hoc, but
|
||||
// * it will otherwise be a nightmare since we don't know which table items are in which class at this point.
|
||||
// */
|
||||
// Class tableClass = tableDef.getClass();
|
||||
// Class parentClass = tableClass.getSuperclass();
|
||||
// if (parentClass.isAssignableFrom(tableClass) == false) {
|
||||
// return null;
|
||||
// }
|
||||
//
|
||||
//
|
||||
// return null;
|
||||
// }
|
||||
|
||||
private String sqlTypeToString(int sqlType, int length) {
|
||||
switch (sqlType) {
|
||||
case Types.ARRAY:
|
||||
return "ARRAY";
|
||||
case Types.BIGINT:
|
||||
return "xs:long";
|
||||
case Types.BINARY:
|
||||
return "BINARY";
|
||||
case Types.BIT:
|
||||
return "BIT";
|
||||
case Types.BLOB:
|
||||
return "BLOB";
|
||||
case Types.BOOLEAN:
|
||||
return "xs:boolean";
|
||||
case Types.CHAR:
|
||||
return "xs:string";
|
||||
case Types.CLOB:
|
||||
return "CLOB";
|
||||
case Types.DATALINK:
|
||||
return "DATALINK";
|
||||
case Types.DATE:
|
||||
return "xs:dateTime";
|
||||
case Types.DECIMAL:
|
||||
return "DECIMAL";
|
||||
case Types.DISTINCT:
|
||||
return "DISTINCT";
|
||||
case Types.DOUBLE:
|
||||
return "xs:double";
|
||||
case Types.FLOAT:
|
||||
return "xs:float";
|
||||
case Types.INTEGER:
|
||||
return "xs:int";
|
||||
case Types.JAVA_OBJECT:
|
||||
return "JAVA_OBJECT";
|
||||
case Types.LONGVARBINARY:
|
||||
return "LONGVARBINARY(" + length + ")";
|
||||
case Types.LONGVARCHAR:
|
||||
return "LONGVARCHAR(" + length + ")";
|
||||
case Types.NULL:
|
||||
return "NULL";
|
||||
case Types.NUMERIC:
|
||||
return "NUMERIC";
|
||||
case Types.OTHER:
|
||||
return "OTHER";
|
||||
case Types.REAL:
|
||||
return "xs:float";
|
||||
case Types.REF:
|
||||
return "REF";
|
||||
case Types.SMALLINT:
|
||||
return "xs:short";
|
||||
case Types.STRUCT:
|
||||
return "STRUCT";
|
||||
case Types.TIME:
|
||||
return "TIME";
|
||||
case Types.TIMESTAMP:
|
||||
return "xs:dateTime";
|
||||
case Types.TINYINT:
|
||||
return "TINYINT";
|
||||
case Types.VARBINARY:
|
||||
return "VARBINARY(" + length + ")";
|
||||
case Types.VARCHAR:
|
||||
return "VARCHAR(" + length + ")";
|
||||
}
|
||||
return null;
|
||||
}
|
||||
}
|
||||
@ -43,7 +43,7 @@ public class EmptyTableDefinition implements Cloneable {
|
||||
this.tableName = tableName;
|
||||
this.setUpdatePolicy(updatePolicy);
|
||||
pamTableItems = new ArrayList<PamTableItem>();
|
||||
pamTableItems.add(indexItem = new PamTableItem(indexColName, Types.INTEGER));
|
||||
pamTableItems.add(indexItem = new PamTableItem(indexColName, Types.INTEGER, "Primary key"));
|
||||
indexItem.setPrimaryKey(true);
|
||||
indexItem.setCounter(true);
|
||||
}
|
||||
|
||||
@ -55,15 +55,15 @@ public class PamTableDefinition extends EmptyTableDefinition implements Cloneabl
|
||||
*/
|
||||
public PamTableDefinition(String tableName, int updatePolicy) {
|
||||
super(tableName, updatePolicy);
|
||||
pamTableItems.add(uid = new PamTableItem("UID", Types.BIGINT));
|
||||
pamTableItems.add(timeStampItem = new PamTableItem(utcColName, Types.TIMESTAMP));
|
||||
pamTableItems.add(timeStampMillis = new PamTableItem("UTCMilliseconds", Types.SMALLINT));
|
||||
pamTableItems.add(localTime = new PamTableItem("PCLocalTime", Types.TIMESTAMP));
|
||||
pamTableItems.add(pcTime = new PamTableItem("PCTime", Types.TIMESTAMP));
|
||||
pamTableItems.add(channelBitmap = new PamTableItem("ChannelBitmap", Types.INTEGER));
|
||||
pamTableItems.add(sequenceBitmap = new PamTableItem("SequenceBitmap", Types.INTEGER));
|
||||
pamTableItems.add(uid = new PamTableItem("UID", Types.BIGINT, "Unique Identifier"));
|
||||
pamTableItems.add(timeStampItem = new PamTableItem(utcColName, Types.TIMESTAMP, "Timestamp UTC"));
|
||||
pamTableItems.add(timeStampMillis = new PamTableItem("UTCMilliseconds", Types.SMALLINT, "Time milliseconds (for databases which do not support millis)"));
|
||||
pamTableItems.add(localTime = new PamTableItem("PCLocalTime", Types.TIMESTAMP, "Local time on PC"));
|
||||
pamTableItems.add(pcTime = new PamTableItem("PCTime", Types.TIMESTAMP, "Time data written, UTC. Same as UTC for real time data, current time for offline file analysis"));
|
||||
pamTableItems.add(channelBitmap = new PamTableItem("ChannelBitmap", Types.INTEGER, "Bitmap of input channels used"));
|
||||
pamTableItems.add(sequenceBitmap = new PamTableItem("SequenceBitmap", Types.INTEGER, "Bitmap of beam or channel outputs used"));
|
||||
if (updatePolicy == SQLLogging.UPDATE_POLICY_WRITENEW) {
|
||||
addTableItem(updateReference = new PamTableItem("UpdateOf", Types.INTEGER));
|
||||
addTableItem(updateReference = new PamTableItem("UpdateOf", Types.INTEGER, "Reference to previous value"));
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -50,6 +50,14 @@ public class PamTableItem implements Cloneable {
|
||||
*/
|
||||
private Object value;
|
||||
|
||||
/**
|
||||
* Test description of field. Can be exported to schema and may
|
||||
* be possible to write into database description fields one day. In any case
|
||||
* it can be useful to the programmer when looking back to see what on earth
|
||||
* code is supposed to be doing.
|
||||
*/
|
||||
private String description;
|
||||
|
||||
/*
|
||||
* Reference to another PamTableItem in a different
|
||||
* table. This must be of the same sqlType as this
|
||||
@ -60,6 +68,11 @@ public class PamTableItem implements Cloneable {
|
||||
*/
|
||||
private PamTableItem crossReferenceItem;
|
||||
|
||||
/**
|
||||
* Generate a table item
|
||||
* @param name name of table item
|
||||
* @param sqlType SQL Type from java.sql.Types, e.g. Types.INTEGER
|
||||
*/
|
||||
public PamTableItem(String name, int sqlType) {
|
||||
super();
|
||||
this.name = name;
|
||||
@ -67,7 +80,28 @@ public class PamTableItem implements Cloneable {
|
||||
this.length = 0;
|
||||
this.required = false;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Generate a table item
|
||||
* @param name name of table item
|
||||
* @param sqlType SQL Type from java.sql.Types, e.g. Types.INTEGER
|
||||
* @param description optional description
|
||||
*/
|
||||
public PamTableItem(String name, int sqlType, String description) {
|
||||
super();
|
||||
this.name = name;
|
||||
this.sqlType = sqlType;
|
||||
this.description = description;
|
||||
this.length = 0;
|
||||
this.required = false;
|
||||
}
|
||||
|
||||
/**
|
||||
* Generate a table item
|
||||
* @param name name of table item
|
||||
* @param sqlType SQL Type from java.sql.Types, e.g. Types.INTEGER
|
||||
* @param length length (only applicable to Types.CHAR types)
|
||||
*/
|
||||
public PamTableItem(String name, int sqlType, int length) {
|
||||
super();
|
||||
this.name = name;
|
||||
@ -76,6 +110,22 @@ public class PamTableItem implements Cloneable {
|
||||
this.required = false;
|
||||
}
|
||||
|
||||
/**
|
||||
* Generate a table item
|
||||
* @param name name of table item
|
||||
* @param sqlType SQL Type from java.sql.Types, e.g. Types.INTEGER
|
||||
* @param length length (only applicable to Types.CHAR types)
|
||||
* @param description optional description
|
||||
*/
|
||||
public PamTableItem(String name, int sqlType, int length, String description) {
|
||||
super();
|
||||
this.name = name;
|
||||
this.sqlType = sqlType;
|
||||
this.length = length;
|
||||
this.description = description;
|
||||
this.required = false;
|
||||
}
|
||||
|
||||
public PamTableItem(String name, int sqlType, int length, boolean required) {
|
||||
super();
|
||||
this.name = name;
|
||||
@ -500,6 +550,20 @@ public class PamTableItem implements Cloneable {
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* @return the description
|
||||
*/
|
||||
public String getDescription() {
|
||||
return description;
|
||||
}
|
||||
|
||||
/**
|
||||
* @param description the description to set
|
||||
*/
|
||||
public void setDescription(String description) {
|
||||
this.description = description;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
@ -2183,5 +2183,12 @@ public abstract class SQLLogging {
|
||||
return subDetection.getSuperDetection(superDataBlock);
|
||||
}
|
||||
|
||||
/**
|
||||
* @return the loggingAddOns
|
||||
*/
|
||||
public ArrayList<SQLLoggingAddon> getLoggingAddOns() {
|
||||
return loggingAddOns;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
@ -1,2 +1,2 @@
|
||||
JavaSearch 1.0
|
||||
TMAP bs=2048 rt=1 fl=-1 id1=6679 id2=1
|
||||
TMAP bs=2048 rt=1 fl=-1 id1=6700 id2=1
|
||||
|
||||
Binary file not shown.
@ -574,6 +574,8 @@
|
||||
|
||||
<mapID target="utilities.SIDEModule.docs.SIDE_Overview_seq" url="utilities/SIDEModule/docs/SIDE_Overview.html#seq"/>
|
||||
|
||||
<mapID target="detectors.clickDetectorHelp.docs.SoundTrapClickDetector" url="detectors/clickDetectorHelp/docs/SoundTrapClickDetector.html"/>
|
||||
|
||||
<mapID target="utilities.spectrogramannotations.docs.using" url="utilities/spectrogramannotations/docs/using.html"/>
|
||||
|
||||
<mapID target="visual_methods.loggerFormsHelp.docs.NMEAINT" url="visual_methods/loggerFormsHelp/docs/NMEAINT.html"/>
|
||||
@ -802,6 +804,8 @@
|
||||
|
||||
<mapID target="visual_methods.loggerFormsHelp.docs.NMEACHAR" url="visual_methods/loggerFormsHelp/docs/NMEACHAR.html"/>
|
||||
|
||||
<mapID target="sound_processing.AcquisitionHelp.docs.sudfiles" url="sound_processing/AcquisitionHelp/docs/sudfiles.html"/>
|
||||
|
||||
<mapID target="sound_processing.LTSA.Docs.LTSADisplays" url="sound_processing/LTSA/Docs/LTSADisplays.html"/>
|
||||
|
||||
<mapID target="localisation.difar.difarLocalisation.docs.difar_PostProcessingTutorial__Toc396467156" url="localisation/difar/difarLocalisation/docs/difar_PostProcessingTutorial.html#_Toc396467156"/>
|
||||
|
||||
@ -1,7 +1,13 @@
|
||||
<?xml version="1.0" encoding="ISO-8859-1" standalone="no"?>
|
||||
<!--generated by JHelpDev Version: 0.63, 14 May 2008, see jhelpdev.sourceforge.net--><!DOCTYPE helpset PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp HelpSet Version 2.0//EN" "http://java.sun.com/products/javahelp/helpset_2_0.dtd">
|
||||
<helpset version="1.0">
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -20,7 +26,13 @@
|
||||
|
||||
|
||||
<title>Help </title>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -39,7 +51,13 @@
|
||||
|
||||
|
||||
<maps>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -60,7 +78,13 @@
|
||||
<homeID>
|
||||
top
|
||||
</homeID>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -79,7 +103,13 @@ top
|
||||
|
||||
|
||||
<mapref location="Map.jhm"/>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -98,7 +128,13 @@ top
|
||||
|
||||
|
||||
</maps>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -117,7 +153,13 @@ top
|
||||
|
||||
|
||||
<view mergetype="javax.help.UniteAppendMerge">
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -138,7 +180,13 @@ top
|
||||
<name>
|
||||
TOC
|
||||
</name>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -159,7 +207,13 @@ TOC
|
||||
<label>
|
||||
TOC
|
||||
</label>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -180,7 +234,13 @@ TOC
|
||||
<type>
|
||||
javax.help.TOCView
|
||||
</type>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -201,7 +261,13 @@ javax.help.TOCView
|
||||
<data>
|
||||
PAMGUARDTOC.xml
|
||||
</data>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -220,7 +286,13 @@ PAMGUARDTOC.xml
|
||||
|
||||
|
||||
</view>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -239,7 +311,13 @@ PAMGUARDTOC.xml
|
||||
|
||||
|
||||
<view>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -260,7 +338,13 @@ PAMGUARDTOC.xml
|
||||
<name>
|
||||
Index
|
||||
</name>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -281,7 +365,13 @@ Index
|
||||
<label>
|
||||
Index
|
||||
</label>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -302,7 +392,13 @@ Index
|
||||
<type>
|
||||
javax.help.IndexView
|
||||
</type>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -323,7 +419,13 @@ javax.help.IndexView
|
||||
<data>
|
||||
PAMGUARDIndex.xml
|
||||
</data>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -342,7 +444,13 @@ PAMGUARDIndex.xml
|
||||
|
||||
|
||||
</view>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -361,7 +469,13 @@ PAMGUARDIndex.xml
|
||||
|
||||
|
||||
<view>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -382,7 +496,13 @@ PAMGUARDIndex.xml
|
||||
<name>
|
||||
Search
|
||||
</name>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -403,7 +523,13 @@ Search
|
||||
<label>
|
||||
Search
|
||||
</label>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -424,7 +550,13 @@ Search
|
||||
<type>
|
||||
javax.help.SearchView
|
||||
</type>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -445,7 +577,13 @@ javax.help.SearchView
|
||||
<data engine="com.sun.java.help.search.DefaultSearchEngine">
|
||||
JavaHelpSearch
|
||||
</data>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -464,7 +602,13 @@ JavaHelpSearch
|
||||
|
||||
|
||||
</view>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -2,6 +2,18 @@
|
||||
<!DOCTYPE index PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp Index Version 1.0//EN" "http://java.sun.com/products/javahelp/index_2_0.dtd"><!--generated by JHelpDev Version: 0.63, 14 May 2008, see jhelpdev.sourceforge.net-->
|
||||
|
||||
<index version="1.0">
|
||||
<indexitem text="SUD Files " target="sound_processing.AcquisitionHelp.docs.sudfiles"/>
|
||||
|
||||
<indexitem text="SoundTrap " target="sound_processing.AcquisitionHelp.docs.sudfiles"/>
|
||||
|
||||
<indexitem text="Sound Trap " target="sound_processing.AcquisitionHelp.docs.sudfiles"/>
|
||||
|
||||
<indexitem text="Click Train " target="detectors.ClickTrainDetector.docs.ClickTrainDetector"/>
|
||||
|
||||
<indexitem text="SUD " target="detectors.clickDetectorHelp.docs.SoundTrapClickDetector"/>
|
||||
|
||||
<indexitem text="SoundTrap " target="detectors.clickDetectorHelp.docs.SoundTrapClickDetector"/>
|
||||
|
||||
<indexitem text="3D Localisation " target="detectors.Pam3DHelp.docs.guiOverview"/>
|
||||
|
||||
<indexitem text="Adding or Editing a Hydrophone " target="utilities.hydrophoneArrayManagerHelp.docs.Array_NewHydrophone"/>
|
||||
|
||||
@ -278,8 +278,10 @@
|
||||
|
||||
<tocitem text="Asio Sound Cards " target="sound_processing.AcquisitionHelp.docs.AcquisitionAsioSoundCard" image="topic"/>
|
||||
|
||||
<tocitem text="Audio Files " target="sound_processing.AcquisitionHelp.docs.AcquisitionFile" image="topic"/>
|
||||
<tocitem text="Audio Files " target="sound_processing.AcquisitionHelp.docs.AcquisitionFile" image="topic">
|
||||
<tocitem text="SUD Files " target="sound_processing.AcquisitionHelp.docs.sudfiles" image="topic"/>
|
||||
|
||||
</tocitem>
|
||||
<tocitem text="Audio File Folders " target="sound_processing.AcquisitionHelp.docs.AcquisitionFileFolder" image="topic"/>
|
||||
|
||||
<tocitem text="File Dates " target="sound_processing.AcquisitionHelp.docs.FileTimeZone" image="topic"/>
|
||||
@ -426,6 +428,8 @@
|
||||
<tocitem text="Create Binary Files Offline " target="utilities.BinaryStore.docs.CreateBinariesOffline" image="topic"/>
|
||||
|
||||
</tocitem>
|
||||
<tocitem text="SoundTrap Click Detector " target="detectors.clickDetectorHelp.docs.SoundTrapClickDetector" image="topic"/>
|
||||
|
||||
</tocitem>
|
||||
<tocitem text="Whistle and Moan Detector ">
|
||||
<tocitem text="Overview " target="detectors.whistleMoanHelp.docs.whistleMoan_Overview" image="topic"/>
|
||||
|
||||
@ -0,0 +1,82 @@
|
||||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
|
||||
<html><head>
|
||||
<link href="../../../pamHelpStylesheet.css" type="text/css" rel="STYLESHEET"><title>Click Classification</title></head>
|
||||
<body><h1>Click Detector</h1>
|
||||
<h2>SoundTrap Click Detector</h2>
|
||||
|
||||
|
||||
<p>If you are using a SountTrap recording device with built in click detection from
|
||||
<a href="https://www.oceaninstruments.co.nz/">Ocean Instruments</a>,
|
||||
you may need to use a modified version of the <a href="ClickDetector_clickDetector.html">Click Detector</a>.
|
||||
</p>
|
||||
<p>The SoundTrap click detector allows you to detect and store clicks at high frequencies (say 384kS/sec), suitable for odontocete echolocation clicks, and
|
||||
at the same time, record audio data files at a lower frequency (e.g. 96 or 48kS/sec). This optimises disk space usage and makes long deployments
|
||||
of several months possible without running out of data storage. </p>
|
||||
<p>Having two sample rates present within a single PAMGuard configuration is possible using
|
||||
<a href="../../../sound_processing/decimatorHelp/docs/decimator_decimator.html">Decimator</</a> modules. However such configurations become particularly
|
||||
complicated to configure when the sample rate of the recorded files is lower than the sample rate of the click detector.</p>
|
||||
<p>We therefore recommend that you use a modified version of the <a href="ClickDetector_clickDetector.html">Click Detector</a>, which manages it's own sample rate and
|
||||
channel information based on information extracted from the SoundTrap data.</p>
|
||||
<p>Note that the SoundTrap click detector should only be used for clicks automatically detected by the SoundTrap. If you want to detect clicks from the
|
||||
SoundTrap recordings, then use a normal <a href="ClickDetector_clickDetector.html">Click Detector</a> in the normal way.</p>
|
||||
|
||||
|
||||
<h3>Creating an instance of the SoundTrap Click Detector</h3>
|
||||
|
||||
<p>
|
||||
From the <strong><em>File>Add modules>Detectors</em></strong> menu, or
|
||||
from the pop-up menu on the data model display, select <i>'SoundTrap Click
|
||||
Detector'</i> near the bottom of the Detectors list. Enter a descriptive name for the new detector and press Ok.
|
||||
</p>
|
||||
|
||||
<h3>Importing SoundTrap Data</h3>
|
||||
<p>SoundTrap data are stored in proprietary files called <a href="../../../sound_processing/AcquisitionHelp/docs/sudfiles.html">SUD files</a>.</p>
|
||||
<p> There are two ways in which you can get data from <a href="../../../sound_processing/AcquisitionHelp/docs/sudfiles.html">SUD files</a> into
|
||||
the SoundTrap Click Detector. </p>
|
||||
|
||||
<h4>The Old Way</h4>
|
||||
<p>The 'standard' way of using SoundTrap data was to inflate all of the data from the compressed SUD files. For details of this process, see the
|
||||
SoundTrap user manuals and the SoundTrap Host software.</p>
|
||||
<p>Normally, several inflated files are generated from each sud file:</p>
|
||||
<ol>
|
||||
<li>A wav file: Audio data in standard wav file format</li>
|
||||
<li>An XML file: Metadata on the SoundTrap configuration, file start times in various formats, etc.</li>
|
||||
<li>If the click detector was running BCL and DWV files, which contain the times of clicks and click waveforms respectively.</li>
|
||||
</ol>
|
||||
<p>To convert the SUD files to the binary storage format used by PAMGuard, working in the
|
||||
<a href="../../../overview/PamMasterHelp/docs/viewerMode.html">PAMGuard Viewer</a>, create a Binary Store, a
|
||||
SoundTrap Click Detector and also create a 'SoundTrap Detector Import' module. Then use the import module to import the BCL and DWV
|
||||
data into PAMGuard. Once imported you can run <a href="ClickDetector_clickClassification.html">Click Classifiers</a>
|
||||
and use other Click Detector offline functions to mark events, etc. </p>
|
||||
<p>If you want to run additional analysis on the WAV file data (for example to
|
||||
<a href="../../../sound_processing/NoiseBands/Docs/NoiseBands.html">make noise measurements</a> or to
|
||||
<a href="../../whistleMoanHelp/docs/whistleMoan_Overview.html">detect whistles</a>),
|
||||
create a different PAMGuard configuration to process those data.<p>
|
||||
|
||||
<h4>The (better) New Way</h4>
|
||||
<p>Current versions of PAMGuard can read <a href="../../../sound_processing/AcquisitionHelp/docs/sudfiles.html">SUD files</a> directly,
|
||||
without first unpacking them into WAV, XML, BCL and DWV files. This not
|
||||
only reduces the amount of disk space you need by about x4, but also saves a lot of time.</p>
|
||||
<p>Better still, you can now set up PAMGuard in normal mode to simultaneously process the audio data in the
|
||||
<a href="../../../sound_processing/AcquisitionHelp/docs/sudfiles.html">SUD file</a> with one set of
|
||||
detectors, and simultaneously extract the click detector data into appropriate files for a SoundTrap Click Detector. </p>
|
||||
|
||||
<p>Start PAMGuard in <a href="../../../overview/PamMasterHelp/docs/normalMode.html">Normal Mode</a> and add a
|
||||
<a href="../../../sound_processing/AcquisitionHelp/docs/AcquisitionOverview.html">Sound Acquisition</a> module.
|
||||
Add a SoundTrap Click Detector, a <a href="../../../utilities/BinaryStore/docs/binarystore_overview.html">Binary Store</a> store and a
|
||||
<a href="../../../utilities/generalDatabaseHelp/docs/database_database.html">Database</a>
|
||||
module (optional). In the <a href="../../../sound_processing/AcquisitionHelp/docs/AcquisitionConfiguration.html">Sound Acquisition dialog</a>
|
||||
select a single SUD file or a folder of SUD files. At this point, the SoundTrap
|
||||
Click Detector will be automatically configured with the correct sample rate (which won't be the sample rate displayed in the Sound Acquisition
|
||||
module). </p>
|
||||
<p>Configure any <a href="ClickDetector_clickClassification.html">Click Classifiers</a> you want to be run on the SoundTrap click data as it is imported.</p>
|
||||
<p>You can then add any other detectors and measurement processes you want to run on the SoundTrap audio data, this may include
|
||||
instances of the normal Click Detector module if you want to detect clicks in the lower frequency audio data.</p>
|
||||
<p>Process the data in the normal way and clicks will automatically be generated within the SoundTrap click detector</p>
|
||||
<p>Further process you data using the <a href="../../../overview/PamMasterHelp/docs/viewerMode.html">PAMGuard Viewer</a> in the normal way.</p>
|
||||
|
||||
|
||||
<br>
|
||||
<br>
|
||||
<br>
|
||||
</body></html>
|
||||
@ -7,7 +7,9 @@
|
||||
|
||||
<h1>Audio Files</h1>
|
||||
<p>As well as analysing data from sound cards in real time, PAMGUARD can be used to analyse archived data
|
||||
from audio filed in WAV or AIF format.</p>
|
||||
from audio filed in <a href="https://en.wikipedia.org/wiki/WAV">WAV</a>,
|
||||
<a href="https://en.wikipedia.org/wiki/Audio_Interchange_File_Format">AIF</a>, <a href="https://en.wikipedia.org/wiki/FLAC">FLAC</a>,
|
||||
or <a href="sudfiles.html">SUD</a> file format.</p>
|
||||
|
||||
<br>
|
||||
<h2>Setting up an Audio File</h2>
|
||||
|
||||
32
src/help/sound_processing/AcquisitionHelp/docs/sudfiles.html
Normal file
32
src/help/sound_processing/AcquisitionHelp/docs/sudfiles.html
Normal file
@ -0,0 +1,32 @@
|
||||
<html>
|
||||
<head>
|
||||
<LINK href="../../../pamHelpStylesheet.css" type=text/css rel=STYLESHEET>
|
||||
<title>SUD Files</title>
|
||||
</head>
|
||||
<body>
|
||||
<h1>SoundTrap data files</h1>
|
||||
<h3>SUD Files</h3>
|
||||
<p>
|
||||
SoundTrap recorders from
|
||||
<a href="https://www.oceaninstruments.co.nz/">Ocean Instruments</a>
|
||||
store data in proprietary files called SUD files. See SoundTrap documentation for information on how to
|
||||
extract SUD files from SoundTrap recorders. </p>
|
||||
|
||||
<p>Earlier versions of PAMGuard required you to 'inflate' the SUD files into standard wav audio files using
|
||||
the <a href="https://www.oceaninstruments.co.nz/downloads/">SoundTrap Host software</a> before they could be processed.</p>
|
||||
<p>The current version of PAMGuard no longer requires this since it can read data directly from the SUD files.</p>
|
||||
<p>Inflating SUD files to WAV files generally required between 3 and 5 times as much disk space and could also take
|
||||
a fair amount of time, so not inflating will save both!</p>
|
||||
|
||||
<h3>Mixing SUD and WAV files</h3>
|
||||
<p>If a SUD file and a WAV file with the same name are in the same folder, then PAMGuard will ignore the SUD file
|
||||
and process the WAV file. Note that in this case, PAMGuard will be unable to extract any metadata from the SUD file
|
||||
and will not extract SoundTrap Click Detections (see below).</p>
|
||||
|
||||
<h3>SoundTrap Click Detector</h3>
|
||||
<p>If you are using the SoundTrap build in click detector (see SoundTrap manuals) then the SUD files will also contain
|
||||
detected clicks.</p> <p>See the help page for the <a href="../../../detectors/clickDetectorHelp/docs/SoundTrapClickDetector.html">SoundTrap Click Detector</a>
|
||||
for information on how to get these clicks from the SUD files into PAMGuard. </p>
|
||||
<br><br><br>
|
||||
</body>
|
||||
</html>
|
||||
@ -144,4 +144,9 @@ public class BuoyStatusData implements Serializable, ManagedParameters {
|
||||
return ps;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
return String.format("Buoy %d(%d) ip %s", buoyId1, buoyId2, ipAddr);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@ -387,6 +387,11 @@ public class BuoyStatusDataUnit extends PamDataUnit {
|
||||
return buoyStatusData;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
return String.format("Status %s\n", buoyStatusData.toString());
|
||||
}
|
||||
|
||||
// /**
|
||||
// * @return the genericStringPairsChanged
|
||||
// */
|
||||
|
||||
@ -770,7 +770,7 @@ public class NetworkReceiver extends PamControlledUnit implements PamSettings, N
|
||||
}
|
||||
|
||||
private NetworkObject interpretPamCommand(NetworkObject receivedData, BuoyStatusDataUnit buoyStatusDataUnit) {
|
||||
// System.out.println("Network command received: " + getPamCommandString(dataId2));
|
||||
// System.out.println("Network command received: " + getPamCommandString(dataId2));
|
||||
buoyStatusDataUnit.setCommandStatus(receivedData.getDataType2());
|
||||
long time = PamCalendar.getTimeInMillis();
|
||||
if (receivedData.getData() != null && receivedData.getDataLength() >= 8) {
|
||||
|
||||
@ -25,13 +25,20 @@
|
||||
package soundtrap;
|
||||
|
||||
import java.awt.Frame;
|
||||
import java.util.ArrayList;
|
||||
|
||||
import javax.swing.JMenu;
|
||||
import javax.swing.JMenuItem;
|
||||
|
||||
import Acquisition.AcquisitionControl;
|
||||
import Acquisition.sud.SUDNotificationManager;
|
||||
import PamController.PamController;
|
||||
import PamguardMVC.PamRawDataBlock;
|
||||
import clickDetector.ClickBTDisplay;
|
||||
import clickDetector.ClickControl;
|
||||
import clickDetector.ClickDisplay;
|
||||
import clickDetector.ClickDisplayManager;
|
||||
import soundtrap.sud.SudFileDWVHandler;
|
||||
|
||||
/**
|
||||
* @author mo55
|
||||
@ -45,6 +52,9 @@ public class STClickControl extends ClickControl {
|
||||
* The private sound acquisition module linked to the Soundtrap click data
|
||||
*/
|
||||
private AcquisitionControl rawSource;
|
||||
|
||||
private SudFileDWVHandler sudFileDWVHandler;
|
||||
|
||||
|
||||
/**
|
||||
* @param name
|
||||
@ -54,6 +64,9 @@ public class STClickControl extends ClickControl {
|
||||
|
||||
// create a private acquisition control that only this module can see
|
||||
rawSource = new AcquisitionControl("Private Sound Acq for Soundtrap Click Detector");
|
||||
|
||||
sudFileDWVHandler = new SudFileDWVHandler(this);
|
||||
sudFileDWVHandler.subscribeSUD();
|
||||
}
|
||||
|
||||
@Override
|
||||
@ -106,6 +119,40 @@ public class STClickControl extends ClickControl {
|
||||
|
||||
return newMenu;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void pamStart() {
|
||||
sudFileDWVHandler.pamStart();
|
||||
super.pamStart();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void pamStop() {
|
||||
sudFileDWVHandler.pamStop();
|
||||
super.pamStop();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void notifyModelChanged(int changeType) {
|
||||
super.notifyModelChanged(changeType);
|
||||
if (changeType == PamController.INITIALIZATION_COMPLETE) {
|
||||
sudFileDWVHandler.subscribeSUD();
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Called when running SUD file data to find and scroll the BT Display's
|
||||
* @param timeMillis
|
||||
*/
|
||||
public void updateDisplayScrollers(long timeMillis) {
|
||||
ClickDisplayManager dispManager = getDisplayManager();
|
||||
ArrayList<ClickDisplay> dispList = dispManager.getWindowList();
|
||||
for (ClickDisplay display : dispList) {
|
||||
if (display instanceof ClickBTDisplay) {
|
||||
((ClickBTDisplay) display).newScrollTimingData(timeMillis);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
59
src/soundtrap/sud/BCLDetectionChunk.java
Normal file
59
src/soundtrap/sud/BCLDetectionChunk.java
Normal file
@ -0,0 +1,59 @@
|
||||
package soundtrap.sud;
|
||||
|
||||
import org.pamguard.x3.sud.Chunk;
|
||||
|
||||
public class BCLDetectionChunk {
|
||||
|
||||
private long javaMillis;
|
||||
private boolean isDetection;
|
||||
private String bclRecord;
|
||||
private Chunk sudChunk;
|
||||
private long javaMicros;
|
||||
|
||||
public BCLDetectionChunk(long javaMillis, long javaMicros, boolean isDetection, String bclRecord, Chunk sudChunk) {
|
||||
super();
|
||||
this.javaMillis = javaMillis;
|
||||
this.javaMicros = javaMicros;
|
||||
this.isDetection = isDetection;
|
||||
this.bclRecord = bclRecord;
|
||||
this.sudChunk = sudChunk;
|
||||
}
|
||||
|
||||
/**
|
||||
* @return the javaMillis
|
||||
*/
|
||||
public long getJavaMillis() {
|
||||
return javaMillis;
|
||||
}
|
||||
|
||||
/**
|
||||
* @return the isDetection
|
||||
*/
|
||||
public boolean isDetection() {
|
||||
return isDetection;
|
||||
}
|
||||
|
||||
/**
|
||||
* @return the bclRecord
|
||||
*/
|
||||
public String getBclRecord() {
|
||||
return bclRecord;
|
||||
}
|
||||
|
||||
/**
|
||||
* @return the sudChunk
|
||||
*/
|
||||
public Chunk getSudChunk() {
|
||||
return sudChunk;
|
||||
}
|
||||
|
||||
/**
|
||||
* @return the javaMicros
|
||||
*/
|
||||
public long getJavaMicros() {
|
||||
return javaMicros;
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
265
src/soundtrap/sud/SudFileDWVHandler.java
Normal file
265
src/soundtrap/sud/SudFileDWVHandler.java
Normal file
@ -0,0 +1,265 @@
|
||||
package soundtrap.sud;
|
||||
|
||||
import java.io.ByteArrayInputStream;
|
||||
import java.io.DataInputStream;
|
||||
import java.io.IOException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.LinkedList;
|
||||
import java.util.List;
|
||||
|
||||
import org.pamguard.x3.sud.Chunk;
|
||||
import org.pamguard.x3.sud.SudAudioInputStream;
|
||||
import org.pamguard.x3.sud.SudDataInputStream;
|
||||
|
||||
import Acquisition.AcquisitionControl;
|
||||
import Acquisition.sud.SUDNotificationHandler;
|
||||
import Acquisition.sud.SUDNotificationManager;
|
||||
import PamController.PamController;
|
||||
import PamUtils.PamCalendar;
|
||||
import clickDetector.ClickDetection;
|
||||
import clickDetector.ClickDetector;
|
||||
import clickDetector.ClickDetector.ChannelGroupDetector;
|
||||
import soundtrap.STClickControl;
|
||||
import wavFiles.ByteConverter;
|
||||
|
||||
/**
|
||||
* Class to handle BCL and DWV data from a SUD file during sud file processing.
|
||||
* SUD files are the compressed data files from soundtraps. The latest PAMGuard
|
||||
* version contains a audioinputstream for SUD files, making it possible to
|
||||
* process them withoug having to first inflate them to wav files. During
|
||||
* 'normal mode' processing, this class will subscribe to packets from the SUD
|
||||
* files, unpack what would normally be BCL and DWV data and generate
|
||||
* appropriate binary output files.
|
||||
*
|
||||
* @author dg50
|
||||
*
|
||||
*/
|
||||
public class SudFileDWVHandler implements SUDNotificationHandler {
|
||||
|
||||
private STClickControl stClickControl;
|
||||
private SudAudioInputStream sudAudioInputStream;
|
||||
|
||||
private int txtCount = 0;
|
||||
|
||||
private List<Chunk> clickChunks = new LinkedList();
|
||||
|
||||
private List<BCLDetectionChunk> bclChunks = new LinkedList();
|
||||
|
||||
int bclDetCount, bclNoiseCount, dwvCount, processedChunks;
|
||||
private long effortStart, fileStartMicros;
|
||||
private double sampleRate;
|
||||
private ByteConverter byteConverter;
|
||||
private ClickDetector clickDetector;
|
||||
private ChannelGroupDetector channelGroupDetector;
|
||||
|
||||
public SudFileDWVHandler(STClickControl stClickControl) {
|
||||
this.stClickControl = stClickControl;
|
||||
clickDetector = stClickControl.getClickDetector();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void newSudInputStream(SudAudioInputStream sudAudioInputStream) {
|
||||
this.sudAudioInputStream = sudAudioInputStream;
|
||||
interpretNewFile(null, sudAudioInputStream);
|
||||
bclDetCount = bclNoiseCount = dwvCount = processedChunks = 0;
|
||||
bclChunks.clear();
|
||||
clickChunks.clear();
|
||||
byteConverter = ByteConverter.createByteConverter(sudAudioInputStream.getFormat());
|
||||
}
|
||||
|
||||
@Override
|
||||
public void interpretNewFile(String newFile, SudAudioInputStream sudAudioInputStream) {
|
||||
// this is the wav sample rate, not the detector sample rate, so don't use it
|
||||
// sampleRate = sudAudioInputStream.getFormat().getFrameRate();
|
||||
// this is the right one
|
||||
sampleRate = sudAudioInputStream.getSudMap().clickDetSampleRate;
|
||||
fileStartMicros = sudAudioInputStream.getSudMap().getFirstChunkTimeMicros();
|
||||
stClickControl.findRawDataBlock().setChannelMap(1);
|
||||
stClickControl.findRawDataBlock().setSampleRate((float) sampleRate, true);
|
||||
stClickControl.getSTAcquisition().acquisitionParameters.sampleRate = (float) sampleRate;
|
||||
// System.out.printf("Open input stream fs = %3.1f\n", sampleRate);
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void sudStreamClosed() {
|
||||
System.out.printf("SUD input stream closed, %d DWV, %d bcl Detectins and %d BCL Noise, %d chunks processed\n",
|
||||
dwvCount, bclDetCount, bclNoiseCount, processedChunks);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void progress(double arg0, int arg1, int arg2) {
|
||||
// TODO Auto-generated method stub
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void chunkProcessed(int chunkID, Chunk sudChunk) {
|
||||
if (sudAudioInputStream == null) {
|
||||
return;
|
||||
}
|
||||
String chunkName = "Unknown";
|
||||
int chunkSize = sudChunk.buffer.length;
|
||||
if (sudAudioInputStream.getChunkIDString(chunkID).equals("wav")) {
|
||||
|
||||
long millis = sudChunk.getChunkHeader().getMillisTime();
|
||||
stClickControl.updateDisplayScrollers(millis);
|
||||
|
||||
if (sudAudioInputStream.isChunkIDWav(chunkID)) {
|
||||
// chunkName = "RECORDINGS";
|
||||
// System.out.printf("Chunk ID %d, size %d, type %s\n", chunkID, chunkSize,
|
||||
// chunkName);
|
||||
// System.out.println("ID: " + chunkID + " This is raw data from detected
|
||||
// CLICKS: " + sudAudioInputStream.getChunkIDString(chunkID));
|
||||
} else {
|
||||
chunkName = "CLICKS";
|
||||
processClickChunk(chunkID, sudChunk);
|
||||
}
|
||||
}
|
||||
|
||||
if (sudAudioInputStream.getChunkIDString(chunkID).equals("csv")) {
|
||||
// System.out.println("CSV data the bytes convert directly to comma delimted data");
|
||||
}
|
||||
if (sudAudioInputStream.getChunkIDString(chunkID).equals("txt")) {
|
||||
processTextChunk(chunkID, sudChunk);
|
||||
txtCount++;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Pairwise byte swap, i.e. change endianness of int16's. Won't work for
|
||||
* anything else.
|
||||
*
|
||||
* @param data
|
||||
*/
|
||||
public void swapEndian(byte[] data) {
|
||||
for (int i = 0; i < data.length; i += 2) {
|
||||
byte b = data[i];
|
||||
data[i] = data[i + 1];
|
||||
data[i + 1] = b;
|
||||
}
|
||||
}
|
||||
|
||||
private void processTextChunk(int chunkID, Chunk sudChunk) {
|
||||
SudDataInputStream dis = new SudDataInputStream(new ByteArrayInputStream(sudChunk.getBuffer()));
|
||||
|
||||
try {
|
||||
while (dis.available() > 0) {
|
||||
long rtime = (dis.readInt()) & 0xffffffffL;
|
||||
long mticks = (dis.readInt()) & 0xffffffffL;
|
||||
int n = dis.readUnsignedShort();
|
||||
|
||||
long javaMillis = (long) rtime * 1000 + mticks / 1000;
|
||||
long javaMicros = (long) rtime * 1000000 + mticks;
|
||||
|
||||
byte[] b = new byte[(n % 2 == 1) ? n + 1 : n];
|
||||
dis.read(b);
|
||||
|
||||
swapEndian(b);
|
||||
|
||||
String s = new String(b, "UTF-8");
|
||||
String[] bits = s.split(",");
|
||||
if (bits[0].equals("E")) {
|
||||
// start or end record.
|
||||
boolean isStart = bits[1].equals("1");
|
||||
if (isStart) {
|
||||
effortStart = javaMicros;
|
||||
}
|
||||
dwvEffort(javaMillis, isStart);
|
||||
} else if (bits[0].equals("D")) {
|
||||
boolean isDet = bits[1].equals("1");
|
||||
if (isDet) {
|
||||
bclDetCount++;
|
||||
String bclText = String.format("%9d,%6d,%s has %d bits", rtime, mticks, s, bits.length);
|
||||
BCLDetectionChunk bclChunk = new BCLDetectionChunk(javaMillis, javaMicros, isDet, bclText,
|
||||
sudChunk);
|
||||
bclChunks.add(bclChunk);
|
||||
} else {
|
||||
bclNoiseCount++;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
} catch (IOException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
convertChunks();
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Convert bcl and dwv data to click detections.
|
||||
*/
|
||||
private void convertChunks() {
|
||||
int nProc = 0;
|
||||
while (bclChunks.size() > 0 && clickChunks.size() > 0) {
|
||||
BCLDetectionChunk bclChunk = bclChunks.remove(0);
|
||||
Chunk dwvChunk = clickChunks.remove(0);
|
||||
makeClick(bclChunk, dwvChunk);
|
||||
nProc++;
|
||||
processedChunks++;
|
||||
}
|
||||
}
|
||||
|
||||
private void makeClick(BCLDetectionChunk bclChunk, Chunk dwvChunk) {
|
||||
long elapsedSamples = (long) ((bclChunk.getJavaMicros() - fileStartMicros) * (sampleRate / 1e6));
|
||||
long millis = bclChunk.getJavaMillis();
|
||||
byte[] rawData = dwvChunk.getBuffer();
|
||||
int nBytes = rawData.length;
|
||||
int nSamples = nBytes / Short.BYTES;
|
||||
double[][] wavData = new double[1][nSamples];
|
||||
byteConverter.bytesToDouble(rawData, wavData, nBytes);
|
||||
|
||||
// channelGroupDetector = clickDetector.getChannelGroupDetector(0);
|
||||
ClickDetection click = new ClickDetection(1, elapsedSamples, nSamples, clickDetector, channelGroupDetector, 1);
|
||||
click.setTimeMilliseconds(millis);
|
||||
click.setWaveData(wavData);
|
||||
|
||||
// if (groupDetector != null) {
|
||||
// groupDetector.
|
||||
// }
|
||||
if (clickDetector.completeClick(click)) {
|
||||
clickDetector.getClickDataBlock().addPamData(click);
|
||||
}
|
||||
}
|
||||
|
||||
private void dwvEffort(long javaMillis, boolean isStart) {
|
||||
System.out.printf("DWV Effort %s at %s\n", isStart ? "Start" : "End", PamCalendar.formatDBDateTime(javaMillis));
|
||||
}
|
||||
|
||||
private void processClickChunk(int chunkID, Chunk sudChunk) {
|
||||
clickChunks.add(sudChunk);
|
||||
dwvCount++;
|
||||
}
|
||||
|
||||
public void pamStart() {
|
||||
subscribeSUD();
|
||||
}
|
||||
|
||||
public void pamStop() {
|
||||
// TODO Auto-generated method stub
|
||||
|
||||
}
|
||||
|
||||
public boolean subscribeSUD() {
|
||||
if (stClickControl.isViewer()) {
|
||||
return false;
|
||||
}
|
||||
AcquisitionControl daq = (AcquisitionControl) PamController.getInstance()
|
||||
.findControlledUnit(AcquisitionControl.unitType);
|
||||
if (daq == null) {
|
||||
return false;
|
||||
}
|
||||
SUDNotificationManager sudManager = daq.getSUDNotificationManager();
|
||||
if (sudManager == null) {
|
||||
return false;
|
||||
}
|
||||
sudManager.addNotificationHandler(this);
|
||||
return true;
|
||||
}
|
||||
|
||||
}
|
||||
@ -183,11 +183,6 @@ public class WhistleMoanControl extends PamControlledUnit implements PamSettings
|
||||
return true;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getModuleSummary() {
|
||||
return whistleToneProcess.getModuleSummary();
|
||||
}
|
||||
|
||||
@Override
|
||||
public Object getShortUnitType() {
|
||||
return "WMD";
|
||||
@ -225,4 +220,9 @@ public class WhistleMoanControl extends PamControlledUnit implements PamSettings
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getModuleSummary(boolean clear) {
|
||||
return whistleToneProcess.getModuleSummary(clear);
|
||||
}
|
||||
}
|
||||
|
||||
@ -968,17 +968,6 @@ public class WhistleToneConnectProcess extends PamProcess {
|
||||
}
|
||||
|
||||
|
||||
public String getModuleSummary() {
|
||||
String sumText = String.format("%d", NSUMMARYPOINTS);
|
||||
for (int i = 0; i < NSUMMARYPOINTS; i++) {
|
||||
sumText += String.format(",%d",whistleSummaryCount[i]);
|
||||
}
|
||||
|
||||
clearSummaryData();
|
||||
return sumText;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* When delay data are written to binary files, int16's are used, but these
|
||||
* must be scaled up to allow for sub-sample timing. How much they can be
|
||||
@ -1099,4 +1088,20 @@ public class WhistleToneConnectProcess extends PamProcess {
|
||||
return fftUnitsOut;
|
||||
}
|
||||
|
||||
/*
|
||||
* replicate Decimus function to give counts of whistles in four evenly spaced frequency
|
||||
* bins.
|
||||
*/
|
||||
public String getModuleSummary(boolean clear) {
|
||||
String sumText = String.format("%d", NSUMMARYPOINTS);
|
||||
for (int i = 0; i < NSUMMARYPOINTS; i++) {
|
||||
sumText += String.format(",%d",whistleSummaryCount[i]);
|
||||
}
|
||||
|
||||
if (clear) {
|
||||
clearSummaryData();
|
||||
}
|
||||
return sumText;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user