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 2022-11-13 17:37:53 +00:00
parent d1af000040
commit d3277be3b1
17 changed files with 327 additions and 250 deletions

View File

@ -15,12 +15,12 @@
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@ -368,8 +368,8 @@ should be something like:</p>
-Xms384m -Xmx4096m -Djava.library.path=lib64 -jar Pamguard_xxxxxx.jar</span></em></p>
<p class=MsoNormal>The -Xms384m -Xmx4096m specify the initial and maximum heap
size for the JVM being used to run Pamguard i.e. how much memory it gets to use.
The default max size usually being too low.</p>
size for the JVM being used to run Pamguard i.e. how much memory it gets to
use. The default max size usually being too low.</p>
<p class=MsoNormal>The -Djava.library.path=lib64 tells the JVM that it should
look in the folder called &quot;lib64&quot; for the required shared libraries (change
@ -381,8 +381,8 @@ a &quot;-m&quot; or &quot;-v&quot; to the list of java arguments. On Windows
just run the appropriately named executable (e.g. PamguardBeta_MixedMode.exe or
PamguardBeta_ViewerMode.exe):</p>
<p class=MsoNormal><em><span style='font-family:"Calibri",sans-serif'>java
-Xms384m -Xmx4096m -Djava.library.path=lib64 -jar PamguardBeta_xxxxxx.jar -v</span></em></p>
<p class=MsoNormal><em><span style='font-family:"Calibri",sans-serif'>java -Xms384m
-Xmx4096m -Djava.library.path=lib64 -jar PamguardBeta_xxxxxx.jar -v</span></em></p>
<p class=MsoNormal><em><span style='font-family:"Calibri",sans-serif'>&nbsp;</span></em></p>
@ -444,7 +444,26 @@ Version 2.00.10 June 2017</a></span></h1>
<h1><span style='font-size:12.0pt'><a href="#_Older_Versions">Older Versions</a></span></h1>
<h1><a name="_Latest_Version_2.02.03_1"></a><a name="_Latest_Version_2.02.05"></a><span
lang=EN-US>Latest Version 2.02.05 October 2022</span></h1>
lang=EN-US>Latest Version 2.02.06 November 2022</span></h1>
<h2><span lang=EN-US>Bug Fix</span></h2>
<p class=MsoNormal><span lang=EN-US>A memory leak has been found which seems to
mostly occur in Viewer mode. Some data on background noise measurements are not
being cleared from memory, so memory will eventually run out. This could happen
after browsing a lot of data, but was most likely when reprocessing files
offline, for example running click classifiers. This is now fixed. </span></p>
<h2><span lang=EN-US>New Features</span></h2>
<p class=MsoNormal><span lang=EN-US>SoundTrap SUD file reading. If youre using
SoundTrap autonomous recorders from Ocean Instruments, you no longer need to decompress
the SoundTrap files prior to processing. This will save time and a lot of disk
space. Extraction of clicks from the inbuilt SoundTrap Click detector an also
happen while processing SUD file data with other detectors, thereby
streamlining the whole processing chain. Read the online Help for details.   </span></p>
<h1><span lang=EN-US>Latest Version 2.02.05 October 2022</span></h1>
<h2><span lang=EN-US>Click Train Detector Features and Bug Fixes</span></h2>
@ -452,8 +471,9 @@ lang=EN-US>Latest Version 2.02.05 October 2022</span></h1>
<p class=MsoNormal><span lang=EN-US>Changes to GUI to make dialog shorter for
low DPI screens. </span></p>
<p class=MsoNormal><span lang=EN-US>Complete rewrite of the classification
system to have nested classifiers which can be enabled or disabled. </span></p>
<p class=MsoNormal><span lang=EN-US>Complete rewrite of the classification system
to have nested classifiers which can be enabled or disabled. </span></p>
<p class=MsoNormal><span lang=EN-US>Changes to classification GUI to
accommodate the new classification system.</span></p>
@ -498,9 +518,9 @@ audio files. </span></p>
<h2><span lang=EN-US>Bug Fixes</span></h2>
<p class=MsoNormal><span lang=EN-US>Soundtrap DWV import. Will now generate binary
files even if DWV file doesn’t exist (which is correct behavior in quiet
conditions when no clicks were detected). </span></p>
<p class=MsoNormal><span lang=EN-US>Soundtrap DWV import. Will now generate
binary files even if DWV file doesnÂt exist (which is correct behavior in
quiet conditions when no clicks were detected). </span></p>
<p class=MsoNormal><span lang=EN-US>Spectrogram. Changes to stop occasional
crashing when restarting processing of wav files. </span></p>
@ -534,8 +554,8 @@ running in real time. Added template names based on file names. </p>
<p class=MsoNormal>#13 Merging files when offline processing file folders: Had
an error introduced in last release which caused it to fail to recognise gaps
between files, meaning that some output data (i.e. after a gap) would have an
incorrect time stamp. This did not affect data if the ‘merge contiguous files’
option was not selected. </p>
incorrect time stamp. This did not affect data if the ÃÂmerge contiguous
filesÃÂ option was not selected. </p>
<p class=MsoNormal>#14 Logger forms data were not plotting correctly. This was
due to the required data selection functions not being fully implemented. This
@ -574,23 +594,23 @@ understand the notes listed for <a href="#_Latest_Beta_Version_2.00.10">Beta
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 16
(OpenJDK release), so you will not need to install a java runtime engine
separately. 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>This version of PAMGuard has been bundled with Java 16 (OpenJDK
release), so you will not need to install a java runtime engine separately.
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 style='margin-bottom:0cm'><span style='font-size:12.0pt;
font-family:"Times New Roman",serif'>&nbsp;</span></p>
<h2>File Format Change</h2>
<p class=MsoNormal>Changes have been made to the binary file format to support
the output of additional noise outputs for certain detectors (See below).
Binary files created with this version will not be compatible with earlier
versions 2.01.### and below. This version will read and may convert earlier
format binary files.</p>
<p class=MsoNormal>Changes have been made to the binary file format to support the
output of additional noise outputs for certain detectors (See below). Binary
files created with this version will not be compatible with earlier versions
2.01.### and below. This version will read and may convert earlier format
binary files.</p>
<p class=MsoNormal style='margin-bottom:0cm'><span style='font-size:12.0pt;
font-family:"Times New Roman",serif'>&nbsp;</span></p>
@ -608,10 +628,10 @@ href="http://www.pamguard.org/downloads.php?cat_id=3">here</a>.</p>
<p class=MsoNormal><b><span lang=EN-US>Detection Group Localiser</span></b><span
lang=EN-US> </span></p>
<p class=MsoNormal>This module has been renamed “Detection Grouper”, so as to
avoid confusion with the Group 3D localizer. This is because the Detection
Grouper is more for organizing data into groups to be localized than it is for
doing localization.</p>
<p class=MsoNormal>This module has been renamed ÓDetection GrouperÔ, so
as to avoid confusion with the Group 3D localizer. This is because the
Detection Grouper is more for organizing data into groups to be localized than
it is for doing localization.</p>
<p class=MsoNormal><b><span lang=EN-US>Minor Bug Fixes</span></b><span
lang=EN-US> </span></p>
@ -729,10 +749,10 @@ included in a future release. </p>
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>17. </span><span
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
An implementation of the Generalized Power Law Detector, developed by Tyler
Helble ([Helble et al., ‘A generalized power-law detection algorithm for humpback
whale vocalizations’, The Journal of the Acoustical Society of America, vol.
131, no. 4, pp. 2682–2699, 2012) is now available. For details, see the online
help </p>
Helble ([Helble et al., ÃÂA generalized power-law detection algorithm for
humpback whale vocalizationsÃÂ, The Journal of the Acoustical Society of
America, vol. 131, no. 4, pp. 2682ÃÂ2699, 2012) is now available. For
details, see the online help </p>
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>18. </span><span
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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>
@ -840,8 +860,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
Added logger form annotation to Spectrogram Annotation module. </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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
Better auto-scaling in Ishmael Detector graphics window. </p>
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
lang=EN-US> </span>Better auto-scaling in Ishmael Detector graphics window. </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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
@ -968,8 +988,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
<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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
Add functionality for bluetooth headsets. </p>
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
lang=EN-US> </span>Add functionality for bluetooth headsets. </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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@ -1093,9 +1113,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
Bug 441. Plot coordinate calculations incorrect in PamAxis.</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
Bug 442. BT Display does not change click symbol color when Colour By
Superdetection is selected.</p>
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
lang=EN-US> </span>Bug 442. BT Display does not change click symbol color when
Colour By Superdetection is selected.</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
@ -1108,8 +1128,8 @@ files.</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
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
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
@ -1182,9 +1202,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nb
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
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
Bug 430. Rocca calculates inflection point parameters incorrectly</p>
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
New display for Gebco Netcdf bathymetry maps.</p>
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -1346,9 +1367,9 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@ -1475,14 +1496,14 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -1632,11 +1654,11 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
@ -1704,8 +1726,8 @@ lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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 UID’s will be used in
both data stores. </span></p>
in both the binary files and in database tables, the same UIDÃÂs 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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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.
&nbsp;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"
&nbsp;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>. &nbsp;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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -2244,19 +2267,19 @@ November 2016</span></h1>
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>1.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Bug 303. Some ASIO sound cards not working with either ASIO system in PAMGuard.
For the PAMGuard ASIO system, this was due to a data format used by some sound
cards never being properly implemented. For the “New ASIO system” which is
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 ÓNew ASIO systemÔ 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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -2475,8 +2498,9 @@ today.&nbsp; </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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -2494,8 +2518,8 @@ style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>Bug 262. Access to SQLite database conversion. This would fail when tables
were present which were not created by PAMGuard. &nbsp;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. &nbsp;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>&nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -3049,12 +3073,11 @@ sonobuoys. See online help for details.&nbsp; </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. &nbsp;</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. &nbsp;</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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).&nbsp; </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).&nbsp; </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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -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.&nbsp; </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&nbsp; 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&nbsp; 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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@ -3932,15 +3955,15 @@ classifier is still available). </p>
Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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.&nbsp; </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.&nbsp; </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.&nbsp; </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.&nbsp; </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.&nbsp; </p>
<p class=MsoNormal><b>Bug fixes</b></p>
<p class=MsoNormal>Speed up of graphics, particularly regarding large quantities
of gps track &nbsp;data</p>
<p class=MsoNormal>Speed up of graphics, particularly regarding large
quantities of gps track &nbsp;data</p>
<p class=MsoNormal>National Instruments cards with names &gt; 20 characters
long are now correctly &nbsp;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>

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@ -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>

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@ -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>=

Binary file not shown.

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@ -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>

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@ -587,7 +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 {

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@ -40,7 +40,7 @@ public class SoundFileTypes {
}
/**
* Get a list of used file types. Reaslistically this
* 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

Binary file not shown.

Binary file not shown.

Binary file not shown.

Binary file not shown.

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@ -1,2 +1,2 @@
JavaSearch 1.0
TMAP bs=2048 rt=1 fl=-1 id1=6697 id2=1
TMAP bs=2048 rt=1 fl=-1 id1=6700 id2=1

Binary file not shown.

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@ -1,7 +1,8 @@
<?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">
@ -25,7 +26,8 @@
<title>Help </title>
@ -49,7 +51,8 @@
<maps>
@ -75,7 +78,8 @@
<homeID>
top
</homeID>
@ -99,7 +103,8 @@ top
<mapref location="Map.jhm"/>
@ -123,7 +128,8 @@ top
</maps>
@ -147,7 +153,8 @@ top
<view mergetype="javax.help.UniteAppendMerge">
@ -173,7 +180,8 @@ top
<name>
TOC
</name>
@ -199,7 +207,8 @@ TOC
<label>
TOC
</label>
@ -225,7 +234,8 @@ TOC
<type>
javax.help.TOCView
</type>
@ -251,7 +261,8 @@ javax.help.TOCView
<data>
PAMGUARDTOC.xml
</data>
@ -275,7 +286,8 @@ PAMGUARDTOC.xml
</view>
@ -299,7 +311,8 @@ PAMGUARDTOC.xml
<view>
@ -325,7 +338,8 @@ PAMGUARDTOC.xml
<name>
Index
</name>
@ -351,7 +365,8 @@ Index
<label>
Index
</label>
@ -377,7 +392,8 @@ Index
<type>
javax.help.IndexView
</type>
@ -403,7 +419,8 @@ javax.help.IndexView
<data>
PAMGUARDIndex.xml
</data>
@ -427,7 +444,8 @@ PAMGUARDIndex.xml
</view>
@ -451,7 +469,8 @@ PAMGUARDIndex.xml
<view>
@ -477,7 +496,8 @@ PAMGUARDIndex.xml
<name>
Search
</name>
@ -503,7 +523,8 @@ Search
<label>
Search
</label>
@ -529,7 +550,8 @@ Search
<type>
javax.help.SearchView
</type>
@ -555,7 +577,8 @@ javax.help.SearchView
<data engine="com.sun.java.help.search.DefaultSearchEngine">
JavaHelpSearch
</data>
@ -579,7 +602,8 @@ JavaHelpSearch
</view>

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@ -2,6 +2,16 @@
<!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"/>

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@ -1,23 +1,21 @@
<!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>
SoundTrap Click Detector
</h1><h2>SoundTrap Click Detector</h2>
<br>
<body><h1>Click Detector</h1>
<h2>SoundTrap Click Detector</h2>
<h3>Overview</h3>
<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 384kHz), suitable for odontocete echolocation clicks, and
at the same time, record audio data files at a lower frequency (e.g. 96 or 48kHz). This optimises disk space usage and makes long deployments
of several months possible with moderate 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
<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
<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>
@ -28,7 +26,7 @@ SoundTrap recordings, then use a normal <a href="ClickDetector_clickDetector.htm
<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 list. Enter a descriptive name for the new detector and press Ok.
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>
@ -50,13 +48,17 @@ SoundTrap recordings, then use a normal <a href="ClickDetector_clickDetector.htm
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 make noise measurements or to detect whistles),
<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 SUD files directly, without first unpacking them into WAV, XML, BCL and DWV files. This not
<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 sud file with one set of
<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

View File

@ -18,6 +18,11 @@ SoundTrap recorders from
<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>