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README.html
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@ -466,9 +466,9 @@ name="_Version_2.02.10_January"></a>Version 2.02.10 January 2024</h1>
<h2><span lang=EN-US>New Features</span></h2>
<p class=MsoNormal><b><span lang=EN-US>Importing modules</span></b><span
lang=EN-US> from other configurations: New options from file menu allowing
import of specific modules, or module settings from other configurations. E.g.
if you had three similar configurations and had set one of them up with a new
lang=EN-US> from other configurations: New options from file menu allowing import
of specific modules, or module settings from other configurations. E.g. if you
had three similar configurations and had set one of them up with a new
detector, or got the click classifier settings set up just right in one of
those configurations, you can import the additional modules or the click
detector settings easily into the other configurations. </span></p>
@ -478,9 +478,8 @@ files) file performance</span></b><span lang=EN-US> when scrolling through
audio data in Viewer mode. </span></p>
<p class=MsoNormal><b><span lang=EN-US>Viewer Launch</span></b><span
lang=EN-US> by right clicking on sqlite database and selecting ‘open with / Pamguard
ViewerMode launcher’ menu option.</span></p>
lang=EN-US> by right clicking on sqlite database and selecting <20>open with / Pamguard
ViewerMode launcher<65> menu option.</span></p>
<h2><span lang=EN-US>Bug Fixes</span></h2>
<p class=MsoNormal><b><span lang=EN-US>Logger Forms</span></b></p>
@ -496,9 +495,9 @@ correctly saving updated bearings to the database. Now fixed. </span></p>
<p class=MsoNormal><b><span lang=EN-US>ROCCA Classifier fixes</span></b></p>
<p class=MsoNormal><span lang=EN-US>Allow Rocca to run without classifiers: Fixed
bug that threw an error if no classifier files were  specified in Rocca Params
dialog</span></p>
<p class=MsoNormal><span lang=EN-US>Allow Rocca to run without classifiers:
Fixed bug that threw an error if no classifier files were &nbsp;specified in
Rocca Params dialog</span></p>
<p class=MsoNormal><span lang=EN-US>Fix memory issue with
RoccaContourDataBlocks not being released for garbage collection</span></p>
@ -563,9 +562,9 @@ handlers to handle corrupt map files. </span></p>
<h2><span lang=EN-US>New Features</span></h2>
<p class=MsoNormal><span lang=EN-US>Restart Options: When you restart
processing of offline files, if output data already exist (binary data of within
database tables) you will be asked if you want to overwrite the data, cancel,
or try to continue from where to left off. </span></p>
processing of offline files, if output data already exist (binary data of
within database tables) you will be asked if you want to overwrite the data,
cancel, or try to continue from where to left off. </span></p>
<p class=MsoNormal><span lang=EN-US>Updated SoundTrap sud file interface so
that PAMGuard now extracts and stores the Click Detector settings from the sud
@ -759,8 +758,9 @@ the TF FX display to crash if no data were displayed.</span></p>
<p class=MsoNormal><span lang=EN-US>See major release notes for V 2.02.01
below. </span></p>
<p class=MsoNormal><span lang=EN-US>Bug 495: TD FX display throws NullPointerException
if user has removed all data units and then moves mouse over display area.</span></p>
<p class=MsoNormal><span lang=EN-US>Bug 495: TD FX display throws
NullPointerException if user has removed all data units and then moves mouse
over display area.</span></p>
<h1><a name="_Latest_Version_2.02.01"></a><span lang=EN-US>Version 2.02.01
October 2021</span></h1>
@ -1369,8 +1369,8 @@ Implemented a simple UDP output for PAMGuard alarms. </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>
Changes to Spectrogram Mark Observers, to allow individual channels to be selected
instead of the spectrogram panel as a whole. </p>
Changes to Spectrogram Mark Observers, to allow individual channels to be
selected instead of the spectrogram panel as a whole. </p>
<p class=MsoListParagraph style='text-indent:-18.0pt'><span lang=EN-US>8. </span><span
lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span><span
@ -1405,9 +1405,9 @@ be compatible with this version, and vice-versa.</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>
Java 12 is better at handling Windows scaling issues on high-DPI displays. Beyond
that, users should not notice much of a difference between this version and
previous beta releases.</p>
Java 12 is better at handling Windows scaling issues on high-DPI displays.
Beyond that, users should not notice much of a difference between this version
and previous beta releases.</p>
<!-- ************************************************************************************************************************** --><!-- ************************************************************************************************************************** -->
@ -1472,8 +1472,8 @@ lang=EN-US> </span>Updates to the Ishmael detectors.</p>
<h1><a name="_Latest_Beta_Version_2.00.16"></a><span lang=EN-US>Beta Version
2.00.16 May 2019</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
<p class=MsoNormal><span lang=EN-US>PAMGuard Version 2 contains major updates.
You should read and 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.</span></p>
@ -1772,10 +1772,10 @@ settings even when user tries to cancel or discard changes</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 387. Map was stopping displaying data based on the start time of data
units. Have changed this to last updated time so that click events will display
if they have been recently modified. Otherwise, long events get lost from the
display.</p>
</span>Bug 387. Map was stopping displaying data based on the start time of
data units. Have changed this to last updated time so that click events will
display if they have been recently modified. Otherwise, long events get lost
from the display.</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;
@ -2111,9 +2111,9 @@ showing. </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>Bug 323. Difar module.</span> Fixed a couple of small bugs
in the DIFAR system which caused it to not work if old configuratins were used.
</p>
</span><span lang=EN-US>Bug 323. Difar module.</span> Fixed a couple of small
bugs in the DIFAR system which caused it to not work if old configuratins were
used. </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;
@ -2262,10 +2262,10 @@ so they will no longer work with older PAMGuard versions.</span></p>
<p class=MsoListParagraph style='margin-left:54.0pt;text-indent:-36.0pt'><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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span><span lang=EN-US>Display colour options will be lost and most data displayed
on the map may default to black. This is due to the above changes to how
colours are managed. Changing back to the colours of your choice is relatively
simple through the PAMGuard GUI. </span></p>
</span><span lang=EN-US>Display colour options will be lost and most data
displayed on the map may default to black. This is due to the above changes to
how colours are managed. Changing back to the colours of your choice is
relatively simple through the PAMGuard GUI. </span></p>
<p class=MsoListParagraph style='margin-left:54.0pt;text-indent:-36.0pt'><span
lang=EN-US>&nbsp;</span></p>
@ -2697,11 +2697,11 @@ planned file format changes and that this is purely a future proofing exercise.<
<p class=MsoListParagraph style='margin-left:38.25pt;text-indent:-20.25pt'>7.<span
style='font-size:7.0pt;font-family:"Times New Roman",serif'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</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>
</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>
<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;
@ -3256,10 +3256,11 @@ 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>
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>
@ -3442,9 +3443,9 @@ whistle.</p>
<p class=MsoNormal><b>New Modules</b></p>
<p class=MsoNormal style='margin-left:36.0pt'>Clip Generator: Saves and displays
short waveform clips around detections. Can work with any detector (or indeed
any other data stream within PAMGuard). &nbsp;</p>
<p class=MsoNormal style='margin-left:36.0pt'>Clip Generator: Saves and
displays short waveform clips around detections. Can work with any detector (or
indeed any other data stream within PAMGuard). &nbsp;</p>
<p class=MsoNormal style='margin-left:36.0pt'>Local time display: displays the
computers local time on the main display panel. </p>
@ -3520,9 +3521,9 @@ information correctly in the binary files. </p>
<p class=MsoNormal style='margin-left:36.0pt'><i>Logger Forms</i></p>
<p class=MsoNormal style='margin-left:36.0pt'>A substantial amount of work has been
carried out on Logger forms, funded by the South West fisheries Science Center.
</p>
<p class=MsoNormal style='margin-left:36.0pt'>A substantial amount of work has
been carried out on Logger forms, funded by the South West fisheries Science
Center. </p>
<p class=MsoNormal style='margin-left:36.0pt'><i>Click Detector</i></p>
@ -3973,9 +3974,9 @@ more displays are set up for offline data viewing in future releases. </p>
<p class=MsoNormal>Viewer data map</p>
<p class=MsoNormal>When using the PAMGUARD viewer an additional panel will be displayed
showing an overview of data quantity (per hour) from the various database
tables connected to PAMGUARD. </p>
<p class=MsoNormal>When using the PAMGUARD viewer an additional panel will be
displayed showing an overview of data quantity (per hour) from the various
database tables connected to PAMGUARD. </p>
<p class=MsoNormal>Spectrogram Display overlays</p>
@ -4185,9 +4186,9 @@ display correctly and amplitude scale updates after scale parameter changes. </p
<p class=MsoNormal><b>Speed improvement</b>. </p>
<p class=MsoNormal>PAMGAURD FFT calculations now use the JTransforms FFT library
which gives a factor 2 speed improvement compared to previous FFT methods used
in PAMGUARD</p>
<p class=MsoNormal>PAMGAURD FFT calculations now use the JTransforms FFT
library which gives a factor 2 speed improvement compared to previous FFT
methods used in PAMGUARD</p>
<p class=MsoNormal><b>New Modules</b></p>
@ -4543,9 +4544,9 @@ localiser (affects stability of click train localiser and whistle localiser in <
<h2>1.2.0 Beta December 2008</h2>
<p class=MsoNormal>This release contains many bug fixes from the PAMGUARD industry
field trial which took place in the Gulf of Mexico on the RV New Venture in
November 2008.</p>
<p class=MsoNormal>This release contains many bug fixes from the PAMGUARD
industry field trial which took place in the Gulf of Mexico on the RV New
Venture in November 2008.</p>
<p class=MsoNormal><b>Bug Fixes</b></p>
@ -4650,8 +4651,8 @@ mouse is moved over the display. Choice of colour maps for 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>Sound playback. Now supported in ASIO sound cards, so you can have sound
coming in through the ASIO card and back out through its headphone socket (after
passing through PAMGUARD filters and other modules) at the same time.</p>
coming in through the ASIO card and back out through its headphone socket
(after passing through PAMGUARD filters and other modules) at the same time.</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;
@ -4671,11 +4672,11 @@ Symbol'>'</span><span style='font-size:7.0pt;font-family:"Times New Roman",serif
<p class=MsoNormal><b>Multithreading</b></p>
<p class=MsoNormal>PAMGUARD now processes data in each module in a different processing
thread. This allows PAMGUARD to use both processor cores on dual or multi core
processor machines. However, multithreading may still cause instability in some
modules. An option is therefore accessible from the main Detection menu to
enable and disable multithreading. </p>
<p class=MsoNormal>PAMGUARD now processes data in each module in a different
processing thread. This allows PAMGUARD to use both processor cores on dual or
multi core processor machines. However, multithreading may still cause
instability in some modules. An option is therefore accessible from the main
Detection menu to enable and disable multithreading. </p>
<p class=MsoNormal><b>New Modules</b></p>

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<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">

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JavaSearch 1.0
TMAP bs=2048 rt=1 fl=-1 id1=6709 id2=1
TMAP bs=2048 rt=1 fl=-1 id1=6727 id2=1

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@ -276,6 +276,8 @@
<mapID target="detectors.clickDetectorHelp.docs.offline_Tools_AmplSel" url="detectors/clickDetectorHelp/docs/offline_Tools.html#AmplSel"/>
<mapID target="utilities.tethys.docs.tethys_quickstart" url="utilities/tethys/docs/tethys_quickstart.html"/>
<mapID target="displays.spectrogramDisplayHelp.docs.UserDisplay_Spectrogram_Overlays" url="displays/spectrogramDisplayHelp/docs/UserDisplay_Spectrogram_Overlays.html"/>
<mapID target="displays.radarDisplayHelp.docs.UserDisplay_Radar_Creating" url="displays/radarDisplayHelp/docs/UserDisplay_Radar_Creating.html"/>

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@ -198,6 +198,8 @@
<tocitem text="Tethys Interface ">
<tocitem text="Tethys Overview " target="utilities.tethys.docs.tethys_overview" image="topic"/>
<tocitem text="Quick Start " target="utilities.tethys.docs.tethys_quickstart" image="topic"/>
<tocitem text="Tethys Server " target="utilities.tethys.docs.tethys_server" image="topic"/>
</tocitem>

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@ -43,9 +43,8 @@ img {
areas as well.
</p>
<p>PAMGuard is compatible with Tethys 3.0, released early in 2024. </p>
<p>The Tethys database is not a replacement for the existing
<p>PAMGuard is compatible with <a href="https://tethys.sdsu.edu/tethys3/">Tethys 3.0</a> or above, released early in 2024. </p>
<p>The Tethys database is not a replacement for the existing
<a href="../../generalDatabaseHelp/docs/database_database.html">PAMGuard Database.</a>
Where the PAMGuard database only contains data from a single instrument or cruise, the Tethys
database contains data from many cruises and projects and can be used to hold a summary of all data
@ -60,8 +59,7 @@ img {
<br><br>
<a href="tethys_configure.html">Next: Configuring the Tethys
Module</a>
<a href="tethys_quickstart.html">Next: Quick Start</a>
</p>
<br>
<br>

80
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@ -0,0 +1,80 @@
<html>
<head>
<LINK href="../../../pamHelpStylesheet.css" type="text/css"
rel="STYLESHEET">
<title>Tethys</title>
</head>
<body>
<h1>Tethys Quick Start</h1>
<p>This 'Quick Start' guide is aimed at people who are already familiar with both Tethys and PAMGuard</p>
<p>The Tethys database is only used in
<a href="../../../overview/PamMasterHelp/docs/viewerMode.html">PAMGUard Viewer mode</a> and is only used to archive project data to a single
centralised database.
It is NOT a replacement for the existing <a href="../../generalDatabaseHelp/docs/database_database.html">PAMGuard database</a>.</p>
<h3>PAMGuard Tethys Module</h3>
<p>Launch PAMGuard in Viewer Mode with an existing set of data.</p>
<p>Add a Tethys module to PAMGuard from the File / Add Modules / Utilities menu. </p>
<p>A new tab panel will show the Tethys interface</p>
<center><img src = "./images/TethysGUI_1.png" width="100%" height="auto"></center>
<p>The tab shows a number of panels for the connection to the server and the various types
of data that will be output to the database. Some of these should summary information on what's in the
current PAMGuard dataset (consisting of your PAMGuard database and binary store), others may be empty until you start to
export to Tethys. </p>
<h3>Tethys Server</h3>
<p>Make sure you have a <a href = "tethys_server.html">Tethys Server</a> running. The PAMGuard interface will
only work with <a href="https://tethys.sdsu.edu/tethys3/">Tethys 3.</a> </p>
<p>Check the server connection. If PAMGuard has correctly connected to the Tethys server, the top panel of the display will be a normal
grey colour. If the connection cannot be made, the panel will be orange.</p>
<p>If required, change the server settings using the "Select Sever" button</p>
<h4>Project and Instrument Information</h4>
<p>Either select an existing "Project", or create a new one.</p>
<p>You also need to give Tethys more information about the instrument(s) or arrays you've deployed than in previous PAMGuard versions. Again, select an
existing instrument, or set up a new one. You'll notice that this information is held with the rest of the PAMGuard array management information.</p>
<h3>Data Export</h3>
<p>It's best to export data in the sequence the panels are laid out in on the PAMGuard display, i.e. Calibrations, then Deployments, and finally Detections.</p>
<h4>Calibrations</h4>
<p>To export the calibration data, press the "Export..." button at the top of the "Instrument Calibration Information" panel.
<p>Most of the calibration data is taken from the array manager and from the sound acquisition module. However, PAMGuard will ask a few questions about
HOW the instrument was calibrated, when it was done and who is responsible. Fill in as much information as you can!
IF the export is successful, a record will show for each hydrophone (or sensor) in your instrument array in the calibration information table:</p>
<center><img src="./images/calibration_information.png"></center>
<h4>Deployments</h4>
<p>PAMGuard will have done it's best to work out the temporal extent of your data by looking in the
<a href="../../generalDatabaseHelp/docs/database_database.html">PAMGuard database</a> and
<a href= "../../BinaryStore/docs/binarystore_overview.html">binary Store</a>. Where data were collected on a regular duty
cycle, or continuously, there should be a single record in the table of recording periods. If data were collected on a more
"ad-hoc" basis, for instance during a boat based survey, there might be many different records in the table.
Occasionally, there may be short recording periods (e.g. while you were testing kit on deck) that you don't want to export. Either select
individual rows that you want to export, or right click on the table and "Select All".</p>
<p>Press the "Export..." button and work through the questions to provide additional information about your data, why it was collected, etc. </p>
<p>Once the document(s) have been exported, the document names will be shown alongside each PAMGuard deployment period</p>
<center><img src="./images/deploymentspanel.png"></center>
<h4>Detections</h4>
<p>The bottom left panel shows a list of different types of PAMGuard data that can be exported and should also show the total numbers of each type of data that are available
within the PAMGuard storage systems. Select the datablock you want to export from and press "Export...". </p>
<p><strong>You really don't want to try to export zillions of data to Tethys</strong> , in the options that will appear you can opt to just export certain types of detections
or summary counts.</p>
<br>
<br>
<p class="prevLink"><a href="tethys_overview.html">Previous: Overview</a></p>
<p class="nextLink"><a href="tethys_server.html">Next: Tethys Server</a></p>
<br>
<br>
<br>
</body>
</html>

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@ -26,7 +26,7 @@
<br>
<br>
<p class="nextLink"><a href="tethys_configure.html">Next: Configuring the Tethys Module</a></p>
<p class="prevLink"><a href="tethys_quickstart.html">Previous: Quick Start</a></p>
<br>
<br>
<br>