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updating Tethys help

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Douglas Gillespie 2024-01-12 18:57:38 +00:00
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commit d05cecaf8b
14 changed files with 89 additions and 7 deletions
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<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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<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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areas as well.
</p>
<p>PAMGuard is compatible with Tethys 3.0, released early in 2024. </p>
<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>

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<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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<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>