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added help details server connection & calibration

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src/help/utilities/tethys/docs/tethys_quickstart.html
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export to Tethys. </p> export to Tethys. </p>
<h3> Connection and Project Details </h3>
<h3>Tethys Server</h3> <p>
<p>Make sure you have a <a href = "tethys_server.html">Tethys Server</a> running. The PAMGuard interface will 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> only work with <a href="https://tethys.sdsu.edu/tethys3/">Tethys
<p>Check the server connection. If PAMGuard has correctly connected to the Tethys server, the top panel of the display will be a normal 3</a> or later. The section below specifies how to set the
grey colour. If the connection cannot be made, the panel will be orange.</p> address of Tethys server address as well as determine if
<p>If required, change the server settings using the "Select Sever" button</p> PAMGuard can communicate successfully with Tethys. (The top
panel will be orange if communication is not working.
</p>
<h4>Tethys Server</h4>
<p>
The Tethys Server field next to the picture of the goddess Tethys
indicates the address of the Tehtys server. To change this field,
click on the gear icon. You will be prompted to provide a computer
address (URL) and a port. The address should start with http://
followed by the machine name or internet protocol address unless
the Tethys server has been configured to use an encrypted
connection. In this case, start the address with https://.
</p>
<p>
By default, PAMGuard will use http://localhost:9779 which
assumes that your Tethys server is running on the same computer as
PAMGuard and that it expects communication on port 9779, the
default port (administrators may change this).
</p>
<p>
If PAMGuard can communicate with the Tethys server, the
Connection and Project panel will be light grey. If
communication is not possible, the panel will be colored
orange. Likely causes for communication failure are:
</p>
<ul>
<li>
The server address or port is incorrect.
</li>
<li>
Tethys has not been started on the server machine. One of the
main reasons that we see this is when the administrator has
not configured Tethys to run automatically as a service. In
that case, when a machine reboots (e.g., for automatic
operaing system updates) the server will not start
automatically. The Tethys manual explains how to configure
Tethys as a service that starts automatically when the machine
boots.
</li>
<li>
Firewall rules do not permit traffic between the machine
executing PAMGuard and the one hosting Tethys on the selected
port. If you do not have adminstrative privileges, you will
need to contact your support team for help.
</li>
</ul>
<h4>Project and Instrument Information</h4> <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 <p>
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> Projects are names used by Tethys to help track work that should
be considered together, such as a series of deployments designed
to answer a specific question or funded under a specific
grant. If you do not already have a project defined in your
PAMGuard database, you can click the "New Project" button in the
"Connection and Project details" section of the Tethys
module. This will start a dialog that asks for a case-sensitive
project name and a geographic region. The geographic region is
for convenience, PAMGuard and Tethys track information by
longitude and latitude, but sometimes it is helpful to query for
information with respect to a geographic name such as Channel
Islands National Marine Sanctuary.
</p>
<p>
The array instrumentation is selected from a drop-down menu next
to the Instruments label. A dropdown menu next to the label
“Instruments” shows the list of hydrophone arrays. These are
likely to have been previously established prior to starting
analysis of your data by using the menu Settings -> Hydrophone
Array.
</p>
<p>
If you are a long-time user of PAMGuard, you will notice
additional fields are required for instrumentation: Instrument
Type and Instrument Id. The type indicates what type of
instrument is being used and may be generic such as a mooring or
array or denote a specific instrument such as a HARP, Rock
Hopper, SoundTrap, etc. The Id is a unique identifier for the
instrument such as a serial number. Note that if you are using
an older PAMGuard database, you may see a blank entry in the
instruments list as these new fields will not have been
populated. Press new/edit to access the instrument settings
from the Tethys module page.
</p>
<h3>Data Export</h3> <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>
<p>To export the calibration data, press the "Export..." button at the top of the "Instrument Calibration Information" panel. It is best to export data in the sequence the panels are laid out in on the PAMGuard display:
<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 </p>
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> <ol>
<li>
Instrument calibration information: exports to the Tethys Calibrations
</li>
<li>
Recording periods and deployment information: exports to Tethys Deployments
</li>
<li>
PAMGuard data blocks: exports to Tethys Detections and/or Localizations.
</li>
</ol>
<h4>Instrument calibration information</h4>
<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.
</p>
<p>
There are two dialogs associated with calibration. The first
asks for a calibration method and has the following fields:
</p>
<ul>
<li>
Method: Must be one of the following options:
<ul>
<li>Reference hydrophone</li>
<li>Manufacturer’s specification</li>
<li>Piston phone</li>
<li>Other calibrated source</li>
<li>Unknown</li>
</ul>
</li>
<li>
Serial number: Hydrophone serial number
</li>
<li>
Quality: Quality assurance value:
<ul>
<li> unverified: The calibration has not been verified </li>
<li> valid: The calibration has been validated as per the quality assurance process </li>
<li> invalid: The calibration was found to be invalid during quality assurance </li>
</ul>
</li>
<li>
QA Comment: Textual description of the quality assurance
process.
</li>
<li>
Calibration method: Textual description of the Method.
</li>
</ul>
<p>
The second calibrations dialog asks for:
</p>
<ul>
<li>
Calibration date: Date the calibration was performed.
</li>
<li>
Update frequency: Must be one of the following:
<ul>
<li>
as-needed: No updates are planned, but if a change is needed the calibration will be updated (defaul)t
</li>
<li>
unplanned: There are no plans to ever update the record.
</li>
<li>
yearly: A yearly review will be conducted to ensure that the record is valid.
</li>
</ul>
</li>
<li>
Technical Person / Data Manager: These two types of data have
the same fields and detail who was responsible for the
calibration and who is responsible for maintaining the record
of the calibration. In many cases, this may be the same
person and copy buttons allow the fields to be duplicated.
<ul>
<li>
Name: Responsible party’s naem
</li>
<li>
Organisation: Organisation to which the party reports
</li>
<li>
Position: Responsible party’s title
</li>
<li>
Email: Email contact information
</li>
</ul>
</li>
</ul>
<p>
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> <center><img src="./images/calibration_information.png"></center>
@ -55,7 +259,7 @@
<a href="../../generalDatabaseHelp/docs/database_database.html">PAMGuard database</a> and <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 <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 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. "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 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> individual rows that you want to export, or right click on the table and "Select All".</p>