Merge pull request #56 from PAMGuard/main

Merge from main

README.html

@@ -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
+lang=EN-US> from other configurations: New options from file menu allowing import
-import of specific modules, or module settings from other configurations. E.g.
+of specific modules, or module settings from other configurations. E.g. if you
-if you had three similar configurations and had set one of them up with a new
+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
+lang=EN-US> by right clicking on sqlite database and selecting <20>open with / Pamguard
-ViewerMode launcher’ menu option.</span></p>
+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
+<p class=MsoNormal><span lang=EN-US>Allow Rocca to run without classifiers:
-bug that threw an error if no classifier files were  specified in Rocca Params
+Fixed bug that threw an error if no classifier files were &nbsp;specified in
-dialog</span></p>
+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
+processing of offline files, if output data already exist (binary data of
-database tables) you will be asked if you want to overwrite the data, cancel,
+within database tables) you will be asked if you want to overwrite the data,
-or try to continue from where to left off. </span></p>
+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
+<p class=MsoNormal><span lang=EN-US>Bug 495: TD FX display throws
-if user has removed all data units and then moves mouse over display area.</span></p>
+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
+Changes to Spectrogram Mark Observers, to allow individual channels to be
-instead of the spectrogram panel as a whole. </p>
+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
+Java 12 is better at handling Windows scaling issues on high-DPI displays.
-that, users should not notice much of a difference between this version and
+Beyond that, users should not notice much of a difference between this version
-previous beta releases.</p>
+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
+<p class=MsoNormal><span lang=EN-US>PAMGuard Version 2 contains major updates.
-should read and understand the notes listed for <a
+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
+</span>Bug 387. Map was stopping displaying data based on the start time of
-units. Have changed this to last updated time so that click events will display
+data units. Have changed this to last updated time so that click events will
-if they have been recently modified. Otherwise, long events get lost from the
+display if they have been recently modified. Otherwise, long events get lost
-display.</p>
+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
+</span><span lang=EN-US>Bug 323. Difar module.</span> Fixed a couple of small
-in the DIFAR system which caused it to not work if old configuratins were used.
+bugs in the DIFAR system which caused it to not work if old configuratins were
-</p>
+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
+</span><span lang=EN-US>Display colour options will be lost and most data
-on the map may default to black. This is due to the above changes to how
+displayed on the map may default to black. This is due to the above changes to
-colours are managed. Changing back to the colours of your choice is relatively
+how colours are managed. Changing back to the colours of your choice is
-simple through the PAMGuard GUI. </span></p>
+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
+</span>Bug 279. GUI Resizing: The whole PAMGuard GUI would suddenly resize to
-very small when a dialog is opened. This has been traced to improper use of a
+something very small when a dialog is opened. This has been traced to improper
-common dialog component SourcePanel which tries to repack its parent Window.
+use of a common dialog component SourcePanel which tries to repack its parent
-Some programmers had inadvertently set it to repack the main PAMGuard GUI
+Window. Some programmers had inadvertently set it to repack the main PAMGuard
-instead. This has been Fixed.</p>
+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.
+University estimates the 3D localisation of clicks using a variety of
-It's primarily been developed to track harbour porpoise in three dimensions
+algorithms. It's primarily been developed to track harbour porpoise in three
-over scales of 10's of metres. While currently only working with output from
+dimensions over scales of 10's of metres. While currently only working with
-the click detector, we hope eventually to extend its use to whistles as well. </p>
+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
+<p class=MsoNormal style='margin-left:36.0pt'>Clip Generator: Saves and
-short waveform clips around detections. Can work with any detector (or indeed
+displays short waveform clips around detections. Can work with any detector (or
-any other data stream within PAMGuard). &nbsp;</p>
+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
+<p class=MsoNormal style='margin-left:36.0pt'>A substantial amount of work has
-carried out on Logger forms, funded by the South West fisheries Science Center.
+been carried out on Logger forms, funded by the South West fisheries Science
-</p>
+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
+<p class=MsoNormal>When using the PAMGUARD viewer an additional panel will be
-showing an overview of data quantity (per hour) from the various database
+displayed showing an overview of data quantity (per hour) from the various
-tables connected to PAMGUARD. </p>
+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
+<p class=MsoNormal>PAMGAURD FFT calculations now use the JTransforms FFT
-which gives a factor 2 speed improvement compared to previous FFT methods used
+library which gives a factor 2 speed improvement compared to previous FFT
-in PAMGUARD</p>
+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
+<p class=MsoNormal>This release contains many bug fixes from the PAMGUARD
-field trial which took place in the Gulf of Mexico on the RV New Venture in
+industry field trial which took place in the Gulf of Mexico on the RV New
-November 2008.</p>
+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
+coming in through the ASIO card and back out through its headphone socket
-passing through PAMGUARD filters and other modules) at the same time.</p>
+(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
+<p class=MsoNormal>PAMGUARD now processes data in each module in a different
-thread. This allows PAMGUARD to use both processor cores on dual or multi core
+processing thread. This allows PAMGUARD to use both processor cores on dual or
-processor machines. However, multithreading may still cause instability in some
+multi core processor machines. However, multithreading may still cause
-modules. An option is therefore accessible from the main Detection menu to
+instability in some modules. An option is therefore accessible from the main
-enable and disable multithreading. </p>
+Detection menu to enable and disable multithreading. </p>
 
 <p class=MsoNormal><b>New Modules</b></p>
 

pom.xml

@@ -1,3 +1,4 @@
+
 <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">

src/help/JavaHelpSearch/SCHEMA

@@ -1,2 +1,2 @@
 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

src/help/Map.jhm

@@ -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"/>

src/help/PAMGUARDTOC.xml

@@ -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>

src/help/utilities/tethys/docs/tethys_overview.html

@@ -43,9 +43,8 @@ img {
 		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
+		<a href="tethys_quickstart.html">Next: Quick Start</a>
-			Module</a>
 	</p>
 	<br>
 	<br>

src/help/utilities/tethys/docs/tethys_quickstart.html

@@ -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>

src/help/utilities/tethys/docs/tethys_server.html

@@ -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>