updated help to include PAMDog

.classpath

@@ -6,7 +6,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/ojdk-21.0.1">
 		<attributes>
 			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>

.project

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
-	<name>PAMGuard_DG</name>
+	<name>PAMGuard</name>
 	<comment></comment>
 	<projects>
 	</projects>

.settings/org.eclipse.jdt.core.prefs

@@ -11,9 +11,9 @@ org.eclipse.jdt.core.codeComplete.staticFinalFieldPrefixes=
 org.eclipse.jdt.core.codeComplete.staticFinalFieldSuffixes=
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
 org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=17
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=19
 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=17
+org.eclipse.jdt.core.compiler.compliance=19
 org.eclipse.jdt.core.compiler.debug.lineNumber=generate
 org.eclipse.jdt.core.compiler.debug.localVariable=generate
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
@@ -23,4 +23,4 @@ org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
 org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=warning
 org.eclipse.jdt.core.compiler.release=enabled
-org.eclipse.jdt.core.compiler.source=17
+org.eclipse.jdt.core.compiler.source=19

src/PamModel/SMRUDevFunctions.java

@@ -55,9 +55,9 @@ public class SMRUDevFunctions {
 		
 		// possible links into module names in table. 
 		// for a dump to go into the main help file, use helpRoot = "../../../";
-		//helpRoot = "../../../";
+		helpRoot = "../../../";
 		// for no output, set null. 
-		helpRoot = null;
+		//helpRoot = null;
 		// for ooutput into main PAMGuard pages, it's probably
 		
 		PamModel model = PamController.getInstance().getModelInterface();

src/help/JavaHelpSearch/SCHEMA

@@ -1,2 +1,2 @@
 JavaSearch 1.0
-TMAP bs=2048 rt=1 fl=-1 id1=7001 id2=1
+TMAP bs=2048 rt=1 fl=-1 id1=7038 id2=1

src/help/Map.jhm

@@ -96,6 +96,8 @@
 
 <mapID target="classifiers.roccaHelp.docs.rocca_ContourExtractionManipulation_manual" url="classifiers/roccaHelp/docs/rocca_ContourExtractionManipulation.html#manual"/>
 
+<mapID target="overview.PamMasterHelp.docs.PamdogHelp" url="overview/PamMasterHelp/docs/PamdogHelp.html"/>
+
 <mapID target="classifiers.roccaHelp.docs.rocca_Configure_rocca_SchoolStatsFile" url="classifiers/roccaHelp/docs/rocca_Configure.html#rocca_SchoolStatsFile"/>
 
 <mapID target="localisation.docs.localisation_tdoa" url="localisation/docs/localisation_tdoa.html"/>

src/help/PAMGUARDTOC - Copy.xml

@@ -14,6 +14,8 @@
 
   <tocitem text="Mixed Mode operation " target="overview.PamMasterHelp.docs.mixedMode" image="topic"/>
 
+  <tocitem text="PAMGuard WatchDog " target="overview.PamMasterHelp.docs.PamdogHelp" image="topic"/>
+
  </tocitem>
  <tocitem text="Core Features ">
   <tocitem text="Graphical User Interface " target="overview.PamMasterHelp.docs.guiOverview" image="topic"/>
@@ -203,8 +205,6 @@
 
    <tocitem text="Tethys Module " target="utilities.tethys.docs.tethys_module" image="topic"/>
 
-   <tocitem text="Tethys Server " target="utilities.tethys.docs.tethys_server" image="topic"/>
-
    <tocitem text="Connecting to Tethys " target="utilities.tethys.docs.connection" image="topic"/>
 
    <tocitem text="Instrument Calibrations " target="utilities.tethys.docs.calibrations" image="topic"/>

src/help/PAMGUARDTOC.xml

@@ -15,6 +15,8 @@
 
   <tocitem text="Mixed Mode operation " target="overview.PamMasterHelp.docs.mixedMode" image="topic"/>
 
+  <tocitem text="PAMGuard WatchDog " target="overview.PamMasterHelp.docs.PamdogHelp" image="topic"/>
+
  </tocitem>
  <tocitem text="Core Features ">
   <tocitem text="Graphical User Interface " target="overview.PamMasterHelp.docs.guiOverview" image="topic"/>

src/help/overview/PamMasterHelp/docs/PamdogHelp.html

@@ -0,0 +1,159 @@
+<!DOCTYPE html>
+<html>
+<head>
+<LINK href="../../../pamHelpStylesheet.css" type=text/css rel=STYLESHEET>
+<title>PamDog Help</title>
+</head>
+<body>
+<h1>PamDog - The PAMGuard Watchdog</h1>
+<h2>Introduction</h2>
+<p>
+PamDog, the <a href="http://www.pamguard.org">PAMGuard</a> watchdog program, can be used when you want to start PAMGuard automatically and want to 
+ensure that it never, ever stops, or if it does stop accidentally due to a fault, it will restart itself.
+</p>
+<p>
+PamDog is particularly useful when a PAM system needs to be left running unattended. 
+</p>
+<p>
+PamDog has only been tested under Windows. Some functions may not be available under other operating systems but the main ones should be OK.
+</p>
+<h2>Installing and Running</h2>
+
+
+<table>
+<tr>
+<td valign="top">
+<p style="text-align:center;"><img src="images/TrayIcon.png"></p>
+</td>
+<td valign="top">
+<p>
+<!PamDog is currently distributed as a single executable jar file. If you have installed Java correctly on your system, 
+then all you have to do is double click on the jar file and PamDog will start.>
+Since PAMGuard release 2.02.03, PamDog has been included in the PAMGuard build, but is not set up to run automatically when 
+Windows starts. To start PamDog, you no longer need to install Java yourself. Simply double click on the file PamguardBeta_WatchDog.exe
+which you'll find in the PAMGuard installation folder (probably C:\Program Files\Pamguard). See below for instructions 
+on making PamDog start with Windows. 
+</p>
+<p>
+By default, no user interface will be displayed. PamDog will run in the background and can be configured via an icon which will appear in 
+the Tray Icon area, that's the little icons down in the bottom right corner of the Windows task bar</p>
+</td>
+</tr>
+</table>
+
+
+<h3>Configuring and Starting PAMGuard</h3>
+<p>If you are using the watchdog DO NOT start PAMGuard in the normal way from the Windows Start menu. PamDog has to 
+start PAMGuard with some specific options enabled so that PamDog and PAMGuard can communicate. These options will not be available  
+if you've started PAMGuard from the Start menu. <p>
+<p>A typical sequence of operations required to use PamDog successfully is as follows:</p>
+<ul>
+<li>With PamDog deactivated, launch PAMGuard from the Start menu in the normal way, configure it how you want, check it's all running OK and save your psf file.</li>
+<li>Close PAMGuard.</li>
+<li>Open the PamDog configuration dialog and configure PamDog with the correct paths and options to Java, the Pamguard executable and your psf file.</li>
+<li>Activate PamDog, sit back and allow PamDog to launch and start PAMGuard.</li> 
+<li>If you need to modify your configuration in anyway, deactivate PamDog and repeat the above steps.</li> 
+</ul>
+
+
+<h3>Starting PamDog Automatically</h3>
+<p>
+You should not run more than one instance of PamDog at a time. Most users will want PamDog to launch automatically when Windows starts. 
+To make PamDog launch automatically, the easiest way is <!copy or move the PamDog.jar file to your Start folder.>
+simply to create a shortcut to the  PamguardBeta_WatchDog.exe program in your Start folder. 
+<p>
+To locate the Start folder click on the Windows Start button, then RIGHT click on 'All Programs'. A small menu should apear. Select 'Open' and
+a Windows explorer window should open in a folder with a name something like
+'C:\Users\*yourusername*\AppData\Roaming\Microsoft\Windows\Start Menu'
+Go into 'Programs' then into 'Startup' so that you're in a folder with a name like
+'C:\Users\*yourusername*\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\Startup'.
+Right click on PamguardBeta_WatchDog.exe and drag across to the Startup folder. Release the mouse and select "Create Shortcuts here" from the menu. Don't 
+drag the actual .exe file across ! 
+</p>
+<p>
+Restart your computer and check that PamDog has started automatically by searching for it in the Tray Icon area.
+</p>
+
+<h2>Configuring</h2>
+<p>
+To configure PamDog, go to the System tray and find the PAMGuard watchdog icon. Click on it to open the configuration dialog or right 
+click on it for other options.
+</p>
+<p>Configuration and control options are spread over three tabs, Control, Pamguard and Java. All controls in the dialog have tool tips - 
+hover the mouse over them and they will provide some information on what they do.<p>
+
+
+<h3>Control</h3>
+<table>
+<tr>
+<td valign="top">
+<p style="text-align:center;"><img src="images/Config1.png"></p>
+</td>
+<td valign="top">
+<p>
+The Control panel controls whether or not the Watchdog is active. If the watchdog is correctly configured and the "Activate Watchdog" 
+button is checked, then PAMGuard will be launched automatically and if PAMGuard is stopped, will immediately restart</p>
+<p><b>Activate Watchdog: </b>Activates or deactivates the watchdog.</p>
+<p><b>UDP Port: </b>UDP (network protocol) port for communication between PamDog and PAMGuard.</p>
+<p><b>Allow system restarts: </b>Will restart Windows if the watchdog fails to start PAMGuard several times in succession. 
+Note that if this option is selected and PAMGuard cannot start for some fundamental reason, such as an acquisition device
+becoming disconnected, then the computer will continually reboot. The reboot cycle is relatively slow so there should always 
+be sufficient time one the computer has restarted to deactivate the watchdog.</p>
+<p><b>open log file folder: </b>Opens a folder containing PAMGuard and PamDog log files. Note that information displayed in 
+the terminal window when PAMGuard is running normally is written to a log file when PAMGuard is launched by PamDog.</p>
+</td>
+</tr>
+</table>
+
+
+<h3>Pamguard</h3>
+<table>
+<tr>
+<td valign="top">
+<p style="text-align:center;"><img src="images/Config2.png"></p>
+</td>
+<td valign="top">
+<p>
+The Pamguard panel controls the location of important PAMGuard files and folders and tells PamDog which PAMGuard configuration file 
+should be used.  
+</p>
+<p><b>Working Directory: </b>The folder containing the PAMGuard executable jar file. Normally this will be something like 
+C:\Program Files\Pamguard64.</p>
+<p><b>Pamguard Executable jar: </b>The main PAMGuard jar file which must be in the <b>Working Directory</b>.</p>
+<p><b>Pamguard Configuration file: </b>The PAMguard configuration (.psf) file.</p>
+<p><b>Library path: </b>The name of a folder containing library files which must be in the <b>Working Directory</b> which will be either <b>lib</b> or <b>lib64</b> for 
+32 or 64 bit versions of PAMGuard and the Java virtual machine.</p>
+<p><b>Other PAMGuard command line options: </b>Leave blank. This is for the use of the PAMGuard development team.</p>
+</td>
+</tr>
+</table>
+
+
+<h3>Java</h3>
+<table>
+<tr>
+<td valign="top">
+<p style="text-align:center;"><img src="images/Config3.png"></p>
+</td>
+<td valign="top">
+<p>
+The Java panel controls the Java virtual machine which is required to run PAMGuard. 
+</p>
+<p><b>Java Executable: </b>The Java runtime executable program. This is always called java.exe and will normally be
+found in a folder with a name like 'C:\Program Files (x86)\Java\jre1.*.*_**\bin' for 32 bit Java versions or 
+'C:\Program Files\Java\jre1.*.*_**\bin' for 64 bit Java versions.  For advanced functionality (including better task 
+killing capabilities), use the java.exe found in a jdk**** folder instead of a jre**** folder.</p>
+<p><b>Min VM Memory: </b>The minimum amount of memory to allocate to the Java virtual machine.</p>
+<p><b>Max VM Memory: </b>The maximum amount of memory to allocate to the Java virtual machine. 32 
+bit versions of Java can have a maximum of 1024 Mega bytes of memory, 64 bit versions can use up
+to 8192 Mega bytes</p>
+<p><b>Other VM command line options: </b>Leave blank. This is for the use of the PAMGuard development team.</p>
+
+</td>
+</tr>
+</table>
+
+
+
+</body>
+</html>

src/help/overview/PamMasterHelp/docs/normalMode.html

@@ -31,22 +31,30 @@ under Windows, the command line for starting PAMGuard Beta version 1.3.02 with 1
 is:  <br><br>
 <center><p>java -jar -mx1024m PAMGuardBeta_1_3_02.jar PAMGuard</p></center> 
 
-<h3>The PSF File</h3>
+<h3>The PSFX File</h3>
 <p>
-PAMGuard saves it's configuration between runs in PAMGuard Settings Files (.psf). 
+PAMGuard saves it's configuration between runs in PAMGuard Settings Files (.psfx). 
 <p>
-Each time you start PAMGuard a dialog will open asking you to select the psf file
+Each time you start PAMGuard a dialog will open asking you to select the psfx file
 you want to use. <p>
 <center><img alt="Start Dialog" src="images/startupDialog.png"/></center></p><br>
 <p>Either select a recently used psf from the drop down list or press the browse button
 to select a psf file stored elsewhere on your system.
 <p>
-Sample psf files may be downloaded from the <a href="http://www.PAMGuard.org">www.PAMGuard.org</a> web site. 
+Sample psfx files may be downloaded from the <a href="http://www.PAMGuard.org">www.PAMGuard.org</a> web site. 
+
+<h3>PAMGuard WatchDog</h3>
+<p>When collecting and processing data in real time you can use the <a href="PamdogHelp.html">PAMGuard WatchDog</a>
+to keep PAMGuard running whatever happens</p>
+
+<h3>Batch Processing</h3>
+<p>If you're processing sets of data offline, you can use the <a href="https://www.pamguard.org/plugins/plugins.html">Batch Processing Plugin</a>
+to run the same configuration file on several different sets of data.</p>
 
 
 <br><br>
 <p CLASS="previousLink"><a href="modules.html">Previous: PAMGuard Modules</a></p>
-<p CLASS="nextLink"><a href="viewerMode.html">Next: PAMGuard Viewer</a></p>
+<p CLASS="nextLink"><a href="viewerMode.html">Next: PAMGuard Viewer.</a></p>
 <br>
 
 </body>

src/quartohelp/QuartoMigrate.java

@@ -50,7 +50,7 @@ public class QuartoMigrate {
 
 	public static void main(String[] args) {
 		QuartoMigrate qm = new QuartoMigrate();
-		qm.convertSource(new File(qm.helpsrc));
+//		qm.convertSource(new File(qm.helpsrc));
 		qm.convertIndex();
 	}
 

src/quartohelp/_quarto.yml

@@ -37,6 +37,7 @@ website:
           - overview/PamMasterHelp/docs/normalMode.qmd
           - overview/PamMasterHelp/docs/viewerMode.qmd
           - overview/PamMasterHelp/docs/mixedMode.qmd
+          - overview/PamMasterHelp/docs/PamdogHelp.qmd
       - section: "Core Features "
         contents:
           - overview/PamMasterHelp/docs/guiOverview.qmd
@@ -155,7 +156,6 @@ website:
             contents:
               - utilities/tethys/docs/tethys_overview.qmd
               - utilities/tethys/docs/tethys_module.qmd
-              - utilities/tethys/docs/tethys_server.qmd
               - utilities/tethys/docs/connection.qmd
               - utilities/tethys/docs/calibrations.qmd
               - utilities/tethys/docs/deployments.qmd
@@ -470,7 +470,7 @@ website:
             contents:
               - visual_methods/loggerFormsHelp/docs/loggerFormsOverview.qmd
               - visual_methods/loggerFormsHelp/docs/designingForms.qmd
-  
+              
 format:
   html:
     theme: cosmo

src/quartohelp/index.qmd

@@ -1,7 +1,8 @@
 ---
 title: "Welcome to PAMGuard Help"
 ---
-
+Welcome to PAMGuard Help
+------------------------
 
 This is a web version of the PAMGuard online help.
 
@@ -9,4 +10,4 @@ Please note that not all of the functionality of the online help system translat
 
 Use the sidebar navigation to find your way through the help pages.
 
-If you cannot see the side bar, expand the width of your browser window and it will appear.
+If you cannot see the side bar, expand the width of your browser window and it will appear.

src/quartohelp/quartohelp.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 69a86409-18e9-40bf-bf10-e22f15d50efd
 
 RestoreWorkspace: Default
 SaveWorkspace: Default