Nearly ready for 2.02.14 release

Added CPOD help.

.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=18
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=17
 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=18
+org.eclipse.jdt.core.compiler.compliance=17
 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=18
+org.eclipse.jdt.core.compiler.source=17

pom.xml

@@ -4,7 +4,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
-  <version>2.02.13c</version>
+  <version>2.02.13d</version>
   <name>Pamguard</name>
   <description>Pamguard using Maven to control dependencies</description>
 	<url>www.pamguard.org</url>

src/PamController/PamguardVersionInfo.java

@@ -31,12 +31,12 @@ public class PamguardVersionInfo {
 	 * Version number, major version.minorversion.sub-release.
 	 * Note: can't go higher than sub-release 'f'
 	 */
-	static public final String version = "2.02.13c";
+	static public final String version = "2.02.13d";
 	
 	/**
 	 * Release date
 	 */
-	static public final String date = "September 2024";
+	static public final String date = "October 2024";
 	
 //	/**
 //	 * Release type - Beta or Core

src/PamModel/PamModel.java

@@ -525,6 +525,7 @@ final public class PamModel implements PamSettings {
 		mi.setModulesMenuGroup(sensorsGroup);
 		mi.setToolTipText("Imports CPOD data");
 		//mi.setHidden(SMRUEnable.isEnable() == false);
+		mi.setHidden(!isViewer);
 		mi.addGUICompatabilityFlag(PamGUIManager.FX); //has FX enabled GUI.
 
 		/*

src/bearinglocaliser/tethys/BearingLocalisationCreator.java

@@ -0,0 +1,33 @@
+package bearinglocaliser.tethys;
+
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.PamDataUnit;
+import nilus.LocalizationType;
+import tethys.localization.LocalizationBuilder;
+import tethys.localization.LocalizationCreator;
+
+public class BearingLocalisationCreator implements LocalizationCreator {
+
+	public BearingLocalisationCreator() {
+		// TODO Auto-generated constructor stub
+	}
+
+	@Override
+	public boolean sortLocalisationCoordinates(LocalizationBuilder localizationBuilder, PamDataBlock dataBlock) {
+		// TODO Auto-generated method stub
+		return false;
+	}
+
+	@Override
+	public LocalizationType createLocalization(LocalizationBuilder localizationBuilder, PamDataUnit dataUnit) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public boolean checkDocument(LocalizationBuilder localizationBuilder) {
+		// TODO Auto-generated method stub
+		return false;
+	}
+
+}

src/help/JavaHelpSearch/SCHEMA

@@ -1,2 +1,2 @@
 JavaSearch 1.0
-TMAP bs=2048 rt=1 fl=-1 id1=6961 id2=1
+TMAP bs=2048 rt=1 fl=-1 id1=6999 id2=1

src/help/Map.jhm

@@ -654,6 +654,8 @@
 
 <mapID target="utilities.listening.docs.Listening_Overview" url="utilities/listening/docs/Listening_Overview.html"/>
 
+<mapID target="sensors.cpod.docs.cpod" url="sensors/cpod/docs/cpod.html"/>
+
 <mapID target="utilities.SIDEModule.docs.SIDE_Overview_tests" url="utilities/SIDEModule/docs/SIDE_Overview.html#tests"/>
 
 <mapID target="overview.PamMasterHelp.docs.modules_utilities" url="overview/PamMasterHelp/docs/modules.html#utilities"/>

src/help/PAMGUARDTOC.xml

@@ -241,6 +241,10 @@
    <tocitem text="Configuration " target="sensors.arrayAccelerometer.docs.accelerometer_configuration" image="topic"/>
 
   </tocitem>
+  <tocitem text="CPOD ">
+   <tocitem text="CPOD Module " target="sensors.cpod.docs.cpod" image="topic"/>
+
+  </tocitem>
  </tocitem>
  <tocitem text="Displays ">
   <tocitem text="Data Selection ">

src/help/sensors/cpod/docs/cpod.html

@@ -0,0 +1,175 @@
+<html>
+<head>
+<LINK href="../../../pamHelpStylesheet.css" type="text/css"
+	rel="STYLESHEET">
+<title>Array Accelerometer</title>
+</head>
+
+<body>
+	<h1 id="cpod-module-help">CPOD module help</h1>
+	<h2 id="introduction">Introduction</h2>
+	<p>
+		CPODs and FPODs are click data loggers widely used in research and
+		industry developed by <a href="https://www.chelonia.co.uk">Chelonia
+			Ltd</a>. PAMGuard&#39;s CPOD module allows users to import CPOD <em>and</em>
+		FPOD data into PAMGuard so it can be viewed using PAMGuard&#39;s
+		visualisation tools. A common use case for this module is to display
+		both CPOD/FPOD data and a lower frequency recording device together -
+		for example a typical PAM setup is to use a CPOD to record high
+		frequency echolocation clicks then a lower frequency recorder (e.g. 96
+		kHz sample rate) to record dolphin whistles, noise, fish sounds etc.
+	</p>
+	<h2 id="quick-overview-of-cpod-fpod-data">Quick overview of
+		CPOD/FPOD data</h2>
+	<p>CPODs and FPODs do not record raw audio - they run a simple on
+		board click detector and then save some basic metrics on each detected
+		click e.g. peak frequency, bandwidth, end frequency etc. FPODs, the
+		successor of CPODs, also record a little extra waveform data on a
+		small subset of detected clicks. Once a CPOD or FPOD has been
+		recovered, it is processed using CPOD.exe or FPOD.exe software
+		respectively which runs a click train classifier. The click train
+		classifier extracts sequences of successive clicks that are likely
+		from the same source, e.g a dolphin, porpoise or echo sounder. It then
+		assigns a likely species to a click train or classes it as unknown.
+		The outputs from the click train detector are saved to a CP3 file
+		which is essentially a file that contains only clicks that have been
+		assigned to click trains.</p>
+	<h2 id="adding-the-cpod-module">Adding the CPOD module</h2>
+	<p>
+		To add the CPOD module go to <strong><em>File-&gt;Add
+				Modules-&gt;Sensors-&gt;CPOD</em></strong>. The module requires the binary storage
+		module in PAMGuard <strong><em>File-&gt; Add
+				modules-&gt;Utilities-&gt;Binary File</em></strong>. Once both the CPOD and Binary
+		file storage modules have been added open the CPOD settings using <strong><em>Settings-&gt;CPOD
+				importer</em></strong>.
+	</p>
+	<h2 id="importing-cpod-fpod-data">Importing CPOD/FPOD data</h2>
+	<p>The module has three possible modes of importing data</p>
+	<ul>
+		<li>Import raw detection data i.e. CP1 or FP1 data. PAMGuard will
+			display the CPOD detection but no click train ID data is available.</li>
+		<li>Import just the click trains data i.e. CP3 or FP3 files -
+			PAMGuard will only import clicks which are part of click trains</li>
+		<li>Import both both raw and click train data (recommended).
+			PAMGuard imports the raw detections then uses the click train data to
+			assign detections to click trains.</li>
+	</ul>
+	<p>
+		Users can use the file button to select a single file (e.g. an FP3
+		file) or the folder button to select a folder of CPOD/FPOD files. If
+		the folder button is used and there are both CP1/FP1 (detections) and
+		CP3/FP3 (click trains) files then PAMGuard will automatically load all
+		files and assign detections to click trains. Once files have imported
+		select <strong><em>Import</em></strong> and the data will be imported
+		into PAMGuard - note this can take some time, especially if importing
+		CP1/FP1 files.
+	</p>
+	<p align="center">
+		<img width="750" height="400"
+			src="resources/cpod_settings_description.png">
+	</p>
+
+	<p>
+		<em>The CPOD module allow users to import CPOD/FPOD data by
+			selecting either individual files or a folder of files</em>
+	</p>
+	<h2 id="visualising-cpod-fpod-data">Visualising CPOD/FPOD data</h2>
+	<p>A broad overview of CPOD data is shown in PAMGuard&#39;s data
+		map which shows a datagram similar to the click detector. The datagram
+		shows the frequency density of CPOD/FPOD clicks constructed from the
+		peak frequency parameter for each click The datagram can be useful for
+		quickly navigating to sections of data that may contain porpoises
+		and/or dolphins.</p>
+	<p>Individual CPOD detections can be viewed in the Time base
+		display in PAMGuard. Add the CPOD module to a plot and then data can
+		be viewed with time using a selection y-axis options such as
+		Amplitude, Amplitude (stem), Frequency, bandwidth etc.</p>
+	<p align="center">
+		<img width="750" height="380"
+			src="resources/cpod_time_display_stem.png">
+	</p>
+	<p align="center">
+		<img width="750" height="380"
+			src="resources/cpod_time_display_amplitude2.png">
+	</p>
+
+	<p>
+		<em>FPOD data visualised in the time base display as a stem plots
+			like FPOD.exe (top) and as a scatter plot of click amplitudes
+			(bottom)</em>
+	</p>
+	<h2 id="data-selector">Data selector</h2>
+	<p>The CPOD module has a custom data selector which provides a
+		unified interface for users to select subsets of CPOD/FPOD data. The
+		data selector has sliders which set the range of various parameters,
+		such as peak frequency and also allows the selection of CPOD/FPOD
+		which belong to a click and those gave been classified to a particular
+		species. Users can use the data selector to, for example, only export
+		clicks classified as dolphin or perhaps plot only clicks with a peak
+		frequency between 100 and 150 kHz on the time display.</p>
+
+	<table>
+		<thead>
+			<tr>
+				<th style="text-align: center">CPOD data selector</th>
+				<th style="text-align: center">CPOD data selector in time
+					display</th>
+			</tr>
+		</thead>
+		<tbody>
+			<tr>
+				<td style="text-align: center"><img
+					src="resources/cpod_data_selector_swing.png" width="500"></td>
+				<td style="text-align: center"><img
+					src="resources/cpod_data_selector_fx.png" width="500"></td>
+			</tr>
+		</tbody>
+	</table>
+	<p>
+		<em>Screenshots of the data selector user interface used
+			throughout PAMGuard. Although the style can change, the data selector
+			is the same throughout PAMGuard</em>
+	</p>
+	<h2 id="exporting-cpod-fpod-data">Exporting CPOD/FPOD data</h2>
+	<p>CPOD and FPOD data can be exported to .RData and .mat using
+		PAMGuard&#39;s exporter.</p>
+	<p align="center">
+		<img width="450" height="600"
+			src="resources/cpod_exporter_dialog_swing.png">
+	</p>
+
+	<p>
+		<em>PAMGuard&#39;s exporter can export CPOD/FPOD clicks to .mat
+			or .RData files. These can be opened in MATLAB, Python, and R
+			respectively</em>
+	</p>
+	<p>
+		The fields saved by the exporter are the same as a standard PAMGuard
+		detection <a href="../../overview/dataexport/docs/dataexport.html">(see
+			exporter help)</a>. The additional fields for CPODs and FPODs are
+	</p>
+	<ul>
+		<li><em>bandwidth</em>: the bandwidth of the click in Hz</li>
+		<li><em>numcycles</em>: the number of cycles fo the click in Hz</li>
+		<li><em>peakfreq</em>: the peak frequency of the click in Hz</li>
+		<li><em>endfreq</em>: the end frequency of the click in Hz</li>
+		<li><em>SPL</em>: the CPOD measure of sound pressure level which
+			is an integer between 0 and 255.</li>
+		<li><em>slope</em>: the slope which is a parameter measured by the
+			CPOD and FPOD.</li>
+		<li><em>wave</em>: this will be empty for most clicks but some
+			clicks from FPODs will have a waveform. Note that this is
+			reconstructed from zero crossings and is NOT a clip from the raw
+			sound data.</li>
+		<li><em>species</em>: if the CPOD is part of a click train then
+			species will be 0 for UNKNOWN, 1 for NBHF, 2 for DOLPHIN and 3 for
+			SONAR. -1 indicates a click is not part of a click train.</li>
+		<li><em>clicktrainID</em>: indicates the click train that the
+			click belongs to. This can be cross referenced with UID column in the
+			PAMGuard database which stores click trains and/or used to as an
+			identifier to associate different clicks together into trains.</li>
+	</ul>
+
+
+</body>
+</html>