Tethys improvements

Better species sel panel in export dialog
updated / corrected help
Sorted 'final' button in export wizard.

src/PamView/wizard/PamWizard.java

@@ -81,7 +81,10 @@ abstract public class PamWizard extends PamDialog {
 		boolean isLast = iCard == wizardCards.size()-1;
 //		getOkButton().setEnabled(!isLast);
 		getOkButton().setText(isLast ? "Finish" : "Next");
+		getOkButton().setToolTipText(isLast ? "Check values and close" : "Next page");
+		prevButton.setToolTipText(iCard == 0 ? null : "Previous page");
 	}
+	
 
 	private boolean checkCurrentCard() {
 		int iCard = getCardIndex();

src/clickDetector/ClickControl.java

@@ -883,7 +883,7 @@ public class ClickControl extends PamControlledUnit implements PamSettings, Loca
 		return true;
 	}
 
-	JMenuBar clickTabMenu = null;
+	JMenuBar tabMenu = null;
 
 	private ClickFFTOrganiser clickFFTDataOrganiser;
 
@@ -893,31 +893,31 @@ public class ClickControl extends PamControlledUnit implements PamSettings, Loca
 	@Override
 	public JMenuBar getTabSpecificMenuBar(Frame parentFrame, JMenuBar standardMenu, PamGui pamGui) {
 		JMenu aMenu;
-		// start bymaking a completely new copy.
+		// start by making a completely new copy.
 		//		if (clickTabMenu == null) {
-		clickTabMenu = standardMenu;
-		for (int i = 0; i < clickTabMenu.getMenuCount(); i++) {
-			if (clickTabMenu.getMenu(i).getText().equals("Display")) {
+		tabMenu = standardMenu;
+		for (int i = 0; i < tabMenu.getMenuCount(); i++) {
+			if (tabMenu.getMenu(i).getText().equals("Display")) {
 				//clickTabMenu.remove(clickTabMenu.getMenu(i));
 
 				aMenu = createDetectionMenu(parentFrame);
 				String txt = aMenu.getText();
 				txt = checkMenuTit(txt, "settings");
 				aMenu.setText(txt);
-				clickTabMenu.add(aMenu, i+1);
+				tabMenu.add(aMenu, i+1);
 
 				aMenu = tabPanelControl.createMenu(parentFrame);
 //				aMenu.setText("Click Display");
 				txt = aMenu.getText();
 				txt = checkMenuTit(txt, "display");
 				aMenu.setText(txt);
-				clickTabMenu.add(aMenu, i+2);
+				tabMenu.add(aMenu, i+2);
 
 				break;
 			}
 		}
 		//		}
-		return clickTabMenu;
+		return tabMenu;
 	}
 
 	/**

src/clickDetector/tethys/ClickTethysDataProvider.java

@@ -16,7 +16,8 @@ public class ClickTethysDataProvider extends AutoTethysProvider {
 
 	@Override
 	public GranularityEnumType[] getAllowedGranularities() {
-		return GranularityEnumType.values(); // everything !
+		GranularityEnumType[] allowed = {GranularityEnumType.CALL, GranularityEnumType.BINNED, GranularityEnumType.ENCOUNTER};
+		return allowed;
 	}
 
 }

src/help/JavaHelpSearch/SCHEMA

@@ -1,2 +1,2 @@
 JavaSearch 1.0
-TMAP bs=2048 rt=1 fl=-1 id1=7071 id2=1
+TMAP bs=2048 rt=1 fl=-1 id1=7076 id2=1

src/help/Map.jhm

@@ -606,6 +606,8 @@
 
 <mapID target="utilities.SIDEModule.docs.SIDE_OpStat" url="utilities/SIDEModule/docs/SIDE_OpStat.html"/>
 
+<mapID target="utilities.tethys.docs.tethys_granularity" url="utilities/tethys/docs/tethys_granularity.html"/>
+
 <mapID target="localisation.group3d.docs.3doutput" url="localisation/group3d/docs/3doutput.html"/>
 
 <mapID target="detectors.gpl.docs.notes" url="detectors/gpl/docs/notes.html"/>

src/help/PAMGUARDTOC.xml

@@ -212,6 +212,8 @@
 
    <tocitem text="Detections and Localizations " target="utilities.tethys.docs.detect_localize" image="topic"/>
 
+   <tocitem text="Granularity " target="utilities.tethys.docs.tethys_granularity" image="topic"/>
+
    <tocitem text="ITIS Species Codes " target="utilities.tethys.docs.tethys_speciescodes" image="topic"/>
 
    <tocitem text="PAMGuard Mapping " target="utilities.tethys.docs.tethys_mappings" image="topic"/>

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

@@ -109,6 +109,10 @@
       populated.  Press new/edit to access the instrument settings
       from the Tethys module page.
     </p>
+    
+    <p>Project names and instrument names are important in maintaining the relationship between
+    a PAMGuard dataset and related documents in Tethys. Read about <a href="tethys_mappings.html">PAMGuard Tethys mappings</a>
+    for further details.</p>
 
     <br>
     <br>

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

@@ -73,14 +73,6 @@ img {
     without affecting the selection state of other blocks.
   <p>
 
-  <p>
-    <em>
-      SUGGESTION:  It looks like we have to highlight these by clicking
-      on them.  As we use select boxes for recording periods, we might
-      want to do the same thing here...  We might want to rename
-      N PAM Datas to N PAM Data as data are already plural.
-    </em>
-  </p>
 
   <h2> Exporting data blocks </h2>
 
@@ -96,14 +88,39 @@ img {
 	 alt="List of details describing the mechanism, parameters, and version of modules used in processing"/>
   </div>
     
+    <br>
   <p>
     There is nothing to change in this summary.  Press Next once you
-    have reviewed it.  The second panel allows specification of your
+    have reviewed it. </p>
+    
+    <img src="./images/stream_species.png">
+    
+    <br>
+    <p>The second panel allows you to check <a href="tethys_speciescodes.html">ITIS species codes and call types</a> 
+    and to select which call types you want to export. </p>
+    
+    
+    <img src="./images/stream_granularity.png">
+    
+    <br>
+    <p>The next panel allows you to chose whether to export Detections, Localizations (if available), or both. Here, you 
+    can also select the <a href="tethys_granularity.html">granularity</a>, which will be a choice of "Call", "Encounter", "Binned", or "Grouped", depending on the 
+    type of data. You can also select an optional data filter which will restrict the output using criteria specific to the 
+    detector you're using. Note that there may be overlap between the data filter and the selections you make in the earlier species
+    selection page.   </p>
+    
+    <img src="./images/stream_description.png">
+    
+    <br>
+    <p>This panel allows specification of your
     objectives, abstract, and method.  Many modules will have
-    pre-populated the method for you.  While it is recommended to populate
-    the objectives and abstract, these fields are optional.
+    pre-populated the method for you.  It is recommended to populate
+    the objectives and abstract with as much information as possible.
   </p>
     
+    <img src="./images/stream_parameters.png">
+    
+    <br>
   <p>
     Press Next to proceed to the next step of the dialog.  You will be asked
     what details you wish to store within the parameters that were used to
@@ -118,7 +135,8 @@ img {
       later date or know whether or not the results of different
       studies can be used together. 
     </li>
-    <li> Data selector only - <strong>not sure what this is</strong> </li>
+    <li> Data selector only - Output only the details of the data filter (if any), for instance that
+    selected only a type of sound, or sounds with a received level above a set minimum.  
     <li>
       Module only - Report the parameters that were set with this
       module.  Only parameters associated with the specific module
@@ -131,21 +149,20 @@ img {
       parameters as well as anything else that is part of the signal processing chain that leads
       to the module.  As an example, a module only setting would not report the parameters that were
       used to generate a spectrogram that was presented to a module for classification, but the
-      full process chain would record these details as well.  Use this option will dramatically
+      full process chain would record these details as well.  Use of this option will dramatically
       increase the potential to reproduce your results, but it will generate a large amount of data
       about the signal processing chain, much of which might not be useful.
     </li>
   </ul>
   
+    <img src="./images/stream_export.png">
+    <br>
   <p>
-    The final page of the dialog has an "Export data" button.  Press
-    this to export the data.  The system will begin generating the
-    Tethys document and the "Export data" button will be relabeled "Export complete"
-    once it is done.  At this point, you can press "Finish" to close
-    the dialog.
+    The final page of the dialog has an "Export data" button.  Press either
+    this, or the Export button at the bottom of the dialog, to export the data.  The system will begin generating the
+    Tethys document and display progress as it works through the data. When complete, it will show a message to indicate that export was 
+    successful, or an error message.  
 
-    <em>Would it make more sense to export when the user presses
-    Finish (or change the Finish button Export)?</em>
   </p>
   
     

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

@@ -0,0 +1,57 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+    "http://www.w3.org/TR/html4/loose.dtd">
+<html lang="en">
+<head>
+
+<link href="../../../pamHelpStylesheet.css" type="text/css"
+	rel="STYLESHEET">
+<title>Detections/Granularity</title>
+<style type="text/css">
+img.wrap {
+	float: left
+}
+
+img.wrapright {
+	float: right
+}
+
+img {
+	float: right;
+}
+</style>
+</head>
+
+<link href="../../../pamHelpStylesheet.css" type="text/css"
+	rel="STYLESHEET">
+<body>
+    <h1>Tethys Granularity</h1>
+    <h2>Tethys Granularity</h2>
+    <p>
+        When exporting Detections to Tethys, you must select the "Granularity" for the exports. This will be one
+        of the following: 
+        <ul>
+        <li>Call - each detected call, or noise measurement is individually output to Tethys.</li>
+        <li>Binned - Counts of calls in fixed time bins are output to Tethys.</li>
+        <li>Encounter - Counts of calls forming and Encounter, that is a period of calling without a predetermined gap between calls. </li>
+        <li>Grouped - A Count of groups of calls associated in some other way (for instance through manual grouping of detections).</li>
+        </ul> 
+    </p>
+    <p>Binned granularity will require you to enter the duration of each bin, and a minimum number of calls for a bin to be output (e.g. you might set this above 
+    1 if there were occasional false positive detections, but when the animals do call, you tend to get lots of them).</p>
+    <p>Encounter granularity will require you to enter a minimum gap between calls which would constitute a new encounter. As with Binned, you also enter
+    a minimum number of calls for a bin to be output</p>
+    
+    <p>
+    Encounter and Binned granularities also offer to output separate records for each detection channel (or hydrophone), or to group detections across channels. The former
+    would be most appropriate for widely spaces hydrophones, where you'd expect different encounters on each hydrophone, whereas the latter would be more suitable if the 
+    hydrophones were spaced close enough together that you'd expect broadly the same detections on them all. </p>   
+     
+    
+    <br>
+   <p class="prevLink"><a href="detect_localize.html">Previous: Detections and Localizations</a></p>
+   <p class="prevLink"><a href="tethys_speciescodes.html">Previous: Species Codes</a></p>
+    <br>
+    <br>
+    <br>
+</body>
+</html>

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

@@ -29,10 +29,10 @@ img {
     <img SRC="images/Tethys-200.png" alt="Tethys mosaic"
 	 style="float: right; margin 10px;"/>
   </div>
-  
+  <br>
   <p>
     PAMGuard is compatible
-    with <a href="https://doi.org/10.5281/zenodo.13626338">Tethys 3.1</a> or
+    with <a href="https://doi.org/10.5281/zenodo.13626338">Tethys 3.2 beta 2</a> or
     later available for download from <a href="https://doi.org/10.5281/zenodo.13626338">Zenodo.</a>
     </p>
     <p>

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

@@ -7,186 +7,199 @@
 
 <body>
 
-  <h1> Species and Call Type Names </h1>
-<br>
- <p> When exporting data from PAMGuard to Tethys, some PAMGuard records
-  will require additional information indicating what type of animal
-  or phenomena were detected.  If a specific call-type was detected,
-  e.g. "Clicks" or "Whistles", these should be noted as well.</p>
-  
-  <h2> Species Names </h2>
-  <p>
-    Tethys uses the <a href="https:itis.gov">Integrated Taxonomic
-    Information System</a> (ITIS) to encode species names as taxonomic
-    serial numbers (TSNs), unique numeric identifiers for species.
-    These data conform with several international coding systems which
-    are described on the <a href="https://itis.gov/standard.html">ITIS
-    standards</a> page.  
-  </p>
+	<h1>Species and Call Type Names</h1>
+	<br>
+	<p>When exporting data from PAMGuard to Tethys, some PAMGuard
+		records will require additional information indicating what type of
+		animal or phenomena were detected. If a specific call-type was
+		detected, e.g. "Clicks" or "Whistles", these should be noted as well.</p>
 
-  <p>
-    It is not uncommon to be unable to describe a call to the genus
-    level.  In such cases, one can use a higher taxonomic level.  For
-    example, beaked whale echolocation clicks are distinctive from the
-    clicks of other toothed whales as their pulses have a
-    frequency-modulated component.  While they can frequently be
-    associated with the family Hyperodontidae, it is not always
-    possible to associate a click to a specific species as many of the
-    at least twenty-two species remain understudied.  In such a case,
-    we would use the TSN for Hyperodontidae, 770799.  While not
-    currently supported by PAMGuard, each species identifier has an
-    optional Group attribute that can be used in an ad-hoc manner to
-    provide additional information.  This can be used to add
-    population markers, tentative genus groups, etc.
-  </p>
+	<h2>Species Names</h2>
+	<p>
+		Tethys uses the <a href="https:itis.gov">Integrated Taxonomic
+			Information System</a> (ITIS) to encode species names as taxonomic serial
+		numbers (TSNs), unique numeric identifiers for species. These data
+		conform with several international coding systems which are described
+		on the <a href="https://itis.gov/standard.html">ITIS standards</a>
+		page.
+	</p>
 
-  <p>
-    ITIS does not describe abiotic sounds, Tethys records such sounds as follows:
-    <ol>
-      <li>
-	For anthropogenic signals, the Tethys convention is to
-	use <em>Homo sapiens</em>, TSN 180092, for the species code
-	and describe the human-generated signal via a call type,
-	e.g. ship, mid-frequency active sonar, etc.
-      </li>
-      <li>
-	Tethys reserves the TSN -10 for geophonic signals.
-	The call type is used to describe the source.  Examples
-	include ambient sound, earthquake, rain, etc.  Note that negative TSNs
-	are not part of the ITIS standard.
-      </li>
-    </ol>
-  </p>
+	<p>It is not uncommon to be unable to describe a call to the genus
+		level. In such cases, one can use a higher taxonomic level. For
+		example, beaked whale echolocation clicks are distinctive from the
+		clicks of other toothed whales as their pulses have a
+		frequency-modulated component. While they can frequently be associated
+		with the family Hyperodontidae, it is not always possible to associate
+		a click to a specific species as many of the at least twenty-two
+		species remain understudied. In such a case, we would use the TSN for
+		Hyperodontidae, 770799. While not currently supported by PAMGuard,
+		each species identifier has an optional Group attribute that can be
+		used in an ad-hoc manner to provide additional information. This can
+		be used to add population markers, tentative genus groups, etc.</p>
 
-  Note that in general, you do not have to worry about remembering
-  TSNs.  Tethys uses TSNs internally, but will translate TSNs to/from
-  Latin names or user-defined abbreviations both when querying and
-  presenting results.
+	<p>ITIS does not describe abiotic sounds, Tethys records such
+		sounds as follows:
+	<ol>
+		<li>For anthropogenic signals, the Tethys convention is to use <em>Homo
+				sapiens</em>, TSN 180092, for the species code and describe the
+			human-generated signal via a call type, e.g. ship, mid-frequency
+			active sonar, etc.
+		</li>
+		<li>Tethys reserves the TSN -10 for geophonic signals. The call
+			type is used to describe the source. Examples include ambient sound,
+			earthquake, rain, etc. Note that negative TSNs are not part of the
+			ITIS standard.</li>
+	</ol>
+	</p>
 
-  <h2> Call types </h2>
+	Note that in general, you do not have to worry about remembering TSNs.
+	Tethys uses TSNs internally, but will translate TSNs to/from Latin
+	names or user-defined abbreviations both when querying and presenting
+	results.
 
-  <p>
-    Some detectors identify specific call types.  When this is the
-    case, users will need to specify the call type name.  While
-    species names are standardized in Tethys, call names do not have a
-    well-defined standard and experts frequently use different names
-    for the same type of call.  Consequently, Tethys does not provide a
-    standard coding for call types and users are free to choose the call
-    type names with which they feel most comfortable.
-  </p>
+	<h2>Call types</h2>
 
-  <p>
-    That said, the authors of Tethys do however provide a list of recommend call
-    types for many species.  These recommendations can be accessed in the
-    <a href="https://ars.els-cdn.com/content/image/1-s2.0-S1574954115001983-mmc1.docx">
-    supplemental information</a> of the open access article "Management of acoustic metadata
-    for bioacoustics," Roch et al. (2016),
-    (<a href="https://doi.org/10.1016/j.ecoinf.2015.12.002">DOI:10.1016/j.ecoinf.2015.12.002</a>).
-  </p>
-  
-  <h2>
-    Export dialog
-  </h2>
+	<p>Some detectors identify specific call types. When this is the
+		case, users will need to specify the call type name. While species
+		names are standardized in Tethys, call names do not have a
+		well-defined standard and experts frequently use different names for
+		the same type of call. Consequently, Tethys does not provide a
+		standard coding for call types and users are free to choose the call
+		type names with which they feel most comfortable.</p>
 
-  <p>
-    During export of records that are species-specific, a dialog will
-    appear that lists the types of events that were found by PAMGuard
-    modules.  This dialog permits users to specify how the ad-hoc species
-    species/call encoding scheme used by PAMGuard modules can be systematically
-    translated to the TSNs and call types are stored in Tethys.
-  </p>
+	<p>
+		That said, the authors of Tethys do however provide a list of
+		recommend call types for many species. These recommendations can be
+		accessed in the <a
+			href="https://ars.els-cdn.com/content/image/1-s2.0-S1574954115001983-mmc1.docx">
+			supplemental information</a> of the open access article "Management of
+		acoustic metadata for bioacoustics," Roch et al. (2016), (<a
+			href="https://doi.org/10.1016/j.ecoinf.2015.12.002">DOI:10.1016/j.ecoinf.2015.12.002</a>).
+	</p>
 
-  <p>
-    PAMGuard events typically are a short name that represents the
-    species and/or potentially a call.  Knowledge of the PAMGuard
-    modules that were run and the data on which they executed will let
-    a user infer what should be recorded.
-    
-    The dialog below shows a sample set of events produced by one or more PAMGuard modules
-    using the names:  HP, DO, SON, KW, UNK, and PHP:
+	<p>
+		Within PAMGuard, different detectors have different numbers of call
+		types. Some, such as the <a
+			href="../../../detectors/whistleMoanHelp/docs/whistleMoan_Overview.html">Whistle
+			and Moan detector</a>, have only one fixed call type "Tonal", for others
+		such as the <a
+			href="../../../detectors/clickDetectorHelp/docs/ClickDetector_clickClassification.html">Click
+			Detector</a>, the user can define any number of different call types in
+		the click classification configuration. The Tethys interface allows
+		the user to map the internal call types from PAMGuard to ITIS species
+		codes and call types.
+	</p>
 
-  <div>
-      <img src="./images/species_codes.png" class=".center"/>
-  </div>
+	<h2>Export dialog</h2>
 
-  The dialog above was produced from detections on data that were
-  recorded near the mouth of the River Tay in Scotland.  Consequently,
-  we can infer that the harbour porpoise that is denoted by "HP" is
-  <em>Phocena phocena</em>, the only harbour porpoise endemic to
-  Scottish waters.
-  </p>
-  
-  An ITIS code and call/sound type can be associated with each event.  The dialog lists:
-  <ul>
-    <li>
-      Name - The ad-hoc name given by the PAMGuard module.  This may not be changed.
-    </li>
+	<p>Before you can export records to Tethys, you must complete a
+		mapping that can translate the ad-hoc encodings defined within
+		PAMGuard to valid ITIS codes and call types. The dialog for these
+		mappings can be accessed in two ways, firstly, in the table of
+		PAMGuard data blocks in the lower left of the display, right click on
+		any row and select the menu item "PAMGuard ITIS Species mapping ...",
+		Otherwise, a similar dialog will appear as a page with the export
+		wizard once you've pressed the "Export ..." button.</p>
 
-    <li>
-      ITIS code -This is the ITIS TSN that is associated with PAMGuard
-      event code.  Click on Find to inovke the TSN
-      search dialog whose behavior is described in the <a href="#TSNLookup">next
-	section</a>.
-      <p>
-	If you happen to know the TSN, you
-	can enter it directly.  Pressing Find after typing the TNS will
-	populate the Latin and English vernauclar names so that you may
-	verify your TSN was entered correctly.
-      </p>
-    </li>
+	<p>PAMGuard events typically are a short name that represents the
+		species and/or potentially a call. Knowledge of the PAMGuard modules
+		that were run and the data on which they executed will let a user
+		infer what should be recorded. The dialog below shows a sample set of
+		species defined in the PAMGuard click detector, where the user has
+		defined the codes Porpoise, BWC, Oo, Pm, UNK, and Zc. Note that the
+		first entry "Click" has been added automatically as a default for when
+		no classification result was returned.
+	<div>
+		<img src="./images/species_codes1a.png" class=".center" />
+	</div>
+	<br> In the dialog above, we can infer that the only porpoise
+	present in the study area was Harbour Porpoise, so have selected ITIS
+	code 180473,
+	<em>Phocoena phocoena</em>. However, the identity of species BWC is
+	unclear, though believed to be some type of beaked whale, so it has
+	been given the code 770799 for
+	<em>Hyperoodontidae</em>.
 
-    <li> Call / sound type - This will default to the code provided by
-      the module but should be updated to specify an appropriate call
-      type or left blank to indicate that the detection is not related
-      to a specific call type.  In the case of a porpoise detector,
-      the likely call type would be "Clicks".
-      <strong>We should double check that no Call element is generated when this is blank.</strong>
-    </li>
-  </ul>
+	</p>
 
-  <p>
-  Once all species names and call/sound types have been identified, press the Okay button.
-  </p>
+	An ITIS code and call/sound type can be associated with each event. The
+	dialog lists:
+	<ul>
+		<li>Name - The ad-hoc name given by the PAMGuard module. This may
+			not be changed.</li>
+
+		<li>ITIS code -This is the ITIS TSN that is associated with
+			PAMGuard event code. Click on Find to inovke the TSN search dialog
+			whose behavior is described in the <a href="#TSNLookup">next
+				section</a>.
+			<p>If you happen to know the TSN, you can enter it directly.
+				Pressing Find after typing the TNS will populate the Latin and
+				English vernauclar names so that you may verify your TSN was entered
+				correctly.</p>
+		</li>
+
+		<li>Call / sound type - This will default to the code provided by
+			the module but should be updated to specify an appropriate call type
+			or left blank to indicate that the detection is not related to a
+			specific call type. In the case of a porpoise detector, the likely
+			call type would be "Clicks". <strong>We should double check
+				that no Call element is generated when this is blank.</strong>
+		</li>
+	</ul>
+
+	<p>Once all species names and call/sound types have been
+		identified, press the Okay button.</p>
 
 
-  
-  <a name="TSNLookup"></a>
-  <h2> Searching for ITIS Taxonomic Serial Numbers (TSNs) </h2>
 
-  <p>
-    As noted above, pressing Find without typing a TSN will bring up a
-    search dialog:
-  </p>
+	<a name="TSNLookup"></a>
+	<h2>Searching for ITIS Taxonomic Serial Numbers (TSNs)</h2>
 
-  <div>
-    <image src="./images/species_search.png" class=".center"/>
-  </div>
-  
-  <p>
-    The top of this dialog has a search box where one can enter either
-    a Latin name or the common name for a species.  The Tethys server
-    will search for all species that match the search-box contents.
-    For many species, there are common name entries in languages
-    other than English, and these are searched as well.
-  </p>
-  <p>
-    Once you press the search button, a list will appear with all
-    matches for your search term.  If there are too many, a scroll bar
-    will permit you to look through the list.  Select the entry that
-    you wish and press OK.  The TSN on the species dialog will be
-    populated along with the Latin name and common names from the ITIS
-    database.
-  </p>
+	<p>As noted above, pressing Find without typing a TSN will bring up
+		a search dialog:</p>
 
+	<div>
+		<image src="./images/species_search.png" class=".center" />
+	</div>
 
-    <br></br>
-    <br></br>
+	<p>The top of this dialog has a search box where one can enter
+		either a Latin name or the common name for a species. The Tethys
+		server will search for all species that match the search-box contents.
+		For many species, there are common name entries in languages other
+		than English, and these are searched as well.</p>
+	<p>Once you press the search button, a list will appear with all
+		matches for your search term. If there are too many, a scroll bar will
+		permit you to look through the list. Select the entry that you wish
+		and press OK. The TSN on the species dialog will be populated along
+		with the Latin name and common names from the ITIS database.</p>
+	<h2>Export and Import</h2>
+	<p>
+		Entering all of these codes can get a little tedious and you'll
+		hopefully also want to be consistent between your different datasets.
+		PAMGuard therefore has options to save the species mapping to a file,
+		which can then be re-imported into a different configuration. 
+		</p>
+		Mappings are stored individually for each PAMGuard datablock and are identified
+		by the datablock name. To Export, go to the "Tethys/Export Species Maps ..." menu
+		and in the dialog, select the maps you want to export.</p>
+<br><br>
+	<div>
+		<image src="./images/exportmap.png" class=".center" />
+	</div>
+	<br>
+	<p>You will be then be asked for the name of a file to export to and data will be saved to that 
+	file. </p>
+	<p>Importing is similar: From the Tethys menu, select "Import Species Maps ... ", you will be asked
+	to select a previously exported file, and can then choose which maps to import.</p>
+		
+		<br></br>
+		<br></br>
+	<p class="prevLink">
+		<a href="detect_localize.html">Previous: Detections &
+			Localizations</a>
+	</p>
+	<p class="nextLink">
+		<a href="tethys_mappings.html">Next: Tethys / PAMGuard mappings</a>
+	</p>
 
-  <p class="prevLink">
-    <a href="detect_localize.html">Previous: Detections & Localizations</a>
-  </p>
-  <p class="nextLink">
-    <a href="tethys_mappings.html">Next: Tethys / PAMGuard mappings</a>
-  </p>
-  
-</body>
+</body>

src/rawDeepLearningClassifier/logging/DLAnnotationSQL.java

@@ -7,6 +7,7 @@ import org.json.JSONArray;
 import org.json.JSONObject;
 
 import PamguardMVC.PamDataUnit;
+import annotation.xml.AnnotationXMLWriter;
 import generalDatabase.EmptyTableDefinition;
 import generalDatabase.PamTableItem;
 import generalDatabase.SQLLoggingAddon;
@@ -163,8 +164,10 @@ public class DLAnnotationSQL implements SQLLoggingAddon   {
 		//to make this a matrix
 		JSONArray classIDArray = new JSONArray();
 		short[] classID  = arrayList.get(0).getClassNames();
-		for (short aClassID : classID) {
-			classIDArray.put(aClassID); 
+		if (classID != null) {
+			for (short aClassID : classID) {
+				classIDArray.put(aClassID); 
+			}
 		}
 
 		jsonObject.put(PREDICTIONS_JSON_KEY, matrixArray);

src/rawDeepLearningClassifier/logging/DLAnnotationType.java

@@ -5,6 +5,7 @@ import annotation.CentralAnnotationsList;
 import annotation.DataAnnotationType;
 import annotation.binary.AnnotationBinaryHandler;
 import annotation.dataselect.AnnotationDataSelCreator;
+import annotation.xml.AnnotationXMLWriter;
 import generalDatabase.SQLLoggingAddon;
 import rawDeepLearningClassifier.DLControl;
 import rawDeepLearningClassifier.dataPlotFX.DLSymbolModifier;
@@ -105,6 +106,12 @@ public class DLAnnotationType extends DataAnnotationType<DLAnnotation>  {
 			return dlDataSelectorCreator;
 		}
 
+		@Override
+		public AnnotationXMLWriter<DLAnnotation> getXMLWriter() {
+			// override since the SQLLogging one seems to output a load of Json. could replace 
+			// with something a bit nicer that makes xml. 
+			return null;
+		}
 		
 
 

src/tethys/TethysControl.java

@@ -18,6 +18,7 @@ import java.util.ArrayList;
 import javax.swing.JFileChooser;
 import javax.swing.JFrame;
 import javax.swing.JMenu;
+import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
 import javax.swing.SwingUtilities;
 import javax.swing.Timer;
@@ -31,6 +32,7 @@ import PamController.PamSettingManager;
 import PamController.PamSettings;
 import PamModel.SMRUEnable;
 import PamUtils.PamFileFilter;
+import PamView.PamGui;
 import PamView.PamTabPanel;
 import PamView.dialog.warn.WarnOnce;
 import PamguardMVC.PamDataBlock;
@@ -161,7 +163,7 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 	 * @param parentFrame
 	 * @return
 	 */
-	public JMenuItem createTethysMenu(Frame parentFrame) {
+	public JMenu createTethysMenu(Frame parentFrame) {
 		JMenu tethysMenu = new JMenu("Tethys");
 //		JMenuItem tethysExport = new JMenuItem("Export ...");
 //		tethysMenu.add(tethysExport);
@@ -216,24 +218,24 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 		});
 		tethysMenu.add(showDeps);
 		
-		JMenuItem cals = new JMenuItem("Export calibrations");
-		cals.addActionListener(new ActionListener() {
-			
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				calibrationHandler.exportAllCalibrations();
-			}
-		});
-		tethysMenu.add(cals);
+//		JMenuItem cals = new JMenuItem("Export calibrations");
+//		cals.addActionListener(new ActionListener() {
+//			
+//			@Override
+//			public void actionPerformed(ActionEvent e) {
+//				calibrationHandler.exportAllCalibrations();
+//			}
+//		});
+//		tethysMenu.add(cals);
 		
 		tethysMenu.addSeparator();
 		JMenuItem mapItem = new JMenuItem("Export species maps ...");
-		mapItem.setToolTipText("Export all species maps (PAMGuard codes to ITIS codes to file for import into other configurations");
+		mapItem.setToolTipText("Export species maps (save PAMGuard species names to ITIS codes mapping to file for import into other configurations)");
 				mapItem.addActionListener(SpeciesMapManager.getInstance().getExportAction(parentFrame));
 		tethysMenu.add(mapItem);
 		
 		mapItem = new JMenuItem("Import species maps ...");
-		mapItem.setToolTipText("Import species maps (PAMGuard codes to ITIS codes to file for import into other configurations");
+		mapItem.setToolTipText("Import species maps (PAMGuard species names to ITIS code mappings exported from other configurations)");
 		mapItem.addActionListener(SpeciesMapManager.getInstance().getImportAction(parentFrame));
 		tethysMenu.add(mapItem);
 		
@@ -248,6 +250,32 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 		return tethysMenu;
 	}
 
+	public JMenuBar getTabSpecificMenuBar(Frame parentFrame, JMenuBar standardMenu, PamGui pamGui) {
+		JMenuItem aMenu;
+		// start by making a completely new copy.
+		//		if (clickTabMenu == null) {
+		JMenuBar tabMenu = standardMenu;
+		try {
+		for (int i = 0; i < tabMenu.getMenuCount(); i++) {
+			if (tabMenu.getMenu(i).getText().equals("Settings")) {
+				//clickTabMenu.remove(clickTabMenu.getMenu(i));
+
+				aMenu = createDetectionMenu(parentFrame);
+				String txt = aMenu.getText();
+				tabMenu.add(aMenu, i+1);
+
+
+				break;
+			}
+		}
+		}
+		catch (Exception e) {
+			return standardMenu;
+		}
+		//		}
+		return tabMenu;
+	}
+
 	protected void openTempDocuments() {
 		File tempFolder = dbxmlConnect.checkTempFolder();
 		if (tempFolder == null) {
@@ -509,6 +537,12 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 				tethysTaskManager.generateTasks();
 			}
 			break;
+		case PamControllerInterface.ADD_CONTROLLEDUNIT:
+		case PamControllerInterface.REMOVE_CONTROLLEDUNIT:
+			if (PamController.getInstance().isInitializationComplete()) {
+				sendStateUpdate(new TethysState(StateType.UPDATESERVER)); 
+			}
+			break;
 		}
 	}
 

src/tethys/calibration/swing/CalibrationProcessCard.java

@@ -94,6 +94,7 @@ public class CalibrationProcessCard extends CalibrationsCard {
 		c.gridx++;
 		c.gridwidth = 2;
 		processPanel.add(version, c);
+		version.setToolTipText("Serial number of calibration equipment");
 		c.gridx = 0;
 		c.gridy++;
 		c.gridwidth = 1;
@@ -107,7 +108,9 @@ public class CalibrationProcessCard extends CalibrationsCard {
 		c.gridwidth = 2;
 		processPanel.add(qaComment, c);
 
-		this.add(BorderLayout.CENTER, makeScrollablePanel(software, "Calibration method"));
+		JScrollPane pane;
+		this.add(BorderLayout.CENTER, pane = makeScrollablePanel(software, "Software / method detail"));
+		pane.setToolTipText("Method detail, including details of any software used / references to published methods, etc.");
 		
 	}
 

src/tethys/detection/DetectionsHandler.java

@@ -811,15 +811,15 @@ public class DetectionsHandler extends CollectionHandler {
 		/**
 		 * Check the species map is OK before doing anything. 
 		 */
-		DataBlockSpeciesManager spManager = dataBlock.getDatablockSpeciesManager();
-		if (spManager != null) {
-			String error = spManager.checkSpeciesMapError();
-			if (error != null) {
-				PamDialog.showWarning(PamController.getMainFrame(), "Datablock species manager error", error);
-				spManager.showSpeciesDialog();
-				return;
-			}
-		}
+//		DataBlockSpeciesManager spManager = dataBlock.getDatablockSpeciesManager();
+//		if (spManager != null) {
+//			String error = spManager.checkSpeciesMapError();
+//			if (error != null) {
+//				PamDialog.showWarning(PamController.getMainFrame(), "Datablock species manager error", error);
+//				spManager.showSpeciesDialog();
+//				return;
+//			}
+//		}
 
 		DetectionsExportWizard.showDialog(tethysControl.getGuiFrame(), tethysControl, dataBlock, true);
 

src/tethys/species/DataBlockSpeciesManager.java

@@ -190,7 +190,7 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> /*implement
 	}
 
 	public void showSpeciesDialog() {
-		DataBlockSpeciesDialog.showDialog(PamController.getMainFrame(), dataBlock);
+		DataBlockSpeciesDialog.showDialog(PamController.getMainFrame(), dataBlock, null);
 	}
 
 	/**
@@ -253,6 +253,18 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> /*implement
 		return null;
 	}
 
+	/**
+	 * Used only in debug mode to clear the species map. Just used while
+	 * debugging so that I can check that it's easy to recreate the map 
+	 * and that dialogs don't go screwy when it's empty. 
+	 */
+	public void clearMap() {
+		if (datablockSpeciesMap == null) {
+			return;
+		}
+		datablockSpeciesMap.clearMap();
+	}
+
 	/*
 	@Override
 	public String getUnitName() {

src/tethys/species/SpeciesMapManager.java

@@ -177,7 +177,7 @@ public class SpeciesMapManager implements PamSettings {
 		return new ActionListener() {
 			@Override
 			public void actionPerformed(ActionEvent e) {
-				importSpeciesMaps(parentFrame);
+				importSpeciesMaps(parentFrame, null);
 			}
 		};
 	}
@@ -190,7 +190,7 @@ public class SpeciesMapManager implements PamSettings {
 	public boolean exportSpeciesMaps(Window parentFrame) {
 		// gather the species maps from the data blocks...
 		gatherSpeciesMaps();
-		GlobalSpeciesMap toExport = SpeciesMapIODialog.showDialog(parentFrame, globalSpeciesMap, true);
+		GlobalSpeciesMap toExport = SpeciesMapIODialog.showDialog(parentFrame, globalSpeciesMap, true, null);
 		if (toExport == null) {
 			return false;
 		}
@@ -238,9 +238,10 @@ public class SpeciesMapManager implements PamSettings {
 	/**
 	 * Import global species maps from selected file. 
 	 * @param parentFrame
+	 * @param selectedBlock specific block, which will get checked by default in the dialog. Can be null
 	 * @return
 	 */
-	public boolean importSpeciesMaps(Window parentFrame) {
+	public boolean importSpeciesMaps(Window parentFrame, String selectedBlock) {
 		JFileChooser chooser = getFileChooser();
 		int ans = chooser.showOpenDialog(parentFrame);
 		if (ans != JFileChooser.APPROVE_OPTION) {
@@ -264,7 +265,7 @@ public class SpeciesMapManager implements PamSettings {
 			return false;
 		}
 
-		GlobalSpeciesMap keptMaps = SpeciesMapIODialog.showDialog(parentFrame, readSpeciesMap, false);
+		GlobalSpeciesMap keptMaps = SpeciesMapIODialog.showDialog(parentFrame, readSpeciesMap, false, selectedBlock);
 		if (keptMaps == null) {
 			return false;
 		}

src/tethys/species/swing/DataBlockSpeciesDialog.java

@@ -18,16 +18,27 @@ import PamView.panel.PamNorthPanel;
 import PamguardMVC.PamDataBlock;
 import tethys.species.SpeciesMapManager;
 
+/**
+ * Dialog to edit ITIS species codes for a datablock. 
+ * @author dg50
+ *
+ */
 public class DataBlockSpeciesDialog extends PamDialog {
 
 	private static final long serialVersionUID = 1L;
 
 	private DataBlockSpeciesPanel speciesPanel;
 	
-	private DataBlockSpeciesDialog(Window parentFrame, PamDataBlock dataBlock) {
+	/**
+	 * Dialog to edit ITIS species codes. 
+	 * @param parentFrame parent window
+	 * @param dataBlock data block 
+	 * @param singleSpecies single species if only one species to be shown. null for all species. 
+	 */
+	private DataBlockSpeciesDialog(Window parentFrame, PamDataBlock dataBlock, String singleSpecies) {
 		super(parentFrame, dataBlock.getDataName() +  " species", false);
 		JPanel mainPanel = new JPanel(new BorderLayout());
-		speciesPanel = new DataBlockSpeciesPanel(dataBlock);
+		speciesPanel = new DataBlockSpeciesPanel(dataBlock, singleSpecies);
 		mainPanel.add(BorderLayout.CENTER, speciesPanel.getDialogComponent());
 		
 		JButton itisButton = new JButton("Go to ITIS web site");
@@ -39,7 +50,7 @@ public class DataBlockSpeciesDialog extends PamDialog {
 			}
 		});
 		JPanel nPanel = new JPanel(new BorderLayout());
-		nPanel.setBorder(new TitledBorder("Code management"));
+		nPanel.setBorder(new TitledBorder("ITIS Code Management"));
 		nPanel.add(BorderLayout.EAST, new PamNorthPanel(itisButton));
 		String otherMsg = 
 				"<html>Specify an ITIS taxonomic serial number (coding)."
@@ -61,8 +72,15 @@ public class DataBlockSpeciesDialog extends PamDialog {
 		PamGui.openURL("https://www.itis.gov");
 	}
 
-	public static void showDialog(Window parentFrame, PamDataBlock dataBlock) {
-		DataBlockSpeciesDialog speciesDialog = new DataBlockSpeciesDialog(parentFrame, dataBlock);
+	/**
+	 * 
+	 * Open Dialog to edit ITIS species codes. 
+	 * @param parentFrame parent window
+	 * @param dataBlock data block 
+	 * @param singleSpecies single species if only one species to be shown. null for all species. 
+	 */
+	public static void showDialog(Window parentFrame, PamDataBlock dataBlock, String singleSpecies) {
+		DataBlockSpeciesDialog speciesDialog = new DataBlockSpeciesDialog(parentFrame, dataBlock, singleSpecies);
 		speciesDialog.setParams();
 		speciesDialog.setVisible(true);
 	}

src/tethys/species/swing/DataBlockSpeciesPanel.java

@@ -26,9 +26,18 @@ public class DataBlockSpeciesPanel implements PamDialogPanel {
 	
 	private ArrayList<SpeciesSubPanel> subPanels = new ArrayList<>();
 
-	public DataBlockSpeciesPanel(PamDataBlock dataBlock) {
+	private String singleSpecies;
+
+	/**
+	 * Panel of info about a species name in PAMGuard relating it to a call type and ITIS 
+	 * code for output to Tethys. 
+	 * @param dataBlock Datablock with a DataBlockSpeciesManager
+	 * @param singleSpecies single species if only one species to be shown. null for all species. 
+	 */
+	public DataBlockSpeciesPanel(PamDataBlock dataBlock, String singleSpecies) {
 		super();
 		this.dataBlock = dataBlock;
+		this.singleSpecies = singleSpecies;
 		mainPanel = new JPanel(new BorderLayout());
 		speciesPanel = new JPanel();
 		JScrollPane scrollPane = new JScrollPane(speciesPanel, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
@@ -53,6 +62,9 @@ public class DataBlockSpeciesPanel implements PamDialogPanel {
 		ArrayList<String> speciesNames = speciesManager.getAllSpeciesCodes();
 		DataBlockSpeciesMap speciesMap = speciesManager.getDatablockSpeciesMap();
 		for (String aSpecies : speciesNames) {
+			if (singleSpecies != null && singleSpecies.equals(aSpecies) == false) {
+				continue;
+			}
 			SpeciesSubPanel subPanel = new SpeciesSubPanel(dataBlock, aSpecies);
 			subPanels.add(subPanel);
 			speciesPanel.add(subPanel.getDialogComponent());

src/tethys/species/swing/SpeciesMapIODialog.java

@@ -34,6 +34,8 @@ public class SpeciesMapIODialog extends PamDialog {
 	
 	private JPanel boxesPanel;
 	
+	private String preselectedBlock;
+	
 	/**
 	 * @param parentFrame
 	 * @param title
@@ -48,7 +50,7 @@ public class SpeciesMapIODialog extends PamDialog {
 		setDialogComponent(boxesPanel);
 	}
 	
-	public static GlobalSpeciesMap showDialog(Window parentFrame, GlobalSpeciesMap speciesMap, boolean export) {
+	public static GlobalSpeciesMap showDialog(Window parentFrame, GlobalSpeciesMap speciesMap, boolean export, String selectedBlock) {
 		if (singleInstance == null) {
 			singleInstance = new SpeciesMapIODialog(parentFrame);
 		}
@@ -56,6 +58,7 @@ public class SpeciesMapIODialog extends PamDialog {
 			singleInstance.showWarning("No Data block species maps are defined");
 			return speciesMap;
 		}
+		singleInstance.preselectedBlock = selectedBlock;
 		singleInstance.setTitle(export ? "Export species maps" : "Import species maps");
 		singleInstance.setParams(speciesMap);
 		singleInstance.setVisible(true);
@@ -86,6 +89,9 @@ public class SpeciesMapIODialog extends PamDialog {
 			c.gridy++;
 			blockBoxes[iBox] = new JCheckBox(item.getKey()); 
 			boxesPanel.add(blockBoxes[iBox], c);	
+			if (item.getKey().equals(preselectedBlock)) {
+				blockBoxes[iBox].setSelected(true);
+			}
 			iBox++;
 		}
 		

src/tethys/swing/DatablockSynchPanel.java

@@ -20,10 +20,11 @@ import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.JScrollPane;
 import javax.swing.JTable;
+import javax.swing.ListSelectionModel;
 import javax.swing.border.TitledBorder;
 import javax.swing.table.AbstractTableModel;
 
-
+import PamModel.SMRUEnable;
 import PamUtils.PamCalendar;
 import PamView.dialog.warn.WarnOnce;
 import PamView.panel.PamPanel;
@@ -49,10 +50,8 @@ public class DatablockSynchPanel extends TethysExportPanel {
 	private ArrayList<DatablockSynchInfo> dataBlockSynchInfo;
 	
 	private ArrayList<StreamTableObserver> tableObservers = new ArrayList<>();
-	
-//	private TippedButton exportButton;
 
-//	private JLabel exportWarning;
+	private int selectedRow = -1;
 	
 	
 	public DatablockSynchPanel(TethysControl tethysControl) {
@@ -65,31 +64,13 @@ public class DatablockSynchPanel extends TethysExportPanel {
 		new SwingTableColumnWidths(tethysControl.getUnitName()+"SynchTable", synchTable);
 		JScrollPane scrollPane = new JScrollPane(synchTable);
 		mainPanel.add(BorderLayout.CENTER, scrollPane);
-//		PamPanel ctrlPanel = new PamPanel(new BorderLayout());
-//		exportButton = new TippedButton("Export ...", "Export Detections document");
-//		exportWarning = new JLabel("  ");
-//		exportWarning.setForeground(Color.RED);
-//		ctrlPanel.add(BorderLayout.WEST, exportButton);
-//		ctrlPanel.add(BorderLayout.CENTER, exportWarning);
-//		mainPanel.add(BorderLayout.NORTH, ctrlPanel);
-
 		
 		synchTable.addMouseListener(new MouseActions());
 		synchTable.addKeyListener(new KeyActions());
+		synchTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 		
-//		exportButton.addActionListener(new ActionListener() {
-//			@Override
-//			public void actionPerformed(ActionEvent e) {
-//				exportData();
-//			}
-//		});
 		enableExportButton();
 	}
-
-//	@Override
-//	public JComponent getComponent() {
-//		return mainPanel;
-//	}
 	
 	private class KeyActions extends KeyAdapter {
 		@Override
@@ -132,6 +113,7 @@ public class DatablockSynchPanel extends TethysExportPanel {
 		if (row < 0) {
 			return row;
 		}
+		selectedRow = row;
 		DatablockSynchInfo synchInfo = dataBlockSynchInfo.get(row);
 //		datablockDetectionsPanel.setDataBlock(synchInfo.getDataBlock());
 		notifyObservers(synchInfo.getDataBlock());
@@ -166,12 +148,15 @@ public class DatablockSynchPanel extends TethysExportPanel {
 			return;
 		}
 
-		PamDataBlock dataBlock = dataBlockSynchInfo.get(rows[0]).getDataBlock();
-		String mapError = checkSpeciesManager(dataBlock);
-		if (mapError != null) {
-			disableExport("Unable to export due to species map error: " + mapError + ". Right click table row to edit species list");
-			return;
-		}
+		/*
+		 * don't do this any more since the species map can be edited within the export Wizard.
+		 */
+//		PamDataBlock dataBlock = dataBlockSynchInfo.get(rows[0]).getDataBlock();
+//		String mapError = checkSpeciesManager(dataBlock);
+//		if (mapError != null) {
+//			disableExport("Unable to export due to species map error: " + mapError + ". Right click table row to edit species list");
+//			return;
+//		}
 		
 		enableExport(true);
 	}
@@ -207,7 +192,7 @@ public class DatablockSynchPanel extends TethysExportPanel {
 			return;
 		}
 		JPopupMenu popMenu = new JPopupMenu();
-		JMenuItem menuItem = new JMenuItem("Species info ...");
+		JMenuItem menuItem = new JMenuItem("PAMGuard ITIS Species mapping ...");
 		menuItem.addActionListener(new ActionListener() {
 			@Override
 			public void actionPerformed(ActionEvent e) {
@@ -215,6 +200,19 @@ public class DatablockSynchPanel extends TethysExportPanel {
 			}
 		});
 		popMenu.add(menuItem);
+		if (SMRUEnable.isDevEnable()) {
+			menuItem = new JMenuItem("Clear species map");
+			menuItem.addActionListener(new ActionListener() {
+				@Override
+				public void actionPerformed(ActionEvent e) {
+					int ans = WarnOnce.showWarning("Delete datamap", "Are you sure ?", WarnOnce.YES_NO_OPTION);
+					if (ans == WarnOnce.OK_OPTION) {
+						speciesManager.clearMap();
+					}
+				}
+			});	
+			popMenu.add(menuItem);
+		}
 		popMenu.show(e.getComponent(), e.getX(), e.getY());
 	}
 
@@ -263,7 +261,7 @@ public class DatablockSynchPanel extends TethysExportPanel {
 
 	private class SynchTableModel extends AbstractTableModel {
 
-		String[] columnNames = {"Data Stream", "N PAM Datas", "PAMGuard Time", "Tethys Documents"};//, "Tethys Time", "Options"};
+		String[] columnNames = {"Select", "Data Stream", "N Data", "PAMGuard Time", "Tethys Documents"};//, "Tethys Time", "Options"};
 		
 		@Override
 		public int getRowCount() {
@@ -278,25 +276,38 @@ public class DatablockSynchPanel extends TethysExportPanel {
 		@Override
 		public String getColumnName(int column) {
 			return columnNames[column];
+		}		
+		
+		@Override
+		public Class<?> getColumnClass(int columnIndex) {
+			if (columnIndex == 0) {
+				return Boolean.class;
+			}
+			return super.getColumnClass(columnIndex);
 		}
 
 		@Override
 		public Object getValueAt(int rowIndex, int columnIndex) {
-			DatablockSynchInfo synchInfo = getSychInfos().get(rowIndex);
-			return getValueAt(synchInfo, columnIndex);
+			if (columnIndex == 0) {
+				return rowIndex == selectedRow;
+			}
+			else {
+				DatablockSynchInfo synchInfo = getSychInfos().get(rowIndex);
+				return getValueAt(synchInfo, columnIndex);
+			}
 		}
 
 		private Object getValueAt(DatablockSynchInfo synchInfo, int columnIndex) {
 			OfflineDataMap dataMap = synchInfo.getDataBlock().getPrimaryDataMap();
 			switch (columnIndex) {
-			case 0:
-				return synchInfo.getDataBlock().getLongDataName();
 			case 1:
+				return synchInfo.getDataBlock().getLongDataName();
+			case 2:
 				if (dataMap == null) {
 					return null;
 				}
 				return synchInfo.getDataBlock().getPrimaryDataMap().getDataCount();
-			case 2:
+			case 3:
 				if (dataMap == null) {
 					return null;
 				}
@@ -306,7 +317,7 @@ public class DatablockSynchPanel extends TethysExportPanel {
 				long start = synchInfo.getDataBlock().getPrimaryDataMap().getFirstDataTime();
 				long stop = synchInfo.getDataBlock().getPrimaryDataMap().getLastDataTime();
 				return String.format("%s - %s", PamCalendar.formatDBDateTime(start), PamCalendar.formatDBDateTime(stop));
-			case 3:
+			case 4:
 				return synchInfo.getDetectionDocumentCount() +  synchInfo.getLocalizationDocumentCount();
 			}
 			return null;

src/tethys/swing/TethysTabPanel.java

@@ -17,7 +17,7 @@ public class TethysTabPanel implements PamTabPanel {
 	
 	@Override
 	public JMenu createMenu(Frame parentFrame) {
-		return null;
+		return tethysContol.createTethysMenu(parentFrame);
 	}
 
 	public TethysTabPanel(TethysControl tethysContol) {

src/tethys/swing/export/CallTypeCard.java

@@ -2,15 +2,23 @@ package tethys.swing.export;
 
 import java.awt.BorderLayout;
 import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.util.ArrayList;
 
+import javax.swing.JButton;
 import javax.swing.JCheckBox;
+import javax.swing.JComponent;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
+import javax.swing.JScrollPane;
 import javax.swing.border.TitledBorder;
 
+import PamController.PamController;
+import PamView.component.PamSettingsIconButton;
 import PamView.dialog.PamGridBagContraints;
 import PamView.dialog.warn.WarnOnce;
+import PamView.panel.PamAlignmentPanel;
 import PamView.wizard.PamWizard;
 import PamguardMVC.PamDataBlock;
 import tethys.TethysControl;
@@ -18,6 +26,8 @@ import tethys.output.StreamExportParams;
 import tethys.species.DataBlockSpeciesManager;
 import tethys.species.DataBlockSpeciesMap;
 import tethys.species.SpeciesMapItem;
+import tethys.species.SpeciesMapManager;
+import tethys.species.swing.DataBlockSpeciesDialog;
 
 /**
  * Wizard card to select call types (species) to export. Only these names will be added to the 
@@ -31,60 +41,183 @@ public class CallTypeCard extends ExportWizardCard {
 //	private DataBlockSpeciesCodes codes;
 	
 	private JCheckBox[] speciesSelection;
+	private JLabel[] itisLabels;
+	private JLabel[] speciesNames;
+	private JLabel[] callTypes;
+	private JCheckBox commonNames;
+	
 	private ArrayList<String> names;
 	
 	private String bitTip = "Select species  / call types to export\n"
 			+ "Only selected types will be added to the Document Effort section";
 
+	private DataBlockSpeciesMap speciesMap;
+
 	public CallTypeCard(TethysControl tethysControl, PamWizard pamWizard, String title, PamDataBlock dataBlock) {
 		super(tethysControl, pamWizard, title, dataBlock);
 		speciesManager = dataBlock.getDatablockSpeciesManager();
-		DataBlockSpeciesMap spMap = speciesManager.getDatablockSpeciesMap();
+		speciesMap = speciesManager.getDatablockSpeciesMap();
 		names = speciesManager.getAllSpeciesCodes();
 		speciesSelection = new JCheckBox[names.size()];
+		itisLabels = new JLabel[names.size()];
+		speciesNames = new JLabel[names.size()];
+		callTypes = new JLabel[names.size()];
 		JPanel spPanel = new JPanel();
-		spPanel.setBorder(new TitledBorder("Species / Call types to export"));
 		spPanel.setLayout(new GridBagLayout());
 		spPanel.setToolTipText(bitTip);
 		PamGridBagContraints c = new PamGridBagContraints();
+		commonNames = new JCheckBox("Species");
+		commonNames.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				fillAllItemInfo();
+			}
+		});
+		String[] tits = {"Select", "PAMGuard Name", "ITIS Code", "Species", "Call Type" };
+		String[] tips = {"Select for export", "Internal PAMGuard Name", "ITIS Species Code", "Species Name (check for common names)", "Call Type (written to Tethys)"};
+		for (int i = 0; i < tits.length; i++) {
+			JComponent lab;
+			if (i == 3) {
+				spPanel.add(lab=commonNames, c);
+			}
+			else {
+				spPanel.add(lab = new JLabel(tits[i], JLabel.LEFT), c);
+			}
+			lab.setToolTipText(tips[i]);
+			c.gridx++;
+		}
 		for (int i = 0; i < names.size(); i++) {
 			c.gridx = 0;
-			speciesSelection[i] = new JCheckBox(names.get(i));
-			spPanel.add(speciesSelection[i], c);
-			SpeciesMapItem item = spMap.getItem(names.get(i));
-			if (item != null) {
-				String latin = item.getLatinName();
-				int itis = item.getItisCode();
-				c.gridx++;
-				spPanel.add(new JLabel(String.format("%d", itis), JLabel.RIGHT), c);
-				c.gridx++;
-				if (latin != null) {
-					spPanel.add(new JLabel(latin));
-				}
-			}
-			
 			c.gridy++;
-		}
+			speciesSelection[i] = new JCheckBox();
+			spPanel.add(speciesSelection[i], c);
+			c.gridx++;
+			spPanel.add(new JLabel(names.get(i)), c);
+			c.gridx++;
+			spPanel.add(itisLabels[i] = new JLabel(), c);
+			c.gridx++;
+			spPanel.add(speciesNames[i] = new JLabel(), c);
+			c.gridx++;
+			spPanel.add(callTypes[i] = new JLabel(), c);
+			fillItemInfo(i);
 
+			c.gridx++;
+			PamSettingsIconButton but = new PamSettingsIconButton();
+			but.setToolTipText("Edit species id and call type");
+			but.addActionListener(new SpeciesAction(i));
+			spPanel.add(but, c);
+		}
+		JPanel nPanel = new PamAlignmentPanel(spPanel, BorderLayout.NORTH);
+		JScrollPane scrollPane = new JScrollPane(nPanel);
+		this.setBorder(new TitledBorder("Species / Call types to export"));
 		this.setLayout(new BorderLayout());
-		this.add(spPanel, BorderLayout.NORTH);
+		this.add(scrollPane, BorderLayout.CENTER);
+		
+		JPanel southPanel = new JPanel(new BorderLayout());
+//		southPanel.setBorder(new TitledBorder("Controls"));
+		JButton importButton = new JButton("Import species mapping");
+		importButton.setToolTipText("Import a species map previously saved from another PAMGuard configuration");
+		importButton.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				importSpeciesMap(importButton);
+			}
+		});
+		southPanel.add(importButton, BorderLayout.WEST);
+		this.add(southPanel, BorderLayout.SOUTH);
+	}
+	
+	private void fillAllItemInfo() {
+		for (int i = 0; i < names.size(); i++) {
+			fillItemInfo(i);
+		}
 	}
 
+	private void fillItemInfo(int itemIndex) {
+		SpeciesMapItem item = speciesMap.getItem(names.get(itemIndex));
+		if (item == null) {
+			itisLabels[itemIndex].setText(null);
+			speciesNames[itemIndex].setText(null);
+			callTypes[itemIndex].setText(null);
+		}
+		else {
+			itisLabels[itemIndex].setText(Integer.valueOf(item.getItisCode()).toString());
+			if (commonNames.isSelected()) {
+				speciesNames[itemIndex].setText(item.getCommonName());
+			}
+			else {
+				speciesNames[itemIndex].setText(item.getLatinName());
+			}
+			callTypes[itemIndex].setText(item.getCallType());
+		}
+		
+	}
+
+	protected void importSpeciesMap(JButton importButton) {
+		SpeciesMapManager mapManager = SpeciesMapManager.getInstance();
+		mapManager.importSpeciesMaps(getPamWizard(), getDataBlock().getLongDataName());
+		// has the map changed ? 
+		DataBlockSpeciesMap newMap = getDataBlock().getDatablockSpeciesManager().getDatablockSpeciesMap();
+		if (newMap != speciesMap) {
+//			System.out.println("Map changed");
+			speciesMap = newMap;
+			fillAllItemInfo();
+		}
+	}
+
+	private class SpeciesAction implements ActionListener {
+
+		private int itemIndex;
+
+		public SpeciesAction(int itemIndex) {
+			this.itemIndex = itemIndex;
+		}
+
+		@Override
+		public void actionPerformed(ActionEvent e) {
+			String name = names.get(itemIndex);
+			DataBlockSpeciesDialog.showDialog(PamController.getMainFrame(), getDataBlock(), name);
+			fillItemInfo(itemIndex);
+		}
+		
+	}
 	@Override
 	public boolean getParams(StreamExportParams cardParams) {
 		int nSel = 0;
+		int nError = 0;
 		for (int i = 0; i < names.size(); i++) {
 			boolean sel = speciesSelection[i].isSelected();
 			cardParams.setSpeciesSelection(names.get(i), sel);
 			if (sel) {
 				nSel++;
 			}
+			if (sel == false) {
+				continue; // don't check items that are not getting exported. 
+			}
+			// check that the item has a valid species code and call type
+			SpeciesMapItem item = speciesMap.getItem(names.get(i));
+			if (item == null) {
+				nError++;
+				continue;
+			}
+			if (item.getItisCode() == 0) {
+				nError ++;
+			}
+			if (item.getCallType() == null || item.getCallType().length() == 0) {
+				nError ++;
+			}
+			
 		}
+		if (nError > 0) {
+			WarnOnce.showWarning("Species / Call type selection", "One or more selected items do not have a valid ITIS code or a Call Type", WarnOnce.WARNING_MESSAGE);
+			return false;
+		}
+		
 		if (nSel == 0) {
 			WarnOnce.showWarning("Species / Call type selection", "You must select at least one species or call type for export", WarnOnce.WARNING_MESSAGE);
-//			return false;
+			return false;
 		}
-		return nSel >= 0;
+		return true;
 	}
 
 	@Override

src/tethys/swing/export/ExportWorkerCard.java

@@ -11,6 +11,7 @@ import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JProgressBar;
 import javax.swing.JTextField;
+import javax.swing.SwingUtilities;
 import javax.swing.border.TitledBorder;
 
 import PamView.dialog.PamGridBagContraints;
@@ -38,6 +39,8 @@ public class ExportWorkerCard extends ExportWizardCard implements DetectionExpor
 	private StreamExportParams streamExportParams;
 
 	private DetectionsExportWizard detectionsExportWizard;
+	
+	private boolean exportDone = false;
 
 	public ExportWorkerCard(DetectionsExportWizard detectionsExportWizard, TethysControl tethysControl, PamDataBlock dataBlock) {
 		super(tethysControl, detectionsExportWizard, "Export", dataBlock);
@@ -103,6 +106,8 @@ public class ExportWorkerCard extends ExportWizardCard implements DetectionExpor
 	}
 
 	protected void exportData() {
+		exportDone = false;
+		
 		DetectionsHandler detHandler = getTethysControl().getDetectionsHandler();
 		
 		detHandler.startExportThread(getDataBlock(), streamExportParams, this);
@@ -116,8 +121,13 @@ public class ExportWorkerCard extends ExportWizardCard implements DetectionExpor
 
 	@Override
 	public boolean getParams(StreamExportParams streamExportParams) {
-		// TODO Auto-generated method stub
-		return true;
+		if (exportDone == false) {
+			exportData();
+			return false;
+		}
+		else {
+			return true;
+		}
 	}
 
 	@Override
@@ -166,6 +176,7 @@ public class ExportWorkerCard extends ExportWizardCard implements DetectionExpor
 			detectionsExportWizard.getCancelButton().setText("Close");
 			detectionsExportWizard.getPreviousButton().setEnabled(false);
 //			getTethysControl().sendStateUpdate(new TethysState(StateType.EXPORTRDATA));
+			exportDone = true;
 			break;
 		case DetectionExportProgress.STATE_WRITING:
 			progressText.setText("Writing to Tethys: " + progress.currentDetections.getId());
@@ -180,6 +191,19 @@ public class ExportWorkerCard extends ExportWizardCard implements DetectionExpor
 		cancel.setEnabled(!stopped);
 		detectionsExportWizard.getCancelButton().setEnabled(stopped);
 		detectionsExportWizard.getPreviousButton().setEnabled(stopped);
+		setButtonName();
+	}
+	
+	private void setButtonName() {
+		String name = exportDone ? "Finish" : "Export";
+		String tip = exportDone ? "Close export wizard" : "Export selected data to Tethys";
+		SwingUtilities.invokeLater(new Runnable() {
+			@Override
+			public void run() {
+				detectionsExportWizard.getOkButton().setText(name);
+				detectionsExportWizard.getOkButton().setToolTipText(tip);
+			}
+		});
 	}
 
 	@Override
@@ -189,7 +213,15 @@ public class ExportWorkerCard extends ExportWizardCard implements DetectionExpor
 		 * we can see here if we're on this or not. 
 		 */
 		super.setVisible(visible);
-		detectionsExportWizard.getOkButton().setEnabled(!visible);
+//		detectionsExportWizard.getOkButton().setEnabled(!visible);
+		if (visible) {
+			// doesn't work because it get's overridden by internal call
+			// to enable controls anyway. 
+			setButtonName();
+		}
+		else {
+			detectionsExportWizard.enableControls(); // sets the button text. 
+		}
 	}
 
 }

src/userDisplay/UserDisplayControl.java

@@ -347,8 +347,8 @@ public class UserDisplayControl extends PamControlledUnit implements
 	@Override
 	public JMenuBar getTabSpecificMenuBar(Frame parentFrame, JMenuBar standardMenu, PamGui pamGui) {
 
-		// always make a new manu - modules may have been added or removed
-		// start bymaking a completely new copy.
+		// always make a new menu - modules may have been added or removed
+		// start by making a completely new copy.
 		spectrogramTabMenu = standardMenu;//pamGui.makeGuiMenu();
 //		if (spectrogramTabMenu == null) {
 			for (int i = 0; i < spectrogramTabMenu.getMenuCount(); i++) {