Update button enablers

And reinstate output of a single deployment document, with non-recording
periods stores in the QA section

And update help TOC for latest help documents.

src/help/JavaHelpSearch/SCHEMA

@@ -1,2 +1,2 @@
 JavaSearch 1.0
-TMAP bs=2048 rt=1 fl=-1 id1=6872 id2=1
+TMAP bs=2048 rt=1 fl=-1 id1=6882 id2=1

src/help/Map.jhm

@@ -54,6 +54,8 @@
 
 <mapID target="classifiers.whistleClassifierHelp.docs.whistleClassifier_Output" url="classifiers/whistleClassifierHelp/docs/whistleClassifier_Output.html"/>
 
+<mapID target="utilities.tethys.docs.calibrations" url="utilities/tethys/docs/calibrations.html"/>
+
 <mapID target="utilities.hydrophoneArrayManagerHelp.docs.Array_Configuration_sec1" url="utilities/hydrophoneArrayManagerHelp/docs/Array_Configuration.html#sec1"/>
 
 <mapID target="sound_processing.fftManagerHelp.docs.noise_removal_medianfilter" url="sound_processing/fftManagerHelp/docs/noise_removal.html#medianfilter"/>
@@ -138,6 +140,8 @@
 
 <mapID target="sound_processing.NoiseBands.Docs.NoiseBands" url="sound_processing/NoiseBands/Docs/NoiseBands.html"/>
 
+<mapID target="utilities.tethys.docs.detect_localize" url="utilities/tethys/docs/detect_localize.html"/>
+
 <mapID target="visual_methods.videoRangeHelp.docs.videoRange_Calibrating" url="visual_methods/videoRangeHelp/docs/videoRange_Calibrating.html"/>
 
 <mapID target="detectors.gpl.docs.detection" url="detectors/gpl/docs/detection.html"/>
@@ -198,6 +202,8 @@
 
 <mapID target="displays.userDisplayHelp.docs.userDisplayPanel" url="displays/userDisplayHelp/docs/userDisplayPanel.html"/>
 
+<mapID target="utilities.tethys.docs.tethys_speciescodes_TSNLookup" url="utilities/tethys/docs/tethys_speciescodes.html#TSNLookup"/>
+
 <mapID target="classifiers.roccaHelp.docs.rocca_Configure_SchoolStats" url="classifiers/roccaHelp/docs/rocca_Configure.html#SchoolStats"/>
 
 <mapID target="visual_methods.loggerFormsHelp.docs.SUBTABS" url="visual_methods/loggerFormsHelp/docs/SUBTABS.html"/>
@@ -276,8 +282,6 @@
 
 <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"/>
@@ -390,6 +394,8 @@
 
 <mapID target="localisation.group3d.docs.3dsimplex" url="localisation/group3d/docs/3dsimplex.html"/>
 
+<mapID target="utilities.tethys.docs.connection" url="utilities/tethys/docs/connection.html"/>
+
 <mapID target="visual_methods.loggerFormsHelp.docs.NOCLEAR" url="visual_methods/loggerFormsHelp/docs/NOCLEAR.html"/>
 
 <mapID target="sound_processing.beamformer.docs.Beamformer_Settings_BF_SourceTab" url="sound_processing/beamformer/docs/Beamformer_Settings.html#BF_SourceTab"/>
@@ -458,6 +464,8 @@
 
 <mapID target="sound_processing.seismicveto.docs.veto_configuration" url="sound_processing/seismicveto/docs/veto_configuration.html"/>
 
+<mapID target="utilities.tethys.docs.deployments" url="utilities/tethys/docs/deployments.html"/>
+
 <mapID target="detectors.whistleMoanHelp.docs.whistleMoan_ConfigNoise_averagesubtraction" url="detectors/whistleMoanHelp/docs/whistleMoan_ConfigNoise.html#averagesubtraction"/>
 
 <mapID target="localisation.largeAperture3D.docs.meal_exercise3_localise" url="localisation/largeAperture3D/docs/meal_exercise3_localise.html"/>
@@ -594,6 +602,8 @@
 
 <mapID target="detectors.gpl.docs.notes" url="detectors/gpl/docs/notes.html"/>
 
+<mapID target="utilities.tethys.docs.tethys_module" url="utilities/tethys/docs/tethys_module.html"/>
+
 <mapID target="sound_processing.fftManagerHelp.docs.FFTEngine_Creating" url="sound_processing/fftManagerHelp/docs/FFTEngine_Creating.html"/>
 
 <mapID target="sound_processing.fftManagerHelp.docs.noise_removal_clickremoval" url="sound_processing/fftManagerHelp/docs/noise_removal.html#clickremoval"/>

src/help/PAMGUARDTOC.xml

@@ -198,10 +198,18 @@
   <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 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"/>
+
+   <tocitem text="Instrument Deployments " target="utilities.tethys.docs.deployments" image="topic"/>
+
+   <tocitem text="Detections and Localizations " target="utilities.tethys.docs.detect_localize" image="topic"/>
+
    <tocitem text="ITIS Species Codes " target="utilities.tethys.docs.tethys_speciescodes" image="topic"/>
 
   </tocitem>

src/tethys/TethysControl.java

@@ -53,7 +53,6 @@ import tethys.output.TethysExportParams;
 import tethys.species.ITISFunctions;
 import tethys.species.SpeciesMapManager;
 import tethys.swing.ProjectDeploymentsDialog;
-import tethys.swing.TethysEnabler;
 import tethys.swing.TethysTabPanel;
 import tethys.swing.XMLStringView;
 import tethys.swing.documents.TethysDocumentsFrame;
@@ -92,12 +91,10 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 	private CalibrationHandler calibrationHandler;
 	
 	private ITISFunctions itisFunctions;
-	private TethysEnabler tethysEnabler;
 
 	public TethysControl(String unitName) {
 		super(unitType, unitName);
 		stateObservers = new ArrayList();
-		tethysEnabler = new TethysEnabler(this);
 		dbxmlConnect = new DBXMLConnect(this);
 		dbxmlQueries = new DBXMLQueries(this, dbxmlConnect);
 		deploymentHandler = new DeploymentHandler(this);
@@ -494,10 +491,10 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 	public ServerStatus checkServer() {
 		ServerStatus serverState = dbxmlConnect.pingServer();
 		if (lastServerStatus == null || lastServerStatus.ok != serverState.ok) {
+			lastServerStatus = serverState; // set before sending notification!
 			sendStateUpdate(new TethysState(StateType.UPDATESERVER));
 		}
-		lastServerStatus = serverState;
+//		lastServerStatus = serverState;
-		tethysEnabler.enableControls(serverState.ok);
 		return serverState;
 	}
 
@@ -704,11 +701,22 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 	}
 
 	/**
-	 * Get a utility class that enables / disables controls depending on server state. 
+	 * @return the lastServerStatus
-	 * @return
 	 */
-	public TethysEnabler getEnabler() {
+	public ServerStatus getLastServerStatus() {
-		return tethysEnabler;
+		return lastServerStatus;
+	}
+	
+	/**
+	 * Quick way for any controls to see that the server is probably OK
+	 * without actually pinging it. 
+	 * @return true if last ping of server was OK
+	 */
+	public boolean isServerOk() {
+		if (lastServerStatus == null) {
+			return false;
+		}
+		return lastServerStatus.ok;
 	}
 
 }

src/tethys/calibration/swing/CalibrationsMainPanel.java

@@ -13,6 +13,7 @@ import javax.swing.border.TitledBorder;
 
 import PamView.panel.PamPanel;
 import tethys.TethysControl;
+import tethys.TethysState;
 import tethys.calibration.CalibrationHandler;
 import tethys.swing.TethysGUIPanel;
 
@@ -41,7 +42,6 @@ public class CalibrationsMainPanel extends TethysGUIPanel {
 		
 		ctrlPanel = new PamPanel(new BorderLayout());
 		exportButton = new JButton("Export ...");
-		tethysControl.getEnabler().addComponent(exportButton);
 		ctrlPanel.add(BorderLayout.WEST, exportButton);
 		warning = new JLabel();
 		ctrlPanel.add(BorderLayout.CENTER, warning);
@@ -64,4 +64,14 @@ public class CalibrationsMainPanel extends TethysGUIPanel {
 		return mainPanel;
 	}
 
+	@Override
+	public void updateState(TethysState tethysState) {
+		super.updateState(tethysState);
+		enableControls();
+	}
+
+	private void enableControls() {
+		exportButton.setEnabled(getTethysControl().isServerOk());
+	}
+
 }

src/tethys/deployment/DeploymentHandler.java

@@ -45,6 +45,9 @@ import dataMap.OfflineDataMapPoint;
 import generalDatabase.DBControlUnit;
 import metadata.MetaDataContol;
 import metadata.PamguardMetaData;
+import nilus.AcousticDataQAType;
+import nilus.AcousticDataQAType.Quality;
+import nilus.AcousticDataQAType.Quality.FrequencyRange;
 import nilus.Audio;
 import nilus.ChannelInfo;
 import nilus.ChannelInfo.DutyCycle;
@@ -403,6 +406,14 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
 	 */
 	private void exportOneDeploymnet(ArrayList<RecordingPeriod> selectedDeployments) {
 		// do the lot, whatever ...
+		Float sampleRate = null;
+		AcquisitionControl daq = (AcquisitionControl) PamController.getInstance().findControlledUnit(AcquisitionControl.class, null);
+		if (daq != null) {
+			DaqSystem system = daq.findDaqSystem(null);
+			AcquisitionParameters daqParams = daq.acquisitionParameters;
+			sampleRate = daqParams.sampleRate;
+		}
+		
 		selectedDeployments = getDeploymentOverview().getRecordingPeriods();
 		int freeId = getTethysControl().getDeploymentHandler().getFirstFreeDeploymentId();
 		RecordingPeriod onePeriod = new RecordingPeriod(selectedDeployments.get(0).getRecordStart(), 
@@ -415,11 +426,37 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
 		deployment.setCruise(globalMeta.getCruise());
 		deployment.setSite(globalMeta.getSite());
 		if (selectedDeployments.size() > 1) {
-			// now need to remove the 
+//			// now need to remove the sampling details - don't though, add invalid periods instead. 
-			SamplingDetails samplingDetails = deployment.getSamplingDetails();
+//			SamplingDetails samplingDetails = deployment.getSamplingDetails();
-			samplingDetails.getChannel().clear();
+//			samplingDetails.getChannel().clear();
-			for (int i = 0; i < selectedDeployments.size(); i++) {
+//			for (int i = 0; i < selectedDeployments.size(); i++) {
-				addSamplingDetails(deployment, selectedDeployments.get(i));
+//				addSamplingDetails(deployment, selectedDeployments.get(i));
+//			}
+			/*
+			 * Instead, we're putting invalid periods into the QA section. 
+			 */
+			AcousticDataQAType qa = deployment.getQualityAssurance();
+			if (qa == null) {
+				deployment.setQualityAssurance(qa = new AcousticDataQAType());
+			}
+			List<Quality> qualityList = qa.getQuality();
+			for (int i = 1; i < selectedDeployments.size(); i++) {
+				long end = selectedDeployments.get(i-1).getRecordStop();
+				long start = selectedDeployments.get(i).getRecordStart();
+				Quality q = new Quality();
+				q.setStart(TethysTimeFuncs.xmlGregCalFromMillis(end));
+				q.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(start));
+				q.setCategory("unusable");
+				if (sampleRate != null) {
+					FrequencyRange f = q.getFrequencyRange();
+					if (f == null) {
+						q.setFrequencyRange(f = new FrequencyRange());
+					}
+					f.setLowHz(0);
+					f.setHighHz(sampleRate/2);
+				}
+				q.setComment("No data (probably off or out of water)");
+				qualityList.add(q);
 			}
 		}
 		DBXMLConnect dbxmlConnect = getTethysControl().getDbxmlConnect();

src/tethys/deployment/swing/DeploymentDataCard.java

@@ -100,9 +100,9 @@ public class DeploymentDataCard extends PamWizardCard {
 		/* 
 		 * temp code to only allow export of multiple documents. 
 		 */
-		exportOptions.separateDeployments = true;
+//		exportOptions.separateDeployments = true;
-		exportOne.setEnabled(false);
+//		exportOne.setEnabled(false);
-		exportOne.setToolTipText("Feature not yet enabled");
+//		exportOne.setToolTipText("Feature not yet enabled");
 		
 		
 		exportOne.setSelected(exportOptions.separateDeployments == false);

src/tethys/swing/DatablockSynchPanel.java

@@ -61,7 +61,6 @@ public class DatablockSynchPanel extends TethysGUIPanel {
 		mainPanel.add(BorderLayout.CENTER, scrollPane);
 		PamPanel ctrlPanel = new PamPanel(new BorderLayout());
 		exportButton = new JButton("Export ...");
-		tethysControl.getEnabler().addComponent(exportButton);
 		ctrlPanel.add(BorderLayout.WEST, exportButton);
 		mainPanel.add(BorderLayout.NORTH, ctrlPanel);
 
@@ -148,7 +147,7 @@ public class DatablockSynchPanel extends TethysGUIPanel {
 		if (deployments == null || deployments.size() == 0) {
 			en = false;
 		}
-		exportButton.setEnabled(en);
+		exportButton.setEnabled(getTethysControl().isServerOk() & en);
 	}
 
 	public void showPopup(MouseEvent e, int row) {
@@ -182,6 +181,9 @@ public class DatablockSynchPanel extends TethysGUIPanel {
 //			dataBlockSynchInfo = null;
 //			getSychInfos();
 //			getTethysControl().coun
+			break;
+		case UPDATESERVER:
+			enableExportButton();
 		}
 		
 		synchTableModel.fireTableDataChanged();

src/tethys/swing/DeploymentExportPanel.java

@@ -100,7 +100,6 @@ public class DeploymentExportPanel extends TethysGUIPanel implements DeploymentT
 		addPair("Set from ", projectDeployments, c);
 		
 		bigExportButton = new JButton("Export selection");
-		tethysControl.getEnabler().addComponent(bigExportButton);
 		bigExportButton.addActionListener(new ActionListener() {
 			@Override
 			public void actionPerformed(ActionEvent e) {
@@ -155,6 +154,9 @@ public class DeploymentExportPanel extends TethysGUIPanel implements DeploymentT
 		case UPDATEMETADATA:
 			setInternal();
 			break;
+		case UPDATESERVER:
+			enableControls();
+			break;
 		}
 	}
 
@@ -245,7 +247,7 @@ public class DeploymentExportPanel extends TethysGUIPanel implements DeploymentT
 
 	private void enableControls() {
 		boolean enable = selectedDeployments != null && selectedDeployments.size() > 0;
-		bigExportButton.setEnabled(enable);
+		bigExportButton.setEnabled(getTethysControl().isServerOk() & enable);
 	}
 
 }

src/tethys/swing/DeploymentsPanel.java

@@ -15,6 +15,7 @@ import javax.swing.border.TitledBorder;
 
 import PamView.panel.PamPanel;
 import tethys.TethysControl;
+import tethys.TethysState;
 import tethys.deployment.DeploymentHandler;
 import tethys.deployment.RecordingPeriod;
 
@@ -57,7 +58,6 @@ public class DeploymentsPanel extends TethysGUIPanel implements DeploymentTableO
 		ctrlButtons.setLayout(new BoxLayout(ctrlButtons, BoxLayout.X_AXIS));
 		optionsButton = new JButton("Options ...");
 		exportButton = new JButton("Export ...");
-		tethysControl.getEnabler().addComponent(exportButton);
 		ctrlButtons.add(optionsButton);
 		ctrlButtons.add(exportButton);
 		ctrlPanel.add(BorderLayout.WEST, ctrlButtons);
@@ -97,15 +97,23 @@ public class DeploymentsPanel extends TethysGUIPanel implements DeploymentTableO
 	public void selectionChanged() {
 		enableExportButton();
 	}
+	
+	
 
 	private void enableExportButton() {
 		ArrayList<RecordingPeriod> selected = pamDeploymentsTable.getSelectedPeriods();
-		// and see if any warnings are needed: basically if anything selected has an output.
+		if (selected == null) {
+			exportButton.setEnabled(false);
+			return;
+		}
 		boolean existing = false;
-		for (RecordingPeriod aPeriod: selected) {
+		if (selected != null) {
-			if (aPeriod.getMatchedTethysDeployment() != null) {
+			// and see if any warnings are needed: basically if anything selected has an output.
-				existing = true;
+			for (RecordingPeriod aPeriod: selected) {
-				break;
+				if (aPeriod.getMatchedTethysDeployment() != null) {
+					existing = true;
+					break;
+				}
 			}
 		}
 		String warning = null;
@@ -114,7 +122,13 @@ public class DeploymentsPanel extends TethysGUIPanel implements DeploymentTableO
 			exportWarning.setText(warning);
 		}
 
-		exportButton.setEnabled(selected.size()>0 & existing == false);
+		exportButton.setEnabled(selected.size()>0 & existing == false && getTethysControl().isServerOk());
+	}
+
+	@Override
+	public void updateState(TethysState tethysState) {
+		super.updateState(tethysState);
+		enableExportButton();
 	}
 
 

src/tethys/swing/PAMGuardDeploymentsTable.java

@@ -326,6 +326,9 @@ public class PAMGuardDeploymentsTable extends TethysGUIPanel {
 	 * @return
 	 */
 	public ArrayList<RecordingPeriod> getSelectedPeriods() {
+		if (deploymentOverview == null) {
+			return null;
+		}
 		ArrayList<RecordingPeriod> allPeriods = deploymentOverview.getRecordingPeriods();
 		ArrayList<RecordingPeriod> selPeriods = new ArrayList();
 		int n = allPeriods.size();

src/tethys/swing/TethysEnabler.java

@@ -1,56 +0,0 @@
-package tethys.swing;
-
-import java.awt.Component;
-import java.util.ArrayList;
-
-import tethys.TethysControl;
-import tethys.TethysState;
-import tethys.TethysState.StateType;
-import tethys.TethysStateObserver;
-
-/**
- * Handle enabling / disabling of any buttons / controls on the GUI. 
- * @author dg50
- *
- */
-public class TethysEnabler implements TethysStateObserver {
-
-	private TethysControl tethysControl;
-	
-	private ArrayList<Component> components = new ArrayList<>();
-
-	/**
-	 * @param tethysControl
-	 */
-	public TethysEnabler(TethysControl tethysControl) {
-		this.tethysControl = tethysControl;
-		tethysControl.addStateObserver(this);
-	}
-	
-	/**
-	 * Add a component to the enable list. 
-	 * @param aComponent
-	 */
-	public synchronized void addComponent(Component aComponent) {
-		components.add(aComponent);
-	}
-	
-	public synchronized void removeComponent(Component aComponent) {
-		components.remove(aComponent);
-	}
-
-	@Override
-	public void updateState(TethysState tethysState) {
-//		if (tethysState.stateType == StateType.UPDATESERVER) {
-//			boolean ok = tethysControl.getDbxmlConnect().pingServer()
-//		}
-	}
-	
-	public synchronized void enableControls(boolean enable) {
-		for (Component c : components) {
-			c.setEnabled(enable);
-		}
-	}
-	
-	
-}