Detections output

more work on detections output.

src/PamguardMVC/DataAutomation.java

@@ -0,0 +1,29 @@
+package PamguardMVC;
+
+/**
+ * @author dg50
+ * Levels of automation for the various datas in PAMGuard. 
+ * Should be used within DataAutomationInfo to perhaps combine with other info in the future. 
+ *
+ */
+public enum DataAutomation {
+
+	AUTOMATIC, MANUAL, MANUALANDAUTOMATIC;
+
+	@Override
+	public String toString() {
+		switch (this) {
+		case AUTOMATIC:
+			return "Automatic";
+		case MANUAL:
+			return "Manual";
+		case MANUALANDAUTOMATIC:
+			return "Manual and automatic";
+		default:
+			break;
+		
+		}
+		return null;
+	}
+	
+}

src/PamguardMVC/DataAutomationInfo.java

@@ -0,0 +1,44 @@
+package PamguardMVC;
+
+/**
+ * Returned by datablocks, though default is null, to give information on how
+ * automatic the process was. 
+ * @author dg50
+ *
+ */
+public class DataAutomationInfo {
+
+	
+	private DataAutomation automation;
+
+	/**
+	 * @param automation
+	 */
+	public DataAutomationInfo(DataAutomation automation) {
+		this.setAutomation(automation);
+	}
+
+	/**
+	 * @return the automation
+	 */
+	public DataAutomation getAutomation() {
+		return automation;
+	}
+
+	/**
+	 * @param automation the automation to set
+	 */
+	public void setAutomation(DataAutomation automation) {
+		this.automation = automation;
+	}
+
+	@Override
+	public String toString() {
+		if (automation == null) {
+			return "Unknown data automation";
+		}
+		return automation.toString();
+	}
+	
+	
+}

src/PamguardMVC/PamDataBlock.java

@@ -3100,11 +3100,12 @@ public class PamDataBlock<Tunit extends PamDataUnit> extends PamObservable {
 	}
 
 	/**
-	 * Set a data provider for Tethys.
+	 * Get the level of automation employed by the generation of these data. 
-	 * @param tethysDataProvider the tethysDataProvider to set
+	 * Should ideally be completed for everything providing data to Tethys. 
+	 * @return level of automation for this data block. 
 	 */
-	public void setTethysDataProvider(TethysDataProvider tethysDataProvider) {
+	public DataAutomationInfo getDataAutomationInfo() {
-		this.tethysDataProvider = tethysDataProvider;
+		return null;
 	}
 	
 	/**

src/RightWhaleEdgeDetector/RWEDataBlock.java

@@ -2,6 +2,8 @@ package RightWhaleEdgeDetector;
 
 import PamView.GroupedDataSource;
 import PamView.GroupedSourceParameters;
+import PamguardMVC.DataAutomation;
+import PamguardMVC.DataAutomationInfo;
 import PamguardMVC.PamProcess;
 import PamguardMVC.dataOffline.OfflineDataLoadInfo;
 import PamguardMVC.dataSelector.DataSelectorCreator;
@@ -77,4 +79,9 @@ public class RWEDataBlock extends AbstractWhistleDataBlock<RWEDataUnit> implemen
 		return rwTethysDataProvider;
 	}
 
+	@Override
+	public DataAutomationInfo getDataAutomationInfo() {
+		return new DataAutomationInfo(DataAutomation.AUTOMATIC);
+	}
+
 }

src/tethys/dbxml/DBXMLQueries.java

@@ -846,6 +846,11 @@ public class DBXMLQueries {
 		description.setMethod(getElementData(result, "Description.Method"));
 		description.setObjectives(getElementData(result, "Description.Objectives"));
 
+		// get the effort start an end
+		String effStart = getElementData(result, "Effort.Start");
+		String effEnd = getElementData(result, "Effort.End");
+		detections.getEffort().setStart(TethysTimeFuncs.fromGregorianXML(effStart));
+		detections.getEffort().setEnd(TethysTimeFuncs.fromGregorianXML(effEnd));
 		// try to find the granularity. 
 		String granularityString = getElementData(result, "Effort.Kind.Granularity");
 		GranularityEnumType granularity = null;

src/tethys/detection/BinnedGranularityHandler.java

@@ -4,6 +4,8 @@ import java.math.BigInteger;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map.Entry;
 import java.util.Set;
 
 import PamguardMVC.PamDataBlock;
@@ -29,9 +31,7 @@ import tethys.species.SpeciesMapItem;
  */
 public class BinnedGranularityHandler extends GranularityHandler {
 
-	private double binDurationSeconds;
+	private long binDurationMillis;
-	
-	private long binStartMillis, binEndMillis;
 	
 	private TethysDataProvider dataProvider;
 
@@ -43,7 +43,7 @@ public class BinnedGranularityHandler extends GranularityHandler {
 			TethysExportParams tethysExportParams, StreamExportParams streamExportParams) {
 		super(tethysControl, dataBlock, tethysExportParams, streamExportParams);
 		
-		binDurationSeconds = streamExportParams.binDurationS;
+		binDurationMillis = (long) (streamExportParams.binDurationS*1000.);
 		dataProvider = dataBlock.getTethysDataProvider(tethysControl);
 		speciesManager = dataBlock.getDatablockSpeciesManager();
 		
@@ -52,61 +52,74 @@ public class BinnedGranularityHandler extends GranularityHandler {
 
 	@Override
 	public void prepare(long timeMillis) {
-		long binStart = DetectionsHandler.roundDownBinStart(timeMillis, (long) (binDurationSeconds*1000));
+//		long binStart = DetectionsHandler.roundDownBinStart(timeMillis, binDurationMillis);
-		startBin(binStart);
+//		startBin(binStart);
 	}
 	
-	private void startBin(long timeMillis) {
+//	private void startBin(long timeMillis) {
-		binStartMillis = timeMillis;
+//		binStartMillis = timeMillis;
-		binEndMillis = binStartMillis + (long) (binDurationSeconds*1000.);
+//		binEndMillis = binStartMillis + binDurationMillis;
-		/*
+//		/*
-		 *  now make a Detection object for every possible species that
+//		 *  now make a Detection object for every possible species that
-		 *  this might throw out. 
+//		 *  this might throw out. 
-		 */
+//		 */
-		ArrayList<String> speciesCodes = speciesManager.getAllSpeciesCodes();
+//		ArrayList<String> speciesCodes = speciesManager.getAllSpeciesCodes();
-		String defaultCode = speciesManager.getDefaultSpeciesCode();
+//		String defaultCode = speciesManager.getDefaultSpeciesCode();
-		Detection det;
+//		Detection det;
-		currentDetections.put(defaultCode, det = new Detection());
+//		currentDetections.put(defaultCode, det = new Detection());
-		det.setStart(TethysTimeFuncs.xmlGregCalFromMillis(binStartMillis));
+//		det.setStart(TethysTimeFuncs.xmlGregCalFromMillis(binStartMillis));
-		det.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(binEndMillis));
+//		det.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(binEndMillis));
-		det.setCount(BigInteger.ZERO);
+//		det.setCount(BigInteger.ZERO);
-		det.setChannel(BigInteger.ZERO);
+//		det.setChannel(BigInteger.ZERO);
-		// add codes at end, just before output. 
+//		// add codes at end, just before output. 
-		if (speciesCodes != null) {
+//		if (speciesCodes != null) {
-			for (String code : speciesCodes) {
+//			for (String code : speciesCodes) {
-				currentDetections.put(code, det = new Detection());
+//				currentDetections.put(code, det = new Detection());
-				det.setStart(TethysTimeFuncs.xmlGregCalFromMillis(binStartMillis));
+//				det.setStart(TethysTimeFuncs.xmlGregCalFromMillis(binStartMillis));
-				det.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(binEndMillis));
+//				det.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(binEndMillis));
-				det.setCount(BigInteger.ZERO);
+//				det.setCount(BigInteger.ZERO);
-				det.setChannel(BigInteger.ZERO);
+//				det.setChannel(BigInteger.ZERO);
-			}
+//			}
-		}
+//		}
-	}
+//	}
 
 	@Override
 	public Detection[] addDataUnit(PamDataUnit dataUnit) {
-		Detection[] detections = null;
+		Detection[] completeDetections = closeBins(dataUnit.getTimeMilliseconds());
-		if (dataUnit.getTimeMilliseconds() >= binEndMillis) {
+		// now look for new ones. First get the species of the dataUnit and find it in the hashmap
-			detections = closeBins(dataUnit.getTimeMilliseconds());
+		String groupName = getCallGroupName(dataUnit);
-			prepare(dataUnit.getTimeMilliseconds());
+		Detection det = currentDetections.get(groupName);
+		if (det == null) {
+			// need to make a new one. 
+			det = new Detection();
+			long binStart = DetectionsHandler.roundDownBinStart(dataUnit.getTimeMilliseconds(), binDurationMillis);
+			det.setStart(TethysTimeFuncs.xmlGregCalFromMillis(binStart));
+			det.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(binStart + binDurationMillis));
+			det.setCount(BigInteger.ONE);
+			det.setChannel(BigInteger.valueOf(dataUnit.getChannelBitmap()));
+			// this should always return something, so am going to crash if it doesn't. 
+			// may revisit this later on if we've unassigned things we don't want to label
+			// in which case they should be rejected earlier than this. 
+			SpeciesMapItem speciesStuff = speciesManager.getSpeciesItem(dataUnit);
+			SpeciesIDType species = new SpeciesIDType();
+			species.setValue(BigInteger.valueOf(speciesStuff.getItisCode()));
+			det.setSpeciesId(species);
+			if (speciesStuff.getCallType() != null) {
+				det.getCall().add(speciesStuff.getCallType());
 			}
-		String speciesCode = speciesManager.getSpeciesCode(dataUnit);
+			currentDetections.put(groupName, det);
-		Detection det = currentDetections.get(speciesCode);
+		}
-		if (det != null) {
+		else {
-			/*
+			// add to current detection. Set new end time and increment count
-			 * Increase the detection count
+			int count = det.getCount().intValue() + 1;
-			 */
-			int count = det.getCount().intValue();
-			count++;
 			det.setCount(BigInteger.valueOf(count));
-			/*
+			int chan = det.getChannel().intValue();
-			 * Add to the channel map too ... 
+			chan |= dataUnit.getChannelBitmap();
-			 */
+			det.setChannel(BigInteger.valueOf(chan));
-			int channel = det.getChannel().intValue();
-			channel |= dataUnit.getChannelBitmap();
-			det.setChannel(BigInteger.valueOf(channel));
 		}
-		return detections;
+
+
+		return completeDetections;
 	}
 
 	/**
@@ -115,33 +128,32 @@ public class BinnedGranularityHandler extends GranularityHandler {
 	 * @param timeMilliseconds
 	 * @return
 	 */
-	private Detection[] closeBins(long timeMilliseconds) {
+	private synchronized Detection[] closeBins(long timeMilliseconds) {
 		Set<String> speciesKeys = currentDetections.keySet();
 		int n = speciesKeys.size();
 		int nGood = 0;
 		DataBlockSpeciesMap speciesMap = speciesManager.getDatablockSpeciesMap();
 		Detection detections[] = new Detection[n];
-		for (String key : speciesKeys) {
+		Iterator<Entry<String, Detection>> iter = currentDetections.entrySet().iterator();
-			Detection det = currentDetections.get(key);
+		while (iter.hasNext()) {
+			Entry<String, Detection> entry = iter.next();
+			Detection det = entry.getValue();
+			long detEnd = TethysTimeFuncs.millisFromGregorianXML(det.getEnd());
+			if (timeMilliseconds < detEnd) {
+				// we're not at the end of the bin, so carry on. 
+				continue;
+			}
+			// we've reached the end of the bin, so remove it from the map
+			iter.remove();
+			// now decide if we want to keep it or not. 
 			int callCount = det.getCount().intValue();
 			if (callCount < Math.max(streamExportParams.minBinCount,1)) {
-				continue;
+				continue; // won't add to output list
-			}
-			SpeciesMapItem speciesStuff = speciesMap.getItem(key); // should be non null!
-			if (speciesStuff == null) {
-				continue;
-			}
-			SpeciesIDType species = new SpeciesIDType();
-			species.setValue(BigInteger.valueOf(speciesStuff.getItisCode()));
-			det.setSpeciesId(species);
-			if (speciesStuff.getCallType() != null) {
-				det.getCall().add(speciesStuff.getCallType());
 			}
+
 			detections[nGood++] = det;
 		}
 		
-		
-		
 		/*
 		 * Clean up the end of the array and return detections that have enough calls.  
 		 */

src/tethys/detection/DetectionsHandler.java

@@ -349,9 +349,9 @@ public class DetectionsHandler {
 	/**
 	 * Round a bin start so that it's aligned correctly with
 	 * day starts. 
-	 * @param binStart
+	 * @param binStart in milliseconds
-	 * @param binInterval
+	 * @param binInterval in milliseconds
-	 * @return
+	 * @return rounded time. 
 	 */
 	public static long roundDownBinStart(long binStart, long binInterval) {
 		binStart/=binInterval;
@@ -441,6 +441,10 @@ public class DetectionsHandler {
 //					currentDetections = null;
 //				}
 			}
+			Detection dets[] = granularityHandler.cleanup(deployment.getAudioEnd());
+			if (dets != null) {
+				exportCount += dets.length;
+			}
 			
 
 
@@ -578,8 +582,9 @@ public class DetectionsHandler {
 			e.printStackTrace();
 			return null;
 		}
+		TethysDataProvider dataProvider = dataBlock.getTethysDataProvider(tethysControl);
 
-		String prefix = deployment.deployment.getId();
+		String prefix = deployment.deployment.getId() + "_" + dataProvider.getDetectionsName();
 		String fullId = "";
 		/*
 		 * Check the document name isn't already used and increment id as necessary.
@@ -599,7 +604,6 @@ public class DetectionsHandler {
 		detections.setDataSource(dataSource);
 		AlgorithmType algorithm = detections.getAlgorithm();
 
-		TethysDataProvider dataProvider = dataBlock.getTethysDataProvider(tethysControl);
 		if (dataProvider != null) {
 			algorithm = dataProvider.getAlgorithm();
 //			detections.setAlgorithm(algorithm);

src/tethys/detection/EncounterGranularityHandler.java

@@ -6,6 +6,7 @@ import java.util.HashMap;
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.Set;
+import java.util.Map.Entry;
 
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
@@ -54,8 +55,8 @@ public class EncounterGranularityHandler extends GranularityHandler {
 	public Detection[] addDataUnit(PamDataUnit dataUnit) {
 		Detection[] completeDetections = checkCurrentEncounters(dataUnit.getTimeMilliseconds());
 		// now look for new ones. First get the species of the dataUnit and find it in the hashmap
-		String speciesCode = speciesManager.getSpeciesCode(dataUnit);
+		String groupName = getCallGroupName(dataUnit);
-		Detection det = currentDetections.get(speciesCode);
+		Detection det = currentDetections.get(groupName);
 		if (det == null) {
 			// need to make a new one. 
 			det = new Detection();
@@ -73,7 +74,7 @@ public class EncounterGranularityHandler extends GranularityHandler {
 			if (speciesStuff.getCallType() != null) {
 				det.getCall().add(speciesStuff.getCallType());
 			}
-			currentDetections.put(speciesCode, det);
+			currentDetections.put(groupName, det);
 		}
 		else {
 			// add to current detection. Set new end time and increment count
@@ -98,16 +99,18 @@ public class EncounterGranularityHandler extends GranularityHandler {
 		Set<String> keys = currentDetections.keySet();
 		int nGood = 0;
 		Detection[] newDetections = new Detection[currentDetections.size()];
-		for (String aKey : keys) {
+		Iterator<Entry<String, Detection>> iter = currentDetections.entrySet().iterator();
-			Detection aDet = currentDetections.get(aKey);
+		while (iter.hasNext()) {
-			Long detEnd = TethysTimeFuncs.millisFromGregorianXML(aDet.getEnd());
+			Entry<String, Detection> entry = iter.next();
+			Detection aDet = entry.getValue();
+			long detEnd = TethysTimeFuncs.millisFromGregorianXML(aDet.getEnd());
 			if (timeMilliseconds-detEnd > maxGapMillis) {
 				// only keep if it's got a min number of calls. 
 				if (aDet.getCount().intValue() >= streamExportParams.minBinCount) {
 					newDetections[nGood++] = aDet;
 				}
 				// remove from set. A new one will be created only when required. 
-				currentDetections.remove(aKey);
+				iter.remove();
 			}
 		}
 

src/tethys/detection/GranularityHandler.java

@@ -7,6 +7,7 @@ import nilus.GranularityEnumType;
 import tethys.TethysControl;
 import tethys.output.StreamExportParams;
 import tethys.output.TethysExportParams;
+import tethys.species.DataBlockSpeciesManager;
 
 public abstract class GranularityHandler {
 
@@ -18,6 +19,8 @@ public abstract class GranularityHandler {
 	
 	protected StreamExportParams streamExportParams;
 
+	private DataBlockSpeciesManager speciesManager;
+
 	/**
 	 * @param tethysControl
 	 * @param dataBlock
@@ -30,6 +33,7 @@ public abstract class GranularityHandler {
 		this.dataBlock = dataBlock;
 		this.tethysExportParams = tethysExportParams;
 		this.streamExportParams = streamExportParams;
+		speciesManager = dataBlock.getDatablockSpeciesManager();
 	}
 	
 	/**
@@ -48,6 +52,23 @@ public abstract class GranularityHandler {
 	 */
 	public abstract Detection[] addDataUnit(PamDataUnit dataUnit);
 	
+	/**
+	 * Get a grouping name for the call. This may just be the calls species code, 
+	 * or it may be appended with the channel number. This is used to find bin and 
+	 * encounter data in HashMaps in 
+	 * @param dataUnit
+	 * @return
+	 */
+	public String getCallGroupName(PamDataUnit dataUnit) {
+		String groupName = speciesManager.getSpeciesCode(dataUnit);
+		if (groupName == null) {
+			groupName = "NullSpecies";
+		}
+		if (streamExportParams.separateChannels) {
+			groupName += String.format("Chan%d", dataUnit.getChannelBitmap());
+		}
+		return groupName;
+	}
 	/**
 	 * Called after end end of all data units to get the last bin / encounter. <p>
 	 * 

src/tethys/output/StreamExportParams.java

@@ -3,15 +3,20 @@ package tethys.output;
 import java.io.IOException;
 import java.io.Serializable;
 
+import PamController.PamController;
+import PamguardMVC.PamDataBlock;
 import nilus.DescriptionType;
 import nilus.GranularityEnumType;
+import tethys.TethysControl;
 import tethys.niluswraps.PDescriptionType;
+import tethys.pamdata.TethysDataProvider;
 
 /**
  * Parameters controlling export of a single stream. 
  * Starts just with a boolean 'selected', but may grow. 
  * These all contain data names rather than references to a Datablock so that 
- * they can be serialised. 
+ * they can be serialised. However, created with TethysControl and datablock
+ * so that some stuff canbe automatically initialised. 
  * @author dg50
  *
  */
@@ -19,24 +24,44 @@ public class StreamExportParams implements Serializable {
 
 	public static final long serialVersionUID = 1L;	
 
-	public StreamExportParams(String longDataName, boolean selected) {
+	/**
-		super();
+	 * Datablock long data name (used instead of datablock
-		this.longDataName = longDataName;
+	 * reference so this object and serialise. 
-		this.selected = selected;
+	 */
-	}
-
 	public String longDataName;
 	
 	public boolean selected;
 	
+	/**
+	 * Granularity type, binned, call, encounter, grouped. 
+	 */
 	public GranularityEnumType granularity = GranularityEnumType.CALL;
 	
+	/**
+	 * Bin duration, seconds. 
+	 */
 	public double binDurationS = 60;
 	
+	/**
+	 * Minimum encounter gap, seconds
+	 */
 	public double encounterGapS = 60;
 	
+	/**
+	 * Minimum count for a bin to be retained. 
+	 */
 	public int minBinCount = 1;
 	
+	/**
+	 * Minimum count for an encounter to be retained. 
+	 */
+	public int minEncounterCount = 1;
+	
+	/**
+	 * Keep channels separate when using binned data. 
+	 */
+	public boolean separateChannels = true;
+	
 	/*
 	 * Can't have this here since it isn't serializable. 
 	 */
@@ -49,6 +74,25 @@ public class StreamExportParams implements Serializable {
 		return detectionDescription;
 	}
 
+	public StreamExportParams(TethysControl tethysControl, PamDataBlock dataBlock, boolean selected) {
+		super();
+		this.longDataName = dataBlock.getLongDataName();
+		this.selected = selected;
+		autoFill(tethysControl, dataBlock);
+	}
+
+	/**
+	 * Try to put some information automatically into the Methods. 
+	 * @param dataBlock2 
+	 * @param tethysControl 
+	 */
+	private void autoFill(TethysControl tethysControl, PamDataBlock dataBlock) {
+		// there should always be a data provider or we'd never have got this far. 
+		TethysDataProvider dataProvider = dataBlock.getTethysDataProvider(tethysControl);
+		PDescriptionType desc = getDetectionDescription();
+		desc.setMethod(dataProvider.getDetectionsMethod());
+	}
+	
 	/**
 	 * Get the nilus detection description
 	 * @return

src/tethys/output/swing/TethysExportDialog.java

@@ -151,7 +151,7 @@ public class TethysExportDialog extends PamDialog {
 		}
 		int nSel = 0;
 		for (DataStreamSet streamSet : dataStreamSets) {
-			StreamExportParams streamOpts = new StreamExportParams(streamSet.dataBlock.getLongDataName(), streamSet.checkBox.isSelected());
+			StreamExportParams streamOpts = new StreamExportParams(tethysControl, streamSet.dataBlock, streamSet.checkBox.isSelected());
 			exportParams.setStreamParams(streamSet.dataBlock, streamOpts);
 			nSel++;
 		}

src/tethys/pamdata/AutoTethysProvider.java

@@ -14,6 +14,7 @@ import PamController.PamSettings;
 import PamController.PamguardVersionInfo;
 import PamController.settings.output.xml.PamguardXMLWriter;
 import PamUtils.XMLUtils;
+import PamguardMVC.DataAutomationInfo;
 import PamguardMVC.DataUnitBaseData;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
@@ -30,6 +31,7 @@ import nilus.Detection;
 import nilus.Detection.Parameters;
 import nilus.Detection.Parameters.UserDefined;
 import nilus.DetectionEffortKind;
+import nilus.GranularityEnumType;
 import nilus.Helper;
 import nilus.SpeciesIDType;
 import tethys.TethysControl;
@@ -90,11 +92,11 @@ public class AutoTethysProvider implements TethysDataProvider {
 		return schema;
 	}
 
-	@Override
+//	@Override
-	public TethysDataPoint getDataPoint(PamDataUnit pamDataUnit) {
+//	public TethysDataPoint getDataPoint(PamDataUnit pamDataUnit) {
-		// TODO Auto-generated method stub
+//		// TODO Auto-generated method stub
-		return null;
+//		return null;
-	}
+//	}
 
 	@Override
 	public DescriptionType getDescription(Deployment deployment, TethysExportParams tethysExportParams) {
@@ -488,4 +490,49 @@ public class AutoTethysProvider implements TethysDataProvider {
 		
 	}
 
+	@Override
+	public String getDetectionsMethod() {
+		/*
+		 *  could really do with knowing what type of detector we're dealing with, i.e. if it's
+		 *  automatic or manual. For most blocks this is fixed, though some may have a mixture of both ! 
+		 */
+		DataAutomationInfo dataAutomation = pamDataBlock.getDataAutomationInfo();
+		String method;
+		PamControlledUnit pcu = pamDataBlock.getParentProcess().getPamControlledUnit();
+		if (dataAutomation == null) {
+			method = String.format("Processing using the PAMGuard %s", pcu.getUnitType());
+		}
+		else {
+			method = String.format("%s processing using the PAMGuard %s", dataAutomation.getAutomation(), pcu.getUnitType());
+		}
+		
+		return method;
+	}
+
+	@Override
+	public GranularityEnumType[] getAllowedGranularities() {
+		GranularityEnumType[] allowed = {GranularityEnumType.CALL, GranularityEnumType.BINNED, GranularityEnumType.ENCOUNTER};
+		return allowed;
+	}
+
+	@Override
+	public String getDetectionsName() {
+		PamProcess process = pamDataBlock.getParentProcess();
+		PamControlledUnit pcu = process.getPamControlledUnit();
+		String pcuName = pcu.getUnitName();
+		String blockName = pamDataBlock.getDataName();
+		String documentName;
+		/**
+		 * If the datablock name is the same as the unit name, no need to repeat onesself. 
+		 */
+		if (pcuName.equals(blockName)) {
+			documentName = new String(pcuName); // copy it, since we're about to modify it!
+		}
+		else {
+			documentName = pcuName + " " + blockName;
+		}
+		documentName = documentName.replace(' ', '_');
+		return documentName;
+	}
+
 }

src/tethys/pamdata/TethysDataProvider.java

@@ -9,6 +9,7 @@ import nilus.Deployment;
 import nilus.DescriptionType;
 import nilus.Detection;
 import nilus.DetectionEffortKind;
+import nilus.GranularityEnumType;
 import tethys.niluswraps.PDeployment;
 import tethys.output.StreamExportParams;
 import tethys.output.TethysExportParams;
@@ -38,8 +39,14 @@ public interface TethysDataProvider {
 	 * @param pamDataUnit
 	 * @return
 	 */
-	public TethysDataPoint getDataPoint(PamDataUnit pamDataUnit);
+//	public TethysDataPoint getDataPoint(PamDataUnit pamDataUnit);
 
+	/**
+	 * Get a standard Method string for each detector. This can be a bit 
+	 * verbose and might even have a reference to a paper ? Is this the best place for this ? 
+	 * @return
+	 */
+	public String getDetectionsMethod();
 
 	/**
 	 * Get DescriptionType object to include in a Tethys Detections document. 
@@ -56,6 +63,22 @@ public interface TethysDataProvider {
 	 */
 	public AlgorithmType getAlgorithm();
 	
+	/**
+	 * Get a list of allowed granularity types for this output 
+	 * @return list of granularities. 
+	 */
+	public GranularityEnumType[] getAllowedGranularities();
+	
+	/**
+	 * Get a name for the detections documents. This will be appended
+	 * to the Deployment name and may also have a number after it. <br>
+	 * Note that the name isn't really important since all the matching between 
+	 * different documents is done internally, but it helps to make everything 
+	 * human readable. 
+	 * @return A name, similar to datablock.getLongDataName(), but no spaces. 
+	 */
+	public String getDetectionsName();
+
 
 	/**
 	 * Create a Tethys Detection object from a PamDataUnit.<br>

src/tethys/swing/DatablockDetectionsPanel.java

@@ -17,6 +17,7 @@ import javax.swing.JTable;
 import javax.swing.border.TitledBorder;
 import javax.swing.table.AbstractTableModel;
 import javax.swing.table.JTableHeader;
+import javax.xml.datatype.XMLGregorianCalendar;
 
 import PamView.PamGui;
 import PamView.dialog.warn.WarnOnce;
@@ -97,10 +98,12 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
         case 1:
         	return "Name of PAMGuard data stream";
         case 2:
-        	return "Output granularity";
+        	return "Effort period";
         case 3:
-        	return "Number of detection elements in document";
+        	return "Output granularity";
         case 4:
+        	return "Number of detection elements in document";
+        case 5:
         	return "Document abstract";
         	
         }
@@ -229,7 +232,7 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 
 	private class TableModel extends AbstractTableModel {
 		
-		private String[] colNames = {"Document", "Detector", "Granularity", "Count", "Abstract"};
+		private String[] colNames = {"Document", "Detector", "Effort", "Granularity", "Count", "Abstract"};
 
 		@Override
 		public int getRowCount() {
@@ -272,6 +275,10 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 				}
 				return pDets.dataBlock.getDataName();
 			case 2:
+				XMLGregorianCalendar start = dets.getEffort().getStart();
+				XMLGregorianCalendar stop = dets.getEffort().getEnd();
+				return start + " to " + stop;
+			case 3:
 				List<DetectionEffortKind> kinds = dets.getEffort().getKind();
 				if (kinds == null) {
 					return null;
@@ -286,9 +293,9 @@ public class DatablockDetectionsPanel extends TethysGUIPanel implements StreamTa
 					}
 				}
 				break;
-			case 3:
-				return pDets.count;
 			case 4:
+				return pDets.count;
+			case 5:
 				return dets.getDescription().getAbstract();
 			}
 			return null;

src/tethys/swing/DatablockSynchPanel.java

@@ -156,7 +156,7 @@ public class DatablockSynchPanel extends TethysGUIPanel {
 
 	private class SynchTableModel extends AbstractTableModel {
 
-		String[] columnNames = {"Data Stream", "N PAM Datas", "PAMGuard Time", "Tethys Documents", "Tethys Time", "Options"};
+		String[] columnNames = {"Data Stream", "N PAM Datas", "PAMGuard Time", "Tethys Documents"};//, "Tethys Time", "Options"};
 		
 		@Override
 		public int getRowCount() {

src/tethys/swing/documents/TethysDocumentTable.java

@@ -14,6 +14,7 @@ import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.JScrollPane;
 import javax.swing.JTable;
+import javax.swing.ListSelectionModel;
 import javax.swing.table.AbstractTableModel;
 
 import PamController.PamController;
@@ -58,6 +59,8 @@ public class TethysDocumentTable implements PamDialogPanel {
 		new SwingTableColumnWidths(tethysControl.getUnitName()+"TethysDocumentsTable", mainTable);
 		this.setCollectionName(collectionName);
 		mainTable.addMouseListener(new TableMouse());
+		mainTable.setRowSelectionAllowed(true);
+		mainTable.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
 	}
 	
 	public void updateTableData() {
@@ -94,6 +97,7 @@ public class TethysDocumentTable implements PamDialogPanel {
 		if (row < 0|| row >= documentNames.size()) {
 			return;
 		}
+		
 		String docName = documentNames.get(row);
 		JPopupMenu popMenu = new JPopupMenu();
 		JMenuItem menuItem = new JMenuItem("Show document " + docName);
@@ -104,6 +108,11 @@ public class TethysDocumentTable implements PamDialogPanel {
 			}
 		});
 		popMenu.add(menuItem);
+		
+
+		int[] rows = mainTable.getSelectedRows();
+		if (rows != null && rows.length == 1) {
+//			docName = documentNames.get(rows[0]);
 			menuItem = new JMenuItem("Delete document " + docName);
 			menuItem.addActionListener(new ActionListener() {
 				@Override
@@ -112,6 +121,18 @@ public class TethysDocumentTable implements PamDialogPanel {
 				}
 			});
 			popMenu.add(menuItem);
+		}
+		else if (rows != null && rows.length > 1) {
+			String mt = String.format("Delete multiple (%d) documents", rows.length);
+			menuItem = new JMenuItem(mt);
+			menuItem.addActionListener(new ActionListener() {
+				@Override
+				public void actionPerformed(ActionEvent e) {
+					deleteDocuments(rows);
+				}
+			});
+			popMenu.add(menuItem);
+		}
 		
 		popMenu.show(e.getComponent(), e.getX(), e.getY());
 	}
@@ -134,6 +155,32 @@ public class TethysDocumentTable implements PamDialogPanel {
 		updateTableData();
 	}
 	
+	private void deleteDocuments(int[] rows) {
+		int ans = WarnOnce.showNamedWarning("deletedoc"+collectionName, PamController.getMainFrame(), "Delete documents", 
+				"Are you sure you want to delete multiple documents ", WarnOnce.OK_CANCEL_OPTION);
+		if (ans != WarnOnce.OK_OPTION) {
+			return;
+		}
+		/*
+		 *  make a new list before anything is deleted since the
+		 *  man list will get updated during deletion and be out of date.  
+		 */
+		String[] docNames = new String[rows.length];
+		for (int i = 0; i < rows.length; i++) {
+			 docNames[i] = documentNames.get(rows[i]);
+		}
+		// now it's safe to delete them. 
+		for (int i = 0; i < docNames.length; i++) {
+			try {
+				tethysControl.getDbxmlConnect().removeDocument(collectionName, docNames[i]);
+			} catch (TethysException e) {
+				System.out.println("Failed to delete " + docNames[i]);
+				System.out.println(e.getMessage());
+			}
+		}
+		updateTableData();
+	}
+
 	private class TableModel extends AbstractTableModel {
 		
 		private String[] columnNames = {"", "Document Id/Name"};

src/tethys/swing/export/DescriptionTypePanel.java

@@ -39,6 +39,13 @@ public class DescriptionTypePanel {
 	
 	private static final int ctrlWidth = 40;
 	
+	public static final String objectivesTip = "What are the objectives of this effort?  Examples:\r\n"
+			+ "Beamform to increase SNR for detection.\r\n"
+			+ "Detect every click of a rare species.\r\n"
+			+ "Verify data quality.";
+	public static final String abstractTip = "Overview of effort.";
+	public static final String methodTip = "High-level description of the method used.";
+	
 	public DescriptionTypePanel(String bordertitle, boolean requireObjective, boolean requireAbstract, boolean requireMethod) {
 		this.requireObjective = requireObjective;
 		this.requireAbstract = requireAbstract;
@@ -51,6 +58,16 @@ public class DescriptionTypePanel {
 		tObjectives = new JTextArea(12, ctrlWidth);
 		tAbstract = new JTextArea(8, ctrlWidth);
 		tMethod = new JTextArea(9, ctrlWidth);
+		tObjectives.setLineWrap(true);
+		tObjectives.setWrapStyleWord(true);
+		tAbstract.setLineWrap(true);
+		tAbstract.setWrapStyleWord(true);
+		tMethod.setLineWrap(true);
+		tMethod.setWrapStyleWord(true);
+		
+		tObjectives.setToolTipText(objectivesTip);
+		tAbstract.setToolTipText(abstractTip);
+		tMethod.setToolTipText(methodTip);
 		
 		mainPanel.setLayout(new BoxLayout(mainPanel, BoxLayout.Y_AXIS));
 		addScrollablePanel(tObjectives, "Objectives");
@@ -78,6 +95,11 @@ public class DescriptionTypePanel {
 			tAbstract.setText(null);
 			tMethod.setText(null);
 		}
+		else {
+			tObjectives.setText(description.getObjectives());
+			tAbstract.setText(description.getAbstract());
+			tMethod.setText(description.getMethod());
+		}
 	}
 	
 	public boolean getParams(PDescriptionType description) {

src/tethys/swing/export/DetectionsExportWizard.java

@@ -39,7 +39,7 @@ public class DetectionsExportWizard extends PamDialog {
 		
 		streamExportParams = tethysControl.getTethysExportParams().getStreamParams(dataBlock);
 		if (streamExportParams == null) {
-			streamExportParams = new StreamExportParams(dataBlock.getLongDataName(), false);
+			streamExportParams = new StreamExportParams(tethysControl, dataBlock, false);
 		}
 		
 		cardLayout = new CardLayout();

src/tethys/swing/export/GranularityCard.java

@@ -30,6 +30,7 @@ import nilus.GranularityEnumType;
 import tethys.TethysControl;
 import tethys.niluswraps.PGranularityType;
 import tethys.output.StreamExportParams;
+import tethys.pamdata.TethysDataProvider;
 
 public class GranularityCard extends ExportWizardCard {
 
@@ -37,7 +38,9 @@ public class GranularityCard extends ExportWizardCard {
 
 	private JTextArea dataSelectionText;
 
-	private JTextField binLength, minCalls, encounterGap;
+	private JTextField binLength, minBinnedCalls, encounterGap, minEncounterCalls;
+	
+	private JRadioButton groupChannels, separateChannels;
 
 	private DataSelector dataSelector;
 
@@ -45,51 +48,68 @@ public class GranularityCard extends ExportWizardCard {
 
 	private int encounterIndex, binnedIndex;
 
+	private GranularityEnumType[] allowedGranularities;
+
 	public GranularityCard(DetectionsExportWizard detectionsExportWizard, TethysControl tethysControl, PamDataBlock dataBlock) {
 		super(tethysControl, "Granularity", dataBlock);
 		this.detectionsExportWizard = detectionsExportWizard;
 		setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
 
+		TethysDataProvider tethysDataProvider = dataBlock.getTethysDataProvider(tethysControl);
 		// granularity
-		GranularityEnumType[] grans = GranularityEnumType.values();
+		allowedGranularities = tethysDataProvider.getAllowedGranularities();
-		granularities = new JRadioButton[grans.length];
+		granularities = new JRadioButton[allowedGranularities.length];
 		JPanel granPanel = new WestAlignedPanel(new GridBagLayout());
 		GridBagConstraints c = new PamGridBagContraints();
 		granPanel.setBorder(new TitledBorder("Granularity"));
 		ButtonGroup granGroup = new ButtonGroup();
 		GranularityChange gc = new GranularityChange();
-		for (int i = 0; i < grans.length; i++) {
+		for (int i = 0; i < allowedGranularities.length; i++) {
 			c.gridx = 0;
-			granularities[i] = new JRadioButton(PGranularityType.prettyString(grans[i]));
+			granularities[i] = new JRadioButton(PGranularityType.prettyString(allowedGranularities[i]));
-			granularities[i].setToolTipText(PGranularityType.toolTip(grans[i]));
+			granularities[i].setToolTipText(PGranularityType.toolTip(allowedGranularities[i]));
 			granularities[i].addActionListener(gc);
 			granPanel.add(granularities[i], c);
 			granGroup.add(granularities[i]);
-			if (grans[i] == GranularityEnumType.BINNED) {
+			if (allowedGranularities[i] == GranularityEnumType.BINNED) {
 				binnedIndex = i;
 				c.gridx++;
-				granPanel.add(new JLabel(" bin duration ", JLabel.RIGHT), c);
+				granPanel.add(new JLabel(" Bin duration ", JLabel.RIGHT), c);
 				c.gridx++;
 				granPanel.add(binLength = new JTextField(5), c);
 				c.gridx++;
-				granPanel.add(new JLabel("(s), min Calls", JLabel.LEFT), c);
+				granPanel.add(new JLabel("(s), Min Calls", JLabel.LEFT), c);
 				c.gridx++;
-				granPanel.add(minCalls = new JTextField(5), c);			
+				granPanel.add(minBinnedCalls = new JTextField(5), c);			
 				binLength.setToolTipText("Time bin duration in seconds");
-				minCalls.setToolTipText("Minimum number of calls for a bin to be output");	
+				minBinnedCalls.setToolTipText("Minimum number of calls for a bin to be output");	
 			}
-			if (grans[i] == GranularityEnumType.ENCOUNTER) {
+			if (allowedGranularities[i] == GranularityEnumType.ENCOUNTER) {
 				encounterIndex = i;
 				c.gridx++;
-				granPanel.add(new JLabel(" min gap ", JLabel.RIGHT), c);
+				granPanel.add(new JLabel(" Minimum gap ", JLabel.RIGHT), c);
 				c.gridx++;
 				granPanel.add(encounterGap = new JTextField(5), c);
 				c.gridx++;
-				granPanel.add(new JLabel("(s) ", JLabel.LEFT), c);
+				granPanel.add(new JLabel("(s), Min Calls", JLabel.LEFT), c);
+				c.gridx++;
+				granPanel.add(minEncounterCalls = new JTextField(5), c);			
 				encounterGap.setToolTipText("Minimum gap between separate encounters");
+				minEncounterCalls.setToolTipText("Minimum number of calls for an encounter to be output");	
 			}
 			c.gridy++;
 		}
+		c.gridx = 1;
+		c.gridwidth = 2;
+		granPanel.add(separateChannels = new JRadioButton("Separate channels"), c);
+		c.gridx += c.gridwidth;
+		granPanel.add(groupChannels = new JRadioButton("Group channels"), c);
+		separateChannels.setToolTipText("Use separate bins/encounters for each detection channel");
+		groupChannels.setToolTipText("Combine detections from different channels into the same bins/encounters");
+		ButtonGroup chanGroup = new ButtonGroup();
+		chanGroup.add(separateChannels);
+		chanGroup.add(groupChannels);
+		
 		this.add(granPanel);
 
 		// data selection
@@ -127,8 +147,12 @@ public class GranularityCard extends ExportWizardCard {
 
 	private void enableControls() {
 		binLength.setEnabled(granularities[binnedIndex].isSelected());
-		minCalls.setEnabled(granularities[binnedIndex].isSelected());
+		minBinnedCalls.setEnabled(granularities[binnedIndex].isSelected());
 		encounterGap.setEnabled(granularities[encounterIndex].isSelected());
+		minEncounterCalls.setEnabled(granularities[encounterIndex].isSelected());
+		boolean binOrencount = granularities[binnedIndex].isSelected() | granularities[encounterIndex].isSelected();
+		separateChannels.setEnabled(binOrencount);
+		groupChannels.setEnabled(binOrencount);
 	}
 
 	protected void newDataSelection() {
@@ -149,10 +173,9 @@ public class GranularityCard extends ExportWizardCard {
 
 	@Override
 	public boolean getParams(StreamExportParams streamExportParams) {
-		GranularityEnumType[] grans = GranularityEnumType.values();
+		for (int i = 0; i < allowedGranularities.length; i++) {
-		for (int i = 0; i < grans.length; i++) {
 			if (granularities[i].isSelected()) {
-				streamExportParams.granularity = grans[i];
+				streamExportParams.granularity = allowedGranularities[i];
 				break;
 			}
 		}
@@ -164,10 +187,10 @@ public class GranularityCard extends ExportWizardCard {
 				return detectionsExportWizard.showWarning("Invalid bin duration parameter");
 			}
 			try {
-				streamExportParams.minBinCount = Integer.valueOf(minCalls.getText());
+				streamExportParams.minBinCount = Integer.valueOf(minBinnedCalls.getText());
 			}
 			catch (NumberFormatException e) {
-				return detectionsExportWizard.showWarning("Invalid minimum call count");
+				return detectionsExportWizard.showWarning("Invalid minimum binned call count");
 			}
 		}
 		if (streamExportParams.granularity == GranularityEnumType.ENCOUNTER) {
@@ -177,20 +200,30 @@ public class GranularityCard extends ExportWizardCard {
 			catch (NumberFormatException e) {
 				return detectionsExportWizard.showWarning("Invalid encounter gap parameter");
 			}
+			try {
+				streamExportParams.minEncounterCount = Integer.valueOf(minEncounterCalls.getText());
 			}
+			catch (NumberFormatException e) {
+				return detectionsExportWizard.showWarning("Invalid minimum encounter call count");
+			}
+		}
+
+		streamExportParams.separateChannels = separateChannels.isSelected();
 		
 		return streamExportParams.granularity != null;
 	}
 
 	@Override
 	public void setParams(StreamExportParams streamExportParams) {
-		GranularityEnumType[] grans = GranularityEnumType.values();
+		for (int i = 0; i < granularities.length; i++) {
-		for (int i = 0; i < grans.length; i++) {
+			granularities[i].setSelected(streamExportParams.granularity == allowedGranularities[i]);
-			granularities[i].setSelected(streamExportParams.granularity == grans[i]);
 		}
 		binLength.setText(String.format("%3.1f", streamExportParams.binDurationS));
-		minCalls.setText(String.format("%d", streamExportParams.minBinCount));
+		minBinnedCalls.setText(String.format("%d", streamExportParams.minBinCount));
 		encounterGap.setText(String.format("%3.1f", streamExportParams.encounterGapS));
+		minEncounterCalls.setText(String.format("%d", streamExportParams.minEncounterCount));
+		separateChannels.setSelected(streamExportParams.separateChannels);
+		groupChannels.setSelected(streamExportParams.separateChannels == false);
 		newDataSelection();
 		enableControls();
 	}