Fix bug in Click Detector target motion analysis

Was crashing if not all click in event were loaded.

src/Localiser/detectionGroupLocaliser/TMGroupLocInfo.java

@@ -159,22 +159,21 @@ public class TMGroupLocInfo implements GroupLocInfo {
 	
 	
 	private void copySubDetections(SuperDetection parentDataUnit, DetectionGroupOptions detectionGroupOptions) {
-		synchronized (parentDataUnit.getSubDetectionSyncronisation()) {
-			int totalUnits = parentDataUnit.getSubDetectionsCount();
-			int keptUnits = totalUnits;
-			if (detectionGroupOptions != null) {
-				if (detectionGroupOptions.getMaxLocalisationPoints() == 0 ||			
-						detectionGroupOptions.getMaxLocalisationPoints() < parentDataUnit.getSubDetectionsCount()) {
-					keptUnits = detectionGroupOptions.getMaxLocalisationPoints();
-				}
-			}
-			subDetectionList = new Vector<>(keptUnits);
-			float keepRat = (float) (totalUnits-1) / (float) (keptUnits-1);
-			for (int i = 0; i < keptUnits; i++) {
-				int unitIndex = Math.round(i*keepRat);
-				subDetectionList.add(parentDataUnit.getSubDetection(unitIndex));
+		ArrayList<PamDataUnit> subDets = parentDataUnit.getSubDetections();
+		int totalUnits = subDets.size();
+		int keptUnits = totalUnits;
+		if (detectionGroupOptions != null) {
+			if (detectionGroupOptions.getMaxLocalisationPoints() == 0 ||			
+					detectionGroupOptions.getMaxLocalisationPoints() < parentDataUnit.getSubDetectionsCount()) {
+				keptUnits = detectionGroupOptions.getMaxLocalisationPoints();
 			}
 		}
+		subDetectionList = new Vector<>(keptUnits);
+		float keepRat = (float) (totalUnits-1) / (float) (keptUnits-1);
+		for (int i = 0; i < keptUnits; i++) {
+			int unitIndex = Math.round(i*keepRat);
+			subDetectionList.add(subDets.get(unitIndex));
+		}
 	}
 
 
@@ -454,7 +453,7 @@ public class TMGroupLocInfo implements GroupLocInfo {
 	 * The real word vectors are relative to the earth surface. Thus they are the bearings vectors 
 	 * from an array, rotated by the true heading, pitch and roll of the array.  
 	 */
-	protected void calculateWorldVectors() {		
+	protected void calculateWorldVectors() {	
 		int nSubDetections=getDetectionCount();
 		rawRealWorldVectors = new PamVector[nSubDetections][];
 		PamVector[] v;

src/PamguardMVC/superdet/SuperDetDataBlock.java

@@ -368,7 +368,7 @@ public class SuperDetDataBlock<Tunit extends SuperDetection, TSubDet extends Pam
 					}
 					if (!found) {
 						superDet = null;
-						System.out.printf("Can't find data unit id %d, UID %d in %s\n", superID, superUID, getDataName());
+						Debug.out.printf("Can't find data unit id %d, UID %d in %s\n", superID, superUID, getDataName());
 					}
 				}
 				if (superDet == null) {
@@ -448,6 +448,9 @@ public class SuperDetDataBlock<Tunit extends SuperDetection, TSubDet extends Pam
 			int iDone = 0;
 			while (duIt.hasNext()) {
 				Tunit aData = duIt.next(); // looping through superdetections.
+//				if (aData.getDatabaseIndex() == 131) {
+//					System.out.println("On event 131");
+//				}
 				if (viewLoadObserver != null) {
 					viewLoadObserver.sayProgress(1, aData.getTimeMilliseconds(), firstTime, lastTime, iDone++);
 				}
@@ -479,6 +482,7 @@ public class SuperDetDataBlock<Tunit extends SuperDetection, TSubDet extends Pam
 						sdInfo.setSubDetection(null);
 					}
 				}
+//				aData.weedMissingSubDetections();
 			}
 		}
 		return true;

src/PamguardMVC/superdet/SuperDetection.java

@@ -278,23 +278,28 @@ public class SuperDetection<T extends PamDataUnit> extends PamDataUnit<T, SuperD
 	 * @return an array list of sub detection data units
 	 */
 	public ArrayList<PamDataUnit<?,?>> getSubDetections() {
-		if (subDetections == null) {
-			return null;
-		}
-		ArrayList<PamDataUnit<?,?>> subDets = new ArrayList<>(getSubDetectionsCount());
-		for (SubdetectionInfo<T> subInfo:subDetections) {
-			T subDet = subInfo.getSubDetection();
-			if (subDet == null) {
-				continue;
+		synchronized (getSubDetectionSyncronisation()) {
+			if (subDetections == null) {
+				return null;
 			}
-			subDets.add(subDet);
+			ArrayList<PamDataUnit<?,?>> subDets = new ArrayList<>(getSubDetectionsCount());
+			for (SubdetectionInfo<T> subInfo:subDetections) {
+				T subDet = subInfo.getSubDetection();
+				if (subDet == null) {
+					continue;
+				}
+				subDets.add(subDet);
+			}
+			return subDets;
 		}
-		return subDets;
 	}
 
 	public T getSubDetection(int ind) {
 		synchronized (subDetectionSyncronisation) {
 			if (subDetections == null) return null;
+			if (ind >= subDetections.size()) {
+				return null;
+			}
 			return subDetections.get(ind).getSubDetection();
 		}
 	}
@@ -484,6 +489,24 @@ public class SuperDetection<T extends PamDataUnit> extends PamDataUnit<T, SuperD
 //		}
 		
 	}
+	
+	/**
+	 * Get a list of sub detections which are actually present. 
+	 * @return list of sub detections which have a non-null sub data unit. 
+	 */
+	public List<SubdetectionInfo<T>> getPresentSubDetections() {
+		ArrayList<SubdetectionInfo<T>> exList = new ArrayList<>(getSubDetectionsCount());
+		synchronized (getSubDetectionSyncronisation()) {
+			for (SubdetectionInfo<T> subInf : subDetections) {
+				if (subInf.getSubDetection() == null) {
+					continue;
+				}
+				exList.add(subInf);
+			}
+			exList.trimToSize();
+		}
+		return exList;
+	}
 
 	/**
 	 * Get the full list of subdetection info's (which may not all 
@@ -550,4 +573,21 @@ public class SuperDetection<T extends PamDataUnit> extends PamDataUnit<T, SuperD
 		}
 	}
 
+	/**
+	 * Remove sub detection infos which have no actual sub detection 
+	 * loaded. Don't use since super dets are supposed to keep the full 
+	 * list even if they don't have loaded subdets. 
+	 */
+//	public void weedMissingSubDetections() {
+//		synchronized (getSubDetectionSyncronisation()) {
+//			ListIterator<SubdetectionInfo<T>> subInfIter = subDetections.listIterator();
+//			while (subInfIter.hasNext()) {
+//				SubdetectionInfo<T> subDetInfo = subInfIter.next();
+//				if (subDetInfo.getSubDetection() == null) {
+//					subInfIter.remove();
+//				}
+//			}
+//		}
+//	}
+
 }

src/clickDetector/offlineFuncs/OfflineEventDataBlock.java

@@ -284,5 +284,17 @@ public class OfflineEventDataBlock extends SuperDetDataBlock<OfflineEventDataUni
 		return (clickDetector.getClickDataBlock() == subDataBlock || clickDetector.getTrackedClicks() == subDataBlock);
 	}
 
+//	int nName = 0;
+//	@Override
+//	public String getDataName() {
+//		// TODO Auto-generated method stub
+//		System.out.println("Call into getDataName " + ++nName);
+//		if (nName == 58) {
+//
+//			System.out.println("Call into getDataName " + ++nName);
+//		}
+//		return super.getDataName();
+//	}
+
 }
 	

src/pamScrollSystem/ViewerScrollerManager.java

@@ -191,9 +191,9 @@ public class ViewerScrollerManager extends AbstractScrollManager implements PamS
 	 */
 	private void loadDataQueueItem(DataLoadQueData dataLoadQueData, int queuePosition, ViewLoadObserver loadObserver) {
 		PamDataBlock dataBlock = dataLoadQueData.getPamDataBlock();
-		if (dataBlock instanceof OfflineEventDataBlock) {
-			System.out.println(dataBlock);
-		}
+//		if (dataBlock instanceof OfflineEventDataBlock) {
+//			System.out.println("in loadDataQueueItem" + dataBlock);
+//		}
 		
 		// 2019-11-12 add a check of the counts to this 'if' statement as well.  If the data start time is negative
 		// (which can indicate that this is a 'special' data block and we should be loading all of it rather than just

src/targetMotionModule/EventRotator.java

@@ -23,8 +23,12 @@ import Stats.LinFit;
  * Step 3 is to rotate all position and angle vectors so that they correspond to 
  * a track as close as possible to the x axis. 
  * @author Doug Gillespie
+ * 
+ * Deprecated. Not used and will probably fall over with system whereby sub detection info
+ * is present, but not all sub detections are. 
  *
  */
+@Deprecated
 @SuppressWarnings("rawtypes") 
 public class EventRotator extends AbstractTargetMotionInformation{
 

src/targetMotionOld/EventRotator.java

@@ -1,9 +1,13 @@
 package targetMotionOld;
 
 import pamMaths.PamVector;
+
+import java.util.List;
+
 import PamDetection.AbstractLocalisation;
 import PamUtils.LatLong;
 import PamguardMVC.PamDataUnit;
+import PamguardMVC.superdet.SubdetectionInfo;
 import PamguardMVC.superdet.SuperDetection;
 import Stats.LinFit;
 
@@ -74,12 +78,18 @@ public class EventRotator {
 	private double[] rotatedArrayAngles;
 
 	private int referenceHydrophones;
+
+	/**
+	 * List of present (actual sub detection is not null) sub detections. 
+	 */
+	private List<SubdetectionInfo<PamDataUnit>> subDetections;
 	/**
 	 * @param pamDetection
 	 */
 	public EventRotator(SuperDetection pamDetection) {
 		super();
 		this.pamDetection = pamDetection;
+		this.subDetections = pamDetection.getPresentSubDetections();
 		rotatedWorldVectors = null;
 		calculateMetrePoints();
 	}
@@ -90,14 +100,14 @@ public class EventRotator {
 	 */
 	private void calculateMetrePoints() {
 		lastUpdateTime = pamDetection.getLastUpdateTime();
-		nSubDetections = pamDetection.getSubDetectionsCount();
+		nSubDetections = subDetections.size();
 		subDetectionOrigins = new PamVector[nSubDetections];
 		subDetectionHeadings = new PamVector[nSubDetections];
 		pointTimes = new long[nSubDetections];
 		if (nSubDetections == 0) {
 			return;
 		}
-		PamDataUnit pd = pamDetection.getSubDetection(0);
+		PamDataUnit pd = subDetections.get(0).getSubDetection();
 		if (pd == null) {
 			return;
 		}
@@ -110,7 +120,10 @@ public class EventRotator {
 		LatLong detOrigin;
 
 		for (int i = 0; i < nSubDetections; i++) {
-			pd = pamDetection.getSubDetection(i);
+			pd = subDetections.get(i).getSubDetection();
+			if (pd == null) {
+				continue;
+			}
 			localisation = pd.getLocalisation();
 			if (localisation == null) {
 				continue;
@@ -152,6 +165,9 @@ public class EventRotator {
 		rotatedOrigins = new PamVector[nSubDetections];
 		rotatedHeadings = new PamVector[nSubDetections];
 		for (int i = 0; i < nSubDetections; i++) {
+			if (subDetectionOrigins[i] == null) {
+				continue;
+			}
 			subDetectionHeadings[i] = new PamVector(Math.cos(Math.PI/2-rotatedArrayAngles[i]), Math.sin(Math.PI/2-rotatedArrayAngles[i]), 0);
 			rotatedOrigins[i] = subDetectionOrigins[i].rotate(-referenceAngle);
 			rotatedArrayAngles[i] = Math.PI/2. - rotatedArrayAngles[i];
@@ -170,7 +186,7 @@ public class EventRotator {
 		PamDataUnit pd;
 		AbstractLocalisation localisation;
 		for (int i = 0; i < nSubDetections; i++) {
-			pd = pamDetection.getSubDetection(i);
+			pd = subDetections.get(i).getSubDetection();
 			localisation = pd.getLocalisation();
 			if (localisation == null) {
 				continue;
@@ -187,7 +203,7 @@ public class EventRotator {
 		PamDataUnit pd;
 		AbstractLocalisation localisation;
 		for (int i = 0; i < nSubDetections; i++) {
-			pd = pamDetection.getSubDetection(i);
+			pd = subDetections.get(i).getSubDetection();
 			localisation = pd.getLocalisation();
 			if (localisation == null) {
 				continue;

src/targetMotionOld/dialog/DialogMap3DSwing.java

@@ -4,6 +4,7 @@ import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
 import java.util.ArrayList;
+import java.util.List;
 
 import javax.swing.JPanel;
 
@@ -18,6 +19,7 @@ import PamUtils.LatLong;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
 import PamguardMVC.dataSelector.DataSelector;
+import PamguardMVC.superdet.SubdetectionInfo;
 import clickDetector.ClickDataBlock;
 import targetMotionOld.TargetMotionLocaliser;
 
@@ -66,9 +68,14 @@ public class DialogMap3DSwing<T extends GroupDetection> extends DialogMap<T> {
 		mapDetData.allAvailable = true;
 		mapDetData.select = true;
 
-		int nSub = currentEvent.getSubDetectionsCount();
+		List<SubdetectionInfo<PamDataUnit>> subDets = currentEvent.getPresentSubDetections();
+		
+		int nSub = subDets.size();
 		for (int i = 0; i < nSub; i++) {
-			PamDataUnit subDet = currentEvent.getSubDetection(i);
+			PamDataUnit subDet = subDets.get(i).getSubDetection();
+			if (subDet == null) {
+				continue;
+			}
 			MapDetectionData subDetData = mapDetectionsManager.findDetectionData(subDet.getParentDataBlock());
 			if (subDetData != null && subDetData != mapDetData) {
 				mapDetData = subDetData;
@@ -81,8 +88,8 @@ public class DialogMap3DSwing<T extends GroupDetection> extends DialogMap<T> {
 		 */
 		LatLong eventCentre = currentEvent.getOriginLatLong(true);
 		if (nSub >= 2) {
-			LatLong ll1 = currentEvent.getSubDetection(0).getOriginLatLong(true);
-			LatLong ll2 = currentEvent.getSubDetection(nSub-1).getOriginLatLong(true);
+			LatLong ll1 = subDets.get(0).getSubDetection().getOriginLatLong(true);
+			LatLong ll2 = subDets.get(nSub-1).getSubDetection().getOriginLatLong(true);
 			if (ll1 != null & ll2 != null) {
 				double lat = (ll1.getLatitude() + ll2.getLatitude())/2.;
 				double lon = (ll1.getLongitude() + ll2.getLongitude())/2.;