Fixes issues #111 and fixes #112 (DIFAR module crashes and ability to use Deep Learning Detections in DIFAR module) (#110)

* Bugfix for OverlayMarks

Check for a null pointer exception in OverlayMarks that was causing a crash on startup.

* Bugfix for null pointer in symbol manager

Fix a bug that I found where the DIFAR module was crashing the symbol manager. Seems that this was due to this subclass of clip generator having a null value for it's uniqueName. I've fixed by checking for null values and assigning a generic symbol when null.

* DeepLearning detections canGenerateClips=true

Set flag in DeepLearning detector so that detections are considered 'clips' by Pamguard. This allows them to be processed automatically in the DIFAR Localisation module (and maybe others).

* DIFAR: bugfix frequency limits for auto-detections

Fix a bug in DIFAR module where the frequency limits of automated detections were not being set properly by the DIFAR module.

* DeepLearning - Bugfix to detection duration

Fix bug in deep learning detector where duration (in samples) was being set to number of samples in a hop instead of the number of samples in a segment.

src/PamView/paneloverlay/overlaymark/OverlayMarkProviders.java

@@ -49,7 +49,7 @@ public class OverlayMarkProviders {
 				continue;
 			}
 			String existingName = marker.getMarkerName();
-			if (existingName.equals(nameToAdd)) {
+			if (existingName!=null && existingName.equals(nameToAdd)) {
 				markProviders.remove(i);
 				break;
 			}

src/PamView/symbol/PamSymbolManager.java

@@ -125,7 +125,7 @@ abstract public class PamSymbolManager<T extends PamSymbolChooser> implements Pa
 		 * This doesn't work since different displays will still need different options based on 
 		 * their projector - so it can work, but need to set the projector.
 		 */
-		if (managedSymbolData.useGeneric) {
+		if (managedSymbolData.useGeneric || displayName==null) {
 			displayName = GENERICNAME;
 		}
 		

src/PamguardMVC/dataSelector/DataSelectorSettings.java

@@ -23,7 +23,9 @@ public class DataSelectorSettings implements Serializable, ManagedParameters {
 		if (selectorParams == null) {
 			selectorParams = new Hashtable<>();
 		}
+		if (name != null) {
 		selectorParams.put(name, params);
+		}
 	}
 	
 	/**

src/difar/DifarProcess.java

@@ -316,11 +316,19 @@ public class DifarProcess extends PamProcess {
 			sP = difarControl.getDifarParameters().findSpeciesParams(difarDataUnit);
 		}
 		difarDataUnit.setDisplaySampleRate(sP.sampleRate);
-		if (!sP.useMarkedBandsForSpectrogramClips){
-			double[] frequency = {sP.processFreqMin, sP.processFreqMax};
-			difarDataUnit.setFrequency(frequency);
+		if (difarDataUnit.triggerName.equals(difarControl.getUnitName())) { // User detection
+			if (!sP.useMarkedBandsForSpectrogramClips ){
+				double[] frequency = {sP.processFreqMin, sP.processFreqMax};
+				difarDataUnit.setFrequency(frequency);
+			}
+		} else { //Check whether to override auto detection freq limits with DIFAR limits
+			if (!sP.useDetectionLimitsForTriggeredDetections ){ // Auto-detection
+				double[] frequency = {sP.processFreqMin, sP.processFreqMax};
+				difarDataUnit.setFrequency(frequency);
+			}
 		}
 		
+		
 		demuxDataUnit(difarDataUnit, demuxWorker, startTime);
 
 		calculateDifarGram(difarDataUnit, demuxWorker, startTime);

src/rawDeepLearningClassifier/dlClassification/DLClassifyProcess.java

@@ -107,7 +107,8 @@ public class DLClassifyProcess extends PamInstantProcess {
 		addOutputDataBlock(dlDetectionDataBlock);
 		dlDetectionDataBlock.setNaturalLifetimeMillis(600*1000); //keep this data for a while.
 		dlDetectionDataBlock.addDataAnnotationType(dlAnnotationType);
-
+		//ClipGeneration allows processing of detections by DIFAR module (and possibly others)
+		dlDetectionDataBlock.setCanClipGenerate(true); 
 		//add custom graphics
 		PamDetectionOverlayGraphics overlayGraphics = new DLGraphics(dlModelResultDataBlock);
 		overlayGraphics.setDetectionData(true);
@@ -483,7 +484,7 @@ public class DLClassifyProcess extends PamInstantProcess {
 
 		DataUnitBaseData basicData  = groupDataBuffer.get(0).getBasicData().clone(); 
 		basicData.setMillisecondDuration(1000.*rawdata[0].length/this.sampleRate);
-		basicData.setSampleDuration((long) (groupDataBuffer.size()*dlControl.getDLParams().sampleHop));
+		basicData.setSampleDuration((long) (groupDataBuffer.size()*dlControl.getDLParams().rawSampleSize));
 
 		//		System.out.println("Model result: " + modelResult.size()); 
 		DLDetection dlDetection = new DLDetection(basicData, rawdata);