Bug fixes to matched click classifier and TDisplayFX

src/dataPlotsFX/scroller/TDAcousticScroller.java

@@ -184,15 +184,21 @@ public class TDAcousticScroller extends AcousticScrollerFX implements PamSetting
 		
 		//add a listener so the visible amount changes of the spinner changes value. 
 		spinner.valueProperty().addListener((obsVal, oldVal, newVal)->{
-			if (spinnerCall) return ; //prevent overflow. 
-			if (newVal<=this.getRangeMillis()) {
-//					Debug.out.println("TDAcousticScroller: TimeRangeSpinner: " + newVal);
-				Platform.runLater(()->{ //why? But seems necessary
-					super.setVisibleMillis(newVal);
-				}); 
-			}
-			else spinner.getValueFactory().decrement(1); //need to use decrement here instead of set time because otherwise arrow buttons
-			//don't work. 
+			if (spinnerCall) return ; //prevent overflow
+			
+			/**
+			 * There are two slightly different modes here- in viewer mode we want the spinner to set
+			 * only the visible range. However in real time mode we want it to set the visible time and
+			 * the data keep time. 
+			 */
+				if (newVal<=this.getRangeMillis() || !isViewer) {
+	//					Debug.out.println("TDAcousticScroller: TimeRangeSpinner: " + newVal);
+					Platform.runLater(()->{ //why? But seems necessary
+						super.setVisibleMillis(newVal);
+						super.setRangeMillis(0, newVal, false); 
+					}); 
+				}
+				else spinner.getValueFactory().decrement(1); //need to use decrement here instead of set time because otherwise arrow buttons
 		});
 	}
 

src/matchedTemplateClassifer/MTClassifier.java

@@ -11,6 +11,9 @@ import com.jmatio.types.MLDouble;
 import com.jmatio.types.MLStructure;
 
 import Filters.SmoothingFilter;
+import Localiser.DelayMeasurementParams;
+import Localiser.algorithms.Correlations;
+import Localiser.algorithms.TimeDelayData;
 import PamModel.parametermanager.ManagedParameters;
 import PamModel.parametermanager.PamParameterSet;
 import PamModel.parametermanager.PrivatePamParameterData;
@@ -92,7 +95,16 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 	 * Decimates waveforms. 
 	 */
 	transient private WavInterpolator wavInterpolator = new WavInterpolator(); 
+	
+	/**
+	 * The delay measurment parameters. 
+	 */
+	private transient DelayMeasurementParams delayMeasurementParams = defualtDelayParams(); 
 
+	/**
+	 * Runs the cross correlation algorithm. 
+	 */
+	private transient Correlations correlations = new Correlations(); 
 	
 	/**
 	 * Default MT classifier 
@@ -101,6 +113,14 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 		fft= new FastFFT();
 	}
 
+	private DelayMeasurementParams defualtDelayParams() {
+		DelayMeasurementParams delayMeasurementParams = new DelayMeasurementParams(); 
+		//delayMeasurementParams.setUpSample(4);
+		delayMeasurementParams.setFftFilterParams(null);
+
+		return delayMeasurementParams;
+	}
+
 	/**
 	 * Get the match waveform FFT for the sampleRate.
 	 * @param fftLength - the FFTlength to use. Bins around waveform peak are used. 
@@ -376,7 +396,7 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 		int fftLength = click.length()*2;
 		
 		ComplexArray matchResult= new ComplexArray(fftLength); 
-		ComplexArray matchTemplate = getWaveformMatchFFT(sR,fftLength); 
+		ComplexArray matchTemplate = getWaveformMatchFFT(sR,fftLength); //remember this is the  complex conjugate
 		
 		//System.out.println("matchTemplate interp: len: " + interpWaveformMatch.length+ " max: " +  PamArrayUtils.max(interpWaveformMatch)); 
 		//System.out.println("matchTemplate: len: " + waveformMatch.waveform.length+ " max: " +  PamArrayUtils.max(waveformMatch.waveform)); 
@@ -386,7 +406,7 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 		}
 		
 		ComplexArray rejectResult= new ComplexArray(fftLength); 
-		ComplexArray rejectTemplate = getWaveformRejectFFT(sR, fftLength); 
+		ComplexArray rejectTemplate = getWaveformRejectFFT(sR, fftLength); //remember this is the  complex conjugate
 		for (int i=0; i<Math.min(rejectTemplate.length(), click.length()); i++) {
 			rejectResult.set(i, click.get(i).times(rejectTemplate.get(i)));
 		}
@@ -395,6 +415,9 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 //		System.out.println("Waveform Reject max: " + PamArrayUtils.max(this.inteprWaveformReject)); 
 		
 		//System.out.println("Click input: " + click.length() + " click template: " + matchTemplate.length());
+		
+	
+
 
 		//must use scaling to get the same result as MATLAB 
 		if (fft==null) fft= new FastFFT();
@@ -424,6 +447,14 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 		double maxmatch=PamArrayUtils.max(matchReal); 
 		double maxreject=PamArrayUtils.max(rejectReal); 
 		
+		
+//		//TEST
+//		if (correlations==null) correlations=new Correlations(); 
+//		TimeDelayData matchResultTD = correlations.getDelay(click,  matchTemplate.conj(), null, sR,  fftLength); 
+//		System.out.println("Old xcorr method: " + maxmatch + " new PG method: " + matchResultTD.getDelayScore()); 
+		
+//		//TEST
+		
 		//if set to "none" then reject template will return a NaN - TODO bit messy and inefficient. 
 		double result; 
 		double maxReject = PamArrayUtils.max(rejectReal); 

src/matchedTemplateClassifer/MTClassifierTest.java

@@ -134,14 +134,25 @@ public class MTClassifierTest {
 			MatchedTemplateResult matchResult = mtclassifier.calcCorrelationMatch(matchClick, sR);
 						
 			
-			System.out.println(String.format("The match correlation for %d is %.5f", i, matchResult.matchCorr)); 
+			System.out.println(String.format("The match correlation for %d is %.5f", i, matchResult.matchCorr));
+//			
+//			 printFFt(matchClick);
+//			 
+//			 System.out.println("-----------------------");
+//			
+//			 ComplexArray matchTemplate = mtclassifier.getWaveformMatchFFT(sR, matchClick.length()*2); 
+//
+//			 printFFt(matchTemplate);
+
+
 		}
 
 	}
 	
 	public static void printFFt(ComplexArray complexArray) {
 		for (int i=0; i<complexArray.length(); i++ ) {
-			System.out.println(complexArray.get(i).toString(6));
+			//System.out.println(complexArray.get(i).toString(6));
+			System.out.println(complexArray.get(i).real + "," + complexArray.get(i).imag);
 		}
 	}
 	

src/matchedTemplateClassifer/offline/MTOfflineProcess.java

@@ -65,6 +65,8 @@ public class MTOfflineProcess {
 		//System.out.println("Click train offline data block " + clickTrainControl.getParentDataBlock());
 		mtOfflineGroup.setPrimaryDataBlock(mtContorl.getParentDataBlock());
 		mtOfflineTask.setParentDataBlock(mtContorl.getParentDataBlock());
+		//need this to make sure annotations trigger saving. 
+        mtOfflineTask.addAffectedDataBlock(mtContorl.getParentDataBlock());
 		
 		//if null open the dialog- also create a new offlineTask group if the datablock has changed. 
 		if (mtOfflineDialog == null) {