Bug fixes to click train detector

Fixed bug with number of coasts in the MHT Kernel
Added an option for amplitude to have a maximum
Removed print statements.

src/PamUtils/TxtFileUtils.java

@@ -6,6 +6,7 @@ import java.io.File;
 import java.io.FileReader;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.text.DecimalFormat;
 import java.text.NumberFormat;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -62,7 +63,7 @@ public class TxtFileUtils {
 		boolean isNaN=false;
 		for (String line : lines) {
 
-			System.out.println(line);
+			//System.out.println(line);
 
 			String[] recordsOnLine = line.split(delimeter);
 
@@ -82,11 +83,15 @@ public class TxtFileUtils {
 						
 //						//This was causing isses with some numbers with e-06...dunno why so switched to parse double
 //						String input = new String(recordsOnLine[i].toCharArray()); 
-//						//System.out.println(input);
+//						System.out.println("|" + recordsOnLine[i] + "|");
 //						dat = nF.parse(input).doubleValue();
 					
-						
-						dat = Double.parseDouble(recordsOnLine[i]);
+						//5/08/2022 - there was a bug here where there is some sort of invisible character that does not appear on the 
+						//print screen - the only way you can tell is the char array is greater than the number of digits - removed all non numeric
+						//characters. 
+						String number = new String(recordsOnLine[i].strip().replaceAll("[^\\d.]", ""));
+						dat = Double.valueOf(number);
+						//dat = DecimalFormat.getNumberInstance().parse(new String(recordsOnLine[i].strip().toCharArray())).doubleValue();
 					}
 				catch (Exception e){
 					e.printStackTrace();

src/clickTrainDetector/IDIInfo.java

@@ -5,6 +5,7 @@ import java.util.List;
 
 import PamUtils.PamArrayUtils;
 import PamguardMVC.PamDataUnit;
+import PamguardMVC.debug.Debug;
 
 /**
  * Holds some basic IDI info on the click train. 
@@ -47,7 +48,7 @@ public class IDIInfo {
 		lastNumber = dataUnits.size();
 
 		if (dataUnits.size()<3) {
-			System.out.println("CTDataUnit: Cannot calculate IDIInfo for less than three data units"); 
+			Debug.out.println("CTDataUnit: Cannot calculate IDIInfo for less than three data units"); 
 			return; 
 		}
 

src/clickTrainDetector/classification/SimpleCTClassification.java

@@ -31,7 +31,6 @@ public class SimpleCTClassification implements CTClassification {
 
 	@Override
 	public String getSummaryString() {
-		// TODO Auto-generated method stub
 		return "SimpleClssf: SpeciesID: " + speciesID + " ClassifierType: " + classifierType;
 	}
 

src/clickTrainDetector/classification/bearingClassifier/BearingClassifier.java

@@ -1,8 +1,8 @@
 package clickTrainDetector.classification.bearingClassifier;
 
-import org.renjin.gcc.runtime.Debug;
 
 import PamUtils.PamArrayUtils;
+import PamguardMVC.debug.Debug;
 import clickTrainDetector.CTDataUnit;
 import clickTrainDetector.ClickTrainControl;
 import clickTrainDetector.classification.CTClassification;
@@ -95,7 +95,7 @@ public class BearingClassifier implements CTClassifier {
 		
 		if (nullcount>clickTrain.getSubDetectionsCount()-4) {
 			//less than three data units with loc results 
-			Debug.println("The bearing classifier has a null count: "); 
+			Debug.out.println("The bearing classifier has a null count: "); 
 			return new BearingClassification(CTClassifier.NOSPECIES, Double.NaN, Double.NaN, Double.NaN);
 		}
 
@@ -111,7 +111,7 @@ public class BearingClassifier implements CTClassifier {
 		double medianBearingD = PamArrayUtils.median(bearingDiff);
 		double stdBearingD = PamArrayUtils.std(bearingDiff);
 		
-		Debug.println("Bearing classifier: No. Detections: " + clickTrain.getSubDetectionsCount() + " medianBearing: " + medianBearingD);
+		Debug.out.println("Bearing classifier: No. Detections: " + clickTrain.getSubDetectionsCount() + " medianBearing: " + medianBearingD);
 
 		int speciesID = CTClassifier.NOSPECIES;
 		boolean passed= true; 
@@ -120,31 +120,31 @@ public class BearingClassifier implements CTClassifier {
 		//is the minimum and maximum bearing in range...
 		if ((min>=bearingClssfrParams.bearingLimMin && min<=bearingClssfrParams.bearingLimMax) ||
 				(max>=bearingClssfrParams.bearingLimMin && max<=bearingClssfrParams.bearingLimMax)) {
-			Debug.println("Passed on min max bearing");
+			Debug.out.println("Passed on min max bearing");
 		}
 		else passed =false; 
 		
 		//mean bearing derivative
 		if (bearingClssfrParams.useMean && meanBearingD>=bearingClssfrParams.minMeanBearingD 
 				&& meanBearingD<=bearingClssfrParams.maxMeanBearingD) {
-			Debug.println("Passed on mean bearing");
+			Debug.out.println("Passed on mean bearing");
 		}
 		else if (bearingClssfrParams.useMean) passed=false; 
 		
 		//median bearing derivative
-		Debug.println("Median Bearing: " + Math.toDegrees(medianBearingD) +
+		Debug.out.println("Median Bearing: " + Math.toDegrees(medianBearingD) +
 				"   minlim: " + Math.toDegrees(bearingClssfrParams.minMedianBearingD)+
 				"   maxlim: " + Math.toDegrees(bearingClssfrParams.maxMedianBearingD)); 
 		if (bearingClssfrParams.useMedian && medianBearingD>=bearingClssfrParams.minMedianBearingD 
 				&& medianBearingD<=bearingClssfrParams.maxMedianBearingD) {
-			Debug.println("Passed on median bearing");
+			Debug.out.println("Passed on median bearing");
 		}
 		else if (bearingClssfrParams.useMedian) passed = false; 
 		
 		//standard deviation derivative
 		if (bearingClssfrParams.useStD && stdBearingD>=bearingClssfrParams.minStdBearingD 
 				&& stdBearingD<=bearingClssfrParams.maxStdBearingD) {
-			Debug.println("Passed on std bearing");
+			Debug.out.println("Passed on std bearing");
 		}
 		else if (bearingClssfrParams.useStD) passed= false; 
 
@@ -152,7 +152,7 @@ public class BearingClassifier implements CTClassifier {
 			speciesID = this.bearingClssfrParams.speciesFlag;
 		}
 		
-		Debug.println("SPECIESID!! " + speciesID);
+		Debug.out.println("SPECIESID!! " + speciesID);
 
 
 		return new BearingClassification(speciesID, meanBearingD, medianBearingD, stdBearingD);

src/clickTrainDetector/clickTrainAlgorithms/mht/MHTGarbageBot.java

@@ -70,11 +70,13 @@ public class MHTGarbageBot {
 		double maxICI = mhtKernel.getMHTParams().maxCoast * mhtKernel.getMHTChi2Provider().getChi2Params().maxICI; 
 		
 		//check the current set of click train possible ICI's 
-				
+		
+		//Debug.out.println("MHTGARBAGEBOT: maxICI " + maxICI + "  " + iciPrev); 
+		
 		//we have reached the hard limit. Save click trains, wipe the detector and start again. 
 		if (mhtKernel.getKCount()>mhtKernel.getMHTParams().nPruneBackStart && (iciPrev>maxICI || mhtKernel.getKCount()>DETECTION_HARD_LIMIT)) {
 			
-//			Debug.out.println("MHTGarbageBot: KERNEL HARD LIMIT"); 
+			//Debug.out.println("MHTGARBAGEBOT: KERNEL HARD LIMIT"); 
 			//check whether the next click has a gap so big that all click trains should be restarted 			
 			//grab tracks
 			mhtKernel.confirmRemainingTracks();

src/clickTrainDetector/clickTrainAlgorithms/mht/MHTKernel.java

@@ -158,10 +158,10 @@ public class MHTKernel<T> {
 			if (verbosity>0) {
 				Debug.out.println("Possiblity matrix size is " + possibleTracks.size() + " x " +  kcount );
 			}
-			//		for (int i=0; i<possibleTracks.size(); i++) {
-			//			System.out.println("Pos " + i +  " chi^2 "+ possibleTracks.get(i).chi2Track + 
-			//					"  " +  printBitSet(possibleTracks.get(i).trackBitSet) );
-			//		}
+//					for (int i=0; i<possibleTracks.size(); i++) {
+//						System.out.println("Pos " + i +  " chi^2 "+ possibleTracks.get(i).chi2Track.getChi2() + 
+//								"  " +  MHTKernel.bitSetString(possibleTracks.get(i).trackBitSet,kcount));
+//					}
 
 			//prune the probability matrix.
 			pruneProbMatrix(false);
@@ -412,6 +412,7 @@ public class MHTKernel<T> {
 					testBranch = newPossibleTracks.get(j); 
 					testBitSet=testBranch.trackBitSet.get(0, kcount-(pruneback));
 
+					
 					//now test whether the current and test branch are the same. 
 					if (testBitSet.equals(currentBitSet)) {
 						indexConfirm[j]=true; 
@@ -423,6 +424,7 @@ public class MHTKernel<T> {
 							indexRemove[j]=true; 	
 						}						
 					}
+					
 				}
 
 				//long time2a=System.currentTimeMillis();
@@ -437,9 +439,11 @@ public class MHTKernel<T> {
 				if (nCoasts>=this.mHTParams.maxCoast || confirmAll || currentBranch.flag==TrackBitSet.JUNK_TRACK) {
 					//the branch needs to be confirmed. 
 
-					//					System.out.println(i + " DONE: "+ String.format("%.3f 		", possibleTracks.get(i).chi2Track.getChi2())+
-					//							"  "  + String.format("%d 	", possibleTracks.get(i).chi2Track.getNCoasts())
-					//								+ MHTKernel.bitSetString(possibleTracks.get(i).trackBitSet, kcount));		
+//					System.out.println(i + " DONE: " + (nCoasts >= this.mHTParams.maxCoast) + "  " + confirmAll + "  "
+//							+ (currentBranch.flag == TrackBitSet.JUNK_TRACK) + " "
+//							+ String.format("%.3f 		", currentBranch.chi2Track.getChi2()) + "  "
+//							+ String.format("%d 	", currentBranch.chi2Track.getNCoasts())
+//							+ MHTKernel.bitSetString(currentBranch.trackBitSet, kcount));
 
 					/**
 					 * 27/02/2020
@@ -460,7 +464,7 @@ public class MHTKernel<T> {
 
 					//add confirmed track
 					confirmedTracks.add(currentBranch); 
-
+					
 					////					//if a branch is confirmed then all the tracks which include it's clicks must also be removed. 
 					////					//test the testBranch against all other branches. TODO - Is this the most efficient code -could add if statements to above loop?
 					for (int j=0; j<newPossibleTracks.size(); j++) {
@@ -471,6 +475,7 @@ public class MHTKernel<T> {
 							indexRemove[j]=true; 	
 						}					
 					}
+					
 				}
 				else {
 					//save as an active track. 
@@ -678,7 +683,7 @@ public class MHTKernel<T> {
 	/**
 	 * 
 	 * Set a new reference index and junk all data before that index. This can be
-	 * useful for long data sets to save memory once all click trains in preceeding
+	 * useful for long data sets to save memory once all click trains in preceding
 	 * data units have been detecteded. Note that the function deletes the currently
 	 * confirmed tracks. These should be extracted beforehand;
 	 * 

src/clickTrainDetector/clickTrainAlgorithms/mht/StandardMHTChi2.java

@@ -5,6 +5,7 @@ import java.util.BitSet;
 
 import PamUtils.PamArrayUtils;
 import PamguardMVC.PamDataUnit;
+import PamguardMVC.debug.Debug;
 import clickTrainDetector.clickTrainAlgorithms.CTAlgorithmInfo;
 import clickTrainDetector.clickTrainAlgorithms.mht.electricalNoiseFilter.ElectricalNoiseFilter;
 import clickTrainDetector.clickTrainAlgorithms.mht.electricalNoiseFilter.SimpleElectricalNoiseFilter;
@@ -225,16 +226,17 @@ public class StandardMHTChi2 implements MHTChi2<PamDataUnit>, Cloneable {
 			getIDIManager().setForceCalc(true);
 			this.lastIDIData = getIDIManager().getIDIStruct(bitSet);
 			
-						
 			//System.out.println("Time diff: " + lastIDIData.timeDiff + "  " + lastIDIData.medianIDI); 
 			
 			nCoasts=(int) Math.floor(lastIDIData.timeDiff/Math.abs(lastIDIData.medianIDI)); 
 		}
 		else if (bitcount==1) {
 			//this stops a single units being stuck in the back of the probability matrix. 
-			nCoasts = (int) Math.floor((newdataUnit.getTimeMilliseconds()/1000.
-					-getIDIManager().getLastTime(bitSet)/this.getChi2Params().maxICI)); 
+			nCoasts = (int) Math.floor(((newdataUnit.getTimeMilliseconds()-getIDIManager().getFirstDataUnit().getTimeMilliseconds())/1000.
+					-getIDIManager().getLastTime(bitSet))/this.getChi2Params().maxICI); 
 		}
+		
+		//System.out.println("nCoasts: " + nCoasts); 
 
 		return nCoasts;
 	}
@@ -332,6 +334,8 @@ public class StandardMHTChi2 implements MHTChi2<PamDataUnit>, Cloneable {
 			
 			double totalTracktime = PamArrayUtils.sum(lastIDIData.idiSeries); 
 			
+			//System.out.println("Total track time: " + totalTracktime);
+			
 			/**
 			* Add a nudge towards longer tracks (remember to cast to double when dividing). Note that 
 			* kcount coefficient is meaningless because all tracks are multiplied by it and x^2 is only used
@@ -341,7 +345,7 @@ public class StandardMHTChi2 implements MHTChi2<PamDataUnit>, Cloneable {
 			//19/03/2020 - fixed a bug; Was multiplying instead of dividing - as such long tracks were being 
 			//discriminated against causing fragmentation...ooops
 			chi2=chi2/Math.pow(totalTracktime/getIDIManager().getTotalTime(),getChi2Params().longTrackExponent);
-			
+			//chi2=chi2/Math.pow(bitSet.cardinality(),getChi2Params().longTrackExponent);
 			
 			
 		}
@@ -374,6 +378,8 @@ public class StandardMHTChi2 implements MHTChi2<PamDataUnit>, Cloneable {
 		//All done. Set the values. 
 		//set the chi2 values. 
 		//long time3=System.nanoTime();
+		//Debug.out.println("Track chi2: " + chi2 + " " + bitcount ); 
+
 		return chi2; 
 	}
 

src/clickTrainDetector/clickTrainAlgorithms/mht/mhtvar/AmplitudeChi2.java

@@ -2,6 +2,9 @@ package clickTrainDetector.clickTrainAlgorithms.mht.mhtvar;
 
 
 import PamguardMVC.PamDataUnit;
+import clickTrainDetector.clickTrainAlgorithms.mht.StandardMHTChi2Params;
+import clickTrainDetector.layout.mht.AmplitudeMHTVarPane;
+import clickTrainDetector.layout.mht.MHTVarSettingsPane;
 
 /**
  * Chi^2 value for dB amplitude of tracks. Measures the chnage in track delta between 
@@ -13,9 +16,14 @@ import PamguardMVC.PamDataUnit;
 @SuppressWarnings("rawtypes")
 public class AmplitudeChi2 extends SimpleChi2VarDelta {
 	
+	private double lastDiff;
+	
+	private AmplitudeChi2Params amplitudeParams;
+
+
 	public AmplitudeChi2() {
 		super();
-		super.setSimpleChiVarParams(defaultSettings());
+		super.setSimpleChiVarParams(amplitudeParams = (AmplitudeChi2Params) defaultSettings());
 	}
 	
 	/**
@@ -23,7 +31,7 @@ public class AmplitudeChi2 extends SimpleChi2VarDelta {
 	 * @return
 	 */
 	private SimpleChi2VarParams defaultSettings() {
-		SimpleChi2VarParams simpleChiVarParams = new SimpleChi2VarParams(getName(), getUnits()); 
+		AmplitudeChi2Params simpleChiVarParams = new AmplitudeChi2Params(getName(), getUnits()); 
 		//simpleChiVarParams.errLimits=new double[] {Double.MIN_VALUE, 100}; 
 		simpleChiVarParams.error=30;
 		simpleChiVarParams.minError=1;
@@ -36,13 +44,15 @@ public class AmplitudeChi2 extends SimpleChi2VarDelta {
 		return "Amplitude";
 	}
 
+
 	@Override
 	public double getDiffValue(PamDataUnit pamDataUnit0, PamDataUnit pamDataUnit1) {
 		//System.out.println("DB: " + pamDataUnit0.getAmplitudeDB());
 		//made this abs so it can deal with increasing then decreasing click trains. i.e.
 		//the click trian is not penalised if it gradually increasing then starts to gradually decrease
 		//in amplitude. 
-		return Math.abs(pamDataUnit0.getAmplitudeDB()-pamDataUnit1.getAmplitudeDB());
+		this.lastDiff = Math.abs(pamDataUnit0.getAmplitudeDB()-pamDataUnit1.getAmplitudeDB());
+		return lastDiff;
 	}
 
 	@Override
@@ -50,6 +60,28 @@ public class AmplitudeChi2 extends SimpleChi2VarDelta {
 		//just a simple static error coefficient. 
 		return super.getError();
 	}
+	
+	@Override
+	public double calcDeltaChi2(double lastDelta, double newDelta, double timeDiff) {
+
+		double chi2 = super.calcDeltaChi2(lastDelta, newDelta, timeDiff); 
+
+		/**
+		 * There was a problem here with using the delta instead of the absolute difference between amplitudes. 
+		 * When using the delta there could be a slow change of amplitude gradient which could lead to giant 
+		 * changes in absolute amplitude. By ensuring this is the absolute 
+		 * value between bearings (lastdiff) then the bearingJump threshold works as it should.
+		 */
+		
+		//System.out.println("Amplitude: " + amplitudeParams.ampJumpEnable + "  " + lastDiff  + "  " + amplitudeParams.maxAmpJump);
+
+		if (lastDiff>amplitudeParams.maxAmpJump && amplitudeParams.ampJumpEnable ) {
+			chi2=chi2+StandardMHTChi2Params.JUNK_TRACK_PENALTY; 
+		}	
+	
+
+		return chi2; 
+	}
 
 
 	@Override
@@ -57,6 +89,27 @@ public class AmplitudeChi2 extends SimpleChi2VarDelta {
 		return "dB";
 	}
 	
+	@Override
+	public void setSimpleChiVarParams(SimpleChi2VarParams params) {
+		if (params==null) amplitudeParams = new AmplitudeChi2Params(getName(), getUnits()); //backwards compatibility
+		else this.amplitudeParams = (AmplitudeChi2Params)  params; ;
+
+		super.setSimpleChiVarParams(params);
+		//save a reference to params so we don;t have to keep casting. 
+	}
+	
+	@Override
+	public void setSettingsObject(Object object) {
+		this.setSimpleChiVarParams((AmplitudeChi2Params) object); 
+	}
+
+	@Override
+	public MHTVarSettingsPane<SimpleChi2VarParams> getSettingsPane() {
+		if (this.settingsPane==null) this.settingsPane= new AmplitudeMHTVarPane(getSimpleChiVarParams(), new ResultConverter()); 
+		settingsPane.setParams(getSimpleChiVarParams());
+		return settingsPane;
+	}
+	
 }
 
 

src/clickTrainDetector/clickTrainAlgorithms/mht/mhtvar/AmplitudeChi2Params.java

@@ -0,0 +1,46 @@
+package clickTrainDetector.clickTrainAlgorithms.mht.mhtvar;
+
+import PamModel.parametermanager.ManagedParameters;
+
+public class AmplitudeChi2Params extends SimpleChi2VarParams  implements ManagedParameters {
+
+
+	
+	public AmplitudeChi2Params(String name, String unitString, double error, double minError, double errorScaleValue) {
+		super(name, unitString, error, minError, errorScaleValue);
+		// TODO Auto-generated constructor stub
+	}
+	public AmplitudeChi2Params(String name, String unitString, double error, double minError) {
+		super(name, unitString, error, minError);
+		// TODO Auto-generated constructor stub
+	}
+	public AmplitudeChi2Params(String name, String unitString) {
+		super(name, unitString);
+		// TODO Auto-generated constructor stub
+	}
+	public AmplitudeChi2Params(String name) {
+		super(name);
+	}
+
+	public AmplitudeChi2Params(SimpleChi2VarParams params) {
+		this(params.name, params.getUnits(), params.error, params.minError, params.errorScaleValue);
+	}
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 1L;
+	
+	/**
+	 * Whether the bearing jump is used. 
+	 */
+	public boolean ampJumpEnable = true;
+	
+	/**
+	 * The maximum allowed bearing bearing jump in a click train in RADIANS
+	 */
+	public double maxAmpJump = 10; //dB
+
+
+	
+}

src/clickTrainDetector/clickTrainAlgorithms/mht/mhtvar/BearingChi2Delta.java

@@ -141,7 +141,7 @@ public class BearingChi2Delta extends SimpleChi2VarDelta {
 
 			if (delta>bearingParams.maxBearingJump) {
 				//System.out.println("Hello!!!! Reverse Bearing");
-				chi2=chi2*StandardMHTChi2Params.JUNK_TRACK_PENALTY; 
+				chi2=chi2+StandardMHTChi2Params.JUNK_TRACK_PENALTY; 
 			}	
 		}
 

src/clickTrainDetector/clickTrainAlgorithms/mht/mhtvar/IDIManager.java

@@ -536,6 +536,10 @@ public class IDIManager {
 		return (this.lastDetection.getTimeMilliseconds()- this.firstDetection.getTimeMilliseconds())/1000.;
 	}
 
+	public PamDataUnit getFirstDataUnit() {
+		return this.firstDetection;
+	}
+
 
 
 

src/clickTrainDetector/clickTrainAlgorithms/mht/mhtvar/LengthChi2.java

@@ -16,7 +16,6 @@ public class LengthChi2 extends SimpleChi2Var {
 
 	@Override
 	public String getName() {
-		// TODO Auto-generated method stub
 		return "Click Length";
 	}
 
@@ -44,7 +43,7 @@ public class LengthChi2 extends SimpleChi2Var {
 		//simpleChiVarParams.errLimits=new double[] {Double.MIN_VALUE, 100}; 
 		simpleChiVarParams.error=0.2;
 		simpleChiVarParams.minError=0.002;
-		simpleChiVarParams.errorScaleValue = SimpleChi2VarParams.SCALE_FACTOR_ICI; 
+		simpleChiVarParams.errorScaleValue = SimpleChi2VarParams.SCALE_FACTOR_ICI*10; 
 		return simpleChiVarParams; 
 	}
 	

src/clickTrainDetector/layout/mht/AdvMHTVarPane.java

@@ -28,7 +28,7 @@ public class AdvMHTVarPane extends DynamicSettingsPane<SimpleChi2VarParams> {
 	/**
 	 * Default divisor of error for min error. 
 	 */
-	private static final Double ERROR_DIVISOR = 10000.0;
+	private static final Double ERROR_DIVISOR = 100.0;
 
 	/**
 	 * The main pane. 

src/clickTrainDetector/layout/mht/AmplitudeChi2AdvPane.java

@@ -0,0 +1,97 @@
+package clickTrainDetector.layout.mht;
+
+import org.controlsfx.control.ToggleSwitch;
+
+import clickTrainDetector.clickTrainAlgorithms.mht.mhtvar.AmplitudeChi2Params;
+import clickTrainDetector.clickTrainAlgorithms.mht.mhtvar.IDIChi2Params;
+import clickTrainDetector.clickTrainAlgorithms.mht.mhtvar.ResultConverter;
+import clickTrainDetector.clickTrainAlgorithms.mht.mhtvar.SimpleChi2VarParams;
+import javafx.scene.control.Label;
+import javafx.scene.control.Spinner;
+import javafx.scene.control.Tooltip;
+import javafx.scene.layout.GridPane;
+import pamViewFX.fxNodes.PamSpinner;
+
+public class AmplitudeChi2AdvPane extends AdvMHTVarPane {
+	
+	private PamSpinner<Double> ampJumpSpinner;
+	private ToggleSwitch ampEnaleSwitch;
+
+
+	public AmplitudeChi2AdvPane(SimpleChi2VarParams simpleChi2Var2, ResultConverter resultConverter) {
+		super(simpleChi2Var2, resultConverter);
+	}
+	
+	
+	@Override
+	protected GridPane createAdvPane() {
+		
+		GridPane gridPane = (GridPane) super.createAdvPane();
+		
+		int gridY=3; 
+
+		gridPane.add(ampEnaleSwitch = new ToggleSwitch("Max jump"), 0, gridY); 
+		ampEnaleSwitch.selectedProperty().addListener((obsVal, newVal, oldVal)->{
+			ampJumpSpinner.setDisable(!ampEnaleSwitch.isSelected());
+		});
+		ampJumpSpinner = new PamSpinner<Double>(0.,Double.MAX_VALUE,0.,1.0); 
+		ampJumpSpinner.getStyleClass().add(Spinner.STYLE_CLASS_SPLIT_ARROWS_HORIZONTAL);
+		ampJumpSpinner.setPrefWidth(90);
+		ampJumpSpinner.valueProperty().addListener((obs,oldVal,newVal)->{
+			notifySettingsListeners();
+		});
+		gridPane.add(ampJumpSpinner, 1, gridY); 
+		gridPane.add(new Label("dB"), 2, gridY); 
+		ampJumpSpinner.setEditable(true);
+		
+		//create tool tip
+		Tooltip errorCoeffTip = new Tooltip(
+						  "The minimum Amplitude defines the maximum decibel jump between two detection allowed in a click train"
+						+ "If an IDI below this minimum occurs in a click train it will incur"
+						+ "a large chi^2 penalty and so the click train is unlikely to be kept"
+						+ "in the hypothesis mix.");
+		errorCoeffTip.setWrapText(true);
+		errorCoeffTip.setPrefWidth(200);
+		ampEnaleSwitch.setTooltip(errorCoeffTip);
+		ampJumpSpinner.setTooltip(errorCoeffTip);
+		
+		ampJumpSpinner.setDisable(!ampEnaleSwitch.isSelected());
+
+
+		return gridPane; 
+	}
+	
+	
+	@Override
+	public AmplitudeChi2Params getParams(SimpleChi2VarParams currParams) {	
+		
+		System.out.println("Get params: AMPLITUDE");
+		
+		AmplitudeChi2Params newParams = new AmplitudeChi2Params(super.getParams(currParams));
+
+		newParams.maxAmpJump = ampJumpSpinner.getValue();
+		newParams.ampJumpEnable = ampEnaleSwitch.isSelected();
+
+		return newParams; 
+	}
+
+
+	@Override
+	public void setParams(SimpleChi2VarParams currParams) {
+		
+		AmplitudeChi2Params newParams;
+		if (currParams instanceof AmplitudeChi2Params) {
+			newParams = (AmplitudeChi2Params) currParams;
+		}
+		else {
+			newParams = new AmplitudeChi2Params(currParams); 
+		}
+		
+		super.setParams(newParams);
+		
+		ampJumpSpinner.setDisable(!ampEnaleSwitch.isSelected()); 
+		ampJumpSpinner.getValueFactory().setValue(newParams.maxAmpJump);		
+		ampEnaleSwitch.setSelected(newParams.ampJumpEnable);
+	}
+
+}

src/clickTrainDetector/layout/mht/AmplitudeMHTVarPane.java

@@ -0,0 +1,22 @@
+package clickTrainDetector.layout.mht;
+
+import clickTrainDetector.clickTrainAlgorithms.mht.mhtvar.ResultConverter;
+import clickTrainDetector.clickTrainAlgorithms.mht.mhtvar.SimpleChi2VarParams;
+
+public class AmplitudeMHTVarPane extends SimpleMHTVarPane {
+
+		public AmplitudeMHTVarPane(SimpleChi2VarParams simpleChi2Var, ResultConverter resultsConverter) {
+			super(simpleChi2Var, resultsConverter);
+			// TODO Auto-generated constructor stub
+		}
+		
+		/**
+		 * Create the advanced settings pane. 
+		 * @return the advanced settings pane. 
+		 */
+		@Override
+		public AdvMHTVarPane createAdvMHTVarPane(SimpleChi2VarParams simpleChi2VarParams, ResultConverter resultConverter) {
+			return new AmplitudeChi2AdvPane(simpleChi2VarParams, resultConverter); 
+		}
+
+}

src/clickTrainDetector/layout/mht/BearingMHTVarPane.java

@@ -8,7 +8,6 @@ public class BearingMHTVarPane extends SimpleMHTVarPane {
 	
 	public BearingMHTVarPane(SimpleChi2VarParams simpleChi2Var, ResultConverter resultsConverter) {
 		super(simpleChi2Var, resultsConverter);
-		// TODO Auto-generated constructor stub
 	}
 	
 	/**

src/clickTrainDetector/layout/mht/CorrelationAdvMHTPane.java

@@ -86,11 +86,11 @@ public class CorrelationAdvMHTPane extends AdvMHTVarPane {
 
 		CorrelationChi2Params newParams = new CorrelationChi2Params(super.getParams(currParams));
 
-		System.out.println("GETPARAMS:fftFilterParams_OLD HIGHPASS: " + newParams.fftFilterParams.highPassFreq);
+		//System.out.println("GETPARAMS:fftFilterParams_OLD HIGHPASS: " + newParams.fftFilterParams.highPassFreq);
 
 		newParams.fftFilterParams=filterPane.getParams(newParams.fftFilterParams); 
 
-		System.out.println("GETPARAMS:fftFilterParams_NEW HIGHPASS: " + newParams.fftFilterParams.highPassFreq);
+		//System.out.println("GETPARAMS:fftFilterParams_NEW HIGHPASS: " + newParams.fftFilterParams.highPassFreq);
 
 		newParams.useFilter=this.useFilterBox.isSelected();
 

src/clickTrainDetector/layout/mht/ICIChi2AdvPane.java

@@ -42,7 +42,8 @@ public class ICIChi2AdvPane  extends AdvMHTVarPane {
 		});
 		gridPane.add(minICISpinner, 1, gridY); 
 		gridPane.add(new Label("ms"), 2, gridY); 
-		
+		minICISpinner.setEditable(true);
+
 		//create tool tip
 		Tooltip errorCoeffTip = new Tooltip(  "The minimum IDI defines a minimum IDI allowed in a click train \n"
 											+ "If an IDI below this minimum occurs in a click train it will incur\n"

src/clickTrainDetector/logging/ClickTrainDetLogging.java

@@ -98,7 +98,7 @@ public class ClickTrainDetLogging extends SuperDetLogging {
 		//average spectrum
 		tableDef.addTableItem(avrg_Spectrum_max = new PamTableItem("avrg_spectrum_max", Types.DOUBLE)); 
 		tableDef.addTableItem(avrg_Spectrum = new PamTableItem("avrg_spectrum", Types.CHAR, 8*DEFAULT_SPECTRUM_LEN)); 
-		tableDef.addTableItem(classifiers = new PamTableItem("classifiers", Types.CHAR, 4096));
+		tableDef.addTableItem(classifiers = new PamTableItem("classifiers", Types.CHAR, 8128));
 
 		//a species flag, this is entirely for user convenience and is NOT read back - the species flag 
 		//is read from the JSON strings when reloading the data unit. If they end being different something has gone 
@@ -279,7 +279,9 @@ public class ClickTrainDetLogging extends SuperDetLogging {
 
 		//set the classifications. 
 		String classifiersData = classifiers.getStringValue();
-
+		
+		//FIXME
+		//System.out.println(classifiersData);
 
 		if (classifiersData!=null && classifiersData.length()>0) {
 			String[] classifiersDatas = classifiersData.split(JSON_DELIMITER);

src/clickTrainDetector/offline/CTProcessDialog.java

@@ -44,7 +44,7 @@ public class CTProcessDialog extends OLProcessDialog {
 			getTaskCheckBoxs()[i].setEnabled(aTask.canRun() && nr);
 			//added extra but here so that only one tasks can be run at a time- may change
 			
-			System.out.println("A task can run: !!" + aTask.canRun() + "  " + aTask.getDataBlock());
+			//System.out.println("A task can run: !!" + aTask.canRun() + "  " + aTask.getDataBlock());
 			//if more tasks are added to the click train detector. 
 			if (aTask.canRun() == false || (aTask!=task && task!=null)) {
 				getTaskCheckBoxs()[i].setSelected(false);

src/matchedTemplateClassifer/ImportTemplateCSV.java

@@ -41,6 +41,7 @@ public class ImportTemplateCSV implements TemplateImport {
 		//the first row is the waveform 
 		double[] waveform = new double[data.get(0).size()];
 		for (int i=0; i<waveform.length; i++) {
+			//System.out.println("i: " + i + " : " +  data.get(0).get(i));
 			waveform[i]=data.get(0).get(i); 
 		}
 		

src/offlineProcessing/OfflineTask.java

@@ -71,7 +71,7 @@ public abstract class OfflineTask<T extends PamDataUnit> {
 		 */
 		PamControlledUnit parentControl = getTaskControlledUnit();
 		if (parentControl == null) {
-			System.out.printf("Offline task %d with datablock %s is not associated with a PAMGuard module\n", getName(), parentDataBlock);
+			System.out.printf("Offline task %s with datablock %s is not associated with a PAMGuard module\n", getName(), parentDataBlock==null ?  "null": parentDataBlock.getDataName());
 		}
 		else {
 			OfflineTaskManager.getManager().registerTask(this);

src/offlineProcessing/logging/TaskLogging.java

@@ -187,20 +187,31 @@ public class TaskLogging {
 		String modType = moduleType.getDeblankedStringValue();
 		String modName = moduleName.getDeblankedStringValue();
 		String tskName = taskName.getDeblankedStringValue();
-		long dStart = SQLTypes.millisFromTimeStamp(dataStart.getValue());
-		long dEnd = SQLTypes.millisFromTimeStamp(dataEnd.getValue());
-		long procEnd = SQLTypes.millisFromTimeStamp(runEnd.getValue());
+
+		Long dEnd = null, dStart = null, procEnd = null; 
+		dStart = SQLTypes.millisFromTimeStamp(dataStart.getValue());
+		dEnd = SQLTypes.millisFromTimeStamp(dataEnd.getValue());
+		procEnd = SQLTypes.millisFromTimeStamp(runEnd.getValue());
+		if (dStart==null && dEnd==null && procEnd==null) return null;
+		
 		String compStatus = completionCode.getDeblankedStringValue();
 		TaskStatus status = null;
+		if (compStatus==null) return null; 
 		try {
 			status = TaskStatus.valueOf(TaskStatus.class, compStatus);
 		}
 		catch (IllegalArgumentException e) {
 			System.out.printf("Uknown completion code \"%s\" for task %s ended at %s\n", compStatus, tskName, PamCalendar.formatDateTime(dEnd));
 		}
+		
 		String taskNote = note.getDeblankedStringValue();
-		OldTaskData monData = new OldTaskData(status, dStart, dEnd, utc, procEnd, taskNote);
-		return monData;
+		if (dStart!=null && dEnd!=null && procEnd!=null) {
+			OldTaskData monData = new OldTaskData(status, dStart, dEnd, utc, procEnd, taskNote);
+			return monData;
+		}
+		else {
+			return null;
+		}
 	}
 	
 	/**

src/soundPlayback/preprocess/PlaybackFilter.java

@@ -74,7 +74,7 @@ public class PlaybackFilter implements PlaybackPreprocess {
 	}
 	
 	public String getTextValue() {
-		System.out.println("Playback control Sample rate:  " + playbackControl.getSourceSampleRate() + " val: " + getValue());
+		//System.out.println("Playback control Sample rate:  " + playbackControl.getSourceSampleRate() + " val: " + getValue());
 		double f = getValue() * playbackControl.getSourceSampleRate();
 		if (f == 0) {
 			return "High pass filter off";