diff --git a/src/matchedTemplateClassifer/MTClassifier.java b/src/matchedTemplateClassifer/MTClassifier.java
index 75f30ef1..b1d43ee5 100644
--- a/src/matchedTemplateClassifer/MTClassifier.java
+++ b/src/matchedTemplateClassifer/MTClassifier.java
@@ -103,9 +103,14 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 		if (waveformMatchFFT==null || currentSr!=sR) {
 			if (fft==null) fft=new FastFFT();
 			
+			
+			//System.out.println("interpWaveform: " + waveformMatch.waveform.length + " sR " + waveformMatch.sR);
+
 			//re-sample the waveform if the sample rate is different
 			this.interpWaveformMatch=interpWaveform(this.waveformMatch, sR); 
 			
+			//System.out.println("interpWaveformMatch: " + interpWaveformMatch.length + " sR " + sR);
+			
 			//normalise
 			//this.interpWaveformMatch=PamArrayUtils.normalise(interpWaveformMatch);
 			
@@ -115,9 +120,11 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 //			System.out.println("MatchNorm: MATCH");
 //			MTClassifierTest.normalizeTest(interpWaveformMatch);
 			
-			//here use the FFT length with the maximum template size. 
-			waveformMatchFFT = fft.rfft(PamArrayUtils.flip(interpWaveformMatch), 
-					length); 
+			waveformMatchFFT = fft.rfft(interpWaveformMatch, length); 
+			
+			//need to calculate the complex conjugate - note that originally I was flipping the array but this means 
+			//the max value does not equal one with identical waveforms...doh. 
+			waveformMatchFFT = waveformMatchFFT.conj();
 //			System.out.println("waveformMatch: " + waveformMatch.waveform.length + 
 //					" interpWaveformMatch: " + interpWaveformMatch.length + " for " +sR + " sr "); 
 
@@ -155,9 +162,11 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 //			MTClassifierTest.printWaveform(inteprWaveformReject);
 			
 			//System.out.println("waveformReject: " +inteprWaveformReject.length +  " fftLength: " +  getFFTLength(sR)); 
+			waveformRejectFFT = fft.rfft(inteprWaveformReject, length); 
 			
-			//must flip the waveform for cross correlation - might as well do this here. 
-			waveformRejectFFT = fft.rfft(PamArrayUtils.flip(inteprWaveformReject), length); 
+			//need to calculate the complex conjugate - note that originally I was flipping the array but this means 
+			//the max value does not equal one with identical waveforms...doh. 
+			waveformRejectFFT = waveformRejectFFT.conj(); 
 		}
 		return waveformRejectFFT; 
 	}
@@ -342,11 +351,9 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 		//set the stored sR
 		currentSr=sR;
 		
-//		System.out.println("Matched click classifier: Waveform click: " + click.length()); 
-//		System.out.println("Matched click classifier: Waveform click: " + click.length()); 
+		//System.out.println("Waveform click: len: " + click.length()); 
 
-//		System.out.println("Waveform Reject max: " + PamArrayUtils.max(this.inteprWaveformReject)); 
-//		System.out.println("Waveform Reject max: " + PamArrayUtils.max(this.inteprWaveformReject)); 
+		//System.out.println("Waveform Reject max: " + PamArrayUtils.max(this.inteprWaveformReject)+ " len " + interpWaveformMatch.length); 
 
 		//int fftLength = getFFTLength(sR);
 		//int fftLength = this.getFFTLength(sR); 
@@ -363,7 +370,10 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 		
 		ComplexArray matchResult= new ComplexArray(fftLength); 
 		ComplexArray matchTemplate = getWaveformMatchFFT(sR,fftLength); 
-		//System.out.println("matchTemplate: Waveform click: " + matchTemplate.length()); 
+		
+		//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)); 
+
 		for (int i=0; i<Math.min(matchTemplate.length(), click.length()); i++) {
 			matchResult.set(i, click.get(i).times(matchTemplate.get(i)));
 		}
@@ -387,13 +397,13 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 		//System.out.println("Inverse MATCH RESULTS");
 	
 		//need to take the real part of the result and multiply by 2 to get same as 
-		//ifft function in MATLAB
+		//ifft function in MATLAB - dunno why this is...
 		double[] matchReal = new double[matchResult.length()]; 
 		double[] rejectReal = new double[rejectResult.length()]; 
 		
 		for (int i=0; i<matchResult.length(); i++) {
-			matchReal[i]=matchResult.getReal(i); 
-			rejectReal[i]=rejectResult.getReal(i); 
+			matchReal[i]=2*matchResult.getReal(i); 
+			rejectReal[i]=2*rejectResult.getReal(i); 
 			//System.out.println("iFFt match result: " + matchResult.get(i) + " iFFT rejectResult: " + rejectResult.get(i) );
 		}
 		
diff --git a/src/matchedTemplateClassifer/MTClassifierTest.java b/src/matchedTemplateClassifer/MTClassifierTest.java
index 90b8a104..df5bce79 100644
--- a/src/matchedTemplateClassifer/MTClassifierTest.java
+++ b/src/matchedTemplateClassifer/MTClassifierTest.java
@@ -72,19 +72,32 @@ public class MTClassifierTest {
 		return struct; 
 	}
 	
+	/**
+	 * Test the correlation of several templates
+	 * @param testWaveform - the waveform to correlate against. 
+	 * @param sR - the sample rate of the waveform. 
+	 * @param templates - the match templates to test. 
+	 */
+	private static void testCorrelation(double[] testWaveform, float sR, ArrayList<MatchTemplate> templates) {
+		testCorrelation(testWaveform,  sR,  templates, MatchedTemplateParams.NORMALIZATION_RMS); 
+	}
+
+	
+	
 	
 	/**
 	 * Test the correlation of several templates
-	 * @param testWaveform
-	 * @param sR
-	 * @param templates
-	 * @return
+	 * @param testWaveform - the waveform to correlate against. 
+	 * @param sR - the sample rate of the waveform. 
+	 * @param templates - the match templates to test. 
+	 * @param normalisation - the normalisation type to use e.g.  MatchedTemplateParams.NORMALIZATION_RMS
 	 */
-	private static void testCorrelation(double[] testWaveform, float sR, ArrayList<MatchTemplate> templates) {
+	private static void testCorrelation(double[] testWaveform, float sR, ArrayList<MatchTemplate> templates, int normalisation) {
 
 		//create the classifier object 
 		for (int i=0; i<templates.size(); i++){
 			MTClassifier mtclassifier = new MTClassifier(); 
+			mtclassifier.normalisation = normalisation; 
 			
 			//System.out.println("Template " + i + " " + templates.get(i));
 			//add templates if inpout 
@@ -97,8 +110,14 @@ public class MTClassifierTest {
 
 			//System.out.println("Waveform len: " +testWaveform.length + " min: " + PamArrayUtils.min(testWaveform) +  " max: " + PamArrayUtils.max(testWaveform)); 
 
+		
 			testWaveform=PamArrayUtils.divide(testWaveform, PamUtils.PamArrayUtils.max(testWaveform));
 			
+			testWaveform = MTClassifier.normaliseWaveform(testWaveform, MatchedTemplateParams.NORMALIZATION_RMS);
+			
+			System.out.println("Waveform max: " + PamArrayUtils.max(testWaveform) + " len: " + testWaveform.length); 
+
+			
 			//calculate the click FFT. 
 			fft = new FastFFT(); 
 			//int fftSize = FastFFT.nextBinaryExp(testWaveform.length/2);
@@ -303,7 +322,10 @@ public class MTClassifierTest {
 		
 	}
 	
-	public static void testMatchCorr() {
+	/**
+	 * Test how the length of the waveform affects the match correlation values
+	 */
+	public static void testMatchCorrLen() {
 		
 		String testClicksPath = "/Users/au671271/MATLAB-Drive/MATLAB/PAMGUARD/matchedclickclassifer/DS2clks_test.mat";
 		String templteFilePath= "/Users/au671271/MATLAB-Drive/MATLAB/PAMGUARD/matchedclickclassifer/DS2templates_test.mat";
@@ -333,6 +355,20 @@ public class MTClassifierTest {
 		
 	}
 	
+	/**
+	 * Test the match corr algorithm by cross correlating a waveform with itself. 
+	 */
+	public static void testMatchCorr() {
+		
+		String templteFilePath= "/Users/au671271/MATLAB-Drive/MATLAB/PAMGUARD/matchedclickclassifer/DS2templates_test.mat";
+		//float sR = 288000; //sample rate in samples per second. 
+
+		ArrayList<MatchTemplate> templates = importTemplates(templteFilePath); 
+		
+		testCorrelation(templates.get(0).waveform,  templates.get(0).sR, templates); 
+		
+	}
+	
 	
 	public static void main(String args[]) {
 		testMatchCorr(); 
diff --git a/src/matchedTemplateClassifer/layoutFX/MTSettingsPane.java b/src/matchedTemplateClassifer/layoutFX/MTSettingsPane.java
index a3cb83b6..2ca0748e 100644
--- a/src/matchedTemplateClassifer/layoutFX/MTSettingsPane.java
+++ b/src/matchedTemplateClassifer/layoutFX/MTSettingsPane.java
@@ -257,7 +257,7 @@ public class MTSettingsPane extends SettingsPane<MatchedTemplateParams> {
 
 		//click normalisation 
 		normBox = new ComboBox<String>();
-		normBox.getItems().addAll("peak to peak", "RMS", "none"); 
+		normBox.getItems().addAll("peak to peak", "norm", "none"); 
 
 		PamHBox clickNormPane= new PamHBox(); 
 		clickNormPane.setSpacing(5);