Merge remote-tracking branch 'origin/main' into Tethys

.classpath

@@ -8,7 +8,6 @@
 	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jre">
 		<attributes>
-			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>

src/PamUtils/PamArrayUtils.java

@@ -22,19 +22,19 @@ public class PamArrayUtils {
 	/**
 	 * Calculate the mean of one dimension within a list of points. <i>e.g.</i> the points might be a list of [x y z] co-ordinates in 
 	 * which case the dim=0 would return the mean of all x points. 
-	 * @param array - a list of points
+	 * @param successJump - a list of points
 	 * @param InitialtoIgnorePercentage: ignore the first percentage of results
 	 * @param dim - the dimension of the point to calculate the average for
 	 * @return the mean of one dimension of the list of the points. 
 	 */
-	public static double mean(ArrayList<double[]> array, double InitialtoIgnorePercentage, int dim){
+	public static double mean(ArrayList<double[]> successJump, double InitialtoIgnorePercentage, int dim){
 
 		double meanTotal=0;
 		int n=0;
-		int forStart=(int) Math.round((InitialtoIgnorePercentage)*array.size());
+		int forStart=(int) Math.round((InitialtoIgnorePercentage)*successJump.size());
 
-		for (int i=forStart; i<array.size();i++){
+		for (int i=forStart; i<successJump.size();i++){
-			meanTotal+= array.get(i)[dim];
+			meanTotal+= successJump.get(i)[dim];
 			n++;
 		}
 
@@ -43,23 +43,24 @@ public class PamArrayUtils {
 		return mean;
 	}
 	
+
 	/**
 	 * Calculate the standard deviation of an array of doubles, ignoring an 'initialtoIgnorePercentage' percentage of jumps
-	 * @param array
+	 * @param successJump
 	 * @param initialtoIgnorePercentage- percentage of initial values to ignore.
 	 * @return standard deviation of array. 
 	 */
-	public static double std(ArrayList<double[]> array, double initialtoIgnorePercentage, int dim){
+	public static double std(ArrayList<double[]> successJump, double initialtoIgnorePercentage, int dim){
 		double std=0.0;
 
 		int n=0;
-		int forStart=(int) Math.round((initialtoIgnorePercentage)*array.size());
+		int forStart=(int) Math.round((initialtoIgnorePercentage)*successJump.size());
 
-		double meanTotal= mean(array,  initialtoIgnorePercentage,  dim);
+		double meanTotal= mean(successJump,  initialtoIgnorePercentage,  dim);
 
 		//calculate standard deviation
-		for (int k=forStart;k<array.size(); k++){
+		for (int k=forStart;k<successJump.size(); k++){
-			std+=Math.pow((array.get(k)[dim]-meanTotal),2);
+			std+=Math.pow((successJump.get(k)[dim]-meanTotal),2);
 		}
 
 		//standard deviation
@@ -448,12 +449,13 @@ public class PamArrayUtils {
 		return new int[] {min, max};
 	}
 
+
 	/**
 	 * Calculate the maximum value in an array 
 	 * @param arr - the array to find the maximum value of. 
 	 * @return the maximum value in the array
 	 */
-	public static double max(double[] arr) {
+	public static double max(float[] arr) {
 		double max = Double.NEGATIVE_INFINITY;
 
 		for(double cur: arr)
@@ -467,7 +469,7 @@ public class PamArrayUtils {
 	 * @param arr - the array to find the maximum value of. 
 	 * @return the maximum value in the array
 	 */
-	public static double max(float[] arr) {
+	public static double max(double[] arr) {
 		double max = Double.NEGATIVE_INFINITY;
 
 		for(double cur: arr)
@@ -490,6 +492,50 @@ public class PamArrayUtils {
 		return max;
 	}
 	
+	/**
+	 * Get the index of the maximum value in an array 
+	 * @param arr  - the array to find the position of the maximum value. 
+	 * m value of. 
+	 * @return the index of the maximum value
+	 */
+	public static int maxPos(double[] arr) {
+		double max = Double.NEGATIVE_INFINITY;
+		int index = -1; 
+		
+		int count = 0; 
+		for(double cur: arr) {
+			if (cur>max) {
+				index = count; 
+				max=cur;
+			}
+			count++; 
+		}
+		
+
+		return index;
+	}
+	
+	/**
+	 * Get the minimum index of an array
+	 * @param arr  - the array to find the position of the maximum value. 
+	 * m value of. 
+	 * @return the index of the minimum value
+	 */
+	public static int minPos(double[] arr) {
+		double max = Double.POSITIVE_INFINITY;
+		int index = -1; 
+		
+		int count = 0; 
+		for(double cur: arr) {
+			if (cur<max) {
+				index = count; 
+				max=cur;
+			}
+			count++; 
+		}
+		return index;
+	}
+
 	/**
 	 * Get the minimum value in an array 
 	 * @param arr  - the array to find the minimu
@@ -505,6 +551,8 @@ public class PamArrayUtils {
 		return min;
 	}
 	
+
+
 	/**
 	 * Get the minimum value in an array 
 	 * @param arr  - the array to find the minimum value of. 
@@ -579,6 +627,27 @@ public class PamArrayUtils {
 		return clone; 
 	}
 	
+	/**
+	 * Split an array based on start index and end index. A new array with index 0
+	 * as start and the last index at end is created and data from the input array
+	 * copied to it.
+	 * 
+	 * @param arr   - the array to split
+	 * @param start - the start index
+	 * @param end   - the end index
+	 * @return the split array.
+	 */
+	public static double[][] split(double[][] arr, int start, int end) {
+		double[][] newArr = new double[end - start][];
+		int n = 0;
+		for (int i = start; i < end; i++) {
+			newArr[n] = arr[i];
+			n++;
+		}
+		return newArr;
+	}
+
+
 	/**
 	 * Sum the elements in an array 
 	 * @param  array - the array to sum.
@@ -855,5 +924,152 @@ public class PamArrayUtils {
 		return arr;
 	}
 
+	/**
+	 * Convert a 2D float array to a 2D double array. 
+	 * @param arrf - the float array
+	 * @return a double array containing the same numbers as arrf. 
+	 */
+	public static double[][] float2Double(float[][] arrf) {
+		double[][] newArray = new double[arrf.length][];
+		for (int i=0; i<arrf.length; i++) {
+			newArray[i] = float2Double(arrf[i]); 
 		}
 		
+		return newArray; 
+	}
+	
+	/**
+	 * Convert a float array to a double array. 
+	 * @param arrd - the double array
+	 * @return a double array containing the same numbers as arrf. 
+	 */
+	public static float[] double2Float(double[] arrd) {
+		float[] arr = new float[arrd.length]; 
+		for (int i=0; i<arr.length; i++) {
+			arr[i] = (float) arrd[i]; 
+		}
+		return arr;
+	}
+	
+	/**
+	 * Convert a 2D float array to a 2D double array. 
+	 * @param arrd - the double array
+	 * @return a double array containing the same numbers as arrf. 
+	 */
+	public static float[][] double2Float(double[][] arrd) {
+		float[][] newArray = new float[arrd.length][];
+		for (int i=0; i<arrd.length; i++) {
+			newArray[i] = double2Float(arrd[i]); 
+		}
+		
+		return newArray; 
+	}
+
+
+	
+	/**
+	 * Check if two int arrays contain the same elements
+	 * @param arr1 - the array to compare to. 
+	 * @param arr2 - the array to be compared. 
+	 */
+	public static boolean arrEquals(int[] arr1, int[] arr2) {
+		if (arr1.length!=arr2.length) return false; 
+		
+		for (int i =0 ;i<arr1.length; i++) {
+			if (arr1[i]!=arr2[i]) return false; 
+		}
+		
+		return true; 
+	}
+	
+	/**
+	 * Check if two double arrays contain the same elements
+	 * @param arr1 - the array to compare to. 
+	 * @param arr2 - the array to be compared. 
+	 */
+	public static boolean arrEquals(double[] arr1, double[] arr2) {
+		if (arr1.length!=arr2.length) return false; 
+		
+		for (int i =0 ;i<arr1.length; i++) {
+			if (arr1[i]!=arr2[i]) return false; 
+		}
+		
+		return true; 
+	}
+
+	/**
+	 * Convert primitive long array to Long object array. 
+	 * @param arr - primitive long array
+	 * @return a Long array 
+	 */
+	public static Long[] primitive2Object(long[] arr) {
+		if (arr==null) return null; 
+		
+		Long[] arrL = new Long[arr.length];
+		for (int i=0; i<arr.length; i++) {
+			arrL[i]=arr[i];
+		}
+		return arrL;
+	}
+	
+	
+
+	/**
+	 * Convert primitive double array to Double object array. 
+	 * @param arr - primitive double array
+	 * @return a Double array 
+	 */
+	public static Double[] primitive2Object(double[] arr) {
+		if (arr==null) return null; 
+		
+		Double[] arrL = new Double[arr.length];
+		for (int i=0; i<arr.length; i++) {
+			arrL[i]=arr[i];
+		}
+		return arrL;
+	}
+	
+
+	/**
+	 * Convert primitive int array to Integer object array. 
+	 * @param arr - primitive int array
+	 * @return a Ineteger array 
+	 */
+	public static Integer[] primitive2Object(int[] arr) {
+		if (arr==null) return null; 
+		
+		Integer[] arrL = new Integer[arr.length];
+		for (int i=0; i<arr.length; i++) {
+			arrL[i]=arr[i];
+		}
+		return arrL;
+	}
+
+
+	public static long[] object2Primitve(Long[] arr) {
+		if (arr==null) return null; 
+		
+		long[] arrL = new long[arr.length];
+		for (int i=0; i<arr.length; i++) {
+			arrL[i]=arr[i].longValue();
+		}
+		return arrL;
+	}
+
+
+
+
+
+	
+	
+	
+
+
+
+
+
+
+
+
+
+}

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.math.BigDecimal;
 import java.text.DecimalFormat;
 import java.text.NumberFormat;
 import java.util.ArrayList;
@@ -89,10 +90,20 @@ public class TxtFileUtils {
 						//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. 
+						
+//						if (recordsOnLine[i].contains("e") || recordsOnLine[i].contains("E")) {
+//							//need to check whether scientific notation might be used here
+////							dat = new BigDecimal(recordsOnLine[i]).doubleValue();
+//							dat =  Double.valueOf(recordsOnLine[i]);
+//						}
+//						else {
+							//note that this gets rid of numbers like 3.84e+05
 							// updated again on 15/11/23 to include - signs, or you end up with the abs(of every number!)
-						String number = new String(recordsOnLine[i].strip().replaceAll("[^\\d.-]", ""));
+							//also added E and e to neglected characters to ensure scientific notation can be used, 
+							String number = new String(recordsOnLine[i].strip().replaceAll("[^Ee\\d.-]", ""));
 							dat = Double.valueOf(number);
 							//dat = DecimalFormat.getNumberInstance().parse(new String(recordsOnLine[i].strip().toCharArray())).doubleValue();
+//						}
 					}
 				catch (Exception e){
 					e.printStackTrace();

src/clickDetector/ClickBTDisplay.java

@@ -395,7 +395,7 @@ public class ClickBTDisplay extends ClickDisplay implements PamObserver, PamSett
 			int subDetInd = superDet.findSubdetectionInfo(clickDetection);
 			for (int i = subDetInd-1; i >= 0; i--) {
 				PamDataUnit subDet = superDet.getSubDetection(i);
-				if (subDet.getChannelBitmap() == clickDetection.getChannelBitmap()) {
+				if (subDet!=null && subDet.getChannelBitmap() == clickDetection.getChannelBitmap()) {
 					double ici = (double) (clickDetection.getTimeMilliseconds() - subDet.getTimeMilliseconds())/1000.;
 					clickDetection.setTempICI(ici);
 					break;

src/clickDetector/layoutFX/clickClassifiers/BasicIdentifierPaneFX.java

@@ -1,13 +1,18 @@
 package clickDetector.layoutFX.clickClassifiers;
 
 import pamViewFX.fxNodes.PamBorderPane;
+import pamViewFX.fxNodes.PamSymbolFX;
 import pamViewFX.fxNodes.flipPane.PamFlipPane;
 import pamViewFX.fxNodes.table.TableSettingsPane;
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
+import javafx.geometry.Insets;
+import javafx.geometry.Point2D;
 import javafx.scene.Node;
+import javafx.scene.canvas.Canvas;
 import javafx.scene.control.Button;
 import javafx.scene.control.Dialog;
+import javafx.scene.control.TableCell;
 import javafx.scene.control.TableColumn;
 import javafx.scene.control.cell.CheckBoxTableCell;
 import clickDetector.BasicClickIdParameters;
@@ -15,6 +20,7 @@ import clickDetector.ClickControl;
 import clickDetector.ClickTypeParams;
 import clickDetector.ClickClassifiers.ClickIdentifier;
 import clickDetector.ClickClassifiers.basic.BasicClickIdentifier;
+import clickDetector.ClickClassifiers.basicSweep.*;
 
 /**
  * Pane for the basic click classifier. 
@@ -37,7 +43,7 @@ public class BasicIdentifierPaneFX implements ClassifyPaneFX {
 	/**
 	 * Pane which holds table data.
 	 */
-	private TableSettingsPane<ClickTypeProperty> settingsPane;
+	protected TableSettingsPane<ClickTypeProperty> clickTypesTable;
 
 	//	/**
 	//	 * Hiding pane which slides out to allow users to change click type settings. 
@@ -103,7 +109,8 @@ public class BasicIdentifierPaneFX implements ClassifyPaneFX {
 	protected Node createSettingsPane(){
 
 		mainHolderPane=new PamBorderPane();
-		mainHolderPane.setCenter(settingsPane=new ClickClassifierTable(clickClassifiers));
+		mainHolderPane.setPadding(new Insets(5,5,5,5));
+		mainHolderPane.setCenter(clickTypesTable=new ClickClassifierTable(clickClassifiers));
 
 		clickTypeHolder=new PamBorderPane();
 		//clickTypeHolder.setPrefWidth(hidingPaneWidth);
@@ -165,9 +172,19 @@ public class BasicIdentifierPaneFX implements ClassifyPaneFX {
 			super(data);
 			//need to set up all the rows.
 
-			TableColumn<ClickTypeProperty,String>  name = new TableColumn<ClickTypeProperty,String>("Name");
+			TableColumn<ClickTypeProperty,String>  icon = new TableColumn<ClickTypeProperty,String>("Name");
-			name.setCellValueFactory(cellData -> cellData.getValue().name);
+			icon.setCellValueFactory(cellData -> cellData.getValue().name);
-			name.setEditable(true);
+			icon.setEditable(false);
+
+			icon.setCellFactory((tableColumn) -> {
+				TableCell<ClickTypeProperty, String> tableCell = new ClickTypeNameCell(); 
+				return tableCell;
+			});
+
+			//			TableColumn<ClickTypeProperty,String>  name = new TableColumn<ClickTypeProperty,String>("Name");
+			//			name.setCellValueFactory(cellData -> cellData.getValue().name);
+			//			name.setEditable(true);
+
 
 			TableColumn<ClickTypeProperty,Number>  code = new TableColumn<ClickTypeProperty,Number>("Species Code");
 			code.setCellValueFactory(cellData -> cellData.getValue().code);
@@ -190,7 +207,7 @@ public class BasicIdentifierPaneFX implements ClassifyPaneFX {
 
 			getTableView().setEditable(true);
 
-			getTableView().getColumns().addAll(checkCol, name, code, discard);
+			getTableView().getColumns().addAll(checkCol, icon, code, discard);
 
 		}
 
@@ -261,7 +278,6 @@ public class BasicIdentifierPaneFX implements ClassifyPaneFX {
 	 */
 	public void setClassifierPane(ClickTypeProperty clickTypeProperty){
 
-		
 		ClickTypePaneFX clickTypePane=new ClickTypePaneFX();
 		clickTypePane.setParams(clickTypeProperty);
 
@@ -270,10 +286,12 @@ public class BasicIdentifierPaneFX implements ClassifyPaneFX {
 		//now need to make sure on closing the pane that settings are saved. Need to 
 		//remove the old click type from the list and add new one in the same position. 
 		getFlipPaneCloseButton().setOnAction((action)->{
-			//System.out.println("CLOSE FLIP PANE");
 			showFlipPane(false);
 			//this should update the click type property in the observable list thus changing the table
 			clickTypePane.getParams(clickTypeProperty);
+
+			//need to refresh table to show symbol. 
+			clickTypesTable.getTableView().refresh();
 		});
 	}
 
@@ -309,7 +327,7 @@ public class BasicIdentifierPaneFX implements ClassifyPaneFX {
 	 * @return table which holds a list of classifiers
 	 */
 	public TableSettingsPane<ClickTypeProperty>  getTablePane() {
-		return this.settingsPane;
+		return this.clickTypesTable;
 	};
 
 	/**
@@ -329,4 +347,48 @@ public class BasicIdentifierPaneFX implements ClassifyPaneFX {
 		return flipPane;
 	}
 
+
+	/**
+	 * Shows a name alongside a graphic showing the current symbol. 
+	 * @author Jamie Macaulay. 
+	 *
+	 */
+	private class  ClickTypeNameCell extends TableCell<ClickTypeProperty, String> {
+
+		/**
+		 * Symbol is drawn on the canvas
+		 */
+		Canvas canvas;
+
+		public static final double SYMBOL_SIZE = 20; 
+
+		public ClickTypeNameCell() {
+			super(); 
+			canvas = new Canvas(SYMBOL_SIZE, SYMBOL_SIZE); 
+		}
+
+
+		@Override
+		protected void updateItem(String item, boolean empty) {
+			super.updateItem(item, empty);
+
+			this.setText(item);
+
+			this.setGraphic(null);
+
+			if (this.getTableRow()!=null && this.getTableRow().getItem()!=null) {
+
+				SweepClassifierSet clickProperty = (SweepClassifierSet) this.getTableRow().getItem().getClickType();
+
+				if (clickProperty.symbol!=null) {
+					canvas.getGraphicsContext2D().clearRect(0, 0, SYMBOL_SIZE, SYMBOL_SIZE);            
+					PamSymbolFX pamSymbolFX = new PamSymbolFX(clickProperty.symbol);
+					pamSymbolFX.draw(canvas.getGraphicsContext2D(), new Point2D(SYMBOL_SIZE/2,SYMBOL_SIZE/2), SYMBOL_SIZE, SYMBOL_SIZE); 
+					this.setGraphic(canvas);
+				}
+			}
+
+		}
+	};
+
 }

src/clickDetector/layoutFX/clickClassifiers/SweepClassifierPaneFX.java

@@ -1,10 +1,16 @@
 package clickDetector.layoutFX.clickClassifiers;
 
 
+
 import clickDetector.ClickControl;
 import clickDetector.ClickClassifiers.basicSweep.SweepClassifier;
 import clickDetector.ClickClassifiers.basicSweep.SweepClassifierParameters;
 import clickDetector.ClickClassifiers.basicSweep.SweepClassifierSet;
+import javafx.scene.text.FontPosture;
+import javafx.scene.text.FontWeight;
+import javafx.scene.layout.Region;
+import javafx.scene.text.Font;
+import javafx.geometry.Insets;
 
 /**
  * Slightly different pane for the sweep classifier.  
@@ -39,10 +45,15 @@ public class SweepClassifierPaneFX extends BasicIdentifierPaneFX {
 	public void setClassifierPane(ClickTypeProperty clickTypeProperty){
 		SweepClassifierSetPaneFX sweepPane=new SweepClassifierSetPaneFX(sweepClickClassifier);
 		
+		//set padding - want the flip pane not to have padding so back button reaches edge of node. 
+		((Region) sweepPane.getContentNode()).setPadding(new Insets(5,5,5,5));
 		
 		//make it so the title of the pane is the same as the name as the classifier
 		getFlipPane().getAdvLabel().textProperty().unbind();
+		
 		getFlipPane().getAdvLabel().textProperty().bind(sweepPane.getNameTextProperty());
+		// removed DG 2023 12 14 since not everything was in this merge that was required Needs to be put back. 
+//		getFlipPane().getPreAdvLabel().graphicProperty().bind(sweepPane.getNameGraphicProperty());
 
 		sweepPane.classifierItemRow = sweepClickClassifier.getSweepClassifierParams().getSetRow((SweepClassifierSet) clickTypeProperty.getClickType());
 		
@@ -54,6 +65,8 @@ public class SweepClassifierPaneFX extends BasicIdentifierPaneFX {
 		getFlipPaneCloseButton().setOnAction((action)->{
 			showFlipPane(false);
 			sweepPane.getParams(clickTypeProperty);
+			//need to refresh table to show symbol. 
+			clickTypesTable.getTableView().refresh();
 		});
 	}
 	

src/matchedTemplateClassifer/ImportTemplateCSV.java

@@ -2,7 +2,9 @@ package matchedTemplateClassifer
 ;
 
 import java.io.File;
+import java.math.BigDecimal;
 import java.util.ArrayList;
+import java.util.Collection;
 
 import PamUtils.PamArrayUtils;
 import PamUtils.TxtFileUtils;
@@ -44,16 +46,21 @@ public class ImportTemplateCSV implements TemplateImport {
 			//System.out.println("i: " + i + " : " +  data.get(0).get(i));
 			waveform[i]=data.get(0).get(i); 
 		}
+//		System.out.println("String sR = " +  data.get(1).get(0)); 
 
-		float sR=data.get(1).get(0).floatValue();
+
+		//used big decimal here because String.,floatValue did not handle numbers like 3.85e05
+		float sR = new BigDecimal(data.get(1).get(0)).floatValue();
+		
+//		float sR=data.get(1).get(0).floatValue();
 		
 		//System.out.println("imported waveform"); 
 		//PamArrayUtils.printArrayRaw(waveform);
 		
 		
 		//now create waveform
-//		System.out.println("Create a waveform with " + waveform.length + " samples with a sample rate of "
+		System.out.println("Import a waveform with " + waveform.length + " samples with a sample rate of "
-//				+ sR + " Hz");
+				+ sR + " Hz ");
 		MatchTemplate matchedTemplate = new MatchTemplate(filePath.getName(), waveform, sR);
 		//TODO		
 		return matchedTemplate; 

src/matchedTemplateClassifer/MTClassifier.java

@@ -146,7 +146,12 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 //			System.out.println("MatchNorm: MATCH");
 //			MTClassifierTest.normalizeTest(interpWaveformMatch);
 			
-			waveformMatchFFT = fft.rfft(interpWaveformMatch, length); 
+			/**
+			 * There is an issue here because, if we have a long template waveform, then it
+			 * will become truncated and the actual waveform may be missed. This means we
+			 * have to use the peak of the template
+			 */
+			waveformMatchFFT = calcTemplateFFT(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. 
@@ -159,6 +164,42 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 	}
 	
 	
+	/**
+	 * Calculate the FFT of an interpolate match template. 
+	 * @param interpTemplateWaveform - the waveform interpolated to the correct sample rate. 
+	 * @param length - the length of the FFT. 
+	 * @return the FFT of the waveform as a complex array. 
+	 */
+	private ComplexArray calcTemplateFFT(double[] interpTemplateWaveform, int length) {
+		
+		ComplexArray fftTemplate;
+		/**
+		 * There is an issue here because, if we have a long template waveform, then it
+		 * will become truncated and the actual waveform may be missed. This means we
+		 * have to use the peak of the template
+		 */
+		if (interpTemplateWaveform.length>length) {
+			//If the template is long then need to find the peak, otherwise we will end up cross correlating with noise at the
+			//start of the template. 
+			//because this is a template and not a random click we don't need to be so clever with how we find peaks. Find 
+			//the maximum and use around that. 
+			int pos = PamArrayUtils.maxPos(interpTemplateWaveform); 
+			
+			int startind = Math.max(0, pos-length/2);
+			int endind = startind+length-1;
+
+			double[] peakTemplate = ArrayUtils.subarray(interpTemplateWaveform, startind, endind); 
+			fftTemplate = fft.rfft(peakTemplate, length);
+		}
+		else {
+			//template waveform is padded by fft function
+			fftTemplate = fft.rfft(interpTemplateWaveform, length); 
+		}
+		
+		return fftTemplate; 
+	}
+	
+
 	
 	/**
 	 * Get the match waveform for the sample rate 
@@ -182,13 +223,17 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 //			this.inteprWaveformReject=PamArrayUtils.divide(inteprWaveformReject, PamArrayUtils.max(inteprWaveformReject));
 			this.inteprWaveformReject = normaliseWaveform(inteprWaveformReject, this.normalisation);
 
-			
 //			System.out.println("MatchNorm: REJECT ");
 //			MTClassifierTest.normalizeTest(inteprWaveformReject);
 //			MTClassifierTest.printWaveform(inteprWaveformReject);
 			
-			//System.out.println("waveformReject: " +inteprWaveformReject.length +  " fftLength: " +  getFFTLength(sR)); 
+			/**
-			waveformRejectFFT = fft.rfft(inteprWaveformReject, length); 
+			 * There is an issue here because, if we have a long template waveform, then it
+			 * will become truncated and the actual waveform may be missed. This means we
+			 * have to use the peak of the template
+			 */
+			waveformRejectFFT = calcTemplateFFT(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. 
@@ -377,7 +422,7 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 		//set the stored sR
 		currentSr=sR;
 		
-		//System.out.println("Waveform click: len: " + click.length()); 
+		System.out.println("Waveform click: len: " + click.length()); 
 
 		//System.out.println("Waveform Reject max: " + PamArrayUtils.max(this.inteprWaveformReject)+ " len " + interpWaveformMatch.length); 
 
@@ -399,7 +444,9 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 		
 //		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)); 
+//		System.out.println("matchTemplate interp: len: " + interpWaveformMatch.length+ " max: " +  PamArrayUtils.max(interpWaveformMatch)); 
 
+		System.out.println("matchTemplate len: " + matchTemplate.length() + " click.length(): "  +click.length()); 
 		for (int i=0; i<Math.min(matchTemplate.length(), click.length()); i++) {
 			matchResult.set(i, click.get(i).times(matchTemplate.get(i)));
 		}
@@ -410,14 +457,11 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 			rejectResult.set(i, click.get(i).times(rejectTemplate.get(i)));
 		}
 		
-//		System.out.println("Waveform Match max: " + PamArrayUtils.max(this.interpWaveformMatch)); 
+		System.out.println("Waveform Match max: " + PamArrayUtils.max(this.interpWaveformMatch)); 
-//		System.out.println("Waveform Reject max: " + PamArrayUtils.max(this.inteprWaveformReject)); 
+		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();
 		fft.ifft(matchResult,  fftLength, true);
@@ -454,17 +498,18 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 		
 //		//TEST
 		
-		//if set to "none" then reject template will return a NaN - TODO bit messy and inefficient. 
+		//if the reject template is set to "none" then reject template will return a NaN 
+		//TODO bit messy and inefficient. 
 		double result; 
-		double maxReject = PamArrayUtils.max(rejectReal); 
+//		double maxReject = PamArrayUtils.max(rejectReal); 
-		if (Double.isNaN(maxReject)) {
+		if (Double.isNaN(maxreject)) {
 			result = PamArrayUtils.max(matchReal);
 		}
 		else {
-			result = PamArrayUtils.max(matchReal)-maxReject; 
+			result = PamArrayUtils.max(matchReal)-maxreject; 
 		}
 
-		//System.out.println("Match corr " + maxmatch + " Reject Corr: " + maxreject);
+		System.out.println("Match corr " + maxmatch + " Reject Corr: " + maxreject);
 
 		MatchedTemplateResult matchTmpResult = new MatchedTemplateResult(); 
 		matchTmpResult.threshold=result; 
@@ -477,17 +522,19 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 	
 	/**
 	 * Get the match waveform for the sample rate 
-	 * @param sR - the sample rate in samples per second
+	 * @param waveformMatch - the template to interpolate or decimate. 
+	 * @param sR - the target sample rate in samples per second
 	 */
 	private double[] interpWaveform(MatchTemplate waveformMatch, double sR) {
 //		System.out.println("Interp waveform: " + " old: " + waveformMatch.sR + " new: " +  sR);
 		
-		if ( waveformMatch.sR>sR) {
+		if (waveformMatch.sR<sR) {
 			//up sample
 			double[] interpWaveformMatch=reSampleWaveform(waveformMatch.waveform, waveformMatch.sR, sR);
 			return interpWaveformMatch; 
 		}
-		else if (waveformMatch.sR<sR){
+		else if (waveformMatch.sR>sR){
+			//decimate
 //			//TODO - make a better decimator?
 //			double[] interpWaveformMatch=reSampleWaveform(waveformMatch.waveform, waveformMatch.sR, sR);
 //			return interpWaveformMatch; 
@@ -495,11 +542,9 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 			return wavInterpolator.decimate(waveformMatch.waveform, waveformMatch.sR, (float) sR); 
 		}
 		else {
-			//nothing needed/ 
+			//nothing needed
 			return waveformMatch.waveform;
 		}		
-		
-			
 	}
 	
 	
@@ -530,7 +575,8 @@ public class MTClassifier implements Serializable, Cloneable, ManagedParameters
 //		// TODO Auto-generated method stub
 //		return PamInterp.interpLinear(x, waveform, xi);
 		
-		return PamInterp.interpWaveform(waveform, 1/binSize); 
+//		System.out.println("Interp waveform: " + binSize); 
+		return PamInterp.interpWaveform(waveform, 1./binSize); 
 		
 	}
 	

src/matchedTemplateClassifer/MTProcess.java

@@ -5,6 +5,7 @@ import java.util.Arrays;
 
 import PamController.PamController;
 import PamDetection.RawDataUnit;
+import PamUtils.PamArrayUtils;
 import PamUtils.complex.ComplexArray;
 import PamView.symbol.PamSymbolManager;
 import PamguardMVC.PamDataBlock;
@@ -288,6 +289,7 @@ public class MTProcess extends PamInstantProcess {
 	@SuppressWarnings("unused")
 	private double[] getWaveData(RawDataHolder clickDetection, int i) {
 		double[] waveform; 
+		
 		if (this.getMTParams().peakSearch) {
 			waveform = createRestrictedLenghtWave(clickDetection,  i, lengthData[i],
 					this.getMTParams().restrictedBins); 
@@ -377,7 +379,14 @@ public class MTProcess extends PamInstantProcess {
 	 */
 	private double[] createRestrictedLenghtWave(RawDataHolder click, int chan, int[] lengthPoints,
 			int restrictedBins) {
-		return createRestrictedLenghtWave(click, chan, lengthPoints, restrictedBins,  getWindow(restrictedBins)); 
+//		System.out.println("Create restricted length wave: " + lengthPoints[0] + " to " + lengthPoints[1]); 
+//		System.out.println("Max before restrict: " + PamArrayUtils.max(click.getWaveData()[chan])); 
+
+		double[] wave = createRestrictedLenghtWave(click, chan, lengthPoints, restrictedBins,  getWindow(restrictedBins)); 
+		
+//		System.out.println("Max after restrict: " + PamArrayUtils.max(click.getWaveData()[chan])); 
+
+		return wave; 
 	}
 
 
@@ -412,7 +421,7 @@ public class MTProcess extends PamInstantProcess {
 
 		ArrayList<MatchedTemplateResult> results = new ArrayList<MatchedTemplateResult>();
 		
-		//System.out.println("Click waveform max: " + PamArrayUtils.max(clickWaveform) + " sample rate: " + sR); 
+		System.out.println("Click waveform max: " + PamArrayUtils.max(clickWaveform) + " sample rate: " + sR); 
 		
 		//normalisation and picking peak has already been performed
 

src/matchedTemplateClassifer/offline/MTClassifierOfflineTask.java

@@ -40,6 +40,10 @@ public class MTClassifierOfflineTask extends OfflineTask<PamDataUnit<?,?>> {
 	@Override
 	public boolean processDataUnit(PamDataUnit dataUnit) {
 
+		try {
+//			System.out.println("MT new data unit: " + dataUnit); 
+
+
 			count++;
 			mtClassifierControl.getMTProcess().newClickData(dataUnit); 
 
@@ -52,7 +56,15 @@ public class MTClassifierOfflineTask extends OfflineTask<PamDataUnit<?,?>> {
 			}
 			dataUnit.updateDataUnit(System.currentTimeMillis());	
 
+
 			return true;
+
+		}
+		catch (Exception e) {
+			e.printStackTrace();
+		}
+		return false;
+
 	}
 
 

src/pamViewFX/fxNodes/PamTabPane.java

@@ -96,10 +96,12 @@ public class PamTabPane extends TabPane {
 	}
 
 	/**
+	 * TODO - the button is removed and then added again it does not seem to appear....
 	 * Set whether a button shows to add tabs to the TabPane
 	 * @param addTabButton - true to show a button next to the last tab which allows new tabs to be added. 
 	 */
 	public void setAddTabButton(boolean addTabButton) {
+		if (this.addTabButton==addTabButton) return;
 		this.addTabButton = addTabButton;
 	}
 	

src/pamViewFX/fxNodes/flipPane/PamFlipPane.java

@@ -1,17 +1,26 @@
 package pamViewFX.fxNodes.flipPane;
 
-import javafx.geometry.Insets;
+import javafx.application.Platform;
+import javafx.beans.value.ChangeListener;
+import javafx.beans.value.ObservableValue;
 import javafx.geometry.Orientation;
 import javafx.geometry.Pos;
+import javafx.scene.Node;
 import javafx.scene.control.Label;
+import javafx.scene.control.Labeled;
+import javafx.scene.control.TextField;
 import javafx.scene.layout.HBox;
 import javafx.scene.layout.Priority;
+import javafx.scene.layout.Region;
 import javafx.scene.paint.Color;
+import javafx.scene.text.Text;
+import javafx.scene.text.TextAlignment;
 import pamViewFX.PamGuiManagerFX;
 import pamViewFX.fxGlyphs.PamGlyphDude;
 import pamViewFX.fxNodes.PamBorderPane;
 import pamViewFX.fxNodes.PamButton;
 import pamViewFX.fxNodes.PamHBox;
+import pamViewFX.fxNodes.utilsFX.TextUtilsFX;
 
 /**
  * Flip pane which has is supposed to be used for advanced settings. The front
@@ -32,15 +41,34 @@ public class PamFlipPane extends FlipPane {
 	
 	private PamBorderPane frontPane;
 	
-	private Label advLabel;
 
 	private PamButton backButton;
 
+	/**
+	 * Text field in the title of the advanced pane. This can be used to change settings. 
+	 */
+	private TextField advLabel;
+
+	/**
+	 * Label which sits before the text field in the advanced settings pane title
+	 */
+	private Label preLabel;
+
+	/**
+	 * Label after the the text field in the advanced pane label - this can be set to say "settings" for example with the text field
+	 * then editable to change the name of a parameter. 
+	 */
+	private Label postLabel;
+	
 
 	public PamFlipPane() {
 		super();
 		this.advPane = createAdvSettingsPane();
 		this.getFront().getChildren().add(frontPane = new PamBorderPane()); 
+		
+//		this.getFront().setStyle("-fx-background-color: grey;");
+//		this.getBack().setStyle("-fx-background-color: grey;");
+
 		this.getBack().getChildren().add(advPane); 
 		this.setFlipTime(FLIP_TIME);
 
@@ -79,6 +107,23 @@ public class PamFlipPane extends FlipPane {
 	}
 	
 	
+	/**
+	 * Set the advanced pane content. 
+	 * @param - the content to set. 
+	 */
+	public void setAdvPaneContent(Node content) {
+		 advPane.setCenter(content);
+	}
+	
+	/**
+	 * Set the front pane content. 
+	 * @param - the content to set. 
+	 */
+	public void setFrontContent(Node content) {
+		frontPane.setCenter(content);
+	}
+
+
 	/**
 	 * Create the advanced settings pane which can be accessed by DAQ panes if needed. 
 	 */
@@ -86,29 +131,70 @@ public class PamFlipPane extends FlipPane {
 		
 		backButton = new PamButton(); 
 		backButton.setGraphic(PamGlyphDude.createPamIcon("mdi2c-chevron-left", Color.WHITE, PamGuiManagerFX.iconSize));
+//		backButton.setStyle("-fx-background-color: -color-base-6"); 
+		//backButton.setStyle("-fx-padding: 0,0,0,0");
 		
 		backButton.setOnAction((action)->{
 		//	System.out.println("FLIP BACK TO FRONT"); 
 			this.flipToFront(); 
 		});
 		
+		//make the back button blue so users can easily see the button. 
+		backButton.setStyle("-fx-background-radius: 0 5 5 0; -fx-border-radius: 0 5 5 0; -fx-background-color: -color-accent-6");
+
 		//backButton.setPrefWidth(150);
-		
 		PamBorderPane advPane = new PamBorderPane(); 
-		advPane.setPadding(new Insets(5,5,5,5));
+		//advPane.setPadding(new Insets(5,5,5,5));
 		
+		
+		// holds the title of the advanced pane. This consists of a label for a graphic,
+		// an editable text field and a label after the editable settings field
+		PamHBox titleHolder = new PamHBox(); 
+		titleHolder.getChildren().addAll(preLabel = new Label(), advLabel = new TextField("Adv. "), postLabel = new Label("Settings"));
+		preLabel.setId("label-title2");
+		postLabel.setId("label-title2");
+		titleHolder.setAlignment(Pos.CENTER);
+		postLabel.setTextAlignment(TextAlignment.LEFT);
+		postLabel.setAlignment(Pos.CENTER_LEFT);
+
+		advLabel.setAlignment(Pos.CENTER);
+//		advLabel.prefColumnCountProperty().bind(advLabel.textProperty().length().subtract(3));
+		// Set Max and Min Width to PREF_SIZE so that the TextField is always PREF
+		advLabel.setMinWidth(Region.USE_PREF_SIZE);
+		advLabel.setMaxWidth(Region.USE_PREF_SIZE);
+		
+		//pretty complicated to make sure the text field is the same size as the text that is being typed. 
+		advLabel.textProperty().addListener((ov, prevText, currText) -> {
+		    // Do this in a Platform.runLater because of Textfield has no padding at first time and so on
+		    Platform.runLater(() -> {
+		        Text text = new Text(currText);
+		        text.setFont(advLabel.getFont()); // Set the same font, so the size is the same
+		        double width = text.getLayoutBounds().getWidth() // This big is the Text in the TextField
+		                + advLabel.getPadding().getLeft() + advLabel.getPadding().getRight() // Add the padding of the TextField
+		                + 2d; // Add some spacing
+		        advLabel.setPrefWidth(width); // Set the width
+		        advLabel.positionCaret(advLabel.getCaretPosition()); // If you remove this line, it flashes a little bit
+		    });
+		});
+		advLabel.setId("label-title2");
+		advLabel.setStyle("-fx-background-color: transparent");
+		
+		titleHolder.setMaxWidth(Double.MAX_VALUE); //need to make sure label is in center. 
+
+		//holds the back button and the title pane. 
 		PamHBox buttonHolder = new PamHBox(); 
-		
 		buttonHolder.setBackground(null);
 		//buttonHolder.setStyle("-fx-background-color: red;");
 		buttonHolder.setAlignment(Pos.CENTER_LEFT);
-		buttonHolder.getChildren().addAll(backButton, advLabel = new Label("Adv. Settings")); 
+		buttonHolder.getChildren().addAll(backButton, titleHolder); 
-		advLabel.setAlignment(Pos.CENTER);
-		advLabel.setMaxWidth(Double.MAX_VALUE); //need to make sure label is in center. 
-		PamGuiManagerFX.titleFont2style(advLabel);
 
 		advLabel.setAlignment(Pos.CENTER);
-		HBox.setHgrow(advLabel, Priority.ALWAYS);
+		advLabel.setMaxWidth(Double.MAX_VALUE); //need to make sure label is in center. 
+//		PamGuiManagerFX.titleFont2style(advLabel);
+
+
+		advLabel.setAlignment(Pos.CENTER);
+		HBox.setHgrow(titleHolder, Priority.ALWAYS);
 		
 		advPane.setTop(buttonHolder);
 		
@@ -117,16 +203,45 @@ public class PamFlipPane extends FlipPane {
 	}
 	
 
-	public Label getAdvLabel() {
+	public TextField getAdvLabel() {
 		return advLabel;
 	}
 
-	public void setAdvLabel(Label advLabel) {
+//	public void setAdvLabel(Label advLabel) {
-		this.advLabel = advLabel;
+//		this.advLabel = advLabel;
-	}
+//	}
 
 	public PamButton getBackButton() {
 		return backButton;
 	}
 	
+	/**
+	 * Get the label located before the editable label in the title
+	 * @return the label before the editable label
+	 */
+	public Label getPreAdvLabel() {
+		return preLabel;
+	}
+	
+	/**
+	 * Get the label located after the editable label in the title
+	 * @return the label after the editable label
+	 */
+	public Label getPostAdvLabel() {
+		return postLabel;
+	}
+
+	/**
+	 * True if the flip pane is showing the front. 
+	 */
+	public boolean isShowingFront() {
+		return super.flipFrontProperty().get();
+	}
+
+	public void setAdvLabelEditable(boolean b) {
+		this.advLabel.setEditable(b); 
+		
+	}
+
+
 }

src/pamViewFX/fxNodes/utilityPanes/FilterPaneFX.java

@@ -143,7 +143,7 @@ public class FilterPaneFX extends SettingsPane<FilterParams> {
 		}
 		else {
 			mainPane.setTop(createFilterPane());
-			mainPane.setBottom(createBodeGraph()); 
+			mainPane.setCenter(createBodeGraph()); 
 		}
 	}
 

src/pamViewFX/fxNodes/utilityPanes/LatLongPane.java

@@ -1,19 +1,24 @@
 package pamViewFX.fxNodes.utilityPanes;
 
+import org.controlsfx.control.SegmentedButton;
+
 import PamController.SettingsPane;
 import PamUtils.LatLong;
 import javafx.geometry.Insets;
+import javafx.geometry.Pos;
 import javafx.scene.Node;
 import javafx.scene.control.Label;
-import javafx.scene.control.RadioButton;
+import javafx.scene.control.Toggle;
-import javafx.scene.control.ToggleGroup;
+import javafx.scene.control.ToggleButton;
-import pamViewFX.fxNodes.PamBorderPane;
+import javafx.scene.text.TextAlignment;
+import pamViewFX.PamGuiManagerFX;
 import pamViewFX.fxNodes.PamHBox;
 import pamViewFX.fxNodes.PamVBox;
 
 /**
  * Pane with controls to to set the values for a Latitude and Longitude. The pane allows users to
  * change the Latitude and Longitude in both Degrees, Decimal minutes and Degrees, Minutes, Seconds
+ * 
  * @author Jamie Macaulay 
  *
  */
@@ -27,37 +32,62 @@ public class LatLongPane extends SettingsPane<LatLong>{
 	/**
 	 * The radio button to select decimal minutes 
 	 */
-	private RadioButton decimalMinutes;
+	private ToggleButton decimalMinutes;
 
 	/**
 	 * Radio button to input minutes and seconds. 
 	 */
-	private RadioButton minutesSeconds;
+	private ToggleButton minutesSeconds;
 
 	/**
 	 * Lat long strip
 	 */
 	private LatLongStrip latStrip, longStrip;
 
-	private PamBorderPane mainPane;
+	private PamVBox mainPane;
+
+	private ToggleButton decimal;
+
+	/**
+	 * Segmented button that also selection of the latitude and longitude format type. 
+	 */
+	private SegmentedButton segmentedButton;
 
 
 	public LatLongPane(String title) {
 		super(null); 
 		
+		
+		mainPane = new PamVBox(); 
+		mainPane.setSpacing(5);
+		mainPane.setAlignment(Pos.CENTER);
+
+		
+		Label titleLabel = new Label(title); 
+		titleLabel.maxWidth(Double.MAX_VALUE);
+		titleLabel.setTextAlignment(TextAlignment.LEFT);
+		PamGuiManagerFX.titleFont2style(titleLabel);
+		mainPane.getChildren().add(titleLabel); 
+
+
 		latLong= new LatLong(); 
 
-		mainPane = new PamBorderPane(); 
+
+		decimalMinutes = new ToggleButton("Degrees, Decimal minutes");
+		minutesSeconds = new ToggleButton("Degrees, Minutes, Seconds");
+		decimal = new ToggleButton("Decimal");
+
+		segmentedButton = new SegmentedButton();    
+		segmentedButton.getButtons().addAll(decimalMinutes, minutesSeconds, decimal);
 
 		PamHBox top = new PamHBox();
 		top.setSpacing(5);
-		top.getChildren().add(new Label("Unit type :"));
+		top.getChildren().add(segmentedButton);
-		top.getChildren().add(decimalMinutes = new RadioButton("Degrees, Decimal minutes"));
-		top.getChildren().add(minutesSeconds = new RadioButton("Degrees, Minutes, Seconds"));
 
-		ToggleGroup bg = new ToggleGroup();
+		//		ToggleGroup bg = new ToggleGroup();
-		decimalMinutes.setToggleGroup(bg);
+		//		decimalMinutes.setToggleGroup(bg);
-		minutesSeconds.setToggleGroup(bg);
+		//		minutesSeconds.setToggleGroup(bg);
+		//		decimal.setToggleGroup(bg);
 
 		decimalMinutes.setOnAction((action)->{
 			actionPerformed(action);
@@ -66,7 +96,12 @@ public class LatLongPane extends SettingsPane<LatLong>{
 		minutesSeconds.setOnAction((action)->{
 			actionPerformed(action);
 		});
-		mainPane.setTop(top);
+
+		decimal.setOnAction((action)->{
+			actionPerformed(action);
+		});
+
+		mainPane.getChildren().add(top); 
 
 		PamVBox cent = new PamVBox();
 		cent.setSpacing(5);
@@ -75,8 +110,12 @@ public class LatLongPane extends SettingsPane<LatLong>{
 		cent.getChildren().add(latStrip = new LatLongStrip(true));
 		cent.getChildren().add(longStrip = new LatLongStrip(false));
 		
-		mainPane.setCenter(cent);
+		//bit of a hack that makes sure controls are aligned for the latitude and longitude. 
+		latStrip.getTitleLabel().prefWidthProperty().bind(longStrip.getTitleLabel().widthProperty());
 
+		mainPane.getChildren().add(cent); 
+
+		decimal.setSelected(true);
 	}
 
 
@@ -85,6 +124,7 @@ public class LatLongPane extends SettingsPane<LatLong>{
 	 */
 	public void actionPerformed(javafx.event.ActionEvent action) {
 
+
 		if (action.getSource() == decimalMinutes) {
 			LatLong.setFormatStyle(LatLong.FORMAT_DECIMALMINUTES);
 		//			if (latStrip != null) {
@@ -105,19 +145,26 @@ public class LatLongPane extends SettingsPane<LatLong>{
 			latStrip.showControls(LatLong.FORMAT_MINUTESSECONDS);
 			longStrip.showControls(LatLong.FORMAT_MINUTESSECONDS);
 		}
-
+		else if (action.getSource() == decimal){
+			LatLong.setFormatStyle(LatLong.FORMAT_DECIMAL);
+			latStrip.showControls(LatLong.FORMAT_DECIMAL);
+			longStrip.showControls(LatLong.FORMAT_DECIMAL);
+		}
 
 	}
 
 
 
 	private void showLatLong() {
+		
 		decimalMinutes	.setSelected(LatLong.getFormatStyle() == LatLong.FORMAT_DECIMALMINUTES);
 		minutesSeconds	.setSelected(LatLong.getFormatStyle() == LatLong.FORMAT_MINUTESSECONDS);
+		decimal			.setSelected(LatLong.getFormatStyle() == LatLong.FORMAT_DECIMAL);
+
 		latStrip		.showControls(LatLong.getFormatStyle() );
 		longStrip		.showControls(LatLong.getFormatStyle() );
-		latStrip.sayValue(latLong.getLatitude());
+		latStrip		.setValue(latLong.getLatitude());
-		longStrip.sayValue(latLong.getLongitude());
+		longStrip		.setValue(latLong.getLongitude());
 	}
 
 
@@ -127,6 +174,21 @@ public class LatLongPane extends SettingsPane<LatLong>{
 	 */
 	@Override
 	public LatLong getParams(LatLong currentParams) {
+		
+		Toggle selectedButton = this.segmentedButton.getToggleGroup().getSelectedToggle();
+		
+		if (selectedButton == decimalMinutes) {
+			LatLong.setFormatStyle(LatLong.FORMAT_DECIMALMINUTES);
+
+		}
+		else if  (selectedButton == minutesSeconds){
+			LatLong.setFormatStyle(LatLong.FORMAT_MINUTESSECONDS);
+	
+		}
+		else if (selectedButton == decimal){
+			LatLong.setFormatStyle(LatLong.FORMAT_DECIMAL);
+		}
+		
 		latLong = new LatLong(latStrip.getValue(), longStrip.getValue());
 		if (Double.isNaN(latLong.getLatitude()) || Double.isNaN(latLong.getLongitude())) {
 			return null;

src/pamViewFX/fxNodes/utilityPanes/LatLongStrip.java

@@ -19,8 +19,8 @@ import pamViewFX.fxNodes.PamHBox;
 public class LatLongStrip extends PamBorderPane {
 
 	Label formattedText;
-	TextField degrees, minutes, seconds, decminutes;
+	TextField degrees, minutes, seconds, decminutes, decimal;
-	Label dl, ml, sl, dml;
+	Label dl, ml, sl, dml, dec;
 	ComboBox<String> nsew;
 	boolean isLatitude;
 	//	boolean decimalMinutes = true;
@@ -35,6 +35,12 @@ public class LatLongStrip extends PamBorderPane {
 	 */
 	private PamHBox decHBox;
 
+	/**
+	 * The format type e.g. LatLong.FORMAT_DECIMALMINUTES.
+	 */
+	private int formatType = LatLong.FORMAT_DECIMALMINUTES;
+	private Label titleLabel;
+
 
 	/**
 	 * Construct a strip of controls to include in a larger dialog. 
@@ -62,23 +68,29 @@ public class LatLongStrip extends PamBorderPane {
 
 	private void createDialogStrip(boolean showBorder) {
 
-		String borderTitle;
+		String title;
-		if (isLatitude) borderTitle = "Latitude";
+		if (isLatitude) title = "Latitude";
-		else borderTitle = "Longitude";
+		else title = "Longitude";
 
-		Label title= new Label(borderTitle);
-		PamGuiManagerFX.titleFont2style(title);
 		//		title.setFont(PamGuiManagerFX.titleFontSize2);
 
 		degrees = new TextField();
+		degrees.setEditable(true);
 		degrees.setPrefColumnCount(4);
 		minutes = new TextField();
 		minutes.setPrefColumnCount(3);
+		minutes.setEditable(true);
 
 		seconds = new TextField();
 		seconds.setPrefColumnCount(6);
+		seconds.setEditable(true);
 		decminutes = new TextField();
 		decminutes.setPrefColumnCount(6);
+		decminutes.setEditable(true);
+
+		decimal=new TextField(); 
+		decimal.setPrefColumnCount(9);
+		decimal.setEditable(true);
 
 		nsew = new ComboBox<String>();
 		nsew.setOnAction((action)->{
@@ -91,6 +103,8 @@ public class LatLongStrip extends PamBorderPane {
 		ml = new Label("min.");
 		sl = new Label("sec.");
 		dml = new Label("dec min.");
+		dec = new Label("decimal deg."); 
+
 		formattedText = new Label("Position");
 		if (isLatitude) {
 			nsew.getItems().add("N");
@@ -117,6 +131,10 @@ public class LatLongStrip extends PamBorderPane {
 			newTypedValues(key); 
 		});
 
+		decimal.setOnKeyPressed((key)->{
+			newTypedValues(key); 
+		});
+
 		nsew.setOnKeyPressed((key)->{
 			newTypedValues(key); 
 		});
@@ -126,50 +144,72 @@ public class LatLongStrip extends PamBorderPane {
 		degHBox.setSpacing(5);
 		degHBox.setAlignment(Pos.CENTER_LEFT);
 
-		this.setRight(nsew);
+		PamHBox holder= new PamHBox(); 
-		this.setCenter(degHBox);
+		holder.setAlignment(Pos.CENTER_LEFT);
+		holder.setSpacing(5);
+		holder.getChildren().addAll(titleLabel = new Label(title), degHBox, nsew); 
+
+		this.setCenter(holder);
 		this.setBottom(formattedText);
 
-		showControls( LatLong.FORMAT_DECIMALMINUTES);
+		showControls(formatType);
 	}
 
 	private void newTypedValues(KeyEvent e) {
 		double v = getValue();
-		// now need to put that into the fields that
-		// are not currently shown so that they are
-		// ready if needed. 
 		
-		if (e != null) {
+		
-			sayValue(v, true);
+//		// now need to put that into the fields that
-		}
+//		// are not currently shown so that they are
+//		// ready if needed. 
+//
+//		if (e != null) {
+//			setValue(v, true);
+//		}
 
 		// and say the formated version
 		sayFormattedValue(v);
 	}
 
 	public void showControls(int formatStyle) {
-		boolean decimal = (formatStyle == LatLong.FORMAT_DECIMALMINUTES);
+		
+		if (formatType==formatStyle) {
+			return;
+		}
+		
+		//important this comes before setting format style. 
+		double currentValue = getValue(); 
+
+		this.formatType = formatStyle; 
+
 		degHBox.getChildren().clear(); 
-		if (decimal) {
+				
+		System.out.println("FORMATSTYLE: " + formatStyle + " val " + currentValue); 
+		
+		switch (formatType) {
+		case LatLong.FORMAT_DECIMALMINUTES:
 			degHBox.getChildren().add(dl); 
 			degHBox.getChildren().add(degrees); 
 			degHBox.getChildren().add(dml); 
 			degHBox.getChildren().add(decminutes); 
-		}
+			break;
-		else {
+		case LatLong.FORMAT_MINUTESSECONDS:
 			degHBox.getChildren().add(dl); 
 			degHBox.getChildren().add(degrees); 
 			degHBox.getChildren().add(ml); 
 			degHBox.getChildren().add(minutes); 
 			degHBox.getChildren().add(sl); 
 			degHBox.getChildren().add(seconds); 
+			break;
+		case LatLong.FORMAT_DECIMAL:
+			degHBox.getChildren().add(dec); 
+			degHBox.getChildren().add(decimal); 
+			break;
+
 		}
-		minutes.setVisible(decimal == false);
+		
-		ml.setVisible(decimal == false);
+		setValue(currentValue);
-		seconds.setVisible(decimal == false);
+		
-		sl.setVisible(decimal == false);
-		decminutes.setVisible(decimal);
-		dml.setVisible(decimal);
 		sayFormattedValue(getValue());
 	}
 
@@ -177,11 +217,13 @@ public class LatLongStrip extends PamBorderPane {
 	 * Set data in the lat long dialog strip
 	 * @param value Lat or Long in decimal degrees.
 	 */
-	public void sayValue(double value) {
+	public void setValue(double value) {
-		sayValue(value, false);
+		setValue(value, false);
 	}
 
-	public void sayValue(double value, boolean hiddenOnly) {
+	public void setValue(double value, boolean hiddenOnly) {
+		
+		System.out.println("Set value: " + value);
 		if (value >= 0) {
 			nsew.getSelectionModel().select(0);
 		}
@@ -192,31 +234,72 @@ public class LatLongStrip extends PamBorderPane {
 		double deg = LatLong.getSignedDegrees(value);
 		//		System.out.println("Deg: " + LatLong.getSignedDegrees(value) + " value: " +value);
 
-		if (degrees.isVisible() == false || !hiddenOnly) degrees.setText(String.format("%d", (int)Math.abs(deg)));
+
-		if (minutes.isVisible() == false || !hiddenOnly) minutes.setText(String.format("%d", LatLong.getIntegerMinutes(value)));
+		//		if (degrees.isVisible() == false || !hiddenOnly) degrees.setText(String.format("%d", (int)Math.abs(deg)));
-		if (decminutes.isVisible() == false || !hiddenOnly) decminutes.setText(String.format("%3.5f", LatLong.getDecimalMinutes(value)));
+		//		if (minutes.isVisible() == false || !hiddenOnly) minutes.setText(String.format("%d", LatLong.getIntegerMinutes(value)));
-		if (seconds.isVisible() == false || !hiddenOnly) seconds.setText(String.format("%3.5f", LatLong.getSeconds(value)));
+		//		if (decminutes.isVisible() == false || !hiddenOnly) decminutes.setText(String.format("%3.5f", LatLong.getDecimalMinutes(value)));
-		if (nsew.isVisible() == false || !hiddenOnly) nsew.getSelectionModel().select(deg >= 0 ? 0 : 1);
+		//		if (seconds.isVisible() == false || !hiddenOnly) seconds.setText(String.format("%3.5f", LatLong.getSeconds(value)));
+		//		if (nsew.isVisible() == false || !hiddenOnly) nsew.getSelectionModel().select(deg >= 0 ? 0 : 1);
+		//		if (decimal.isVisible() == false || !hiddenOnly) decimal.setText(String.format("%.8f", value));
+
+		switch (formatType) {
+		case LatLong.FORMAT_DECIMALMINUTES:
+
+			degrees.setText(String.format("%d", (int)Math.abs(deg)));
+			decminutes.setText(String.format("%3.5f", LatLong.getDecimalMinutes(value)));
+
+			break;
+		case LatLong.FORMAT_MINUTESSECONDS:
+
+			degrees.setText(String.format("%d", (int)Math.abs(deg)));
+			minutes.setText(String.format("%d", LatLong.getIntegerMinutes(value)));
+			seconds.setText(String.format("%3.5f", LatLong.getSeconds(value)));
+
+			break;
+		case LatLong.FORMAT_DECIMAL:
+			
+			decimal.setText(String.format("%.8f", value));
+			
+			break;
+
+		}
+
 		sayFormattedValue(value);
 	}
 
 	/**
-	 * Get the value for the latitude and longitude 
+	 * Get the value for the latitude or longitude in decimal
-	 * @return the value. 
+	 * @return the value - the value in decimal
 	 */
 	public double getValue() {
+		
 		double deg = 0;
 		double min = 0;
 		double sec = 0;
 		double sin = 1.;
+		
 		if (nsew.getSelectionModel().getSelectedIndex() == 1) sin = -1.;
+
+
+		if (formatType == LatLong.FORMAT_DECIMAL){
+			try {
+				deg = Double.valueOf(decimal.getText());
+				return deg; 
+			}
+			catch (NumberFormatException ex) {
+				return Double.NaN;
+			}
+		}
+
 		try {
 			deg = Integer.valueOf(degrees.getText());
 		}
 		catch (NumberFormatException Ex) {
 			return Double.NaN;
 		}
-		if (LatLong.getFormatStyle() == LatLong.FORMAT_DECIMALMINUTES){
+
+
+		if (formatType == LatLong.FORMAT_DECIMALMINUTES){
 			try {
 				min = Double.valueOf(decminutes.getText());
 			}
@@ -237,6 +320,7 @@ public class LatLongStrip extends PamBorderPane {
 			catch (NumberFormatException ex) {
 				return Double.NaN;
 			}
+
 		}
 		deg += min/60 + sec/3600;
 		deg *= sin;
@@ -251,6 +335,7 @@ public class LatLongStrip extends PamBorderPane {
 		minutes.setText("");
 		seconds.setText("");
 		decminutes.setText("");
+		decimal.setText("");
 	}
 
 
@@ -281,5 +366,16 @@ public class LatLongStrip extends PamBorderPane {
 		seconds.setDisable(!enabled);
 		decminutes.setDisable(!enabled);
 		nsew.setDisable(!enabled);
+		decimal.setDisable(!enabled);
 	}
+
+	/**
+	 * Get the title label. 
+	 * @return the title label. 
+	 */
+	public Label getTitleLabel() {
+		return titleLabel;
+	}
+
+
 }

src/pamViewFX/fxNodes/utilsFX/TextUtilsFX.java

@@ -0,0 +1,40 @@
+package pamViewFX.fxNodes.utilsFX;
+
+import javafx.scene.text.Font;
+import javafx.scene.text.Text;
+import javafx.scene.text.TextBoundsType;
+
+public class TextUtilsFX {
+
+    static final Text helper;
+    static final double DEFAULT_WRAPPING_WIDTH;
+    static final double DEFAULT_LINE_SPACING;
+    static final String DEFAULT_TEXT;
+    static final TextBoundsType DEFAULT_BOUNDS_TYPE;
+    static {
+        helper = new Text();
+        DEFAULT_WRAPPING_WIDTH = helper.getWrappingWidth();
+        DEFAULT_LINE_SPACING = helper.getLineSpacing();
+        DEFAULT_TEXT = helper.getText();
+        DEFAULT_BOUNDS_TYPE = helper.getBoundsType();
+    }
+
+    public static double computeTextWidth(Font font, String text, double help0) {
+        // Toolkit.getToolkit().getFontLoader().computeStringWidth(field.getText(),
+        // field.getFont());
+
+        helper.setText(text);
+        helper.setFont(font);
+
+        helper.setWrappingWidth(0.0D);
+        helper.setLineSpacing(0.0D);
+        double d = Math.min(helper.prefWidth(-1.0D), help0);
+        helper.setWrappingWidth((int) Math.ceil(d));
+        d = Math.ceil(helper.getLayoutBounds().getWidth());
+
+        helper.setWrappingWidth(DEFAULT_WRAPPING_WIDTH);
+        helper.setLineSpacing(DEFAULT_LINE_SPACING);
+        helper.setText(DEFAULT_TEXT);
+        return d;
+    }
+}