Merge pull request #11 from PAMGuard/main

Fixes to CTD

pom.xml

@@ -4,7 +4,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
-  <version>2.02.04a</version>
+  <version>2.02.04f</version>
   <name>Pamguard Java12+</name>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
 	<url>www.pamguard.org</url>

src/PamView/symbol/PamSymbolManager.java

@@ -222,6 +222,9 @@ abstract public class PamSymbolManager<T extends PamSymbolChooser> implements Pa
 	 * @param psc
 	 */
 	private void addSuperDetectionModifiers(PamSymbolChooser psc) {
+		/**
+		 * This is going in an infinite loop. Need to do something to stop it !
+		 */
 		ArrayList<SuperDetDataBlock> superDetBlocks = OfflineSuperDetFilter.findPossibleSuperDetections(getPamDataBlock());
 		
 //		Debug.out.println("The number of super det datablock is: " + superDetBlocks + " for the chooser: " +  psc); 
@@ -233,6 +236,12 @@ abstract public class PamSymbolManager<T extends PamSymbolChooser> implements Pa
 			if (superMan == null) {
 				continue;
 			}
+			if (superBlock == getPamDataBlock()) {
+				continue;
+			}
+			if (superBlock.getClass() == getPamDataBlock().getClass()) {
+				continue;
+			}
 //			Debug.out.println("The number of super det datablock superMan: " + superMan +  " for the chooser: " +  psc); 
 
 			PamSymbolChooser superSC = superMan.getSymbolChooser("Super det': " + psc.getDisplayName(), psc.getProjector());

src/clickTrainDetector/CTDetectionGroupDataUnit.java

@@ -46,6 +46,7 @@ public abstract class CTDetectionGroupDataUnit extends DetectionGroupDataUnit im
 	public int addSubDetections(List<PamDataUnit> list) {
 		int h = super.addSubDetections(list);
 		this.calcMinMaxAng();
+		
 		//make sure there is a non null start sample otherwise
 		//the click trian detector will crash in real time mode. 
 //		this.calcStartSample(); 

src/clickTrainDetector/ClickTrainProcess.java

@@ -86,13 +86,20 @@ public class ClickTrainProcess extends PamInstantProcess {
 
 		//TODO - this is a bit messy. Ideally probably should have the datablock's long name in the settings but 
 		//this would break previous configurations...
-		sourceDataBlock = PamController.getInstance().getDataBlock(ClickDetection.class, 
-				getClickTrainParams().dataSourceName);
+//		sourceDataBlock = PamController.getInstance().getDataBlock(ClickDetection.class, 
+//				getClickTrainParams().dataSourceName);
+		/*
+		 * Identify by long name since that is unique, otherwise doesn't work with multiple click detectors. 
+		 */
+		sourceDataBlock = PamController.getInstance().getDataBlockByLongName(getClickTrainParams().dataSourceName);
+		if (sourceDataBlock == null) {
+			// otherwise find any click detector. 
+			sourceDataBlock = PamController.getInstance().getDataBlock(ClickDetection.class, 0);
+		}
 
 		if (sourceDataBlock==null) {
 			sourceDataBlock = PamController.getInstance().getDataBlock(CPODClick.class, 
 					getClickTrainParams().dataSourceName);
-
 		}
 		
 		//System.out.println("CPOD sample rate: " + sourceDataBlock.getSampleRate()); 

src/clickTrainDetector/classification/bearingClassifier/BearingClassifier.java

@@ -154,7 +154,6 @@ public class BearingClassifier implements CTClassifier {
 		
 		Debug.out.println("SPECIESID!! " + speciesID);
 
-
 		return new BearingClassification(speciesID, meanBearingD, medianBearingD, stdBearingD);
 	}
 

src/clickTrainDetector/classification/standardClassifier/StandardClassifier.java

@@ -116,7 +116,7 @@ public class StandardClassifier implements CTClassifier {
 		for (int i=0; i<classifiers.size(); i++) {
 			if (standardClssfrParams.ctClassifierParams[i]==null) {
 				//set default settings
-				standardClssfrParams.ctClassifierParams[i]= classifiers.get(i).getParams(); 
+				standardClssfrParams.ctClassifierParams[i] = classifiers.get(i).getParams(); 
 			}
 			else {
 				//the standard classifier should have settings set. 
@@ -178,6 +178,7 @@ public class StandardClassifier implements CTClassifier {
 	}
 
 	public StandardClassifierParams getParams() {
+		
 		return standardClssfrParams;
 	}
 

src/clickTrainDetector/clickTrainAlgorithms/mht/MHTKernel.java

@@ -848,6 +848,7 @@ public class MHTKernel<T> {
 	 */
 	public T getLastDataUnit() {
 		if (this.dataUnits==null) return null;
+		if (this.dataUnits.size()<1) return null; 
 		return dataUnits.get(dataUnits.size()-1);
 	}
 

src/clickTrainDetector/layout/CTFXGUI.java

@@ -61,7 +61,7 @@ public class CTFXGUI  extends PamControlledGUIFX {
 			//data source may have potentially changed. e.g. by a datamodelfx Need to set in params.
 			//System.out.println("FFTControl: CHANGED_PROCESS_SETTINGS : " +fftProcess.getParentDataBlock());
 					if (clickTrainControl.getClickTrainProcess().getParentDataBlock()!=null){
-						clickTrainControl.getClickTrainParams().dataSourceName=clickTrainControl.getClickTrainProcess().getParentDataBlock().getDataName();
+						clickTrainControl.getClickTrainParams().dataSourceName=clickTrainControl.getClickTrainProcess().getParentDataBlock().getLongDataName();
 					}
 					else clickTrainControl.getClickTrainParams().dataSourceName="";
 			break;

src/clickTrainDetector/layout/CTSwingGUI.java

@@ -94,7 +94,7 @@ public class CTSwingGUI extends PamControlledGUISwing {
 
 	@Override
 	public JMenuItem createDetectionMenu(Frame parentFrame) {
-		JMenu submenu = new JMenu("Click Train Detector");
+		JMenu submenu = new JMenu(clickTrainControl.getUnitName());
 
 		JMenuItem menuItem = new JMenuItem("Detection Settings ..."); 
 

src/clickTrainDetector/layout/ClickTrainAlgorithmPaneFX.java

@@ -408,7 +408,7 @@ public class ClickTrainAlgorithmPaneFX extends SettingsPane<ClickTrainParams> {
 	public ClickTrainParams getParams(ClickTrainParams currParams) {
 		try {
 			currParams.dataSourceIndex = sourcePane.getSourceIndex();
-			currParams.dataSourceName = sourcePane.getSourceName();
+			currParams.dataSourceName = sourcePane.getSourceLongName();
 			
 			
 			//use the data selector. 
@@ -511,7 +511,7 @@ public class ClickTrainAlgorithmPaneFX extends SettingsPane<ClickTrainParams> {
 
 		// and fill in the data source list (may have changed - or might in later versions)
 		ArrayList<PamDataBlock> rd = PamController.getInstance().getDataBlocks(ClickDetection.class, true); 
-		PamDataBlock  datablock = PamController.getInstance().getRawDataBlock(clickTrainParams.dataSourceName);
+		PamDataBlock  datablock = PamController.getInstance().getDataBlockByLongName(clickTrainParams.dataSourceName);
 		
 		//use the data selector. 
 		dataSelectorCheckBox.setSelected(clickTrainParams.useDataSelector); 

src/clickTrainDetector/layout/classification/CTClassifierPane.java

@@ -170,12 +170,17 @@ public class CTClassifierPane extends PamBorderPane {
 //				break; 
 //			}
 //		}
+		
 		classifierListBox.getSelectionModel().select(params.type);
+		
+
 		setClassifierPane(params.type);
 		
 		//species Id
 		setBasicParams(params);
 		
+
+		
 		//		//when setting parameters have to figure out what pane to create first!
 		//		currentClassifier = clickTrainControl.getClassifierManager().createClassifier(params.type); 
 		//		//Classifier pane
@@ -197,7 +202,9 @@ public class CTClassifierPane extends PamBorderPane {
 	 */
 	private void setClassifierPane(CTClassifierType ctClassifierType) {
 		if (ctClassifierType==null) return;
+		
 		currentClassifier = clickTrainControl.getClassifierManager().createClassifier(ctClassifierType); 
+
 		//Classifier pane- this also sets parameters for the classifier specific pane
 		if (currentClassifier.getCTClassifierGraphics()!=null) {
 			settingsHolder.setCenter(currentClassifier.getCTClassifierGraphics().getCTClassifierPane());		

src/clickTrainDetector/layout/classification/CTClassifiersPane.java

@@ -228,6 +228,7 @@ public class CTClassifiersPane extends PamBorderPane {
 
 				//set the parameters. 
 				tab = (ClassifierTab) pamTabPane.getTabs().get(i); 
+				
 				//set the parameters for the tab.
 				tab.getCTClassifierPane().setParams(clickTrainParams.ctClassifierParams[i]);
 			}

src/clickTrainDetector/layout/classification/bearingClassifier/BearingClassifierGraphics.java

@@ -41,7 +41,7 @@ public class BearingClassifierGraphics implements CTClassifierGraphics {
 			bearingClassifierPane = new BearingClassifierPane(bearingClassifer);
 		}
 		//params are set here. 
-		bearingClassifierPane.setParams(bearingClassifer.getParams());
+		//bearingClassifierPane.setParams(bearingClassifer.getParams()); <- warning - causes an error in which params are overriden
 		return (Pane) bearingClassifierPane.getContentNode();
 	}
 

src/clickTrainDetector/layout/classification/bearingClassifier/BearingClassifierPane.java

@@ -105,7 +105,7 @@ public class BearingClassifierPane extends  SettingsPane<BearingClassifierParams
 		currParams.minStdBearingD =  Math.toRadians(params.min.doubleValue());
 		currParams.maxStdBearingD =  Math.toRadians(params.max.doubleValue());
 		currParams.useStD = params.enabled;
-
+		
 		return currParams;
 	}
 
@@ -126,6 +126,7 @@ public class BearingClassifierPane extends  SettingsPane<BearingClassifierParams
 
 	@Override
 	public void setParams(BearingClassifierParams input) {
+		
 		//bearing limits
 		this.bearingLims.setParams(Math.toDegrees(input.bearingLimMin), Math.toDegrees(input.bearingLimMax), true);
 		

src/clickTrainDetector/layout/dataselector/CTDataSelectPanel.java

@@ -366,7 +366,7 @@ public class CTDataSelectPanel implements PamDialogPanel {
 			return true; 
 		}
 		catch (Exception e) {
-			e.printStackTrace();
+//			e.printStackTrace();
 			return false;
 		}
 	}

src/detectionPlotFX/plots/SpectrumPlot.java

@@ -134,9 +134,12 @@ public abstract class  SpectrumPlot <D extends PamDataUnit> implements Detection
 		this.sR=sR;  
 
 		int[] minmax = getAxisMinMaxSamples(plotProjector);
-		
-		if (minmax[1]>=data.getSampleDuration()) minmax[1]=(int) (data.getSampleDuration()-1);
+	
+		if (data.getSampleDuration()!=null) {	
+			if (minmax[1]>=data.getSampleDuration()) minmax[1]=(int) (data.getSampleDuration()-1);
+		}
 		if (minmax[0]<0 || minmax[0]>=minmax[1]) minmax[0]=0;
+	
 		
 		//System.out.println("Min max: " + minmax[0] + "  " + minmax[1]);
 

src/pamViewFX/fxNodes/utilsFX/PamUtilsFX.java

@@ -14,7 +14,9 @@ import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 import javax.swing.JPopupMenu;
+import javax.swing.JPopupMenu.Separator;
 import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JSeparator;
 import javax.swing.SwingUtilities;
 
 import PamView.PamSymbol;
@@ -197,6 +199,12 @@ public class PamUtilsFX {
 			if (JMenuItem.class.isAssignableFrom(item.getClass())) {
 				itemList.add(swingMenuItemToFX( (JMenuItem) item));
 			}
+			else {
+				Component unkItem = item;
+				if (item instanceof Separator) {
+//					MenuItem mi = new Separator();
+				}
+			}
 		}
 		
 		return itemList;
@@ -300,6 +308,9 @@ public class PamUtilsFX {
 			radioItem.setSelected(((JRadioButtonMenuItem) swingItem).isSelected());
 			
 		}
+//		else if (swingItem.getClass() == JSeparator.class) {
+//			
+//		}
 		if (fxItem == null) {
 			return null;
 		}