Merge branch 'main' into main

pom.xml

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

src/PamController/PamguardVersionInfo.java

@@ -31,12 +31,12 @@ public class PamguardVersionInfo {
 	 * Version number, major version.minorversion.sub-release.
 	 * Note: can't go higher than sub-release 'f'
 	 */
-	static public final String version = "2.02.04aa";
+	static public final String version = "2.02.04ac";
 	
 	/**
 	 * Release date
 	 */
-	static public final String date = "13 September 2022";
+	static public final String date = "22 September 2022";
 	
 //	/**
 //	 * Release type - Beta or Core

src/clickTrainDetector/classification/CTClassifierManager.java

@@ -238,10 +238,10 @@ public class CTClassifierManager {
 				continue; 
 			}
 			
-			if (ctParams[i].uniqueID ==null) {
-				//old versions may not have a unique ID so needs to be added. 
-				ctParams[i].uniqueID = UUID.randomUUID().toString();
-			}
+//			if (ctParams[i].uniqueID ==null) {
+//				//old versions may not have a unique ID so needs to be added. 
+//				ctParams[i].uniqueID = UUID.randomUUID().toString();
+//			}
 			aClassifier.setParams(ctParams[i]); 
 			cTClassifiers.add(aClassifier); 
 		}

src/clickTrainDetector/classification/simplechi2classifier/Chi2ThresholdClassifier.java

@@ -123,7 +123,8 @@ public class Chi2ThresholdClassifier implements CTClassifier {
 			//create the data selector
 			//System.out.println("Data selector: " + dataSelector); 
 			if (source!=null) {
-				dataSelector=source.getDataSelectCreator().getDataSelector(clickTrainControl.getUnitName() +  " " + clssfrParams.uniqueID
+				
+				dataSelector=source.getDataSelectCreator().getDataSelector(clickTrainControl.getUnitName() +  "_" + clssfrParams.classifierName
 						+ "_X2_threshold_classifier", false, null);
 			}
 			else {

src/clickTrainDetector/dataselector/CTDataSelector.java

@@ -10,6 +10,7 @@ import clickTrainDetector.CTDataUnit;
 import clickTrainDetector.CTDetectionGroupDataUnit;
 import clickTrainDetector.ClickTrainControl;
 import clickTrainDetector.ClickTrainDataBlock;
+import clickTrainDetector.classification.CTClassification;
 import clickTrainDetector.layout.dataselector.CTDataSelectPane;
 import clickTrainDetector.layout.dataselector.CTDataSelectPanel;
 import pamViewFX.fxSettingsPanes.DynamicSettingsPane;
@@ -112,8 +113,8 @@ public class CTDataSelector extends DataSelector {
 		
 		if (ctSelectParams.needsLoc && !pamDataUnit.getLocalisation().hasLocContent(LocContents.HAS_RANGE)) return 0; 
 
-		
 		return 1;
+		
 	}
 
 	/**
@@ -123,19 +124,38 @@ public class CTDataSelector extends DataSelector {
 	 */
 	private boolean isClassified(CTDetectionGroupDataUnit ctDataUnit) {
 
-		if (!ctSelectParams.needsClassification) return true; 
-
+		if (ctSelectParams.allowAnyClassification) return true; 
+		
 		if (ctDataUnit instanceof CTDataUnit) {
 
 			CTDataUnit clickTrain = (CTDataUnit) ctDataUnit; 
 
 			if (clickTrain.ctClassifications==null) return false; 
 
-			//iterate through all the classifiers and allowed classification types. 
-			for (int i=0; i<ctSelectParams.classifier.length; i++) {
-				for (int j=0; j<clickTrain.ctClassifications.size(); j++) {
-					if (clickTrain.ctClassifications.get(j).getSpeciesID()==ctSelectParams.classifier[i]) {
-						return true; 
+			int nClass = clickTrain.ctClassifications.size();
+			if (ctSelectParams.allowMultipleChoices == false) {
+				int clsInd = clickTrain.getClassificationIndex();
+				if (clsInd < 0) {
+					return false;
+				}
+				if (clsInd >= clickTrain.ctClassifications.size()) {
+					return false;
+				}
+				CTClassification singleClass = clickTrain.ctClassifications.get(clsInd);
+				for (int i = 0; i < ctSelectParams.classifier.length; i++) {
+					if (ctSelectParams.classifier[i] == singleClass.getSpeciesID()) {
+						return true;
+					}
+				}
+				return false;
+			}
+			else {
+				//iterate through all the classifiers and allowed classification types. 
+				for (int i=0; i<ctSelectParams.classifier.length; i++) {
+					for (int j=0; j<nClass; j++) {
+						if (clickTrain.ctClassifications.get(j).getSpeciesID()==ctSelectParams.classifier[i]) {
+							return true; 
+						}
 					}
 				}
 			}

src/clickTrainDetector/dataselector/CTSelectParams.java

@@ -35,9 +35,22 @@ public class CTSelectParams extends DataSelectParams implements Serializable, Cl
 	public int minSubDetections = 10; 
 	
 	/**
-	 * True of the click train detector needs a classifcation
+	 * True of the click train detector needs a classifcation No !!!!
+	 * This 'needsClassification' variable was been used the wrong way around throughout and is screwing the classiifer. 
+	 * I've therefore replaced it with the variable allowAll which is how this is actually used !
+	 * Given that anything using this would have has screwed logic, I don't care if I break 
+	 * a config or two ! DG 22/9/22
 	 */
-	public boolean needsClassification = false; 
+	public boolean allowAnyClassification = false; 
+//	private boolean needsClassification = false; 
+	
+	/**
+	 * In the data selector, if this is false it will only look at the best classifier, i.e. the
+	 * one with the best classifier score. If set true it will check every species above min
+	 * score even if it's not the first classification choice. 
+	 */
+	public boolean allowMultipleChoices = false;
+	
 	
 	/**
 	 * The classifier type(s) to select

src/clickTrainDetector/layout/dataselector/CTDataSelectPanel.java

@@ -77,6 +77,8 @@ public class CTDataSelectPanel implements PamDialogPanel {
 	private JPanel classification;
 
 	private JCheckBox[] classifierCheckBoxes;
+	
+	private JCheckBox allowMultipleChoices; // 
 
 	private JCheckBox unclassifiedCheckBox;
 
@@ -232,6 +234,12 @@ public class CTDataSelectPanel implements PamDialogPanel {
 			classifierCheckBoxes[i].setSelected(true); //default should be selected
 			constraints.gridy++; 
 		}	
+		
+		constraints.gridy++;
+		classification.add(allowMultipleChoices = new JCheckBox("Allow multiple classification options"), constraints);
+		allowMultipleChoices.setToolTipText("If not selected, then only the first choice classification is compared to the " +
+		"selected list. If selected, then all classifiers passing minimum score may be used");
+		
 		classification.validate(); //make sure everything is laid out properly.
 		
 		setClassifierParams(); 
@@ -245,6 +253,7 @@ public class CTDataSelectPanel implements PamDialogPanel {
 				classifierCheckBoxes[i].setEnabled(!unclassifiedCheckBox.isSelected());
 			}
 		}
+		allowMultipleChoices.setEnabled(!unclassifiedCheckBox.isSelected());
 	}
 	
 	
@@ -253,7 +262,7 @@ public class CTDataSelectPanel implements PamDialogPanel {
 	 */
 	private void setClassifierParams() {
 		
-		unclassifiedCheckBox.setSelected(currentParams.needsClassification ); 
+		unclassifiedCheckBox.setSelected(currentParams.allowAnyClassification ); 
 
 		if (currentParams.classifier==null ) {
 			for (int i=0; i<classifierCheckBoxes.length; i++) {
@@ -270,6 +279,7 @@ public class CTDataSelectPanel implements PamDialogPanel {
 				}
 			}
 		}
+		allowMultipleChoices.setSelected(currentParams.allowMultipleChoices);
 
 	}
 		
@@ -278,7 +288,9 @@ public class CTDataSelectPanel implements PamDialogPanel {
 	 * Get the parameters for the classifiers to  use. 	
 	 */
 	private void getClassifierParams() {
-			currentParams.needsClassification  = unclassifiedCheckBox.isSelected(); 
+			currentParams.allowAnyClassification  = unclassifiedCheckBox.isSelected(); 
+			
+			currentParams.allowMultipleChoices = allowMultipleChoices.isSelected();
 			
 			int count = 0; 
 			for (int i=0; i<classifierCheckBoxes.length; i++) {

src/generalDatabase/pamCursor/PamCursor.java

@@ -489,7 +489,7 @@ abstract public class PamCursor {
 			preparedUpdateStatement.setObject(iCol + 1, tableDef.getIndexItem().getValue());
 			int result = preparedUpdateStatement.executeUpdate();
 			if (result<1) {
-				System.out.println("update db result = " + String.valueOf(result));
+//				System.out.println("update db result = " + String.valueOf(result));
 				String msg = String.format("There was a problem updating row %d in table %s", 
 						tableDef.getIndexItem().getValue(), tableDef.getTableName());
 				PamWarning dispWarning = new PamWarning("Database Error", msg, 2);