Merge pull request #20 from PAMGuard/main

Get CTD bug fix

.classpath

@@ -16,5 +16,6 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="lib" path="/X3/src/org"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

src/Acquisition/pamAudio/PamAudioSystem.java

@@ -45,6 +45,14 @@ public class PamAudioSystem {
 				
 			}
 		}
+		else if (file != null && isSudFile(file)) {
+			try {
+				return new SudAudioFileReader().getAudioInputStream(file);
+			}
+			catch (UnsupportedAudioFileException e) {
+				
+			}
+		}
 		try {
 		return AudioSystem.getAudioInputStream(file);
 		}
@@ -77,4 +85,20 @@ public class PamAudioSystem {
 		return (end.equals(".flac"));
 	}
 	
+	/**
+	 * Check whether a file is a .sud file. This is the file format used
+	 * by SoundTraps which contains X3 compressed data. 
+	 * @param file - the file to check. 
+	 * @return  true if a .sud file. 
+	 */
+	private static boolean isSudFile(File file) {
+		String name = file.getName();
+		if (name.length() < 5) {
+			return false;
+		}
+		String end = name.substring(name.length()-5).toLowerCase();
+		return (end.equals(".sud"));
+	}
+
+
 }

src/Acquisition/pamAudio/SudAudioFileReader.java

@@ -0,0 +1,23 @@
+package Acquisition.pamAudio;
+
+import java.io.File;
+import java.io.IOException;
+
+import javax.sound.sampled.AudioInputStream;
+import javax.sound.sampled.UnsupportedAudioFileException;
+
+/**
+ * Audio file reader for a .sud file. .sud files are a file format used by SoundTraps which contain
+ * blocks of X3 compressed data. 
+ * @author Jamie Macaulay
+ *
+ */
+public class SudAudioFileReader {
+
+	
+	public AudioInputStream getAudioInputStream(File file) throws UnsupportedAudioFileException, IOException {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+}

src/Acquisition/pamAudio/WavFileInputStream.java

@@ -79,6 +79,8 @@ public class WavFileInputStream extends AudioInputStream {
 		
 		return new WavFileInputStream(wavHeader, inputStream, audioFormat, nFrames);
 	}
+	
+	
 	static AudioFormat.Encoding getEncoding(int formatCode) {
 		switch (formatCode) {
 		case 1:

src/PamUtils/PamAudioFileFilter.java

@@ -15,6 +15,7 @@ public class PamAudioFileFilter extends PamFileFilter {
 //		addFileType(".AIFF");
 //		addFileType(".FLAC");
 		addFileType(".flac");
+		addFileType(".sud");
 	}
 
 }

src/clickTrainDetector/classification/CTClassifierParams.java

@@ -22,7 +22,8 @@ public class CTClassifierParams implements Cloneable, Serializable, ManagedParam
 	
 	
 	public CTClassifierParams() {
-//		this.uniqueID = UUID.randomUUID().toString(); // see comment below 
+		//this.uniqueID = UUID.randomUUID().toString();
+		//System.out.println("Create classifier params: " + uniqueID); 
 	}
 	
 	
@@ -32,13 +33,10 @@ public class CTClassifierParams implements Cloneable, Serializable, ManagedParam
 	public String classifierName = ""; 
 	
 	
-//	/**
-//	 * A unique ID for the classifier that never changes. This is important for accessing data selectors. 
-//	 * GET RID OF THIS, Every time you make a new set of params you get a new ID and it then creates a new 
-//	 * classifier selector with default settings, so the classifier selectors never work. 
-//	Classifier selectors need to be names on something that's not oging to change, so the module name and the classifier species ame. 
-//	 */
-//	public String uniqueID; 
+	/**
+	 * A unique ID for the classifier that never changes. This is important for accessing data selectors. 
+	 */
+	public String uniqueID =  UUID.randomUUID().toString();
 	
 	
 	/**

src/clickTrainDetector/classification/bearingClassifier/BearingClassifierParams.java

@@ -17,6 +17,7 @@ public class BearingClassifierParams extends CTClassifierParams implements Manag
 	public BearingClassifierParams(){
 		super();
 		type = CTClassifierType.BEARINGCLASSIFIER; 
+		//System.out.println("Bearing classifier params");
 	}
 
 	/**

src/clickTrainDetector/classification/idiClassifier/IDIClassifierParams.java

@@ -11,6 +11,8 @@ public class IDIClassifierParams extends CTClassifierParams implements Serializa
 	public IDIClassifierParams(){
 		super();
 		type = CTClassifierType.IDICLASSIFIER; 
+		//System.out.println("IDI classifier params: " + this);
+
 	}
 	
 	/**

src/clickTrainDetector/classification/simplechi2classifier/Chi2ThresholdClassifier.java

@@ -44,7 +44,7 @@ public class Chi2ThresholdClassifier implements CTClassifier {
 	public Chi2ThresholdClassifier(ClickTrainControl clickTrainControl, int defaultSpeciesID) {
 		this.clickTrainControl=clickTrainControl; 
 		clssfrParams.speciesFlag=defaultSpeciesID; 
-		createDataSelector(clickTrainControl.getParentDataBlock());
+		//createDataSelector(clickTrainControl.getParentDataBlock());
 	}
 
 	
@@ -110,12 +110,15 @@ public class Chi2ThresholdClassifier implements CTClassifier {
 	}
 
 
+
 	/**
 	 * Get the data selector. 
 	 * @param source - the source data block 
 	 * @return the data selector.
 	 */
 	public void createDataSelector(PamDataBlock<?> source) {
+		//System.out.println("Create data selector " +" " + clssfrParams.classifierName + "  " + clssfrParams.speciesFlag + " " + clssfrParams.uniqueID ); 
+
 		if (dataSelector==null || dataSelector.getPamDataBlock()!=source) {
 			//create the data selector
 			//System.out.println("Data selector: " + dataSelector); 
@@ -123,7 +126,6 @@ public class Chi2ThresholdClassifier implements CTClassifier {
 				
 				dataSelector=source.getDataSelectCreator().getDataSelector(clickTrainControl.getUnitName() +  "_" + clssfrParams.classifierName
 						+ "_X2_threshold_classifier", false, null);
-				//System.out.println("Data selector: " + dataSelector); 
 			}
 			else {
 				dataSelector=null; 
@@ -198,7 +200,6 @@ public class Chi2ThresholdClassifier implements CTClassifier {
 
 	@Override
 	public void setParams(CTClassifierParams ctClassifierParams) {
-		// TODO Auto-generated method stub
 		this.clssfrParams=(Chi2ThresholdParams) ctClassifierParams;
 	}
 

src/clickTrainDetector/classification/simplechi2classifier/Chi2ThresholdParams.java

@@ -20,6 +20,7 @@ public class Chi2ThresholdParams extends CTClassifierParams implements ManagedPa
 	public Chi2ThresholdParams(){
 		super();
 		super.type=CTClassifierType.CHI2THRESHOLD;
+		//System.out.println("Chi2thrwesh classifier params: " + this);
 	}
 	
 	/**

src/clickTrainDetector/classification/standardClassifier/StandardClassifier.java

@@ -74,7 +74,7 @@ public class StandardClassifier implements CTClassifier {
 	private void createClassifiers() {
 		classifiers = new ArrayList<CTClassifier>(); 
 
-		
+		//System.out.println("------CREATE CLASSIFIERS: -------"); 
 		//do this so that is CLASSIFIER_TYPES changes order things still work. 
 		for (int i=0; i<CLASSIFIER_TYPES.length; i++) {
 
@@ -104,6 +104,7 @@ public class StandardClassifier implements CTClassifier {
 	 */
 	private void setClassifierParams() {
 		
+		
 		if (standardClssfrParams.ctClassifierParams ==null || standardClssfrParams.ctClassifierParams.length != classifiers.size()) {
 			standardClssfrParams.ctClassifierParams = new CTClassifierParams[classifiers.size()];  
 			standardClssfrParams.enable = new boolean[classifiers.size()]; 
@@ -119,6 +120,11 @@ public class StandardClassifier implements CTClassifier {
 				standardClssfrParams.ctClassifierParams[i] = classifiers.get(i).getParams(); 
 			}
 			else {
+				
+				//set the current species ID and name for convenience
+				standardClssfrParams.ctClassifierParams[i].classifierName=standardClssfrParams.classifierName;
+				standardClssfrParams.ctClassifierParams[i].speciesFlag=standardClssfrParams.speciesFlag;
+
 				//the standard classifier should have settings set. 
 				classifiers.get(i).setParams(standardClssfrParams.ctClassifierParams[i]); 
 			}

src/clickTrainDetector/classification/standardClassifier/StandardClassifierParams.java

@@ -33,6 +33,7 @@ public class StandardClassifierParams extends CTClassifierParams {
 		///very important to set this or else the clasifier manager does not
 		//know which classifier to create. 
 		type = CTClassifierType.STANDARDCLASSIFIER; 
+		//System.out.println("Standard classifier params: " + this);
 	}
 
 	

src/clickTrainDetector/classification/templateClassifier/TemplateClassifierParams.java

@@ -26,6 +26,7 @@ public class TemplateClassifierParams extends CTClassifierParams implements Mana
 		super.type=CTClassifierType.TEMPLATECLASSIFIER;
 //		chi2ThresholdParams = new Chi2ThresholdParams();  
 //		template = DefualtSpectrumTemplates.getTemplate(SpectrumTemplateType.BEAKED_WHALE);
+		//System.out.println("Template classifier params: " + this);
 	}
 	
 	

src/clickTrainDetector/layout/classification/simplechi2classifier/SimpleCTClassifierPane.java

@@ -76,6 +76,8 @@ public class SimpleCTClassifierPane extends SettingsPane<Chi2ThresholdParams>  {
 	 */
 	private ControlField<Double> minPercClicks;
 
+	private Chi2ThresholdParams currParams;
+
 	public SimpleCTClassifierPane(Chi2ThresholdClassifier simpleChi2Classifier) {
 		super(null);
 		this.simpleChi2Classifier=simpleChi2Classifier; 
@@ -214,6 +216,9 @@ public class SimpleCTClassifierPane extends SettingsPane<Chi2ThresholdParams>  {
 	public Chi2ThresholdParams getParams(Chi2ThresholdParams currParams) {
 		//System.out.println("Get PERC spinner value; " + minPercClicks.getSpinner().getValue());
 		
+		//System.out.println("Chi2 pane get params: " + this.currParams.speciesFlag + "  " + this.currParams.uniqueID + "  " + this.currParams); 
+		
+
 		currParams.chi2Threshold=chi2Threshold.getSpinner().getValue(); 
 		//HACK - for some reason Integer spinner is returning a double
 		currParams.minClicks=minClicks.getSpinner().getValue().intValue(); 
@@ -224,17 +229,25 @@ public class SimpleCTClassifierPane extends SettingsPane<Chi2ThresholdParams>  {
 			simpleChi2Classifier.getDataSelector().getDialogPaneFX().getParams(true); 
 		}
 		
-		return currParams;
+		currParams.uniqueID = this.currParams.uniqueID; 
+		
+		return currParams=this.currParams;
 	}
 
 	@Override
 	public void setParams(Chi2ThresholdParams input) {
 		
+		this.currParams = input; 
+		
+		//System.out.println("Chi2 pane set params: " + this.currParams.speciesFlag + "  " +  currParams.uniqueID + "  " + currParams); 
+		
 		chi2Threshold.getSpinner().getValueFactory().setValue(input.chi2Threshold);
 		//HACK - for some reason Integer spinner is returning a double
 		minClicks.getSpinner().getValueFactory().setValue((double) input.minClicks);
 		minTime.getSpinner().getValueFactory().setValue(input.minTime);
 		minPercClicks.getSpinner().getValueFactory().setValue(input.minPercentage*100.);
+		
+		
 	}
 
 	@Override

src/clickTrainDetector/layout/classification/standardClassifier/StandardClassifierGraphics.java

@@ -64,7 +64,6 @@ public class StandardClassifierGraphics implements CTClassifierGraphics {
 	@Override
 	public void setParams(CTClassifierParams params) {
 		standardClassifierPane.setParams((StandardClassifierParams) params);
-		
 	}
 
 }

src/clickTrainDetector/layout/classification/standardClassifier/StandardClassifierPane.java

@@ -84,7 +84,15 @@ public class StandardClassifierPane extends  SettingsPane<StandardClassifierPara
 	@Override
 	public void setParams(StandardClassifierParams input) {
 		for (int i=0; i<standardClassifier.getClassifiers().size(); i++) {
+			
+			standardClassifier.getClassifiers().get(i).setParams(input.ctClassifierParams[i]);
+			/**
+			 * It is important to set this here because otherwise the params can be out of sync with the classifer class. Usually this
+			 * is not an issue because they are set later, however, if there is a paramter that does not have a correpsonding UI control, then
+			 * this may change back to default - thus we have to explicitlly set here. (Note this caused issues with the uniqueID data selector string)
+			 */
 			standardClassifier.getClassifiers().get(i).getCTClassifierGraphics().setParams(input.ctClassifierParams[i]);
+
 			enableSwitch[i].setSelected(input.enable[i]);
 			disableClassifierPane(i); 
 		}

src/clickTrainDetector/layout/mht/AmplitudeChi2AdvPane.java

@@ -65,8 +65,6 @@ public class AmplitudeChi2AdvPane extends AdvMHTVarPane {
 	@Override
 	public AmplitudeChi2Params getParams(SimpleChi2VarParams currParams) {	
 				
-		System.out.println("Get params: AMPLITUDE");
-		
 		AmplitudeChi2Params newParams = new AmplitudeChi2Params(super.getParams(currParams));
 
 		newParams.maxAmpJump = ampJumpSpinner.getValue();

src/rawDeepLearningClassifier/dlClassification/DLLocalisation.java

@@ -27,8 +27,8 @@ public class DLLocalisation extends AbstractLocalisation {
 		this.angles = bearingAnnotation.getBearingLocalisation().getAngles(); 
 		this.setSubArrayType(bearingAnnotation.getBearingLocalisation().getSubArrayType()); 
 		
-		System.out.println("Loc content!: " + this.getLocContents().hasLocContent(LocContents.HAS_AMBIGUITY) + " angles: " + angles.length); 
-		PamUtils.PamArrayUtils.printArray(angles);
+		//System.out.println("Loc content!: " + this.getLocContents().hasLocContent(LocContents.HAS_AMBIGUITY) + " angles: " + angles.length); 
+		//PamUtils.PamArrayUtils.printArray(angles);
 	}
 	
 	@Override

src/rawDeepLearningClassifier/dlClassification/DLTaskThread.java

@@ -58,7 +58,7 @@ public abstract class DLTaskThread extends Thread {
 					for (int i =0; i<modelResult.size(); i++) {
 //						modelResult.get(i).setClassNameID(getClassNameIDs()); 
 //						modelResult.get(i).setBinaryClassification(isBinaryResult(modelResult.get(i))); 
-						newResult(modelResult.get(i), groupedRawData.get(i));
+						newDLResult(modelResult.get(i), groupedRawData.get(i));
 					}
 
 				}
@@ -79,7 +79,7 @@ public abstract class DLTaskThread extends Thread {
 	 * @param soundSpotResult - the new result.
 	 * @param groupedRawData - the grouped data unit. 
 	 */
-	public abstract void newResult(GenericPrediction soundSpotResult, GroupedRawData groupedRawData); 
+	public abstract void newDLResult(GenericPrediction soundSpotResult, GroupedRawData groupedRawData); 
 
 	/**
 	 * Get the grouped data queue

src/rawDeepLearningClassifier/dlClassification/animalSpot/SoundSpotClassifier.java

@@ -161,7 +161,7 @@ public class SoundSpotClassifier implements DLClassiferModel, PamSettings {
 		}
 
 		@Override
-		public void newResult(GenericPrediction soundSpotResult, GroupedRawData groupedRawData) {
+		public void newDLResult(GenericPrediction soundSpotResult, GroupedRawData groupedRawData) {
 			soundSpotResult.setClassNameID(getClassNameIDs()); 
 			soundSpotResult.setBinaryClassification(isBinaryResult(soundSpotResult)); 
 			newResult(soundSpotResult, groupedRawData);
@@ -241,11 +241,12 @@ public class SoundSpotClassifier implements DLClassiferModel, PamSettings {
 	 * @param modelResult - the model result;
 	 * @param groupedRawData - the grouped raw data. 
 	 */
-	private void newResult(GenericPrediction modelResult, GroupedRawData groupedRawData) {
+	protected void newResult(GenericPrediction modelResult, GroupedRawData groupedRawData) {
 		this.dlControl.getDLClassifyProcess().newModelResult(modelResult, groupedRawData);
 	}
 	
 
+
 	@Override
 	public void prepModel() {
 		//System.out.println("PrepModel! !!!");

src/rawDeepLearningClassifier/dlClassification/genericModel/GenericDLClassifier.java

@@ -323,7 +323,7 @@ public class GenericDLClassifier implements DLClassiferModel, PamSettings {
 		}
 
 		@Override
-		public void newResult(GenericPrediction modelResult, GroupedRawData groupedRawData) {
+		public void newDLResult(GenericPrediction modelResult, GroupedRawData groupedRawData) {
 			modelResult.setClassNameID(getClassNameIDs(genericModelParams)); 
 			modelResult.setBinaryClassification(isBinaryResult(modelResult, genericModelParams)); 
 			newResult(modelResult, groupedRawData);
@@ -331,6 +331,15 @@ public class GenericDLClassifier implements DLClassiferModel, PamSettings {
 
 	}
 	
+	/**
+	 * Send a new result form the thread queue to the process. 
+	 * @param modelResult - the model result;
+	 * @param groupedRawData - the grouped raw data. 
+	 */
+	protected void newResult(GenericPrediction modelResult, GroupedRawData groupedRawData) {
+		this.dlControl.getDLClassifyProcess().newModelResult(modelResult, groupedRawData);
+	}
+	
 	/**
 	 * Get the class name IDs
 	 * @return an array of class name IDs

src/rawDeepLearningClassifier/dlClassification/ketos/KetosClassifier.java

@@ -169,7 +169,7 @@ public class KetosClassifier implements DLClassiferModel, PamSettings {
 		}
 
 		@Override
-		public void newResult(GenericPrediction soundSpotResult, GroupedRawData groupedRawData) {
+		public void newDLResult(GenericPrediction soundSpotResult, GroupedRawData groupedRawData) {
 			soundSpotResult.setClassNameID(GenericDLClassifier.getClassNameIDs(ketosDLParams)); 
 			soundSpotResult.setBinaryClassification(GenericDLClassifier.isBinaryResult(soundSpotResult, ketosDLParams)); 
 			newResult(soundSpotResult, groupedRawData);
@@ -177,6 +177,15 @@ public class KetosClassifier implements DLClassiferModel, PamSettings {
 
 	}
 	
+	/**
+	 * Send a new result form the thread queue to the process. 
+	 * @param modelResult - the model result;
+	 * @param groupedRawData - the grouped raw data. 
+	 */
+	protected void newResult(GenericPrediction modelResult, GroupedRawData groupedRawData) {
+		this.dlControl.getDLClassifyProcess().newModelResult(modelResult, groupedRawData);
+	}
+
 
 	@Override
 	public void closeModel() {