From 941737a7ab66b605a948203900a0d05f9444fbee Mon Sep 17 00:00:00 2001
From: Jamie Mac <macster110@gmail.com>
Date: Fri, 18 Feb 2022 16:22:34 +0000
Subject: [PATCH] Updates and bug fixes to click train detector and CPOD
 importer

---
 .../classification/CTClassifierManager.java   | 13 +++--
 .../classification/CTClassifierParams.java    |  2 +-
 .../idiClassifier/IDIClassification.java      |  2 +-
 .../idiClassifier/IDIClassifier.java          |  8 ++-
 .../Chi2CTClassification.java                 |  2 +-
 .../StandardClassification.java               | 15 ++----
 .../StandardClassificationJSON.java           | 54 +++++++++++++++++++
 .../StandardClassifier.java                   | 42 ++++++++++++---
 .../StandardClassifierParams.java             |  9 ++++
 .../mht/mhtMAT/MHTClassifierMAT.java          |  3 +-
 .../StandardClassifierPane.java               | 19 ++++---
 src/cpod/fx/CPODSettingsPane.java             |  5 ++
 .../menuOptions/MLExport/MLClickExport.java   |  4 --
 .../overlaymark/popUpMenu/TDMenuPane.java     |  6 +--
 14 files changed, 142 insertions(+), 42 deletions(-)

diff --git a/src/clickTrainDetector/classification/CTClassifierManager.java b/src/clickTrainDetector/classification/CTClassifierManager.java
index 45261fdd..1c0af211 100644
--- a/src/clickTrainDetector/classification/CTClassifierManager.java
+++ b/src/clickTrainDetector/classification/CTClassifierManager.java
@@ -158,7 +158,7 @@ public class CTClassifierManager {
 		//first check the pre-classifier
 		Chi2CTClassification classification = this.preClassifier.classifyClickTrain(ctDataUnit); 
 		
-		Debug.out.println("Pre classifier: " + PamCalendar.formatDateTime(ctDataUnit.getTimeMilliseconds()) + " N. " + ctDataUnit.getSubDetectionsCount() + "UID first: " + ctDataUnit.getSubDetection(0).getUID() ); 
+		System.out.println("Pre classifier: " + PamCalendar.formatDateTime(ctDataUnit.getTimeMilliseconds()) + " N. " + ctDataUnit.getSubDetectionsCount() + "UID first: " + ctDataUnit.getSubDetection(0).getUID() ); 
 
 		if (classification.getSpeciesID()==CTClassifier.NOSPECIES) {
 			System.out.println("No SPECIES: chi^2" + ctDataUnit.getCTChi2()); 
@@ -189,12 +189,18 @@ public class CTClassifierManager {
 		ctDataUnit.clearClassifiers();
 		ctDataUnit.setClassificationIndex(-1);
 		
+		System.out.println("Classify species: Num classifier " +  this.cTClassifiers.size()); 
 
-		for (int i=0; i<clickTrainControl.getCurrentClassifiers().size(); i++) {
+		for (int i=0; i<this.cTClassifiers.size(); i++) {
 			
 		
+			System.out.println("Classifier: " + i); 
+
 			//the first classifier 
-			ctclassification = clickTrainControl.getCurrentClassifiers().get(i).classifyClickTrain(ctDataUnit);
+			ctclassification = this.cTClassifiers.get(i).classifyClickTrain(ctDataUnit);
+			
+			System.out.println("Classifier complete: SPECIES: " + ctclassification.getSpeciesID()); 
+
 			
 //			Debug.out.println(i + " ClassifierManager: Classify a click train data unit: " + ctDataUnit  + " parent data block: " +
 //					" " + ctDataUnit.getnSubDetections()); 
@@ -202,6 +208,7 @@ public class CTClassifierManager {
 			
 			//set the species flag but only if this is the first time the ct data unit has been classified. 
 			if (ctclassification.getSpeciesID()>CTClassifier.NOSPECIES && !hasBeenClssfd) {
+				System.out.println("Set classiifcation index: " + i); 
 				ctDataUnit.setClassificationIndex(i); //set the classification index. 
 				hasBeenClssfd = true; 
 			}
diff --git a/src/clickTrainDetector/classification/CTClassifierParams.java b/src/clickTrainDetector/classification/CTClassifierParams.java
index bb746b10..81af2483 100644
--- a/src/clickTrainDetector/classification/CTClassifierParams.java
+++ b/src/clickTrainDetector/classification/CTClassifierParams.java
@@ -32,7 +32,7 @@ public class CTClassifierParams implements Cloneable, Serializable, ManagedParam
 	public int speciesFlag = 1; 
 	
 	/**
-	 * Easy way to know which classifier the parameter class belong to rather than big instancof statement
+	 * Easy way to know which classifier the parameter class belong to rather than big instance of statement
 	 */
 	public CTClassifierType type; 
 	
diff --git a/src/clickTrainDetector/classification/idiClassifier/IDIClassification.java b/src/clickTrainDetector/classification/idiClassifier/IDIClassification.java
index 2c394c7a..11ded86f 100644
--- a/src/clickTrainDetector/classification/idiClassifier/IDIClassification.java
+++ b/src/clickTrainDetector/classification/idiClassifier/IDIClassification.java
@@ -81,7 +81,7 @@ public class IDIClassification implements CTClassification {
 
 	@Override
 	public String getSummaryString() {
-		return  String.format("IDI Classifier: Mean IDI %.4f\u00B0/s Median IDI %.4f\u00B0/s Std IDI%.4f\u00B0/s",
+		return  String.format("IDI Classifier: Mean IDI %.5fs Median IDI %.5fs Std IDI%.5fs",
 				meanIDI, medianIDI, stdIDI);
 	}
 
diff --git a/src/clickTrainDetector/classification/idiClassifier/IDIClassifier.java b/src/clickTrainDetector/classification/idiClassifier/IDIClassifier.java
index 57b720ed..ce870aeb 100644
--- a/src/clickTrainDetector/classification/idiClassifier/IDIClassifier.java
+++ b/src/clickTrainDetector/classification/idiClassifier/IDIClassifier.java
@@ -37,7 +37,13 @@ public class IDIClassifier implements CTClassifier {
 		//check IDI classification is passed
 		boolean passesIDI = checkIDIMeasurements(clickTrain); 
 		
-		return null;
+		int speciesID = CTClassifier.NOSPECIES; 
+		if (passesIDI) {
+			speciesID =  idiParams.speciesFlag; 
+		}
+		
+		return new IDIClassification( speciesID,  clickTrain.getIDIInfo().medianIDI,   clickTrain.getIDIInfo().meanIDI,   clickTrain.getIDIInfo().stdIDI);
+		
 	}
 
 	@Override
diff --git a/src/clickTrainDetector/classification/simplechi2classifier/Chi2CTClassification.java b/src/clickTrainDetector/classification/simplechi2classifier/Chi2CTClassification.java
index c478ad3e..22ef818e 100644
--- a/src/clickTrainDetector/classification/simplechi2classifier/Chi2CTClassification.java
+++ b/src/clickTrainDetector/classification/simplechi2classifier/Chi2CTClassification.java
@@ -50,7 +50,7 @@ public class Chi2CTClassification implements CTClassification {
 
 	@Override
 	public String getSummaryString() {
-		return "Simple X\u00b2 Clssfr: Species ID: " + this.getSpeciesID();
+		return "X\u00b2 Clssfr: Species ID: " + this.getSpeciesID();
 	}
 	
 	@Override
diff --git a/src/clickTrainDetector/classification/standardClassifier/StandardClassification.java b/src/clickTrainDetector/classification/standardClassifier/StandardClassification.java
index 804d169a..554f2b0c 100644
--- a/src/clickTrainDetector/classification/standardClassifier/StandardClassification.java
+++ b/src/clickTrainDetector/classification/standardClassifier/StandardClassification.java
@@ -1,10 +1,8 @@
 package clickTrainDetector.classification.standardClassifier;
 
-import clickTrainDetector.ClickTrainControl;
 import clickTrainDetector.classification.CTClassification;
 import clickTrainDetector.classification.CTClassifierType;
 import clickTrainDetector.classification.ClassifierJSONLogging;
-import clickTrainDetector.classification.bearingClassifier.BearingClassifierJSON;
 
 /**
  * A classification object for a standard classification 
@@ -14,12 +12,6 @@ import clickTrainDetector.classification.bearingClassifier.BearingClassifierJSON
  */
 public class StandardClassification implements CTClassification {
 	
-	/**
-	 * Reference to the click control. 
-	 */
-	private ClickTrainControl clickTrainControl;
-	
-
 	/**
 	 * The current species ID.
 	 */
@@ -31,17 +23,16 @@ public class StandardClassification implements CTClassification {
 	private CTClassification[] ctClassifications;
 	
 	
-
 	/**
 	 * Standard classifier JSON logging. 
 	 */
 	private StandardClassificationJSON standardClassifierJSONLogging; 
 	
 	
-	public StandardClassification(ClickTrainControl clickTrainControl, CTClassification[] ctClassifications, int speciesID) {
-		this.clickTrainControl=clickTrainControl; 
+	public StandardClassification(CTClassification[] ctClassifications, int speciesID) {
 		this.ctClassifications=ctClassifications; 
-		standardClassifierJSONLogging = new StandardClassificationJSON(); 
+		standardClassifierJSONLogging = new StandardClassificationJSON(ctClassifications); 
+		this.speciesID=speciesID; 
 
 	}
 
diff --git a/src/clickTrainDetector/classification/standardClassifier/StandardClassificationJSON.java b/src/clickTrainDetector/classification/standardClassifier/StandardClassificationJSON.java
index 58643085..3016ba2d 100644
--- a/src/clickTrainDetector/classification/standardClassifier/StandardClassificationJSON.java
+++ b/src/clickTrainDetector/classification/standardClassifier/StandardClassificationJSON.java
@@ -1,9 +1,63 @@
 package clickTrainDetector.classification.standardClassifier;
 
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.databind.JsonNode;
+
+import clickTrainDetector.classification.CTClassification;
 import clickTrainDetector.classification.SimpleClassifierJSONLogging;
 
+
+/**
+ * Standard classification JSON logging
+ * 
+ * @author Jamie Macaulay 
+ *
+ */
 public class StandardClassificationJSON extends SimpleClassifierJSONLogging {	
 	
+	private CTClassification[] standardClassifier;
+
+	/**
+	 * Create the JSON logging for standard classifier. 
+	 * @param ctClassifications - the standard classifier.
+	 */
+	public StandardClassificationJSON(CTClassification[] ctClassifications) {
+		this.standardClassifier=ctClassifications; 
+	}
+	
+
+	@Override
+	public void writeJSONData(JsonGenerator jg, CTClassification ctClassification) {
+		for (int i=0; i<standardClassifier.length; i++) {
+			((SimpleClassifierJSONLogging) standardClassifier[i].getJSONLogging()).writeJSONData(jg, standardClassifier[i]);
+		}
+	}
+	
+	
+	@Override
+	public CTClassification createClassification(JsonNode jTree) {
+		
+		JsonNode na = jTree.findValue("SPECIES");
+		int speciesID;
+		if (na != null ) {
+			speciesID = na.asInt(); 
+		}
+		else {
+			System.err.println("Cannot load template classifier");
+			return null; 
+		}
+
+		CTClassification[] ctClassification = new CTClassification[standardClassifier.length]; 
+		for (int i=0; i<standardClassifier.length; i++) {
+			ctClassification[i] = ((SimpleClassifierJSONLogging) standardClassifier[i].getJSONLogging()).createClassification(jTree);
+		}
+		
+		StandardClassification stClassification = 
+				new StandardClassification(ctClassification, speciesID); 
+		
+		return stClassification; 
+	}
+
 	
 
 
diff --git a/src/clickTrainDetector/classification/standardClassifier/StandardClassifier.java b/src/clickTrainDetector/classification/standardClassifier/StandardClassifier.java
index 3aa92dea..bc510c4d 100644
--- a/src/clickTrainDetector/classification/standardClassifier/StandardClassifier.java
+++ b/src/clickTrainDetector/classification/standardClassifier/StandardClassifier.java
@@ -25,6 +25,12 @@ import clickTrainDetector.layout.classification.standardClassifier.StandardClass
  */
 public class StandardClassifier implements CTClassifier {
 	
+	/**
+	 * It's quite complicated to keep track of the species ID for all sub classifier but just set them 
+	 * to 1 to check whether the classifier has passed or not, 
+	 */
+	public int SUB_CLASSIFIER_SPECIESID = 1; 
+	
 	/**
 	 * The bearing classifier parameters. 
 	 */
@@ -52,7 +58,6 @@ public class StandardClassifier implements CTClassifier {
 		
 		//load the settings
 		createClassifiers(); 
-
 	}
 	
 	/**
@@ -61,13 +66,13 @@ public class StandardClassifier implements CTClassifier {
 	private void createClassifiers() {
 		classifiers = new ArrayList<CTClassifier>(); 
 		
-		classifiers.add(new Chi2ThresholdClassifier(clickTrainControl, standardClssfrParams.speciesFlag));
+		classifiers.add(new Chi2ThresholdClassifier(clickTrainControl, SUB_CLASSIFIER_SPECIESID));
 		
-		classifiers.add(new IDIClassifier(clickTrainControl, standardClssfrParams.speciesFlag));
+		classifiers.add(new IDIClassifier(clickTrainControl,SUB_CLASSIFIER_SPECIESID));
 			
-		classifiers.add(new CTTemplateClassifier(clickTrainControl, standardClssfrParams.speciesFlag));
+		classifiers.add(new CTTemplateClassifier(clickTrainControl, SUB_CLASSIFIER_SPECIESID));
 		
-		classifiers.add(new BearingClassifier(clickTrainControl, standardClssfrParams.speciesFlag));
+		classifiers.add(new BearingClassifier(clickTrainControl, SUB_CLASSIFIER_SPECIESID));
 		
 		setClassifierParams();
 	}
@@ -101,11 +106,32 @@ public class StandardClassifier implements CTClassifier {
 	@Override
 	public CTClassification classifyClickTrain(CTDataUnit clickTrain) {
 		
+		int speciesID = standardClssfrParams.speciesFlag; 
 		
-		//all classifiers have to pass.  
-		
+		System.out.println("Standard Classificiation: " ); 
 	
-		return null;
+		//all classifiers have to pass.  
+		CTClassification[] ctClassification = new CTClassification[classifiers.size()]; 
+		for (int i=0; i<classifiers.size(); i++) {
+			
+			ctClassification[i] = classifiers.get(i).classifyClickTrain(clickTrain); 
+			
+			System.out.println("Standard Classificiation: " + i + "  speciesID: " + ctClassification[i].getSpeciesID() 
+					+ "  sub species: "+ classifiers.get(i).getParams().speciesFlag + " standard species: " +speciesID + " use? : " + standardClssfrParams.enable[i]); 
+
+			if (standardClssfrParams.enable[i]) {
+				if (ctClassification[i].getSpeciesID() != SUB_CLASSIFIER_SPECIESID){
+					speciesID = CTClassifier.NOSPECIES;
+				}
+			}
+		}
+	
+		System.out.println("SPECIES ID: " + speciesID); 
+
+		//create the classification. 
+		StandardClassification classification = new StandardClassification(ctClassification, speciesID); 
+	
+		return classification;
 	}
 
 	@Override
diff --git a/src/clickTrainDetector/classification/standardClassifier/StandardClassifierParams.java b/src/clickTrainDetector/classification/standardClassifier/StandardClassifierParams.java
index 9f878080..a3d13e0e 100644
--- a/src/clickTrainDetector/classification/standardClassifier/StandardClassifierParams.java
+++ b/src/clickTrainDetector/classification/standardClassifier/StandardClassifierParams.java
@@ -1,6 +1,7 @@
 package clickTrainDetector.classification.standardClassifier;
 
 import clickTrainDetector.classification.CTClassifierParams;
+import clickTrainDetector.classification.CTClassifierType;
 
 
 /**
@@ -24,6 +25,14 @@ public class StandardClassifierParams extends CTClassifierParams {
 	 */
 	public boolean[] enable; 
 	
+	
+	public StandardClassifierParams(){
+		///very important to set this or else the clasifier manager does not
+		//know which classifier to create. 
+		type = CTClassifierType.STANDARDCLASSIFIER; 
+	}
+
+	
 //	
 //	/**
 //	 * Standard classifier parameters.
diff --git a/src/clickTrainDetector/clickTrainAlgorithms/mht/mhtMAT/MHTClassifierMAT.java b/src/clickTrainDetector/clickTrainAlgorithms/mht/mhtMAT/MHTClassifierMAT.java
index efde044f..277175b7 100644
--- a/src/clickTrainDetector/clickTrainAlgorithms/mht/mhtMAT/MHTClassifierMAT.java
+++ b/src/clickTrainDetector/clickTrainAlgorithms/mht/mhtMAT/MHTClassifierMAT.java
@@ -66,10 +66,9 @@ public class MHTClassifierMAT {
 			classification  = cTClassifiers.get(i).classifyClickTrain(dataUnit); 
 			dataUnit.addCtClassification(classification);
 			
-//			System.out.println("Classification " + classification.getSpeciesID() + " speciesID " + cTClassifiers.get(i).getSpeciesID()); 
+			System.out.println("Classification " + classification.getSpeciesID() + " speciesID " + cTClassifiers.get(i).getSpeciesID()); 
 
 			if (classification.getSpeciesID()>CTClassifier.NOSPECIES && !hasBeenClssfd) {
-//				System.out.println("Set classiifcation index: " + i); 
 				dataUnit.setClassificationIndex(i); //set the classification index. 
 				hasBeenClssfd = true; 
 			}
diff --git a/src/clickTrainDetector/layout/classification/standardClassifier/StandardClassifierPane.java b/src/clickTrainDetector/layout/classification/standardClassifier/StandardClassifierPane.java
index 0d621cf5..7393fbeb 100644
--- a/src/clickTrainDetector/layout/classification/standardClassifier/StandardClassifierPane.java
+++ b/src/clickTrainDetector/layout/classification/standardClassifier/StandardClassifierPane.java
@@ -26,6 +26,8 @@ public class StandardClassifierPane extends  SettingsPane<StandardClassifierPara
 
 	private PamToggleSwitch[] enableSwitch;
 
+	private Label[] labels;
+
 	public StandardClassifierPane(StandardClassifier standardClassifier) {
 		super(null);
 		this.standardClassifier = standardClassifier; 
@@ -37,32 +39,36 @@ public class StandardClassifierPane extends  SettingsPane<StandardClassifierPara
 		PamVBox vBox = new PamVBox(); 
 		vBox.setSpacing(5);
 
+		labels = new Label[standardClassifier.getClassifiers().size()]; 
 		enableSwitch = new PamToggleSwitch[standardClassifier.getClassifiers().size()]; 
 		for (int i=0; i<standardClassifier.getClassifiers().size(); i++) {
 
 			enableSwitch[i] = new PamToggleSwitch(""); 
 			
-			Label label = new Label(standardClassifier.getClassifiers().get(i).getName()); 
-			PamGuiManagerFX.titleFont2style(label);
+			labels[i] = new Label(standardClassifier.getClassifiers().get(i).getName()); 
+			PamGuiManagerFX.titleFont2style(labels[i]);
 
 			final int ii = i; 
 			enableSwitch[i].selectedProperty().addListener((obsVal, oldVal, newVal)->{
 				standardClassifier.getClassifiers().get(ii).getCTClassifierGraphics().getCTClassifierPane().setDisable(!enableSwitch[ii].isSelected());
-				label.setDisable(!enableSwitch[ii].isSelected()); 
+				labels[ii].setDisable(!enableSwitch[ii].isSelected()); 
 			});
 
 			PamHBox hBox = new PamHBox(); 
 			hBox.setSpacing(5);
 
-			hBox.getChildren().addAll(enableSwitch[i], label); 
+			hBox.getChildren().addAll(enableSwitch[i], labels[i]); 
 			
-
-
 			vBox.getChildren().addAll(hBox, standardClassifier.getClassifiers().get(i).getCTClassifierGraphics().getCTClassifierPane());
 		}
 
 		return vBox; 
 	} 
+	
+	private void disableClassifierPane(int ii) {
+		standardClassifier.getClassifiers().get(ii).getCTClassifierGraphics().getCTClassifierPane().setDisable(!enableSwitch[ii].isSelected());
+		labels[ii].setDisable(!enableSwitch[ii].isSelected()); 
+	}
 
 	@Override
 	public StandardClassifierParams getParams(StandardClassifierParams currParams) {
@@ -78,6 +84,7 @@ public class StandardClassifierPane extends  SettingsPane<StandardClassifierPara
 		for (int i=0; i<standardClassifier.getClassifiers().size(); i++) {
 			standardClassifier.getClassifiers().get(i).getCTClassifierGraphics().setParams(input.ctClassifierParams[i]);
 			enableSwitch[i].setSelected(input.enable[i]);
+			disableClassifierPane(i); 
 		}
 	}
 
diff --git a/src/cpod/fx/CPODSettingsPane.java b/src/cpod/fx/CPODSettingsPane.java
index b6d0cad5..59a6ffde 100644
--- a/src/cpod/fx/CPODSettingsPane.java
+++ b/src/cpod/fx/CPODSettingsPane.java
@@ -402,10 +402,15 @@ public class CPODSettingsPane extends SettingsPane<CPODParams> {
 
 		//have a look through the files and check that there are some files to import. 		
 		for (int i=0; i<CPODFileType.values().length; i++) {
+			try {
 			List<File> cp1 = (List<File>) FileUtils.listFiles(folder, 
 					new String[]{CPODFileType.values()[i].getText()}, this.subFolder.isSelected());
 			System.out.println("Files out: " + cp1);
 			files.addAll(cp1); 
+			}
+			catch (Exception e) {
+				System.err.println("Current directory does not exist: " + folder ); 
+			}
 		}
 	}
 
diff --git a/src/dataPlotsFX/overlaymark/menuOptions/MLExport/MLClickExport.java b/src/dataPlotsFX/overlaymark/menuOptions/MLExport/MLClickExport.java
index 9cb1aa4b..d86e3d7a 100644
--- a/src/dataPlotsFX/overlaymark/menuOptions/MLExport/MLClickExport.java
+++ b/src/dataPlotsFX/overlaymark/menuOptions/MLExport/MLClickExport.java
@@ -1,15 +1,11 @@
 package dataPlotsFX.overlaymark.menuOptions.MLExport;
 
-import com.jmatio.types.MLDouble;
 import com.jmatio.types.MLInt32;
-import com.jmatio.types.MLInt64;
 import com.jmatio.types.MLInt8;
 import com.jmatio.types.MLStructure;
 
-import PamUtils.PamUtils;
 import PamguardMVC.PamDataUnit;
 import clickDetector.ClickDetection;
-import whistlesAndMoans.ConnectedRegionDataUnit;
 
 /**
  * Export a click to a MATLAB structure. 
diff --git a/src/dataPlotsFX/overlaymark/popUpMenu/TDMenuPane.java b/src/dataPlotsFX/overlaymark/popUpMenu/TDMenuPane.java
index 756b5f55..ff2df930 100644
--- a/src/dataPlotsFX/overlaymark/popUpMenu/TDMenuPane.java
+++ b/src/dataPlotsFX/overlaymark/popUpMenu/TDMenuPane.java
@@ -49,7 +49,7 @@ import pamViewFX.fxStyles.PamStylesManagerFX;
  */
 public class TDMenuPane extends PamBorderPane {
 
-	public static final int menuWidth=200; 
+	public static final int MENU_WIDTH=200; 
 
 	/**
 	 * The current data units. 
@@ -333,10 +333,10 @@ public class TDMenuPane extends PamBorderPane {
 
 		flipPane.getFront().getChildren().add(menuPane); 
 		flipPane.getBack().getChildren().add(infoPane); 
-		flipPane.setPrefWidth(menuWidth);
+		flipPane.setPrefWidth(MENU_WIDTH);
 
 		PamBorderPane holder = new PamBorderPane(flipPane); 
-		holder.setPrefWidth(menuWidth);
+		holder.setPrefWidth(MENU_WIDTH);
 
 
 		return holder;