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Updates and bug fixes to click train detector and CPOD importer

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This commit is contained in:
Jamie Mac 2022-02-18 16:22:34 +00:00
parent fa52548746
commit 941737a7ab
14 changed files with 142 additions and 42 deletions
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13
src/clickTrainDetector/classification/CTClassifierManager.java
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@ -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;
}

2
src/clickTrainDetector/classification/CTClassifierParams.java
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@ -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;

2
src/clickTrainDetector/classification/idiClassifier/IDIClassification.java
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@ -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);
}

8
src/clickTrainDetector/classification/idiClassifier/IDIClassifier.java
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@ -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

2
src/clickTrainDetector/classification/simplechi2classifier/Chi2CTClassification.java
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@ -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

15
src/clickTrainDetector/classification/standardClassifier/StandardClassification.java
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@ -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;
}

54
src/clickTrainDetector/classification/standardClassifier/StandardClassificationJSON.java
View File

@ -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;
}

42
src/clickTrainDetector/classification/standardClassifier/StandardClassifier.java
View File

@ -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

9
src/clickTrainDetector/classification/standardClassifier/StandardClassifierParams.java
View File

@ -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.

3
src/clickTrainDetector/clickTrainAlgorithms/mht/mhtMAT/MHTClassifierMAT.java
View File

@ -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;
}

19
src/clickTrainDetector/layout/classification/standardClassifier/StandardClassifierPane.java
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@ -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);
}
}

5
src/cpod/fx/CPODSettingsPane.java
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@ -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 );
}
}
}

4
src/dataPlotsFX/overlaymark/menuOptions/MLExport/MLClickExport.java
View File

@ -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.

6
src/dataPlotsFX/overlaymark/popUpMenu/TDMenuPane.java
View File

@ -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;