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Bug fixes (#31)

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* Updates to click train detector

New GUI for click train classification - more intuitive and allows users to build more powerful classifiers.
CPOD data can now build average waveforms.
CPOD click trains can be viewed in TDisplayFX pop up menu displays
Fixed Peak Frequency symbol chooser so it saves the colour box settings

* Screenshots

* Updates and bug fixes to click train detector and CPOD importer

* Updates to click train detector

New GUI for click train classification - more intuitive and allows users to build more powerful classifiers.
CPOD data can now build average waveforms.
CPOD click trains can be viewed in TDisplayFX pop up menu displays
Fixed Peak Frequency symbol chooser so it saves the colour box settings

* Updates and bug fixes to click train detector and CPOD importer

* Fix standard classifier JSON logging

* Merge fixes to click train detector

* Updates to click train detector

New GUI for click train classification - more intuitive and allows users to build more powerful classifiers.
CPOD data can now build average waveforms.
CPOD click trains can be viewed in TDisplayFX pop up menu displays
Fixed Peak Frequency symbol chooser so it saves the colour box settings

* Screenshots

* Updates and bug fixes to click train detector and CPOD importer

* Updates to click train detector

New GUI for click train classification - more intuitive and allows users to build more powerful classifiers.
CPOD data can now build average waveforms.
CPOD click trains can be viewed in TDisplayFX pop up menu displays
Fixed Peak Frequency symbol chooser so it saves the colour box settings

* Screenshots

* Updates and bug fixes to click train detector and CPOD importer

* Fix standard classifier JSON logging

* Google humpback whale deep learning classifier

Google's humpback whale deep learning classifier can now be imported.
Updated TDisplayFX to make the data selection panes cleaner and clearer.
Updated the TDisplayFX so that predicitons from deep learning models now have some display options e.g. changing colour.

* Bug fix to UI

* Updates to FX GUI

* Bug fixes

Click train detector now registers click train if there are no longer any click detections for a significant period of time.

Jitter in wrap spectrogram for TDisplayFX fixed

Deep learning module compatible with bearing localiser

Updates to FX GUI
This commit is contained in:
Jamie Mac 2022-04-28 10:52:03 +01:00 committed by GitHub
parent c4ee5f389b
commit d85d9078a1
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
31 changed files with 516 additions and 113 deletions
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2
.classpath
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@ -6,7 +6,7 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/Java 17">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>

2
.gitignore vendored
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@ -36,5 +36,3 @@ target/WMM.COF
settings.xml
.classpath
.classpath
.classpath

6
.settings/org.eclipse.jdt.core.prefs
View File

@ -1,11 +1,11 @@
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.targetPlatform=11
org.eclipse.jdt.core.compiler.compliance=11
org.eclipse.jdt.core.compiler.codegen.targetPlatform=16
org.eclipse.jdt.core.compiler.compliance=16
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=warning
org.eclipse.jdt.core.compiler.release=enabled
org.eclipse.jdt.core.compiler.source=11
org.eclipse.jdt.core.compiler.source=16

2
src/Acquisition/FolderInputSystem.java
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@ -421,7 +421,7 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings{
}
}
protected String getCurrentFolder() {
public String getCurrentFolder() {
if (folderInputParameters.recentFiles.size() == 0) {
return null;
}

12
src/Acquisition/layoutFX/AcquisitionPaneFX.java
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@ -145,6 +145,7 @@ public class AcquisitionPaneFX extends SettingsPane<AcquisitionParameters>{
public AcquisitionPaneFX(AcquisitionControl aquisitionControl){
super(null);
mainPane = new PamBorderPane();
mainPane.setPrefWidth(400);
this.acquisitionControl=aquisitionControl;
this.acquisitionParameters=acquisitionControl.getAcquisitionParameters();
@ -153,7 +154,7 @@ public class AcquisitionPaneFX extends SettingsPane<AcquisitionParameters>{
flipPane=new FlipPane();
flipPane.setFlipDirection(Orientation.HORIZONTAL);
flipPane.setFlipTime(250); //default is 700ms- way too high
//flipPane.prefWidthProperty().bind(mainPane.widthProperty());
if (aquisitionControl.isViewer()){
this.mainPane.setCenter(createViewerModePane());
@ -166,9 +167,7 @@ public class AcquisitionPaneFX extends SettingsPane<AcquisitionParameters>{
//create the advanced flip pane.
advancedSettingPane = createAdvSettingsPane();
flipPane.getBack().getChildren().add(advancedSettingPane);
System.out.println("MAKE PANE: " + acquisitionParameters.getDaqSystemType());
//System.out.println("MAKE PANE: " + acquisitionParameters.getDaqSystemType());
}
@ -194,7 +193,7 @@ public class AcquisitionPaneFX extends SettingsPane<AcquisitionParameters>{
buttonHolder.setAlignment(Pos.CENTER_LEFT);
buttonHolder.getChildren().addAll(back, advLabel = new Label("Adv. Settings"));
advLabel.setAlignment(Pos.CENTER);
advLabel.setMaxWidth(Double.MAX_VALUE); //nneed ot make sure label is in center.
advLabel.setMaxWidth(Double.MAX_VALUE); //need to make sure label is in center.
PamGuiManagerFX.titleFont2style(advLabel);
advLabel.setAlignment(Pos.CENTER);
@ -264,7 +263,6 @@ public class AcquisitionPaneFX extends SettingsPane<AcquisitionParameters>{
//TODO- this is a bit CUMBERSOME and maybe fixed in new version of JavaFX
//need to get stage and resize because new controls may have been added.
if (mainPane!=null && mainPane.getScene()!=null) {
Stage stage = (Stage) mainPane.getScene().getWindow();
stage.sizeToScene();
@ -498,7 +496,7 @@ public class AcquisitionPaneFX extends SettingsPane<AcquisitionParameters>{
acquisitionControl.getOfflineFileServer().setOfflineFileParameters(ofp);
}
System.out.println("Get Params: Open Aquisition dialog: " + acquisitionParameters.getDaqSystemType());
//System.out.println("Get Params: Open Aquisition dialog: " + acquisitionParameters.getDaqSystemType());
return acquisitionParameters;
}

273
src/Acquisition/layoutFX/CheckWavHeadersPane.java Normal file
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@ -0,0 +1,273 @@
package Acquisition.layoutFX;
import java.io.File;
import java.util.ArrayList;
import Acquisition.AudioFileFuncs;
import Acquisition.FolderInputSystem;
import Acquisition.WavFileFuncs;
import PamUtils.PamAudioFileFilter;
import javafx.geometry.Insets;
import javafx.beans.property.SimpleDoubleProperty;
import javafx.concurrent.Task;
import javafx.geometry.Pos;
import javafx.scene.control.Label;
import javafx.scene.control.ProgressBar;
import javafx.scene.control.ScrollPane;
import javafx.scene.control.ScrollPane.ScrollBarPolicy;
import javafx.scene.control.TextArea;
import javafx.scene.layout.Priority;
import pamViewFX.PamGuiManagerFX;
import pamViewFX.fxGlyphs.PamGlyphDude;
import pamViewFX.fxNodes.PamBorderPane;
import pamViewFX.fxNodes.PamButton;
import pamViewFX.fxNodes.PamHBox;
import pamViewFX.fxNodes.PamVBox;
/**
* Pane with controls to fix wave file headers.
* @author Jamie Macaulay
*
*/
public class CheckWavHeadersPane extends PamBorderPane {
/**
* The text area.
*/
private TextArea textArea;
/**
* The folder name label.
*/
private Label folderName;
/**
* Progress bar showing progress of file write.
*/
private ProgressBar progressBar;
private boolean running, ran;
/**
* Check file workers.
*/
private CheckFiles checkFilesWorker;
/**
* The files.
*/
private ArrayList<File> allFiles = new ArrayList<File>();
/**
* The folder input system.
*/
private FolderInputSystem folderInputSystem;
/**
* Look at sub folders.
*/
private boolean subFolders;
/**
* The folder.
*/
private File folder;
/**
* The number of files.
*/
private int nFiles;
private int doneFiles;
private int nErrors;
/**
* Simple double property.
*/
private SimpleDoubleProperty progressProperty = new SimpleDoubleProperty(0);
/**
* Constructor for the CheckWavHeadersPane
* @param folderInputSystem - the folder input system.
*/
public CheckWavHeadersPane(FolderInputSystem folderInputSystem) {
//this.setCenter(new Label("Hello fix wav pane"));
PamVBox mainPane = new PamVBox();
mainPane.setSpacing(5);
this.folderInputSystem=folderInputSystem;
folderName = new Label(" ");
PamGuiManagerFX.titleFont2style(folderName);
textArea = new TextArea();
textArea.setEditable(false);
ScrollPane scrollPane = new ScrollPane(textArea);
scrollPane.setHbarPolicy(ScrollBarPolicy.NEVER);
//scrollPane.setPrefSize(322, 300);
this.setCenter(scrollPane);
PamHBox pamHBox = new PamHBox();
pamHBox.setAlignment(Pos.CENTER_LEFT);
pamHBox.setSpacing(5);
PamButton runButton = new PamButton();
runButton.setGraphic(PamGlyphDude.createPamIcon("mdi2p-play"));
runButton.setOnAction((action)->{
checkFiles();
});
progressBar = new ProgressBar();
PamHBox.setHgrow(progressBar, Priority.ALWAYS);
progressBar.prefHeightProperty().bind(runButton.heightProperty());
pamHBox.getChildren().addAll(runButton, progressBar);
progressBar.setMaxWidth(Double.MAX_VALUE);
mainPane.getChildren().addAll(folderName, textArea, pamHBox);
this.setPadding(new Insets(5,0,5,15));
}
private void setParams() {
running = ran = false;
subFolders = folderInputSystem.getFolderInputParameters().subFolders;
if (subFolders) {
folderName.setText(folderInputSystem.getCurrentFolder() + " + sub folders");
}
else {
folderName.setText(folderInputSystem.getCurrentFolder());
}
folder = new File(folderInputSystem.getCurrentFolder());
textArea.setText(" ");
allFiles.clear();
nFiles = countFiles(folder);
progressBar.setProgress(0);
progressBar.progressProperty().bind(progressProperty);
//progressBar.setMaximum(Math.max(nFiles, 1));
enableControls();
}
private int countFiles(File folder) {
int nF = 0;
File[] files = folder.listFiles(new PamAudioFileFilter());
if (files == null) return 0;
File file;
for (int i = 0; i < files.length; i++) {
file = files[i];
if (file.isDirectory() && subFolders) {
System.out.println(file.getAbsoluteFile());
nF += countFiles(file.getAbsoluteFile());
}
else if (file.isFile()) {
allFiles.add(file);
nF++;
}
}
return nF;
}
/**
* Return true if there is an error
* @param aFile file to check, aif or wav
* @return true if there is an error
*/
private int checkFile(File aFile) {
if (aFile.exists() == false || aFile.isDirectory() == true) {
return AudioFileFuncs.FILE_DOESNTEXIST;
}
String fileName = aFile.getName();
// get the bit after the dot
int dotPos = fileName.lastIndexOf('.');
if (dotPos < 0) {
return AudioFileFuncs.FILE_UNKNOWNTYPE;
}
String fileEnd = fileName.substring(dotPos+1);
if (fileEnd.equalsIgnoreCase("wav")) {
return checkWavFile(aFile);
}
else if (fileEnd.equalsIgnoreCase("aif")) {
return checkAifFile(aFile);
}
return AudioFileFuncs.FILE_UNKNOWNTYPE;
}
private void enableControls() {
//getOkButton().setEnabled(nFiles > 0 & running == false && ran == false);
//getCancelButton().setEnabled(running == false);
}
private void checkFiles() {
running = true;
textArea.setText(String.format("Checking %d files ...\n", nFiles));
doneFiles = 0;
nErrors = 0;
enableControls();
checkFilesWorker = new CheckFiles();
}
private void jobDone() {
running = false;
ran = true;
enableControls();
textArea.appendText(String.format("\n\n%d file headers contained errors", nErrors));
}
private int checkAifFile(File file) {
return AudioFileFuncs.FILE_CANTOPEN;
}
private int checkWavFile(File aFile) {
return WavFileFuncs.checkHeader(aFile, true);
}
private class CheckFiles extends Task<Integer> {
@Override
protected Integer call() throws Exception {
try {
/*
* need to loop over files again
* for each file, report on progress with it's name and
* whether or not it had an error
*/
int error;
File aFile;
for (int i = 0; i < allFiles.size(); i++) {
error = checkFile(aFile = allFiles.get(i));
//progressBar.progressProperty().bind(null);
progressProperty.setValue(100*i/(double) allFiles.size());
}
return null;
}
catch (Exception e) {
e.printStackTrace();
return null;
}
}
@Override
protected void done() {
super.done();
jobDone();
}
}
}

19
src/Acquisition/layoutFX/FixWavPane.java
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@ -1,19 +0,0 @@
package Acquisition.layoutFX;
import Acquisition.FolderInputSystem;
import javafx.scene.control.Label;
import pamViewFX.fxNodes.PamBorderPane;
/**
* Pane with controls to fix wave file headers.
* @author Jamie Macaulay
*
*/
public class FixWavPane extends PamBorderPane {
public FixWavPane(FolderInputSystem folderInputSystem) {
this.setCenter(new Label("Hello fix wav pane"));
}
}

17
src/Acquisition/layoutFX/FolderInputPane.java
View File

@ -143,7 +143,7 @@ public class FolderInputPane extends DAQSettingsPane<FolderInputParameters>{
/**
* Pane to fix the headers of wave files.
*/
private FixWavPane fixWavPane;
private CheckWavHeadersPane fixWavPane;
/**
* Toggle button for merging contigious files
@ -166,6 +166,7 @@ public class FolderInputPane extends DAQSettingsPane<FolderInputParameters>{
this.folderInputSystem=folderInputSystem2;
this.acquisitionPaneFX = acquisitionPaneFX;
this.mainPane=createDAQPane();
this.mainPane.setPrefWidth(300);
}
/**
@ -198,7 +199,7 @@ public class FolderInputPane extends DAQSettingsPane<FolderInputParameters>{
browseFileButton.setGraphic(Glyph.create("FontAwesome|FILES_ALT").
size(PamGuiManagerFX.iconSize).color(Color.WHITE.darker()));
browseFileButton.prefHeightProperty().bind(fileSelectBox.heightProperty()); //make browse button same height as combo box.
browseFileButton.setMinWidth(30);
browseFileButton.setMinWidth(35);
browseFileButton.setOnAction( (action) ->{
selectFolder(false);
});
@ -208,7 +209,7 @@ public class FolderInputPane extends DAQSettingsPane<FolderInputParameters>{
browseFolderButton.setGraphic(Glyph.create("FontAwesome|FOLDER").
size(PamGuiManagerFX.iconSize).color(Color.WHITE.darker()));
browseFolderButton.prefHeightProperty().bind(fileSelectBox.heightProperty()); //make browse button same height as combo box.
browseFolderButton.setMinWidth(30);
browseFolderButton.setMinWidth(35);
browseFolderButton.setOnAction( (action) ->{
selectFolder(true);
});
@ -244,7 +245,7 @@ public class FolderInputPane extends DAQSettingsPane<FolderInputParameters>{
fileDateStrip.prefWidthProperty().bind(pamVBox.widthProperty());
fixWavPane = new FixWavPane(folderInputSystem);
fixWavPane = new CheckWavHeadersPane(folderInputSystem);
Label utilsLabel=new Label("Sound file utilities");
PamGuiManagerFX.titleFont2style(utilsLabel);
@ -323,10 +324,11 @@ public class FolderInputPane extends DAQSettingsPane<FolderInputParameters>{
table.setEditable(true);
TableColumn<WavFileType, Boolean > useWavFileColumn = new TableColumn<>( "Use file" );
TableColumn<WavFileType, Boolean > useWavFileColumn = new TableColumn<>( "Use" );
useWavFileColumn.setCellValueFactory(cellData -> cellData.getValue().useWavFileProperty());
useWavFileColumn.setCellFactory( tc -> new CheckBoxTableCell<>());
useWavFileColumn.setEditable(true);
useWavFileColumn.setMaxWidth(40);
TableColumn<WavFileType, String > fileNameColumn = new TableColumn<WavFileType, String >("File Name");
fileNameColumn.setCellValueFactory( f -> new SimpleStringProperty(f.getValue().getName()));
@ -342,12 +344,13 @@ public class FolderInputPane extends DAQSettingsPane<FolderInputParameters>{
TableColumn<WavFileType, Float > durationColumn = new TableColumn<WavFileType, Float > ("Duration");
durationColumn.setCellValueFactory(cellData -> new SimpleFloatProperty(cellData.getValue().getDurationInSeconds()).asObject());
TableColumn<WavFileType, Float > sampleRateColumn = new TableColumn<WavFileType, Float > ("Sample Rate");
TableColumn<WavFileType, Float > sampleRateColumn = new TableColumn<WavFileType, Float > ("sR");
sampleRateColumn.setCellValueFactory(cellData -> new SimpleFloatProperty(cellData.getValue().getAudioInfo().getSampleRate()).asObject());
//
TableColumn<WavFileType, Integer > chanColumn = new TableColumn<WavFileType, Integer > ("No. Channels");
TableColumn<WavFileType, Integer > chanColumn = new TableColumn<WavFileType, Integer > ("Chan");
chanColumn.setCellValueFactory(cellData -> new SimpleIntegerProperty(cellData.getValue().getAudioInfo().getChannels()).asObject());
useWavFileColumn.setPrefWidth(70);
TableColumn<WavFileType, String > typeColumn = new TableColumn<WavFileType, String > ("Type");

1
src/Localiser/controls/RawOrFFTPane.java
View File

@ -62,6 +62,7 @@ public class RawOrFFTPane extends SettingsPane<RawOrFFTParamsInterface> {
// BorderPane.setMargin(fftSourcePane, new Insets(15, 0, 0, 0));
beamDataSourcePane = new SourcePaneFX(FFTDataUnit.class, false, false);
beamDataSourcePane.addSourceType(RawDataUnit.class, false);
beamDataSourcePane.setMaxWidth(Double.POSITIVE_INFINITY);
/*
*
sourceList.setMaxWidth(Double.MAX_VALUE);

4
src/PamView/symbol/StandardSymbolChooser.java
View File

@ -10,6 +10,7 @@ import javax.swing.JCheckBoxMenuItem;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import PamUtils.PamArrayUtils;
import PamView.GeneralProjector;
import PamView.GeneralProjector.ParameterType;
import PamView.dialog.GenericSwingDialog;
@ -63,7 +64,8 @@ public class StandardSymbolChooser extends PamSymbolChooser {
ArrayList<SymbolModifier> modifiers = getSymbolModifiers();
// System.out.println("StandardSymbolChooser: " + modifiers.size() + " Defualt shape: " + options.symbolData.symbol);
// System.out.println("StandardSymbolOptions: " + options);
// System.out.println("StandardSymbolOptions: " + mord.length + " " + this.getSymbolManager() + " " + options);
// PamArrayUtils.printArray(mord);
if (modifiers == null || modifiers.size() == 0) {
return symbolData;

3
src/PamView/symbol/StandardSymbolOptions.java
View File

@ -4,6 +4,7 @@ import java.awt.Color;
import java.io.Serializable;
import java.util.HashMap;
import PamUtils.PamArrayUtils;
import PamView.symbol.modifier.SymbolModifier;
import PamView.symbol.modifier.SymbolModifierParams;
@ -138,7 +139,7 @@ public class StandardSymbolOptions extends PamSymbolOptions implements Serializa
* @return the modifierOrder
*/
public int[] getModifierOrder(StandardSymbolChooser symbolChooser) {
if (modifierOrder == null || modifierOrder.length != symbolChooser.getSymbolModifiers().size()) {
if (modifierOrder == null || modifierOrder.length != symbolChooser.getSymbolModifiers().size() || PamArrayUtils.contains(modifierOrder, -1)) {
modifierOrder = new int[symbolChooser.getSymbolModifiers().size()];
for (int i = 0; i < modifierOrder.length; i++) {
modifierOrder[i] = i;

3
src/PamguardMVC/PamProcess.java
View File

@ -40,9 +40,6 @@ import javax.swing.Timer;
import networkTransfer.receive.BuoyStatusDataUnit;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import PamController.PamControlledUnit;
import PamController.PamController;
import PamController.PamControllerInterface;

6
src/bearinglocaliser/dialog/BearLocAlgorithmPane.java
View File

@ -21,6 +21,7 @@ import javafx.scene.control.ChoiceBox;
import javafx.scene.control.Label;
import javafx.scene.control.Tooltip;
import javafx.scene.layout.GridPane;
import javafx.scene.layout.Priority;
import pamViewFX.PamGuiManagerFX;
import pamViewFX.fxGlyphs.PamGlyphDude;
import pamViewFX.fxNodes.PamBorderPane;
@ -41,7 +42,7 @@ public class BearLocAlgorithmPane extends SettingsPane<BearingLocaliserParams> {
this.bfLocControl = bfLocControl;
algoPane = new GridPane();
algoPane.setVgap(2);
algoPane.setHgap(12);
algoPane.setHgap(5);
// algoPane.setPadding(new Insets(2, 12, 2, 12));
mainPane = new PamBorderPane(new PamTitledBorderPane("Algorithm selection", algoPane));
mainPane.setPadding(new Insets(10, 5, 10, 5));
@ -140,6 +141,9 @@ public class BearLocAlgorithmPane extends SettingsPane<BearingLocaliserParams> {
algoPane.add(idLab = new Label(String.format("%d", i)), 0, iRow);
GridPane.setHalignment(idLab, HPos.CENTER);
algoSelection[i] = new ChoiceBox<>();
algoSelection[i].setMaxWidth(Double.POSITIVE_INFINITY);
algoSelection[i].setPrefWidth(150);
GridPane.setHgrow(algoSelection[i], Priority.ALWAYS); //stop the choice box from changing size on selection
for (BearingAlgorithmProvider anAlgo:allAlgorithms) {
algoSelection[i].getItems().add(anAlgo.getStaticProperties().getName());
}

1
src/bearinglocaliser/dialog/BearLocGroupPane.java
View File

@ -74,6 +74,7 @@ public class BearLocGroupPane extends SettingsPane<BearingLocaliserParams> {
@Override
public void setParams(BearingLocaliserParams params) {
System.out.println("Bearing Localiser: params: " + params.getChannelBitmap());
groupedChannelPanel.setParams(params.getRawOrFFTSourceParameters());
doAllGroups.setSelected(params.doAllGroups);
}

3
src/bearinglocaliser/dialog/BearLocSourcePane.java
View File

@ -26,6 +26,7 @@ import javafx.scene.control.TextField;
import javafx.scene.control.ToggleGroup;
import javafx.scene.layout.BorderPane;
import javafx.scene.layout.GridPane;
import javafx.scene.layout.Priority;
import pamViewFX.fxNodes.PamBorderPane;
import pamViewFX.fxNodes.PamGridPane;
import pamViewFX.fxNodes.PamTextField;
@ -50,6 +51,8 @@ public class BearLocSourcePane extends SettingsPane<BearingLocaliserParams> {
// sourcePane.setVgap(3);
// sourcePane.setHgap(4);
detSourcePane = new SourcePaneFX(PamDetection.class, false, true);
detSourcePane.setMaxWidth(Double.POSITIVE_INFINITY);
GridPane.setHgrow(detSourcePane, Priority.ALWAYS);
// sourcePane.add(detSourcePane, 0, 2);
sourcePane.add(detSourcePane, 0, 0);
mainPane.setTop(new PamTitledBorderPane("Detection Source", sourcePane));

3
src/clickTrainDetector/CTClassificationProcess.java
View File

@ -118,8 +118,7 @@ public class CTClassificationProcess extends PamInstantProcess {
@Override
public void pamStart() {
System.out.println("-----||||| This parent block: " + this.getParentDataBlock() + " " + this.getParentProcess());
//System.out.println("-----||||| This parent block: " + this.getParentDataBlock() + " " + this.getParentProcess());
}
@Override

10
src/clickTrainDetector/ClickTrainControl.java
View File

@ -66,6 +66,11 @@ public class ClickTrainControl extends PamControlledUnit implements PamSettings
*/
public static final int NEW_PARENT_DATABLOCK= 3;
/**
* The PAMGuard clock has been updated.
*/
public static final int CLOCK_UPDATE = 4;
/**
* Reference to the click train process.
*/
@ -233,7 +238,7 @@ public class ClickTrainControl extends PamControlledUnit implements PamSettings
}
for (int i=0; i<this.clickTrainAlgorithms.size(); i++) {
clickTrainAlgorithms.get(i).update(ClickTrainControl.NEW_PARAMS);
clickTrainAlgorithms.get(i).update(ClickTrainControl.NEW_PARAMS, null);
}
//set up the classifier parameters
@ -326,7 +331,7 @@ public class ClickTrainControl extends PamControlledUnit implements PamSettings
*/
public void update(int flag) {
for (int i=0; i<this.clickTrainAlgorithms.size(); i++) {
clickTrainAlgorithms.get(i).update(flag);
clickTrainAlgorithms.get(i).update(flag, null);
}
}
@ -537,6 +542,7 @@ public class ClickTrainControl extends PamControlledUnit implements PamSettings
return clAlgorithmInfoManager;
}

7
src/clickTrainDetector/ClickTrainProcess.java
View File

@ -182,6 +182,13 @@ public class ClickTrainProcess extends PamInstantProcess {
public ClickTrainControl getClickTrainControl() {
return this.clickTrainControl;
}
@Override
public void masterClockUpdate(long timeMilliseconds, long sampleNumber) {
super.masterClockUpdate(timeMilliseconds, sampleNumber);
this.clickTrainControl.getCurrentCTAlgorithm().update(ClickTrainControl.CLOCK_UPDATE, Long.valueOf(timeMilliseconds));
}
// /**

3
src/clickTrainDetector/clickTrainAlgorithms/ClickTrainAlgorithm.java
View File

@ -32,9 +32,10 @@ public interface ClickTrainAlgorithm {
/**
* Send update flag to the algorithm
* @param object - an object to add to update
* @param flag - the flag.
*/
public void update(int i);
public void update(int i, Object object);
/**
* Get logging class for click algorithm specific information.

2
src/clickTrainDetector/clickTrainAlgorithms/classificationRatio/RatioClickTrainAlgorithm.java
View File

@ -44,7 +44,7 @@ public class RatioClickTrainAlgorithm implements ClickTrainAlgorithm {
}
@Override
public void update(int i) {
public void update(int i, Object data) {
// TODO Auto-generated method stub
}

2
src/clickTrainDetector/clickTrainAlgorithms/mht/MHTChi2Params.java
View File

@ -15,7 +15,7 @@ public class MHTChi2Params implements Cloneable, Serializable, ManagedParameters
*/
private static final long serialVersionUID = 1L;
/**
* The absolute maximum ICI for a click train
* The absolute maximum ICI for a click train in seconds!
*/
public double maxICI = 0.4;

40
src/clickTrainDetector/clickTrainAlgorithms/mht/MHTClickTrainAlgorithm.java
View File

@ -217,6 +217,25 @@ public class MHTClickTrainAlgorithm implements ClickTrainAlgorithm, PamSettings
}
}
}
/**
* Check for garbage collection based on the current time. This is used when, for example, no click are detected for a
* long period.
* @param timeMillis - the time in millis
* @param mhtAlgorithm - the channel based MHTAlgorithm.
*/
private void checkCTGarbageCollect(long timeMillis, MHTAlgorithm mhtAlgorithm) {
boolean isGarbage = this.mhtGarbageBot.checkCTGarbageCollect(timeMillis, mhtAlgorithm.getMHTKernal());
if (isGarbage) {
//grab tracks
mhtAlgorithm.getMHTKernal().confirmRemainingTracks();
grabDoneTrains(mhtAlgorithm);
//reset the kernel;
mhtAlgorithm.getMHTKernal().clearKernel();
}
}
// /**
// * Get the interval between the new unit and the last unit.
@ -396,7 +415,7 @@ public class MHTClickTrainAlgorithm implements ClickTrainAlgorithm, PamSettings
* Update the algorithm
* @param flag- flag indicating the update type.
*/
public void update(int flag) {
public void update(int flag, Object info) {
switch (flag) {
case ClickTrainControl.PROCESSING_START:
@ -437,10 +456,16 @@ public class MHTClickTrainAlgorithm implements ClickTrainAlgorithm, PamSettings
case ClickTrainControl.NEW_PARAMS:
setupAlgorithm();
break;
case ClickTrainControl.CLOCK_UPDATE:
for (int i=0; i<this.mHTAlgorithms.size(); i++) {
checkCTGarbageCollect((Long) info, mHTAlgorithms.get(i));
}
break;
}
}
/**
* Set up the algorithm.
*/
@ -547,13 +572,12 @@ public class MHTClickTrainAlgorithm implements ClickTrainAlgorithm, PamSettings
*/
public void printSettings() {
System.out.println("/********MHT PARAMS*******/");
pamMHTChi2.printSettings();
mhtKernal.getMHTParams().printSettings();
System.out.println("/*************************/");
Debug.out.println("/********MHT PARAMS*******/");
if (Debug.isPrintDebug()) {
pamMHTChi2.printSettings();
mhtKernal.getMHTParams().printSettings();
}
Debug.out.println("/*************************/");
// //MHT kernel params
// System.out.println("npruneback: " + mhtKernal.getMHTParams().nPruneback);

23
src/clickTrainDetector/clickTrainAlgorithms/mht/MHTGarbageBot.java
View File

@ -59,8 +59,8 @@ public class MHTGarbageBot {
* then the possibility matrix will simply keep resizing and click train
* detector will run indefinitely.
*
* @param - the new data unit
* @param -the channel based MHTAlgorithm.
* @param dataUnit - the new data unit
* @param mhtKernel - the current MHT Kernel.
* @return - true if a garbage collection task was executed.
*/
public boolean checkCTGarbageCollect(PamDataUnit dataUnit, MHTKernel<PamDataUnit> mhtKernel) {
@ -126,6 +126,25 @@ public class MHTGarbageBot {
return false;
}
/**
* Check whether a garbage collection of the hypothesis matrix is required based on current time rather than the current data unit.
* @param currentTimemillis - the current time in millis
* @param mhtKernel - the MHT kernel
* @return true if a garbage collect is required.
*/
public boolean checkCTGarbageCollect(long currentTimemillis, MHTKernel<PamDataUnit> mhtKernel) {
if (mhtKernel.getLastDataUnit()==null) return false;
if ((currentTimemillis - mhtKernel.getLastDataUnit().getTimeMilliseconds())
>mhtKernel.getMHTParams().maxCoast*mhtKernel.getMHTChi2Provider().getChi2Params().maxICI*1000.) {
return true;
}
return false;
}
/**
* Get the interval between the new unit and the last unit.
* @param dataUnit - get the data units.

6
src/clickTrainDetector/layout/ClickTrainAlgorithmPaneFX.java
View File

@ -263,7 +263,7 @@ public class ClickTrainAlgorithmPaneFX extends SettingsPane<ClickTrainParams> {
clickTrainControl.createDataSelector(sourcePane.getSource());
System.out.println("ClickTrainAlgorithmPaneFX: Detection Selector: " + clickTrainControl.getDataSelector() + " " + sourcePane.getSource());
//System.out.println("ClickTrainAlgorithmPaneFX: Detection Selector: " + clickTrainControl.getDataSelector() + " " + sourcePane.getSource());
if (clickTrainControl.getDataSelector()!=null) {
Label dataSelectorLabel = new Label("Detection Selector");
@ -557,8 +557,8 @@ public class ClickTrainAlgorithmPaneFX extends SettingsPane<ClickTrainParams> {
this.ctClassifierHolder.setParams(clickTrainParams);
//notify the algorithm of updates.
System.out.println("getSelectedCTAlgorithm(): " + getSelectedCTAlgorithm());
System.out.println("getSelectedCTAlgorithm().getClickTrainGraphics(): " + getSelectedCTAlgorithm().getClickTrainGraphics());
// System.out.println("getSelectedCTAlgorithm(): " + getSelectedCTAlgorithm());
// System.out.println("getSelectedCTAlgorithm().getClickTrainGraphics(): " + getSelectedCTAlgorithm().getClickTrainGraphics());
getSelectedCTAlgorithm().getClickTrainGraphics().notifyUpdate(ClickTrainControl.NEW_PARENT_DATABLOCK,
sourcePane.getDataBlockBox().getSelectionModel().getSelectedItem());

83
src/dataPlotsFX/scrollingPlot2D/Scrolling2DPlotDataFX.java
View File

@ -571,13 +571,17 @@ public class Scrolling2DPlotDataFX {
/****Some useful variables used all the time**/
//Note - "imageXX" indicates that the number refers to pixels in the writable images
// - "screenXX" indicates the number refers to pixels on the screen.
//time axis
private double tScale; // the time scale in pixels per millisecond.
// private long wrapLengthMillis; //the length of the left wrap section in millis
private double wrapScreenPix; //the number of screen pixels the wrap takes up
private double wrapImagePixdw; //the length of the wrap section in spectrogram image pixels (not time display pixels)
private double imagePixdw; // the width of the screen in image pixels.
private double imagestart; //the start of time image
private double imageStart1; //the start of time image
private double imageStart2; //the start of the image for the second wrap segment
private double endScreenPix; //the end of the screen in pixels. This s not just timePixels
private double nImagePixs;//the number of pixels on image in memory, from zero to current location of pointer.
//the number of screen pixels corresponding to the current position on the writable image to zero.
@ -585,10 +589,19 @@ public class Scrolling2DPlotDataFX {
private double scrollEndTime; //the current time.
//location to start drawing image on screen from.
private double screenStartPix;
//freq axis
/**Frequency (vertical) axis***/
private double freqPixels;
private double imageFP1, imageFP2;
private double freqWidth;
/*
* The maximum pixel jitter allowed. The calculated image start position can jitter because
* of rounding errors. MAX_PIXEL_JITTER ensures that the image location is kep constant for
* different frames by assumin that any chnage below MAX_PIXEL_JITTER is a rounding error and not
* a change in the display.
*/
private double MAX_PIXEL_JITTER = 3; //pixels
public double drawSpectrogramWrap(GraphicsContext g2d, double timePixels, double freqPixels, PamAxisFX timeAxis,
@ -609,69 +622,89 @@ public class Scrolling2DPlotDataFX {
//the length of the wrap section in spectrogram image pixels (not time display pixels)
wrapImagePixdw=wrapScreenPix/(timeScale * 1000. * tScale * timeCompression);
imagePixdw = timePixels/(timeScale * 1000. * tScale * timeCompression);
// System.out.println(String.format(" timeScale %.3f timeCompression %d timePixels %.3f wrapImagePixdw %.3f",
// timeScale, timeCompression, timePixels, wrapImagePixdw));
imagePixdw= timePixels/(timeScale * 1000. * tScale * timeCompression);
//the start of time image
imagestart=imageXPos+1-wrapImagePixdw;
/**
* Because everything related to pixel measurements is a double in JavaFX we sometimes
* get a rounding issue which means the wrap display. The way to get around this is to only
* change the imageStart whenever the displays finishes wrapping. It's a bit of a HACK but it
* works.
*/
double imageStart=imageXPos+1-wrapImagePixdw;
if (Math.abs(imageStart-this.imageStart1)>=MAX_PIXEL_JITTER) {
//System.out.println("Reset image start: " + imageStart + " " + this.imageStart1);
this.imageStart1=imageStart;
}
//location to start drawing image on screne from.
screenStartPix=0;
if (imagestart<-1){
if (this.imageStart1<-1){
//gotta shift the start of the screen a bit if there is not enough image
screenStartPix=(Math.abs(imagestart))*timeScale * 1000. * tScale * timeCompression;
screenStartPix=(Math.abs(imageStart1))*timeScale * 1000. * tScale * timeCompression;
}
// System.out.println("imageXPos: "+imageXPos+"wrapLengthMillis: "+wrapLengthMillis+ " wrapScreenPix "+wrapScreenPix+
// " wrapScreenPixdw: "+wrapScreenPix+ " wrapImagePixdw: "+wrapImagePixdw+ " imagestart: "+
// imagestart + "nScreenPix: "+nScreenPix);
//System.out.println(String.format(" imageStart %.4f imageXPos %.4f imagePixdw %.4f", imageStart1,imageXPos, imagePixdw ));
/**
* Lift as much as possible into first section
*/
g2d.drawImage(writableImage, Math.max(0,imagestart), freqBinRange[1], wrapImagePixdw, freqWidth,
g2d.drawImage(writableImage, Math.max(0,this.imageStart1), freqBinRange[1], wrapImagePixdw, freqWidth,
screenStartPix, imageFP1, wrapScreenPix, imageFP2);
if (imagestart<-1){
if (imageStart1<-1){
/**
* If this occurs, the image is negative, i.e. we have to go back and fill a bit in from the end of the image in the wrap section.
*/
g2d.drawImage(writableImage, writableImage.getWidth()+imagestart, freqBinRange[1], Math.abs(imagestart), freqWidth,
g2d.drawImage(writableImage, writableImage.getWidth()+ imageStart1, freqBinRange[1], Math.abs(imageStart1), freqWidth,
0, imageFP1, screenStartPix, imageFP2);
}
//System.out.println(String.format(" totalXDraw %d wrapImagePixdw %.2f", totalXDraw,wrapImagePixdw ));
if (totalXDraw>imagePixdw){
imagestart=imageXPos+1-imagePixdw;
/**
* Because imageStart1 has remained clamped to prevent jitter in the image, we have to add a compensation factor
* to prevent jitter on the other half of the image. The compensation factor is the difference between the clamped
* start of the image (imageStart1) and the true image start (imagesStart)
*/
imageStart2= imageXPos +1 - imagePixdw- (imageStart-this.imageStart1);
//System.out.println(String.format(" imageStart %.4f imageXPos %.4f imagePixdw %.4f", imageStart,imageXPos, imagePixdw ));
screenStartPix= wrapScreenPix;
imagePixdw=imagePixdw-wrapImagePixdw;
if (imagestart<-1){
imagePixdw=imagePixdw - wrapImagePixdw;
if (imageStart2<-1){
/**
* Cannot fill the entire area in one go without going into negative parts of the image.
*/
screenStartPix=wrapScreenPix+(Math.abs(imagestart))*timeScale * 1000. * tScale * timeCompression;
imagePixdw=imagePixdw+imagestart;
screenStartPix=wrapScreenPix+(Math.abs(imageStart2))*timeScale * 1000. * tScale * timeCompression;
imagePixdw=imagePixdw+imageStart2;
}
//System.out.println(String.format(" imagestart %.3f imagePixdw %.3f screenstart %.3f", imagestart, imagePixdw,(timePixels-(endScreenPix-timePixels)+wrapScreenPix)));
//System.out.println(String.format(" imagestart %.3f imagePixdw %.3f screenStartPix %.3f imageXPos %.3f", imageStart2, imagePixdw, screenStartPix, imageXPos));
/**
* Now draw the data after the wrap line. i.e. the older part of the image
*/
g2d.drawImage(writableImage, Math.max(0,imagestart), freqBinRange[1], imagePixdw, freqWidth,
g2d.drawImage(writableImage, Math.max(0,imageStart2), freqBinRange[1], imagePixdw, freqWidth,
screenStartPix, imageFP1, timePixels-screenStartPix, imageFP2);
if (imagestart<-1){
if (imageStart2<-1){
/**
* Fill the remaining section with the negative parts of the image
*/
g2d.drawImage(writableImage, writableImage.getWidth()+imagestart, freqBinRange[1], Math.abs(imagestart), freqWidth,
g2d.drawImage(writableImage, writableImage.getWidth()+imageStart2, freqBinRange[1], Math.abs(imageStart2), freqWidth,
wrapScreenPix, imageFP1, screenStartPix-wrapScreenPix, imageFP2);
}

9
src/pamViewFX/fxNodes/utilityPanes/GroupedChannelPaneFX.java
View File

@ -207,11 +207,11 @@ public class GroupedChannelPaneFX {
}
protected void showChannels(int channels) {
//remove all channels from vertical box pane.
channelListPane.getChildren().removeAll(channelListPane.getChildren());
channelListPane.getChildren().remove(selectAll);
channelListPane.getChildren().remove(selectAll);
channelListPane.add(selectAll,0,0);
for (int i = 0; i < Math.min(PamConstants.MAX_CHANNELS, channelBoxes.length); i++) {
@ -306,13 +306,16 @@ public class GroupedChannelPaneFX {
}
public void setParams(GroupedSourceParameters params) {
/**
* First try to find the source datablock and from there set up
* the panel.
*/
*/
PamController pamController = PamController.getInstance();
sourceDataBlock = pamController.getDataBlockByLongName(params.getDataSource());
setSourceDataBlock(sourceDataBlock);
if (sourceDataBlock != null) {
// showChannels(sourceDataBlock.getChannelMap());
showChannels(sourceDataBlock.getSequenceMap());

2
src/pamViewFX/fxNodes/utilityPanes/MinMaxPane.java
View File

@ -2,6 +2,7 @@ package pamViewFX.fxNodes.utilityPanes;
import java.io.Serializable;
import javafx.geometry.Pos;
import javafx.scene.control.CheckBox;
import javafx.scene.control.Label;
import javafx.scene.control.Spinner;
@ -57,6 +58,7 @@ public class MinMaxPane<T extends Number> extends PamBorderPane {
PamHBox pamHBox = new PamHBox();
pamHBox.setSpacing(5);
pamHBox.setAlignment(Pos.CENTER_LEFT);
//e
checkBox = new CheckBox(varName);

5
src/pamViewFX/symbol/StandardSymbolOptionsPane.java
View File

@ -5,6 +5,7 @@ import java.util.List;
import org.controlsfx.control.ToggleSwitch;
import PamUtils.PamArrayUtils;
import PamView.symbol.ManagedSymbolData;
import PamView.symbol.PamSymbolChooser;
import PamView.symbol.PamSymbolManager;
@ -248,6 +249,10 @@ public class StandardSymbolOptionsPane extends FXSymbolOptionsPane<StandardSymbo
for (int i=0; i<modifierorder.length; i++ ) {
modifierorder[i] = getWhichChooser().getSymbolModifiers().indexOf(sortedPanelist.get(i).getSymbolModifier());
}
// System.out.println("Modifier Order: " + standardSymbolManager);
// PamArrayUtils.printArray(modifierorder);
return modifierorder;
}

58
src/rawDeepLearningClassifier/dlClassification/DLClassifyProcess.java
View File

@ -14,6 +14,7 @@ import PamguardMVC.PamObservable;
import PamguardMVC.PamProcess;
import binaryFileStorage.DataUnitFileInformation;
import rawDeepLearningClassifier.DLControl;
import rawDeepLearningClassifier.RawDLParams;
import rawDeepLearningClassifier.layoutFX.DLDetectionGraphics;
import rawDeepLearningClassifier.layoutFX.DLGraphics;
import rawDeepLearningClassifier.logging.DLAnnotation;
@ -127,7 +128,7 @@ public class DLClassifyProcess extends PamInstantProcess {
*/
private void setupClassifierProcess() {
System.out.println("Setup raw deep learning classiifer process: ");
//System.out.println("Setup raw deep learning classiifer process: ");
if (dlControl.getDLParams()==null) {
System.err.println("SegmenterProcess.setupSegmenter: The DLParams are null???");
@ -138,6 +139,11 @@ public class DLClassifyProcess extends PamInstantProcess {
System.err.println("Raw Deep Learning Classifier: The grouped source parameters were null."
+ " A new instance has been created: Possible de-serialization error.");
}
//important for downstream processes such as the bearing localiser.
dlModelResultDataBlock.setChannelMap(dlControl.getDLParams().groupedSourceParams.getChannelBitmap());
dlDetectionDataBlock.setChannelMap(dlControl.getDLParams().groupedSourceParams.getChannelBitmap());
int[] chanGroups = dlControl.getDLParams().groupedSourceParams.getChannelGroups();
@ -159,6 +165,20 @@ public class DLClassifyProcess extends PamInstantProcess {
public void prepareProcess() {
setupClassifierProcess();
}
/**
* called for every process once the system model has been created.
* this is a good time to check out and find input data blocks and
* similar tasks.
*
*/
@Override
public void setupProcess() {
setupClassifierProcess();
super.setupProcess();
}
/*
@ -233,7 +253,6 @@ public class DLClassifyProcess extends PamInstantProcess {
//1) It's over a max time
//2) Contains different parent data units (if not from raw data).
GroupedRawData lastUnit = classificationBuffer2.get(classificationBuffer2.size()-1);
if (!(lastUnit.getParentDataUnit() instanceof RawDataUnit) && lastUnit.getParentDataUnit()!=rawDataUnit.getParentDataUnit()) {
@ -255,7 +274,7 @@ public class DLClassifyProcess extends PamInstantProcess {
// if (timeDiff>=this.dlControl.getDLParams().maxBufferTime) {
//we are over the max buffer size.
System.out.println("DLClassifyProcess: warning: buffer is over max time gap");
//System.out.println("DLClassifyProcess: warning: buffer is over max time gap");
return true;
}
@ -280,7 +299,8 @@ public class DLClassifyProcess extends PamInstantProcess {
}
/**
* Create a data unit form a model result.
* Create a data unit form a model result. This is called whenever data passes a prediction threshold.
*
* @param modelResult - the model result.
* @param pamRawData - the raw data unit which the model result came from.
*/
@ -288,7 +308,7 @@ public class DLClassifyProcess extends PamInstantProcess {
//the model result may be null if the classifier uses a new thread.
//System.out.println("New segment: parent UID: " + pamRawData.getParentDataUnit().getUID() + " Prediciton: " + modelResult.getPrediction()[4]);
//System.out.println("New segment: parent UID: " + pamRawData.getParentDataUnit().getUID() + " Prediciton: " + modelResult.getPrediction()[0]+ " " + getSourceParams().countChannelGroups());
//create a new data unit - always add to the model result section.
DLDataUnit dlDataUnit = new DLDataUnit(pamRawData.getTimeMilliseconds(), pamRawData.getChannelBitmap(),
@ -303,11 +323,14 @@ public class DLClassifyProcess extends PamInstantProcess {
//need to implement multiple groups.
for (int i=0; i<getSourceParams().countChannelGroups(); i++) {
// System.out.println("RawDataIn: chan: " + pamRawData.getChannelBitmap()+ " " +
// PamUtils.hasChannel(getSourceParams().getGroupChannels(i), pamRawData.getChannelBitmap()) +
// " grouped source: " +getSourceParams().getGroupChannels(i));
// System.out.println("RawDataIn: chan: " + pamRawData.getChannelBitmap()+ " " +
// PamUtils.hasChannel(getSourceParams().getGroupChannels(i), pamRawData.getChannelBitmap()) +
// " grouped source: " +getSourceParams().getGroupChannels(i) + " Channels OK? "
// +PamUtils.hasChannel(getSourceParams().getGroupChannels(i), PamUtils.getSingleChannel(pamRawData.getChannelBitmap()))
// + " groupchan: " + getSourceParams().getGroupChannels(i) + " " + PamUtils.getLowestChannel(pamRawData.getChannelBitmap())
// + " chan bitmap: " + pamRawData.getChannelBitmap());
if (PamUtils.hasChannel(getSourceParams().getGroupChannels(i), PamUtils.getSingleChannel(pamRawData.getChannelBitmap()))) {
if (PamUtils.hasChannel(getSourceParams().getGroupChannels(i), PamUtils.getLowestChannel(pamRawData.getChannelBitmap()))) {
/***
* The are two options here.
@ -316,6 +339,8 @@ public class DLClassifyProcess extends PamInstantProcess {
* 2) Annotated an existing data unit with a deep learning annotation.
*/
if (pamRawData.getParentDataUnit() instanceof RawDataUnit) {
/****Make our own data units****/
if (dlDataUnit.getPredicitionResult().isBinaryClassification()) {
//if the model result has a binary classification then it is added to the data buffer unless the data
//buffer has reached a maximum size. In that case the data is saved.
@ -345,9 +370,11 @@ public class DLClassifyProcess extends PamInstantProcess {
}
}
else {
//need to go by the parent data unit for merging data not the segments.
/****Add annotation to existing data unit (e.g. click, clip or other RawDataHolder)****/
//Need to go by the parent data unit for merging data not the segments. Note that we may still add multiple
//predicitions to a single data unit depending on how many segments it contains.
//System.out.println("New model data " + pamRawData.getParentDataUnit().getUID() + " " + groupDataBuffer[i].size() + " " + modelResultDataBuffer[i].size());
System.out.println("New model data " + pamRawData.getParentDataUnit().getUID() + " " + groupDataBuffer[i].size() + " " + modelResultDataBuffer[i].size());
if (pamRawData.getParentDataUnit()!=lastParentDataUnit[i]) {
//save any data
@ -371,7 +398,6 @@ public class DLClassifyProcess extends PamInstantProcess {
lastParentDataUnit[i]=pamRawData.getParentDataUnit();
groupDataBuffer[i].add(pamRawData);
modelResultDataBuffer[i].add(modelResult);
//System.out.println("Buffer click annotation to " + lastParentDataUnit[i].getUID() + " " + groupDataBuffer[i].size());
}
}
@ -558,4 +584,12 @@ public class DLClassifyProcess extends PamInstantProcess {
return dlAnnotationType;
}
/**
* Get the parameters for the raw deep learning module.
* @return the parameters object for the raw deep learning classifier.
*/
public RawDLParams getDLParams() {
return this.dlControl.getDLParams();
}
}

17
src/rawDeepLearningClassifier/dlClassification/DLDetectionDataBlock.java
View File

@ -1,8 +1,8 @@
package rawDeepLearningClassifier.dlClassification;
import PamView.GroupedDataSource;
import PamView.GroupedSourceParameters;
import PamguardMVC.AcousticDataBlock;
import PamguardMVC.PamDataBlock;
import PamguardMVC.PamProcess;
/**
* Holds classified data units from deep learning model.
@ -10,11 +10,18 @@ import PamguardMVC.PamProcess;
* @author Jamie Macaulay
*
*/
public class DLDetectionDataBlock extends AcousticDataBlock<DLDetection> {
public class DLDetectionDataBlock extends AcousticDataBlock<DLDetection> implements GroupedDataSource {
public DLDetectionDataBlock(String dataName, PamProcess parentProcess, int channelMap) {
private DLClassifyProcess dlClassifyProcess;
public DLDetectionDataBlock(String dataName, DLClassifyProcess parentProcess, int channelMap) {
super(DLDetection.class, dataName, parentProcess, channelMap);
this.dlClassifyProcess = parentProcess;
}
@Override
public GroupedSourceParameters getGroupSourceParameters() {
return dlClassifyProcess.getDLParams().groupedSourceParams;
}

5
src/rawDeepLearningClassifier/segmenter/SegmenterProcess.java
View File

@ -375,7 +375,7 @@ public class SegmenterProcess extends PamProcess {
if (currentRawChunks[i]==null) {
//create a new data unit - should only be called once after initial start.
currentRawChunks[i] = new GroupedRawData(timeMilliseconds, getSourceParams() .getGroupChannels(i),
currentRawChunks[i] = new GroupedRawData(timeMilliseconds, getSourceParams().getGroupChannels(i),
startSampleTime, dlControl.getDLParams().rawSampleSize, dlControl.getDLParams().rawSampleSize);
currentRawChunks[i].setParentDataUnit(unit);;
}
@ -388,7 +388,7 @@ public class SegmenterProcess extends PamProcess {
//current time milliseconds is referenced from the first chunk with samples added. But, this can mean, especially for long period of times and multiple
//chunks that things get a bit out of sync. So make a quick check to ensure that time millis is roughly correct. If not then fix.
if (Math.abs(((double) currentRawChunks[i].getTimeMilliseconds() + 1000.*currentRawChunks[i].getRawDataPointer()[0]/this.getSampleRate()) - timeMilliseconds)>MAX_MILLIS_DRIFT) {
Debug.out.println("DL SEGMENTER: RESETTING TIME: ");
//Debug.out.println("DL SEGMENTER: RESETTING TIME: ");
currentRawChunks[i].setTimeMilliseconds((long) (timeMilliseconds - 1000.*currentRawChunks[i].getRawDataPointer()[0]/this.getSampleRate()));
currentRawChunks[i].setStartSample(startSampleTime-currentRawChunks[i].getRawDataPointer()[0]);
}
@ -690,6 +690,7 @@ public class SegmenterProcess extends PamProcess {
for (int i =0; i<rawData.length; i++) {
rawData[i] = new double[samplesize];
}
}
/**