Updates to deep learning and PAMGuardFX GUI

pom.xml

@@ -309,7 +309,7 @@
 	<dependency>
 		<groupId>io.github.macster110</groupId>
 		<artifactId>jdl4pam</artifactId>
-		<version>0.0.99b</version>
+		<version>0.0.99d</version>
 	</dependency> 
 			
 	<!-- https://mvnrepository.com/artifact/gov.nist.math/jama -->

src/PamController/PamSettingManager.java

@@ -55,16 +55,6 @@ import pamguard.GlobalArguments;
 //import org.w3c.dom.Node;
 //import com.thoughtworks.xstream.XStream;
 
-
-
-
-
-
-
-
-import java.io.StringWriter;
-
-
 //import javax.xml.transform.OutputKeys;
 //import javax.xml.transform.Transformer;
 //import javax.xml.transform.TransformerException;
@@ -73,13 +63,6 @@ import java.io.StringWriter;
 //import javax.xml.transform.stream.StreamResult;
 
 
-
-
-
-
-
-
-
 //import sun.jdbc.odbc.OdbcDef;
 import tipOfTheDay.TipOfTheDayManager;
 //import javax.swing.filechooser.FileFilter;
@@ -90,11 +73,7 @@ import PamController.settings.SettingsNameChanger;
 import PamUtils.PamCalendar;
 import PamUtils.PamFileChooser;
 import PamUtils.PamFileFilter;
-import PamUtils.Splash;
-import PamView.PamGui;
 import PamView.dialog.warn.WarnOnce;
-import amplifier.AmpDialog;
-import amplifier.AmpParameters;
 
 //import PamUtils.PamFileFilter;
 
@@ -172,6 +151,7 @@ public class PamSettingManager {
 	static public final String fileEnd = "psf";
 	static public final String fileEndx = "psfx";
 	static public final String fileEndXML = "psfxml";
+	
 	private static boolean saveAsPSFX = true;
 
 	static public String getCurrentSettingsFileEnd() {
@@ -220,11 +200,12 @@ public class PamSettingManager {
 	/**
 	 * Save settings to a psf file
 	 */
-	static private final int SAVE_PSF = 0x1;
+	static public final int SAVE_PSF = 0x1;
+	
 	/**
 	 * Save settings to database tables (if available).
 	 */
-	static private final int SAVE_DATABASE = 0x2;
+	static public final int SAVE_DATABASE = 0x2;
 
 	/**
 	 * running in remote mode, default normal
@@ -800,7 +781,6 @@ public class PamSettingManager {
 		/*
 		 * then save it to a single XML file
 		 */
-
 		//XML file test
 
 		objectToXMLFile(pamSettingsList,file);

src/dataMap/layoutFX/DataMapPaneFX.java

@@ -178,12 +178,13 @@ public class DataMapPaneFX extends PamBorderPane implements UserDisplayNodeFX {
 	 * Called from ScalePanel when anything 
 	 * to do with scaling changes. 
 	 */
+	@Deprecated
 	public void scaleChanged() {
 		if (scalePane == null || scrollingDataPanel == null) {
 			return;
 		}
 		scalePane.getParams(dataMapControl.dataMapParameters);
-		scrollingDataPanel.scaleChange();
+		//scrollingDataPanel.scaleChange();
 	}
 
 	@Override

src/dataMap/layoutFX/DataStreamPaneFX.java

@@ -1,6 +1,5 @@
 package dataMap.layoutFX;
 
-import java.awt.Insets;
 import java.util.Arrays;
 import java.util.Iterator;
 
@@ -159,11 +158,12 @@ public class DataStreamPaneFX extends PamBorderPane {
 		
 		showButton = new PamButton();
 		showButton.setStyle("-fx-padding: 0 10 0 10; -fx-border-radius: 0 0 0 0; -fx-background-radius: 0 0 0 0;");
-		showButton.setGraphic(PamGlyphDude.createPamIcon("mdi2c-chevron-down", 18));
 		showButton.setOnAction((action)->{
 			this.setCollapsed(!this.isCollapsed()); 
+			setButtonGraphic();
 		});
-		
+		 setButtonGraphic();
+		 
 		pane.setLeft(showButton);
 		
 		pane.setPrefHeight(PREF_HEADER_HEIGHT);
@@ -172,6 +172,18 @@ public class DataStreamPaneFX extends PamBorderPane {
 	}
 	
 	
+	
+	
+	private void setButtonGraphic() {
+		if (this.isCollapsed()) {
+			showButton.setGraphic(PamGlyphDude.createPamIcon("mdi2c-chevron-down", (int) PREF_HEADER_HEIGHT-2));
+		}
+		else {
+			showButton.setGraphic(PamGlyphDude.createPamIcon("mdi2c-chevron-up", (int) PREF_HEADER_HEIGHT-2));
+		}
+		
+	}
+
 	/**
 	 * @return the dataGraph
 	 */

src/dataMap/layoutFX/ScrollingDataPaneFX.java

@@ -223,6 +223,9 @@ public class ScrollingDataPaneFX extends PamBorderPane {
 		timeScrollBar.getTextBox().setPrefWidth(100);
 
 		timeScrollBar.setPrefHeight(50);
+		
+		//set this to zero just so that we know if it has been set or not
+		timeScrollBar.setVisibleAmount(0.);
 
 		holder.setCenter(timeScrollBar);
 		holder.setBottom(timeLabelPane);
@@ -388,7 +391,12 @@ public class ScrollingDataPaneFX extends PamBorderPane {
 		timeScrollBar.setMaxVal(Math.max(dataSeconds, screenSeconds)*1000L);
 		timeScrollBar.setBlockIncrement(Math.max(1, screenSeconds * 4/5));
 		//			timeScrollBar.setUnitIncrement(Math.max(1, screenSeconds / 20));
-		timeScrollBar.setVisibleAmount(screenSeconds*1000L);
+		
+		//there might already have a visible amount in which case we do not wish to change. This is a bit of a hack 
+		//to figure out whether the visible amount has already been set. 
+		if (timeScrollBar.getVisibleAmount()==0) {
+			timeScrollBar.setVisibleAmount(screenSeconds*1000L);
+		}
 		timeScrollBar.setCurrentValue(currentPos);
 		
 		//now paint the canvas to show the data. 
@@ -479,13 +487,13 @@ public class ScrollingDataPaneFX extends PamBorderPane {
 		return dataMapPaneFX;
 	}
 
-	int lastHScaleChoice=-1; 
-	public void scaleChange() {
-		if (lastHScaleChoice != dataMapControl.dataMapParameters.hScaleChoice) {
-			lastHScaleChoice = dataMapControl.dataMapParameters.hScaleChoice;
-			setupScrollBar();
-		}
-		this.notifyScrollChange();
-	}
+//	int lastHScaleChoice=-1; 
+//	public void scaleChange() {
+//		if (lastHScaleChoice != dataMapControl.dataMapParameters.hScaleChoice) {
+//			lastHScaleChoice = dataMapControl.dataMapParameters.hScaleChoice;
+//			setupScrollBar();
+//		}
+//		this.notifyScrollChange();
+//	}
 
 }

src/pamViewFX/PamGuiFX.java

@@ -476,9 +476,11 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 			PamHBox playControls=new PamHBox();
 			recordButton=new PamButton();
 //			recordButton.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.CIRCLE, Color.LIMEGREEN, PamGuiManagerFX.iconSize));
-			recordButton.setGraphic(PamGlyphDude.createPamIcon("mdi2c-checkbox-blank-circle", Color.LIMEGREEN, PamGuiManagerFX.iconSize));
+			recordButton.setGraphic(PamGlyphDude.createPamIcon("mdi2r-record-circle", Color.RED, PamGuiManagerFX.iconSize));
 			recordButton.getStyleClass().add("transparent-button");
-			recordButton.setStyle(" -fx-background-radius: 50;");
+			
+			//recordButton.setStyle(" -fx-background-radius: 50;");
+			
 			recordButton.setOnAction((action)->{
 				if (PamController.getInstance().getPamStatus()==PamController.PAM_RUNNING){
 					PamController.getInstance().pamStop();
@@ -487,6 +489,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 				else {
 					PamController.getInstance().pamStart();
 					pamGuiManagerFX.setPamRunning(true);
+					
 				}
 			});
 
@@ -494,7 +497,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 //			playButton.setGraphic(PamGlyphDude.createPamGlyph(FontAwesomeIcon.PLAY, Color.BLACK, PamGuiManagerFX.iconSize));
 			playButton.setGraphic(PamGlyphDude.createPamIcon("mdi2p-play", Color.BLACK, PamGuiManagerFX.iconSize));
 			playButton.getStyleClass().add("transparent-button");
-			playButton.setStyle(" -fx-background-radius: 50;");
+			//playButton.setStyle(" -fx-background-radius: 50;");
 			playButton.setOnAction((action)->{
 				//TODO
 				//start pamguard
@@ -505,7 +508,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 			playControls.getChildren().addAll(recordButton,playButton);
 			playControls.setSpacing(10);
 			playControls.setPadding(new Insets(0,10,0,20));
-			playControls.getStyleClass().add("pane-opaque");
+//			playControls.getStyleClass().add("pane-opaque");
 			playControls.setPrefHeight(prefHeight);
 			playControls.setAlignment(Pos.CENTER);
 			
@@ -514,7 +517,7 @@ public class PamGuiFX extends StackPane implements PamViewInterface {
 			rightHBox.setAlignment(Pos.CENTER_LEFT);
 			rightHBox.setPadding(new Insets(0,10,0,20));
 			rightHBox.setSpacing(5);
-			rightHBox.getStyleClass().add("pane-opaque");
+//			rightHBox.getStyleClass().add("pane-opaque");
 			
 			editWindows=new ToggleSwitch("Resize"); 
 			//HACK,

src/pamViewFX/PamLauncherFXApp.java

@@ -0,0 +1,24 @@
+package pamViewFX;
+
+import javafx.application.Application;
+import javafx.scene.Scene;
+import javafx.scene.layout.StackPane;
+import javafx.stage.Stage;
+
+public class PamLauncherFXApp extends Application {
+	
+    public static void main(String[] args) {
+        launch(args);
+    }
+    
+    @Override
+    public void start(Stage primaryStage) {
+        primaryStage.setTitle("PAMGuard Launcher");
+      
+        
+        StackPane root = new StackPane();
+        root.getChildren().add(new PamLauncherPane());
+        primaryStage.setScene(new Scene(root, 500, 250));
+        primaryStage.show();
+    }
+}

src/pamViewFX/PamLauncherFXAppLauncher.java

@@ -0,0 +1,9 @@
+package pamViewFX;
+
+public class PamLauncherFXAppLauncher {
+	
+	public static void main(String[] args) {
+		PamLauncherFXApp.main(args);
+	}
+
+}

src/pamViewFX/PamLauncherPane.java

@@ -0,0 +1,27 @@
+package pamViewFX;
+
+import javafx.scene.image.Image;
+import javafx.scene.image.ImageView;
+import pamViewFX.fxNodes.PamBorderPane;
+import pamViewFX.fxNodes.PamButton;
+
+/**
+ * Shows a launcher pane which allows a user to open a real time or viewer configuration. 
+ */
+public class PamLauncherPane extends PamBorderPane {
+	
+	public PamLauncherPane() {
+		
+		PamButton buttonNormal = new PamButton("Real time");
+		buttonNormal.setGraphic(buttonNormal);
+		
+		 Image img = new Image("./src/Resources/pamguardIcon.png");
+	      ImageView view = new ImageView(img);
+	      
+	      buttonNormal.setGraphic(view);
+		
+		this.setLeft(buttonNormal);
+		
+	}
+
+}

src/pamViewFX/PamSettingsMenuPane.java

@@ -2,6 +2,7 @@ package pamViewFX;
 
 import generalDatabase.DBControlUnit;
 
+import java.io.File;
 import java.util.Optional;
 
 import binaryFileStorage.BinaryStore;
@@ -16,7 +17,8 @@ import PamController.StorageParameters;
 import PamController.soundMedium.GlobalMedium;
 import PamController.soundMedium.GlobalMedium.SoundMedium;
 import PamModel.PamModuleInfo;
-import PamView.dialog.warn.WarnOnce;
+import PamUtils.PamFileFilter;
+import pamViewFX.fxGlyphs.PamGlyphDude;
 import pamViewFX.fxNodes.PamButton;
 import pamViewFX.fxNodes.PamVBox;
 import pamViewFX.fxNodes.PamHBox;
@@ -34,10 +36,13 @@ import javafx.scene.control.MenuButton;
 import javafx.scene.control.MenuItem;
 import javafx.scene.control.Separator;
 import javafx.scene.text.TextAlignment;
+import javafx.stage.FileChooser;
+import javafx.stage.FileChooser.ExtensionFilter;
 import javafx.scene.control.ToggleButton;
 import javafx.scene.control.ToggleGroup;
 import javafx.scene.control.Tooltip;
 import javafx.scene.layout.Priority;
+import javafx.scene.paint.Color;
 
 /**
  * Pane which holds settings menu. All primary settings are accessed from this pane which sits in a hiding pane to the right 
@@ -81,13 +86,16 @@ public class PamSettingsMenuPane extends PamVBox {
 			PamSettingManager.getInstance().saveSettings(null);
 		});
 		styleButton(saveConfig);
+		saveConfig.setGraphic(PamGlyphDude.createPamIcon("mdi2c-content-save-outline", 
+				PamGuiManagerFX.iconSize));
 		
 		PamButton saveConfigAs=new PamButton("Save as..."); 
 		saveConfigAs.setOnAction((action)->{
-			PamSettingManager.getInstance().saveSettingsAs(null);
+			saveSettingsAs();
 		});
 		styleButton(saveConfigAs);
-		
+		saveConfigAs.setGraphic(PamGlyphDude.createPamIcon("mdi2c-content-save-move-outline", 
+			 PamGuiManagerFX.iconSize));
 		
 		//Air or water mode
 		ToggleButton toggleButton1 = new ToggleButton("Water");
@@ -97,6 +105,7 @@ public class PamSettingsMenuPane extends PamVBox {
 			if (PamController.getInstance().getGlobalMediumManager().getGlobalMediumParameters().currentMedium==SoundMedium.Water) return; //do nothing. 
 				PamController.getInstance().getGlobalMediumManager().setCurrentMedium(SoundMedium.Water);
 		});
+		
 
 	    ToggleButton toggleButton2 = new ToggleButton("Air");
 	    toggleButton2.setPrefWidth(60);
@@ -114,6 +123,8 @@ public class PamSettingsMenuPane extends PamVBox {
 	    Label mediumLabel = new Label("Sound Medium"); 
 	    mediumLabel.setAlignment(Pos.CENTER_LEFT);
 	    mediumLabel.setPadding(new Insets(0,0,0,15));
+	    mediumLabel.setGraphic(PamGlyphDude.createPamIcon("mdi2w-waves", 
+			 PamGuiManagerFX.iconSize));
 		//styleButton(mediumLabel);
 
 	    
@@ -132,9 +143,13 @@ public class PamSettingsMenuPane extends PamVBox {
 		
 		PamButton generalSettings=new PamButton("General Settings..."); 
 		styleButton(generalSettings);
+		generalSettings.setGraphic(PamGlyphDude.createPamIcon("mdi2c-cog", 
+					 PamGuiManagerFX.iconSize));
 		
 		MenuButton settings=new MenuButton("Module Settings"); 
 		settings.setPopupSide(Side.RIGHT);
+		settings.setGraphic(PamGlyphDude.createPamIcon("mdi2c-cogs", 
+				 PamGuiManagerFX.iconSize));
 //		settings.setStyle("-fx-background-radius: 0;"
 //				+ " -fx-border-color: transparent; -fx-padding: 0 0 0 0;");
 		
@@ -173,6 +188,8 @@ public class PamSettingsMenuPane extends PamVBox {
 			}
 		}); 
 		styleButton(database);
+		database.setGraphic(PamGlyphDude.createPamIcon("mdi2d-database", 
+				 PamGuiManagerFX.iconSize));
 
 		PamButton binaryStorage=new PamButton("Binary Storage..."); 
 		binaryStorage.setOnAction((action)->{
@@ -193,6 +210,8 @@ public class PamSettingsMenuPane extends PamVBox {
 			}
 		}); 
 		styleButton(binaryStorage);
+		binaryStorage.setGraphic(PamGlyphDude.createPamIcon("mdi2f-file-table", 
+				 PamGuiManagerFX.iconSize));
 
 		PamButton storageManager=new PamButton("Storage Manager..."); 
 		storageManager.setOnAction((action)->{
@@ -204,24 +223,35 @@ public class PamSettingsMenuPane extends PamVBox {
 			}
 		});
 		styleButton(storageManager);
+		storageManager.setGraphic(PamGlyphDude.createPamIcon("mdi2d-database-cog", 
+				 PamGuiManagerFX.iconSize));		
 		
 		PamButton help=new PamButton("Help...");
 		styleButton(help);
+		help.setGraphic(PamGlyphDude.createPamIcon("mdi2h-help-circle-outline", 
+				 PamGuiManagerFX.iconSize));	
 		
 		PamButton about=new PamButton("About..."); 
 		styleButton(about);
-		
+		about.setGraphic(PamGlyphDude.createPamIcon("mdi2i-information-outline", 
+				 PamGuiManagerFX.iconSize));
 //		PamButton tip=new PamButton("Tip of the day..."); 
 //		styleButton(tip);
 		
 		PamButton website=new PamButton("Website"); 
 		styleButton(website);
+		website.setGraphic(PamGlyphDude.createPamIcon("mdi2e-earth", 
+				 PamGuiManagerFX.iconSize));
 		
 		PamButton contact=new PamButton("Found a bug?"); 
 		styleButton(contact);
+		contact.setGraphic(PamGlyphDude.createPamIcon("mdi2b-bug", 
+				 PamGuiManagerFX.iconSize));
 		
 		PamButton checkForUpdates=new PamButton("Check for updates"); 
 		styleButton(checkForUpdates);
+		checkForUpdates.setGraphic(PamGlyphDude.createPamIcon("mdi2r-refresh", 
+				 PamGuiManagerFX.iconSize));
 		
 		this.getChildren().addAll(settingsLabel,saveConfig,saveConfigAs, new Separator(),  mediumToggleBox, generalSettings, settings, new Separator(), 
 				storageManager, database, binaryStorage, new Separator(), help, checkForUpdates, website, contact, about);
@@ -268,4 +298,55 @@ public class PamSettingsMenuPane extends PamVBox {
 		}
 	}
 	
+	
+	/**
+	 * Save settings to a new psf file.
+	 * @param frame parent frame for dialog.
+	 */
+	public void saveSettingsAs() {
+		/*
+		 * get a new file name, set that as the current file
+		 * then write all settings to it.
+		 */
+		File file = null;
+		String currentfileName  = PamSettingManager.getInstance().getSettingsFileName();
+		if (currentfileName != null) {
+			file =new File(currentfileName);
+		}
+		
+		FileChooser fileChooser = new FileChooser();
+		 fileChooser.setTitle("Open Resource File");
+		 fileChooser.getExtensionFilters().addAll(
+		         new ExtensionFilter("PAMGuard settings files", "*.xml", "*.psfx"));
+		 if (currentfileName!=null) {
+			 fileChooser.setInitialDirectory(file);
+		 }
+		 
+		 File selectedFile = fileChooser.showOpenDialog(this.getScene().getWindow());
+		 
+		 if (selectedFile == null) {
+		    return;
+		 }
+		 
+		 selectedFile = PamFileFilter.checkFileEnd(selectedFile, PamSettingManager.getCurrentSettingsFileEnd(), true);
+
+
+		System.out.println("Saving settings to file " + selectedFile.getAbsolutePath());
+
+		// Insert the new file into the top of the recent psf file list.  Also check
+		// if we are running remotely, which probably means the user double-clicked on
+		// a psf to start Pamguard.  In that case, change the remotePSF pointer to
+		// the new file as well
+		PamSettingManager.getInstance().setDefaultFile(selectedFile.getAbsolutePath());
+		
+		if (PamSettingManager.remote_psf != null) {
+			PamSettingManager.remote_psf = selectedFile.getAbsolutePath();
+		}
+
+		PamSettingManager.getInstance().saveSettings(PamSettingManager.SAVE_PSF);
+
+		PamController.getInstance().getGuiFrameManager().sortFrameTitles();
+
+	}
+	
 }

src/pamguard/PAMGuard_sqlite.java

@@ -1,39 +0,0 @@
-package pamguard;
-
-import java.sql.Connection;
-import java.sql.SQLException;
-
-import org.sqlite.SQLiteConfig;
-
-import generalDatabase.sqlite.SqliteSQLTypes;
-
-public class PAMGuard_sqlite {
-	
-	public static void main(String[] args) {
-		
-		String dbName = "/Users/jdjm/Desktop/section2_cpod/hyskeir_pamguard.sqlite3";
-		/*
-		 * Don't use the driver manager, but open from the built in command in
-		 * SQLiteConfig. This will then correctly set the dateformat of the database. 
-		 */
-		SQLiteConfig config = new SQLiteConfig();
-		config.setSharedCache(true);
-		config.enableRecursiveTriggers(true);
-		config.enableLoadExtension(true);
-		config.setDateClass(SqliteSQLTypes.dateClass.getValue());
-		config.setDateStringFormat(SQLiteConfig.DEFAULT_DATE_STRING_FORMAT);
-
-		Connection con = null;
-		try {
-			con = config.createConnection("jdbc:sqlite:" + dbName);
-			con.setAutoCommit(false);
-		} catch (SQLException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-		
-		System.out.println("Connection: " + con);
-		
-	}
-
-}

src/test/rawDeepLearningClassifier/ClickDLTest.java

@@ -10,10 +10,7 @@ import org.jamdev.jdl4pam.transforms.SimpleTransformParams;
 import org.jamdev.jdl4pam.transforms.DLTransform.DLTransformType;
 import org.junit.jupiter.api.Test;
 
-import PamDetection.RawDataUnit;
 import PamUtils.PamArrayUtils;
-import PamguardMVC.RawDataHolder;
-import matchedTemplateClassifer.MatchTemplate;
 import rawDeepLearningClassifier.dlClassification.genericModel.GenericModelParams;
 import rawDeepLearningClassifier.dlClassification.genericModel.GenericModelWorker;
 import rawDeepLearningClassifier.dlClassification.genericModel.StandardPrediction;
@@ -25,7 +22,7 @@ import us.hebi.matlab.mat.types.Struct;
 
 public class ClickDLTest {
 
-	
+
 	@Test
 	public void clickDLTest() {
 		
@@ -39,7 +36,6 @@ public class ClickDLTest {
 
 		Path path = Paths.get(relModelPath);
 
-
 		GenericModelWorker genericModelWorker = new GenericModelWorker(); 
 
 		GenericModelParams genericModelParams = new GenericModelParams(); 
@@ -54,7 +50,6 @@ public class ClickDLTest {
 		genericModelParams.dlTransfromParams = dlTransformParamsArr;
 		genericModelParams.dlTransfroms = DLTransformsFactory.makeDLTransforms((ArrayList<DLTransfromParams>)genericModelParams.dlTransfromParams); 
 		
-		
 		//create the clicks. 
 		path = Paths.get(clicksPath);
 		ArrayList<GroupedRawData> clicks = importClicks(path.toAbsolutePath().normalize().toString(),  SAMPLE_RATE); 

src/test/resources/rawDeepLearningClassifier/Generic/risso_click/ReadMe.rtf

@@ -0,0 +1,9 @@
+{\rtf1\ansi\ansicpg1252\cocoartf2761
+\cocoatextscaling0\cocoaplatform0{\fonttbl\f0\fnil\fcharset0 Menlo-Regular;}
+{\colortbl;\red255\green255\blue255;\red0\green0\blue0;\red255\green255\blue255;}
+{\*\expandedcolortbl;;\cssrgb\c0\c0\c0;\cssrgb\c100000\c100000\c99985\c0;}
+\paperw11900\paperh16840\margl1440\margr1440\vieww11220\viewh8100\viewkind0
+\deftab720
+\pard\pardeftab720\partightenfactor0
+
+\f0\fs24 \cf2 \cb3 clickwave.wav is a Rissos dolphin click with a prediction of 0.8221 for channel 0 and 0.9631 for channel 1. }