Merge branch 'main' into main

src/generalDatabase/SQLLogging.java

@@ -2000,6 +2000,10 @@ public abstract class SQLLogging {
 				}
 				PamSubtableData subtableData = new PamSubtableData();
 				long utc = SQLTypes.millisFromTimeStamp(subtableTableDef.getTimeStampItem().getValue());
+				if (utc % 1000 == 0) {
+					int millis = subtableTableDef.getTimeStampMillis().getIntegerValue();
+					utc += millis;
+				}
 				subtableData.setChildUTC(utc);
 				subtableData.setParentID(subtableTableDef.getParentID().getIntegerValue());
 				subtableData.setParentUID(subtableTableDef.getParentUID().getLongValue());

src/generalDatabase/UTCTimestamp.java

@@ -0,0 +1,30 @@
+package generalDatabase;
+
+import java.sql.Timestamp;
+import java.time.LocalDateTime;
+
+/**
+ * Override standard Timestamp class and stop it making UTC corrections as it writes to database
+ * @author dg50
+ *
+ */
+public class UTCTimestamp extends Timestamp {
+
+	private static final long serialVersionUID = 1L;
+
+	public UTCTimestamp(long time) {
+		super(time);
+		// TODO Auto-generated constructor stub
+	}
+
+	@Override
+	public long getTime() {
+		return super.getTime();
+	}
+
+	@Override
+	public LocalDateTime toLocalDateTime() {
+		return super.toLocalDateTime();
+	}
+
+}

src/generalDatabase/sqlite/SqliteSQLTypes.java

@@ -44,6 +44,31 @@ public class SqliteSQLTypes extends SQLTypes {
 		return super.systemSqlType(sqlType);
 	}
 	
+	@Override
+	public Object getTimeStamp(Long timeMillis) {
+		/**
+		 * This has just got nasty WRT time zones. 
+		 * When the TimeStamp is written to database it uses the default time zone correction, which of course 
+		 * I don't want since I only do UTC. I was therefore subtracting this off before creating the ts 
+		 * so that it all worked fine when it was added back on again. 
+		 * This was fine for many years until someone processed data from exactly when the clocks went 
+		 * forward in the spring. Because the data were just after the clocks going forward, it took off
+		 * an hour, then failed to add it back on again since the time was now before daylight saving. 
+		 * Amazed this has never happened before. Well done G and E ! I can fix it by setting the 
+		 * default time zone to UTC when PAMGuard starts, but note that all future references to local time
+		 * will then be UTC. If I try to change it temporarily it doesn't help since the Timestamp always 
+		 * goes to the default, so it needs to be on UTC at the moment data are written to the database, not
+		 * just in this function. 
+		 * 
+		 * Seems that for SQLite we can get away with a string, for MySQL we need a TimeStamp object still 
+		 */
+//		return timeMillis;
+		if (timeMillis == null) {
+			return null;
+		}
+		return PamCalendar.formatDBDateTime(timeMillis, true);
+	}
+	
 	@Override
 	public String formatDBDateTimeQueryString(long timeMilliseconds) {
 		switch (dateClass) {

src/whistleClassifier/WhistleClasificationDataBlock.java

@@ -2,12 +2,25 @@ package whistleClassifier;
 
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamProcess;
+import PamguardMVC.dataSelector.DataSelectorCreator;
+import whistleClassifier.dataselect.WslClsDataSelectCreator;
 
 public class WhistleClasificationDataBlock extends PamDataBlock<WhistleClassificationDataUnit> {
+	
+	private WslClsDataSelectCreator dataSelectCreator;
+	private WhistleClassifierControl wslClassifierControl;
 
-	public WhistleClasificationDataBlock(PamProcess parentProcess, int channelMap) {
+	public WhistleClasificationDataBlock(WhistleClassifierControl wslClassifierControl, PamProcess parentProcess, int channelMap) {
 		super(WhistleClassificationDataUnit.class, "Whistle Classification", parentProcess, channelMap);
+		this.wslClassifierControl = wslClassifierControl;
+	}
 
+	@Override
+	public DataSelectorCreator getDataSelectCreator() {
+		if (dataSelectCreator == null) {
+			dataSelectCreator = new WslClsDataSelectCreator(wslClassifierControl, this);
+		}
+		return dataSelectCreator;
 	}
 
 }

src/whistleClassifier/WhistleClassificationDataUnit.java

@@ -1,9 +1,10 @@
 package whistleClassifier;
 
+import PamDetection.PamDetection;
 import PamguardMVC.AcousticDataUnit;
 import PamguardMVC.PamDataUnit;
 
-public class WhistleClassificationDataUnit extends PamDataUnit<PamDataUnit,PamDataUnit> implements AcousticDataUnit {
+public class WhistleClassificationDataUnit extends PamDataUnit<PamDataUnit,PamDataUnit> implements AcousticDataUnit, PamDetection {
 	
 	private double[] speciesLogLikelihoods;
 	

src/whistleClassifier/WhistleClassifierProcess.java

@@ -65,7 +65,7 @@ public class WhistleClassifierProcess extends PamProcess {
 
 		this.whistleClassifierControl  = whistleClassifierControl;
 
-		whistleClasificationDataBlock = new WhistleClasificationDataBlock(this, 3);
+		whistleClasificationDataBlock = new WhistleClasificationDataBlock(whistleClassifierControl, this, 3);
 
 		addOutputDataBlock(whistleClasificationDataBlock);
 

src/whistleClassifier/dataselect/SppClsSelectParams.java

@@ -0,0 +1,35 @@
+package whistleClassifier.dataselect;
+
+import java.io.Serializable;
+
+/**
+ * Data selector params for a single species. 
+ * @author dg50
+ *
+ */
+public class SppClsSelectParams implements Serializable, Cloneable {
+
+	private static final long serialVersionUID = 1L;
+	
+	public String name;
+	public boolean selected;
+	public double minScore;
+	
+	public SppClsSelectParams(String name, boolean selected, double minScore) {
+		super();
+		this.name = name;
+		this.selected = selected;
+		this.minScore = minScore;
+	}
+
+	@Override
+	protected SppClsSelectParams clone() {
+		try {
+			return (SppClsSelectParams) super.clone();
+		} catch (CloneNotSupportedException e) {
+			e.printStackTrace();
+			return null;
+		}
+	}
+
+}

src/whistleClassifier/dataselect/WslClsDataSelectCreator.java

@@ -0,0 +1,31 @@
+package whistleClassifier.dataselect;
+
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.dataSelector.DataSelectParams;
+import PamguardMVC.dataSelector.DataSelector;
+import PamguardMVC.dataSelector.DataSelectorCreator;
+import whistleClassifier.WhistleClasificationDataBlock;
+import whistleClassifier.WhistleClassifierControl;
+
+public class WslClsDataSelectCreator extends DataSelectorCreator {
+
+	private WhistleClassifierControl wslClassifierControl;
+	private WhistleClasificationDataBlock wslClassifierDataBlock;
+
+	public WslClsDataSelectCreator(WhistleClassifierControl wslClassifierControl, WhistleClasificationDataBlock pamDataBlock) {
+		super(pamDataBlock);
+		this.wslClassifierControl = wslClassifierControl;
+		this.wslClassifierDataBlock = pamDataBlock;
+	}
+
+	@Override
+	public DataSelector createDataSelector(String selectorName, boolean allowScores, String selectorType) {
+		return new WslClsDataSelector(wslClassifierControl, wslClassifierDataBlock, selectorName, allowScores);
+	}
+
+	@Override
+	public DataSelectParams createNewParams(String name) {
+		return new WslClsSelectorParams();
+	}
+
+}

src/whistleClassifier/dataselect/WslClsDataSelector.java

@@ -0,0 +1,70 @@
+package whistleClassifier.dataselect;
+
+import PamView.dialog.PamDialogPanel;
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.PamDataUnit;
+import PamguardMVC.dataSelector.DataSelectParams;
+import PamguardMVC.dataSelector.DataSelector;
+import pamViewFX.fxSettingsPanes.DynamicSettingsPane;
+import whistleClassifier.WhistleClassificationDataUnit;
+import whistleClassifier.WhistleClassifierControl;
+
+/**
+ * Species selector for whistle classifier. Currently only does yes / no, will 
+ * maybe one day be extended to allow scores as well. 
+ * @author dg50
+ *
+ */
+public class WslClsDataSelector extends DataSelector {
+
+	private WhistleClassifierControl wslClassifierControl;
+	
+	private WslClsSelectorParams wcsParams = new WslClsSelectorParams();
+
+	public WslClsDataSelector(WhistleClassifierControl wslClassifierControl, PamDataBlock pamDataBlock, String selectorName, boolean allowScores) {
+		super(pamDataBlock, selectorName, allowScores);
+		this.wslClassifierControl = wslClassifierControl;
+	}
+	
+
+	@Override
+	public void setParams(DataSelectParams dataSelectParams) {
+		if (dataSelectParams instanceof WslClsSelectorParams) {
+			wcsParams = (WslClsSelectorParams) dataSelectParams;
+		}
+	}
+
+	@Override
+	public WslClsSelectorParams getParams() {
+		return wcsParams;
+	}
+
+	@Override
+	public PamDialogPanel getDialogPanel() {
+		return new WslClsDialogPanel(wslClassifierControl, this);
+	}
+
+	@Override
+	public DynamicSettingsPane<Boolean> getDialogPaneFX() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public double scoreData(PamDataUnit pamDataUnit) {
+		WhistleClassificationDataUnit wcdu = (WhistleClassificationDataUnit) pamDataUnit;
+		String species = wcdu.getSpecies();
+//		score = wcdu.get
+		SppClsSelectParams sppParams = wcsParams.getSppParams(species);
+//		if ()
+//		if (sppParams.selected == false) {
+//			return 0;
+//		}
+//		if (isAllowScores()) {
+//			return sppP
+//		}
+//		wslClassifierControl.getWhistleClassificationParameters().
+		return sppParams.selected ? 1 : 0;
+	}
+
+}

src/whistleClassifier/dataselect/WslClsDialogPanel.java

@@ -0,0 +1,132 @@
+package whistleClassifier.dataselect;
+
+import java.awt.BorderLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+
+import javax.swing.JCheckBox;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.border.TitledBorder;
+
+import PamView.dialog.PamDialog;
+import PamView.dialog.PamDialogPanel;
+import PamView.dialog.PamGridBagContraints;
+import PamguardMVC.dataSelector.DataSelectParams;
+import whistleClassifier.FragmentClassifierParams;
+import whistleClassifier.WhistleClassificationParameters;
+import whistleClassifier.WhistleClassifierControl;
+
+/**
+ * dialog for whistle classifier data selector
+ * @author dg50
+ *
+ */
+public class WslClsDialogPanel implements PamDialogPanel {
+
+	private WhistleClassifierControl wslClassifierControl;
+	private WslClsDataSelector wslClsDataSelector;
+	
+	private JPanel mainPanel;
+	
+	private JPanel sppPanel;
+	
+	private JCheckBox[] speciesBoxes;
+	
+	private JTextField[] speciesScores;
+
+	public WslClsDialogPanel(WhistleClassifierControl wslClassifierControl, WslClsDataSelector wslClsDataSelector) {
+		this.wslClassifierControl = wslClassifierControl;
+		this.wslClsDataSelector = wslClsDataSelector;
+		
+		this.mainPanel = new JPanel(new BorderLayout());
+		mainPanel.setBorder(new TitledBorder("Select species"));
+		
+		sppPanel = new JPanel(new GridBagLayout());
+		mainPanel.add(BorderLayout.CENTER, sppPanel);
+	}
+
+	@Override
+	public JComponent getDialogComponent() {
+		return mainPanel;
+	}
+
+	@Override
+	public void setParams() {
+		WhistleClassificationParameters wslParams = wslClassifierControl.getWhistleClassificationParameters();
+		WslClsSelectorParams selParams = wslClsDataSelector.getParams();
+		if (wslParams == null) {
+			return;
+		}
+		FragmentClassifierParams fragParams = wslParams.fragmentClassifierParams;
+		if (fragParams == null) {
+			return;
+		}
+		fillSppPanel(wslParams, selParams);
+	}
+
+	private void fillSppPanel(WhistleClassificationParameters wslParams, WslClsSelectorParams selParams) {
+		boolean allowScores = wslClsDataSelector.isAllowScores();
+		sppPanel.removeAll();
+		String[] sppList = wslParams.fragmentClassifierParams.getSpeciesList();
+		if (sppList == null) {
+			return;
+		}
+		int nSpp = sppList.length;
+		speciesBoxes = new JCheckBox[nSpp];
+		speciesScores = new JTextField[nSpp];
+		GridBagConstraints c = new PamGridBagContraints();
+		sppPanel.add(new JLabel("Species", JLabel.CENTER), c);
+		if (allowScores) {
+			c.gridx++;
+			JLabel lab = new JLabel(" Min score ", JLabel.CENTER);
+			lab.setToolTipText("Minimum classification score (between 0 and 1)");
+			sppPanel.add(lab , c);
+		}
+		for (int i = 0; i < nSpp; i++) {
+			speciesBoxes[i] = new JCheckBox(sppList[i]);
+			speciesScores[i] = new JTextField(3);
+			c.gridx = 0;
+			c.gridy++;
+			sppPanel.add(speciesBoxes[i], c);
+			if (allowScores) {
+				c.gridx++;
+				sppPanel.add(speciesScores[i], c);
+			}
+			SppClsSelectParams sppSel = selParams.getSppParams(sppList[i]);
+			speciesBoxes[i].setSelected(sppSel.selected);
+			speciesScores[i].setText(String.format("%3.2f", sppSel.minScore));
+		}
+	}
+
+	@Override
+	public boolean getParams() {
+		WslClsSelectorParams selParams = wslClsDataSelector.getParams();
+		boolean allowScores = wslClsDataSelector.isAllowScores();
+		if (speciesBoxes == null) {
+			return false;
+		}
+		int nSpp = speciesBoxes.length;
+		for (int i = 0; i < nSpp; i++) {
+			String name = speciesBoxes[i].getText();
+			boolean sel = speciesBoxes[i].isSelected();
+			double score = 0;
+			if (allowScores) {
+				try {
+					score = Double.valueOf(speciesScores[i].getText());
+				}
+				catch (NumberFormatException e) {
+					score = -1;
+				}
+			}
+			if (score < 0 || score > 1) {
+				return PamDialog.showWarning(null, "Invalid score value for " + name, "Score values must be betwween 0 and 1");
+			}
+			selParams.setSppParams(name, new SppClsSelectParams(name, sel, score));
+		}
+		return true;
+	}
+
+}

src/whistleClassifier/dataselect/WslClsSelectorParams.java

@@ -0,0 +1,46 @@
+package whistleClassifier.dataselect;
+
+import java.io.Serializable;
+import java.util.HashMap;
+
+import PamguardMVC.dataSelector.DataSelectParams;
+
+public class WslClsSelectorParams extends DataSelectParams implements Cloneable, Serializable {
+
+	private static final long serialVersionUID = 1L;
+	
+	private HashMap<String, SppClsSelectParams> sppParamsTable = new HashMap<>();
+
+	public WslClsSelectorParams() {
+		// TODO Auto-generated constructor stub
+	}
+
+	@Override
+	public WslClsSelectorParams clone()  {
+		try {
+			return (WslClsSelectorParams) super.clone();
+		} catch (CloneNotSupportedException e) {
+			e.printStackTrace();
+			return null;
+		}
+	}
+	
+	public void setSppParams(String sppName, SppClsSelectParams params) {
+		if (sppParamsTable == null) {
+			sppParamsTable = new HashMap<String, SppClsSelectParams>();
+		}
+		sppParamsTable.put(sppName, params);
+	}
+	
+	public SppClsSelectParams getSppParams(String sppName) {
+		if (sppParamsTable == null) {
+			sppParamsTable = new HashMap<String, SppClsSelectParams>();
+		}
+		SppClsSelectParams sppParams = sppParamsTable.get(sppName);
+		if (sppParams == null) {
+			sppParams = new SppClsSelectParams(sppName, false, 0);
+		}
+		return sppParams;
+	}
+
+}