Merge pull request #67 from PAMGuard/main

Pull fixes from main

dependency-reduced-pom.xml

@@ -4,7 +4,7 @@
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
   <name>Pamguard Java12+</name>
-  <version>2.02.10</version>
+  <version>2.02.10b</version>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
   <url>www.pamguard.org</url>
   <organization>

pom.xml

@@ -5,7 +5,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.pamguard</groupId>
   <artifactId>Pamguard</artifactId>
-  <version>2.02.10</version>
+  <version>2.02.10b</version>
   <name>Pamguard Java12+</name>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
 	<url>www.pamguard.org</url>
@@ -748,7 +748,7 @@
 		<dependency>
 			<groupId>net.sf.ucanaccess</groupId>
 			<artifactId>ucanaccess</artifactId>
-			<version>4.0.4</version>
+			<version>5.0.1</version>
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/nz.ac.waikato.cms.weka/weka-dev -->

src/Array/HydrophoneDataBlock.java

@@ -53,7 +53,7 @@ public class HydrophoneDataBlock extends PamDataBlock<HydrophoneDataUnit> {
 	 */
 	@Override
 	public int getNumRequiredBeforeLoadTime() {
-		return ArrayManager.getArrayManager().getCurrentArray().getHydrophoneCount();
+		return ArrayManager.getArrayManager().getCurrentArray().getHydrophoneCount()*2;
 	}
 
 

src/Array/HydrophoneProcess.java

@@ -3,6 +3,7 @@ package Array;
 import pamScrollSystem.AbstractScrollManager;
 import PamUtils.PamCalendar;
 import PamView.symbol.StandardSymbolManager;
+import PamguardMVC.PamConstants;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamProcess;
 
@@ -42,7 +43,7 @@ public class HydrophoneProcess extends PamProcess{
 		
 		@Override
 		public void addOutputDataBlock(PamDataBlock outputDataBlock){
-			AbstractScrollManager.getScrollManager().addToSpecialDatablock(outputDataBlock);
+			AbstractScrollManager.getScrollManager().addToSpecialDatablock(outputDataBlock, 60000, 0);
 			super.addOutputDataBlock(outputDataBlock);
 		}
 		

src/PamController/PamControlledUnitSettings.java

@@ -403,4 +403,9 @@ public class PamControlledUnitSettings implements Serializable, ManagedParameter
 		return ps;
 	}
 
+	@Override
+	public String toString() {
+		return String.format("Type %s; Name %s, Data ", getUnitType(), getUnitName()) + getSettings();
+	}
+
 }

src/PamController/PamSettingManager.java

@@ -384,6 +384,8 @@ public class PamSettingManager {
 			boolean[] usedSettings,	PamSettings user) {
 		if (settingsList == null) return null;
 		// go through the list and see if any match this module. Avoid repeats.
+//		String unitName = user.getUnitName();
+//		String unitType = user.getUnitType();
 		for (int i = 0; i < settingsList.size(); i++) {
 			if (usedSettings != null && usedSettings[i]) continue;
 			if (isSettingsUnit(user, settingsList.get(i))) {
@@ -393,6 +395,7 @@ public class PamSettingManager {
 				return settingsList.get(i);
 			}
 		}
+		
 		/*
 		 * To improve complex module loading where settings may be saved by multiple sub-modules, in
 		 * July 2015 many modules which had fixed settings had their settings names and types changed !
@@ -1482,11 +1485,20 @@ public class PamSettingManager {
 		if (settings.getUnitName() == null || settingsUser.getUnitName() == null) return false;
 		if (settings.getUnitType() == null || settingsUser.getUnitType() == null) return false;
 
-
-		if (settings.getUnitName().equals(settingsUser.getUnitName())
-				&& settings.getUnitType().equals(settingsUser.getUnitType())
-				&& settings.versionNo == settingsUser.getSettingsVersion()){
-			return true;
+		/*
+		 *  some of the settings names used in Viewer mode have become too long, notably
+		 *  in some data selectors which are using a datablocks long data name. This 
+		 *  screws things up, so moving to a begins with rather than equals for the name. 
+		 */
+		String name = settingsUser.getUnitName();
+		String type = settingsUser.getUnitType();
+		long version = settingsUser.getSettingsVersion();
+		
+		if (settings.getUnitType().equals(type)
+				&& settings.versionNo == version){
+			if (name.startsWith(settings.getUnitName())) {
+				return true;
+			}
 		}
 
 		return false;

src/PamController/PamguardVersionInfo.java

@@ -31,7 +31,7 @@ public class PamguardVersionInfo {
 	 * Version number, major version.minorversion.sub-release.
 	 * Note: can't go higher than sub-release 'f'
 	 */
-	static public final String version = "2.02.10";
+	static public final String version = "2.02.10b";
 	
 	/**
 	 * Release date

src/PamModel/parametermanager/PamParameterSet.java

@@ -10,7 +10,6 @@ import java.util.Collection;
 import java.util.Hashtable;
 import java.util.List;
 
-import binaryFileStorage.BinaryStoreSettings;
 
 /**
  * Description of the parameters within a class. Primarily holds a list
@@ -51,6 +50,17 @@ public class PamParameterSet {
 		hiddenFields = new ArrayList<>();
 	}
 
+	/**
+	 * Automatically generate a parameter set for a class. Will include all public fields and 
+	 * any private or protected fields for which a getter can be found that has a similar enough name
+	 * @param parentObject class to generate description for. Exception is anything that's listed 
+	 * in the STANDARD_MODIFIER_EXCLUSIONS list (FINAL or STATIC).
+	 * @return Created parameter set. 
+	 */
+	@Deprecated 
+	public static PamParameterSet autoGenerate(Object parentObject) {
+		return autoGenerate(parentObject, ParameterSetType.DETECTOR);
+	}
 	/**
 	 * Automatically generate a parameter set for a class. Will include all public fields and 
 	 * any private or protected fields for which a getter can be found that has a similar enough name

src/PamguardMVC/dataSelector/CompoundParams.java

@@ -19,4 +19,10 @@ public class CompoundParams extends DataSelectParams {
 	public DataSelectParams getSelectorParams(DataSelector dataSelector) {
 		return selectorParams.get(dataSelector.getLongSelectorName());
 	}
+
+	@Override
+	public int getCombinationFlag() {
+		return DATA_SELECT_AND;
+	}
+	
 }

src/PamguardMVC/dataSelector/DataSelectorCreator.java

@@ -200,7 +200,14 @@ public abstract class DataSelectorCreator implements PamSettings {
 			return allSelectors.get(0);
 		}
 		else {
-			return new CompoundDataSelector(pamDataBlock, allSelectors, selectorName, allowScores, selectorType);
+			CompoundDataSelector selector = new CompoundDataSelector(pamDataBlock, allSelectors, selectorName, allowScores, selectorType);
+			// not needed since it get's done after this call anyway. 
+//			DataSelectParams params = dataSelectorSettings.getParams(selectorName);
+//			if (params instanceof CompoundParams) {
+//				selector.setParams(params);
+//			}
+			
+			return selector;
 		}
 	}
 	

src/binaryFileStorage/BinaryOutputStream.java

@@ -505,7 +505,9 @@ public class BinaryOutputStream {
 	 */
 	public synchronized boolean storeData(DataOutputStream outputStream, int objectId, DataUnitBaseData baseData, BinaryObjectData binaryObjectData) {
 		if (lastObjectType == BinaryTypes.MODULE_FOOTER) {
-			System.out.printf("Storing binary object type %d in file %s with no module header\n", objectId, outputStream == null ? null : outputStream.toString());
+			System.out.printf("Storing binary object at %s from %s in file %s with no module header\n", 
+					PamCalendar.formatDBDateTime(baseData.getTimeMilliseconds()),
+					parentDataBlock.getDataName(), outputStream == null ? null : outputStream.toString());
 		}
 		byte[] data = binaryObjectData.getData();
 		int objectLength = binaryObjectData.getDataLength();

src/clickDetector/ClickDisplayManager.java

@@ -407,8 +407,13 @@ public class ClickDisplayManager implements PamSettings {
 
 	public Serializable getSettingsReference() {
 		cdmp.countEverything(this);
+		cdmp.saveDisplayLocations(getWindowList());
 		return cdmp;
 	}
+	
+	public void restoreWindowSizes() {
+		cdmp.restoreWindowSizes(getWindowList());
+	}
 
 	public int countDisplays(Class displayType) {
 		int count = 0;

src/clickDetector/ClickDisplayManagerParameters2.java

@@ -1,8 +1,13 @@
 package clickDetector;
 
+import java.awt.Dimension;
+import java.awt.Point;
+import java.awt.Rectangle;
 import java.io.Serializable;
 import java.lang.reflect.Field;
+import java.util.ArrayList;
 
+import Layout.PamInternalFrame;
 import clickDetector.IDI_Display.IDIHistogramImage;
 
 import PamController.PamController;
@@ -35,6 +40,10 @@ public class ClickDisplayManagerParameters2 implements Cloneable, Serializable,
 	
 	private boolean initialised = false;
 	
+	private boolean manualWindowSizes = false;
+	
+	private ArrayList<WindowSizeData> windowSizes = new ArrayList();
+	
 	public ClickDisplayManagerParameters2() {
 		setDefaults();
 	}
@@ -159,6 +168,11 @@ public class ClickDisplayManagerParameters2 implements Cloneable, Serializable,
 		return null;
 	}
 
+	/**
+	 * This populates the serialised settings with lists of how many displays of 
+	 * each type there are. 
+	 * @param clickDisplayManager
+	 */
 	public void countEverything(ClickDisplayManager clickDisplayManager) {
 		lastMode = PamController.getInstance().getRunMode();
 		if (lastMode >= NMODES) lastMode = 0;
@@ -208,4 +222,101 @@ public class ClickDisplayManagerParameters2 implements Cloneable, Serializable,
 		return ps;
 	}
 
+	/**
+	 * Save windows sizes in an array list. 
+	 * @param windowList
+	 */
+	public void saveDisplayLocations(ArrayList<ClickDisplay> windowList) {
+		if (windowList == null) {
+			return;
+		}
+		getWindowSizes(); // make sure the array is created
+		windowSizes.clear();
+		for (ClickDisplay disp : windowList) {
+			Point loc = disp.getFrame().getLocation();
+			Dimension sz = disp.getFrame().getSize();
+			String cls = disp.getClass().toString();
+			windowSizes.add(new WindowSizeData(cls, loc, sz));
+		}
+	}
+	
+	/**
+	 * Try to restore window locations and sizes from a stored list. 
+	 * @param windowList
+	 * @return
+	 */
+	public boolean restoreWindowSizes(ArrayList<ClickDisplay> windowList){
+		if (windowSizes == null || windowList == null) {
+			return false;
+		}
+		int resized = 0;
+		for (ClickDisplay disp : windowList) {
+			PamInternalFrame frame = disp.getFrame();
+			String cls = disp.getClass().toString();
+			// find an element in the list with that class.
+			WindowSizeData sizeData = null;
+			for (int i = 0; i < windowSizes.size(); i++) {
+				if (windowSizes.get(i).windowClass.equals(cls)) {
+					sizeData = windowSizes.remove(i);
+					break;
+				}
+			}
+			if (sizeData != null) {
+				frame.setLocation(sizeData.location);
+				frame.setSize(sizeData.size);
+				resized ++;
+			}
+		}
+		return resized > 0;
+	}
+	
+	
+	
+	/**
+	 * @return the windowSizes
+	 */
+	public ArrayList<WindowSizeData> getWindowSizes() {
+		if (windowSizes == null) {
+			windowSizes = new ArrayList<>();
+		}
+		return windowSizes;
+	}
+
+
+
+	/**
+	 * @return the manualWindowSizes
+	 */
+	public boolean isManualWindowSizes() {
+		return manualWindowSizes;
+	}
+
+	/**
+	 * @param manualWindowSizes the manualWindowSizes to set
+	 */
+	public void setManualWindowSizes(boolean manualWindowSizes) {
+		this.manualWindowSizes = manualWindowSizes;
+	}
+
+
+
+	private class WindowSizeData implements Serializable {
+		
+		static public final long serialVersionUID = 1;
+		
+		protected String windowClass;
+		
+		public WindowSizeData(String windowClass, Point location, Dimension size) {
+			super();
+			this.windowClass = windowClass;
+			this.location = location;
+			this.size = size;
+		}
+
+		protected Point location;
+		
+		protected Dimension size;
+		
+	}
+
 }

src/clickDetector/ClickTabPanel.java

@@ -72,9 +72,19 @@ public class ClickTabPanel extends JDesktopPane implements ComponentListener {
 	public void componentMoved(ComponentEvent e) {
 	}
 	
+	/**
+	 * This get's called during startup when the window is created and will 
+	 * automatically resize everything. IT may get called 2 or 3 times at startup
+	 * as components such as the side bar sort themselves out. 
+	 */
 	public void componentResized(ComponentEvent e) {
 		// if (++resizeCount < 5) {
-		arrangeWindows();
+		if (clickTabPanelControl.clickDisplayManager.cdmp.isManualWindowSizes() == false) {
+			arrangeWindows();
+		}
+		else {
+			clickTabPanelControl.clickDisplayManager.restoreWindowSizes();
+		}
 		// }
 	}
 	

src/clickDetector/ClickTabPanelControl.java

@@ -26,6 +26,7 @@ import java.awt.Frame;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 
+import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JComponent;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
@@ -117,11 +118,29 @@ public class ClickTabPanelControl implements PamTabPanel {
 		
 		menu.add(clickDisplayManager.getModulesMenu());
 		
-		menuItem = new JMenuItem("Arrange Windows ...");
+		menu.add(clickControl.angleVetoes.getDisplayMenuItem(parentFrame));
+		
+		menu.addSeparator();
+		
+		JCheckBoxMenuItem autoArrange = new JCheckBoxMenuItem("Auto arrange windows");
+		autoArrange.setSelected(clickDisplayManager.cdmp.isManualWindowSizes() == false);
+		autoArrange.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				clickDisplayManager.cdmp.setManualWindowSizes(autoArrange.isSelected() == false);
+				if (autoArrange.isSelected()) {
+					clickPanel.arrangeWindows();
+				}
+			}
+		});
+		autoArrange.setToolTipText("Automatically arrange windows in a standard layout whenever the display dimensions change");
+		menu.add(autoArrange);
+		
+		menuItem = new JMenuItem("Arrange Windows Now");
 		menuItem.addActionListener(new ArrangeWindows(parentFrame));
+		menuItem.setToolTipText("Automatically arrange windows in a standard layout");
 		menu.add(menuItem);
 		
-		menu.add(clickControl.angleVetoes.getDisplayMenuItem(parentFrame));
 
 		return menu;
 	}

src/detectiongrouplocaliser/DetectionGroupProcess.java

@@ -458,6 +458,7 @@ public class DetectionGroupProcess extends PamProcess {
 		detectionGroupDataBlock.saveViewerData();
 		int nUpdates = 0;
 		int nOK = 0;
+		int consecutiveOK = 0;
 		System.out.printf("Checking %d data units in %s ", detectionGroupDataBlock.getUnitsCount(), detectionGroupDataBlock.getDataName());
 		synchronized (detectionGroupDataBlock.getSynchLock()) {
 			ListIterator<DetectionGroupDataUnit> it = detectionGroupDataBlock.getListIterator(0);
@@ -466,11 +467,16 @@ public class DetectionGroupProcess extends PamProcess {
 				boolean ok = checkDataIntegrity(du, false);
 				if (ok) {
 					nUpdates++;
+					consecutiveOK = 0;
 				}
 				else {
 					nOK++;
+					consecutiveOK++;
 				}
 				System.out.printf(".");
+				if (consecutiveOK % 80 == 0) {
+					System.out.printf("\n");
+				}
 			}
 		}
 		System.out.printf("\n%s: %d out of %d data units required corrections\n", detectionGroupDataBlock.getDataName(), nUpdates, nUpdates+nOK);
@@ -486,7 +492,7 @@ public class DetectionGroupProcess extends PamProcess {
 		subTabLogging = detectionGroupLogging.getSubLogging();
 		PamConnection con = DBControlUnit.findConnection();
 		String desc = String.format("Detection group UID %d at %s", du.getUID(), PamCalendar.formatDBDateTime(du.getTimeMilliseconds()));
-		String idList = "( " + du.getUID() + " )";
+		String idList = "( " + du.getDatabaseIndex() + " )";
 		ArrayList<PamSubtableData> stData = subTabLogging.loadSubtableData(con, detectionGroupLogging, idList, null);
 		if (stData == null) {
 			System.out.println("Error loading sub table data for event uid " + du.getUID());

src/generalDatabase/SQLLogging.java

@@ -2002,7 +2002,7 @@ public abstract class SQLLogging {
 	 * 
 	 * @param con database connection
 	 * @param parentLogging super detection logging instance.
-	 * @param uidList list of UID's in the parent data that have been loaded. 
+	 * @param idList list of ID's in the parent data that have been loaded. Note Id, NOT UID 
 	 * @return list of all PamSubtableData items
 	 */
 	public ArrayList<PamSubtableData> loadSubtableData(PamConnection con, SQLLogging parentLogging, String idList, ViewLoadObserver loadObserver) {
@@ -2034,6 +2034,13 @@ public abstract class SQLLogging {
 		return loadSubtableData(con, subtableResults, loadObserver);
 	}
 
+	/**
+	 * Get a sub table result set. Note that this is based on ID, not UID
+	 * @param con connection
+	 * @param parentLogging parent logging system
+	 * @param parentIdList ParentID list. Note that this is ID, not UID, <br>i.e. the query is  WHERE ParentID IN ...
+	 * @return child table result set
+	 */
 	private ResultSet createSubTableResultSet(PamConnection con, SQLLogging parentLogging,
 			String parentIdList) {
 		String clause = String.format(" WHERE ParentID IN %s ORDER BY UTC, UTCMilliseconds", parentIdList);

src/generalDatabase/lookupTables/LookUpTables.java

@@ -3,10 +3,13 @@ package generalDatabase.lookupTables;
 import java.awt.Color;
 import java.awt.Window;
 import java.sql.Connection;
+import java.sql.ResultSet;
 import java.sql.SQLException;
+import java.sql.Statement;
 import java.sql.Types;
 import java.util.ArrayList;
 import java.util.ListIterator;
+import java.util.Vector;
 
 import PamController.PamController;
 import PamView.dialog.warn.WarnOnce;
@@ -101,9 +104,101 @@ public class LookUpTables {
 		checkedTableConnection = null;
 		if (dbControlUnit.getDbProcess().checkTable(lutTableDef)) {
 			checkedTableConnection = con;
-			return true;
 		}
-		return false;
+		
+		checkTableRepeats(con, lutTableDef);
+		
+		return checkedTableConnection != null;
+	}
+
+	/**
+	 * for some reason some repeats have got into the LUT and need to be removed
+	 * or it really messes stuff up. So check it automatically. 
+	 * @param con
+	 * @param lutTableDef2
+	 */
+	private boolean checkTableRepeats(PamConnection con, EmptyTableDefinition lutTableDef) {
+		/*
+		 * first get a list of unique topics, then check them one at a time. 
+		 */
+		ArrayList<String> topics = getTopicList(con, lutTableDef);
+		if (topics == null) {
+			return false;
+		}
+		
+		for (String topic : topics) {
+			checkTopicRepeats(con, lutTableDef, topic);
+		}
+		return true;
+	}
+	
+	private void checkTopicRepeats(PamConnection con, EmptyTableDefinition lutTableDef2, String topic) {
+		LookupList lutList = getLookupList(topic);
+		Vector<LookupItem> list = lutList.getList();
+		int n = list.size();
+		boolean[] isRepeat = new boolean[n];
+		int nRepeat = 0;
+		// search for repeats.
+		for (int i = 0; i < n-1; i++) {
+			String code = list.get(i).getCode().trim();
+			for (int j = i+1; j < n; j++) {
+				String code2 = list.get(j).getCode().trim();
+				if (code.equals(code2)) {
+					isRepeat[j] = true;
+					nRepeat++;
+				}
+			}
+		}
+		if (nRepeat == 0) {
+			return;
+		}
+		// make a clause to delete the repeats. 
+		String sql = null;
+		for (int i = 0; i < n; i++) {
+			if (isRepeat[i] == false) {
+				continue;
+			}
+			if (sql == null) {
+				sql = String.format("DELETE FROM %s WHERE Id IN (%d", lutTableDef.getTableName(), list.get(i).getDatabaseId());
+			}
+			else {
+				sql = sql + String.format(",%d", list.get(i).getDatabaseId());
+			}
+		}
+		sql += ")";
+		boolean ok = false;
+		try {
+			Statement stmt = con.getConnection().createStatement();
+			ok = stmt.execute(sql);
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+	}
+
+	private ArrayList<String> getTopicList(PamConnection con, EmptyTableDefinition lutTableDef) {
+		if (con == null) {
+			return null;
+		}
+		ArrayList<String> topics = new ArrayList<>();
+		String qStr = "SELECT DISTINCT Topic FROM  " + lutTableDef.getTableName();
+		try {
+			Statement stmt = con.getConnection().createStatement();
+			boolean ok = stmt.execute(qStr);
+			if (ok == false) {
+				return null;
+			}
+			ResultSet results = stmt.getResultSet();
+			while (results.next()) {
+				String topic = results.getString(1);
+				topics.add(topic);
+			}
+		} catch (SQLException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+			return null;
+		}
+		return topics;
 	}
 
 	public LookupList createLookupList(PamCursor resultSet, String topic) {

src/generalDatabase/ucanAccess/UCanAccessSystem.java

@@ -153,7 +153,7 @@ public class UCanAccessSystem extends BaseAccessSystem implements PamSettings {
 			String conStr = "jdbc:ucanaccess://"
 					+ fl.getAbsolutePath() + passwordEntry+noMem;
 			System.out.println("UCanAccess connection string = " + conStr);
-			conn = DriverManager.getConnection(conStr);
+			conn = DriverManager.getConnection(conStr,"","");
 			conn.setAutoCommit(false);
 		} catch (Exception e) {
 			e.printStackTrace();

src/loggerForms/FormDescription.java

@@ -1598,7 +1598,9 @@ public class FormDescription implements Cloneable, Comparable<FormDescription> {
 			normalForm.destroyForm();
 		}
 		if (hiddenForm != null) {
-			normalForm.destroyForm();
+			if (normalForm != null) {
+				normalForm.destroyForm();
+			}
 		}
 		if (subtabForms != null) {
 			for (LoggerForm aForm:subtabForms) {

src/loggerForms/LoggerForm.java

@@ -21,6 +21,7 @@ import javax.swing.BoxLayout;
 import javax.swing.JButton;
 import javax.swing.JComponent;
 import javax.swing.JOptionPane;
+import javax.swing.JPanel;
 import javax.swing.JRootPane;
 import javax.swing.JScrollPane;
 import javax.swing.Timer;
@@ -529,7 +530,10 @@ public class LoggerForm{
 				innerCenterPanel.add(currentRow);
 				currentRow = new LoggerFormPanel(this, new FlowLayout(FlowLayout.LEFT));
 			}else{
-				currentRow.add(c.makeComponent(this));
+				JPanel component = c.makeComponent(this);
+				if (component != null) {
+					currentRow.add(component);
+				}
 			}
 
 		}