Species map i/o

src/tethys/TethysControl.java

@@ -51,6 +51,7 @@ import tethys.output.TethysExportParams;
 import tethys.output.TethysExporter;
 import tethys.output.swing.TethysExportDialog;
 import tethys.species.ITISFunctions;
+import tethys.species.SpeciesMapManager;
 import tethys.swing.ProjectDeploymentsDialog;
 import tethys.swing.TethysTabPanel;
 import tethys.swing.XMLStringView;
@@ -200,6 +201,18 @@ public class TethysControl extends PamControlledUnit implements PamSettings, Tet
 			}
 		});
 		tethysMenu.add(showDeps);
+		
+		tethysMenu.addSeparator();
+		JMenuItem mapItem = new JMenuItem("Export species maps ...");
+		mapItem.setToolTipText("Export all species maps (PAMGuard codes to ITIS codes to file for import into other configurations");
+				mapItem.addActionListener(SpeciesMapManager.getInstance().getExportAction(parentFrame));
+		tethysMenu.add(mapItem);
+		
+		mapItem = new JMenuItem("Import species maps ...");
+		mapItem.setToolTipText("Import species maps (PAMGuard codes to ITIS codes to file for import into other configurations");
+		mapItem.addActionListener(SpeciesMapManager.getInstance().getImportAction(parentFrame));
+		tethysMenu.add(mapItem);
+		
 		return tethysMenu;
 	}
 

src/tethys/detection/DetectionsHandler.java

@@ -6,9 +6,11 @@ import java.util.List;
 import javax.swing.SwingWorker;
 
 import PamController.PamControlledUnit;
+import PamController.PamController;
 import PamController.PamguardVersionInfo;
 import PamModel.PamPluginInterface;
 import PamUtils.PamCalendar;
+import PamView.dialog.PamDialog;
 import PamView.dialog.warn.WarnOnce;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
@@ -40,6 +42,7 @@ import tethys.niluswraps.TethysCollections;
 import tethys.output.StreamExportParams;
 import tethys.output.TethysExportParams;
 import tethys.pamdata.TethysDataProvider;
+import tethys.species.DataBlockSpeciesManager;
 
 /**
  * Functions for handling output of Detections documents. 
@@ -203,6 +206,7 @@ public class DetectionsHandler {
 	 * @param exportWorkerCard
 	 */
 	public void startExportThread(PamDataBlock pamDataBlock, StreamExportParams streamExportParams, DetectionExportObserver exportObserver) {
+
 		checkGranularity(pamDataBlock, streamExportParams);
 		tethysControl.getTethysExportParams().setStreamParams(pamDataBlock, streamExportParams);
 		activeExport = true;

src/tethys/pamdata/AutoTethysProvider.java

@@ -247,6 +247,9 @@ abstract public class AutoTethysProvider implements TethysDataProvider {
 		Detection detection = new Detection();
 		detection.setStart(TethysTimeFuncs.xmlGregCalFromMillis(dataUnit.getTimeMilliseconds()));
 		detection.setEnd(TethysTimeFuncs.xmlGregCalFromMillis(dataUnit.getEndTimeInMilliseconds()));
+		if (dataUnit.getEndTimeInMilliseconds() < dataUnit.getTimeMilliseconds()) {
+			System.out.printf("Error UID %d, end %s before start %s\n", dataUnit.getUID(), detection.getEnd(), detection.getStart());
+		}
 
 		DataBlockSpeciesManager speciesManager = pamDataBlock.getDatablockSpeciesManager();
 		SpeciesMapItem speciesItem = null;

src/tethys/species/DataBlockSpeciesManager.java

@@ -27,6 +27,7 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> {
 	/**
 	 * The serialised bit. Always exists (or should be created) even if there
 	 * are no real species, via a defaultdefaultSpecies. 
+	 * Don't keep a local copy though since it may have been 
 	 */
 	private DataBlockSpeciesMap datablockSpeciesMap;
 	
@@ -194,4 +195,28 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> {
 	public void setDefaultSpeciesCode(String defaultName) {
 		this.defaultSpeciesCode = defaultName;
 	}
+	
+	/**
+	 * Check the species map. Only return true if every species code
+	 * has a map item. Otherwise it's not safe to export. 
+	 * @return null if all codes have a lookup, otherwise some sort of useful error information
+	 */
+	public String checkSpeciesMapError() {
+		ArrayList<String> codes = getAllSpeciesCodes();
+		if (codes == null || codes.size() == 0) {
+			return "No defined species codes"; // I guess that's OK ? 
+		}
+		DataBlockSpeciesMap spMap = getDatablockSpeciesMap();
+		if (spMap == null) {
+			return "No species map";
+		}
+		
+		for (String aCode : codes) {
+			SpeciesMapItem item = spMap.getItem(aCode);
+			if (item == null) {
+				return "No Species item for species code " + aCode;
+			}
+		}
+		return null;
+	}
 }

src/tethys/species/SpeciesMapManager.java

@@ -1,17 +1,32 @@
 package tethys.species;
 
+import java.awt.Window;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
 import java.io.Serializable;
 import java.util.ArrayList;
 
+import javax.swing.JFileChooser;
+
 import PamController.PamControlledUnitSettings;
 import PamController.PamController;
+import PamController.PamFolders;
 import PamController.PamSettingManager;
 import PamController.PamSettings;
+import PamUtils.PamFileFilter;
+import PamView.dialog.warn.WarnOnce;
 import PamguardMVC.PamDataBlock;
 
 /**
  * Master manager for species maps which will eventually allow for export and import from XML
- * documents, databases and other things ...
+ * documents, databases and other things ...<br>
+ * (Perhaps not as XML, will simply output the serialized map - easier. 
  * @author dg50
  *
  */
@@ -19,10 +34,23 @@ public class SpeciesMapManager implements PamSettings {
 	
 	private static SpeciesMapManager singleInstance = null;
 	
+	/**
+	 * Synch object to survive multithreading. 
+	 */
 	private static Object synch = new Object(); 
 	
+	/**
+	 * Map of all species maps. 
+	 */
 	private GlobalSpeciesMap globalSpeciesMap;
 
+	private JFileChooser ioFileChooser;
+	
+	/**
+	 * file end type for map files 
+	 */
+	public static final String mapFileEnd = ".spmap";
+
 	private SpeciesMapManager() {
 		PamSettingManager.getInstance().registerSettings(this);
 	}
@@ -101,4 +129,124 @@ public class SpeciesMapManager implements PamSettings {
 			return false;
 		}
 	}
+	
+	public ActionListener getExportAction(Window parentFrame) {
+		return new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				exportSpeciesMaps(parentFrame);
+			}
+		};
+	}
+
+	public ActionListener getImportAction(Window parentFrame) {
+		return new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				importSpeciesMaps(parentFrame);
+			}
+		};
+	}
+	
+	/**
+	 * Export all species maps to a serialized object file. 
+	 * @param parentFrame 
+	 * @return
+	 */
+	public boolean exportSpeciesMaps(Window parentFrame) {
+		JFileChooser chooser = getFileChooser();
+		int ans = chooser.showSaveDialog(parentFrame);
+		if (ans != JFileChooser.APPROVE_OPTION) {
+			return false;
+		}
+		File opFile = chooser.getSelectedFile();
+		opFile = PamFileFilter.checkFileEnd(opFile, mapFileEnd, true);
+		// write it. 
+		try {
+			ObjectOutputStream op = new ObjectOutputStream(new FileOutputStream(opFile));
+			op.writeObject(getSettingsReference());
+			op.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+			return false;
+		}
+		
+		
+		return true;
+	}
+	
+	/**
+	 * Get a file chooser, which will remember folders, etc. while PAMGuard is open 
+	 * @return file chooser. 
+	 */
+	private JFileChooser getFileChooser() {
+		if (ioFileChooser != null) {
+			return ioFileChooser;
+		}
+		PamFileFilter fileFilter = new PamFileFilter("Species map files", mapFileEnd);
+		ioFileChooser = new JFileChooser();
+		ioFileChooser.setFileFilter(fileFilter);
+		ioFileChooser.setCurrentDirectory(new File(PamFolders.getDefaultProjectFolder()));
+		return ioFileChooser;
+	}
+	
+	/**
+	 * Import global species maps from selected file. 
+	 * @param parentFrame
+	 * @return
+	 */
+	public boolean importSpeciesMaps(Window parentFrame) {
+		JFileChooser chooser = getFileChooser();
+		int ans = chooser.showOpenDialog(parentFrame);
+		if (ans != JFileChooser.APPROVE_OPTION) {
+			return false;
+		}
+		File ipFile = chooser.getSelectedFile();
+		ipFile = PamFileFilter.checkFileEnd(ipFile, mapFileEnd, true);
+		GlobalSpeciesMap readSpeciesMap = null;
+		// read it. 
+		try {
+			ObjectInputStream ip = new ObjectInputStream(new FileInputStream(ipFile));
+			readSpeciesMap = (GlobalSpeciesMap) ip.readObject();
+		} catch (IOException e) {
+			e.printStackTrace();
+			return false;
+		} catch (ClassNotFoundException e) {
+			e.printStackTrace();
+			return false;
+		} catch (Exception e) {
+			e.printStackTrace();
+			return false;
+		}
+		
+		return handleNewSpeciesMap(readSpeciesMap);
+	}
+
+	private boolean handleNewSpeciesMap(GlobalSpeciesMap readSpeciesMap) {
+		if (readSpeciesMap == null) {
+			return false;
+		}
+		// could put in a dialog to only select parts of the map if we wanted to ? 
+		int ans = WarnOnce.showWarning("Global Species Map", 
+				"Do you want to overwrite ALL PAMGaurd species maps with the imported data ?",
+				WarnOnce.YES_NO_OPTION);
+		if (ans == WarnOnce.CANCEL_OPTION) {
+			return false;
+		}
+		globalSpeciesMap = readSpeciesMap;
+		// no wupdate all datablock maps since they keep their own copies. 
+		ArrayList<PamDataBlock> allDatablocks = PamController.getInstance().getDataBlocks();
+		for (PamDataBlock aBlock : allDatablocks) {
+			DataBlockSpeciesManager spManager = aBlock.getDatablockSpeciesManager();
+			if (spManager == null) {
+				continue;
+			}
+			DataBlockSpeciesMap blockMap = globalSpeciesMap.get(aBlock);
+			if (blockMap != null) {
+				spManager.setDatablockSpeciesMap(blockMap);
+			}
+		}
+		
+		return true;
+	}
 }

src/tethys/species/swing/DataBlockSpeciesDialog.java

@@ -1,17 +1,20 @@
 package tethys.species.swing;
 
 import java.awt.BorderLayout;
+import java.awt.FlowLayout;
 import java.awt.Window;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 
 import javax.swing.JButton;
 import javax.swing.JPanel;
+import javax.swing.border.TitledBorder;
 
 import PamController.PamController;
 import PamView.PamGui;
 import PamView.dialog.PamDialog;
 import PamguardMVC.PamDataBlock;
+import tethys.species.SpeciesMapManager;
 
 public class DataBlockSpeciesDialog extends PamDialog {
 
@@ -24,6 +27,7 @@ public class DataBlockSpeciesDialog extends PamDialog {
 		JPanel mainPanel = new JPanel(new BorderLayout());
 		speciesPanel = new DataBlockSpeciesPanel(dataBlock);
 		mainPanel.add(BorderLayout.CENTER, speciesPanel.getDialogComponent());
+		
 		JButton itisButton = new JButton("Go to ITIS web site");
 		itisButton.setToolTipText("Go to ITIS website to search for species codes");
 		itisButton.addActionListener(new ActionListener() {
@@ -33,9 +37,21 @@ public class DataBlockSpeciesDialog extends PamDialog {
 			}
 		});
 		JPanel nPanel = new JPanel(new BorderLayout());
+		nPanel.setBorder(new TitledBorder("Code management"));
 		nPanel.add(BorderLayout.EAST, itisButton);
+//		JPanel nwBit = new JPanel(new FlowLayout());
+//		JButton exportButton = new JButton("Export");
+//		exportButton.addActionListener(SpeciesMapManager.getInstance().getExportAction(parentFrame));
+//		nwBit.add(exportButton);
+//		JButton importButton = new JButton("Import");
+//		importButton.addActionListener(SpeciesMapManager.getInstance().getImportAction(parentFrame));
+//		nwBit.add(importButton);
+//		nPanel.add(BorderLayout.WEST, nwBit);
+		
+		
 		mainPanel.add(BorderLayout.NORTH, nPanel);
 		setDialogComponent(mainPanel);
+		setResizable(true);
 	}
 	
 	protected void gotoITIS() {

src/tethys/species/swing/DataBlockSpeciesPanel.java

@@ -6,6 +6,7 @@ import java.util.ArrayList;
 import javax.swing.BoxLayout;
 import javax.swing.JComponent;
 import javax.swing.JPanel;
+import javax.swing.JScrollPane;
 import javax.swing.border.TitledBorder;
 
 import PamView.dialog.PamDialogPanel;
@@ -30,7 +31,8 @@ public class DataBlockSpeciesPanel implements PamDialogPanel {
 		this.dataBlock = dataBlock;
 		mainPanel = new JPanel(new BorderLayout());
 		speciesPanel = new JPanel();
-		mainPanel.add(speciesPanel, BorderLayout.CENTER);
+		JScrollPane scrollPane = new JScrollPane(speciesPanel, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+		mainPanel.add(scrollPane, BorderLayout.CENTER);
 		mainPanel.setBorder(new TitledBorder(dataBlock.getDataName()));
 	}
 

src/tethys/swing/DetectionsExportPanel.java

@@ -11,10 +11,13 @@ import javax.swing.JComponent;
 import javax.swing.JPanel;
 import javax.swing.border.TitledBorder;
 
+import PamController.PamController;
+import PamView.dialog.PamDialog;
 import PamView.dialog.PamGridBagContraints;
 import PamView.panel.PamAlignmentPanel;
 import PamguardMVC.PamDataBlock;
 import tethys.TethysControl;
+import tethys.species.DataBlockSpeciesManager;
 import tethys.swing.export.DetectionsExportWizard;
 
 public class DetectionsExportPanel extends TethysGUIPanel implements StreamTableObserver {
@@ -53,6 +56,20 @@ public class DetectionsExportPanel extends TethysGUIPanel implements StreamTable
 		if (selectedDataBlock == null) {
 			return;
 		}
+		
+		/**
+		 * Check the species map is OK before doing anything. 
+		 */
+		DataBlockSpeciesManager spManager = selectedDataBlock.getDatablockSpeciesManager();
+		if (spManager != null) {
+			String error = spManager.checkSpeciesMapError();
+			if (error != null) {
+				PamDialog.showWarning(PamController.getMainFrame(), "Datablock species manager error", error);
+				spManager.showSpeciesDialog();
+				return;
+			}
+		}
+		
 		DetectionsExportWizard.showDialog(getTethysControl().getGuiFrame(), getTethysControl(), selectedDataBlock);
 	}