Species info

Sort out of species info which hopefully now deals with all
eventualities.

src/RightWhaleEdgeDetector/species/RWSpeciesManager.java

@@ -3,7 +3,8 @@ package RightWhaleEdgeDetector.species;
 import PamguardMVC.PamDataBlock;
 import RightWhaleEdgeDetector.RWEDataUnit;
 import tethys.species.DataBlockSpeciesManager;
-import tethys.species.DataBlockSpeciesTypes;
+import tethys.species.DataBlockSpeciesCodes;
+import tethys.species.SpeciesMapItem;
 
 public class RWSpeciesManager extends DataBlockSpeciesManager<RWEDataUnit> {
 	
@@ -11,15 +12,16 @@ public class RWSpeciesManager extends DataBlockSpeciesManager<RWEDataUnit> {
 
 	public RWSpeciesManager(PamDataBlock<RWEDataUnit> dataBlock) {
 		super(dataBlock);
+		setDefaultDefaultSpecies(new SpeciesMapItem(RWSpeciesTypes.eubalaena, RWSpeciesTypes.onlyType, RWSpeciesTypes.defaultName));
 	}
 
 	@Override
-	public DataBlockSpeciesTypes getSpeciesTypes() {
-		return rwSpeciesTypes;
+	public DataBlockSpeciesCodes getSpeciesCodes() {
+		return null;
 	}
 
 	@Override
-	public String getSpeciesString(RWEDataUnit dataUnit) {
+	public String getSpeciesCode(RWEDataUnit dataUnit) {
 		return RWSpeciesTypes.onlyType;
 	}
 

src/RightWhaleEdgeDetector/species/RWSpeciesTypes.java

@@ -1,15 +1,17 @@
 package RightWhaleEdgeDetector.species;
 
-import tethys.species.DataBlockSpeciesTypes;
+import tethys.species.DataBlockSpeciesCodes;
 
-public class RWSpeciesTypes extends DataBlockSpeciesTypes {
+public class RWSpeciesTypes extends DataBlockSpeciesCodes {
 	
 	public static final String onlyType = "Up call";
 	
-	private static final int glacialis = 180536;
+	public static final int eubalaena = 180536;
+	
+	public static final String defaultName = "Right Whale";
 
 	public RWSpeciesTypes() {
-		super(glacialis, onlyType);
+		super(eubalaena, defaultName, onlyType);
 	}
 
 }

src/clickDetector/ClickClassifiers/ClickBlockSpeciesManager.java

@@ -4,7 +4,7 @@ import clickDetector.ClickControl;
 import clickDetector.ClickDataBlock;
 import clickDetector.ClickDetection;
 import tethys.species.DataBlockSpeciesManager;
-import tethys.species.DataBlockSpeciesTypes;
+import tethys.species.DataBlockSpeciesCodes;
 import tethys.species.ITISTypes;
 import tethys.species.SpeciesMapItem;
 
@@ -16,11 +16,11 @@ public class ClickBlockSpeciesManager extends DataBlockSpeciesManager<ClickDetec
 		super(clickDataBlock);
 		this.clickControl = clickControl;
 		setDefaultDefaultSpecies(new SpeciesMapItem(ITISTypes.UNKNOWN, "Unknown", "Unknown"));
-		setDefaultName("Unknown");
+		setDefaultSpeciesCode("Unknown");
 	}
 
 	@Override
-	public DataBlockSpeciesTypes getSpeciesTypes() {
+	public DataBlockSpeciesCodes getSpeciesCodes() {
 		ClickTypeMasterManager masterManager = clickControl.getClickTypeMasterManager();
 		if (masterManager == null) {
 			return null;
@@ -28,16 +28,16 @@ public class ClickBlockSpeciesManager extends DataBlockSpeciesManager<ClickDetec
 		String[] speciesList = masterManager.getSpeciesList();
 		// add the default
 		String[] fullList = new String[speciesList.length+1];
-		fullList[0] = getDefaultName();
+		fullList[0] = getDefaultSpeciesCode();
 		for (int i = 0; i < speciesList.length; i++) {
 			fullList[i+1] = speciesList[i];
 		}
 		
-		return new DataBlockSpeciesTypes("Click", fullList);
+		return new DataBlockSpeciesCodes("Click", fullList);
 	}
 
 	@Override
-	public String getSpeciesString(ClickDetection dataUnit) {
+	public String getSpeciesCode(ClickDetection dataUnit) {
 		ClickTypeMasterManager masterManager = clickControl.getClickTypeMasterManager();
 		if (masterManager == null) {
 			return null;

src/pamMaths/PamVector.java

@@ -382,7 +382,7 @@ public class PamVector implements Serializable, Cloneable, PamCoordinate, Manage
 	 * @return magnitude of those dimensions only. 
 	 */
 	public double norm(int nDim) {
-		return Math.sqrt(normSquared(2));
+		return Math.sqrt(normSquared(nDim));
 	}
 	/**
 	 * 

src/tethys/species/DataBlockSpeciesCodes.java

@@ -9,11 +9,12 @@ import java.util.ArrayList;
  * @author dg50
  *
  */
-public class DataBlockSpeciesTypes {
+public class DataBlockSpeciesCodes {
 
 	/**
 	 * List of species names / codes associated with this data block. These can be translated, 
 	 * via a HashMap to more detailed objects which include an ITIS code. 
+	 * These are the internal codes of each detector - whatever it uses. 
 	 */
 	private ArrayList<String> speciesNames;
 	
@@ -31,7 +32,7 @@ public class DataBlockSpeciesTypes {
 	/**
 	 * @param defaultType
 	 */
-	public DataBlockSpeciesTypes(String defaultType) {
+	public DataBlockSpeciesCodes(String defaultType) {
 		this.defaultType = defaultType;
 	}
 
@@ -39,8 +40,10 @@ public class DataBlockSpeciesTypes {
 	 * @param itisDefault
 	 * @param defaultType
 	 */
-	public DataBlockSpeciesTypes(int itisDefault, String defaultType) {
+	public DataBlockSpeciesCodes(int itisDefault, String defaultName, String defaultType) {
 		this.itisDefault = itisDefault;
+		speciesNames = new ArrayList<>();
+		speciesNames.add(defaultName);
 		this.defaultType = defaultType;
 	}
 
@@ -48,7 +51,7 @@ public class DataBlockSpeciesTypes {
 	 * constructor to use with a array of String names. 
 	 * @param speciesList
 	 */
-	public DataBlockSpeciesTypes(String defaultType, String[] speciesList) {
+	public DataBlockSpeciesCodes(String defaultType, String[] speciesList) {
 		this.defaultType = defaultType;
 		if (speciesList == null) {
 			speciesNames = new ArrayList<>();

src/tethys/species/DataBlockSpeciesManager.java

@@ -1,5 +1,7 @@
 package tethys.species;
 
+import java.util.ArrayList;
+
 import PamController.PamController;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
@@ -7,31 +9,86 @@ import tethys.species.swing.DataBlockSpeciesDialog;
 
 /**
  * Manage species conversion for a single datablock.
+ *
+ * there seem to be three types of manager:<br>
+ * 1. Datablocks which have a totally free list of species codes, such as the click detector, or whistle classifier <br>
+ * 1a. A slight variation on this is blocks which have a list and also a default for data units which aren't classified.<br>
+ * 2. Datablocks which have a single type which may be unknown or partially known, but we want the possibility of overriding it.
+ * e.g. the whistle detector may default to odontocete, but may be overridden to a mystecete species.<br> 
+ * 3. Datablocks with no information, or where the list from (1.) is empty. <p>
+ * In all cases, we need to handle this reasonably sensibly. The code list is always the start of this and must 
+ * always return something, even if it's 'unknown'. 
+ *
  * @author dg50
  *
  */
 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. 
+	 */
 	private DataBlockSpeciesMap datablockSpeciesMap;
 	
 	private PamDataBlock<T> dataBlock;
 	
-	private String defaultName = null;
+	/*
+	 * Below are three ways of getting species codes. At least ONE of these 
+	 * must return something. 
+	 */
 
+	/**
+	 * Object that contains a list of species codes. This may be fluid
+	 * between configurations and may change during a session, e.g. through
+	 * the addition of a new click type or changes to the whistle classifier settings. 
+	 * @return object containing a list of species types. 
+	 */
+	public abstract DataBlockSpeciesCodes getSpeciesCodes();
+	
+	/**
+	 * A default species code. Can be null, in which case it won't be used or 
+	 * can be set to something like 'Unknown'
+	 */
+	private String defaultSpeciesCode = null;
+	
+	/**
+	 * For use in detectors that have a strong default species, but no 
+	 * real list of different species codes. Can be left null. 
+	 */
 	private SpeciesMapItem defaultDefaultSpecies = null;
 
-	public abstract DataBlockSpeciesTypes getSpeciesTypes();
 	
-	public abstract String getSpeciesString(T dataUnit);
+	/**
+	 * Gets a species string for a specific data unit, This is abstracted
+	 * since different detectors store this in non standard ways. The result of 
+	 * this should be within the set provided by getSpeciesCodes() which can then 
+	 * be used in the DataBlockSpeciesMap to look up an itis code. 
+	 * @param dataUnit
+	 * @return A species code for a specific data unit. May be null (e.g. for an unclassified click)
+	 */
+	public abstract String getSpeciesCode(T dataUnit);
 
 	public DataBlockSpeciesManager(PamDataBlock<T> dataBlock) {
 		super();
 		this.dataBlock = dataBlock;
 		datablockSpeciesMap = SpeciesMapManager.getInstance().getSpeciesMap(dataBlock);
+//		datablockSpeciesMap.clearMap();
+		clearMapNulls();
+		checkMapDefault();
+	}
+	
+	/**
+	 * Clear up some old maps which have got a null null default. 
+	 */
+	private void clearMapNulls() {
+		SpeciesMapItem nullVal = datablockSpeciesMap.getItem(null);
+		if (nullVal == null) {
+			datablockSpeciesMap.removeItem(null);
+		}
 	}
 
 	public SpeciesMapItem getSpeciesItem(T dataUnit) {
-		String speciesString = getSpeciesString(dataUnit);
+		String speciesString = getSpeciesCode(dataUnit);
 		if (speciesString == null) {
 			return getDefaultDefaultSpecies();
 		}
@@ -42,6 +99,30 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> {
 		return speciesMap.getItem(speciesString);
 	}
 	
+	/**
+	 * Get all PAMGuard species codes, which may come from the DataBlockSpeciesCodes 
+	 * object, or the defaultSpeciesCode, or the defaultDefaultSpecies name. Ideally, 
+	 * at least one of these should have something, or we'll stick in an "Unknown"
+	 * @return
+	 */
+	public ArrayList<String> getAllSpeciesCodes() {
+		ArrayList<String> allCodes = new ArrayList<String>();
+		if (defaultSpeciesCode != null) {
+			allCodes.add(defaultSpeciesCode);
+		}
+		if (defaultDefaultSpecies != null) {
+			allCodes.add(defaultDefaultSpecies.getPamguardName());
+		}
+		DataBlockSpeciesCodes codeList = getSpeciesCodes();
+		if (codeList != null) {
+			allCodes.addAll(codeList.getSpeciesNames());
+		}
+		if (allCodes.size() == 0) {
+			allCodes.add("Unknown");
+		}
+		return allCodes;
+	}
+	
 	public DataBlockSpeciesMap getDatablockSpeciesMap() {
 		if (datablockSpeciesMap == null) {
 			datablockSpeciesMap = new DataBlockSpeciesMap();
@@ -51,9 +132,16 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> {
 	}
 
 	private void checkMapDefault() {
-		SpeciesMapItem defaultItem = datablockSpeciesMap.getItem(getDefaultName());
+//		SpeciesMapItem defaultItem = datablockSpeciesMap.getItem(getDefaultSpeciesCode());
+//		if (defaultItem == null) {
+//			datablockSpeciesMap.putItem(getDefaultSpeciesCode(), getDefaultDefaultSpecies());
+//		}
+		if (defaultDefaultSpecies == null) {
+			return;
+		}
+		SpeciesMapItem defaultItem = datablockSpeciesMap.getItem(defaultDefaultSpecies.getPamguardName());
 		if (defaultItem == null) {
-			datablockSpeciesMap.putItem(getDefaultName(), getDefaultDefaultSpecies());
+			datablockSpeciesMap.putItem(defaultDefaultSpecies.getPamguardName(), defaultDefaultSpecies);
 		}
 	}
 
@@ -84,19 +172,20 @@ abstract public class DataBlockSpeciesManager<T extends PamDataUnit> {
 	 */
 	public void setDefaultDefaultSpecies(SpeciesMapItem defaultDefaultSpecies) {
 		this.defaultDefaultSpecies = defaultDefaultSpecies;
+		checkMapDefault();
 	}
 
 	/**
 	 * @return the defaultName
 	 */
-	public String getDefaultName() {
-		return defaultName;
+	public String getDefaultSpeciesCode() {
+		return defaultSpeciesCode;
 	}
 
 	/**
 	 * @param defaultName the defaultName to set
 	 */
-	public void setDefaultName(String defaultName) {
-		this.defaultName = defaultName;
+	public void setDefaultSpeciesCode(String defaultName) {
+		this.defaultSpeciesCode = defaultName;
 	}
 }

src/tethys/species/DataBlockSpeciesMap.java

@@ -4,7 +4,10 @@ import java.io.Serializable;
 import java.util.HashMap;
 
 /**
- * Species map for a specified data block
+ * Species map for a specified data block <p>
+ * This is the bit that can be serialised, and is primarily (only) a hash table of 
+ * SpeciesMapItems which relate String species codes for a detector to more 
+ * details itis and scientific name information.   
  * @author dg50
  *
  */
@@ -34,4 +37,8 @@ public class DataBlockSpeciesMap implements Serializable {
 		speciesTable.remove(key);
 	}
 	
+	public void clearMap() {
+		speciesTable.clear();
+	}
+
 }

src/tethys/species/SpeciesTest.java

@@ -129,9 +129,9 @@ public class SpeciesTest {
 	private void runJson() {
 //		String jQ = "{\"return\":[\"Deployment\"],\"select\":[{\"op\":\"=\",\"operands\":[\"Deployment/Project\",\"DCLDE2022\"],\"optype\":\"binary\"}],\"enclose\":1}";
 //		String jQ = "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"=\",\"operands\":[\"ranks/rank/tsn\",\"180488\"],\"optype\":\"binary\"}],\"enclose\":1}";
-		String jQ = "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"=\",\"operands\":[\"ranks/rank/tsn\",\"180488\"],\"optype\":\"binary\"}],\"enclose\":1}";
+//		String jQ = "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"=\",\"operands\":[\"ranks/rank/tsn\",\"180488\"],\"optype\":\"binary\"}],\"enclose\":1}";
 //		String jQ = "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"=\",\"operands\":[\"ranks/rank/completename\",\"Physeter macrocephalus\"],\"optype\":\"binary\"}],\"enclose\":1}";
-//		String jQ = "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"dbxml:contains\",\"operands\":[\"ranks/rank/completename\",\"Sperm\"],\"optype\":\"function\"}],\"enclose\":1}";
+		String jQ = "{\"return\":[\"ranks/rank\"],\"select\":[{\"op\":\"dbxml:contains\",\"operands\":[\"ranks/rank/completename\",\"Sperm\"],\"optype\":\"function\"}],\"enclose\":1}";
 
 		System.out.println(jQ);
 

src/tethys/species/swing/DataBlockSpeciesPanel.java

@@ -12,7 +12,7 @@ import PamView.dialog.PamDialogPanel;
 import PamguardMVC.PamDataBlock;
 import tethys.species.DataBlockSpeciesManager;
 import tethys.species.DataBlockSpeciesMap;
-import tethys.species.DataBlockSpeciesTypes;
+import tethys.species.DataBlockSpeciesCodes;
 import tethys.species.SpeciesMapItem;
 
 public class DataBlockSpeciesPanel implements PamDialogPanel {
@@ -46,8 +46,8 @@ public class DataBlockSpeciesPanel implements PamDialogPanel {
 		subPanels.clear();
 		
 		DataBlockSpeciesManager speciesManager = dataBlock.getDatablockSpeciesManager();
-		DataBlockSpeciesTypes speciesTypes = speciesManager.getSpeciesTypes();
-		ArrayList<String> speciesNames = speciesTypes.getSpeciesNames();
+//		DataBlockSpeciesCodes speciesTypes = speciesManager.getSpeciesCodes();
+		ArrayList<String> speciesNames = speciesManager.getAllSpeciesCodes();
 		DataBlockSpeciesMap speciesMap = speciesManager.getDatablockSpeciesMap();
 		for (String aSpecies : speciesNames) {
 			SpeciesSubPanel subPanel = new SpeciesSubPanel(aSpecies);

src/tethys/species/swing/SpeciesSubPanel.java

@@ -139,7 +139,7 @@ public class SpeciesSubPanel {
 			tsn = Integer.valueOf(itisCode.getText());
 		}
 		catch (NumberFormatException e) {
-			PamDialog.showWarning(PamController.getMainFrame(), pamguardName.getText(), "You must specified an ITIS taxanomic code");
+			PamDialog.showWarning(PamController.getMainFrame(), pamguardName.getText(), "You must specify an ITIS taxanomic code");
 			return null;
 		}
 		latin = latinName.getText();
@@ -149,7 +149,8 @@ public class SpeciesSubPanel {
 			PamDialog.showWarning(PamController.getMainFrame(), pamguardName.getText(), "You must specified a call type");
 			return null;			
 		}
-		return new SpeciesMapItem(tsn, callType, pamguardName.getText(), latin, vernacular);
+		String pamName = pamguardName.getText().replace("\"", "");
+		return new SpeciesMapItem(tsn, callType, pamName, latin, vernacular);
 	}
 
 }

src/whistlesAndMoans/species/WhistleSpeciesManager.java

@@ -3,7 +3,7 @@ package whistlesAndMoans.species;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
 import tethys.species.DataBlockSpeciesManager;
-import tethys.species.DataBlockSpeciesTypes;
+import tethys.species.DataBlockSpeciesCodes;
 import tethys.species.ITISTypes;
 import tethys.species.SpeciesMapItem;
 import whistlesAndMoans.ConnectedRegionDataUnit;
@@ -15,19 +15,20 @@ public class WhistleSpeciesManager extends DataBlockSpeciesManager<ConnectedRegi
 
 	public WhistleSpeciesManager(PamDataBlock<ConnectedRegionDataUnit> dataBlock) {
 		super(dataBlock);
-		setDefaultDefaultSpecies(new SpeciesMapItem(180404, "Tonal", "Odontocete"));
+		setDefaultDefaultSpecies(new SpeciesMapItem(180404, "Tonal", "Tonal"));
 	}
 
 	@Override
-	public DataBlockSpeciesTypes getSpeciesTypes() {
-		String spList[] = {"Unknown"};
-
-		DataBlockSpeciesTypes whistleSpeciesTypes = new DataBlockSpeciesTypes("Tonal", spList);
-		return whistleSpeciesTypes;
+	public DataBlockSpeciesCodes getSpeciesCodes() {
+//		String spList[] = {"Unknown"};
+//
+//		DataBlockSpeciesCodes whistleSpeciesTypes = new DataBlockSpeciesCodes("Tonal", spList);
+//		return whistleSpeciesTypes;
+		return null;
 	}
 
 	@Override
-	public String getSpeciesString(ConnectedRegionDataUnit dataUnit) {
+	public String getSpeciesCode(ConnectedRegionDataUnit dataUnit) {
 		return defaultName;
 	}