Compute distances to table rows WIP

src/main/java/org/embl/mobie/lib/annotation/Annotation.java

@@ -49,9 +49,12 @@ public interface Annotation extends Location
 	// (typically: feature = column in an annotation table)
 	Double getNumber( String feature );
 
-	// For adding manual annotations
+	// For adding text annotations
 	void setString( String columnName, String value );
 
+	// For adding numeric annotations
+	void setNumber( String columnName, double value );
+
 	// Transform the spatial coordinates of this annotation.
 	// Note that there are also methods to transform annotations,
 	// which create a copy of the annotation;

src/main/java/org/embl/mobie/lib/bdv/view/SliceViewer.java

@@ -149,13 +149,13 @@ private void installContextMenuAndKeyboardShortCuts( )
 		final Set< String > actionsKeys = sacService.getActionsKeys();
 
 		final ArrayList< String > actions = new ArrayList< String >();
-		actions.add( sacService.getCommandName( ScreenShotMakerCommand.class ) );
-		actions.add( sacService.getCommandName( ShowRasterImagesCommand.class ) );
-		actions.add( sacService.getCommandName( ViewerTransformLoggerCommand.class ) );
-		actions.add( sacService.getCommandName( SourceInfoLoggerCommand.class ) );
-		actions.add( sacService.getCommandName( BigWarpRegistrationCommand.class ) );
-		actions.add( sacService.getCommandName( ManualRegistrationCommand.class ) );
-		actions.add( sacService.getCommandName( FlipCommand.class ) );
+		actions.add( SourceAndConverterService.getCommandName( ScreenShotMakerCommand.class ) );
+		actions.add( SourceAndConverterService.getCommandName( ShowRasterImagesCommand.class ) );
+		actions.add( SourceAndConverterService.getCommandName( ViewerTransformLoggerCommand.class ) );
+		actions.add( SourceAndConverterService.getCommandName( SourceInfoLoggerCommand.class ) );
+		actions.add( SourceAndConverterService.getCommandName( BigWarpRegistrationCommand.class ) );
+		actions.add( SourceAndConverterService.getCommandName( ManualRegistrationCommand.class ) );
+		actions.add( SourceAndConverterService.getCommandName( FlipCommand.class ) );
 		actions.add( UNDO_SEGMENT_SELECTIONS );
 		actions.add( LOAD_ADDITIONAL_VIEWS );
 		actions.add( SAVE_CURRENT_SETTINGS_AS_VIEW );

src/main/java/org/embl/mobie/lib/table/AnnotationTableModel.java

@@ -73,6 +73,7 @@ default ValuePair< Double, Double > getColumnMinMax( String columnName, ArrayLis
 	Pair< Double, Double > getMinMax( String columnName ); // for contrast limits during rendering
 	ArrayList< A > annotations();
 	void addStringColumn( String columnName );
+	void addNumericColumn( String columnName );
 	StorageLocation getStorageLocation();
 	void transform( AffineTransform3D affineTransform3D );
 	void addAnnotationListener(  AnnotationListener< A > listener );

src/main/java/org/embl/mobie/lib/table/ConcatenatedAnnotationTableModel.java

@@ -158,6 +158,24 @@ public void addStringColumn( String columnName )
 			listener.columnsAdded( null );
 	}
 
+	@Override
+	public void addNumericColumn( String columnName )
+	{
+		if ( columnNames().contains( columnName ) )
+			return;
+
+		for ( AnnotationTableModel< A > tableModel : tableModels )
+		{
+			if ( ! tableModel.columnNames().contains( columnName ) )
+			{
+				tableModel.addNumericColumn( columnName );
+			}
+		}
+
+		for ( AnnotationListener< A > listener : listeners.list )
+			listener.columnsAdded( null );
+	}
+
 	@Override
 	public StorageLocation getStorageLocation()
 	{

src/main/java/org/embl/mobie/lib/table/DefaultAnnotatedSegment.java

@@ -152,8 +152,14 @@ public void setString( String columnName, String value )
 		// TODO current implementation would require making
 		//  the static field mutable, which would not
 		//  work for multiple tables using the DefaultAnnotatedSegment
-//		columnToValue.put( columnName, value );
-//		columnToClass.put( columnName, String.class );
+		//	columnToValue.put( columnName, value );
+		//	columnToClass.put( columnName, String.class );
+		throw new UnsupportedOperationException( "Adding values to " + this.getClass() + " is not implemented." );
+	}
+
+	@Override
+	public void setNumber( String columnName, double value )
+	{
 		throw new UnsupportedOperationException( "Adding values to " + this.getClass() + " is not implemented." );
 	}
 

src/main/java/org/embl/mobie/lib/table/DistanceComputer.java

@@ -0,0 +1,42 @@
+package org.embl.mobie.lib.table;
+
+import ij.gui.GenericDialog;
+import org.embl.mobie.lib.annotation.Annotation;
+import org.embl.mobie.lib.select.SelectionModel;
+
+import java.util.Set;
+
+public class DistanceComputer
+{
+    public static < A extends Annotation > void showUI( AnnotationTableModel< A > tableModel, SelectionModel< A > selectionModel )
+    {
+        // show dialog
+        //
+        final GenericDialog gd = new GenericDialog( "" );
+        gd.addStringField( "Distance Columns RegEx", ".*" );
+        gd.addStringField( "Results Column Name", "distance" );
+        gd.showDialog();
+        if( gd.wasCanceled() ) return;
+        final String columnsRegEx = gd.getNextChoice();
+        final String resultColumnName = gd.getNextString();
+
+        // TODO
+//        tableModel.addNumericColumn( resultColumnName );
+//
+//        selectedColumns = tableModel.columnNames().stream() // TODO: select columns that match columnsRegEx
+//
+//        // for all selected selectedColumns compute the average or median value
+//        // of all selectedAnnotations
+//        Set< A > selectedAnnotations = selectionModel.getSelected();
+//        for ( A annotation : selectedAnnotations )
+//        {
+//            annotation.getNumber( column ) // TODO
+//        }
+//
+//        // for all annotations compute the Euclidean distance
+//        // to the above computed average of the selected annotations
+//
+//        tableModel.annotations()
+//        tableModel.annotation( index ).setString(  );
+    }
+}

src/main/java/org/embl/mobie/lib/table/LazyAnnotatedSegmentTableModel.java

@@ -138,6 +138,12 @@ public void addStringColumn( String columnName )
 		throw new UnsupportedOperationException( this.getClass().getName() + " does not support adding table columns." );
 	}
 
+	@Override
+	public void addNumericColumn( String columnName )
+	{
+		throw new UnsupportedOperationException( this.getClass().getName() + " does not support adding table columns." );
+	}
+
 	@Override
 	public StorageLocation getStorageLocation()
 	{
@@ -154,7 +160,7 @@ public synchronized void transform( AffineTransform3D affineTransform3D )
 	public void addAnnotationListener( AnnotationListener< AnnotatedSegment > listener )
 	{
 		listeners.add( listener );
-		if ( annotations.size() > 0 )
+		if ( ! annotations.isEmpty() )
 			listener.annotationsAdded( annotations );
 	}
 

src/main/java/org/embl/mobie/lib/table/TableView.java

@@ -32,7 +32,6 @@
 import de.embl.cba.tables.TableUIs;
 import ij.IJ;
 import ij.gui.GenericDialog;
-import loci.poi.hssf.extractor.ExcelExtractor;
 import org.embl.mobie.io.util.IOHelper;
 import org.embl.mobie.lib.annotation.AnnotationUI;
 import org.embl.mobie.lib.annotation.Annotation;
@@ -53,10 +52,7 @@
 import org.embl.mobie.lib.ui.UserInterfaceHelper;
 
 import javax.swing.*;
-import javax.swing.event.TableModelEvent;
-import javax.swing.event.TableModelListener;
 import javax.swing.table.DefaultTableCellRenderer;
-import javax.swing.table.TableColumnModel;
 import java.awt.*;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
@@ -169,6 +165,8 @@ private JMenuBar createMenuBar()
 			// menuBar.add( createPlotMenu() ); we have this already in the MoBIE UI
 		}
 
+		menuBar.add( createComputeMenu() );
+
 		return menuBar;
 	}
 
@@ -182,6 +180,13 @@ private JMenu createSelectionMenu()
 		return menu;
 	}
 
+	private JMenu createComputeMenu()
+	{
+		JMenu menu = new JMenu( "Compute" );
+		menu.add( createComputeDistanceMenuItem() );
+		return menu;
+	}
+
 	private JMenu createAnnotateMenu()
 	{
 		JMenu menu = new JMenu( "Annotate" );
@@ -241,9 +246,7 @@ private JMenuItem createAddStringColumnMenuItem()
 	{
 		final JMenuItem menuItem = new JMenuItem( "Add Text Column..." );
 		menuItem.addActionListener( e ->
-				new Thread( () -> {
-					showAddStringColumnDialog();
-				}).start()
+				new Thread( this::showAddStringColumnDialog ).start()
 		);
 		return menuItem;
 	}
@@ -318,12 +321,20 @@ private JMenuItem createSelectAllMenuItem()
 		return menuItem;
 	}
 
+	private JMenuItem createComputeDistanceMenuItem()
+	{
+		final JMenuItem menuItem = new JMenuItem( "Compute Distance to Selected Rows..." );
+		menuItem.addActionListener( e ->
+				SwingUtilities.invokeLater( ()
+						-> DistanceComputer.showUI( tableModel, selectionModel ) ) );
+		return menuItem;
+	}
+
 	private JMenuItem createSelectEqualToMenuItem()
 	{
 		final JMenuItem menuItem = new JMenuItem( "Select Equal To..." );
 		menuItem.addActionListener( e ->
-				SwingUtilities.invokeLater( () ->
-						selectEqualTo() ) );
+				SwingUtilities.invokeLater( this::selectEqualTo ) );
 		return menuItem;
 	}
 

src/main/java/org/embl/mobie/lib/table/TransformedAnnotationTableModel.java

@@ -151,6 +151,12 @@ public void addStringColumn( String columnName )
 		tableModel.addStringColumn( columnName );
 	}
 
+	@Override
+	public void addNumericColumn( String columnName )
+	{
+		tableModel.addNumericColumn( columnName );
+	}
+
 	@Override
 	public StorageLocation getStorageLocation()
 	{

src/main/java/org/embl/mobie/lib/table/saw/AbstractTableSawAnnotation.java

@@ -51,8 +51,7 @@ public Object getValue( String feature )
 	{
 		try
 		{
-			final Object object = model.getTable().get( rowIndex, model.getTable().columnIndex( feature ) );
-			return object;
+            return model.getTable().get( rowIndex, model.getTable().columnIndex( feature ) );
 		}
 		catch ( Exception e )
 		{
@@ -72,4 +71,10 @@ public void setString( String columnName, String value )
 		model.getTable().stringColumn( columnName ).set( rowIndex, value );
 	}
 
+	@Override
+	public void setNumber( String columnName, double value )
+	{
+		model.getTable().doubleColumn( columnName ).set( rowIndex, value );
+	}
+
 }

src/main/java/org/embl/mobie/lib/table/saw/TableSawAnnotationTableModel.java

@@ -40,6 +40,7 @@
 import org.embl.mobie.lib.table.DefaultValues;
 import org.embl.mobie.lib.table.TableDataFormat;
 import tech.tablesaw.api.ColumnType;
+import tech.tablesaw.api.DoubleColumn;
 import tech.tablesaw.api.StringColumn;
 import tech.tablesaw.api.Table;
 
@@ -352,6 +353,23 @@ public void addStringColumn( String columnName )
 			listener.columnsAdded( Collections.singleton( columnName ) );
 	}
 
+	@Override
+	public void addNumericColumn( String columnName )
+	{
+		update();
+
+		if ( table.containsColumn( columnName ) )
+			throw new UnsupportedOperationException("Column " + columnName + " exists already.");
+
+		final double[] doubles = new double[ table.rowCount() ];
+		Arrays.fill( doubles, 0.0 );
+		final DoubleColumn doubleColumn = DoubleColumn.create( columnName, doubles );
+		table.addColumns( doubleColumn );
+
+		for ( AnnotationListener< A > listener : listeners.list )
+			listener.columnsAdded( Collections.singleton( columnName ) );
+	}
+
 	@Override
 	public StorageLocation getStorageLocation()
 	{

src/main/java/org/embl/mobie/lib/transform/AffineTransformedAnnotatedSegment.java

@@ -144,6 +144,12 @@ public void setString( String columnName, String value )
 		annotatedSegment.setString( columnName, value );
 	}
 
+	@Override
+	public void setNumber( String columnName, double value )
+	{
+		annotatedSegment.setNumber( columnName, value );
+	}
+
 	@Override
 	public void transform( AffineTransform3D affineTransform3D )
 	{