Compute distances WIP

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

@@ -1,42 +1,135 @@
 package org.embl.mobie.lib.table;
 
+import ij.IJ;
 import ij.gui.GenericDialog;
+import net.imglib2.type.numeric.ARGBType;
+import net.imglib2.util.Pair;
+import net.imglib2.util.ValuePair;
 import org.embl.mobie.lib.annotation.Annotation;
+import org.embl.mobie.lib.color.ColoringModels;
+import org.embl.mobie.lib.color.MobieColoringModel;
+import org.embl.mobie.lib.color.NumericAnnotationColoringModel;
+import org.embl.mobie.lib.color.lut.LUTs;
 import org.embl.mobie.lib.select.SelectionModel;
+import org.jetbrains.annotations.NotNull;
+import org.scijava.util.ColorRGB;
 
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 import java.util.Set;
+import java.util.stream.Collectors;
 
 public class DistanceComputer
 {
-    public static < A extends Annotation > void showUI( AnnotationTableModel< A > tableModel, SelectionModel< A > selectionModel )
+    public static < A extends Annotation > void showUI( AnnotationTableModel< A > tableModel, SelectionModel< A > selectionModel, MobieColoringModel< A > coloringModel )
     {
         // show dialog
         //
         final GenericDialog gd = new GenericDialog( "" );
-        gd.addStringField( "Distance Columns RegEx", ".*" );
+        gd.addStringField( "Distance Columns RegEx", "anchor_.*" );
         gd.addStringField( "Results Column Name", "distance" );
+        gd.addCheckbox( "Color by Distances", true );
         gd.showDialog();
         if( gd.wasCanceled() ) return;
-        final String columnsRegEx = gd.getNextChoice();
+        final String columnNamesRegEx = gd.getNextString();
         final String resultColumnName = gd.getNextString();
+        boolean colorByDistances = gd.getNextBoolean();
+
+        List< String > selectedColumnNames = tableModel.columnNames().stream()
+                .filter( columnName -> columnName.matches( columnNamesRegEx ) )
+                .collect( Collectors.toList() );
+
+        if ( selectedColumnNames.isEmpty() )
+        {
+            IJ.log( "The regular expression " + columnNamesRegEx + " did not match any column names." );
+            return;
+        }
+
+        // for all selected selectedColumns compute the average or median value
+        // of all selectedAnnotations and store this in a Map< ColumnName, double >
+        Set< A > selectedAnnotations = selectionModel.getSelected();
+
+        // TODO provide options for other averaging methods, e.g. median
+        Map< String, Double > columnAverages = averageSelectedAnnotations( selectedColumnNames, selectedAnnotations );
+
+        // for all annotations compute the Euclidean distance
+        // to the above computed average of the selected annotations
+        tableModel.addNumericColumn( resultColumnName );
+
+        long start = System.currentTimeMillis();
+        computeEuclidanDistances( tableModel, selectedColumnNames, columnAverages, resultColumnName );
+        String distanceMetric = "Euclidan";
+        IJ.log( "Computed the " + distanceMetric + " distance of " + selectedColumnNames.size()
+                + " features for " + tableModel.annotations().size() + " annotations in " +
+                ( System.currentTimeMillis() - start ) + " ms.");
+
+        if ( colorByDistances )
+        {
+            NumericAnnotationColoringModel< A > numericModel =
+                    ColoringModels.createNumericModel(
+                            resultColumnName,
+                            LUTs.BLUE_WHITE_RED,
+                            tableModel.getMinMax( resultColumnName ),
+                            true );
+            coloringModel.setColoringModel( numericModel );
+            coloringModel.setOpacityNotSelected( 1.0 );
+            coloringModel.setSelectionColor( new ARGBType( ARGBType.rgba( 255, 255, 0, 255 ) ) );
+        }
+
+    }
+
+    @NotNull
+    private static < A extends Annotation > Map< String, Double > averageSelectedAnnotations( List< String > selectedColumnNames, Set< A > selectedAnnotations )
+    {
+        Map<String, Double> columnAverages = new HashMap<>();
+        for (String column : selectedColumnNames ) {
+            double sum = selectedAnnotations.stream()
+                    .mapToDouble(annotation -> annotation.getNumber(column).doubleValue())
+                    .sum();
+            double average = sum / selectedAnnotations.size();
+            columnAverages.put(column, average);
+        }
+        return columnAverages;
+    }
+
+    @NotNull
+    private static < A extends Annotation > Map< String, Double > medianSelectedAnnotations( List< String > selectedColumnNames, Set< A > selectedAnnotations )
+    {
+        Map<String, Double> columnMedians = new HashMap<>();
+        for (String column : selectedColumnNames) {
+            List<Double> values = selectedAnnotations.stream()
+                    .map(annotation -> annotation.getNumber(column).doubleValue())
+                    .sorted()
+                    .collect(Collectors.toList());
+            double median;
+            int size = values.size();
+            if (size % 2 == 0) {
+                median = (values.get(size / 2 - 1) + values.get(size / 2)) / 2.0;
+            } else {
+                median = values.get(size / 2);
+            }
+            columnMedians.put(column, median);
+        }
+        return columnMedians;
+    }
+
+    private static < A extends Annotation > void computeEuclidanDistances( AnnotationTableModel< A > tableModel, List< String > selectedColumnNames, Map< String, Double > columnAverages, String resultColumnName )
+    {
+        // Compute Euclidean distances
+        List< A > annotations = tableModel.annotations();
+
+        for ( A annotation : annotations )
+        {
+            double sumOfSquares = 0.0;
+            for ( String column : selectedColumnNames ) {
+                final double value = annotation.getNumber(column).doubleValue();
+                final double average = columnAverages.get(column);
+                sumOfSquares += Math.pow(value - average, 2);
+            }
+            final double euclideanDistance = Math.sqrt( sumOfSquares );
+            annotation.setNumber( resultColumnName, euclideanDistance);
+        }
 
-        // 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/SwingTableModel.java

@@ -101,12 +101,16 @@ public Object getValueAt( int rowIndex, int columnIndex )
 	@Override
 	public void setValueAt( Object aValue, int rowIndex, int columnIndex )
 	{
+		final String columnName = getColumnName( columnIndex );
 		final Class< ? > columnClass = getColumnClass( columnIndex );
 		if ( columnClass.equals( String.class ) )
 		{
-			final String columnName = getColumnName( columnIndex );
 			tableModel.annotations().get( rowIndex ).setString( columnName, aValue.toString() );
 		}
+		else if ( columnClass.isAssignableFrom( Number.class ) )
+		{
+			tableModel.annotations().get( rowIndex ).setNumber( columnName, ( Double ) aValue );
+		}
 	}
 
 	@Override

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

@@ -326,7 +326,7 @@ private JMenuItem createComputeDistanceMenuItem()
 		final JMenuItem menuItem = new JMenuItem( "Compute Distance to Selected Rows..." );
 		menuItem.addActionListener( e ->
 				SwingUtilities.invokeLater( ()
-						-> DistanceComputer.showUI( tableModel, selectionModel ) ) );
+						-> DistanceComputer.showUI( tableModel, selectionModel, coloringModel ) ) );
 		return menuItem;
 	}