Fix spots rendering for 2-D data

src/main/java/org/embl/mobie/MoBIE.java

@@ -39,7 +39,6 @@
 import org.embl.mobie.io.ImageDataFormat;
 import org.embl.mobie.io.imagedata.ImageData;
 import org.embl.mobie.io.util.IOHelper;
-import org.embl.mobie.io.util.S3Utils;
 import org.embl.mobie.lib.*;
 import org.embl.mobie.lib.bdv.BdvViewingMode;
 import org.embl.mobie.lib.data.*;
@@ -698,9 +697,10 @@ private void initDataSource( DataSource dataSource, String log )
 
 		if ( dataSource instanceof SpotDataSource )
 		{
+
 			// build spots image from spots table
 			final SpotImageCreator spotImageCreator = new SpotImageCreator( ( SpotDataSource ) dataSource, this );
-			DataStore.addImage( spotImageCreator.create() );
+			DataStore.addImage( spotImageCreator.get() );
 		}
 
 		if ( dataSource instanceof RegionTableSource )

src/main/java/org/embl/mobie/lib/SpotImageCreator.java

@@ -44,28 +44,41 @@
 
 public class SpotImageCreator
 {
+	private final SpotDataSource spotDataSource;
+	private final MoBIE moBIE;
 	private SpotAnnotationImage< AnnotatedSpot > spotAnnotationImage;
 
 	public SpotImageCreator( SpotDataSource dataSource, MoBIE moBIE )
 	{
-		final SpotDataSource spotDataSource = dataSource;
-		final StorageLocation tableLocation = moBIE.getTableLocation( spotDataSource.tableData );
-		final TableDataFormat tableFormat = moBIE.getTableDataFormat( spotDataSource.tableData );
+		this.spotDataSource = dataSource;
+		this.moBIE = moBIE;
+	}
 
-		Table table = TableOpener.open( tableLocation, tableFormat );
+	public SpotAnnotationImage< AnnotatedSpot > get()
+	{
+		if ( spotAnnotationImage == null )
+		{
+			final StorageLocation tableLocation = moBIE.getTableLocation( spotDataSource.tableData );
+			final TableDataFormat tableFormat = moBIE.getTableDataFormat( spotDataSource.tableData );
 
-		// TODO: maybe make the spot column names mapping configurable?
-		final TableSawAnnotationCreator< TableSawAnnotatedSpot > annotationCreator = new TableSawAnnotatedSpotCreator( table );
+			Table table = TableOpener.open( tableLocation, tableFormat );
 
-		final TableSawAnnotationTableModel< AnnotatedSpot > tableModel = new TableSawAnnotationTableModel( dataSource.getName(), annotationCreator, tableLocation, tableFormat, table );
+			// TODO: maybe make the spot column names mapping configurable?
+			final TableSawAnnotationCreator< TableSawAnnotatedSpot > annotationCreator = new TableSawAnnotatedSpotCreator( table );
 
-		final DefaultAnnData< AnnotatedSpot > spotAnnData = new DefaultAnnData<>( tableModel );
+			final TableSawAnnotationTableModel< AnnotatedSpot > tableModel =
+					new TableSawAnnotationTableModel(
+							spotDataSource.getName(),
+							annotationCreator,
+							tableLocation,
+							tableFormat,
+							table );
 
-		spotAnnotationImage = new SpotAnnotationImage( spotDataSource.getName(), spotAnnData, 1.0, spotDataSource.boundingBoxMin, spotDataSource.boundingBoxMax );
-	}
+			final DefaultAnnData< AnnotatedSpot > spotAnnData = new DefaultAnnData<>( tableModel );
+
+			spotAnnotationImage = new SpotAnnotationImage( spotDataSource.getName(), spotAnnData, 1.0, spotDataSource.boundingBoxMin, spotDataSource.boundingBoxMax );
+		}
 
-	public SpotAnnotationImage< AnnotatedSpot > create()
-	{
 		return spotAnnotationImage;
 	}
 }

src/main/java/org/embl/mobie/lib/data/CollectionTableDataSetter.java

@@ -101,16 +101,15 @@ else if ( dataType.equals( CollectionTableConstants.SPOTS )  )
                         );
                 dataset.putDataSource( spotDataSource );
 
-                // build spots image from spots table
-                final SpotImageCreator spotImageCreator = new SpotImageCreator(
-                        spotDataSource,
-                        MoBIE.getInstance() );
-
-                SpotAnnotationImage< AnnotatedSpot > spotImage = spotImageCreator.create();
-                DataStore.addImage( spotImage );
+//                // build spots image from spots table
+//                final SpotImageCreator spotImageCreator = new SpotImageCreator(
+//                        spotDataSource,
+//                        MoBIE.getInstance() );
+//                SpotAnnotationImage< AnnotatedSpot > spotImage = spotImageCreator.create();
+//                DataStore.addImage( spotImage );
 
                 SpotDisplay< AnnotatedRegion > spotDisplay = new SpotDisplay<>( name );
-                spotDisplay.sources = Collections.singletonList( spotImage.getName() );
+                spotDisplay.sources = Collections.singletonList( spotDataSource.getName() );
                 display = spotDisplay;
             }
             else // default: intensities

src/main/java/org/embl/mobie/lib/image/SpotAnnotationImage.java

@@ -31,18 +31,16 @@
 import bdv.tools.transformation.TransformedSource;
 import bdv.viewer.Source;
 import mpicbg.spim.data.sequence.FinalVoxelDimensions;
-import net.imglib2.Interval;
-import net.imglib2.KDTree;
-import net.imglib2.RealLocalizable;
-import net.imglib2.Sampler;
-import net.imglib2.Volatile;
+import net.imglib2.*;
 import net.imglib2.neighborsearch.RadiusNeighborSearchOnKDTree;
 import net.imglib2.position.FunctionRealRandomAccessible;
 import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.realtransform.RealViews;
 import net.imglib2.roi.RealMaskRealInterval;
 import net.imglib2.roi.geom.GeomMasks;
 import net.imglib2.type.numeric.integer.UnsignedIntType;
 import net.imglib2.util.Intervals;
+import net.imglib2.view.Views;
 import org.embl.mobie.lib.annotation.AnnotatedSpot;
 import org.embl.mobie.lib.source.AnnotationType;
 import org.embl.mobie.lib.source.RealRandomAccessibleIntervalTimelapseSource;
@@ -92,23 +90,47 @@ public void setRadius( double radius )
 	private void createImage()
 	{
 		final ArrayList< AS > annotations = annData.getTable().annotations();
+		System.out.println("Building KDTree with numElements = " + annotations.size());
 		kdTree = new KDTree( annotations, annotations );
 
 		if ( boundingBoxMin == null )
-			boundingBoxMin = kdTree.minAsDoubleArray();
+		{
+			boundingBoxMin = new double[ 3 ];
+			kdTree.realMin( boundingBoxMin );
+		}
 
 		if ( boundingBoxMax == null )
-			boundingBoxMax = kdTree.maxAsDoubleArray();
+		{
+			boundingBoxMax = new double[ 3 ];
+			kdTree.realMax( boundingBoxMax );
+		}
 
 		mask = GeomMasks.closedBox( boundingBoxMin, boundingBoxMax );
 
 		// TODO: code duplication with RegionLabelImage
 		final ArrayList< Integer > timePoints = configureTimePoints();
 		final Interval interval = Intervals.smallestContainingInterval( getMask() );
 		final AS annotatedSpot = annData.getTable().annotation( 0 );
-		final FunctionRealRandomAccessible< AnnotationType< AS > > realRandomAccessible = new FunctionRealRandomAccessible( 3, new LocationToAnnotatedSpotSupplier(), () -> new AnnotationType<>( annotatedSpot ) );
+
+		RealRandomAccessible< AnnotationType< AS > > rra =
+				new FunctionRealRandomAccessible(
+						kdTree.numDimensions(),
+						new LocationToAnnotatedSpotSupplier(),
+						() -> new AnnotationType<>( annotatedSpot ) );
 		//final RealRandomAccessible interpolate = Views.interpolate( new NearestNeighborSearchOnKDTree( kdTree ), new NearestNeighborSearchInterpolatorFactory() );
-		source = new RealRandomAccessibleIntervalTimelapseSource( realRandomAccessible, interval, new AnnotationType<>( annotatedSpot ), new AffineTransform3D(), name, true, null, new FinalVoxelDimensions( "", 1, 1, 1 ) );
+
+		if ( kdTree.numDimensions() == 2 )
+			rra = RealViews.addDimension( rra );
+
+		source = new RealRandomAccessibleIntervalTimelapseSource(
+				rra,
+				interval,
+				new AnnotationType<>( annotatedSpot ),
+				new AffineTransform3D(),
+				name,
+				true,
+				null,
+				new FinalVoxelDimensions( "", 1, 1, 1 ) );
 	}
 
 	@Override

src/main/java/org/embl/mobie/lib/serialize/View.java

@@ -109,8 +109,6 @@ public Map< String, Object > getSources()
 
 			if ( display instanceof SpotDisplay )
 			{
-				// TODO:
-				//   https://github.com/mobie/mobie.github.io/issues/88
 				final SpotDisplay< ? > spotDisplay = ( SpotDisplay< ? > ) display;
 				for ( String source : spotDisplay.sources )
 					sources.put( source, display );

src/main/java/org/embl/mobie/lib/source/AbstractBoundarySource.java

@@ -125,6 +125,15 @@ public RealRandomAccessible< T > getInterpolatedSource( final int t, final int l
     protected ArrayList< Integer > boundaryDimensions()
     {
         final ArrayList< Integer > dimensions = new ArrayList<>();
+
+        if ( source.getSource( 0,0 ).dimension( 2 ) == 1 )
+        {
+            // 2D source
+            dimensions.add( 0 );
+            dimensions.add( 1 );
+            return dimensions;
+        }
+
         if ( bounds != null )
         {
             // check whether the source is effectively 2D,
@@ -136,22 +145,15 @@ protected ArrayList< Integer > boundaryDimensions()
                 if ( sourceWidth > 3 * boundaryWidth )
                     dimensions.add( d );
             }
-        }
-        else if ( source.getSource( 0,0 ).dimension( 2 ) == 1 )
-        {
-            // 2D source
-            dimensions.add( 0 );
-            dimensions.add( 1 );
-        }
-        else
-        {
-            // 3D source
-            dimensions.add( 0 );
-            dimensions.add( 1 );
-            dimensions.add( 2 );
+            return dimensions;
         }
 
+        // 3D source
+        dimensions.add( 0 );
+        dimensions.add( 1 );
+        dimensions.add( 2 );
         return dimensions;
+
     }
 
     protected double[] pixelBoundaryWidth( int t, int level )

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

@@ -90,6 +90,7 @@ public static Table open( StorageLocation storageLocation, String chunk, TableDa
 				return (Table) storageLocation.data;
 			case TSV:
 			case CSV:
+			case PARQUET:
 			default:
 				return openTableFile( storageLocation, chunk, tableDataFormat );
 		}

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

@@ -60,10 +60,10 @@ public TableSawAnnotatedSpotCreator( Table table )
 	public TableSawAnnotatedSpot create( TableSawAnnotationTableModel< TableSawAnnotatedSpot > model, int rowIndex )
 	{
 		final Table table = model.getTable();
-		final float[] position = new float[ 3 ];
+		int numDimensions = zColumnIndex > -1 ? 3 : 2;
+		final float[] position = new float[ numDimensions ];
 		position[ 0 ] = ((Number) table.get( rowIndex, xColumnIndex )).floatValue();
 		position[ 1 ] = ((Number) table.get( rowIndex, yColumnIndex )).floatValue();
-
 		// FIXME kdTree issue: https://imagesc.zulipchat.com/#narrow/stream/327240-ImgLib2/topic/kdTree.20issue
 		if ( zColumnIndex > -1 )
 			position[ 2 ] = ((Number) table.get( rowIndex, zColumnIndex )).floatValue() + (float) ( 1e-3 * Math.random() );