WIP

src/main/java/org/embl/mobie/lib/hcs/HCSPlateAdder.java

@@ -227,6 +227,6 @@ private String getSiteID( Plate plate, Channel channel, Well well, Site site )
 
 	private String getWellID( Plate plate, Channel channel, Well well )
 	{
-		return Strings.join( "-", Arrays.asList( plate.getName(), "ch" + channel.getName(), "w" + well.getName() ) );
+		return Strings.join( "-", Arrays.asList( plate.getName(), channel.getName(), well.getName() ) );
 	}
 }

src/main/java/org/embl/mobie/lib/hcs/Plate.java

@@ -59,6 +59,7 @@
 import java.util.concurrent.ExecutionException;
 import java.util.stream.Collectors;
 import java.util.stream.IntStream;
+import java.util.stream.Stream;
 
 import static org.embl.mobie.lib.MoBIEHelper.computeMinMax;
 
@@ -111,8 +112,9 @@ public Plate( String hcsDirectory, @Nullable VoxelDimensions voxelDimensions ) t
 			}
 
 			imagePaths = OMEZarrHCSHelper.imagePathsFromMetadata( hcsDirectory );
-
-			ImageData< ? > imageData = ImageDataOpener.open( imagePaths.get( 0 ), imageDataFormat, ThreadHelper.sharedQueue );
+			Collections.sort( imagePaths );
+			String referenceImagePath = imagePaths.get( 0 );
+			ImageData< ? > imageData = ImageDataOpener.open( referenceImagePath, imageDataFormat, ThreadHelper.sharedQueue );
 			int numChannels = imageData.getNumDatasets();
 			List< String > channelNames = IntStream.range( 0, numChannels )
 					.mapToObj( imageData::getName )
@@ -311,7 +313,7 @@ private void buildPlateMap( List< String > imagePaths )
 						IJ.log( "" );
 						final Map< String, Entity > attributes = viewSetup.getAttributes();
 						IJ.log( "Image index:" + imageIndex );
-						IJ.log( "Series index: " + ( ( SeriesIndex ) attributes.get( "seriesindex" ) ).getId() );
+						IJ.log( "Series index: " + attributes.get( "seriesindex" ).getId() );
 						IJ.log( "Setup name: " + viewSetup.getName() );
 						IJ.log( "File name: " + new File( imagePath ).getName() );
 						site = new Site( siteGroup, imageDataFormat, spimDataPlate, imageIndex );

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

@@ -127,6 +127,7 @@ public void removeTableModelListener( TableModelListener l )
 
 	public void tableChanged()
 	{
+		// https://github.com/mobie/mobie-viewer-fiji/issues/1146
 		for ( TableModelListener listener : tableModelListeners )
 		{
 			final TableModelEvent tableModelEvent = new TableModelEvent( this, TableModelEvent.HEADER_ROW );

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

@@ -28,6 +28,7 @@
  */
 package org.embl.mobie.lib.table;
 
+import IceInternal.Ex;
 import de.embl.cba.tables.Logger;
 import de.embl.cba.tables.TableUIs;
 import ij.IJ;
@@ -111,6 +112,7 @@ public void close()
 
 	public void show()
 	{
+
 		// Prefetch the columns and wait a bit as this hopefully makes it less likely that
 		// there are errors thrown by Java Swing when rendering the table window
 		// below during frame.pack()
@@ -119,8 +121,10 @@ public void show()
 		for ( int columnIndex = 0; columnIndex < columnCount; columnIndex++ )
 		{
 			TableColumn column = columnModel.getColumn( columnIndex );
+			if ( column == null )
+				throw new NullPointerException("");
 		}
-		IJ.log( "Showing table " + tableName + " with " + columnCount + " columns.");
+		IJ.log( "Showing table \"" + tableName + "\" with " + columnCount + " columns.");
 		IJ.wait( 200 );
 
 		final JPanel panel = new JPanel( new GridLayout( 1, 0 ) );
@@ -130,7 +134,6 @@ public void show()
 				JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED );
 		panel.add( scrollPane );
 
-		jTable.setAutoResizeMode( JTable.AUTO_RESIZE_OFF );
 		panel.updateUI();
 		panel.setOpaque( true );
 
@@ -139,31 +142,37 @@ public void show()
 		frame.setJMenuBar( menuBar );
 		frame.setContentPane( panel );
 
-		// Display the window
 		try
 		{
-			frame.pack();
+			// Adding a delay
+			Timer timer = new Timer(200, e -> {
+				frame.pack();
+				frame.setVisible(true);
+			});
+			timer.setRepeats(false);
+			timer.start();
 		}
 		catch ( Exception e )
 		{
 			IJ.log("Error showing table: " + tableName );
 		}
 
-		// Replace closing by making it invisible
 		frame.setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
 		frame.addWindowListener( new WindowAdapter() {
 			public void windowClosing( WindowEvent ev) {
 				frame.setVisible( false );
 			}
-		});
+		});	//frame.pack();
 	}
 
 	private void configureJTable()
 	{
 		swingTableModel = new SwingTableModel( tableModel );
 		jTable = new JTable( swingTableModel );
+		TableColumnModel columnModel = jTable.getColumnModel();
+		TableColumn column = columnModel.getColumn( 0 );
 		jTable.updateUI();
-		jTable.setPreferredScrollableViewportSize( new Dimension(500, 200) );
+		jTable.setPreferredScrollableViewportSize( new Dimension( 500, 200 ) );
 		jTable.setFillsViewportHeight( true );
 		jTable.setAutoCreateRowSorter( true );
 		jTable.setRowSelectionAllowed( true );
@@ -316,8 +325,11 @@ private synchronized void updateTable()
 	{
 		if ( jTable == null ) return;
 
+		// https://github.com/mobie/mobie-viewer-fiji/issues/1146
 		swingTableModel.tableChanged();
-		repaintTable();
+
+		if ( jTable.isVisible() )
+			repaintTable();
 	}
 
 	private JMenuItem createSaveTableAsMenuItem()
@@ -850,28 +862,38 @@ private synchronized void repaintTable()
 	@Override
 	public void annotationsAdded( Collection< A > annotations )
 	{
+		// https://github.com/mobie/mobie-viewer-fiji/issues/1146
 		updateTable();
 	}
 
 	@Override
 	public synchronized void columnsAdded( Collection< String > columns )
 	{
-		updateTable();
-		// TODO: errors such as
-		// Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 31 >= 31
-		//	at java.util.Vector.elementAt(Vector.java:479)
-		//	at javax.swing.table.DefaultTableColumnModel
-//		For debugging:
-//		final List< String > columnNames = tableModel.columnNames();
-//		final int swingColumnCount = swingTableModel.getColumnCount();
-//		final TableColumnModel columnModel = jTable.getColumnModel();
-//		final int jTableColumnCount = columnModel.getColumnCount();
-////		IJ.wait( 100 ); // maybe this avoids the updating error?
-//		for ( int i = 0; i < columnNames.size(); i++ )
-//		{
-//			System.out.println( columnNames.get( i ) );
-//			System.out.println( swingTableModel.getColumnName( i ) );
-//			System.out.println( jTable.getColumnName( i ) );
-//		}
+		try
+		{
+			updateTable();
+		}
+		catch ( Exception e )
+		{
+			// TODO: errors such as
+			// Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 31 >= 31
+			//	at java.util.Vector.elementAt(Vector.java:479)
+			//	at javax.swing.table.DefaultTableColumnModel
+			// For debugging:
+			System.out.println("Error updating " + tableName );
+			final List< String > columnNames = tableModel.columnNames();
+			final int swingColumnCount = swingTableModel.getColumnCount();
+			final TableColumnModel columnModel = jTable.getColumnModel();
+			final int jTableColumnCount = columnModel.getColumnCount();
+			IJ.wait( 100 ); // maybe this avoids the updating error?
+			for ( int i = 0; i < columnNames.size(); i++ )
+			{
+				System.out.println( columnNames.get( i ) );
+				System.out.println( swingTableModel.getColumnName( i ) );
+				System.out.println( jTable.getColumnName( i ) );
+			}
+			throw new RuntimeException( e );
+		}
+
 	}
 }

src/main/java/org/embl/mobie/lib/view/ViewManager.java

@@ -342,18 +342,12 @@ public void initData( View view )
 				final MergedGridTransformation mergedGridTransformation = ( MergedGridTransformation ) transformOrDisplay;
 				if ( mergedGridTransformation.metadataSource != null )
 				{
-					if ( dataSourceName.equals( mergedGridTransformation.metadataSource ) )
-						dataSource.preInit( true );
-					else
-						dataSource.preInit( false );
+                    dataSource.preInit( dataSourceName.equals( mergedGridTransformation.metadataSource ) );
 				}
 				else // no metadata source specified, use the first in the grid as metadata source
 				{
 					final String firstImageInGrid = mergedGridTransformation.getSources().get( 0 );
-					if ( dataSourceName.equals( firstImageInGrid ) )
-						dataSource.preInit( true );
-					else
-						dataSource.preInit( false );
+                    dataSource.preInit( dataSourceName.equals( firstImageInGrid ) );
 				}
 			}
 			else
@@ -709,18 +703,18 @@ private void initImageVolumeViewer( ImageDisplay< ? > imageDisplay )
 	private void initTableView( AbstractAnnotationDisplay< ? extends Annotation > display )
 	{
 		display.tableView = new TableView( display );
+		display.selectionModel.listeners().add( display.tableView );
+		display.coloringModel.listeners().add( display.tableView );
+
 		// TODO: currently we must show the table here
 		//   in order to instantiate the window.
 		//   This window is needed in {@code UserInterfaceHelper}
 		//   in the function {@code createWindowVisibilityCheckbox},
 		//   in which the table window will be
 		//   hidden, if {@code display.showTable == false}.
 		//   It would be good if we would not have to show it.
-
 		display.tableView.show();
 		setTablePosition( display.sliceViewer.getWindow(), display.tableView.getWindow() );
-		display.selectionModel.listeners().add( display.tableView );
-		display.coloringModel.listeners().add( display.tableView );
 	}
 
 	private void setTablePosition( Window reference, Window table )

src/test/java/debug/DebugIssue1066.java

@@ -43,7 +43,11 @@ public static void main( String[] args ) throws IOException
 		imageJ.ui().showUI();
 
 		OpenHCSDatasetCommand command = new OpenHCSDatasetCommand();
-		command.hcsDirectory = "/Users/tischer/Downloads/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr";
+		//command.hcsDirectory = "/Users/tischer/Downloads/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr";
+
+		// https://forum.image.sc/t/ome-zarr-hcs-with-labels-on-s3/97327/3
+		command.hcsDirectory = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0001A/2551.zarr";
+
 		command.run();
 	}
 }