Merge pull request #1046 from mobie/issue1044

Issue1044

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

@@ -21,25 +21,26 @@
 
 public class AnnotatedLabelImageCreator
 {
-	private final MoBIE moBIE;
 	private AnnotationLabelImage< TableSawAnnotatedSegment > annotatedLabelImage;
 
 	public AnnotatedLabelImageCreator( MoBIE moBIE, SegmentationDataSource dataSource, Image< ? > image )
 	{
-		this.moBIE = moBIE;
-
 		if ( dataSource.tableData != null )
 		{
+			//System.out.println(dataSource.getName() + ": initialising.." );
+
 			final StorageLocation tableLocation = moBIE.getTableLocation( dataSource.tableData );
 			final TableDataFormat tableFormat =  moBIE.getTableDataFormat( dataSource.tableData );
 
+			//System.out.println( dataSource.getName() + ": pre-init: " + dataSource.preInit() );
+
 			Table table = dataSource.preInit() ?
 					TableOpener.open( tableLocation, tableFormat ) : null;
 
-			SegmentColumnNames segmentColumnNames = table != null ?
-					TableDataFormat.getSegmentColumnNames( table.columnNames() ) : null;
+			//SegmentColumnNames segmentColumnNames = table != null ?
+			//		TableDataFormat.getSegmentColumnNames( table.columnNames() ) : null;
 
-			final TableSawAnnotatedSegmentCreator annotationCreator = new TableSawAnnotatedSegmentCreator( segmentColumnNames, table );
+			final TableSawAnnotatedSegmentCreator annotationCreator = new TableSawAnnotatedSegmentCreator( table );
 
 			final TableSawAnnotationTableModel< TableSawAnnotatedSegment >  tableModel = new TableSawAnnotationTableModel( dataSource.getName(), annotationCreator, tableLocation, tableFormat, table );
 

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

@@ -52,9 +52,6 @@ public interface Annotation extends Location
 	// For adding manual annotations
 	void setString( String columnName, String value );
 
-	// For merging tables.
-	String[] idColumns();
-
 	// 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/image/StitchedImage.java

@@ -222,12 +222,12 @@ private void setPositions( List< ? extends Image< T > > images, List< int[] > po
 			this.positions = new ArrayList<>();
 			for ( int[] position : positions )
 			{
-				final int[] thisPosition = new int[ 2 ];
+				final int[] zeroMinPosition = new int[ 2 ];
 				for ( int d = 0; d < 2; d++ )
 				{
-					thisPosition[ d ] = position[ d ] - min[ d ];
+					zeroMinPosition[ d ] = position[ d ] - min[ d ];
 				}
-				this.positions.add( thisPosition );
+				this.positions.add( zeroMinPosition );
 			}
 		}
 	}
@@ -490,8 +490,8 @@ protected Map< Integer, List< RandomAccessibleInterval< V > > > stitchVolatileTi
 			{
 				final V background = volatileType.createVariable();
 				background.setValid( true );
-				final FunctionRandomAccessible< V > stichedTimepointAtLevel = new FunctionRandomAccessible( 3, new VolatileValueFromTilesFetcherSupplier( tileStore, t, level, background ).get(), () -> volatileType.createVariable() );
-				final IntervalView< V > rai = Views.interval( stichedTimepointAtLevel, getInterval( level ) );
+				final FunctionRandomAccessible< V > stitchedTimepointAtLevel = new FunctionRandomAccessible( 3, new VolatileValueFromTilesFetcherSupplier( tileStore, t, level, background ).get(), () -> volatileType.createVariable() );
+				final IntervalView< V > rai = Views.interval( stitchedTimepointAtLevel, getInterval( level ) );
 				stitched.get( t ).add( rai );
 			}
 		}

src/main/java/org/embl/mobie/lib/serialize/transformation/AbstractGridTransformation.java

@@ -34,8 +34,8 @@ public abstract class AbstractGridTransformation implements Transformation
 {
 	// Serialization
 
-	public List< int[] > positions;
+	public List< int[] > positions; // x,y positions of the image tiles
 
-	public double margin = 0.1; // 0.1;
+	public double margin = 0.1;
 
 }

src/main/java/org/embl/mobie/lib/serialize/transformation/MergedGridTransformation.java

@@ -32,17 +32,18 @@
 
 public class MergedGridTransformation extends AbstractGridTransformation
 {
-	// Serialization TODO: make fields private and add getter and setter methods
+	// Serialization
 
 	public List< String > sources; // required
 
-	private String mergedGridSourceName = "merged image"; // required => name of corresponding StitchedImage
-
 	public String metadataSource; // optional, this improves performance (a lot)
 
 	public boolean centerAtOrigin = false; // TODO: should actually be true, but: https://github.com/mobie/mobie-viewer-fiji/issues/685#issuecomment-1108179599
 
+	private String mergedGridSourceName = "merged image"; // required => name of corresponding StitchedImage
+
 	// Runtime
+
 	public transient int timepoints = 1; // the number of timepoints that the sources span
 
 	public transient boolean lazyLoadTables = true;

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

@@ -106,8 +106,8 @@ public void loadTableChunk( String tableChunk )
 		for ( AnnotationTableModel< A > tableModel : tableModels )
 			tableModel.loadTableChunk( tableChunk );
 
-		// TODO: it is not logical that this method does not trigger
-		//   an annotation listener...
+		for ( AnnotationListener< A > listener : listeners.list )
+			listener.columnsAdded( null );
 	}
 
 	@Override

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

@@ -157,12 +157,6 @@ public void setString( String columnName, String value )
 		throw new UnsupportedOperationException( "Adding values to " + this.getClass() + " is not implemented." );
 	}
 
-	@Override
-	public String[] idColumns()
-	{
-		return idColumns;
-	}
-
 	@Override
 	public void transform( AffineTransform3D affineTransform3D )
 	{

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

@@ -128,12 +128,6 @@ public String source()
 		return source;
 	}
 
-	@Override
-	public String[] idColumns()
-	{
-		return idColumns;
-	}
-
 	@Override
 	public void transform( AffineTransform3D affineTransform3D )
 	{

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

@@ -31,6 +31,7 @@
 import org.embl.mobie.lib.table.ColumnNames;
 import tech.tablesaw.api.Table;
 
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 
@@ -40,6 +41,7 @@ public class TableSawAnnotatedRegionCreator implements TableSawAnnotationCreator
 	private final int timePointColumnIndex;
 	private final double relativeDilation;
 	private int regionIdColumnIndex;
+	private ArrayList< String > idColumns;
 
 	public TableSawAnnotatedRegionCreator( Table table, Map< String, List< String > > regionIdToImageNames, double relativeDilation )
 	{
@@ -48,6 +50,9 @@ public TableSawAnnotatedRegionCreator( Table table, Map< String, List< String >
 		this.regionIdToImageNames = regionIdToImageNames;
 		regionIdColumnIndex = columnNames.indexOf( ColumnNames.REGION_ID );
 		timePointColumnIndex = columnNames.indexOf( ColumnNames.TIMEPOINT );
+		idColumns = new ArrayList<>();
+		idColumns.add( ColumnNames.REGION_ID );
+		idColumns.add( ColumnNames.TIMEPOINT );
 	}
 
 	@Override
@@ -71,4 +76,10 @@ public int[] removeColumns()
 	{
 		return new int[ 0 ];
 	}
+
+	@Override
+	public List< String > getIDColumns()
+	{
+		return idColumns;
+	}
 }

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

@@ -134,12 +134,6 @@ public String source()
 		return source;
 	}
 
-	@Override
-	public String[] idColumns()
-	{
-		return idColumns;
-	}
-
 	@Override
 	public void transform( AffineTransform3D affineTransform3D )
 	{

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

@@ -34,6 +34,7 @@
 import tech.tablesaw.api.Table;
 
 import javax.annotation.Nullable;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.concurrent.atomic.AtomicBoolean;
@@ -51,12 +52,11 @@ public class TableSawAnnotatedSegmentCreator implements TableSawAnnotationCreato
 	private AtomicBoolean columnsInitialised = new AtomicBoolean( false );
 	private boolean is3D;
 	private boolean hasBoundingBox;
+	private ArrayList< String > idColumns;
 
-	public TableSawAnnotatedSegmentCreator(
-			@Nullable SegmentColumnNames segmentColumnNames,
-			@Nullable Table table )
+	public TableSawAnnotatedSegmentCreator( @Nullable Table table )
 	{
-		this.segmentColumnNames = segmentColumnNames;
+		//this.segmentColumnNames = segmentColumnNames;
 		if ( table != null )
 			initColumns( table );
 	}
@@ -67,8 +67,12 @@ private synchronized void initColumns( Table table )
 
 		final List< String > columnNames = table.columnNames();
 
-		if ( segmentColumnNames == null )
-			segmentColumnNames = TableDataFormat.getSegmentColumnNames( columnNames );
+		segmentColumnNames = TableDataFormat.getSegmentColumnNames( columnNames );
+
+		idColumns = new ArrayList<>();
+		idColumns.add( segmentColumnNames.labelIdColumn() );
+		idColumns.add( segmentColumnNames.timePointColumn() );
+		idColumns.add( segmentColumnNames.labelImageColumn() );
 
 		labelIdColumnIndex = columnNames.indexOf( segmentColumnNames.labelIdColumn() );
 		if ( labelIdColumnIndex == -1 )
@@ -94,6 +98,7 @@ private synchronized void initColumns( Table table )
 
 		hasBoundingBox = bbMinColumnIndices[ 0 ] > -1;
 
+
 	}
 
 	@Override
@@ -153,4 +158,10 @@ private FinalRealInterval boundingBox( Table table, int rowIndex )
 
 		return boundingBox;
 	}
+
+	@Override
+	public List< String > getIDColumns()
+	{
+		return idColumns;
+	}
 }

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

@@ -102,12 +102,6 @@ public String source()
 		return source;
 	}
 
-	@Override
-	public String[] idColumns()
-	{
-		return idColumns;
-	}
-
 	@Override
 	public void transform( AffineTransform3D affineTransform3D )
 	{

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

@@ -31,6 +31,7 @@
 import org.embl.mobie.lib.table.ColumnNames;
 import tech.tablesaw.api.Table;
 
+import java.util.ArrayList;
 import java.util.List;
 
 public class TableSawAnnotatedSpotCreator implements TableSawAnnotationCreator< TableSawAnnotatedSpot >
@@ -40,6 +41,7 @@ public class TableSawAnnotatedSpotCreator implements TableSawAnnotationCreator<
 	private final int yColumnIndex;
 	private final int zColumnIndex;
 	private int timePointColumnIndex;
+	private ArrayList< String > idColumns;
 
 	public TableSawAnnotatedSpotCreator( Table table )
 	{
@@ -49,6 +51,9 @@ public TableSawAnnotatedSpotCreator( Table table )
 		yColumnIndex = columnNames.indexOf( ColumnNames.SPOT_Y );
 		zColumnIndex = columnNames.indexOf( ColumnNames.SPOT_Z );
 		timePointColumnIndex = columnNames.indexOf( ColumnNames.TIMEPOINT );
+		idColumns = new ArrayList<>();
+		idColumns.add( ColumnNames.SPOT_ID );
+		idColumns.add( ColumnNames.TIMEPOINT );
 	}
 
 	@Override
@@ -77,4 +82,10 @@ public int[] removeColumns()
 	{
 		return new int[]{ xColumnIndex, yColumnIndex, zColumnIndex };
 	}
+
+	@Override
+	public List< String > getIDColumns()
+	{
+		return idColumns;
+	}
 }

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

@@ -30,10 +30,14 @@
 
 import org.embl.mobie.lib.annotation.Annotation;
 
+import java.util.List;
+
 
 public interface TableSawAnnotationCreator< A extends Annotation >
 {
 	A create( TableSawAnnotationTableModel< A > tableModel, int rowIndex );
 
 	int[] removeColumns();
+
+	List< String > getIDColumns();
 }

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

@@ -171,14 +171,16 @@ private void joinTable( Table additionalTable )
 	{
 		// join additional table
 		// some columns, e.g. timepoint, are optional and thus
-		// are only used for merging if they are actually present
+		// may be missing in the parent table;
+		// thus we only use columns for merging that are actually present
 		final List< String > columnNames = table.columnNames();
-		final List< String > mergeByColumnNames = Arrays.stream( annotation( 0 ).idColumns() ).filter( column -> columnNames.contains( column ) ).collect( Collectors.toList() );
+		//final String[] idColumns = annotation( 0 ).idColumns();
+		final List< String > idColumns = annotationCreator.getIDColumns();
+		final List< String > mergeByColumnNames = idColumns.stream().filter( column -> columnNames.contains( column ) ).collect( Collectors.toList() );
 
-		// note that the below joining changes the table object,
+		// the below table merging changes the table object,
 		// thus other classes that need that table object
-		// need to retrieve the new one using the {@code getTable()}
-		// method
+		// need to retrieve the new table using {@code getTable()}
 		try
 		{
 			final List< String > additionalColumnNames = additionalTable.columnNames().stream().filter( col -> ! mergeByColumnNames.contains( col ) ).collect( Collectors.toList() );

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

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

src/test/java/debug/DebugIssue1044.java

@@ -0,0 +1,19 @@
+package debug;
+
+import net.imagej.ImageJ;
+import org.embl.mobie.MoBIE;
+import org.embl.mobie.MoBIESettings;
+
+import java.io.IOException;
+
+public class DebugIssue1044
+{
+	public static void main( String[] args ) throws IOException
+	{
+		final ImageJ imageJ = new ImageJ();
+		imageJ.ui().showUI();
+
+		new MoBIE("/Users/tischer/Downloads/minimal-mobie/minimal-mobie-project", MoBIESettings.settings().view( "segmentations" ) );// .getViewManager().show( "cell-segmentation" );
+
+	}
+}