perf: better memory cleanup

* seems to address the worst offenders
* some of this cleanup is likely overkill

see #134

src/main/java/bdv/gui/BigWarpViewerFrame.java

@@ -96,7 +96,7 @@ public BigWarpViewerFrame(
 	}
 
 	public BigWarpViewerFrame(
-			BigWarp<?> bw,
+			final BigWarp<?> bw,
 			final int width, final int height,
 			final List< SourceAndConverter< ? > > sources,
 			final List< ConverterSetup > converterSetups,
@@ -256,4 +256,16 @@ public Behaviours getTransformBehaviours()
 		return transformBehaviours;
 	}
 
+	@Override
+	public void dispose()
+	{
+		super.dispose();
+		keybindings.removeActionMap("bw");
+		keybindings.removeInputMap("bw");
+		keybindings.removeActionMap("bwv");
+		keybindings.removeInputMap("bwv");
+		keybindings.removeActionMap("navigation");
+		keybindings.removeInputMap("navigation");
+	}
+
 }

src/main/java/bdv/gui/LandmarkKeyboardProcessor.java

@@ -24,15 +24,13 @@
 import java.awt.KeyEventPostProcessor;
 import java.awt.event.KeyEvent;
 
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.realtransform.AffineTransform3D;
 import bigwarp.BigWarp;
 
 public class LandmarkKeyboardProcessor implements KeyEventPostProcessor 
 {
-	BigWarp bw;
+	BigWarp<?> bw;
 
-	public LandmarkKeyboardProcessor( BigWarp bw )
+	public LandmarkKeyboardProcessor( BigWarp<?> bw )
 	{
 		this.bw = bw;
 	}
@@ -53,4 +51,9 @@ public boolean postProcessKeyEvent(KeyEvent ke ) {
 		return false;
 	}
 
+	public void dispose() {
+
+		bw = null;
+	}
+
 }

src/main/java/bdv/viewer/BigWarpOverlay.java

@@ -140,7 +140,6 @@ public void paint( final Graphics2D g )
 				textBoxColor = Color.BLACK;
 				textBoxColorHl = new Color( color.getRed(), color.getGreen(), color.getBlue(), 255 );
 				textBoxColor = new Color( color.getRed(), color.getGreen(), color.getBlue(), 128 );
-
 			}
 
 			final int nRows = landmarkModel.getRowCount();
@@ -161,7 +160,7 @@ public void paint( final Graphics2D g )
 				// otherwise, take the fixed point
 				boolean copySuccess = false;
 				if( isMoving ) {
-					if( viewer.isInFixedImageSpace() ) {
+					if( !isMoving ) {
 						if( landmarkModel.isWarped(index))
 							copySuccess = landmarkModel.copyWarpedPointSafe(spot, index);
 						else

src/main/java/bdv/viewer/BigWarpViewerPanel.java

@@ -23,21 +23,18 @@
 
 import bdv.cache.CacheControl;
 import bdv.gui.BigWarpViewerOptions;
-import bdv.img.WarpedSource;
 import bdv.util.Affine3DHelpers;
 import bdv.util.Prefs;
 import bdv.viewer.animate.RotationAnimator;
 import bdv.viewer.animate.SimilarityTransformAnimator3D;
 import bdv.viewer.overlay.BigWarpMaskSphereOverlay;
 import bigwarp.BigWarp;
 import bigwarp.BigWarpData;
-import bigwarp.source.SourceInfo;
 import bigwarp.util.Rotation2DHelpers;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.List;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.realtransform.Translation3D;
 
@@ -49,8 +46,6 @@ public class BigWarpViewerPanel extends ViewerPanel
 
 	public static final int TARGET_GROUP_INDEX = 1;
 
-	protected final BigWarpData<?> bwData;
-
 	protected BigWarpViewerSettings viewerSettings;
 
 	protected BigWarpOverlay overlay;
@@ -89,7 +84,6 @@ public BigWarpViewerPanel( final BigWarpData bwData, final BigWarpViewerSettings
 	{
 		// TODO compiler complains if the first argument is 'final BigWarpData<?> bwData'
 		super( bwData.sources, 1, cache, optional.getViewerOptions( isMoving ) );
-		this.bwData = bwData;
 		this.viewerSettings = viewerSettings;
 		this.isMoving = isMoving;
 		this.updateOnDrag = !isMoving; // update on drag only for the fixed
@@ -103,8 +97,6 @@ public BigWarpViewerPanel( final BigWarpData bwData, final BigWarpViewerSettings
 				dragOverlay.paint( ( Graphics2D ) g );
 			}
 		} );
-
-		//updateGrouping();
 	}
 
 	@Override
@@ -130,16 +122,6 @@ public void precomputeRotations2d( final AffineTransform3D initialViewTransform
 		}
 	}
 
-//	public void toggleTextOverlayVisible()
-//	{
-//		textOverlayVisible = !textOverlayVisible;
-//	}
-//
-//	public void toggleBoxOverlayVisible()
-//	{
-//		boxOverlayVisible = !boxOverlayVisible;
-//	}
-
 	public void setHoveredIndex( int index )
 	{
 		if( index != overlay.getHoveredIndex() )
@@ -164,59 +146,13 @@ public void setHoveredIndex( int index )
 	@Deprecated
 	public int updateGrouping()
 	{
-		final SynchronizedViewerState state = state();
-		synchronized ( state )
-		{
-			final List< SourceAndConverter< ? > > moving = new ArrayList<>();
-			final List< SourceAndConverter< ? > > target = new ArrayList<>();
-
-			int idx = 0;
-			for ( final SourceInfo sourceInfo : bwData.sourceInfos.values() )
-			{
-				if (sourceInfo.isMoving()) {
-					moving.add( state.getSources().get( idx ) );
-				} else {
-					target.add( state.getSources().get( idx ) );
-				}
-				idx++;
-			}
-
-			state.clearGroups();
-
-			final SourceGroup movingGroup = new SourceGroup();
-			state.addGroup( movingGroup );
-			state.setGroupName( movingGroup, "moving images" );
-			state.addSourcesToGroup( moving, movingGroup );
-
-			final SourceGroup targetGroup = new SourceGroup();
-			state.addGroup( targetGroup );
-			state.setGroupName( targetGroup, "fixed images" );
-			state.addSourcesToGroup( target, targetGroup );
-
-			// make only moving and target image groups active in fused mode
-			state.setGroupActive( movingGroup, true );
-			state.setGroupActive( targetGroup, true );
-
-			// only turn grouping enabled by default if there are multiple moving or
-			// target images
-			if ( moving.size() > 1 || target.size() > 1 )
-				state.setDisplayMode( state.getDisplayMode().withGrouping( true ) );
-
-			state.setCurrentGroup( isMoving ? movingGroup : targetGroup );
-
-			// TODO: This does not what the javadoc says. Change javadoc? Return void.
-			return state.getGroups().size();
-		}
+		return -1;
 	}
 
+	@Deprecated
 	public boolean isInFixedImageSpace()
 	{
-		if( bwData.numMovingSources() < 1 )
-			return true;
-		else
-		{
-			return !isMoving || ( ( WarpedSource< ? > ) ( ( bwData.getMovingSource( 0 )).getSpimSource() ) ).isTransformed();
-		}
+		return !isMoving;
 	}
 
 	public boolean doUpdateOnDrag()

src/main/java/bigwarp/BigWarp.java

@@ -39,7 +39,6 @@
 import java.io.FileWriter;
 import java.io.IOException;
 import java.lang.reflect.Field;
-import java.lang.reflect.InvocationTargetException;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.text.SimpleDateFormat;
@@ -231,10 +230,11 @@ public class BigWarp< T >
 
 	protected BigWarpData< T > data;
 
-	protected final SetupAssignments setupAssignments;
-	protected final WarpVisFrame warpVisDialog;
+	protected SetupAssignments setupAssignments;
 
-	protected final HelpDialog helpDialog;
+	protected WarpVisFrame warpVisDialog;
+
+	protected HelpDialog helpDialog;
 
 	private final KeymapManager keymapManager;
 
@@ -310,6 +310,8 @@ public class BigWarp< T >
 
 	protected MaskedSourceEditorMouseListener maskSourceMouseListenerQ;
 
+	private LandmarkKeyboardProcessor keyboardProc;
+
 	protected BigWarpMessageAnimator message;
 
 	protected final Set< KeyEventPostProcessor > keyEventPostProcessorSet = new HashSet< KeyEventPostProcessor >();
@@ -359,7 +361,7 @@ public class BigWarp< T >
 
 	protected FileDialog fileDialog;
 
-	final JFileChooser fileChooser;
+	protected final JFileChooser fileChooser;
 
 	protected File autoSaveDirectory;
 
@@ -615,7 +617,6 @@ public boolean accept( final File f )
 
 		tableActions = new BigWarpActions( inputTriggerConfig, "bw-table" );
 		BigWarpActions.installTableActions( tableActions, getLandmarkFrame().getKeybindings(), this );
-//		UnmappedNavigationActions.install( tableActions, options.values.is2D() );
 
 		keymap.updateListeners().add( () -> {
 
@@ -681,7 +682,6 @@ public boolean accept( final File f )
 		createMovingTargetGroups();
 		viewerP.state().setCurrentGroup( mvgGrp );
 		viewerQ.state().setCurrentGroup( tgtGrp );
-//		viewerQ.state().changeListeners().add(warpVisDialog.transformGraphPanel);
 
 		SwingUtilities.invokeLater( () -> {
 			viewerFrameP.setVisible( true );
@@ -1087,8 +1087,10 @@ public void removeKeyEventPostProcessor( final KeyEventPostProcessor ke )
 
 	public void closeAll()
 	{
-		final ArrayList< KeyEventPostProcessor > ks = new ArrayList< KeyEventPostProcessor >( keyEventPostProcessorSet );
-		for ( final KeyEventPostProcessor ke : ks )
+		// This method is probably total overkill, but helps avoid an actual
+		// memory leak
+
+		for ( final KeyEventPostProcessor ke : keyEventPostProcessorSet )
 			removeKeyEventPostProcessor( ke );
 
 		repeatedKeyEventsFixer.remove();
@@ -1103,6 +1105,21 @@ public void closeAll()
 		viewerFrameP.dispose();
 		viewerFrameQ.dispose();
 		landmarkFrame.dispose();
+
+		warpVisDialog.dispose();
+		warpVisDialog = null;
+
+		helpDialog.dispose();
+		helpDialog = null;
+
+		keyboardProc.dispose();
+		keyboardProc = null;
+
+		solverThread.interrupt();
+		solverThread = null;
+
+		data.cleanUp();
+		data = null;
 	}
 
 	public void setUpdateWarpOnChange( final boolean updateWarpOnPtChange )
@@ -2674,7 +2691,8 @@ public PlateauSphericalMaskSource getTransformPlateauMaskSource()
 
 	public void setupKeyListener()
 	{
-		KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventPostProcessor( new LandmarkKeyboardProcessor( this ) );
+		keyboardProc = new LandmarkKeyboardProcessor( this ) ;
+		KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventPostProcessor( keyboardProc );
 	}
 
 	public void setWarpVisGridType( final GridSource.GRID_TYPE type )

src/main/java/bigwarp/BigWarpData.java

@@ -30,7 +30,6 @@
 import net.imglib2.realtransform.InvertibleWrapped2DTransformAs3D;
 import net.imglib2.realtransform.RealTransform;
 import net.imglib2.realtransform.Wrapped2DTransformAs3D;
-import net.imglib2.util.Intervals;
 
 public class BigWarpData< T >
 {
@@ -234,6 +233,14 @@ public void wrapUp()
 	{
 	}
 
+	public void cleanUp()
+	{
+		System.out.println("data clean up");
+		sources.clear();
+		sourceInfos.clear();
+		converterSetups.clear();
+	}
+
 	void addSource( Source<T> src, boolean isMoving )
 	{
 		addSource( src, isMoving, null );