Merge pull request #291 from saalfeldlab/fix-deadlock-at-startup

[BUGFIX] Fix deadlock at startup (#239 #288), thanks to @igorpisarev in #291

Author: hanslovsky

src/main/java/bdv/fx/viewer/ViewerPanelFX.java

@@ -29,6 +29,21 @@
  */
 package bdv.fx.viewer;
 
+import java.lang.invoke.MethodHandles;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.concurrent.CopyOnWriteArrayList;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.ThreadFactory;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.function.Function;
+
+import org.janelia.saalfeldlab.paintera.data.axisorder.AxisOrder;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import bdv.cache.CacheControl;
 import bdv.fx.viewer.render.RenderUnit;
 import bdv.viewer.Interpolation;
@@ -39,7 +54,6 @@
 import javafx.beans.property.ReadOnlyBooleanProperty;
 import javafx.beans.property.ReadOnlyDoubleProperty;
 import javafx.collections.FXCollections;
-import javafx.collections.ListChangeListener;
 import javafx.collections.ObservableList;
 import javafx.scene.Node;
 import javafx.scene.layout.StackPane;
@@ -51,19 +65,6 @@
 import net.imglib2.RealPositionable;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.ui.TransformListener;
-import org.janelia.saalfeldlab.paintera.data.axisorder.AxisOrder;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import java.lang.invoke.MethodHandles;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.concurrent.CopyOnWriteArrayList;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.ThreadFactory;
-import java.util.concurrent.atomic.AtomicInteger;
-import java.util.function.Function;
 
 /**
  * @author Philipp Hanslovsky
@@ -87,6 +88,7 @@ public class ViewerPanelFX
 	private final OverlayPane<?> overlayPane = new OverlayPane<>();
 
 	private final ViewerState state;
+
 	private final AffineTransform3D viewerTransform;
 
 	private ThreadGroup threadGroup;
@@ -184,17 +186,11 @@ public ViewerPanelFX(
 		this.renderingExecutorService = Executors.newFixedThreadPool(optional.values.getNumRenderingThreads(), new RenderThreadFactory());
 		options = optional.values;
 
-		this.state = new ViewerState(axisOrder);
-
-		state.numTimepoints.set(numTimepoints);
-
 		threadGroup = new ThreadGroup(this.toString());
 		viewerTransform = new AffineTransform3D();
 
 		transformListeners = new CopyOnWriteArrayList<>();
 
-		state.sourcesAndConverters.addListener((ListChangeListener<SourceAndConverter<?>>) c -> requestRepaint());
-
 		mouseTracker.installInto(this);
 
 		this.renderUnit = new RenderUnit(
@@ -214,9 +210,14 @@ public ViewerPanelFX(
 		this.heightProperty().addListener((obs, oldv, newv) -> this.renderUnit.setDimensions((long)getWidth(), (long)getHeight()));
 		setWidth(options.getWidth());
 		setHeight(options.getHeight());
-		setAllSources(sources);
+
 		// TODO why is this necessary?
 		transformListeners.add(tf -> getDisplay().drawOverlays());
+
+		this.state = new ViewerState(axisOrder, numTimepoints);
+		state.addListener(obs -> requestRepaint());
+
+		setAllSources(sources);
 	}
 
 	/**
@@ -225,10 +226,7 @@ public ViewerPanelFX(
 	 */
 	public void setAllSources(final Collection<? extends SourceAndConverter<?>> sources)
 	{
-		synchronized (state)
-		{
-			this.state.sourcesAndConverters.setAll(sources);
-		}
+		this.state.setSources(sources);
 	}
 
 	/**
@@ -350,13 +348,9 @@ public void requestRepaint(final long[] min, final long[] max)
 	public synchronized void transformChanged(final AffineTransform3D transform)
 	{
 		viewerTransform.set(transform);
-		synchronized (state)
-		{
-		    state.setViewerTransform(transform);
-		}
+		state.setViewerTransform(transform);
 		for (final TransformListener<AffineTransform3D> l : transformListeners)
 			l.transformChanged(viewerTransform);
-		requestRepaint();
 	}
 
 	/**

src/main/java/bdv/fx/viewer/ViewerState.java

@@ -1,63 +1,81 @@
 package bdv.fx.viewer;
 
+import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 import java.util.function.Function;
-import java.util.stream.Collectors;
+
+import org.janelia.saalfeldlab.fx.ObservableWithListenersList;
+import org.janelia.saalfeldlab.paintera.data.axisorder.AxisOrder;
 
 import bdv.util.MipmapTransforms;
 import bdv.viewer.Source;
 import bdv.viewer.SourceAndConverter;
-import javafx.beans.property.IntegerProperty;
-import javafx.beans.property.ReadOnlyIntegerProperty;
-import javafx.beans.property.SimpleIntegerProperty;
-import javafx.collections.FXCollections;
-import javafx.collections.ListChangeListener;
-import javafx.collections.ObservableList;
-import javafx.collections.ObservableMap;
 import net.imglib2.realtransform.AffineTransform3D;
-import org.janelia.saalfeldlab.paintera.data.axisorder.AxisOrder;
 
-public class ViewerState
+public class ViewerState extends ObservableWithListenersList
 {
 
 	private final AffineTransform3D viewerTransform = new AffineTransform3D();
 
-	protected final IntegerProperty timepoint = new SimpleIntegerProperty(0);
+	private final List<SourceAndConverter<?>> sourcesAndConverters = new ArrayList<>();
 
-	protected final IntegerProperty numTimepoints = new SimpleIntegerProperty(1);
+	private final Function<Source<?>, AxisOrder> axisOrder;
 
-	protected final ObservableList<SourceAndConverter<?>> sourcesAndConverters = FXCollections.observableArrayList();
+	private final int numTimepoints;
 
-	private final Function<Source<?>, AxisOrder> axisOrder;
+	private int timepoint;
 
-	protected final ObservableMap<Source<?>, SourceAndConverter<?>> sources = asMap(
-			sourcesAndConverters,
-			SourceAndConverter::getSpimSource
-	                                                                               );
+	public ViewerState(final Function<Source<?>, AxisOrder> axisOrder, final int numTimepoints)
+	{
+		this.axisOrder = axisOrder;
+		this.numTimepoints = numTimepoints;
+	}
 
-	protected synchronized void setViewerTransform(final AffineTransform3D to)
+	protected void setViewerTransform(final AffineTransform3D to)
 	{
-		this.viewerTransform.set(to);
+		synchronized (this)
+		{
+			this.viewerTransform.set(to);
+		}
+		stateChanged();
 	}
 
 	public synchronized void getViewerTransform(final AffineTransform3D to)
 	{
 		to.set(this.viewerTransform);
 	}
 
-	public ReadOnlyIntegerProperty timepointProperty()
+	public void setTimepoint(final int timepoint)
+	{
+		synchronized (this)
+		{
+			this.timepoint = timepoint;
+		}
+		stateChanged();
+	}
+
+	public synchronized int getTimepoint()
 	{
 		return this.timepoint;
 	}
 
-	public List<SourceAndConverter<?>> getSources()
+	public synchronized List<SourceAndConverter<?>> getSources()
 	{
 		return Collections.unmodifiableList(sourcesAndConverters);
 	}
 
+	public void setSources(final Collection<? extends SourceAndConverter<?>> newSources)
+	{
+		synchronized (this)
+		{
+			this.sourcesAndConverters.clear();
+			this.sourcesAndConverters.addAll(newSources);
+		}
+		stateChanged();
+	}
+
 	public synchronized int getBestMipMapLevel(final AffineTransform3D screenScaleTransform, final Source<?> source,
 	                                           final int timepoint)
 	{
@@ -70,54 +88,25 @@ public synchronized int getBestMipMapLevel(final AffineTransform3D screenScaleTr
 
 	public synchronized int getBestMipMapLevel(final AffineTransform3D screenScaleTransform, final Source<?> source)
 	{
-		return getBestMipMapLevel(screenScaleTransform, source, timepoint.get());
+		return getBestMipMapLevel(screenScaleTransform, source, timepoint);
 	}
 
 	public synchronized int getBestMipMapLevel(final AffineTransform3D screenScaleTransform, final int sourceIndex)
 	{
 		return getBestMipMapLevel(screenScaleTransform, sourcesAndConverters.get(sourceIndex).getSpimSource());
 	}
 
-	public ViewerState(final Function<Source<?>, AxisOrder> axisOrder)
-	{
-		this.axisOrder = axisOrder;
-	}
-
 	public synchronized ViewerState copy()
 	{
-		final ViewerState state = new ViewerState(this.axisOrder);
-		state.viewerTransform.set(viewerTransform);
-		state.timepoint.set(timepoint.get());
-		state.numTimepoints.set(numTimepoints.get());
-		state.sourcesAndConverters.setAll(sourcesAndConverters);
+		final ViewerState state = new ViewerState(this.axisOrder, this.numTimepoints);
+		state.setViewerTransform(this.viewerTransform);
+		state.setTimepoint(this.timepoint);
+		state.setSources(this.sourcesAndConverters);
 		return state;
 	}
 
-	public static <S, T> ObservableList<T> mapObservableList(final ObservableList<? extends S> source, final
-	Function<S, T> mapping)
-	{
-		final ObservableList<T> target = FXCollections.observableArrayList();
-		source.addListener((ListChangeListener<? super S>) change -> target.setAll(source.stream().map(mapping)
-				.collect(
-				Collectors.toList())));
-		return target;
-	}
-
-	public static <S, T> ObservableMap<T, S> asMap(final ObservableList<? extends S> source, final Function<S, T>
-			generateKeyFromValue)
-	{
-		final ObservableMap<T, S> target = FXCollections.observableHashMap();
-		source.addListener((ListChangeListener<? super S>) change -> {
-			final Map<T, S> tmp = new HashMap<>();
-			source.forEach(s -> tmp.put(generateKeyFromValue.apply(s), s));
-			target.putAll(tmp);
-		});
-		return target;
-	}
-
-	public AxisOrder axisOrder(final Source<?> source)
+	public synchronized AxisOrder axisOrder(final Source<?> source)
 	{
 		return this.axisOrder.apply(source);
 	}
-
 }

src/main/java/bdv/fx/viewer/multibox/MultiBoxOverlayRendererFX.java

@@ -153,7 +153,7 @@ public synchronized void setViewerState(final ViewerState viewerState)
 	{
 		synchronized (viewerState)
 		{
-			final int timepoint = viewerState.timepointProperty().get();
+			final int timepoint = viewerState.getTimepoint();
 
 			final int numSources        = this.allSources.size();
 			final int numPresentSources = (int) IntStream.range(

src/main/java/bdv/fx/viewer/render/RenderUnit.java

@@ -236,7 +236,7 @@ public void paint()
 				synchronized (viewerState)
 				{
 					viewerState.getViewerTransform(viewerTransform);
-					timepoint = viewerState.timepointProperty().get();
+					timepoint = viewerState.getTimepoint();
 					sacs.addAll(viewerState.getSources());
 				}
 			}

src/main/java/org/janelia/saalfeldlab/paintera/control/ShapeInterpolationMode.java

@@ -378,7 +378,7 @@ public boolean isModeOn()
 
 	private void createMask() throws MaskInUse
 	{
-		final int time = activeViewer.getState().timepointProperty().get();
+		final int time = activeViewer.getState().getTimepoint();
 		final int level = MASK_SCALE_LEVEL;
 		final MaskInfo<UnsignedLongType> maskInfo = new MaskInfo<>(time, level, new UnsignedLongType(newLabelId));
 		mask = source.generateMask(maskInfo, FOREGROUND_CHECK);
@@ -935,7 +935,7 @@ private UnsignedLongType getMaskValue(final double x, final double y)
 	private D getDataValue(final double x, final double y)
 	{
 		final RealPoint sourcePos = getSourceCoordinates(x, y);
-		final int time = activeViewer.getState().timepointProperty().get();
+		final int time = activeViewer.getState().getTimepoint();
 		final int level = MASK_SCALE_LEVEL;
 		final RandomAccessibleInterval<D> data = source.getDataSource(time, level);
 		final RandomAccess<D> dataAccess = data.randomAccess();
@@ -947,7 +947,7 @@ private D getDataValue(final double x, final double y)
 	private AffineTransform3D getMaskTransform()
 	{
 		final AffineTransform3D maskTransform = new AffineTransform3D();
-		final int time = activeViewer.getState().timepointProperty().get();
+		final int time = activeViewer.getState().getTimepoint();
 		final int level = MASK_SCALE_LEVEL;
 		source.getSourceTransform(time, level, maskTransform);
 		return maskTransform;
@@ -979,7 +979,7 @@ private AffineTransform3D getMaskDisplayTransformIgnoreScaling(final int targetL
 		if (targetLevel != maskLevel)
 		{
 			// scale with respect to the given mipmap level
-			final int time = activeViewer.getState().timepointProperty().get();
+			final int time = activeViewer.getState().getTimepoint();
 			final Scale3D relativeScaleTransform = new Scale3D(DataSource.getRelativeScales(source, time, maskLevel, targetLevel));
 			maskMipmapDisplayTransform.preConcatenate(relativeScaleTransform.inverse());
 		}
@@ -1000,7 +1000,7 @@ private AffineTransform3D getMaskDisplayTransformIgnoreScaling()
 		Arrays.setAll(viewerScale, d -> Affine3DHelpers.extractScale(viewerTransform, d));
 		final Scale3D scalingTransform = new Scale3D(viewerScale);
 		// neutralize mask scaling if there is any
-		final int time = activeViewer.getState().timepointProperty().get();
+		final int time = activeViewer.getState().getTimepoint();
 		final int level = MASK_SCALE_LEVEL;
 		scalingTransform.concatenate(new Scale3D(DataSource.getScale(source, time, level)));
 		// build the resulting transform

src/main/java/org/janelia/saalfeldlab/paintera/control/paint/FloodFill.java

@@ -162,7 +162,7 @@ private void fillAt(final double x, final double y, final long fill)
 
 		final int               level          = 0;
 		final AffineTransform3D labelTransform = new AffineTransform3D();
-		final int               time           = viewerState.timepointProperty().get();
+		final int               time           = viewerState.getTimepoint();
 		source.getSourceTransform(time, level, labelTransform);
 
 		final RealPoint rp = setCoordinates(x, y, viewer, labelTransform);

src/main/java/org/janelia/saalfeldlab/paintera/control/paint/FloodFill2D.java

@@ -162,7 +162,7 @@ public <T extends IntegerType<T>> void fillAt(final double x, final double y, fi
 		}
 
 		final int level = 0;
-		final int time = viewerState.timepointProperty().get();
+		final int time = viewerState.getTimepoint();
 		final MaskInfo<UnsignedLongType> maskInfo = new MaskInfo<>(time, level, new UnsignedLongType(fill));
 
 		final Scene  scene          = viewer.getScene();

src/main/java/org/janelia/saalfeldlab/paintera/control/paint/RestrictPainting.java

@@ -137,7 +137,7 @@ public void restrictTo(final double x, final double y)
 		synchronized (viewerState)
 		{
 			level = viewerState.getBestMipMapLevel(screenScaleTransform, sourceInfo.currentSourceIndexInVisibleSources().get());
-			time = viewerState.timepointProperty().get();
+			time = viewerState.getTimepoint();
 		}
 		final AffineTransform3D labelTransform = new AffineTransform3D();
 		source.getSourceTransform(time, level, labelTransform);