Alpha Masks

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>40.0.0</version>
+		<version>41.0.0</version>
 		<relativePath />
 	</parent>
 
@@ -143,8 +143,7 @@
 		<license.licenseName>bsd_2</license.licenseName>
 		<license.copyrightOwners>BigDataViewer developers.</license.copyrightOwners>
 
-		<imglib2.version>7.1.5</imglib2.version>
-		<imglib2-algorithm.version>0.18.1</imglib2-algorithm.version>
+		<imglib2.version>8.0.0</imglib2.version>
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>

src/main/java/bdv/AbstractSpimSource.java

@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -34,6 +34,7 @@
 import java.util.Set;
 
 import bdv.viewer.Interpolation;
+import bdv.viewer.MaskUtils;
 import bdv.viewer.Source;
 import mpicbg.spim.data.generic.AbstractSpimData;
 import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
@@ -52,7 +53,11 @@
 import net.imglib2.interpolation.randomaccess.ClampingNLinearInterpolatorFactory;
 import net.imglib2.interpolation.randomaccess.NearestNeighborInterpolatorFactory;
 import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.type.mask.Masked;
+import net.imglib2.type.numeric.ARGBType;
 import net.imglib2.type.numeric.NumericType;
+import net.imglib2.type.volatiles.VolatileARGBType;
+import net.imglib2.util.Cast;
 import net.imglib2.view.Views;
 
 public abstract class AbstractSpimSource< T extends NumericType< T > > implements Source< T >
@@ -129,19 +134,14 @@ public boolean equals( final Object obj )
 
 	private final int numMipmapLevels;
 
-	private final static int numInterpolationMethods = 2;
-
-	private final static int iNearestNeighborMethod = 0;
-
-	private final static int iNLinearMethod = 1;
-
-	private final InterpolatorFactory< T, RandomAccessible< T > >[] interpolatorFactories;
-
 	private final UncheckedCache< ImgKey, RandomAccessibleInterval< T > > cachedSources;
 
 	private final UncheckedCache< ImgKey, RealRandomAccessible< T > > cachedInterpolatedSources;
 
-	@SuppressWarnings( "unchecked" )
+	private final UncheckedCache< ImgKey, RandomAccessibleInterval< ? extends Masked< T >  > > cachedMaskedSources;
+
+	private final UncheckedCache< ImgKey, RealRandomAccessible< ? extends Masked< T > > > cachedInterpolatedMaskedSources;
+
 	public AbstractSpimSource( final AbstractSpimData< ? > spimData, final int setupId, final String name )
 	{
 		this.setupId = setupId;
@@ -155,35 +155,54 @@ public AbstractSpimSource( final AbstractSpimData< ? > spimData, final int setup
 		voxelDimensions = seq.getViewSetups().get( setupId ).getVoxelSize();
 		numMipmapLevels = ( ( ViewerImgLoader ) seq.getImgLoader() ).getSetupImgLoader( setupId ).numMipmapLevels();
 
-		interpolatorFactories = new InterpolatorFactory[ numInterpolationMethods ];
-		interpolatorFactories[ iNearestNeighborMethod ] = new NearestNeighborInterpolatorFactory<>();
-		interpolatorFactories[ iNLinearMethod ] = new ClampingNLinearInterpolatorFactory<>();
-
-		final CacheLoader< ImgKey, RandomAccessibleInterval< T > > loader = key -> {
-			return getImage( timePointsOrdered.get( key.timepoint ).getId(), key.level );
-		};
+		final CacheLoader< ImgKey, RandomAccessibleInterval< T > > loader = key ->
+				getImage( timePointsOrdered.get( key.timepoint ).getId(), key.level );
 		cachedSources = Caches.unchecked( Caches.withLoader(
 				new BoundedSoftRefLoaderCache<>( 3 * numMipmapLevels ),
 				loader ) );
 
-		final CacheLoader< ImgKey, RealRandomAccessible< T > > interpolLoader = key -> {
-			final T zero = getType().createVariable();
-			zero.setZero();
-			final int i = key.method == Interpolation.NLINEAR ? iNLinearMethod : iNearestNeighborMethod;
-			final InterpolatorFactory< T, RandomAccessible< T > > factory = interpolatorFactories[ i ];
-			return Views.interpolate( Views.extendValue( getSource( key.timepoint, key.level ), zero ), factory );
-		};
+		final CacheLoader< ImgKey, RealRandomAccessible< T > > interpolLoader = key ->
+				Views.interpolate( Views.extendZero( getSource( key.timepoint, key.level, key.threadGroup ) ), interpolator( key.method ) );
 		cachedInterpolatedSources = Caches.unchecked( Caches.withLoader(
-				new BoundedSoftRefLoaderCache<>( 3 * numMipmapLevels * numInterpolationMethods ),
+				new BoundedSoftRefLoaderCache<>( 3 * numMipmapLevels * Interpolation.values().length ),
 				interpolLoader ) );
 
+		final CacheLoader< ImgKey, RandomAccessibleInterval< ? extends Masked< T > > > maskedLoader = key ->
+				Masked.withConstant( getSource( key.timepoint, key.level, key.threadGroup ), 1 );
+		cachedMaskedSources = Caches.unchecked( Caches.withLoader(
+				new BoundedSoftRefLoaderCache<>( 3 * numMipmapLevels ),
+				maskedLoader ) );
+
+		final CacheLoader< ImgKey, RealRandomAccessible< ? extends Masked< T > > > maskedInterpolLoader = key -> {
+			if ( getType() instanceof ARGBType || getType() instanceof VolatileARGBType )
+			{
+				// TODO: How to correctly handle ARGBType sources?  We could make a
+				//       Masked<ARGBType> wrapper that uses the ARGBType's A as mask?
+				return Masked.withConstant( getInterpolatedSource( key.timepoint, key.level, key.method, key.threadGroup ), 1 );
+			}
+			else
+			{
+				return MaskUtils.extendAndInterpolateMasked( Cast.unchecked( getMaskedSource( key.timepoint, key.level, key.threadGroup ) ), key.method );
+			}
+		};
+		cachedInterpolatedMaskedSources = Caches.unchecked( Caches.withLoader(
+				new BoundedSoftRefLoaderCache<>( 3 * numMipmapLevels * Interpolation.values().length ),
+				maskedInterpolLoader ) );
+
 		currentSourceTransforms = new AffineTransform3D[ numMipmapLevels ];
 		for ( int level = 0; level < numMipmapLevels; level++ )
 			currentSourceTransforms[ level ] = new AffineTransform3D();
 
 		currentTimePointIndex = -1;
 	}
 
+	private static < T extends NumericType< T > > InterpolatorFactory< T, RandomAccessible< T > > interpolator( final Interpolation method )
+	{
+		return method == Interpolation.NEARESTNEIGHBOR
+				? new NearestNeighborInterpolatorFactory<>()
+				: new ClampingNLinearInterpolatorFactory<>();
+	}
+
 	void loadTimepoint( final int timepointIndex )
 	{
 		currentTimePointIndex = timepointIndex;
@@ -291,4 +310,34 @@ public void reload()
 	{
 		currentTimePointIndex = -1;
 	}
+
+	@Override
+	public RandomAccessibleInterval< ? extends Masked< T > > getMaskedSource( final int t, final int level )
+	{
+		return getMaskedSource( t, level, Thread.currentThread().getThreadGroup() );
+	}
+
+	public synchronized RandomAccessibleInterval< ? extends Masked< T > > getMaskedSource( final int t, final int level, final ThreadGroup threadGroup )
+	{
+		if ( t != currentTimePointIndex )
+			loadTimepoint( t );
+		return currentTimePointIsPresent
+				? cachedMaskedSources.get( new ImgKey( t, level, null, threadGroup ) )
+				: null;
+	}
+
+	@Override
+	public RealRandomAccessible< ? extends Masked< T > > getInterpolatedMaskedSource( int t, int level, final Interpolation method )
+	{
+		return getInterpolatedMaskedSource( t, level, method, Thread.currentThread().getThreadGroup() );
+	}
+
+	public synchronized RealRandomAccessible< ? extends Masked< T > > getInterpolatedMaskedSource( final int t, final int level, final Interpolation method, final ThreadGroup threadGroup )
+	{
+		if ( t != currentTimePointIndex )
+			loadTimepoint( t );
+		return currentTimePointIsPresent
+				? cachedInterpolatedMaskedSources.get( new ImgKey( t, level, method, threadGroup ) )
+				: null;
+	}
 }

src/main/java/bdv/tools/InitializeViewerState.java

@@ -36,6 +36,7 @@
 import net.imglib2.histogram.Histogram1d;
 import net.imglib2.histogram.Real1dBinMapper;
 import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.type.numeric.integer.UnsignedShortType;
 import net.imglib2.util.LinAlgHelpers;
@@ -198,34 +199,47 @@ public static Bounds estimateSourceRange( final Source< ? > source, final int ti
 		{
 			@SuppressWarnings( "unchecked" )
 			final RandomAccessibleInterval< UnsignedShortType > img = ( RandomAccessibleInterval< UnsignedShortType > ) source.getSource( timepoint, source.getNumMipmapLevels() - 1 );
-			final long z = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 2;
-
-			final int numBins = 6535;
-			final Histogram1d< ? > histogram = new Histogram1d<>( Views.hyperSlice( img, 2, z ), new Real1dBinMapper<>( 0, 65535, numBins, false ) );
-			final DiscreteFrequencyDistribution dfd = histogram.dfd();
-			final long[] bin = new long[] { 0 };
-			double cumulative = 0;
-			int i = 0;
-			for ( ; i < numBins && cumulative < cumulativeMinCutoff; ++i )
-			{
-				bin[ 0 ] = i;
-				cumulative += dfd.relativeFrequency( bin );
-			}
-			final int min = i * 65535 / numBins;
-			for ( ; i < numBins && cumulative < cumulativeMaxCutoff; ++i )
-			{
-				bin[ 0 ] = i;
-				cumulative += dfd.relativeFrequency( bin );
-			}
-			final int max = i * 65535 / numBins;
-			return new Bounds( min, max );
+			return estimateBounds( img, cumulativeMinCutoff, cumulativeMaxCutoff);
 		}
 		else if ( type instanceof UnsignedByteType )
 			return new Bounds( 0, 255 );
 		else
 			return new Bounds( 0, 65535 );
 	}
 
+	/**
+	 * @param img
+	 * 		3D image, histogram of the center plane is used for estimating instensity range.
+	 * @param cumulativeMinCutoff
+	 * 		fraction of pixels that are allowed to be saturated at the lower end of the range.
+	 * @param cumulativeMaxCutoff
+	 * 		fraction of pixels that are allowed to be saturated at the upper end of the range.
+	 */
+	private static < T extends RealType< T > > Bounds estimateBounds( final RandomAccessibleInterval< T > img, final double cumulativeMinCutoff, final double cumulativeMaxCutoff )
+	{
+		final long z = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 2;
+
+		final int numBins = 6535;
+		final Histogram1d< ? > histogram = new Histogram1d<>( Views.hyperSlice( img, 2, z ), new Real1dBinMapper<>( 0, 65535, numBins, false ) );
+		final DiscreteFrequencyDistribution dfd = histogram.dfd();
+		final long[] bin = new long[] { 0 };
+		double cumulative = 0;
+		int i = 0;
+		for ( ; i < numBins && cumulative < cumulativeMinCutoff; ++i )
+		{
+			bin[ 0 ] = i;
+			cumulative += dfd.relativeFrequency( bin );
+		}
+		final int min = i * 65535 / numBins;
+		for ( ; i < numBins && cumulative < cumulativeMaxCutoff; ++i )
+		{
+			bin[ 0 ] = i;
+			cumulative += dfd.relativeFrequency( bin );
+		}
+		final int max = i * 65535 / numBins;
+		return new Bounds( min, max );
+	}
+
 	@Deprecated
 	public static AffineTransform3D initTransform( final int viewerWidth, final int viewerHeight, final boolean zoomedIn, final bdv.viewer.state.ViewerState state )
 	{

src/main/java/bdv/tools/RecordMaxProjectionDialog.java

@@ -367,7 +367,7 @@ public int getHeight()
 		final MyTarget target = new MyTarget();
 		final MultiResolutionRenderer renderer = new MultiResolutionRenderer(
 				target, () -> {}, new double[] { 1 }, 0, 1, null, false,
-				viewer.getOptionValues().getAccumulateProjectorFactory(), new CacheControl.Dummy() );
+				new CacheControl.Dummy() );
 		progressWriter.setProgress( 0 );
 		for ( int timepoint = minTimepointIndex; timepoint <= maxTimepointIndex; ++timepoint )
 		{

src/main/java/bdv/tools/RecordMovieDialog.java

@@ -301,7 +301,7 @@ public int getHeight()
 		final MyTarget target = new MyTarget();
 		final MultiResolutionRenderer renderer = new MultiResolutionRenderer(
 				target, () -> {}, new double[] { 1 }, 0, 1, null, false,
-				viewer.getOptionValues().getAccumulateProjectorFactory(), new CacheControl.Dummy() );
+				new CacheControl.Dummy() );
 		progressWriter.setProgress( 0 );
 		for ( int timepoint = minTimepointIndex; timepoint <= maxTimepointIndex; ++timepoint )
 		{

src/main/java/bdv/tools/boundingbox/TransformedBoxPlaceHolderSource.java

@@ -37,8 +37,8 @@
 import net.imglib2.RealLocalizable;
 import net.imglib2.RealRandomAccess;
 import net.imglib2.RealRandomAccessible;
-import net.imglib2.Sampler;
 import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.type.mask.Masked;
 import net.imglib2.type.numeric.integer.UnsignedShortType;
 import net.imglib2.util.Intervals;
 import net.imglib2.view.Views;
@@ -106,6 +106,18 @@ public RealRandomAccessible< Void > getInterpolatedSource( final int t, final in
 		return rra;
 	}
 
+	@Override
+	public RandomAccessibleInterval< ? extends Masked< Void > > getMaskedSource( final int t, final int level )
+	{
+		return Views.interval( Views.raster( Masked.withConstant( rra, 0 ) ), Intervals.smallestContainingInterval( bbSource.getInterval() ) );
+	}
+
+	@Override
+	public RealRandomAccessible< ? extends Masked< Void > > getInterpolatedMaskedSource( final int t, final int level, final Interpolation method )
+	{
+		return Masked.withConstant( rra, 0 );
+	}
+
 	@Override
 	public void getSourceTransform( final int t, final int level, final AffineTransform3D transform )
 	{

src/main/java/bdv/tools/transformation/TransformedSource.java

@@ -36,6 +36,7 @@
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.RealRandomAccessible;
 import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.type.mask.Masked;
 
 /**
  * A {@link Source} that wraps another {@link Source} and allows to decorate it
@@ -295,4 +296,16 @@ public Source< T > getWrappedSource()
 	{
 		return source;
 	}
+
+	@Override
+	public RandomAccessibleInterval< ? extends Masked< T > > getMaskedSource( final int t, final int level )
+	{
+		return source.getMaskedSource( t, level );
+	}
+
+	@Override
+	public RealRandomAccessible< ? extends Masked< T > > getInterpolatedMaskedSource( final int t, final int level, final Interpolation method )
+	{
+		return source.getInterpolatedMaskedSource( t, level, method );
+	}
 }