Merge branch 'master' into stepsize

src/main/java/net/preibisch/mvrecon/fiji/plugin/interestpointdetection/DifferenceOfGUI.java

@@ -485,7 +485,8 @@ protected ImagePlus getImagePlusForInteractive( final String dialogHeader )
 		RandomAccessibleInterval<RealType<?>> imgGeneric = DownsampleTools.openAndDownsample(
 			spimData.getSequenceDescription().getImgLoader(),
 			viewDescription,
-			new long[] { downsampleXY, downsampleXY, downsampleZ } ).getA();
+			new long[] { downsampleXY, downsampleXY, downsampleZ },
+			true ).getA();
 
 		if ( imgGeneric == null )
 		{

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyDHMImgLoader.java

@@ -31,7 +31,6 @@
 import ij.io.Opener;
 import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
 import mpicbg.spim.data.generic.sequence.BasicViewDescription;
-import mpicbg.spim.data.generic.sequence.BasicViewSetup;
 import mpicbg.spim.data.sequence.Channel;
 import mpicbg.spim.data.sequence.ViewId;
 import mpicbg.spim.data.sequence.VoxelDimensions;
@@ -98,9 +97,9 @@ public LegacyDHMImgLoader(
 	public RandomAccessibleInterval< FloatType > getFloatImage( final ViewId view, final boolean normalize )
 	{
 		if ( normalize )
-			return ImgLib2Tools.normalizeVirtual( getImage( view ) );
+			return ImgLib2Tools.normalizeVirtualRAI( getImage( view ) );
 		else
-			return ImgLib2Tools.convertVirtual( getImage( view ) );
+			return ImgLib2Tools.convertVirtualRAI( getImage( view ) );
 	}
 
 	@Override

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyFileMapImgLoaderLOCI.java

@@ -61,7 +61,6 @@
 import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.img.Img;
-import net.imglib2.img.ImgFactory;
 import net.imglib2.img.array.ArrayImg;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
@@ -139,9 +138,9 @@ public LegacyFileMapImgLoaderLOCI(
 	public RandomAccessibleInterval< FloatType > getFloatImage(ViewId view, boolean normalize)
 	{
 		if ( normalize )
-			return ImgLib2Tools.normalizeVirtual( getImage( view ) );
+			return ImgLib2Tools.normalizeVirtualRAI( getImage( view ) );
 		else
-			return ImgLib2Tools.convertVirtual( getImage( view ) );
+			return ImgLib2Tools.convertVirtualRAI( getImage( view ) );
 	}
 
 

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyLightSheetZ1ImgLoader.java

@@ -86,9 +86,9 @@ public LegacyLightSheetZ1ImgLoader(
 	public RandomAccessibleInterval< FloatType > getFloatImage( final ViewId view, final boolean normalize )
 	{
 		if ( normalize )
-			return ImgLib2Tools.normalizeVirtual( getImage( view ) );
+			return ImgLib2Tools.normalizeVirtualRAI( getImage( view ) );
 		else
-			return ImgLib2Tools.convertVirtual( getImage( view ) );
+			return ImgLib2Tools.convertVirtualRAI( getImage( view ) );
 	}
 
 	@Override

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyMicroManagerImgLoader.java

@@ -121,9 +121,9 @@ final public static < T extends RealType< T > & NativeType< T > > void populateI
 	public RandomAccessibleInterval< FloatType > getFloatImage( final ViewId view, final boolean normalize )
 	{
 		if ( normalize )
-			return ImgLib2Tools.normalizeVirtual( getImage( view ) );
+			return ImgLib2Tools.normalizeVirtualRAI( getImage( view ) );
 		else
-			return ImgLib2Tools.convertVirtual( getImage( view ) );
+			return ImgLib2Tools.convertVirtualRAI( getImage( view ) );
 	}
 
 	@Override

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyStackImgLoaderIJ.java

@@ -91,9 +91,9 @@ public static ImagePlus open( File file )
 	public RandomAccessibleInterval< FloatType > getFloatImage( final ViewId view, final boolean normalize )
 	{
 		if ( normalize )
-			return ImgLib2Tools.normalizeVirtual( getImage( view ) );
+			return ImgLib2Tools.normalizeVirtualRAI( getImage( view ) );
 		else
-			return ImgLib2Tools.convertVirtual( getImage( view ) );
+			return ImgLib2Tools.convertVirtualRAI( getImage( view ) );
 	}
 
 	/**

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyStackImgLoaderLOCI.java

@@ -82,9 +82,9 @@ public LegacyStackImgLoaderLOCI(
 	public RandomAccessibleInterval< FloatType > getFloatImage( final ViewId view, final boolean normalize )
 	{
 		if ( normalize )
-			return ImgLib2Tools.normalizeVirtual( getImage( view ) );
+			return ImgLib2Tools.normalizeVirtualRAI( getImage( view ) );
 		else
-			return ImgLib2Tools.convertVirtual( getImage( view ) );
+			return ImgLib2Tools.convertVirtualRAI( getImage( view ) );
 	}
 
 	/**

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/SimViewSetupImgLoader.java

@@ -88,9 +88,9 @@ public SimViewSetupImgLoader(
 	public RandomAccessibleInterval<FloatType> getFloatImage( final int timepointId, final boolean normalize, ImgLoaderHint... hints )
 	{
 		if ( normalize )
-			return ImgLib2Tools.normalizeVirtual( getImage( timepointId, hints ) );
+			return ImgLib2Tools.normalizeVirtualRAI( getImage( timepointId, hints ) );
 		else
-			return ImgLib2Tools.convertVirtual( getImage( timepointId, hints ) );
+			return ImgLib2Tools.convertVirtualRAI( getImage( timepointId, hints ) );
 	}
 
 	@Override

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/filemap2/FileMapImgLoaderLOCI2.java

@@ -220,9 +220,9 @@ public RandomAccessibleInterval< FloatType > getFloatImage(int timepointId, bool
 				ImgLoaderHint... hints)
 		{
 			if ( normalize )
-				return ImgLib2Tools.normalizeVirtual( getImage( timepointId, hints ) );
+				return ImgLib2Tools.normalizeVirtualRAI( getImage( timepointId, hints ) );
 			else
-				return ImgLib2Tools.convertVirtual( getImage( timepointId, hints ) );
+				return ImgLib2Tools.convertVirtualRAI( getImage( timepointId, hints ) );
 		}
 
 		@Override

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/splitting/SplitMultiResolutionSetupImgLoader.java

@@ -96,7 +96,7 @@ public RandomAccessibleInterval< FloatType > getFloatImage( final int timepointI
 		// TODO: this is stupid, remove capablitity to get FloatType images!
 		if ( normalize )
 		{
-			return ImgLib2Tools.normalizeVirtual( img );
+			return ImgLib2Tools.normalizeVirtualRAI( img );
 		}
 		else
 		{

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/splitting/SplitSetupImgLoader.java

@@ -70,7 +70,7 @@ public RandomAccessibleInterval< FloatType > getFloatImage( final int timepointI
 		// TODO: this is stupid, remove capablitity to get FloatType images!
 		if ( normalize )
 		{
-			return ImgLib2Tools.normalizeVirtual( img );
+			return ImgLib2Tools.normalizeVirtualRAI( img );
 		}
 		else
 		{

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/splitting/SplitViewerSetupImgLoader.java

@@ -156,9 +156,9 @@ public UnsignedShortType getImageType()
 	public RandomAccessibleInterval< FloatType > getFloatImage( final int timepointId, final boolean normalize, final ImgLoaderHint... hints )
 	{
 		if ( normalize )
-			return ImgLib2Tools.normalizeVirtual( getImage( timepointId, hints ) );
+			return ImgLib2Tools.normalizeVirtualRAI( getImage( timepointId, hints ) );
 		else
-			return ImgLib2Tools.convertVirtual( getImage( timepointId, hints ) );
+			return ImgLib2Tools.convertVirtualRAI( getImage( timepointId, hints ) );
 	}
 
 	@Override

src/main/java/net/preibisch/mvrecon/fiji/spimdata/interestpoints/InterestPointsN5.java

@@ -372,6 +372,16 @@ protected boolean loadInterestPoints()
 			final RandomAccessibleInterval< DoubleType > locData = N5Utils.open( n5, locDataset );
 			final int n = (int)locData.dimension( 0 );
 
+			// empty list
+			if ( n == 0 )
+			{
+				this.interestPoints = new ArrayList<>();
+				modifiedInterestPoints = false;
+
+				n5.close();
+				return true;
+			}
+
 			final RandomAccess< UnsignedLongType > idRA = idData.randomAccess();
 			final RandomAccess< DoubleType > locRA = locData.randomAccess();
 

src/main/java/net/preibisch/mvrecon/process/downsampling/DownsampleTools.java

@@ -34,11 +34,15 @@
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.util.LinAlgHelpers;
+import net.imglib2.type.numeric.real.FloatType;
 import net.imglib2.util.Pair;
 import net.imglib2.util.Util;
 import net.imglib2.util.ValuePair;
+import net.imglib2.view.Views;
 import net.preibisch.legacy.io.IOFunctions;
 import net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint;
+import net.preibisch.mvrecon.process.downsampling.lazy.LazyDownsample2x;
+import net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2;
 
 public class DownsampleTools
 {
@@ -382,7 +386,7 @@ public static AffineTransform3D getMipMapTransform(
 	{
 		final AffineTransform3D mmt = new AffineTransform3D();
 
-		openAndDownsample( imgLoader, vd, mmt, downsampleFactors, true );
+		openAndDownsample( imgLoader, vd, mmt, downsampleFactors, true, false );
 
 		return mmt;
 	}
@@ -394,17 +398,19 @@ public static AffineTransform3D getMipMapTransform(
 	 * @param imgLoader the imgloader
 	 * @param vd the view id
 	 * @param downsampleFactors - specify which downsampling in each dimension (e.g. 1,2,4,8 )
+	 * @param virtualDownsampling - use virtual downsampling if the requested downsamplefactors are not precomputed
 	 * @return opened image and the mipmap transform
 	 */
 	@SuppressWarnings({ "rawtypes" })
 	public static Pair<RandomAccessibleInterval, AffineTransform3D> openAndDownsample(
 			final BasicImgLoader imgLoader,
 			final ViewId vd,
-			final long[] downsampleFactors )
+			final long[] downsampleFactors,
+			final boolean virtualDownsampling )
 	{
 		final AffineTransform3D mipMapTransform = new AffineTransform3D();
 
-		final RandomAccessibleInterval img = openAndDownsample(imgLoader, vd, mipMapTransform, downsampleFactors, false );
+		final RandomAccessibleInterval img = openAndDownsample(imgLoader, vd, mipMapTransform, downsampleFactors, false, virtualDownsampling );
 
 		return new ValuePair<RandomAccessibleInterval, AffineTransform3D>( img, mipMapTransform );
 	}
@@ -417,6 +423,7 @@ public static Pair<RandomAccessibleInterval, AffineTransform3D> openAndDownsampl
 	 * @param vd the view id
 	 * @param mipMapTransform - will be filled if downsampling is performed, otherwise identity transform
 	 * @param downsampleFactors - specify which downsampling in each dimension (e.g. 1,2,4,8 )
+	 * @param virtualDownsampling - use virtual downsampling if the requested downsamplefactors are not precomputed
 	 * @param transformOnly - if true does not open any images but only provides the mipMapTransform (METHOD WILL RETURN NULL!)
 	 * @return opened image
 	 */
@@ -426,14 +433,9 @@ private static RandomAccessibleInterval openAndDownsample(
 			final ViewId vd,
 			final AffineTransform3D mipMapTransform,
 			long[] downsampleFactors,
-			final boolean transformOnly ) // only for ImgLib1 legacy code
+			final boolean transformOnly, // only for ImgLib1 legacy code
+			final boolean virtualDownsampling )
 	{
-
-		//if ( !transformOnly )
-		//	IOFunctions.println(
-		//		"(" + new Date(System.currentTimeMillis()) + "): "
-		//		+ "Requesting Img from ImgLoader (tp=" + vd.getTimePointId() + ", setup=" + vd.getViewSetupId() + "), downsampling: " + Util.printCoordinates( downsampleFactors ) );
-
 		long dsx = downsampleFactors[0];
 		long dsy = downsampleFactors[1];
 		long dsz = (downsampleFactors.length > 2) ? downsampleFactors[ 2 ] : 1;
@@ -473,31 +475,14 @@ private static RandomAccessibleInterval openAndDownsample(
 
 			if ( !transformOnly )
 			{
-				//IOFunctions.println(
-				//		"(" + new Date(System.currentTimeMillis()) + "): " +
-				//		"Using precomputed Multiresolution Images [" + fx + "x" + fy + "x" + fz + "], " +
-				//		"Remaining downsampling [" + dsx + "x" + dsy + "x" + dsz + "]" );
-
-				//if ( openAsFloat )
-				//	input = ImgLib2Tools.convertVirtual( (RandomAccessibleInterval)mrImgLoader.getSetupImgLoader( vd.getViewSetupId() ).getImage( vd.getTimePointId(), bestLevel ) );
-				//else
-					input = mrImgLoader.getSetupImgLoader( vd.getViewSetupId() ).getImage( vd.getTimePointId(), bestLevel );
+				input = mrImgLoader.getSetupImgLoader( vd.getViewSetupId() ).getImage( vd.getTimePointId(), bestLevel );
 			}
 		}
 		else
 		{
 			if ( !transformOnly )
 			{
-				//IOFunctions.println(
-				//		"(" + new Date(System.currentTimeMillis()) + "): " +
-				//		"Using precomputed Multiresolution Images [1x1x1], " +
-				//		"Remaining downsampling [" + dsx + "x" + dsy + "x" + dsz + "]" );
-
-				// we only need to do the complete opening when we do not perform additional downsampling below
-				//if ( openAsFloat )
-				//	input = ImgLib2Tools.convertVirtual( (RandomAccessibleInterval)imgLoader.getSetupImgLoader( vd.getViewSetupId() ).getImage( vd.getTimePointId() ) );
-				//else
-					input = imgLoader.getSetupImgLoader( vd.getViewSetupId() ).getImage( vd.getTimePointId() );
+				input = imgLoader.getSetupImgLoader( vd.getViewSetupId() ).getImage( vd.getTimePointId() );
 			}
 
 			if ( mipMapTransform != null )
@@ -509,7 +494,7 @@ private static RandomAccessibleInterval openAndDownsample(
 			// the additional downsampling (performed below)
 			final AffineTransform3D additonalDS = new AffineTransform3D();
 			additonalDS.set( dsx, 0.0, 0.0, 0.0, 0.0, dsy, 0.0, 0.0, 0.0, 0.0, dsz, 0.0 );
-	
+
 			// we need to concatenate since when correcting for the downsampling we first multiply by whatever
 			// the manual downsampling did, and just then by the scaling+offset of the HDF5
 			//
@@ -522,15 +507,29 @@ private static RandomAccessibleInterval openAndDownsample(
 
 		if ( !transformOnly )
 		{
-			// note: every pixel is read exactly once, therefore caching the virtual input would not give any advantages
-			for ( ;dsx > 1; dsx /= 2 )
-				input = Downsample.simple2x( input, new boolean[]{ true, false, false } );
+			if ( virtualDownsampling )
+			{
+				for ( ;dsx > 1; dsx /= 2 )
+					input = LazyDownsample2x.init( Views.extendBorder( input ), input, new FloatType(), DoGImgLib2.blockSize, 0 );
 
-			for ( ;dsy > 1; dsy /= 2 )
-				input = Downsample.simple2x( input, new boolean[]{ false, true, false } );
+				for ( ;dsy > 1; dsy /= 2 )
+					input = LazyDownsample2x.init( Views.extendBorder( input ), input, new FloatType(), DoGImgLib2.blockSize, 1 );
 
-			for ( ;dsz > 1; dsz /= 2 )
-				input = Downsample.simple2x( input, new boolean[]{ false, false, true } );
+				for ( ;dsz > 1; dsz /= 2 )
+					input = LazyDownsample2x.init( Views.extendBorder( input ), input, new FloatType(), DoGImgLib2.blockSize, 2 );
+			}
+			else
+			{
+				// note: every pixel is read exactly once, therefore caching the virtual input would not give any advantages
+				for ( ;dsx > 1; dsx /= 2 )
+					input = Downsample.simple2x( input, new boolean[]{ true, false, false } );
+
+				for ( ;dsy > 1; dsy /= 2 )
+					input = Downsample.simple2x( input, new boolean[]{ false, true, false } );
+
+				for ( ;dsz > 1; dsz /= 2 )
+					input = Downsample.simple2x( input, new boolean[]{ false, false, true } );
+			}
 		}
 
 		return input;

src/main/java/net/preibisch/mvrecon/process/interestpointdetection/methods/dog/DoG.java

@@ -29,6 +29,7 @@
 import ij.IJ;
 import mpicbg.spim.data.sequence.ViewDescription;
 import mpicbg.spim.data.sequence.ViewId;
+import net.imglib2.FinalInterval;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.type.NativeType;
@@ -60,7 +61,7 @@ public static HashMap< ViewId, List< InterestPoint >> findInterestPoints( final
 		return interestPoints;
 	}
 
-	/**
+	/*
 	 * finds all interest points and returns them as InterestPoints (which is a mpicbg Point and implements RealLocalizable),
 	 * by default returns world coordinates
 	 *
@@ -92,8 +93,9 @@ public static < T extends RealType< T > & NativeType< T > > List< InterestPoint
 		// compute Difference-of-Gaussian (includes normalization)
 		//
 		List< InterestPoint > ips = DoGImgLib2.computeDoG(
-				Views.zeroMin( input ),
+				Views.extendMirrorSingle( Views.zeroMin( input ) ),
 				null,
+				new FinalInterval( Views.zeroMin( input ) ),
 				sigma,
 				threshold,
 				1, // 0 = no subpixel localization, 1 = quadratic fit
@@ -140,18 +142,19 @@ public static void addInterestPoints( final HashMap< ViewId, List< InterestPoint
 
 				final ExecutorService service = Threads.createFixedExecutorService( Threads.numThreads() );
 
-				// TODO: downsampling is not virtual!
+				// downsampling is not virtual!
 				@SuppressWarnings({"rawtypes" })
 				final Pair<RandomAccessibleInterval, AffineTransform3D> input =
 						DownsampleTools.openAndDownsample(
 								dog.imgloader,
 								vd,
-								new long[] { dog.downsampleXY, dog.downsampleXY, dog.downsampleZ } );
+								new long[] { dog.downsampleXY, dog.downsampleXY, dog.downsampleZ },
+								false );
 
-				@SuppressWarnings("unchecked")
 				List< InterestPoint > ips = DoGImgLib2.computeDoG(
-							input.getA(),
+							Views.extendMirrorSingle( input.getA() ),
 							null, // mask
+							new FinalInterval( input.getA() ),
 							dog.sigma,
 							dog.threshold,
 							dog.localization,