DoG detection takes RandomAccessible's instead of RandomAccessibleInt…

…erval's (so OutOfBounds - or not - can be defined outside)
PreibischLab · Feb 29, 2024 · 3b071be · 3b071be
1 parent 94aa958
commit 3b071be
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Showing 14 changed files with 67 additions and 55 deletions.
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyDHMImgLoader.java b/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

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyFileMapImgLoaderLOCI.java b/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 ) );
 	}
 
 

diff --git a/...main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyLightSheetZ1ImgLoader.java b/...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

diff --git a/...main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyMicroManagerImgLoader.java b/...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

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyStackImgLoaderIJ.java b/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 ) );
 	}
 
 	/**

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyStackImgLoaderLOCI.java b/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 ) );
 	}
 
 	/**

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/SimViewSetupImgLoader.java b/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

diff --git a/...n/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/filemap2/FileMapImgLoaderLOCI2.java b/...n/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

diff --git a/...ibisch/mvrecon/fiji/spimdata/imgloaders/splitting/SplitMultiResolutionSetupImgLoader.java b/...ibisch/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
 		{

diff --git a/...in/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/splitting/SplitSetupImgLoader.java b/...in/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
 		{

diff --git a/...a/net/preibisch/mvrecon/fiji/spimdata/imgloaders/splitting/SplitViewerSetupImgLoader.java b/...a/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

diff --git a/src/main/java/net/preibisch/mvrecon/process/interestpointdetection/methods/dog/DoG.java b/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
@@ -150,8 +152,9 @@ public static void addInterestPoints( final HashMap< ViewId, List< InterestPoint
 
 				@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,

diff --git a/...ain/java/net/preibisch/mvrecon/process/interestpointdetection/methods/dog/DoGImgLib2.java b/...ain/java/net/preibisch/mvrecon/process/interestpointdetection/methods/dog/DoGImgLib2.java
@@ -53,11 +53,9 @@
 import net.imglib2.img.array.ArrayImg;
 import net.imglib2.img.array.ArrayImgFactory;
 import net.imglib2.img.array.ArrayImgs;
-import net.imglib2.img.basictypeaccess.AccessFlags;
 import net.imglib2.img.basictypeaccess.array.FloatArray;
 import net.imglib2.img.cell.CellImgFactory;
 import net.imglib2.img.display.imagej.ImageJFunctions;
-import net.imglib2.type.NativeType;
 import net.imglib2.type.Type;
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.real.FloatType;
@@ -82,7 +80,6 @@
 import net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss.LazyGauss;
 import net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss.LazyWeightedGauss;
 import util.ImgLib2Tools;
-import util.Lazy;
 
 public class DoGImgLib2
 {
@@ -112,7 +109,7 @@ public static void main ( String[] args )
 
 		// 1388x1040x81 = 116925120
 		final ArrayList<InterestPoint> points = 
-				computeDoG(inputCropped, null, 2.000, 0.03, 1/*localization*/, false /*findMin*/, true /*findMax*/, 0, 255, Executors.newFixedThreadPool( 8 ) );
+				computeDoG( Views.extendMirrorDouble( inputCropped ), Views.extendZero( mask ), new FinalInterval( inputCropped ), 2.000, 0.03, 1/*localization*/, false /*findMin*/, true /*findMax*/, 0, 255, Executors.newFixedThreadPool( 8 ) );
 
 		System.out.println( System.currentTimeMillis() - time );
 
@@ -141,8 +138,9 @@ public static < T extends RealType< T > > int radiusDoG( final double sigma )
 	}
 
 	public static < T extends RealType< T > > ArrayList< InterestPoint > computeDoG(
-			final RandomAccessibleInterval< T > input,
-			final RandomAccessibleInterval< T > mask,
+			final RandomAccessible< T > input,
+			final RandomAccessible< T > mask,
+			final Interval interval,
 			final double sigma,
 			final double threshold,
 			final int localization,
@@ -152,12 +150,13 @@ public static < T extends RealType< T > > ArrayList< InterestPoint > computeDoG(
 			final double maxIntensity,
 			final ExecutorService service )
 	{
-		return computeDoG(input, mask, sigma, threshold, localization, findMin, findMax, minIntensity, maxIntensity, blockSize, service, null, null, false, 0.0 );
+		return computeDoG(input, mask, interval, sigma, threshold, localization, findMin, findMax, minIntensity, maxIntensity, blockSize, service, null, null, false, 0.0 );
 	}
 
 	public static < T extends RealType< T > > ArrayList< InterestPoint > computeDoG(
-			final RandomAccessibleInterval< T > input,
-			final RandomAccessibleInterval< T > mask,
+			final RandomAccessible< T > input,
+			final RandomAccessible< T > mask,
+			final Interval interval,
 			final double sigma,
 			final double threshold,
 			final int localization,
@@ -189,9 +188,9 @@ public static < T extends RealType< T > > ArrayList< InterestPoint > computeDoG(
 			final float[] minmax;
 
 			if ( mask == null )
-				minmax = FusionTools.minMax( input, service );
+				minmax = FusionTools.minMax( Views.interval( input, interval ), service );
 			else
-				minmax = minMax( input, mask, service );
+				minmax = minMax( Views.interval( input, interval ), Views.interval( mask, interval ), service );
 
 			min = minmax[ 0 ];
 			max = minmax[ 1 ];
@@ -206,7 +205,7 @@ public static < T extends RealType< T > > ArrayList< InterestPoint > computeDoG(
 			IOFunctions.println( "(" + new Date(System.currentTimeMillis()) + "): min intensity = " + min + ", max intensity = " + max );
 
 		// normalize image
-		final RandomAccessibleInterval< FloatType > inputFloat = ImgLib2Tools.normalizeVirtual( input, min, max );
+		final RandomAccessible< FloatType > inputFloat = ImgLib2Tools.normalizeVirtual( input, min, max );
 
 		final float k = LaPlaceFunctions.computeK( 4 );
 		final float K_MIN1_INV = LaPlaceFunctions.computeKWeight(k);
@@ -232,33 +231,33 @@ public static < T extends RealType< T > > ArrayList< InterestPoint > computeDoG(
 				"threshold=" + minPeakValue + ", sigma1=" + Util.printCoordinates( sigma1 ) + ", sigma2=" + Util.printCoordinates( sigma2 ) + ")" );
 
 		final long[] minInterval = new long[ inputFloat.numDimensions() ];
-		inputFloat.min( minInterval );
+		interval.min( minInterval );
 
 		final RandomAccessibleInterval< FloatType > gauss1, gauss2;
-		final RandomAccessibleInterval< FloatType > maskFloat;
+		final RandomAccessible< FloatType > maskFloat;
 
 		if ( mask == null )
 		{
 			maskFloat = null;
 
 			if ( cuda == null )
 			{
-				gauss1 = LazyGauss.init( Views.extendMirrorDouble( inputFloat ), new FinalInterval( inputFloat ), new FloatType(), sigma1, blockSize );
-				gauss2 = LazyGauss.init( Views.extendMirrorDouble( inputFloat ), new FinalInterval( inputFloat ), new FloatType(), sigma2, blockSize );
+				gauss1 = LazyGauss.init( inputFloat, interval, new FloatType(), sigma1, blockSize );
+				gauss2 = LazyGauss.init( inputFloat, interval , new FloatType(), sigma2, blockSize );
 			}
 			else
 			{
 				// TODO: untested
-				gauss1 = computeGaussCUDA( inputFloat, sigma1, cuda, cudaDevice, accurateCUDA, percentGPUMem );
-				gauss2 = computeGaussCUDA( inputFloat, sigma2, cuda, cudaDevice, accurateCUDA, percentGPUMem );
+				gauss1 = computeGaussCUDA( Views.interval( inputFloat, interval ), sigma1, cuda, cudaDevice, accurateCUDA, percentGPUMem );
+				gauss2 = computeGaussCUDA( Views.interval( inputFloat, interval ), sigma2, cuda, cudaDevice, accurateCUDA, percentGPUMem );
 			}
 		}
 		else
 		{
-			maskFloat = Converters.convertRAI( mask, (i,o) -> o.set( i.getRealFloat() ), new FloatType());//ImgLib2Tools.convertVirtual( mask );
+			maskFloat = Converters.convert( mask, (i,o) -> o.set( i.getRealFloat() ), new FloatType());//ImgLib2Tools.convertVirtual( mask );
 
-			gauss1 = LazyWeightedGauss.init( Views.extendMirrorSingle( inputFloat ), Views.extendZero( maskFloat ), new FinalInterval( inputFloat ), new FloatType(), sigma1, blockSize );
-			gauss2 = LazyWeightedGauss.init( Views.extendMirrorSingle( inputFloat ), Views.extendZero( maskFloat ), new FinalInterval( inputFloat ), new FloatType(), sigma2, blockSize );
+			gauss1 = LazyWeightedGauss.init( inputFloat, maskFloat, interval, new FloatType(), sigma1, blockSize ); // mask zero oobs
+			gauss2 = LazyWeightedGauss.init( inputFloat, maskFloat, interval, new FloatType(), sigma2, blockSize );
 		}
 
 		final RandomAccessibleInterval< FloatType > dog = Converters.convert(gauss2, gauss1, new BiConverter<FloatType, FloatType, FloatType>()
@@ -277,7 +276,7 @@ public void convert( final FloatType inputA, final FloatType inputB, final Float
 		if ( !silent )
 			IOFunctions.println("(" + new Date(System.currentTimeMillis()) + "): Detecting peaks." );
 
-		final ArrayList< SimplePeak > peaks = findPeaks( dogCached, maskFloat, minInitialPeakValue, service );
+		final ArrayList< SimplePeak > peaks = findPeaks( dogCached, Views.interval( maskFloat, interval ), minInitialPeakValue, service );
 
 		if ( !silent )
 			IOFunctions.println("(" + new Date(System.currentTimeMillis()) + "): Found " + peaks.size() + " initial peaks (before refinement)." );

diff --git a/src/main/java/util/ImgLib2Tools.java b/src/main/java/util/ImgLib2Tools.java
@@ -22,6 +22,7 @@
  */
 package util;
 
+import net.imglib2.RandomAccessible;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.converter.Converters;
 import net.imglib2.type.numeric.RealType;
@@ -30,17 +31,28 @@
 
 public class ImgLib2Tools
 {
-	public static final < T extends RealType< T > > RandomAccessibleInterval<FloatType> convertVirtual( final RandomAccessibleInterval< T > img )
+	public static final < T extends RealType< T > > RandomAccessibleInterval<FloatType> convertVirtualRAI( final RandomAccessibleInterval< T > img )
 	{
 		return Converters.convertRAI( img, (i,o) -> o.set( i.getRealFloat() ), new FloatType());
-		/*
-		return new ConvertedRandomAccessibleInterval<T, FloatType>(
+	}
+
+	public static final < T extends RealType< T > > RandomAccessible<FloatType> convertVirtual( final RandomAccessible< T > img )
+	{
+		return Converters.convert( img, (i,o) -> o.set( i.getRealFloat() ), new FloatType());
+	}
+
+	public static final < T extends RealType< T > > RandomAccessible<FloatType> normalizeVirtual( final RandomAccessible< T > img, final double min, final double max )
+	{
+		final float minf = (float)min;
+		final float maxf = (float)max;
+
+		return Converters.convert(
 				img,
-				new RealFloatConverter<T>(),
-				new FloatType() );*/
+				( input, output ) -> output.set( ( input.getRealFloat() - minf ) / ( maxf - minf ) ),
+				new FloatType() );
 	}
 
-	public static final < T extends RealType< T > > RandomAccessibleInterval<FloatType> normalizeVirtual( final RandomAccessibleInterval< T > img, final double min, final double max )
+	public static final < T extends RealType< T > > RandomAccessibleInterval<FloatType> normalizeVirtualRAI( final RandomAccessibleInterval< T > img, final double min, final double max )
 	{
 		final float minf = (float)min;
 		final float maxf = (float)max;
@@ -51,7 +63,7 @@ public static final < T extends RealType< T > > RandomAccessibleInterval<FloatTy
 				new FloatType() );
 	}
 
-	public static final < T extends RealType< T > > RandomAccessibleInterval<FloatType> normalizeVirtual( final RandomAccessibleInterval< T > img )
+	public static final < T extends RealType< T > > RandomAccessibleInterval<FloatType> normalizeVirtualRAI( final RandomAccessibleInterval< T > img )
 	{
 		double min = Double.MAX_VALUE;
 		double max = -Double.MAX_VALUE;
@@ -67,6 +79,6 @@ public static final < T extends RealType< T > > RandomAccessibleInterval<FloatTy
 				max = v;
 		}
 
-		return normalizeVirtual( img, min, max );
+		return normalizeVirtualRAI( img, min, max );
 	}
 }