add support of 32-bit images

pom.xml

@@ -47,6 +47,11 @@
 			<url>https://ulrik.is/writing</url>
 			<properties><id>skalarproduktraum</id></properties>
 		</contributor>
+		<contributor>
+			<name>Eugene Katrukha</name>
+			<url>https://imagej.net/people/ekatrukha</url>
+			<properties><id>ekatrukha</id></properties>
+		</contributor>
 	</contributors>
 
 	<mailingLists>

src/main/java/bvv/core/blocks/ByteUtils.java

@@ -43,6 +43,7 @@ public class ByteUtils
 	private static final long BUFFER_ADDRESS_OFFSET;
 	private static final long BYTE_ARRAY_OFFSET;
 	private static final long SHORT_ARRAY_OFFSET;
+	private static final long FLOAT_ARRAY_OFFSET;
 
 	static
 	{
@@ -66,6 +67,7 @@ public Unsafe run() throws Exception
 
 			BYTE_ARRAY_OFFSET = UNSAFE.arrayBaseOffset( byte[].class );
 			SHORT_ARRAY_OFFSET = UNSAFE.arrayBaseOffset( short[].class );
+			FLOAT_ARRAY_OFFSET = UNSAFE.arrayBaseOffset( float[].class );
 		}
 		catch ( final Exception ex )
 		{
@@ -98,6 +100,17 @@ public static void copyBytes( final byte[] src, final long dst, final long sox,
 	{
 		UNSAFE.copyMemory( src, BYTE_ARRAY_OFFSET + sox, null, dst, csx );
 	}
+
+	public static void setFloats( final float src, final long dst, final long csx )
+	{
+		for ( int i = 0; i < csx; ++i )
+			UNSAFE.putFloat( dst + 4 * i, src );
+	}
+
+	public static void copyFloats( final float[] src, final long dst, final long sox, final long csx )
+	{
+		UNSAFE.copyMemory( src, FLOAT_ARRAY_OFFSET + 4 * sox, null, dst, 4 * csx );
+	}
 
 	public interface Address
 	{

src/main/java/bvv/core/blocks/CopySubArrayImp.java

@@ -66,6 +66,23 @@ public void copysubarray3d( final byte[] src, final int sox, final int soy, fina
 			copysubarray3dn( copy, sox, soy, soz, ssx, ssy, dox, doy, doz, dsx, dsy, csx, csy, csz );
 		}
 	}
+
+	public static class FloatToAddress implements CopySubArray< float[], ByteUtils.Address >
+	{
+		@Override
+		public void clearsubarray3d( final ByteUtils.Address dst, final int dox, final int doy, final int doz, final int dsx, final int dsy, final int csx, final int csy, final int csz )
+		{
+			final ArrayFill fill = ( o, l ) -> ByteUtils.setFloats( 0, dst.getAddress() + 4 * o, l );
+			fillsubarray3dn( fill, dox, doy, doz, dsx, dsy, csx, csy, csz );
+		}
+
+		@Override
+		public void copysubarray3d( final float[] src, final int sox, final int soy, final int soz, final int ssx, final int ssy, final ByteUtils.Address dst, final int dox, final int doy, final int doz, final int dsx, final int dsy, final int csx, final int csy, final int csz )
+		{
+			final ArrayCopy copy = ( so, o, l ) -> ByteUtils.copyFloats( src, dst.getAddress() + 4 * o, so, l );
+			copysubarray3dn( copy, sox, soy, soz, ssx, ssy, dox, doy, doz, dsx, dsy, csx, csy, csz );
+		}
+	}
 
 	static void copysubarray3dn(
 			ArrayCopy copysubarray1dn,

src/main/java/bvv/core/blocks/TileAccess.java

@@ -44,6 +44,7 @@
 
 import static net.imglib2.type.PrimitiveType.BYTE;
 import static net.imglib2.type.PrimitiveType.SHORT;
+import static net.imglib2.type.PrimitiveType.FLOAT;
 
 /**
  * Copy blocks from a {@link ResolutionLevel3D} source to an {@link UploadBuffer}.
@@ -137,6 +138,16 @@ else if ( cellimg && primitive == BYTE && cacheSpec.format() == Texture.Internal
 						cacheSpec
 				);
 			}
+			else if ( cellimg && primitive == FLOAT && cacheSpec.format() == Texture.InternalFormat.R32F )
+			{
+				return new TileAccess<>(
+						volatil
+								? new GridDataAccessImp.VolatileCells<>( ( AbstractCellImg ) img )
+								: new GridDataAccessImp.Cells<>( ( AbstractCellImg ) img ),
+						new CopySubArrayImp.FloatToAddress(),
+						cacheSpec
+				);
+			}
 		}
 
 		throw new UnsupportedOperationException( "pixel and/or image type not supported (yet)." );
@@ -150,7 +161,7 @@ public static boolean isSupportedType( final Object type )
 		{
 			final PrimitiveType primitive = ( ( NativeType ) type ).getNativeTypeFactory().getPrimitiveType();
 			final Fraction epp = ( ( NativeType ) type ).getEntitiesPerPixel();
-			return ( primitive == SHORT || primitive == BYTE ) && epp.getNumerator() == epp.getDenominator();
+			return ( primitive == SHORT || primitive == BYTE || primitive == FLOAT ) && epp.getNumerator() == epp.getDenominator();
 		}
 
 		return false;

src/main/java/bvv/core/cache/TextureCache.java

@@ -316,6 +316,13 @@ private void initializeBlockedTiles( ArrayList< TileFillTask > tileFillTasks )
 				return true;
 			} , () -> true ), oobTile ) );
 		}
+		if(spec.format() == InternalFormat.R32F)
+		{
+			tileFillTasks.add( new TileFillTask( new DefaultFillTask( oobDummyKey, buf -> {
+				ByteUtils.setFloats( 0, buf.getAddress(), elementsPerTile );
+				return true;
+			} , () -> true ), oobTile ) );
+		}
 	}
 
 	private List< Tile > assignFillTiles( final int size, final int currentTimestamp )

src/main/java/bvv/core/render/DefaultSimpleStackManager.java

@@ -30,6 +30,7 @@
 
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
+import java.nio.FloatBuffer;
 import java.nio.IntBuffer;
 import java.nio.ShortBuffer;
 import java.util.HashMap;
@@ -41,6 +42,7 @@
 import net.imglib2.type.numeric.ARGBType;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.type.numeric.integer.UnsignedShortType;
+import net.imglib2.type.numeric.real.FloatType;
 import net.imglib2.util.Intervals;
 import net.imglib2.view.Views;
 
@@ -54,13 +56,15 @@ public class DefaultSimpleStackManager implements SimpleStackManager
 {
 	private final HashMap< SimpleStack3D< ? >, VolumeTextureU16 > texturesU16;
 	private final HashMap< SimpleStack3D< ? >, VolumeTextureU8 > texturesU8;
+	private final HashMap< SimpleStack3D< ? >, VolumeTextureU32 > texturesU32;
 	private final HashMap< SimpleStack3D< ? >, VolumeTextureRGBA8 > texturesRGBA8;
 
 	private final HashMap< Texture3D, Integer > timestamps;
 	private int currentTimestamp;
 
 	public DefaultSimpleStackManager()
 	{
+		texturesU32 = new HashMap<>();
 		texturesU16 = new HashMap<>();
 		texturesU8 = new HashMap<>();
 		texturesRGBA8 = new HashMap<>();
@@ -90,6 +94,12 @@ else if ( type instanceof UnsignedByteType )
 			sourceMax = new Vector3f( image.max( 0 ), image.max( 1 ), image.max( 2 ) );
 			sourceMin = new Vector3f( image.min( 0 ), image.min( 1 ), image.min( 2 ) );
 		}
+		else if ( type instanceof FloatType )
+		{
+			texture = texturesU32.computeIfAbsent( stack, s -> uploadToTextureU32( context, ( RandomAccessibleInterval< FloatType > ) image ) );
+			sourceMax = new Vector3f( image.max( 0 ), image.max( 1 ), image.max( 2 ) );
+			sourceMin = new Vector3f( image.min( 0 ), image.min( 1 ), image.min( 2 ) );
+		}
 		else if ( type instanceof ARGBType )
 		{
 			texture = texturesRGBA8.computeIfAbsent( stack, s -> uploadToTextureRGBA8( context, ( RandomAccessibleInterval< ARGBType > ) image ) );
@@ -162,6 +172,30 @@ private static void copyToBufferU16( final RandomAccessibleInterval< UnsignedSho
 		while ( cursor.hasNext() )
 			sdata.put( i++, cursor.next().getShort() );
 	}
+
+	private static VolumeTextureU32 uploadToTextureU32( final GpuContext context, final RandomAccessibleInterval< FloatType > rai )
+	{
+		final VolumeTextureU32 texture = new VolumeTextureU32();
+		texture.init( Intervals.dimensionsAsIntArray( rai ) );
+
+		final int numBytes = ( int ) ( 4 * Intervals.numElements( rai ) );
+		final ByteBuffer data = ByteBuffer.allocateDirect( numBytes ); // allocate a bit more than needed...
+		data.order( ByteOrder.nativeOrder() );
+		copyToBufferU32( rai, data );
+		texture.upload( context, data );
+		return texture;
+	}
+
+	private static void copyToBufferU32( final RandomAccessibleInterval< FloatType  > rai, final ByteBuffer buffer )
+	{
+		// TODO handle specific RAI types more efficiently
+		// TODO multithreading
+		final Cursor< FloatType > cursor = Views.flatIterable( rai ).cursor();
+		final FloatBuffer sdata = buffer.asFloatBuffer();
+		int i = 0;
+		while ( cursor.hasNext() )
+			sdata.put( i++, cursor.next().getRealFloat() );
+	}
 
 	private static VolumeTextureU8 uploadToTextureU8( final GpuContext context, final RandomAccessibleInterval< UnsignedByteType > rai )
 	{

src/main/java/bvv/core/render/MultiVolumeShaderMip.java

@@ -184,6 +184,7 @@ public MultiVolumeShaderMip( VolumeShaderSignature signature, final boolean useD
 			switch ( volumeSignature.getPixelType() )
 			{
 			default:
+			case SFLOAT:
 			case USHORT:
 			case UBYTE:
 				convert = templateConvert.instantiate();
@@ -520,6 +521,9 @@ public ConverterSegment( final SegmentedShader prog, final Segment segment, fina
 			case ARGB:
 				rangeScale = 0xff;
 				break;
+			case SFLOAT:
+				rangeScale = 1.0;
+				break;
 			}
 		}
 

src/main/java/bvv/core/render/VolumeRenderer.java

@@ -37,17 +37,20 @@
 import static com.jogamp.opengl.GL.GL_UNPACK_ALIGNMENT;
 import static bvv.core.backend.Texture.InternalFormat.R8;
 import static bvv.core.backend.Texture.InternalFormat.R16;
+import static bvv.core.backend.Texture.InternalFormat.R32F;
 import static bvv.core.render.VolumeRenderer.RepaintType.DITHER;
 import static bvv.core.render.VolumeRenderer.RepaintType.FULL;
 import static bvv.core.render.VolumeRenderer.RepaintType.LOAD;
 import static bvv.core.render.VolumeRenderer.RepaintType.NONE;
 import static bvv.core.render.VolumeShaderSignature.PixelType.ARGB;
 import static bvv.core.render.VolumeShaderSignature.PixelType.UBYTE;
 import static bvv.core.render.VolumeShaderSignature.PixelType.USHORT;
+import static bvv.core.render.VolumeShaderSignature.PixelType.SFLOAT;
 import static bvv.core.multires.SourceStacks.SourceStackType.MULTIRESOLUTION;
 import static bvv.core.multires.SourceStacks.SourceStackType.SIMPLE;
 import static net.imglib2.type.PrimitiveType.BYTE;
 import static net.imglib2.type.PrimitiveType.SHORT;
+import static net.imglib2.type.PrimitiveType.FLOAT;
 
 import bvv.core.backend.Texture.InternalFormat;
 import bvv.core.cache.CacheSpec;
@@ -69,8 +72,10 @@
 import net.imglib2.type.numeric.ARGBType;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.type.numeric.integer.UnsignedShortType;
+import net.imglib2.type.numeric.real.FloatType;
 import net.imglib2.type.volatiles.VolatileUnsignedByteType;
 import net.imglib2.type.volatiles.VolatileUnsignedShortType;
+import net.imglib2.type.volatiles.VolatileFloatType;
 
 import org.joml.Matrix4f;
 
@@ -145,6 +150,8 @@ void request( final RepaintType type )
 	private final TextureCacheAndPboChain cacheR8;
 
 	private final TextureCacheAndPboChain cacheR16;
+
+	private final TextureCacheAndPboChain cacheR32F;
 
 	private final ForkJoinPool forkJoinPool;
 
@@ -208,6 +215,7 @@ public VolumeRenderer(
 		// used for the first time.
 		cacheR8 = new TextureCacheAndPboChain( R8, cacheBlockSize, maxCacheSizeInMB );
 		cacheR16 = new TextureCacheAndPboChain( R16, cacheBlockSize, maxCacheSizeInMB );
+		cacheR32F = new TextureCacheAndPboChain( R32F, cacheBlockSize, maxCacheSizeInMB );
 
 		final int parallelism = Math.max( 1, Runtime.getRuntime().availableProcessors() / 2 );
 		forkJoinPool = new ForkJoinPool( parallelism );
@@ -306,6 +314,8 @@ else if ( type == LOAD )
 						volumeSignatures.add( new VolumeSignature( MULTIRESOLUTION, USHORT ) );
 					else if ( ( pixelType instanceof UnsignedByteType ) || ( pixelType instanceof VolatileUnsignedByteType ) )
 						volumeSignatures.add( new VolumeSignature( MULTIRESOLUTION, UBYTE ) );
+					else if ( ( pixelType instanceof FloatType ) || ( pixelType instanceof VolatileFloatType ) )
+						volumeSignatures.add( new VolumeSignature( MULTIRESOLUTION, SFLOAT ) );
 					else
 						throw new IllegalArgumentException( "Multiresolution stack with pixel type " + pixelType.getClass().getName() + " unsupported in BigVolumeViewer." );
 				}
@@ -316,6 +326,8 @@ else if ( stack instanceof SimpleStack3D )
 						volumeSignatures.add( new VolumeSignature( SIMPLE, USHORT ) );
 					else if ( pixelType instanceof UnsignedByteType )
 						volumeSignatures.add( new VolumeSignature( SIMPLE, UBYTE ) );
+					else if ( pixelType instanceof FloatType )
+						volumeSignatures.add( new VolumeSignature( SIMPLE, SFLOAT ) );
 					else if ( pixelType instanceof ARGBType )
 						volumeSignatures.add( new VolumeSignature( SIMPLE, ARGB ) );
 					else
@@ -523,6 +535,9 @@ private void updateBlocks(
 
 		final List< MultiResolutionStack3D< ? > > multiResStacksR16 = new ArrayList<>();
 		final List< VolumeBlocks > volumesR16 = new ArrayList<>();
+
+		final List< MultiResolutionStack3D< ? > > multiResStacksR32 = new ArrayList<>();
+		final List< VolumeBlocks > volumesR32 = new ArrayList<>();
 
 		for ( int i = 0; i < multiResStacks.size(); i++ )
 		{
@@ -539,6 +554,11 @@ else if ( primitiveType == SHORT )
 				multiResStacksR16.add( stack );
 				volumesR16.add( volume );
 			}
+			else if ( primitiveType == FLOAT )
+			{
+				multiResStacksR32.add( stack );
+				volumesR32.add( volume );
+			}
 			else
 			{
 				throw new IllegalArgumentException();
@@ -548,6 +568,8 @@ else if ( primitiveType == SHORT )
 		boolean complete = true;
 		complete &= updateBlocks( context, multiResStacksR8, volumesR8, cacheR8, forkJoinPool, renderWidth, pv );
 		complete &= updateBlocks( context, multiResStacksR16, volumesR16, cacheR16, forkJoinPool, renderWidth, pv );
+		complete &= updateBlocks( context, multiResStacksR32, volumesR32, cacheR32F, forkJoinPool, renderWidth, pv );
+
 		if ( !complete )
 			nextRequestedRepaint.request( LOAD );
 	}

src/main/java/bvv/core/render/VolumeShaderSignature.java

@@ -36,6 +36,7 @@ public final class VolumeShaderSignature
 {
 	public enum PixelType
 	{
+		SFLOAT,
 		USHORT,
 		UBYTE,
 		ARGB