Correct displayed sources bounds

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

@@ -262,7 +262,7 @@ public static Map< SegmentType, SegmentTemplate > getDefaultSegments( boolean us
 				"lutSampler", "blockScales", "lutSize", "lutOffset", "sampleVolume" ) );
 		segments.put( SegmentType.SampleVolume, new SegmentTemplate(
 				"sample_volume_simple.frag",
-				"im", "sourcemax", "intersectBoundingBox",
+				"im", "sourcemin", "sourcemax", "intersectBoundingBox",
 				"volume", "sampleVolume" ) );
 		segments.put( SegmentType.SampleRGBAVolume, new SegmentTemplate(
 				"sample_volume_simple_rgba.frag",
@@ -632,20 +632,23 @@ static class VolumeSimpleSegment extends VolumeSegment
 	{
 		private final UniformSampler uniformVolumeSampler;
 		private final UniformMatrix4f uniformIm;
+		private final Uniform3f uniformSourcemin;
 		private final Uniform3f uniformSourcemax;
 
 		public VolumeSimpleSegment( final SegmentedShader prog, final Segment volume )
 		{
 			super( volume );
 			uniformVolumeSampler = prog.getUniformSampler( volume, "volume" );
 			uniformIm = prog.getUniformMatrix4f( volume, "im" );
+			uniformSourcemin = prog.getUniform3f( volume, "sourcemin" );
 			uniformSourcemax = prog.getUniform3f( volume, "sourcemax" );
 		}
 
 		public void setData( SimpleVolume volume )
 		{
 			uniformVolumeSampler.set( volume.getVolumeTexture() );
 			uniformIm.set( volume.getIms() );
+			uniformSourcemin.set( volume.getSourceMin() );
 			uniformSourcemax.set( volume.getSourceMax() );
 		}
 	}

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

@@ -61,7 +61,7 @@ public SimpleVolume( final Texture3D texture, final AffineTransform3D sourceTran
 		this.texture = texture;
 		this.sourceToWorld = sourceTransform;
 		this.sourceMax = sourceMax.sub( sourceMin, new Vector3f() );
-
+		this.sourceMax.add( 0.5f, 0.5f, 0.5f );
 		AffineTransform3D t = new AffineTransform3D();
 		t.translate( sourceMin.x(), sourceMin.y(), sourceMin.z() );
 		t.preConcatenate( sourceTransform );
@@ -101,6 +101,11 @@ public double getVoxelSizeInWorldCoordinates()
 		}
 		return voxelSize;
 	}
+
+	public Vector3f getSourceMin()
+	{
+		return new Vector3f(-0.5f, -0.5f, -0.5f);
+	}
 
 	public Vector3f getSourceMax()
 	{

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

@@ -259,15 +259,15 @@ public Matrix4f getIms()
 	public Vector3f getSourceLevelMin()
 	{
 		final Interval lbb = multiResolutionStack.resolutions().get( baseLevel ).getImage();
-		final Vector3f sourceLevelMin = new Vector3f( lbb.min( 0 ), lbb.min( 1 ), lbb.min( 2 ) );
+		final Vector3f sourceLevelMin = new Vector3f( lbb.min( 0 ) - 0.5f, lbb.min( 1 ) - 0.5f, lbb.min( 2 ) - 0.5f );
 		return sourceLevelMin;
 	}
 
 	// TODO: revise / remove
 	public Vector3f getSourceLevelMax()
 	{
 		final Interval lbb = multiResolutionStack.resolutions().get( baseLevel ).getImage();
-		final Vector3f sourceLevelMax = new Vector3f( lbb.max( 0 ), lbb.max( 1 ), lbb.max( 2 ) );
+		final Vector3f sourceLevelMax = new Vector3f( lbb.max( 0 ) + 0.5f, lbb.max( 1 ) + 0.5f, lbb.max( 2 ) + 0.5f );
 		return sourceLevelMax;
 	}
 

src/main/resources/bvv/core/render/sample_volume_blocks.frag

@@ -36,8 +36,7 @@ float sampleVolume( vec4 wpos )
 	vec3 B0 = lutv.xyz * paddedBlockSize + cachePadOffset;
 	vec3 sj = blockScales[ lutv.w ];
 
-	vec3 c0 = B0 + mod( pos * sj, blockSize ) + 0.5 * sj;
-	                                       // + 0.5 ( sj - 1 )   + 0.5 for tex coord offset
+	vec3 c0 = B0 + mod( pos * sj, blockSize );
 
 	return texture( volumeCache, c0 / cacheSize ).r;
-}
+}

src/main/resources/bvv/core/render/sample_volume_simple.frag

@@ -1,11 +1,12 @@
 uniform mat4 im;
+uniform vec3 sourcemin;
 uniform vec3 sourcemax;
 
 void intersectBoundingBox( vec4 wfront, vec4 wback, out float tnear, out float tfar )
 {
 	vec4 mfront = im * wfront;
 	vec4 mback = im * wback;
-	intersectBox( mfront.xyz, (mback - mfront).xyz, vec3( 0, 0, 0 ), sourcemax, tnear, tfar );
+	intersectBox( mfront.xyz, (mback - mfront).xyz, sourcemin, sourcemax, tnear, tfar );
 }
 
 uniform sampler3D volume;

src/main/resources/bvv/core/render/sample_volume_simple_rgba.frag

@@ -1,11 +1,12 @@
 uniform mat4 im;
+uniform vec3 sourcemin;
 uniform vec3 sourcemax;
 
 void intersectBoundingBox( vec4 wfront, vec4 wback, out float tnear, out float tfar )
 {
 	vec4 mfront = im * wfront;
 	vec4 mback = im * wback;
-	intersectBox( mfront.xyz, (mback - mfront).xyz, vec3( 0, 0, 0 ), sourcemax, tnear, tfar );
+	intersectBox( mfront.xyz, (mback - mfront).xyz, sourcemin, sourcemax, tnear, tfar );
 }
 
 uniform sampler3D volume;

src/test/java/bvv/debug/DebugSpimData.java

@@ -0,0 +1,36 @@
+package bvv.debug;
+
+import java.util.List;
+
+import bdv.spimdata.SpimDataMinimal;
+import bdv.spimdata.XmlIoSpimDataMinimal;
+import bvv.vistools.Bvv;
+import bvv.vistools.BvvFunctions;
+import bvv.vistools.BvvOptions;
+import bvv.vistools.BvvStackSource;
+import mpicbg.spim.data.SpimDataException;
+
+public class DebugSpimData
+{
+	public static void main( final String[] args )
+	{
+		final String xmlFilename8bit = "/home/eugene/Desktop/projects/BigTrace/BigTrace_data/t1-head_8bit.xml";
+		final String xmlFilename16bit = "/home/eugene/Desktop/projects/BVB/points/mastodon/datasethdf5.xml";
+
+		SpimDataMinimal spimData8bit = null;
+		SpimDataMinimal spimData16bit = null;
+
+		try {
+			spimData8bit = new XmlIoSpimDataMinimal().load( xmlFilename8bit );
+			spimData16bit = new XmlIoSpimDataMinimal().load( xmlFilename16bit );
+		} catch (SpimDataException e) {
+			e.printStackTrace();
+		}
+		final Bvv bvv = BvvFunctions.show(BvvOptions.options().frameTitle( "Test spimdata" ));
+		List< BvvStackSource< ? > > bvvSources8bit = BvvFunctions.show( spimData8bit, BvvOptions.options().addTo( bvv ) );
+		bvvSources8bit.get( 0 ).setDisplayRange( 0, 255 );
+		List< BvvStackSource< ? > > bvvSources16bit = BvvFunctions.show( spimData16bit, BvvOptions.options().addTo( bvv ) );
+		bvvSources16bit.get( 0 ).setDisplayRange( 0, 700 );
+
+	}
+}

src/test/java/bvv/debug/GenerateVolumes.java

@@ -0,0 +1,85 @@
+package bvv.debug;
+
+import net.imglib2.Cursor;
+import net.imglib2.cache.img.ReadOnlyCachedCellImgFactory;
+import net.imglib2.cache.img.ReadOnlyCachedCellImgOptions;
+import net.imglib2.img.Img;
+import net.imglib2.img.array.ArrayImg;
+import net.imglib2.img.array.ArrayImgFactory;
+import net.imglib2.img.array.ArrayLocalizingCursor;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+
+public class GenerateVolumes
+{
+
+	static < T extends RealType< T > & NativeType< T >> ArrayImg< T, ? > makeSimpleRAI(final T type, final int nEdge, final double minAmp, final double maxAmp, final boolean bConstantMax)
+	{
+		final long[] dims = new long[] {nEdge, nEdge, nEdge};
+		ArrayImgFactory<T> factoryImg = new ArrayImgFactory<>(type);
+		ArrayImg< T, ? > img = factoryImg.create( dims );
+		ArrayLocalizingCursor< T > cursor = img.localizingCursor();
+		double period = nEdge * 0.5 + Math.random() *  nEdge * 0.5;
+
+		final double [] pos = new double[3];
+		while(cursor.hasNext())
+		{
+			cursor.fwd();
+			cursor.localize( pos );
+			if(bConstantMax)
+			{
+				cursor.get().setReal( maxAmp ); 
+			}
+			else
+			{
+				double val = gyroid(pos, period, minAmp, maxAmp);
+				cursor.get().setReal( val ); 
+			}
+		}
+		return img;
+	}
+
+	/** creates a 3D cube volume with nEdge size filled with gyroid in the range of minAmp and maxAmp.
+	 *  The period of gyroid randomly varies from 0.5 to 1.0 nEdge
+	 *  If bConstantMax is true, single values volume filled with maxAmp**/
+	static < T extends RealType< T > & NativeType< T >> Img< T > makeCachedCellImg(final T type, final int nEdge, final double minAmp, final double maxAmp, final boolean bConstantMax)
+	{
+		final long[] dims = new long[] {nEdge, nEdge, nEdge};
+		final ReadOnlyCachedCellImgFactory factory = new ReadOnlyCachedCellImgFactory(
+				ReadOnlyCachedCellImgOptions.options().cellDimensions( 32 ) );
+		double period = nEdge * 0.5 + Math.random() *  nEdge * 0.5;
+		final Img< T > cellimg = factory.create( dims, type, cell -> {
+			Cursor< T > cursor = cell.localizingCursor();
+			final double [] pos = new double[3];
+			while(cursor.hasNext())
+			{
+				cursor.fwd();
+				cursor.localize( pos );
+				if( bConstantMax)
+				{
+					cursor.get().setReal( maxAmp ); 
+				}
+				else
+				{
+					final double val = gyroid(pos, period, minAmp, maxAmp);
+					cursor.get().setReal( val ); 					
+				}
+			}
+			//Thread.sleep( 80 );
+		});
+
+		return cellimg;
+	}
+
+
+	static double gyroid(final double [] pos, final double period, final double minAmp, final double maxAmp) 
+	{
+		double w = 2.0 * Math.PI / period;
+
+		double g = Math.sin(pos[0] * w ) * Math.cos(pos[1] * w) 
+				+ Math.sin(pos[1] * w ) * Math.cos(pos[2] * w ) 
+				+ Math.sin(pos[2] * w ) * Math.cos(pos[0] * w );
+		g = Math.pow((Math.tanh( g ) + 1) * 0.5, 7);
+		return g  * (maxAmp - minAmp) + minAmp;
+	}
+}

src/test/java/bvv/debug/TestHalfPixel.java

@@ -0,0 +1,45 @@
+package bvv.debug;
+
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.type.numeric.integer.UnsignedByteType;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
+
+import bdv.util.volatiles.VolatileViews;
+import bvv.vistools.Bvv;
+import bvv.vistools.BvvFunctions;
+import bvv.vistools.BvvOptions;
+import bvv.vistools.BvvStackSource;
+
+public class TestHalfPixel
+{
+	public static void main( final String[] args )
+	{
+		Bvv bvv = BvvFunctions.show( BvvOptions.options().frameTitle( "Test half pixel" ));
+		UnsignedByteType type = new UnsignedByteType();
+		final int nFillValue = 255;
+
+		//UnsignedShortType type = new UnsignedShortType();
+		//final int nFillValue = 65535;
+
+		int nEdge = 3;
+		//make a 5x5 constant intensity blocks
+		final RandomAccessibleInterval< ? > rai = GenerateVolumes.makeSimpleRAI(type, nEdge, 0, nFillValue, true );
+		final RandomAccessibleInterval< ? > cachedRai = GenerateVolumes.makeCachedCellImg(type, nEdge, 0, nFillValue, true );
+
+		BvvStackSource< ? > raiCS = BvvFunctions.show( rai, 
+				"simple RAI", 
+				BvvOptions.options().addTo( bvv ));
+		AffineTransform3D t = new AffineTransform3D();
+		t.translate( nEdge, 0.0, 0.0 );
+
+		BvvStackSource< ? > cachedRaiCS = BvvFunctions.show( VolatileViews.wrapAsVolatile(cachedRai), 
+				"cached RAI", 
+				BvvOptions.options().addTo( bvv ).sourceTransform( t ));
+		AffineTransform3D viewT = bvv.getBvvHandle().getViewerPanel().state().getViewerTransform();
+		viewT.scale( 0.5 );
+		viewT.translate( 80., 140.0, 0.0 );
+		bvv.getBvvHandle().getViewerPanel().state().setViewerTransform( viewT );
+
+	}
+}