volume box boundary and half pixel multires shift

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

@@ -8,7 +8,7 @@ void intersectBoundingBox( vec4 wfront, vec4 wback, out float tnear, out float t
 {
 	vec4 mfront = im * wfront;
 	vec4 mback = im * wback;
-	intersectBox( mfront.xyz, (mback - mfront).xyz, sourcemin, sourcemax, tnear, tfar );
+	intersectBox( mfront.xyz, (mback - mfront).xyz, sourcemin-0.5, sourcemax+0.5, tnear, tfar );
 }
 
 uniform usampler3D lutSampler;
@@ -18,7 +18,11 @@ uniform vec3 lutOffset;
 
 float sampleVolume( vec4 wpos, sampler3D volumeCache, vec3 cacheSize, vec3 blockSize, vec3 paddedBlockSize, vec3 padOffset )
 {
-	vec3 pos = (im * wpos).xyz + 0.5;
+	vec3 pos = (im * wpos).xyz ;
+	vec3 over = pos * step(0.0,pos) - pos;
+	float zerofade = 1.0;
+	pos = over + pos;
+	zerofade = (1.0-over.x)*(1.0-over.y)*(1-over.z);	
 	vec3 q = floor( pos / blockSize ) - lutOffset + 0.5;
 
 	uvec4 lutv = texture( lutSampler, q / lutSize );
@@ -28,5 +32,5 @@ float sampleVolume( vec4 wpos, sampler3D volumeCache, vec3 cacheSize, vec3 block
 	vec3 c0 = B0 + mod( pos * sj, blockSize ) + 0.5 * sj;
 	                                       // + 0.5 ( sj - 1 )   + 0.5 for tex coord offset
 
-	return texture( volumeCache, c0 / cacheSize ).r;
+	return zerofade*texture( volumeCache, c0 / cacheSize ).r;
 }

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

@@ -5,7 +5,7 @@ void intersectBoundingBox( vec4 wfront, vec4 wback, out float tnear, out float t
 {
 	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, vec3( -0.5, -0.5, -0.5 ), sourcemax+0.5, tnear, tfar );
 }
 
 uniform sampler3D volume;

src/test/java/bvv/debug/DebugHalfPixel.java

@@ -0,0 +1,43 @@
+package bvv.debug;
+
+import java.util.List;
+
+import net.imglib2.img.Img;
+import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.type.numeric.ARGBType;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
+
+import bdv.spimdata.SpimDataMinimal;
+import bdv.spimdata.XmlIoSpimDataMinimal;
+import bvv.vistools.Bvv;
+import bvv.vistools.BvvFunctions;
+import bvv.vistools.BvvHandle;
+import bvv.vistools.BvvStackSource;
+
+import ij.IJ;
+import ij.ImagePlus;
+import mpicbg.spim.data.SpimDataException;
+
+public class DebugHalfPixel
+{
+	public static void main( final String[] args )
+	{
+		//load multires
+		final String xmlFilename = "src/test/resources/halfpixeltest/cliptest1ch.xml";
+		SpimDataMinimal spimData = null;
+		try {
+			spimData = new XmlIoSpimDataMinimal().load( xmlFilename );
+		} catch (SpimDataException e) {
+			e.printStackTrace();
+		}		
+		List< BvvStackSource< ? > > sources = BvvFunctions.show( spimData );
+		sources.get( 0 ).setColor( new ARGBType(0x0000FF00) );
+		BvvHandle handle = sources.get( 0 ).getBvvHandle();
+
+		//load simple stack
+		final ImagePlus imp = IJ.openImage( "src/test/resources/halfpixeltest/cliptest1ch.tif" );
+		final Img< UnsignedShortType > img = ImageJFunctions.wrapShort( imp );
+		final BvvStackSource< UnsignedShortType > source = BvvFunctions.show( img, "SimpleStack", Bvv.options().addTo( handle ) );
+		source.setColor( new ARGBType(0x00FF0000) );
+	}
+}

src/test/resources/halfpixeltest/cliptest1ch.xml

@@ -0,0 +1,40 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<SpimData version="0.2">
+  <BasePath type="relative">.</BasePath>
+  <SequenceDescription>
+    <ImageLoader format="bdv.hdf5">
+      <hdf5 type="relative">cliptest1ch.h5</hdf5>
+    </ImageLoader>
+    <ViewSetups>
+      <ViewSetup>
+        <id>0</id>
+        <name>channel 1</name>
+        <size>4 2 10</size>
+        <voxelSize>
+          <unit>micron</unit>
+          <size>1.0 1.0 1.0</size>
+        </voxelSize>
+        <attributes>
+          <channel>1</channel>
+        </attributes>
+      </ViewSetup>
+      <Attributes name="channel">
+        <Channel>
+          <id>1</id>
+          <name>1</name>
+        </Channel>
+      </Attributes>
+    </ViewSetups>
+    <Timepoints type="range">
+      <first>0</first>
+      <last>0</last>
+    </Timepoints>
+  </SequenceDescription>
+  <ViewRegistrations>
+    <ViewRegistration timepoint="0" setup="0">
+      <ViewTransform type="affine">
+        <affine>1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0</affine>
+      </ViewTransform>
+    </ViewRegistration>
+  </ViewRegistrations>
+</SpimData>