fixed formalizm of preintegration to the correct one

src/main/java/bdv/jogl/VolumeRenderer/ShaderPrograms/MultiVolumeRenderer.java

@@ -9,7 +9,6 @@ import java.nio.IntBuffer;
 import java.util.HashMap;
 import java.util.Map;
 
-
 import bdv.jogl.VolumeRenderer.GLErrorHandler;
 import bdv.jogl.VolumeRenderer.Scene.Texture;
 import bdv.jogl.VolumeRenderer.ShaderPrograms.ShaderSources.ISourceListener;
@@ -18,6 +17,7 @@ import bdv.jogl.VolumeRenderer.ShaderPrograms.ShaderSources.functions.accumulato
 import bdv.jogl.VolumeRenderer.ShaderPrograms.ShaderSources.functions.accumulator.MaximumVolumeAccumulator;
 import bdv.jogl.VolumeRenderer.TransferFunctions.TransferFunction1D;
 import bdv.jogl.VolumeRenderer.TransferFunctions.TransferFunctionAdapter;
+import bdv.jogl.VolumeRenderer.TransferFunctions.sampler.ITransferFunctionSampler;
 import bdv.jogl.VolumeRenderer.utils.GeometryUtils;
 import bdv.jogl.VolumeRenderer.utils.VolumeDataManager;
 import bdv.jogl.VolumeRenderer.utils.VolumeDataManagerAdapter;
@@ -54,8 +54,6 @@ public class MultiVolumeRenderer extends AbstractShaderSceneElement{
 
 	private TransferFunction1D tf;
 
-	private Texture colorTexture;
-
 	private boolean isColorUpdateable;
 
 	private boolean isEyeUpdateable = true;
@@ -106,6 +104,8 @@ public class MultiVolumeRenderer extends AbstractShaderSceneElement{
 
 	private float[] slice2Dplane;
 
+	private ITransferFunctionSampler currentSampler;
+	
 	public void setDrawRect(AABBox rect){
 		drawCubeTransformation = getTransformationRepresentAABBox(rect);
 		drawRect  = rect;
@@ -416,7 +416,7 @@ public class MultiVolumeRenderer extends AbstractShaderSceneElement{
 			diagVec[i]/=sizeDim;
 		}
 
-		length = VectorUtil.normVec3(diagVec);
+		length = runLength;//VectorUtil.normVec3(diagVec);
 
 		gl2.glUniform1f(getLocation(suvTransferFuntionSize), length);
 		GLErrorHandler.assertGL(gl2);
@@ -626,12 +626,9 @@ public class MultiVolumeRenderer extends AbstractShaderSceneElement{
 			volumeTextureMap.put(i, t);
 			GLErrorHandler.assertGL(gl2);
 		}
-		location = getLocation(suvColorTexture);
-		colorTexture = new Texture(GL2.GL_TEXTURE_1D,location,GL2.GL_RGBA,GL2.GL_RGBA,GL2.GL_FLOAT);
-		colorTexture.genTexture(gl2);
-		colorTexture.setTexParameteri(gl2,GL2.GL_TEXTURE_MAG_FILTER, GL2.GL_LINEAR);
-		colorTexture.setTexParameteri(gl2, GL2.GL_TEXTURE_MIN_FILTER, GL2.GL_LINEAR);
-		colorTexture.setTexParameteri(gl2, GL2.GL_TEXTURE_WRAP_S, GL2.GL_CLAMP_TO_BORDER);
+		this.currentSampler = tf.getSampler();
+		currentSampler.init(gl2, getLocation(suvColorTexture));
+
 	}
 
 	@Override
@@ -672,10 +669,12 @@ public class MultiVolumeRenderer extends AbstractShaderSceneElement{
 		}
 
 		//get Buffer last key is the highest number 
-		FloatBuffer buffer = tf.getTexture(length/(float)samples); 
+		//FloatBuffer buffer = tf.getTexture(length/(float)samples); 
 
+		tf.getSampler().updateData(gl2,tf, length/(float)samples);
+		
 		//upload data
-		colorTexture.update(gl2, 0, buffer, new int[]{buffer.capacity()/4});
+
 		//gl2.glBindTexture(GL2.GL_TEXTURE_1D, 0);
 		isColorUpdateable = false;
 	}
@@ -698,6 +697,7 @@ public class MultiVolumeRenderer extends AbstractShaderSceneElement{
 	 */
 	public void setTransferFunction(final TransferFunction1D tf){
 		this.tf = tf;
+
 		this.tf.addTransferFunctionListener(new TransferFunctionAdapter() {
 
 			@Override
@@ -736,8 +736,9 @@ public class MultiVolumeRenderer extends AbstractShaderSceneElement{
 
 	@Override
 	protected void disposeSubClass(GL4 gl2) {
-		colorTexture.delete(gl2);
+	
 
+		currentSampler.dispose(gl2);
 		for(Texture texture: volumeTextureMap.values() ){
 			texture.delete(gl2);
 		}

src/main/java/bdv/jogl/VolumeRenderer/ShaderPrograms/ShaderSources/functions/transferfunctioninterpreter/PreIntegrationInterpreter.java

@@ -8,38 +8,13 @@ public class PreIntegrationInterpreter extends AbstractTransferFunctionInterpret
 	public String[] declaration() {
 		String dec[] ={
 				"#line "+Thread.currentThread().getStackTrace()[1].getLineNumber()+ " 10",
-				"uniform sampler1D "+suvColorTexture+";",
-				"const float minValue = 0.000001;",
-				"const float minValueHalf = minValue/2.0;",
+				"uniform sampler2D "+suvColorTexture+";",
 				"float texoffset = 1.0/(2.0*"+suvMaxVolumeValue+");",
 				"float texnorm = ("+suvMaxVolumeValue+"-1.0)/"+suvMaxVolumeValue+";",
 				"",
 				"vec4 "+getFunctionName()+"(float vbegin, float vend, float distance){",
-				"	if(vbegin - vend < minValue){",
-				"		if(vbegin - minValueHalf < 0.0){",
-				"			vend+= minValue*10.0;",	
-				"		}else{",	
-				"			if(vend +minValueHalf > 1.0){",
-				"				vbegin-=minValue*10.0;",
-				"			}else{",			
-				"				vend+=minValueHalf*10.0;",
-				"				vbegin-=minValueHalf*10.0;",
-				"			}",
-				"		}",	
-				"	}",
-				"	vec4 iFront = texture("+suvColorTexture+",vbegin*texnorm + texoffset);",
-				"	vec4 iBack = texture("+suvColorTexture+",vend*texnorm + texoffset);",
-				"	vec4 color = vec4(0.0);",				
-				"	vec4 iDiff = distance/(vend - vbegin) * (iBack - iFront);",
-				"",
-				"	//alpha desample",
-				"	color.a = 1.0 - exp(-iDiff.a);",
-				"",
-				"	//rgb desample",
-				"	color.rgb = iDiff.rgb;",
-				"	return color;",
-				"}",
-				""
+				"	return texture("+suvColorTexture+",vec2(vbegin*texnorm + texoffset,vend*texnorm + texoffset)).rgba;",
+				"}"
 		};
 		return dec;
 	}

src/main/java/bdv/jogl/VolumeRenderer/TransferFunctions/TransferFunction1D.java

@@ -353,9 +353,7 @@ public class TransferFunction1D {
 		fireColorChangedEventAll();
 	}
 
-	public FloatBuffer getTexture(float f){
-		return sampler.sample(this, f);
-	}
+
 
 	public IFunction getTransferFunctionShaderCode(){
 		return sampler.getShaderCode();

src/main/java/bdv/jogl/VolumeRenderer/TransferFunctions/sampler/ITransferFunctionSampler.java

@@ -2,6 +2,8 @@ package bdv.jogl.VolumeRenderer.TransferFunctions.sampler;
 
 import java.nio.FloatBuffer;
 
+import com.jogamp.opengl.GL4;
+
 import bdv.jogl.VolumeRenderer.ShaderPrograms.ShaderSources.functions.IFunction;
 import bdv.jogl.VolumeRenderer.TransferFunctions.TransferFunction1D;
 
@@ -11,6 +13,15 @@ import bdv.jogl.VolumeRenderer.TransferFunctions.TransferFunction1D;
  *
  */
 public interface ITransferFunctionSampler {
+	
+	public void init(GL4 gl, int colorTextureId);
+	
+	
+	public void dispose(GL4 gl);
+
+	public void updateData(GL4 gl,TransferFunction1D transferFunction, float sampleStep);
+
+	
 	/**
 	 * Retruns the desampling shader code
 	 * @return

src/main/java/bdv/jogl/VolumeRenderer/TransferFunctions/sampler/PreIntegrationSampler.java

@@ -2,18 +2,24 @@ package bdv.jogl.VolumeRenderer.TransferFunctions.sampler;
 
 import java.awt.Color;
 import java.nio.FloatBuffer;
+import java.util.ArrayList;
 import java.util.TreeMap;
 
 import com.jogamp.common.nio.Buffers;
+import com.jogamp.opengl.GL2;
+import com.jogamp.opengl.GL4;
 
+import bdv.jogl.VolumeRenderer.Scene.Texture;
 import bdv.jogl.VolumeRenderer.ShaderPrograms.ShaderSources.functions.IFunction;
 import bdv.jogl.VolumeRenderer.ShaderPrograms.ShaderSources.functions.transferfunctioninterpreter.PreIntegrationInterpreter;
 import bdv.jogl.VolumeRenderer.TransferFunctions.TransferFunction1D;
+import static bdv.jogl.VolumeRenderer.ShaderPrograms.ShaderSources.MultiVolumeRendererShaderSource.suvColorTexture;
 import static bdv.jogl.VolumeRenderer.utils.WindowUtils.getNormalizedColor;
 
 public class PreIntegrationSampler implements ITransferFunctionSampler {
 
 	private final PreIntegrationInterpreter desampler = new PreIntegrationInterpreter();
+	private Texture colorTexture;
 
 	@Override
 	public IFunction getShaderCode() {
@@ -44,20 +50,40 @@ public class PreIntegrationSampler implements ITransferFunctionSampler {
 		return stepSize/2.f * (a1+a2);
 	}
 	
+	@Override
+	public void init(GL4 gl, int colorTextureId) {
+		colorTexture = new Texture(GL2.GL_TEXTURE_2D,colorTextureId,GL2.GL_RGBA,GL2.GL_RGBA,GL2.GL_FLOAT);
+		colorTexture.genTexture(gl);
+		colorTexture.setTexParameteri(gl,GL2.GL_TEXTURE_MAG_FILTER, GL2.GL_LINEAR);
+		colorTexture.setTexParameteri(gl, GL2.GL_TEXTURE_MIN_FILTER, GL2.GL_LINEAR);
+		colorTexture.setTexParameteri(gl, GL2.GL_TEXTURE_WRAP_S, GL2.GL_CLAMP_TO_BORDER);
+		colorTexture.setTexParameteri(gl, GL2.GL_TEXTURE_WRAP_T, GL2.GL_CLAMP_TO_BORDER);
+	}
+	
+	@Override
+	public void updateData(GL4 gl, TransferFunction1D transferFunction,
+			float sampleStep) {
+		FloatBuffer buffer = sample(transferFunction, sampleStep);
+		int dim[] = new int[]{(int)Math.round(Math.sqrt(buffer.capacity()/4)),(int)Math.round(Math.sqrt(buffer.capacity()/4))};
+		colorTexture.update(gl, 0, buffer,dim );
+		
+	}
 	
 	@Override
-	public FloatBuffer sample(TransferFunction1D transferFunction, float stepSize) {
+	public FloatBuffer sample( TransferFunction1D transferFunction, float stepSize) {
 		//http://www.uni-koblenz.de/~cg/Studienarbeiten/SA_MariusErdt.pdf
 		
 		int sampleStep=1;
 		TreeMap<Integer, Color> colorMap = transferFunction.getTexturColor();
-		//get Buffer last key is the highest number 
-		FloatBuffer buffer = Buffers.newDirectFloatBuffer(((colorMap.lastKey()-colorMap.firstKey())+1)*4);
 
+
+		
 		//make samples
 		Integer intervalBegin = colorMap.firstKey();
 		float[] integral = {0,0,0,0};
-		buffer.put(integral.clone());
+		ArrayList <float[]> integalsOfS = new ArrayList<float[]>();
+		ArrayList <float[]> colors = new ArrayList<float[]>();
+
 		//iterate candidates
 		for(Integer intervalEnd: colorMap.keySet()){
 			if(intervalEnd == intervalBegin){
@@ -78,27 +104,84 @@ public class PreIntegrationSampler implements ITransferFunctionSampler {
 			float[] formerSampleColor = intervalBeginColor.clone();
 		
 			//sample linear
-			for(float step = intervalBegin; step < intervalEnd; step+=sampleStep ){
-				
+			for(int step = intervalBegin; step < intervalEnd; step++ ){
+				colors.add(sampleColor);
 				//increment color
 				for(int i =0; i< sampleColor.length; i++){
-					sampleColor[i]+= intervalColorGradient[i]*sampleStep;
+					sampleColor[i]+= intervalColorGradient[i];
 				}
 				
+				
 				//absorbation integral
-				integral[3] += calcAbsorbationIntegral(formerSampleColor[3], sampleColor[3], stepSize);
+				integral[3] += calcAbsorbationIntegral(formerSampleColor[3], sampleColor[3], 1);
 				
 				//color integral
 				for(int i = 0; i< 3; i++){
 					integral[i] +=calcColorChannelIntegral(formerSampleColor[i], sampleColor[i], 
-							formerSampleColor[3], sampleColor[3], stepSize);
+							formerSampleColor[3], sampleColor[3], 1);
 				}
-				buffer.put(integral.clone());
+				integalsOfS.add(integral.clone());
 				formerSampleColor = sampleColor.clone();
 			}
 			intervalBegin = intervalEnd;
 		}
+		
+		//get Buffer last key is the highest number 
+		FloatBuffer buffer = Buffers.newDirectFloatBuffer((int)Math.pow(integalsOfS.size(), 2)*4);
+		//classification
+		for(int sb = 0; sb < integalsOfS.size(); sb++){
+			for(int sf = 0; sf < integalsOfS.size(); sf++){
+				float rgba[] = {0,0,0,0};
+				if(sf!=sb){
+					float integralFront[] = integalsOfS.get(sf);
+					float integralBack[] = integalsOfS.get(sb);
+					for(int i =0; i< rgba.length; i++){
+						rgba[i] = stepSize/(float)(sb - sf) * (integralBack[i] - integralFront[i]);
+					}
+				}else{
+					//rgba = colors.get(sf).clone();
+					for(int i =0; i< rgba.length; i++){
+						rgba[i] *=stepSize;
+					}
+					
+				}
+				rgba[3] = (float) (1.f - Math.exp(-rgba[3]));
+				buffer.put(rgba.clone());
+			}
+		}
+		
 		buffer.rewind();
 		return buffer;
+		
+	}
+	/*"	if(vbegin - vend < minValue){",
+	"		if(vbegin - minValueHalf < 0.0){",
+	"			vend+= minValue*10.0;",	
+	"		}else{",	
+	"			if(vend +minValueHalf > 1.0){",
+	"				vbegin-=minValue*10.0;",
+	"			}else{",			
+	"				vend+=minValueHalf*10.0;",
+	"				vbegin-=minValueHalf*10.0;",
+	"			}",
+	"		}",	
+	"	}",
+	"	vec4 iFront = texture("+suvColorTexture+",vbegin*texnorm + texoffset);",
+	"	vec4 iBack = texture("+suvColorTexture+",vend*texnorm + texoffset);",
+	"	vec4 color = vec4(0.0);",				
+	"	vec4 iDiff = distance/(vend - vbegin) * (iBack - iFront);",
+	"",
+	"	//alpha desample",
+	"	color.a = 1.0 - exp(-iDiff.a);",
+	"",
+	"	//rgb desample",
+	"	color.rgb = iDiff.rgb;",
+	"	return color;",
+	"}",*/
+
+	@Override
+	public void dispose(GL4 gl) {
+		colorTexture.delete(gl);
+		
 	}
 }

src/main/java/bdv/jogl/VolumeRenderer/TransferFunctions/sampler/RegularSampler.java

@@ -5,7 +5,10 @@ import java.nio.FloatBuffer;
 import java.util.TreeMap;
 
 import com.jogamp.common.nio.Buffers;
+import com.jogamp.opengl.GL2;
+import com.jogamp.opengl.GL4;
 
+import bdv.jogl.VolumeRenderer.Scene.Texture;
 import bdv.jogl.VolumeRenderer.ShaderPrograms.ShaderSources.functions.IFunction;
 import bdv.jogl.VolumeRenderer.ShaderPrograms.ShaderSources.functions.transferfunctioninterpreter.RegularTransferFunctionInterpreter;
 import bdv.jogl.VolumeRenderer.TransferFunctions.TransferFunction1D;
@@ -17,7 +20,24 @@ import static bdv.jogl.VolumeRenderer.utils.WindowUtils.getNormalizedColor;
  */
 public class RegularSampler implements ITransferFunctionSampler {
 	
-	private final RegularTransferFunctionInterpreter desampler = new RegularTransferFunctionInterpreter();  
+	private final RegularTransferFunctionInterpreter desampler = new RegularTransferFunctionInterpreter();
+	private Texture colorTexture;  
+	
+	@Override
+	public void init(GL4 gl, int colorTextureId) {
+		colorTexture = new Texture(GL2.GL_TEXTURE_1D,colorTextureId,GL2.GL_RGBA,GL2.GL_RGBA,GL2.GL_FLOAT);
+		colorTexture.genTexture(gl);
+		colorTexture.setTexParameteri(gl,GL2.GL_TEXTURE_MAG_FILTER, GL2.GL_LINEAR);
+		colorTexture.setTexParameteri(gl, GL2.GL_TEXTURE_MIN_FILTER, GL2.GL_LINEAR);
+		colorTexture.setTexParameteri(gl, GL2.GL_TEXTURE_WRAP_S, GL2.GL_CLAMP_TO_BORDER);
+	}
+	
+	@Override
+	public void updateData(GL4 gl, TransferFunction1D transferFunction,
+			float sampleStep) {
+		FloatBuffer buffer = sample( transferFunction, sampleStep);
+		colorTexture.update(gl, 0, buffer, new int[]{buffer.capacity()/4});
+	}
 	
 	/**
 	 * Samples tf data and returns 1d texture
@@ -25,6 +45,7 @@ public class RegularSampler implements ITransferFunctionSampler {
 	 * @param sampleStep
 	 * @return
 	 */
+	
 	public FloatBuffer sample(TransferFunction1D transferFunction, float sampleStep){
 		TreeMap<Integer, Color> colorMap = transferFunction.getTexturColor();
 		//get Buffer last key is the highest number 
@@ -67,6 +88,7 @@ public class RegularSampler implements ITransferFunctionSampler {
 
 		buffer.rewind();
 		return buffer;
+
 	};
 	
 	/**
@@ -76,5 +98,10 @@ public class RegularSampler implements ITransferFunctionSampler {
 	public IFunction getShaderCode(){
 		return desampler;
 	}
-	
+
+	@Override
+	public void dispose(GL4 gl) {
+		colorTexture.delete(gl);
+		
+	}
 }

src/main/java/bdv/jogl/VolumeRenderer/gui/GLWindow/GLWindow.java

@@ -341,7 +341,7 @@ public class GLWindow extends JFrame {
 
 
 		//sample size
-		setSize(640,580);
+		setSize(600,600);
 
 		getContentPane().add(glCanvas);