cdec cleanup, remove bayesian stuff, parsing stuff

8 files changed, 0 insertions, 325 deletions

diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/CompositeStopingCriteria.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/CompositeStopingCriteria.java
deleted file mode 100644
index 15760f18..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/CompositeStopingCriteria.java
+++ /dev/null
@@ -1,33 +0,0 @@
-package optimization.stopCriteria;
-
-import java.util.ArrayList;
-
-import optimization.gradientBasedMethods.Objective;
-
-public class CompositeStopingCriteria implements StopingCriteria {
-	
-	ArrayList<StopingCriteria> criterias;
-	
-	public CompositeStopingCriteria() {
-		criterias = new ArrayList<StopingCriteria>();
-	}
-	
-	public void add(StopingCriteria criteria){
-		criterias.add(criteria);
-	}
-	
-	public boolean stopOptimization(Objective obj){
-		for(StopingCriteria criteria: criterias){
-			if(criteria.stopOptimization(obj)){
-				return true;
-			}
-		}
-		return false;
-	}
-	
-	public void reset(){
-		for(StopingCriteria criteria: criterias){
-			criteria.reset();
-		}
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/GradientL2Norm.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/GradientL2Norm.java
deleted file mode 100644
index 534ff833..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/GradientL2Norm.java
+++ /dev/null
@@ -1,30 +0,0 @@
-package optimization.stopCriteria;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.util.MathUtils;
-
-public class GradientL2Norm implements StopingCriteria{
-	
-	/**
-	 * Stop if gradientNorm/(originalGradientNorm) smaller
-	 * than gradientConvergenceValue
-	 */
-	protected double gradientConvergenceValue;
-	
-	
-	public GradientL2Norm(double gradientConvergenceValue){
-		this.gradientConvergenceValue = gradientConvergenceValue;
-	}
-	
-	public void reset(){}
-	
-	public boolean stopOptimization(Objective obj){
-		double norm = MathUtils.L2Norm(obj.gradient);
-		if(norm < gradientConvergenceValue){
-			System.out.println("Gradient norm below treshold");
-			return true;
-		}
-		return false;
-		
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedGradientL2Norm.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedGradientL2Norm.java
deleted file mode 100644
index 4a489641..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedGradientL2Norm.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package optimization.stopCriteria;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.gradientBasedMethods.ProjectedObjective;
-import optimization.util.MathUtils;
-
-/**
- * Divides the norm by the norm at the begining of the iteration
- * @author javg
- *
- */
-public class NormalizedGradientL2Norm extends GradientL2Norm{
-	
-	/**
-	 * Stop if gradientNorm/(originalGradientNorm) smaller
-	 * than gradientConvergenceValue
-	 */
-	protected double originalGradientNorm = -1;
-	
-	public void reset(){
-		originalGradientNorm = -1;
-	}
-	public NormalizedGradientL2Norm(double gradientConvergenceValue){
-		super(gradientConvergenceValue);
-	}
-	
-	
-	 
-	
-	public boolean stopOptimization(Objective obj){
-			double norm = MathUtils.L2Norm(obj.gradient);
-			if(originalGradientNorm == -1){
-				originalGradientNorm = norm;
-			}
-			if(originalGradientNorm < 1E-10){
-				System.out.println("Gradient norm is zero " +  originalGradientNorm);
-				return true;
-			}
-			double normalizedNorm = 1.0*norm/originalGradientNorm;
-			if( normalizedNorm < gradientConvergenceValue){
-				System.out.println("Gradient norm below normalized normtreshold: " + norm + " original: " + originalGradientNorm + " normalized norm: " + normalizedNorm);
-				return true;
-			}else{
-//				System.out.println("projected gradient norm: " + norm);
-				return false;
-			}
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedProjectedGradientL2Norm.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedProjectedGradientL2Norm.java
deleted file mode 100644
index 5ae554c2..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedProjectedGradientL2Norm.java
+++ /dev/null
@@ -1,60 +0,0 @@
-package optimization.stopCriteria;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.gradientBasedMethods.ProjectedObjective;
-import optimization.util.MathUtils;
-
-/**
- * Divides the norm by the norm at the begining of the iteration
- * @author javg
- *
- */
-public class NormalizedProjectedGradientL2Norm extends ProjectedGradientL2Norm{
-	
-	/**
-	 * Stop if gradientNorm/(originalGradientNorm) smaller
-	 * than gradientConvergenceValue
-	 */
-	double originalProjectedNorm = -1;
-	
-	public NormalizedProjectedGradientL2Norm(double gradientConvergenceValue){
-		super(gradientConvergenceValue);
-	}
-	
-	public void reset(){
-		originalProjectedNorm = -1;
-	}
-	
-	
-	 double[] projectGradient(ProjectedObjective obj){
-		
-		if(obj.auxParameters == null){
-			obj.auxParameters = new double[obj.getNumParameters()];
-		}
-		System.arraycopy(obj.getParameters(), 0, obj.auxParameters, 0, obj.getNumParameters());
-		MathUtils.minusEquals(obj.auxParameters, obj.gradient, 1);
-		obj.auxParameters = obj.projectPoint(obj.auxParameters);
-		MathUtils.minusEquals(obj.auxParameters,obj.getParameters(),1);
-		return obj.auxParameters;
-	}
-	
-	public boolean stopOptimization(Objective obj){
-		if(obj instanceof ProjectedObjective) {
-			ProjectedObjective o = (ProjectedObjective) obj;
-			double norm = MathUtils.L2Norm(projectGradient(o));
-			if(originalProjectedNorm == -1){
-				originalProjectedNorm = norm;
-			}
-			double normalizedNorm = 1.0*norm/originalProjectedNorm;
-			if( normalizedNorm < gradientConvergenceValue){
-				System.out.println("Gradient norm below normalized normtreshold: " + norm + " original: " + originalProjectedNorm + " normalized norm: " + normalizedNorm);
-				return true;
-			}else{
-//				System.out.println("projected gradient norm: " + norm);
-				return false;
-			}
-		}
-		System.out.println("Not a projected objective");
-		throw new RuntimeException();
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedValueDifference.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedValueDifference.java
deleted file mode 100644
index 6dbbc50d..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/NormalizedValueDifference.java
+++ /dev/null
@@ -1,54 +0,0 @@
-package optimization.stopCriteria;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.util.MathUtils;
-
-public class NormalizedValueDifference implements StopingCriteria{
-	
-	/**
-	 * Stop if the different between values is smaller than a treshold
-	 */
-	protected double valueConvergenceValue=0.01;
-	protected double previousValue = Double.NaN;
-	protected double currentValue = Double.NaN;
-	
-	public NormalizedValueDifference(double valueConvergenceValue){
-		this.valueConvergenceValue = valueConvergenceValue;
-	}
-	
-	public void reset(){
-		previousValue = Double.NaN;
-		currentValue = Double.NaN;
-	}
-
-	
-	public boolean stopOptimization(Objective obj){
-		if(Double.isNaN(currentValue)){
-			currentValue = obj.getValue();
-			return false;
-		}else {
-			previousValue = currentValue;
-			currentValue = obj.getValue();
-			if(previousValue != 0){
-				double valueDiff = Math.abs(previousValue - currentValue)/Math.abs(previousValue);
-				if( valueDiff  < valueConvergenceValue){
-					System.out.println("Leaving different in values is to small: Prev " 
-							+ (previousValue/previousValue) + " Curr: " + (currentValue/previousValue) 
-							+ " diff: " + valueDiff);
-					return true;
-				}
-			}else{
-				double valueDiff = Math.abs(previousValue - currentValue);
-				if( valueDiff  < valueConvergenceValue){
-					System.out.println("Leaving different in values is to small: Prev " 
-							+ (previousValue) + " Curr: " + (currentValue) 
-							+ " diff: " + valueDiff);
-					return true;
-				}
-			}
-
-			return false;
-		}
-		
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/ProjectedGradientL2Norm.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/ProjectedGradientL2Norm.java
deleted file mode 100644
index aadf1fd5..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/ProjectedGradientL2Norm.java
+++ /dev/null
@@ -1,51 +0,0 @@
-package optimization.stopCriteria;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.gradientBasedMethods.ProjectedObjective;
-import optimization.util.MathUtils;
-
-public class ProjectedGradientL2Norm implements StopingCriteria{
-	
-	/**
-	 * Stop if gradientNorm/(originalGradientNorm) smaller
-	 * than gradientConvergenceValue
-	 */
-	protected double gradientConvergenceValue;
-	
-	
-	public ProjectedGradientL2Norm(double gradientConvergenceValue){
-		this.gradientConvergenceValue = gradientConvergenceValue;
-	}
-	
-	public void reset(){
-		
-	}
-	
-	 double[] projectGradient(ProjectedObjective obj){
-		
-		if(obj.auxParameters == null){
-			obj.auxParameters = new double[obj.getNumParameters()];
-		}
-		System.arraycopy(obj.getParameters(), 0, obj.auxParameters, 0, obj.getNumParameters());
-		MathUtils.minusEquals(obj.auxParameters, obj.gradient, 1);
-		obj.auxParameters = obj.projectPoint(obj.auxParameters);
-		MathUtils.minusEquals(obj.auxParameters,obj.getParameters(),1);
-		return obj.auxParameters;
-	}
-	
-	public boolean stopOptimization(Objective obj){
-		if(obj instanceof ProjectedObjective) {
-			ProjectedObjective o = (ProjectedObjective) obj;
-			double norm = MathUtils.L2Norm(projectGradient(o));
-			if(norm < gradientConvergenceValue){
-	//			System.out.println("Gradient norm below treshold: " + norm);
-				return true;
-			}else{
-//				System.out.println("projected gradient norm: " + norm);
-				return false;
-			}
-		}
-		System.out.println("Not a projected objective");
-		throw new RuntimeException();
-	}
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/StopingCriteria.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/StopingCriteria.java
deleted file mode 100644
index 10cf0522..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/StopingCriteria.java
+++ /dev/null
@@ -1,8 +0,0 @@
-package optimization.stopCriteria;
-
-import optimization.gradientBasedMethods.Objective;
-
-public interface StopingCriteria {
-	public boolean stopOptimization(Objective obj);
-	public void reset();
-}
diff --git a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/ValueDifference.java b/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/ValueDifference.java
deleted file mode 100644
index e5d07229..00000000
--- a/gi/posterior-regularisation/prjava/src/optimization/stopCriteria/ValueDifference.java
+++ /dev/null
@@ -1,41 +0,0 @@
-package optimization.stopCriteria;
-
-import optimization.gradientBasedMethods.Objective;
-import optimization.util.MathUtils;
-
-public class ValueDifference implements StopingCriteria{
-	
-	/**
-	 * Stop if the different between values is smaller than a treshold
-	 */
-	protected double valueConvergenceValue=0.01;
-	protected double previousValue = Double.NaN;
-	protected double currentValue = Double.NaN;
-	
-	public ValueDifference(double valueConvergenceValue){
-		this.valueConvergenceValue = valueConvergenceValue;
-	}
-	
-	public void reset(){
-		previousValue = Double.NaN;
-		currentValue = Double.NaN;
-	}
-	
-	public boolean stopOptimization(Objective obj){
-		if(Double.isNaN(currentValue)){
-			currentValue = obj.getValue();
-			return false;
-		}else {
-			previousValue = currentValue;
-			currentValue = obj.getValue();
-			if(previousValue - currentValue   < valueConvergenceValue){
-//				System.out.println("Leaving different in values is to small: Prev " 
-//						+ previousValue + " Curr: " + currentValue 
-//						+ " diff: " + (previousValue - currentValue));
-				return true;
-			}
-			return false;
-		}
-		
-	}
-}