Merge remote branch 'upstream/master'

Conflicts:
	Jamroot
	bjam
	decoder/Jamfile
	decoder/cdec.cc
	dpmert/Jamfile
	jam-files/sanity.jam
	klm/lm/Jamfile
	klm/util/Jamfile
	mira/Jamfile

4 files changed, 0 insertions, 319 deletions

diff --git a/gi/posterior-regularisation/prjava/src/test/CorpusTest.java b/gi/posterior-regularisation/prjava/src/test/CorpusTest.java
deleted file mode 100644
index b4c3041f..00000000
--- a/gi/posterior-regularisation/prjava/src/test/CorpusTest.java
+++ /dev/null
@@ -1,60 +0,0 @@
-package test;

-

-import java.util.Arrays;

-import java.util.HashMap;

-

-import data.Corpus;

-import hmm.POS;

-

-public class CorpusTest {

-

-	public static void main(String[] args) {

-		Corpus c=new Corpus(POS.trainFilename);

-

-		

-		int idx=30;

-		

-		

-		HashMap<String, Integer>vocab=

-			(HashMap<String, Integer>) io.SerializedObjects.readSerializedObject(Corpus.alphaFilename);

-		

-		HashMap<String, Integer>tagVocab=

-			(HashMap<String, Integer>) io.SerializedObjects.readSerializedObject(Corpus.tagalphaFilename);

-		

-		

-		String [] dict=new String [vocab.size()+1];

-		for(String key:vocab.keySet()){

-			dict[vocab.get(key)]=key;

-		}

-		dict[dict.length-1]=Corpus.UNK_TOK;

-		

-		String [] tagdict=new String [tagVocab.size()+1];

-		for(String key:tagVocab.keySet()){

-			tagdict[tagVocab.get(key)]=key;

-		}

-		tagdict[tagdict.length-1]=Corpus.UNK_TOK;

-		

-		String[] sent=c.get(idx);

-		int []data=c.getInt(idx);

-		

-		

-		String []roundtrip=new String [sent.length];

-		for(int i=0;i<sent.length;i++){

-			roundtrip[i]=dict[data[i]];

-		}

-		System.out.println(Arrays.toString(sent));

-		System.out.println(Arrays.toString(roundtrip));

-		

-		sent=c.tag.get(idx);

-		data=c.tagData.get(idx);

-		

-		

-		roundtrip=new String [sent.length];

-		for(int i=0;i<sent.length;i++){

-			roundtrip[i]=tagdict[data[i]];

-		}

-		System.out.println(Arrays.toString(sent));

-		System.out.println(Arrays.toString(roundtrip));

-	}

-

-}

diff --git a/gi/posterior-regularisation/prjava/src/test/HMMModelStats.java b/gi/posterior-regularisation/prjava/src/test/HMMModelStats.java
deleted file mode 100644
index d54525c8..00000000
--- a/gi/posterior-regularisation/prjava/src/test/HMMModelStats.java
+++ /dev/null
@@ -1,105 +0,0 @@
-package test;

-

-import hmm.HMM;

-import hmm.POS;

-

-import java.io.File;

-import java.io.FileNotFoundException;

-import java.io.IOException;

-import java.io.PrintStream;

-import java.util.ArrayList;

-import java.util.Collections;

-import java.util.HashMap;

-

-import data.Corpus;

-

-public class HMMModelStats {

-

-	public static String modelFilename="../posdata/posModel.out";

-	public static String alphaFilename="../posdata/corpus.alphabet";

-	public static String statsFilename="../posdata/model.stats";

-

-	public static final int NUM_WORD=50;

-	

-	public static String testFilename="../posdata/en_test.conll";

-	

-	public static double [][]maxwt;

-	

-	public static void main(String[] args) {

-		HashMap<String, Integer>vocab=

-			(HashMap<String, Integer>) io.SerializedObjects.readSerializedObject(alphaFilename);

-		

-		Corpus test=new Corpus(testFilename,vocab);

-		

-		String [] dict=new String [vocab.size()+1];

-		for(String key:vocab.keySet()){

-			dict[vocab.get(key)]=key;

-		}

-		dict[dict.length-1]=Corpus.UNK_TOK;

-		

-		HMM hmm=new HMM();

-		hmm.readModel(modelFilename);

-

-		

-		

-		PrintStream ps = null;

-		try {

-			ps = io.FileUtil.printstream(new File(statsFilename));

-		} catch (IOException e) {

-			e.printStackTrace();

-			System.exit(1);

-		}

-		

-		double [][] emit=hmm.getEmitProb();

-		for(int i=0;i<emit.length;i++){

-			ArrayList<IntDoublePair>l=new ArrayList<IntDoublePair>();

-			for(int j=0;j<emit[i].length;j++){

-				l.add(new IntDoublePair(j,emit[i][j]));

-			}

-			Collections.sort(l);

-			ps.println(i);

-			for(int j=0;j<NUM_WORD;j++){

-				if(j>=dict.length){

-					break;

-				}

-				ps.print(dict[l.get(j).idx]+"\t");

-				if((1+j)%10==0){

-					ps.println();

-				}

-			}

-			ps.println("\n");

-		}

-		

-		checkMaxwt(hmm,ps,test.getAllData());

-		

-		int terminalSym=vocab.get(Corpus .END_SYM);

-		//sample 10 sentences

-		for(int i=0;i<10;i++){

-			int []sent=hmm.sample(terminalSym);

-			for(int j=0;j<sent.length;j++){

-				ps.print(dict[sent[j]]+"\t");

-			}

-			ps.println();

-		}

-		

-		ps.close();

-		

-	}

-	

-	public static void checkMaxwt(HMM hmm,PrintStream ps,int [][]data){

-		double [][]emit=hmm.getEmitProb();

-		maxwt=new double[emit.length][emit[0].length];

-		

-		hmm.computeMaxwt(maxwt,data);

-		double sum=0;

-		for(int i=0;i<maxwt.length;i++){

-			for(int j=0;j<maxwt.length;j++){

-				sum+=maxwt[i][j];

-			}

-		}

-		

-		ps.println("max w t P(w_i|t): "+sum);

-		

-	}

-	

-}

diff --git a/gi/posterior-regularisation/prjava/src/test/IntDoublePair.java b/gi/posterior-regularisation/prjava/src/test/IntDoublePair.java
deleted file mode 100644
index 3f9f0ad7..00000000
--- a/gi/posterior-regularisation/prjava/src/test/IntDoublePair.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package test;

-

-public class IntDoublePair implements Comparable{

-	double val;

-	int idx;

-	public int compareTo(Object o){

-		if(o instanceof IntDoublePair){

-			IntDoublePair pair=(IntDoublePair)o;

-			if(pair.val>val){

-				return 1;

-			}

-			if(pair.val<val){

-				return -1;

-			}

-			return 0;

-		}

-		return -1;

-	}

-	public IntDoublePair(int i,double v){

-		val=v;

-		idx=i;

-	}

-}

diff --git a/gi/posterior-regularisation/prjava/src/test/X2y2WithConstraints.java b/gi/posterior-regularisation/prjava/src/test/X2y2WithConstraints.java
deleted file mode 100644
index 9059a59e..00000000
--- a/gi/posterior-regularisation/prjava/src/test/X2y2WithConstraints.java
+++ /dev/null
@@ -1,131 +0,0 @@
-package test;

-

-

-

-import optimization.gradientBasedMethods.ProjectedGradientDescent;

-import optimization.gradientBasedMethods.ProjectedObjective;

-import optimization.gradientBasedMethods.stats.OptimizerStats;

-import optimization.linesearch.ArmijoLineSearchMinimizationAlongProjectionArc;

-import optimization.linesearch.InterpolationPickFirstStep;

-import optimization.linesearch.LineSearchMethod;

-import optimization.projections.BoundsProjection;

-import optimization.projections.Projection;

-import optimization.projections.SimplexProjection;

-import optimization.stopCriteria.CompositeStopingCriteria;

-import optimization.stopCriteria.GradientL2Norm;

-import optimization.stopCriteria.ProjectedGradientL2Norm;

-import optimization.stopCriteria.StopingCriteria;

-import optimization.stopCriteria.ValueDifference;

-

-

-/**

- * @author javg

- * 

- * 

- *ax2+ b(y2 -displacement)

- */

-public class X2y2WithConstraints extends ProjectedObjective{

-

-

-	double a, b;

-	double dx;

-	double dy;

-	Projection projection;

-	

-	

-	public X2y2WithConstraints(double a, double b, double[] params, double dx, double dy, Projection proj){

-		//projection = new BoundsProjection(0.2,Double.MAX_VALUE);

-		super();

-		projection = proj;	

-		this.a = a;

-		this.b = b;

-		this.dx = dx;

-		this.dy = dy;

-		setInitialParameters(params);

-		System.out.println("Function " +a+"(x-"+dx+")^2 + "+b+"(y-"+dy+")^2");

-		System.out.println("Gradient " +(2*a)+"(x-"+dx+") ; "+(b*2)+"(y-"+dy+")");

-		printParameters();

-		projection.project(parameters);

-		printParameters();

-		gradient = new double[2];

-	}

-	

-	public double getValue() {

-		functionCalls++;

-		return a*(parameters[0]-dx)*(parameters[0]-dx)+b*((parameters[1]-dy)*(parameters[1]-dy));

-	}

-

-	public double[] getGradient() {

-		if(gradient == null){

-			gradient = new double[2];

-		}

-		gradientCalls++;

-		gradient[0]=2*a*(parameters[0]-dx);

-		gradient[1]=2*b*(parameters[1]-dy);

-		return gradient;

-	}

-	

-	

-	public double[] projectPoint(double[] point) {

-		double[] newPoint = point.clone();

-		projection.project(newPoint);

-		return newPoint;

-	}	

-	

-	public void optimizeWithProjectedGradientDescent(LineSearchMethod ls, OptimizerStats stats, X2y2WithConstraints o){

-		ProjectedGradientDescent optimizer = new ProjectedGradientDescent(ls);

-		StopingCriteria stopGrad = new ProjectedGradientL2Norm(0.001);

-		StopingCriteria stopValue = new ValueDifference(0.001);

-		CompositeStopingCriteria compositeStop = new CompositeStopingCriteria();

-		compositeStop.add(stopGrad);

-		compositeStop.add(stopValue);

-		

-		optimizer.setMaxIterations(5);

-		boolean succed = optimizer.optimize(o,stats,compositeStop);

-		System.out.println("Ended optimzation Projected Gradient Descent\n" + stats.prettyPrint(1));

-		System.out.println("Solution: " + " x0 " + o.parameters[0]+ " x1 " + o.parameters[1]);

-		if(succed){

-			System.out.println("Ended optimization in " + optimizer.getCurrentIteration());

-		}else{

-			System.out.println("Failed to optimize");

-		}

-	}

-	

-	

-	

-	public String toString(){

-		

-		return "P1: " + parameters[0] + " P2: " + parameters[1] + " value " + getValue() + " grad (" + getGradient()[0] + ":" + getGradient()[1]+")";

-	}

-	

-	public static void main(String[] args) {

-		double a = 1;

-		double b=1;

-		double x0 = 0;

-		double y0  =1;

-		double dx = 0.5;

-		double dy = 0.2	;

-		double [] parameters = new double[2];

-		parameters[0] = x0;

-		parameters[1] = y0;

-		X2y2WithConstraints o = new X2y2WithConstraints(a,b,parameters,dx,dy, 

-				new SimplexProjection(0.5)

-				//new BoundsProjection(0.0,0.4)

-		);

-		System.out.println("Starting optimization " + " x0 " + o.parameters[0]+ " x1 " + o.parameters[1] + " a " + a + " b "+b );

-		o.setDebugLevel(4);

-		

-		LineSearchMethod ls = new ArmijoLineSearchMinimizationAlongProjectionArc(new InterpolationPickFirstStep(1));

-		

-		OptimizerStats stats = new OptimizerStats();

-		o.optimizeWithProjectedGradientDescent(ls, stats, o);

-		

-//		o = new x2y2WithConstraints(a,b,x0,y0,dx,dy);

-//		stats = new OptimizerStats();

-//		o.optimizeWithSpectralProjectedGradientDescent(stats, o);

-	}

-	

-	

-	

-	

-}