Added formal command line options & new main class.

git-svn-id: https://ws10smt.googlecode.com/svn/trunk@200 ec762483-ff6d-05da-a07a-a48fb63a330f

12 files changed, 194 insertions, 108 deletions

diff --git a/gi/posterior-regularisation/prjava/build.xml b/gi/posterior-regularisation/prjava/build.xml
index c9ed2e8d..40199144 100644
--- a/gi/posterior-regularisation/prjava/build.xml
+++ b/gi/posterior-regularisation/prjava/build.xml
@@ -6,6 +6,7 @@
   <path id="classpath">
       <pathelement location="lib/trove-2.0.2.jar"/>
       <pathelement location="lib/optimization.jar"/>
+      <pathelement location="lib/jopt-simple-3.2.jar"/>
   </path>
 
   <target name="init">
diff --git a/gi/posterior-regularisation/prjava/prjava-20100707.jar b/gi/posterior-regularisation/prjava/prjava-20100707.jar
deleted file mode 100644
index 195374d9..00000000
--- a/gi/posterior-regularisation/prjava/prjava-20100707.jar
+++ /dev/null
diff --git a/gi/posterior-regularisation/prjava/prjava-20100707_1.jar b/gi/posterior-regularisation/prjava/prjava-20100707_1.jar
deleted file mode 100644
index a65f4d43..00000000
--- a/gi/posterior-regularisation/prjava/prjava-20100707_1.jar
+++ /dev/null
diff --git a/gi/posterior-regularisation/prjava/src/arr/F.java b/gi/posterior-regularisation/prjava/src/arr/F.java
index 5821af42..7f2b140a 100644
--- a/gi/posterior-regularisation/prjava/src/arr/F.java
+++ b/gi/posterior-regularisation/prjava/src/arr/F.java
@@ -3,7 +3,7 @@ package arr;
 import java.util.Random;

 

 public class F {

-	private static Random rng = new Random(); //(9562724l);

+	public static Random rng = new Random();

 	

 	public static void randomise(double probs[])

 	{

diff --git a/gi/posterior-regularisation/prjava/src/io/FileUtil.java b/gi/posterior-regularisation/prjava/src/io/FileUtil.java
index 67ce571e..81e7747b 100644
--- a/gi/posterior-regularisation/prjava/src/io/FileUtil.java
+++ b/gi/posterior-regularisation/prjava/src/io/FileUtil.java
@@ -3,7 +3,24 @@ import java.util.*;
 import java.util.zip.GZIPInputStream;

 import java.util.zip.GZIPOutputStream;

 import java.io.*;

-public class FileUtil {

+public class FileUtil 

+{

+	public static BufferedReader reader(File file) throws FileNotFoundException, IOException

+	{

+		if (file.getName().endsWith(".gz"))

+			return new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(file))));

+		else

+			return new BufferedReader(new FileReader(file));

+	}

+	

+	public static PrintStream printstream(File file) throws FileNotFoundException, IOException

+	{

+		if (file.getName().endsWith(".gz"))

+			return new PrintStream(new GZIPOutputStream(new FileOutputStream(file)));

+		else

+			return new PrintStream(new FileOutputStream(file));

+	}

+

 	public static Scanner openInFile(String filename){

 		Scanner localsc=null;

 		try

@@ -16,34 +33,6 @@ public class FileUtil {
 		return localsc;

 	}

 	

-	public static BufferedReader openBufferedReader(String filename){

-		BufferedReader r=null;

-		try

-		{

-			if (filename.endsWith(".gz"))

-				r=(new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(new File(filename))))));

-			else

-				r=(new BufferedReader(new FileReader(new File(filename))));

-		}catch(IOException ioe){

-			System.out.println(ioe.getMessage());

-		}

-		return r;		

-	}

-	

-	public static PrintStream  openOutFile(String filename){

-		PrintStream localps=null;

-		try

-		{

-			if (filename.endsWith(".gz"))

-				localps=new PrintStream (new GZIPOutputStream(new FileOutputStream(filename)));

-			else

-				localps=new PrintStream (new FileOutputStream(filename));

-

-		}catch(IOException ioe){

-			System.out.println(ioe.getMessage());

-		}

-		return localps;

-	}

 	public static FileInputStream openInputStream(String infilename){

 		FileInputStream fis=null;

 		try {

diff --git a/gi/posterior-regularisation/prjava/src/phrase/Corpus.java b/gi/posterior-regularisation/prjava/src/phrase/Corpus.java
index d5e856ca..81264ab9 100644
--- a/gi/posterior-regularisation/prjava/src/phrase/Corpus.java
+++ b/gi/posterior-regularisation/prjava/src/phrase/Corpus.java
@@ -217,5 +217,11 @@ public class Corpus
 		}
 		
 		return c;
+	}
+
+	public void printStats(PrintStream out) 
+	{
+		out.println("Corpus has " + edges.size() + " edges " + phraseLexicon.size() + " phrases " 
+				+ contextLexicon.size() + " contexts and " + wordLexicon.size() + " word types");
 	}	
-}
+}
\ No newline at end of file
diff --git a/gi/posterior-regularisation/prjava/src/phrase/PhraseCluster.java b/gi/posterior-regularisation/prjava/src/phrase/PhraseCluster.java
index 63a60682..7d7c46dd 100644
--- a/gi/posterior-regularisation/prjava/src/phrase/PhraseCluster.java
+++ b/gi/posterior-regularisation/prjava/src/phrase/PhraseCluster.java
@@ -25,73 +25,6 @@ public class PhraseCluster {
 	// pi[phrase][tag] = p(tag | phrase)

 	private double pi[][];

 	

-	public static void main(String[] args) 

-	{

-		String input_fname = args[0];

-		int tags = Integer.parseInt(args[1]);

-		String output_fname = args[2];

-		int iterations = Integer.parseInt(args[3]);

-		double scalePT = Double.parseDouble(args[4]);

-		double scaleCT = Double.parseDouble(args[5]);

-		int threads = Integer.parseInt(args[6]);

-		boolean runEM = Boolean.parseBoolean(args[7]);

-		

-		assert(tags >= 2);

-		assert(scalePT >= 0);

-		assert(scaleCT >= 0);

-		

-		Corpus corpus = null;

-		try {

-			corpus = Corpus.readFromFile(FileUtil.openBufferedReader(input_fname));

-		} catch (IOException e) {

-			System.err.println("Failed to open input file: " + input_fname);

-			e.printStackTrace();

-			System.exit(1);

-		}

-		PhraseCluster cluster = new PhraseCluster(tags, corpus, scalePT, scaleCT, threads);

-		

-		//PhraseObjective.ps = FileUtil.openOutFile(outputDir + "/phrase_stat.out");

-		

-		double last = 0;

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

-			

-			double o;

-			if (runEM || i < 3) 

-				o = cluster.EM();

-			else if (scaleCT == 0)

-			{

-				if (threads >= 1)

-					o = cluster.PREM_phrase_constraints_parallel();

-				else

-					o = cluster.PREM_phrase_constraints();

-			}

-			else 

-				o = cluster.PREM_phrase_context_constraints();

-			

-			//PhraseObjective.ps.

-			System.out.println("ITER: "+i+" objective: " + o);

-			last = o;

-		}

-		

-		double pl1lmax = cluster.phrase_l1lmax();

-		double cl1lmax = cluster.context_l1lmax();

-		System.out.println("Final posterior phrase l1lmax " + pl1lmax + " context l1lmax " + cl1lmax);

-		if (runEM) System.out.println("With PR objective " + (last - scalePT*pl1lmax - scaleCT*cl1lmax));

-		

-		PrintStream ps=io.FileUtil.openOutFile(output_fname);

-		cluster.displayPosterior(ps);

-		ps.close();

-		

-		//PhraseObjective.ps.close();

-

-		//ps = io.FileUtil.openOutFile(outputDir + "/parameters.out");

-		//cluster.displayModelParam(ps);

-		//ps.close();

-		

-		if (cluster.pool != null)

-			cluster.pool.shutdown();

-	}

-

 	public PhraseCluster(int numCluster, Corpus corpus, double scalep, double scalec, int threads){

 		K=numCluster;

 		c=corpus;

@@ -134,7 +67,7 @@ public class PhraseCluster {
 				double p[]=posterior(edge);

 				double z = arr.F.l1norm(p);

 				assert z > 0;

-				loglikelihood+=Math.log(z);

+				loglikelihood += edge.getCount() * Math.log(z);

 				arr.F.l1normalize(p);

 				

 				int count = edge.getCount();

@@ -150,7 +83,7 @@ public class PhraseCluster {
 			}

 		}

 		

-		System.out.println("Log likelihood: "+loglikelihood);

+		//System.out.println("Log likelihood: "+loglikelihood);

 		

 		//M

 		for(double [][]i:exp_emit){

diff --git a/gi/posterior-regularisation/prjava/src/phrase/PhraseContextObjective.java b/gi/posterior-regularisation/prjava/src/phrase/PhraseContextObjective.java
index fbf43a7f..15bd29c2 100644
--- a/gi/posterior-regularisation/prjava/src/phrase/PhraseContextObjective.java
+++ b/gi/posterior-regularisation/prjava/src/phrase/PhraseContextObjective.java
@@ -26,7 +26,7 @@ import phrase.Corpus.Edge;
 public class PhraseContextObjective extends ProjectedObjective

 {

 	private static final double GRAD_DIFF = 0.00002;

-	private static double INIT_STEP_SIZE = 10;

+	private static double INIT_STEP_SIZE = 300;

 	private static double VAL_DIFF = 1e-4; // FIXME needs to be tuned

 	private static int ITERATIONS = 100;

 	

diff --git a/gi/posterior-regularisation/prjava/src/phrase/PhraseCorpus.java b/gi/posterior-regularisation/prjava/src/phrase/PhraseCorpus.java
index 11e948ff..903e47c8 100644
--- a/gi/posterior-regularisation/prjava/src/phrase/PhraseCorpus.java
+++ b/gi/posterior-regularisation/prjava/src/phrase/PhraseCorpus.java
@@ -1,7 +1,11 @@
 package phrase;

 

+import io.FileUtil;

+

 import java.io.BufferedInputStream;

 import java.io.BufferedReader;

+import java.io.File;

+import java.io.FileNotFoundException;

 import java.io.IOException;

 import java.io.PrintStream;

 import java.util.ArrayList;

@@ -20,8 +24,9 @@ public class PhraseCorpus
 	public int data[][][];

 	public int numContexts;	

 

-	public PhraseCorpus(String filename){

-		BufferedReader r=io.FileUtil.openBufferedReader(filename);

+	public PhraseCorpus(String filename) throws FileNotFoundException, IOException

+	{

+		BufferedReader r = FileUtil.reader(new File(filename));

 		

 		phraseLex=new HashMap<String,Integer>();

 		wordLex=new HashMap<String,Integer>();

@@ -84,8 +89,9 @@ public class PhraseCorpus
 	}

 	

 	//for debugging

-	public void saveLex(String lexFilename){

-		PrintStream ps=io.FileUtil.openOutFile(lexFilename);

+	public void saveLex(String lexFilename) throws FileNotFoundException, IOException

+	{

+		PrintStream ps = FileUtil.printstream(new File(lexFilename));

 		ps.println("Phrase Lexicon");

 		ps.println(phraseLex.size());

 		printDict(phraseLex,ps);

@@ -175,7 +181,8 @@ public class PhraseCorpus
 		return null;

 	}

 

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

+	public static void main(String[] args) throws Exception 

+	{

 		String LEX_FILENAME="../pdata/lex.out";

 		String DATA_FILENAME="../pdata/btec.con";

 		PhraseCorpus c=new PhraseCorpus(DATA_FILENAME);

diff --git a/gi/posterior-regularisation/prjava/src/phrase/PhraseObjective.java b/gi/posterior-regularisation/prjava/src/phrase/PhraseObjective.java
index 0a76e2dc..3314f74a 100644
--- a/gi/posterior-regularisation/prjava/src/phrase/PhraseObjective.java
+++ b/gi/posterior-regularisation/prjava/src/phrase/PhraseObjective.java
@@ -21,7 +21,7 @@ import optimization.util.MathUtils;
 public class PhraseObjective extends ProjectedObjective

 {

 	static final double GRAD_DIFF = 0.00002;

-	static double INIT_STEP_SIZE = 10;

+	static double INIT_STEP_SIZE = 300;

 	static double VAL_DIFF = 1e-4; // FIXME needs to be tuned - and this might be too weak

 	static int ITERATIONS = 100;

 	//private double c1=0.0001; // wolf stuff

diff --git a/gi/posterior-regularisation/prjava/src/phrase/Trainer.java b/gi/posterior-regularisation/prjava/src/phrase/Trainer.java
new file mode 100644
index 00000000..b19f3fb9
--- /dev/null
+++ b/gi/posterior-regularisation/prjava/src/phrase/Trainer.java
@@ -0,0 +1,150 @@
+package phrase;
+
+import io.FileUtil;
+import joptsimple.OptionParser;
+import joptsimple.OptionSet;
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.util.Random;
+
+import arr.F;
+
+public class Trainer 
+{
+	public static void main(String[] args) 
+	{
+        OptionParser parser = new OptionParser();
+        parser.accepts("help");
+        parser.accepts("in").withRequiredArg().ofType(File.class);
+        parser.accepts("out").withRequiredArg().ofType(File.class);
+        parser.accepts("parameters").withRequiredArg().ofType(File.class);
+        parser.accepts("topics").withRequiredArg().ofType(Integer.class).defaultsTo(5);
+        parser.accepts("em-iterations").withRequiredArg().ofType(Integer.class).defaultsTo(5);
+        parser.accepts("pr-iterations").withRequiredArg().ofType(Integer.class).defaultsTo(0);
+        parser.accepts("threads").withRequiredArg().ofType(Integer.class).defaultsTo(0);
+        parser.accepts("scale-phrase").withRequiredArg().ofType(Double.class).defaultsTo(5.0);
+        parser.accepts("scale-context").withRequiredArg().ofType(Double.class).defaultsTo(0.0);
+        parser.accepts("seed").withRequiredArg().ofType(Long.class).defaultsTo(0l);
+        parser.accepts("convergence-threshold").withRequiredArg().ofType(Double.class).defaultsTo(1e-6);
+        OptionSet options = parser.parse(args);
+
+        if (options.has("help") || !options.has("in"))
+        {
+        	try {
+				parser.printHelpOn(System.err);
+			} catch (IOException e) {
+				System.err.println("This should never happen. Really.");
+				e.printStackTrace();
+			}
+        	System.exit(1);     
+        }
+		
+		int tags = (Integer) options.valueOf("topics");
+		int em_iterations = (Integer) options.valueOf("em-iterations");
+		int pr_iterations = (Integer) options.valueOf("pr-iterations");
+		double scale_phrase = (Double) options.valueOf("scale-phrase");
+		double scale_context = (Double) options.valueOf("scale-context");
+		int threads = (Integer) options.valueOf("threads");
+		double threshold = (Double) options.valueOf("convergence-threshold");
+		
+		if (options.has("seed"))
+			F.rng = new Random((Long) options.valueOf("seed"));
+		
+		if (tags <= 1 || scale_phrase < 0 || scale_context < 0 || threshold < 0)
+		{
+			System.err.println("Invalid arguments. Try again!");
+			System.exit(1);
+		}
+		
+		Corpus corpus = null;
+		File infile = (File) options.valueOf("in");
+		try {
+			System.out.println("Reading concordance from " + infile);
+			corpus = Corpus.readFromFile(FileUtil.reader(infile));
+			corpus.printStats(System.out);
+		} catch (IOException e) {
+			System.err.println("Failed to open input file: " + infile);
+			e.printStackTrace();
+			System.exit(1);
+		}
+		
+ 		System.out.println("Running with " + tags + " tags " +
+ 				"for " + em_iterations + " EM and " + pr_iterations + " PR iterations " +
+ 				"with scale " + scale_phrase + " phrase and " + scale_context + " context " +
+ 				"and " + threads + " threads");
+ 		System.out.println();
+		
+		PhraseCluster cluster = new PhraseCluster(tags, corpus, scale_phrase, scale_context, threads);
+				
+		double last = 0;
+		for (int i=0; i<em_iterations+pr_iterations; i++)
+		{
+			double o;
+			if (i < em_iterations) 
+				o = cluster.EM();
+			else if (scale_context == 0)
+			{
+				if (threads >= 1)
+					o = cluster.PREM_phrase_constraints_parallel();
+				else
+					o = cluster.PREM_phrase_constraints();
+			}
+			else 
+				o = cluster.PREM_phrase_context_constraints();
+			
+			System.out.println("ITER: "+i+" objective: " + o);
+			
+			if (i != 0 && Math.abs((o - last) / o) < threshold)
+			{
+				last = o;
+				if (i < em_iterations)
+				{
+					i = em_iterations - 1;
+					continue;
+				}
+				else
+					break;
+			}
+			last = o;
+		}
+		
+		double pl1lmax = cluster.phrase_l1lmax();
+		double cl1lmax = cluster.context_l1lmax();
+		System.out.println("\nFinal posterior phrase l1lmax " + pl1lmax + " context l1lmax " + cl1lmax);
+		if (pr_iterations == 0) 
+			System.out.println("With PR objective " + (last - scale_phrase*pl1lmax - scale_context*cl1lmax));
+		
+		if (options.has("out"))
+		{
+			File outfile = (File) options.valueOf("out");
+			try {
+				PrintStream ps = FileUtil.printstream(outfile);
+				cluster.displayPosterior(ps);
+				ps.close();
+			} catch (IOException e) {
+				System.err.println("Failed to open output file: " + outfile);
+				e.printStackTrace();
+				System.exit(1);
+			}
+		}
+
+		if (options.has("parameters"))
+		{
+			File outfile = (File) options.valueOf("parameters");
+			PrintStream ps;
+			try {
+				ps = FileUtil.printstream(outfile);
+				cluster.displayModelParam(ps);
+				ps.close();
+			} catch (IOException e) {
+				System.err.println("Failed to open output parameters file: " + outfile);
+				e.printStackTrace();
+				System.exit(1);
+			}
+		}
+		
+		if (cluster.pool != null)
+			cluster.pool.shutdown();
+	}
+}
diff --git a/gi/posterior-regularisation/prjava/train-PR-cluster.sh b/gi/posterior-regularisation/prjava/train-PR-cluster.sh
index b86d564b..41bb403f 100755
--- a/gi/posterior-regularisation/prjava/train-PR-cluster.sh
+++ b/gi/posterior-regularisation/prjava/train-PR-cluster.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
 d=`dirname $0`
-java -ea -Xmx8g -cp $d/prjava.jar:$d/lib/trove-2.0.2.jar:$d/lib/optimization.jar phrase.PhraseCluster $*
+java -ea -Xmx8g -cp $d/prjava.jar:$d/lib/trove-2.0.2.jar:$d/lib/optimization.jar:$d/lib/jopt-simple-3.2.jar phrase.Trainer $*