Replaced System.err.print* with logger api

Author: thammegowda

src/main/java/org/apache/joshua/adagrad/AdaGradCore.java

@@ -50,21 +50,25 @@
 import org.apache.joshua.util.StreamGobbler;
 
 import EDU.oswego.cs.dl.util.concurrent.ConcurrentHashMap;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * This code was originally written by Yuan Cao, who copied the MERT code to produce this file.
  */
 
 public class AdaGradCore {
-  private final JoshuaConfiguration joshuaConfiguration;
-  private TreeSet<Integer>[] indicesOfInterest_all;
-
-  private final static DecimalFormat f4 = new DecimalFormat("###0.0000");
-  private final Runtime myRuntime = Runtime.getRuntime();
 
+  private static final Logger LOG = LoggerFactory.getLogger(AdaGradCore.class);
   private final static double NegInf = (-1.0 / 0.0);
   private final static double PosInf = (+1.0 / 0.0);
   private final static double epsilon = 1.0 / 1000000;
+  private final static DecimalFormat f4 = new DecimalFormat("###0.0000");
+
+  private final JoshuaConfiguration joshuaConfiguration;
+  private final Runtime myRuntime = Runtime.getRuntime();
+
+  private TreeSet<Integer>[] indicesOfInterest_all;
 
   private int progress;
 
@@ -1928,12 +1932,8 @@ private boolean copyFile(String origFileName, String newFileName) {
        * inFile.close(); outFile.close();
        */
       return true;
-    } catch (FileNotFoundException e) {
-      System.err.println("FileNotFoundException in AdaGradCore.copyFile(String,String): "
-          + e.getMessage());
-      return false;
     } catch (IOException e) {
-      System.err.println("IOException in AdaGradCore.copyFile(String,String): " + e.getMessage());
+      LOG.error(e.getMessage(), e);
       return false;
     }
   }

src/main/java/org/apache/joshua/decoder/Decoder.java

@@ -239,13 +239,12 @@ private void handleMetadata(MetaDataException meta) throws IOException {
         // Change a decoder weight
         String[] tokens = meta.tokens();
         if (tokens.length != 3) {
-          System.err.println("* Error: weight change requires three tokens");
+          LOG.error("weight change requires three tokens");
         } else {
           float old_weight = Decoder.weights.getWeight(tokens[1]);
           Decoder.weights.set(tokens[1], Float.parseFloat(tokens[2]));
-          System.err.println(String.format("@set_weight: %s %.3f -> %.3f",
-              tokens[1], old_weight,
-              Decoder.weights.getWeight(tokens[1])));
+          LOG.error("@set_weight: {} {} -> {}", tokens[1], old_weight,
+              Decoder.weights.getWeight(tokens[1]));
         }
 
         // TODO: return a JSON object with this weight or all weights
@@ -256,15 +255,15 @@ private void handleMetadata(MetaDataException meta) throws IOException {
 
         String[] tokens = meta.tokens();
 
-        System.err.println(String.format("%s = %f", tokens[1], Decoder.weights.getWeight(tokens[1])));
+        LOG.error("{} = {}", tokens[1], Decoder.weights.getWeight(tokens[1]));
 
         out.write("".getBytes());
 
       } else if (meta.type().equals("add_rule")) {
         String tokens[] = meta.tokens(" \\|\\|\\| ");
 
         if (tokens.length != 2) {
-          System.err.println("* INVALID RULE '" + meta.tokenString() + "'");;
+          LOG.error("* INVALID RULE '{}'", meta);
           out.write("bad rule".getBytes());
           return;
         }

src/main/java/org/apache/joshua/decoder/NbestMinRiskReranker.java

@@ -31,7 +31,8 @@
 
 import org.apache.joshua.util.Ngram;
 import org.apache.joshua.util.Regex;
-
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * this class implements: (1) nbest min risk (MBR) reranking using BLEU as a gain funtion.
@@ -46,6 +47,8 @@
  */
 public class NbestMinRiskReranker {
 
+  private static final Logger LOG = LoggerFactory.getLogger(NbestMinRiskReranker.class);
+
   // TODO: this functionality is not implemented yet; default is to produce 1best without any
   // feature scores;
   boolean produceRerankedNbest = false;
@@ -67,7 +70,7 @@ public NbestMinRiskReranker(boolean produceRerankedNbest, double scalingFactor)
 
 
   public String processOneSent(List<String> nbest, int sentID) {
-    System.err.println("Now process sentence " + sentID);
+    LOG.info("Now process sentence {}", sentID);
 
     // step-0: preprocess
     // assumption: each hyp has a formate:
@@ -77,7 +80,7 @@ public String processOneSent(List<String> nbest, int sentID) {
     if (nbest.size() == 1) {
       String[] fields = Regex.threeBarsWithSpace.split(nbest.get(0));
       if (fields[1].equals("") || Regex.spaces.matches(fields[1])) {
-        System.err.println(String.format("-> sentence is empty"));
+        LOG.warn("-> sentence is empty");
         return "";
       }
     } 
@@ -171,7 +174,7 @@ public String processOneSent(List<String> nbest, int sentID) {
        */
     }
 
-    System.err.println("best gain: " + bestGain);
+    LOG.info("best gain: {}", bestGain);
     if (null == bestHyp) {
       throw new RuntimeException("mbr reranked one best is null, must be wrong");
     }
@@ -311,8 +314,10 @@ public static void main(String[] args) throws IOException {
     // If you don't know what to use for scaling factor, try using 1
 
     if (args.length < 2) {
-      System.err
-          .println("usage: java NbestMinRiskReranker <produce_reranked_nbest> <scaling_factor> [numThreads]");
+      String msg = "usage: java NbestMinRiskReranker <produce_reranked_nbest> <scaling_factor> "
+          + "[numThreads]";
+      System.err.println(msg);
+      LOG.error(msg);
       return;
     }
     long startTime = System.currentTimeMillis();
@@ -324,7 +329,7 @@ public static void main(String[] args) throws IOException {
     NbestMinRiskReranker mbrReranker =
         new NbestMinRiskReranker(produceRerankedNbest, scalingFactor);
 
-    System.err.println("##############running mbr reranking");
+    LOG.info("Running mbr reranking");
 
     int oldSentID = -1;
     List<String> nbest = new ArrayList<String>();
@@ -390,18 +395,15 @@ public static void main(String[] args) throws IOException {
           String best_hyp = result.toString();
           System.out.println(best_hyp);
         }
-
-
       } catch (InterruptedException e) {
-        e.printStackTrace();
+        LOG.error(e.getMessage(), e);
       }
-
     }
 
     scanner.close();
 
-    System.err.println("Total running time (seconds) is "
-        + (System.currentTimeMillis() - startTime) / 1000.0);
+    LOG.info("Total running time (seconds) is {} ",
+        (System.currentTimeMillis() - startTime) / 1000.0);
   }
 
   private class RankerTask implements Runnable {

src/main/java/org/apache/joshua/decoder/chart_parser/ComputeNodeResult.java

@@ -31,6 +31,8 @@
 import org.apache.joshua.decoder.hypergraph.HGNode;
 import org.apache.joshua.decoder.hypergraph.HyperEdge;
 import org.apache.joshua.decoder.segment_file.Sentence;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * This class computes the cost of applying a rule.
@@ -41,6 +43,8 @@
 
 public class ComputeNodeResult {
 
+  private static final Logger LOG = LoggerFactory.getLogger(ComputeNodeResult.class);
+
   // The cost incurred by the rule itself (and all associated feature functions)
   private float transitionCost;
 
@@ -67,11 +71,9 @@ public ComputeNodeResult(List<FeatureFunction> featureFunctions, Rule rule, List
     // whatever costs we incur applying this rule to create a new hyperedge.
     float viterbiCost = 0.0f;
 
-    if (Decoder.VERBOSE >= 4) {
-      System.err.println("ComputeNodeResult():");
-      System.err.println("-> RULE " + rule);
-    }
-      
+    LOG.debug("ComputeNodeResult():");
+    LOG.info("-> RULE {}", rule);
+
     /*
      * Here we sum the accumulated cost of each of the tail nodes. The total cost of the new
      * hyperedge (the inside or Viterbi cost) is the sum of these nodes plus the cost of the
@@ -80,10 +82,8 @@ public ComputeNodeResult(List<FeatureFunction> featureFunctions, Rule rule, List
      */
     if (null != tailNodes) {
       for (HGNode item : tailNodes) {
-        if (Decoder.VERBOSE >= 4) {
-          System.err.println("  -> item.bestedge: " + item);
-          System.err.println("-> TAIL NODE " + item);
-        }        
+        LOG.info("-> item.bestedge: {}", item);
+        LOG.info("-> TAIL NODE {}", item);
         viterbiCost += item.bestHyperedge.getBestDerivationScore();
       }
     }
@@ -105,11 +105,10 @@ public ComputeNodeResult(List<FeatureFunction> featureFunctions, Rule rule, List
 
       DPState newState = feature.compute(rule, tailNodes, i, j, sourcePath, sentence, acc);
       transitionCost += acc.getScore();
-      
-      if (Decoder.VERBOSE >= 4)
-        System.err.println(String.format("-> FEATURE %s = %.3f * %.3f = %.3f", 
-            feature.getName(), acc.getScore() / Decoder.weights.getSparse(feature.getName()),
-            Decoder.weights.getSparse(feature.getName()), acc.getScore()));
+
+      LOG.debug("FEATURE {} = {} * {} = {}", feature.getName(),
+          acc.getScore() / Decoder.weights.getSparse(feature.getName()),
+          Decoder.weights.getSparse(feature.getName()), acc.getScore());
 
       if (feature.isStateful()) {
         futureCostEstimate += feature.estimateFutureCost(rule, newState, sentence);
@@ -118,9 +117,7 @@ public ComputeNodeResult(List<FeatureFunction> featureFunctions, Rule rule, List
     }
 
     viterbiCost += transitionCost;
-
-    if (Decoder.VERBOSE >= 4)
-      System.err.println(String.format("-> COST = %.3f", transitionCost));
+    LOG.debug("-> COST = {}", transitionCost);
 
     // Set the final results.
     this.pruningCostEstimate = viterbiCost + futureCostEstimate;

src/main/java/org/apache/joshua/decoder/ff/RuleCountBin.java

@@ -27,12 +27,16 @@
 import org.apache.joshua.decoder.ff.tm.Rule;
 import org.apache.joshua.decoder.hypergraph.HGNode;
 import org.apache.joshua.decoder.segment_file.Sentence;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /*
  * This feature computes a bin for the rule and activates a feature for it. It requires access to
  * the index of the RarityPenalty field, from which the rule count can be computed.
  */
 public class RuleCountBin extends StatelessFF {
+
+  private static final Logger LOG = LoggerFactory.getLogger(RuleCountBin.class);
   private int field = -1;
 
   public RuleCountBin(FeatureVector weights, String[] args, JoshuaConfiguration config) {
@@ -61,7 +65,7 @@ public DPState compute(Rule rule, List<HGNode> tailNodes, int i, int j, SourcePa
       }
     }
 
-    System.err.println(String.format("RuleCountBin(%f) = %d ==> %s", rarityPenalty, count, feature));
+    LOG.debug("RuleCountBin({}) = {} ==> {}", rarityPenalty, count, feature);
 
     acc.add(feature, 1.0f);
 

src/main/java/org/apache/joshua/decoder/ff/fragmentlm/FragmentLMFF.java

@@ -36,6 +36,8 @@
 import org.apache.joshua.decoder.hypergraph.HGNode;
 import org.apache.joshua.decoder.hypergraph.HyperEdge;
 import org.apache.joshua.decoder.segment_file.Sentence;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Feature function that reads in a list of language model fragments and matches them against the
@@ -68,6 +70,8 @@
  */
 public class FragmentLMFF extends StatefulFF {
 
+  private static final Logger LOG = LoggerFactory.getLogger(FragmentLMFF.class);
+
   /*
    * When building a fragment from a rule rooted in the hypergraph, this parameter determines how
    * deep we'll go. Smaller values mean less hypergraph traversal but may also limit the LM
@@ -131,8 +135,7 @@ public FragmentLMFF(FeatureVector weights, String[] args, JoshuaConfiguration co
       throw new RuntimeException(String.format("* WARNING: couldn't read fragment LM file '%s'",
           fragmentLMFile), e);
     }
-    System.err.println(String.format("FragmentLMFF: Read %d LM fragments from '%s'", numFragments,
-        fragmentLMFile));
+    LOG.info("FragmentLMFF: Read {} LM fragments from '{}'", numFragments, fragmentLMFile);
   }
 
   /**
@@ -147,19 +150,18 @@ public void addLMFragment(Tree fragment) {
     int fragmentDepth = fragment.getDepth();
 
     if (MAX_DEPTH != 0 && fragmentDepth > MAX_DEPTH) {
-      System.err.println(String.format("  Skipping fragment %s (depth %d > %d)", fragment,
-          fragmentDepth, MAX_DEPTH));
+      LOG.warn("Skipping fragment {} (depth {} > {})", fragment, fragmentDepth, MAX_DEPTH);
       return;
     }
 
     if (MIN_LEX_DEPTH > 1 && fragment.isLexicalized() && fragmentDepth < MIN_LEX_DEPTH) {
-      System.err.println(String.format("  Skipping fragment %s (lex depth %d < %d)", fragment,
-          fragmentDepth, MIN_LEX_DEPTH));
+      LOG.warn("Skipping fragment {} (lex depth {} < {})", fragment, fragmentDepth, MIN_LEX_DEPTH);
       return;
     }
 
-    if (lmFragments.get(fragment.getRule()) == null)
+    if (lmFragments.get(fragment.getRule()) == null) {
       lmFragments.put(fragment.getRule(), new ArrayList<Tree>());
+    }
     lmFragments.get(fragment.getRule()).add(fragment);
     numFragments++;
   }
@@ -314,7 +316,7 @@ public static void main(String[] args) {
 
     Tree tree = Tree.buildTree(ruleS, tailNodes, 1);
     boolean matched = fragmentLMFF.match(fragment, tree);
-    System.err.println(String.format("Does\n  %s match\n  %s??\n  -> %s", fragment, tree, matched));
+    LOG.info("Does\n  {} match\n  {}??\n  -> {}", fragment, tree, matched);
   }
 
   /**

src/main/java/org/apache/joshua/decoder/ff/fragmentlm/Tree.java

@@ -550,10 +550,12 @@ public static Tree buildTree(Rule rule, DerivationState[] derivationStates, int
     }
 
     tree = tree.shallowClone();
-    
-    System.err.println(String.format("buildTree(%s)", tree));
-    for (int i = 0; i < derivationStates.length; i++) {
-      System.err.println(String.format("  -> %d: %s", i, derivationStates[i]));
+
+    if (LOG.isDebugEnabled()) {
+      LOG.debug("buildTree({})", tree);
+      for (int i = 0; i < derivationStates.length; i++) {
+        LOG.debug("  -> {}: {}", i, derivationStates[i]);
+      }
     }
 
     List<Tree> frontier = tree.getNonterminalYield();
@@ -630,7 +632,7 @@ public static Tree buildTree(DerivationState derivationState, int maxDepth) {
 
     tree = tree.shallowClone();
 
-    System.err.println(String.format("buildTree(%s)", tree));
+    LOG.debug("buildTree({})", tree);
 
     if (rule.getArity() > 0 && maxDepth > 0) {
       List<Tree> frontier = tree.getNonterminalYield();

src/main/java/org/apache/joshua/decoder/ff/lm/KenLM.java

@@ -21,6 +21,8 @@
 import org.apache.joshua.corpus.Vocabulary;
 import org.apache.joshua.decoder.ff.lm.NGramLanguageModel;
 import org.apache.joshua.decoder.ff.state_maintenance.KenLMState;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * JNI wrapper for KenLM. This version of KenLM supports two use cases, implemented by the separate
@@ -34,17 +36,19 @@
 
 public class KenLM implements NGramLanguageModel, Comparable<KenLM> {
 
+  private static final Logger LOG = LoggerFactory.getLogger(KenLM.class);
+
   static {
     try {
       System.loadLibrary("ken");
     } catch (UnsatisfiedLinkError e) {
       //TODO: send these prints to LOG.err
-      System.err.println("* FATAL: Can't find libken.so (libken.dylib on OS X) in $JOSHUA/lib");
-      System.err.println("*        This probably means that the KenLM library didn't compile.");
-      System.err.println("*        Make sure that BOOST_ROOT is set to the root of your boost");
-      System.err.println("*        installation (it's not /opt/local/, the default), change to");
-      System.err.println("*        $JOSHUA, and type 'ant kenlm'. If problems persist, see the");
-      System.err.println("*        website (joshua-decoder.org).");
+      LOG.error("* FATAL: Can't find libken.so (libken.dylib on OS X) in $JOSHUA/lib");
+      LOG.error("*        This probably means that the KenLM library didn't compile.");
+      LOG.error("*        Make sure that BOOST_ROOT is set to the root of your boost");
+      LOG.error("*        installation (it's not /opt/local/, the default), change to");
+      LOG.error("*        $JOSHUA, and type 'ant kenlm'. If problems persist, see the");
+      LOG.error("*        website (joshua-decoder.org)."); //FIXME: update link to newer url
       throw new RuntimeException(e);
     }
   }