/**
   * The basic method for splitting off a clause of a tree. This modifies the tree in place. This
   * method addtionally follows ref edges.
   *
   * @param tree The tree to split a clause from.
   * @param toKeep The edge representing the clause to keep.
   */
  @SuppressWarnings("unchecked")
  private void simpleClause(SemanticGraph tree, SemanticGraphEdge toKeep) {
    splitToChildOfEdge(tree, toKeep);

    // Follow 'ref' edges
    Map<IndexedWord, IndexedWord> refReplaceMap = new HashMap<>();
    // (find replacements)
    for (IndexedWord vertex : tree.vertexSet()) {
      for (SemanticGraphEdge edge : extraEdgesByDependent.get(vertex)) {
        if ("ref".equals(edge.getRelation().toString())
            && // it's a ref edge...
            !tree.containsVertex(
                edge.getGovernor())) { // ...that doesn't already exist in the tree.
          refReplaceMap.put(vertex, edge.getGovernor());
        }
      }
    }
    // (do replacements)
    for (Map.Entry<IndexedWord, IndexedWord> entry : refReplaceMap.entrySet()) {
      Iterator<SemanticGraphEdge> iter = tree.incomingEdgeIterator(entry.getKey());
      if (!iter.hasNext()) {
        continue;
      }
      SemanticGraphEdge incomingEdge = iter.next();
      IndexedWord governor = incomingEdge.getGovernor();
      tree.removeVertex(entry.getKey());
      addSubtree(
          tree,
          governor,
          incomingEdge.getRelation().toString(),
          this.tree,
          entry.getValue(),
          this.tree.incomingEdgeList(tree.getFirstRoot()));
    }
  }
 /** Re-order the action space based on the specified order of names. */
 private Collection<Action> orderActions(Collection<Action> actionSpace, List<String> order) {
   List<Action> tmp = new ArrayList<>(actionSpace);
   List<Action> out = new ArrayList<>();
   for (String key : order) {
     Iterator<Action> iter = tmp.iterator();
     while (iter.hasNext()) {
       Action a = iter.next();
       if (a.signature().equals(key)) {
         out.add(a);
         iter.remove();
       }
     }
   }
   out.addAll(tmp);
   return out;
 }
Example #3
0
  public Object formResult() {
    Set brs = new HashSet();
    Set urs = new HashSet();
    // scan each rule / history pair
    int ruleCount = 0;
    for (Iterator pairI = rulePairs.keySet().iterator(); pairI.hasNext(); ) {
      if (ruleCount % 100 == 0) {
        System.err.println("Rules multiplied: " + ruleCount);
      }
      ruleCount++;
      Pair rulePair = (Pair) pairI.next();
      Rule baseRule = (Rule) rulePair.first;
      String baseLabel = (String) ruleToLabel.get(baseRule);
      List history = (List) rulePair.second;
      double totalProb = 0;
      for (int depth = 1; depth <= HISTORY_DEPTH() && depth <= history.size(); depth++) {
        List subHistory = history.subList(0, depth);
        double c_label = labelPairs.getCount(new Pair(baseLabel, subHistory));
        double c_rule = rulePairs.getCount(new Pair(baseRule, subHistory));
        // System.out.println("Multiplying out "+baseRule+" with history "+subHistory);
        // System.out.println("Count of "+baseLabel+" with "+subHistory+" is "+c_label);
        // System.out.println("Count of "+baseRule+" with "+subHistory+" is "+c_rule );

        double prob = (1.0 / HISTORY_DEPTH()) * (c_rule) / (c_label);
        totalProb += prob;
        for (int childDepth = 0; childDepth <= Math.min(HISTORY_DEPTH() - 1, depth); childDepth++) {
          Rule rule = specifyRule(baseRule, subHistory, childDepth);
          rule.score = (float) Math.log(totalProb);
          // System.out.println("Created  "+rule+" with score "+rule.score);
          if (rule instanceof UnaryRule) {
            urs.add(rule);
          } else {
            brs.add(rule);
          }
        }
      }
    }
    System.out.println("Total states: " + stateNumberer.total());
    BinaryGrammar bg = new BinaryGrammar(stateNumberer.total());
    UnaryGrammar ug = new UnaryGrammar(stateNumberer.total());
    for (Iterator brI = brs.iterator(); brI.hasNext(); ) {
      BinaryRule br = (BinaryRule) brI.next();
      bg.addRule(br);
    }
    for (Iterator urI = urs.iterator(); urI.hasNext(); ) {
      UnaryRule ur = (UnaryRule) urI.next();
      ug.addRule(ur);
    }
    return new Pair(ug, bg);
  }
  @Override
  public void finishTraining() {
    lex.finishTraining();

    int numTags = tagIndex.size();
    POSes = new HashSet<String>(tagIndex.objectsList());
    initialPOSDist = Distribution.laplaceSmoothedDistribution(initial, numTags, 0.5);
    markovPOSDists = new HashMap<String, Distribution>();
    Set entries = ruleCounter.lowestLevelCounterEntrySet();
    for (Iterator iter = entries.iterator(); iter.hasNext(); ) {
      Map.Entry entry = (Map.Entry) iter.next();
      //      Map.Entry<List<String>, Counter> entry = (Map.Entry<List<String>, Counter>)
      // iter.next();
      Distribution d =
          Distribution.laplaceSmoothedDistribution((ClassicCounter) entry.getValue(), numTags, 0.5);
      markovPOSDists.put(((List<String>) entry.getKey()).get(0), d);
    }
  }
Example #5
0
 public XBarGrammarProjection(BinaryGrammar bg, UnaryGrammar ug) {
   Map<BinaryRule, BinaryRule> binaryRules = new HashMap<BinaryRule, BinaryRule>();
   Map<UnaryRule, UnaryRule> unaryRules = new HashMap<UnaryRule, UnaryRule>();
   sourceUG = ug;
   sourceBG = bg;
   sourceNumberer = Numberer.getGlobalNumberer(bg.stateSpace());
   targetNumberer = Numberer.getGlobalNumberer(bg.stateSpace() + "-xbar");
   projection = new int[sourceNumberer.total()];
   scanStates(sourceNumberer, targetNumberer);
   targetBG = new BinaryGrammar(targetNumberer.total(), bg.stateSpace() + "-xbar");
   targetUG = new UnaryGrammar(targetNumberer.total());
   for (Iterator<BinaryRule> brI = bg.iterator(); brI.hasNext(); ) {
     BinaryRule rule = projectBinaryRule(brI.next());
     Rule old = binaryRules.get(rule);
     if (old == null || rule.score > old.score) {
       binaryRules.put(rule, rule);
     }
   }
   for (BinaryRule br : binaryRules.keySet()) {
     targetBG.addRule(br);
     // System.out.println("BR: "+targetNumberer.object(br.parent)+" ->
     // "+targetNumberer.object(br.leftChild)+" "+targetNumberer.object(br.rightChild)+" %%
     // "+br.score);
   }
   targetBG.splitRules();
   for (int parent = 0; parent < sourceNumberer.total(); parent++) {
     for (Iterator<UnaryRule> urI = ug.ruleIteratorByParent(parent); urI.hasNext(); ) {
       UnaryRule sourceRule = urI.next();
       UnaryRule rule = projectUnaryRule(sourceRule);
       Rule old = unaryRules.get(rule);
       if (old == null || rule.score > old.score) {
         unaryRules.put(rule, rule);
       }
       /*
         if (((UnaryRule)rule).child == targetNumberer.number("PRP") &&
           ((String)sourceNumberer.object(rule.parent)).charAt(0) == 'N') {
         System.out.println("Source UR: "+sourceRule+" %% "+sourceRule.score);
         System.out.println("Score of "+rule+"is now: "+((UnaryRule)unaryRules.get(rule)).score);
       }
       */
     }
   }
   for (UnaryRule ur : unaryRules.keySet()) {
     targetUG.addRule(ur);
     // System.out.println("UR: "+targetNumberer.object(ur.parent)+" ->
     // "+targetNumberer.object(ur.child)+" %% "+ur.score);
   }
   targetUG.purgeRules();
   System.out.println(
       "Projected "
           + sourceNumberer.total()
           + " states to "
           + targetNumberer.total()
           + " states.");
 }
 private Distribution<Integer> getSegmentedWordLengthDistribution(Treebank tb) {
   // CharacterLevelTagExtender ext = new CharacterLevelTagExtender();
   ClassicCounter<Integer> c = new ClassicCounter<Integer>();
   for (Iterator iterator = tb.iterator(); iterator.hasNext(); ) {
     Tree gold = (Tree) iterator.next();
     StringBuilder goldChars = new StringBuilder();
     ArrayList goldYield = gold.yield();
     for (Iterator wordIter = goldYield.iterator(); wordIter.hasNext(); ) {
       Word word = (Word) wordIter.next();
       goldChars.append(word);
     }
     List<HasWord> ourWords = segment(goldChars.toString());
     for (int i = 0; i < ourWords.size(); i++) {
       c.incrementCount(Integer.valueOf(ourWords.get(i).word().length()));
     }
   }
   return Distribution.getDistribution(c);
 }
Example #7
0
  /**
   * Prints out all matches of a semgrex pattern on a file of dependencies. <br>
   * Usage:<br>
   * java edu.stanford.nlp.semgraph.semgrex.SemgrexPattern [args] <br>
   * See the help() function for a list of possible arguments to provide.
   */
  public static void main(String[] args) throws IOException {
    Map<String, Integer> flagMap = Generics.newHashMap();

    flagMap.put(PATTERN, 1);
    flagMap.put(TREE_FILE, 1);
    flagMap.put(MODE, 1);
    flagMap.put(EXTRAS, 1);
    flagMap.put(CONLLU_FILE, 1);
    flagMap.put(OUTPUT_FORMAT_OPTION, 1);

    Map<String, String[]> argsMap = StringUtils.argsToMap(args, flagMap);
    args = argsMap.get(null);

    // TODO: allow patterns to be extracted from a file
    if (!(argsMap.containsKey(PATTERN)) || argsMap.get(PATTERN).length == 0) {
      help();
      System.exit(2);
    }
    SemgrexPattern semgrex = SemgrexPattern.compile(argsMap.get(PATTERN)[0]);

    String modeString = DEFAULT_MODE;
    if (argsMap.containsKey(MODE) && argsMap.get(MODE).length > 0) {
      modeString = argsMap.get(MODE)[0].toUpperCase();
    }
    SemanticGraphFactory.Mode mode = SemanticGraphFactory.Mode.valueOf(modeString);

    String outputFormatString = DEFAULT_OUTPUT_FORMAT;
    if (argsMap.containsKey(OUTPUT_FORMAT_OPTION) && argsMap.get(OUTPUT_FORMAT_OPTION).length > 0) {
      outputFormatString = argsMap.get(OUTPUT_FORMAT_OPTION)[0].toUpperCase();
    }
    OutputFormat outputFormat = OutputFormat.valueOf(outputFormatString);

    boolean useExtras = true;
    if (argsMap.containsKey(EXTRAS) && argsMap.get(EXTRAS).length > 0) {
      useExtras = Boolean.valueOf(argsMap.get(EXTRAS)[0]);
    }

    List<SemanticGraph> graphs = Generics.newArrayList();
    // TODO: allow other sources of graphs, such as dependency files
    if (argsMap.containsKey(TREE_FILE) && argsMap.get(TREE_FILE).length > 0) {
      for (String treeFile : argsMap.get(TREE_FILE)) {
        System.err.println("Loading file " + treeFile);
        MemoryTreebank treebank = new MemoryTreebank(new TreeNormalizer());
        treebank.loadPath(treeFile);
        for (Tree tree : treebank) {
          // TODO: allow other languages... this defaults to English
          SemanticGraph graph =
              SemanticGraphFactory.makeFromTree(
                  tree,
                  mode,
                  useExtras
                      ? GrammaticalStructure.Extras.MAXIMAL
                      : GrammaticalStructure.Extras.NONE,
                  true);
          graphs.add(graph);
        }
      }
    }

    if (argsMap.containsKey(CONLLU_FILE) && argsMap.get(CONLLU_FILE).length > 0) {
      CoNLLUDocumentReader reader = new CoNLLUDocumentReader();
      for (String conlluFile : argsMap.get(CONLLU_FILE)) {
        System.err.println("Loading file " + conlluFile);
        Iterator<SemanticGraph> it = reader.getIterator(IOUtils.readerFromString(conlluFile));

        while (it.hasNext()) {
          SemanticGraph graph = it.next();
          graphs.add(graph);
        }
      }
    }

    for (SemanticGraph graph : graphs) {
      SemgrexMatcher matcher = semgrex.matcher(graph);
      if (!(matcher.find())) {
        continue;
      }

      if (outputFormat == OutputFormat.LIST) {
        System.err.println("Matched graph:");
        System.err.println(graph.toString(SemanticGraph.OutputFormat.LIST));
        boolean found = true;
        while (found) {
          System.err.println(
              "Matches at: " + matcher.getMatch().value() + "-" + matcher.getMatch().index());
          List<String> nodeNames = Generics.newArrayList();
          nodeNames.addAll(matcher.getNodeNames());
          Collections.sort(nodeNames);
          for (String name : nodeNames) {
            System.err.println(
                "  "
                    + name
                    + ": "
                    + matcher.getNode(name).value()
                    + "-"
                    + matcher.getNode(name).index());
          }
          System.err.println();
          found = matcher.find();
        }
      } else if (outputFormat == OutputFormat.OFFSET) {
        if (graph.vertexListSorted().isEmpty()) {
          continue;
        }
        System.out.printf(
            "+%d %s%n",
            graph.vertexListSorted().get(0).get(CoreAnnotations.LineNumberAnnotation.class),
            argsMap.get(CONLLU_FILE)[0]);
      }
    }
  }
Example #8
0
  public static void main(String[] args) {
    Options op = new Options(new EnglishTreebankParserParams());
    // op.tlpParams may be changed to something else later, so don't use it till
    // after options are parsed.

    System.out.println("Currently " + new Date());
    System.out.print("Invoked with arguments:");
    for (String arg : args) {
      System.out.print(" " + arg);
    }
    System.out.println();

    String path = "/u/nlp/stuff/corpora/Treebank3/parsed/mrg/wsj";
    int trainLow = 200, trainHigh = 2199, testLow = 2200, testHigh = 2219;
    String serializeFile = null;

    int i = 0;
    while (i < args.length && args[i].startsWith("-")) {
      if (args[i].equalsIgnoreCase("-path") && (i + 1 < args.length)) {
        path = args[i + 1];
        i += 2;
      } else if (args[i].equalsIgnoreCase("-train") && (i + 2 < args.length)) {
        trainLow = Integer.parseInt(args[i + 1]);
        trainHigh = Integer.parseInt(args[i + 2]);
        i += 3;
      } else if (args[i].equalsIgnoreCase("-test") && (i + 2 < args.length)) {
        testLow = Integer.parseInt(args[i + 1]);
        testHigh = Integer.parseInt(args[i + 2]);
        i += 3;
      } else if (args[i].equalsIgnoreCase("-serialize") && (i + 1 < args.length)) {
        serializeFile = args[i + 1];
        i += 2;
      } else if (args[i].equalsIgnoreCase("-tLPP") && (i + 1 < args.length)) {
        try {
          op.tlpParams = (TreebankLangParserParams) Class.forName(args[i + 1]).newInstance();
        } catch (ClassNotFoundException e) {
          System.err.println("Class not found: " + args[i + 1]);
        } catch (InstantiationException e) {
          System.err.println("Couldn't instantiate: " + args[i + 1] + ": " + e.toString());
        } catch (IllegalAccessException e) {
          System.err.println("illegal access" + e);
        }
        i += 2;
      } else if (args[i].equals("-encoding")) {
        // sets encoding for TreebankLangParserParams
        op.tlpParams.setInputEncoding(args[i + 1]);
        op.tlpParams.setOutputEncoding(args[i + 1]);
        i += 2;
      } else {
        i = op.setOptionOrWarn(args, i);
      }
    }
    // System.out.println(tlpParams.getClass());
    TreebankLanguagePack tlp = op.tlpParams.treebankLanguagePack();

    Train.sisterSplitters = new HashSet(Arrays.asList(op.tlpParams.sisterSplitters()));
    //    BinarizerFactory.TreeAnnotator.setTreebankLang(tlpParams);
    PrintWriter pw = op.tlpParams.pw();

    Test.display();
    Train.display();
    op.display();
    op.tlpParams.display();

    // setup tree transforms
    Treebank trainTreebank = op.tlpParams.memoryTreebank();
    MemoryTreebank testTreebank = op.tlpParams.testMemoryTreebank();
    // Treebank blippTreebank = ((EnglishTreebankParserParams) tlpParams).diskTreebank();
    // String blippPath = "/afs/ir.stanford.edu/data/linguistic-data/BLLIP-WSJ/";
    // blippTreebank.loadPath(blippPath, "", true);

    Timing.startTime();
    System.err.print("Reading trees...");
    testTreebank.loadPath(path, new NumberRangeFileFilter(testLow, testHigh, true));
    if (Test.increasingLength) {
      Collections.sort(testTreebank, new TreeLengthComparator());
    }

    trainTreebank.loadPath(path, new NumberRangeFileFilter(trainLow, trainHigh, true));
    Timing.tick("done.");
    System.err.print("Binarizing trees...");
    TreeAnnotatorAndBinarizer binarizer = null;
    if (!Train.leftToRight) {
      binarizer =
          new TreeAnnotatorAndBinarizer(op.tlpParams, op.forceCNF, !Train.outsideFactor(), true);
    } else {
      binarizer =
          new TreeAnnotatorAndBinarizer(
              op.tlpParams.headFinder(),
              new LeftHeadFinder(),
              op.tlpParams,
              op.forceCNF,
              !Train.outsideFactor(),
              true);
    }
    CollinsPuncTransformer collinsPuncTransformer = null;
    if (Train.collinsPunc) {
      collinsPuncTransformer = new CollinsPuncTransformer(tlp);
    }
    TreeTransformer debinarizer = new Debinarizer(op.forceCNF);
    List<Tree> binaryTrainTrees = new ArrayList<Tree>();

    if (Train.selectiveSplit) {
      Train.splitters =
          ParentAnnotationStats.getSplitCategories(
              trainTreebank,
              Train.tagSelectiveSplit,
              0,
              Train.selectiveSplitCutOff,
              Train.tagSelectiveSplitCutOff,
              op.tlpParams.treebankLanguagePack());
      if (Train.deleteSplitters != null) {
        List<String> deleted = new ArrayList<String>();
        for (String del : Train.deleteSplitters) {
          String baseDel = tlp.basicCategory(del);
          boolean checkBasic = del.equals(baseDel);
          for (Iterator<String> it = Train.splitters.iterator(); it.hasNext(); ) {
            String elem = it.next();
            String baseElem = tlp.basicCategory(elem);
            boolean delStr = checkBasic && baseElem.equals(baseDel) || elem.equals(del);
            if (delStr) {
              it.remove();
              deleted.add(elem);
            }
          }
        }
        System.err.println("Removed from vertical splitters: " + deleted);
      }
    }
    if (Train.selectivePostSplit) {
      TreeTransformer myTransformer = new TreeAnnotator(op.tlpParams.headFinder(), op.tlpParams);
      Treebank annotatedTB = trainTreebank.transform(myTransformer);
      Train.postSplitters =
          ParentAnnotationStats.getSplitCategories(
              annotatedTB,
              true,
              0,
              Train.selectivePostSplitCutOff,
              Train.tagSelectivePostSplitCutOff,
              op.tlpParams.treebankLanguagePack());
    }

    if (Train.hSelSplit) {
      binarizer.setDoSelectiveSplit(false);
      for (Tree tree : trainTreebank) {
        if (Train.collinsPunc) {
          tree = collinsPuncTransformer.transformTree(tree);
        }
        // tree.pennPrint(tlpParams.pw());
        tree = binarizer.transformTree(tree);
        // binaryTrainTrees.add(tree);
      }
      binarizer.setDoSelectiveSplit(true);
    }
    for (Tree tree : trainTreebank) {
      if (Train.collinsPunc) {
        tree = collinsPuncTransformer.transformTree(tree);
      }
      tree = binarizer.transformTree(tree);
      binaryTrainTrees.add(tree);
    }
    if (Test.verbose) {
      binarizer.dumpStats();
    }

    List<Tree> binaryTestTrees = new ArrayList<Tree>();
    for (Tree tree : testTreebank) {
      if (Train.collinsPunc) {
        tree = collinsPuncTransformer.transformTree(tree);
      }
      tree = binarizer.transformTree(tree);
      binaryTestTrees.add(tree);
    }
    Timing.tick("done."); // binarization
    BinaryGrammar bg = null;
    UnaryGrammar ug = null;
    DependencyGrammar dg = null;
    // DependencyGrammar dgBLIPP = null;
    Lexicon lex = null;
    // extract grammars
    Extractor bgExtractor = new BinaryGrammarExtractor();
    // Extractor bgExtractor = new SmoothedBinaryGrammarExtractor();//new BinaryGrammarExtractor();
    // Extractor lexExtractor = new LexiconExtractor();

    // Extractor dgExtractor = new DependencyMemGrammarExtractor();

    Extractor dgExtractor = new MLEDependencyGrammarExtractor(op);
    if (op.doPCFG) {
      System.err.print("Extracting PCFG...");
      Pair bgug = null;
      if (Train.cheatPCFG) {
        List allTrees = new ArrayList(binaryTrainTrees);
        allTrees.addAll(binaryTestTrees);
        bgug = (Pair) bgExtractor.extract(allTrees);
      } else {
        bgug = (Pair) bgExtractor.extract(binaryTrainTrees);
      }
      bg = (BinaryGrammar) bgug.second;
      bg.splitRules();
      ug = (UnaryGrammar) bgug.first;
      ug.purgeRules();
      Timing.tick("done.");
    }
    System.err.print("Extracting Lexicon...");
    lex = op.tlpParams.lex(op.lexOptions);
    lex.train(binaryTrainTrees);
    Timing.tick("done.");

    if (op.doDep) {
      System.err.print("Extracting Dependencies...");
      binaryTrainTrees.clear();
      // dgBLIPP = (DependencyGrammar) dgExtractor.extract(new
      // ConcatenationIterator(trainTreebank.iterator(),blippTreebank.iterator()),new
      // TransformTreeDependency(tlpParams,true));

      DependencyGrammar dg1 =
          (DependencyGrammar)
              dgExtractor.extract(
                  trainTreebank.iterator(), new TransformTreeDependency(op.tlpParams, true));
      // dgBLIPP=(DependencyGrammar)dgExtractor.extract(blippTreebank.iterator(),new
      // TransformTreeDependency(tlpParams));

      // dg = (DependencyGrammar) dgExtractor.extract(new
      // ConcatenationIterator(trainTreebank.iterator(),blippTreebank.iterator()),new
      // TransformTreeDependency(tlpParams));
      // dg=new DependencyGrammarCombination(dg1,dgBLIPP,2);
      // dg = (DependencyGrammar) dgExtractor.extract(binaryTrainTrees); //uses information whether
      // the words are known or not, discards unknown words
      Timing.tick("done.");
      // System.out.print("Extracting Unknown Word Model...");
      // UnknownWordModel uwm = (UnknownWordModel)uwmExtractor.extract(binaryTrainTrees);
      // Timing.tick("done.");
      System.out.print("Tuning Dependency Model...");
      dg.tune(binaryTestTrees);
      // System.out.println("TUNE DEPS: "+tuneDeps);
      Timing.tick("done.");
    }

    BinaryGrammar boundBG = bg;
    UnaryGrammar boundUG = ug;

    GrammarProjection gp = new NullGrammarProjection(bg, ug);

    // serialization
    if (serializeFile != null) {
      System.err.print("Serializing parser...");
      LexicalizedParser.saveParserDataToSerialized(
          new ParserData(lex, bg, ug, dg, Numberer.getNumberers(), op), serializeFile);
      Timing.tick("done.");
    }

    // test: pcfg-parse and output

    ExhaustivePCFGParser parser = null;
    if (op.doPCFG) {
      parser = new ExhaustivePCFGParser(boundBG, boundUG, lex, op);
    }

    ExhaustiveDependencyParser dparser =
        ((op.doDep && !Test.useFastFactored) ? new ExhaustiveDependencyParser(dg, lex, op) : null);

    Scorer scorer = (op.doPCFG ? new TwinScorer(new ProjectionScorer(parser, gp), dparser) : null);
    // Scorer scorer = parser;
    BiLexPCFGParser bparser = null;
    if (op.doPCFG && op.doDep) {
      bparser =
          (Test.useN5)
              ? new BiLexPCFGParser.N5BiLexPCFGParser(
                  scorer, parser, dparser, bg, ug, dg, lex, op, gp)
              : new BiLexPCFGParser(scorer, parser, dparser, bg, ug, dg, lex, op, gp);
    }

    LabeledConstituentEval pcfgPE = new LabeledConstituentEval("pcfg  PE", true, tlp);
    LabeledConstituentEval comboPE = new LabeledConstituentEval("combo PE", true, tlp);
    AbstractEval pcfgCB = new LabeledConstituentEval.CBEval("pcfg  CB", true, tlp);

    AbstractEval pcfgTE = new AbstractEval.TaggingEval("pcfg  TE");
    AbstractEval comboTE = new AbstractEval.TaggingEval("combo TE");
    AbstractEval pcfgTEnoPunct = new AbstractEval.TaggingEval("pcfg nopunct TE");
    AbstractEval comboTEnoPunct = new AbstractEval.TaggingEval("combo nopunct TE");
    AbstractEval depTE = new AbstractEval.TaggingEval("depnd TE");

    AbstractEval depDE =
        new AbstractEval.DependencyEval("depnd DE", true, tlp.punctuationWordAcceptFilter());
    AbstractEval comboDE =
        new AbstractEval.DependencyEval("combo DE", true, tlp.punctuationWordAcceptFilter());

    if (Test.evalb) {
      EvalB.initEVALBfiles(op.tlpParams);
    }

    // int[] countByLength = new int[Test.maxLength+1];

    // use a reflection ruse, so one can run this without needing the tagger
    // edu.stanford.nlp.process.SentenceTagger tagger = (Test.preTag ? new
    // edu.stanford.nlp.process.SentenceTagger("/u/nlp/data/tagger.params/wsj0-21.holder") : null);
    SentenceProcessor tagger = null;
    if (Test.preTag) {
      try {
        Class[] argsClass = new Class[] {String.class};
        Object[] arguments =
            new Object[] {"/u/nlp/data/pos-tagger/wsj3t0-18-bidirectional/train-wsj-0-18.holder"};
        tagger =
            (SentenceProcessor)
                Class.forName("edu.stanford.nlp.tagger.maxent.MaxentTagger")
                    .getConstructor(argsClass)
                    .newInstance(arguments);
      } catch (Exception e) {
        System.err.println(e);
        System.err.println("Warning: No pretagging of sentences will be done.");
      }
    }

    for (int tNum = 0, ttSize = testTreebank.size(); tNum < ttSize; tNum++) {
      Tree tree = testTreebank.get(tNum);
      int testTreeLen = tree.yield().size();
      if (testTreeLen > Test.maxLength) {
        continue;
      }
      Tree binaryTree = binaryTestTrees.get(tNum);
      // countByLength[testTreeLen]++;
      System.out.println("-------------------------------------");
      System.out.println("Number: " + (tNum + 1));
      System.out.println("Length: " + testTreeLen);

      // tree.pennPrint(pw);
      // System.out.println("XXXX The binary tree is");
      // binaryTree.pennPrint(pw);
      // System.out.println("Here are the tags in the lexicon:");
      // System.out.println(lex.showTags());
      // System.out.println("Here's the tagnumberer:");
      // System.out.println(Numberer.getGlobalNumberer("tags").toString());

      long timeMil1 = System.currentTimeMillis();
      Timing.tick("Starting parse.");
      if (op.doPCFG) {
        // System.err.println(Test.forceTags);
        if (Test.forceTags) {
          if (tagger != null) {
            // System.out.println("Using a tagger to set tags");
            // System.out.println("Tagged sentence as: " +
            // tagger.processSentence(cutLast(wordify(binaryTree.yield()))).toString(false));
            parser.parse(addLast(tagger.processSentence(cutLast(wordify(binaryTree.yield())))));
          } else {
            // System.out.println("Forcing tags to match input.");
            parser.parse(cleanTags(binaryTree.taggedYield(), tlp));
          }
        } else {
          // System.out.println("XXXX Parsing " + binaryTree.yield());
          parser.parse(binaryTree.yield());
        }
        // Timing.tick("Done with pcfg phase.");
      }
      if (op.doDep) {
        dparser.parse(binaryTree.yield());
        // Timing.tick("Done with dependency phase.");
      }
      boolean bothPassed = false;
      if (op.doPCFG && op.doDep) {
        bothPassed = bparser.parse(binaryTree.yield());
        // Timing.tick("Done with combination phase.");
      }
      long timeMil2 = System.currentTimeMillis();
      long elapsed = timeMil2 - timeMil1;
      System.err.println("Time: " + ((int) (elapsed / 100)) / 10.00 + " sec.");
      // System.out.println("PCFG Best Parse:");
      Tree tree2b = null;
      Tree tree2 = null;
      // System.out.println("Got full best parse...");
      if (op.doPCFG) {
        tree2b = parser.getBestParse();
        tree2 = debinarizer.transformTree(tree2b);
      }
      // System.out.println("Debinarized parse...");
      // tree2.pennPrint();
      // System.out.println("DepG Best Parse:");
      Tree tree3 = null;
      Tree tree3db = null;
      if (op.doDep) {
        tree3 = dparser.getBestParse();
        // was: but wrong Tree tree3db = debinarizer.transformTree(tree2);
        tree3db = debinarizer.transformTree(tree3);
        tree3.pennPrint(pw);
      }
      // tree.pennPrint();
      // ((Tree)binaryTrainTrees.get(tNum)).pennPrint();
      // System.out.println("Combo Best Parse:");
      Tree tree4 = null;
      if (op.doPCFG && op.doDep) {
        try {
          tree4 = bparser.getBestParse();
          if (tree4 == null) {
            tree4 = tree2b;
          }
        } catch (NullPointerException e) {
          System.err.println("Blocked, using PCFG parse!");
          tree4 = tree2b;
        }
      }
      if (op.doPCFG && !bothPassed) {
        tree4 = tree2b;
      }
      // tree4.pennPrint();
      if (op.doDep) {
        depDE.evaluate(tree3, binaryTree, pw);
        depTE.evaluate(tree3db, tree, pw);
      }
      TreeTransformer tc = op.tlpParams.collinizer();
      TreeTransformer tcEvalb = op.tlpParams.collinizerEvalb();
      Tree tree4b = null;
      if (op.doPCFG) {
        // System.out.println("XXXX Best PCFG was: ");
        // tree2.pennPrint();
        // System.out.println("XXXX Transformed best PCFG is: ");
        // tc.transformTree(tree2).pennPrint();
        // System.out.println("True Best Parse:");
        // tree.pennPrint();
        // tc.transformTree(tree).pennPrint();
        pcfgPE.evaluate(tc.transformTree(tree2), tc.transformTree(tree), pw);
        pcfgCB.evaluate(tc.transformTree(tree2), tc.transformTree(tree), pw);
        if (op.doDep) {
          comboDE.evaluate((bothPassed ? tree4 : tree3), binaryTree, pw);
          tree4b = tree4;
          tree4 = debinarizer.transformTree(tree4);
          if (op.nodePrune) {
            NodePruner np = new NodePruner(parser, debinarizer);
            tree4 = np.prune(tree4);
          }
          // tree4.pennPrint();
          comboPE.evaluate(tc.transformTree(tree4), tc.transformTree(tree), pw);
        }
        // pcfgTE.evaluate(tree2, tree);
        pcfgTE.evaluate(tcEvalb.transformTree(tree2), tcEvalb.transformTree(tree), pw);
        pcfgTEnoPunct.evaluate(tc.transformTree(tree2), tc.transformTree(tree), pw);

        if (op.doDep) {
          comboTE.evaluate(tcEvalb.transformTree(tree4), tcEvalb.transformTree(tree), pw);
          comboTEnoPunct.evaluate(tc.transformTree(tree4), tc.transformTree(tree), pw);
        }
        System.out.println("PCFG only: " + parser.scoreBinarizedTree(tree2b, 0));

        // tc.transformTree(tree2).pennPrint();
        tree2.pennPrint(pw);

        if (op.doDep) {
          System.out.println("Combo: " + parser.scoreBinarizedTree(tree4b, 0));
          // tc.transformTree(tree4).pennPrint(pw);
          tree4.pennPrint(pw);
        }
        System.out.println("Correct:" + parser.scoreBinarizedTree(binaryTree, 0));
        /*
        if (parser.scoreBinarizedTree(tree2b,true) < parser.scoreBinarizedTree(binaryTree,true)) {
          System.out.println("SCORE INVERSION");
          parser.validateBinarizedTree(binaryTree,0);
        }
        */
        tree.pennPrint(pw);
      } // end if doPCFG

      if (Test.evalb) {
        if (op.doPCFG && op.doDep) {
          EvalB.writeEVALBline(tcEvalb.transformTree(tree), tcEvalb.transformTree(tree4));
        } else if (op.doPCFG) {
          EvalB.writeEVALBline(tcEvalb.transformTree(tree), tcEvalb.transformTree(tree2));
        } else if (op.doDep) {
          EvalB.writeEVALBline(tcEvalb.transformTree(tree), tcEvalb.transformTree(tree3db));
        }
      }
    } // end for each tree in test treebank

    if (Test.evalb) {
      EvalB.closeEVALBfiles();
    }

    // Test.display();
    if (op.doPCFG) {
      pcfgPE.display(false, pw);
      System.out.println("Grammar size: " + Numberer.getGlobalNumberer("states").total());
      pcfgCB.display(false, pw);
      if (op.doDep) {
        comboPE.display(false, pw);
      }
      pcfgTE.display(false, pw);
      pcfgTEnoPunct.display(false, pw);
      if (op.doDep) {
        comboTE.display(false, pw);
        comboTEnoPunct.display(false, pw);
      }
    }
    if (op.doDep) {
      depTE.display(false, pw);
      depDE.display(false, pw);
    }
    if (op.doPCFG && op.doDep) {
      comboDE.display(false, pw);
    }
    // pcfgPE.printGoodBad();
  }
  // CDM 2007: I wonder what this does differently from segmentWordsWithMarkov???
  private ArrayList<TaggedWord> basicSegmentWords(String s) {
    int length = s.length();
    //    Set<String> POSes = (Set<String>) POSDistribution.keySet();  // 1.5
    // best score of span
    double[][] scores = new double[length][length + 1];
    // best (last index of) first word for this span
    int[][] splitBacktrace = new int[length][length + 1];
    // best tag for word over this span
    int[][] POSbacktrace = new int[length][length + 1];
    for (int i = 0; i < length; i++) {
      Arrays.fill(scores[i], Double.NEGATIVE_INFINITY);
    }
    // first fill in word probabilities
    for (int diff = 1; diff <= 10; diff++) {
      for (int start = 0; start + diff <= length; start++) {
        int end = start + diff;
        StringBuilder wordBuf = new StringBuilder();
        for (int pos = start; pos < end; pos++) {
          wordBuf.append(s.charAt(pos));
        }
        String word = wordBuf.toString();
        //        for (String tag : POSes) {  // 1.5
        for (Iterator<String> iter = POSes.iterator(); iter.hasNext(); ) {
          String tag = iter.next();
          IntTaggedWord itw = new IntTaggedWord(word, tag, wordIndex, tagIndex);
          double newScore =
              lex.score(itw, 0, word, null) + Math.log(lex.getPOSDistribution().probabilityOf(tag));
          if (newScore > scores[start][end]) {
            scores[start][end] = newScore;
            splitBacktrace[start][end] = end;
            POSbacktrace[start][end] = itw.tag();
          }
        }
      }
    }
    // now fill in word combination probabilities
    for (int diff = 2; diff <= length; diff++) {
      for (int start = 0; start + diff <= length; start++) {
        int end = start + diff;
        for (int split = start + 1; split < end && split - start <= 10; split++) {
          if (splitBacktrace[start][split] != split) {
            continue; // only consider words on left
          }
          double newScore = scores[start][split] + scores[split][end];
          if (newScore > scores[start][end]) {
            scores[start][end] = newScore;
            splitBacktrace[start][end] = split;
          }
        }
      }
    }

    List<TaggedWord> words = new ArrayList<TaggedWord>();
    int start = 0;
    while (start < length) {
      int end = splitBacktrace[start][length];
      StringBuilder wordBuf = new StringBuilder();
      for (int pos = start; pos < end; pos++) {
        wordBuf.append(s.charAt(pos));
      }
      String word = wordBuf.toString();
      String tag = tagIndex.get(POSbacktrace[start][end]);

      words.add(new TaggedWord(word, tag));
      start = end;
    }

    return new ArrayList<TaggedWord>(words);
  }