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

1 files changed, 0 insertions, 543 deletions

diff --git a/gi/pf/brat.cc b/gi/pf/brat.cc
deleted file mode 100644
index 832f22cf..00000000
--- a/gi/pf/brat.cc
+++ /dev/null
@@ -1,543 +0,0 @@
-#include <iostream>
-#include <tr1/memory>
-#include <queue>
-
-#include <boost/functional.hpp>
-#include <boost/multi_array.hpp>
-#include <boost/program_options.hpp>
-#include <boost/program_options/variables_map.hpp>
-
-#include "viterbi.h"
-#include "hg.h"
-#include "trule.h"
-#include "tdict.h"
-#include "filelib.h"
-#include "dict.h"
-#include "sampler.h"
-#include "ccrp_nt.h"
-#include "cfg_wfst_composer.h"
-
-using namespace std;
-using namespace tr1;
-namespace po = boost::program_options;
-
-static unsigned kMAX_SRC_PHRASE;
-static unsigned kMAX_TRG_PHRASE;
-struct FSTState;
-
-double log_poisson(unsigned x, const double& lambda) {
-  assert(lambda > 0.0);
-  return log(lambda) * x - lgamma(x + 1) - lambda;
-}
-
-struct ConditionalBase {
-  explicit ConditionalBase(const double m1mixture, const unsigned vocab_e_size, const string& model1fname) :
-      kM1MIXTURE(m1mixture),
-      kUNIFORM_MIXTURE(1.0 - m1mixture),
-      kUNIFORM_TARGET(1.0 / vocab_e_size),
-      kNULL(TD::Convert("<eps>")) {
-    assert(m1mixture >= 0.0 && m1mixture <= 1.0);
-    assert(vocab_e_size > 0);
-    LoadModel1(model1fname);
-  }
-
-  void LoadModel1(const string& fname) {
-    cerr << "Loading Model 1 parameters from " << fname << " ..." << endl;
-    ReadFile rf(fname);
-    istream& in = *rf.stream();
-    string line;
-    unsigned lc = 0;
-    while(getline(in, line)) {
-      ++lc;
-      int cur = 0;
-      int start = 0;
-      while(cur < line.size() && line[cur] != ' ') { ++cur; }
-      assert(cur != line.size());
-      line[cur] = 0;
-      const WordID src = TD::Convert(&line[0]);
-      ++cur;
-      start = cur;
-      while(cur < line.size() && line[cur] != ' ') { ++cur; }
-      assert(cur != line.size());
-      line[cur] = 0;
-      WordID trg = TD::Convert(&line[start]);
-      const double logprob = strtod(&line[cur + 1], NULL);
-      if (src >= ttable.size()) ttable.resize(src + 1);
-      ttable[src][trg].logeq(logprob);
-    }
-    cerr << "  read " << lc << " parameters.\n";
-  }
-
-  // return logp0 of rule.e_ | rule.f_
-  prob_t operator()(const TRule& rule) const {
-    const int flen = rule.f_.size();
-    const int elen = rule.e_.size();
-    prob_t uniform_src_alignment; uniform_src_alignment.logeq(-log(flen + 1));
-    prob_t p;
-    p.logeq(log_poisson(elen, flen + 0.01));       // elen | flen          ~Pois(flen + 0.01)
-    for (int i = 0; i < elen; ++i) {               // for each position i in e-RHS
-      const WordID trg = rule.e_[i];
-      prob_t tp = prob_t::Zero();
-      for (int j = -1; j < flen; ++j) {
-        const WordID src = j < 0 ? kNULL : rule.f_[j];
-        const map<WordID, prob_t>::const_iterator it = ttable[src].find(trg);
-        if (it != ttable[src].end()) {
-          tp += kM1MIXTURE * it->second;
-        }
-        tp += kUNIFORM_MIXTURE * kUNIFORM_TARGET;
-      }
-      tp *= uniform_src_alignment;                 //     draw a_i         ~uniform
-      p *= tp;                                     //     draw e_i         ~Model1(f_a_i) / uniform
-    }
-    return p;
-  }
-
-  const prob_t kM1MIXTURE;  // Model 1 mixture component
-  const prob_t kUNIFORM_MIXTURE; // uniform mixture component
-  const prob_t kUNIFORM_TARGET;
-  const WordID kNULL;
-  vector<map<WordID, prob_t> > ttable;
-};
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  opts.add_options()
-        ("samples,s",po::value<unsigned>()->default_value(1000),"Number of samples")
-        ("input,i",po::value<string>(),"Read parallel data from")
-        ("max_src_phrase",po::value<unsigned>()->default_value(3),"Maximum length of source language phrases")
-        ("max_trg_phrase",po::value<unsigned>()->default_value(3),"Maximum length of target language phrases")
-        ("model1,m",po::value<string>(),"Model 1 parameters (used in base distribution)")
-        ("model1_interpolation_weight",po::value<double>()->default_value(0.95),"Mixing proportion of model 1 with uniform target distribution")
-        ("random_seed,S",po::value<uint32_t>(), "Random seed");
-  po::options_description clo("Command line options");
-  clo.add_options()
-        ("config", po::value<string>(), "Configuration file")
-        ("help,h", "Print this help message and exit");
-  po::options_description dconfig_options, dcmdline_options;
-  dconfig_options.add(opts);
-  dcmdline_options.add(opts).add(clo);
-  
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  if (conf->count("config")) {
-    ifstream config((*conf)["config"].as<string>().c_str());
-    po::store(po::parse_config_file(config, dconfig_options), *conf);
-  }
-  po::notify(*conf);
-
-  if (conf->count("help") || (conf->count("input") == 0)) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-}
-
-void ReadParallelCorpus(const string& filename,
-                vector<vector<WordID> >* f,
-                vector<vector<int> >* e,
-                set<int>* vocab_f,
-                set<int>* vocab_e) {
-  f->clear();
-  e->clear();
-  vocab_f->clear();
-  vocab_e->clear();
-  istream* in;
-  if (filename == "-")
-    in = &cin;
-  else
-    in = new ifstream(filename.c_str());
-  assert(*in);
-  string line;
-  const WordID kDIV = TD::Convert("|||");
-  vector<WordID> tmp;
-  while(*in) {
-    getline(*in, line);
-    if (line.empty() && !*in) break;
-    e->push_back(vector<int>());
-    f->push_back(vector<int>());
-    vector<int>& le = e->back();
-    vector<int>& lf = f->back();
-    tmp.clear();
-    TD::ConvertSentence(line, &tmp);
-    bool isf = true;
-    for (unsigned i = 0; i < tmp.size(); ++i) {
-      const int cur = tmp[i];
-      if (isf) {
-        if (kDIV == cur) { isf = false; } else {
-          lf.push_back(cur);
-          vocab_f->insert(cur);
-        }
-      } else {
-        assert(cur != kDIV);
-        le.push_back(cur);
-        vocab_e->insert(cur);
-      }
-    }
-    assert(isf == false);
-  }
-  if (in != &cin) delete in;
-}
-
-struct UniphraseLM {
-  UniphraseLM(const vector<vector<int> >& corpus,
-              const set<int>& vocab,
-              const po::variables_map& conf) :
-    phrases_(1,1),
-    gen_(1,1),
-    corpus_(corpus),
-    uniform_word_(1.0 / vocab.size()),
-    gen_p0_(0.5),
-    p_end_(0.5),
-    use_poisson_(conf.count("poisson_length") > 0) {}
-
-  void ResampleHyperparameters(MT19937* rng) {
-    phrases_.resample_hyperparameters(rng);
-    gen_.resample_hyperparameters(rng);
-    cerr << " " << phrases_.alpha();
-  }
-
-  CCRP_NoTable<vector<int> > phrases_;
-  CCRP_NoTable<bool> gen_;
-  vector<vector<bool> > z_;   // z_[i] is there a phrase boundary after the ith word
-  const vector<vector<int> >& corpus_;
-  const double uniform_word_;
-  const double gen_p0_;
-  const double p_end_; // in base length distribution, p of the end of a phrase
-  const bool use_poisson_;
-};
-
-struct Reachability {
-  boost::multi_array<bool, 4> edges;  // edges[src_covered][trg_covered][x][trg_delta] is this edge worth exploring?
-  boost::multi_array<short, 2> max_src_delta; // msd[src_covered][trg_covered] -- the largest src delta that's valid
-
-  Reachability(int srclen, int trglen, int src_max_phrase_len, int trg_max_phrase_len) :
-      edges(boost::extents[srclen][trglen][src_max_phrase_len+1][trg_max_phrase_len+1]),
-      max_src_delta(boost::extents[srclen][trglen]) {
-    ComputeReachability(srclen, trglen, src_max_phrase_len, trg_max_phrase_len);
-  }
-
- private:
-  struct SState {
-    SState() : prev_src_covered(), prev_trg_covered() {}
-    SState(int i, int j) : prev_src_covered(i), prev_trg_covered(j) {}
-    int prev_src_covered;
-    int prev_trg_covered;
-  };
-
-  struct NState {
-    NState() : next_src_covered(), next_trg_covered() {}
-    NState(int i, int j) : next_src_covered(i), next_trg_covered(j) {}
-    int next_src_covered;
-    int next_trg_covered;
-  };
-
-  void ComputeReachability(int srclen, int trglen, int src_max_phrase_len, int trg_max_phrase_len) {
-    typedef boost::multi_array<vector<SState>, 2> array_type;
-    array_type a(boost::extents[srclen + 1][trglen + 1]);
-    a[0][0].push_back(SState());
-    for (int i = 0; i < srclen; ++i) {
-      for (int j = 0; j < trglen; ++j) {
-        if (a[i][j].size() == 0) continue;
-        const SState prev(i,j);
-        for (int k = 1; k <= src_max_phrase_len; ++k) {
-          if ((i + k) > srclen) continue;
-          for (int l = 1; l <= trg_max_phrase_len; ++l) {
-            if ((j + l) > trglen) continue;
-            a[i + k][j + l].push_back(prev);
-          }
-        }
-      }
-    }
-    a[0][0].clear();
-    cerr << "Final cell contains " << a[srclen][trglen].size() << " back pointers\n";
-    assert(a[srclen][trglen].size() > 0);
-
-    typedef boost::multi_array<bool, 2> rarray_type;
-    rarray_type r(boost::extents[srclen + 1][trglen + 1]);
-//    typedef boost::multi_array<vector<NState>, 2> narray_type;
-//    narray_type b(boost::extents[srclen + 1][trglen + 1]);
-    r[srclen][trglen] = true;
-    for (int i = srclen; i >= 0; --i) {
-      for (int j = trglen; j >= 0; --j) {
-        vector<SState>& prevs = a[i][j];
-        if (!r[i][j]) { prevs.clear(); }
-//        const NState nstate(i,j);
-        for (int k = 0; k < prevs.size(); ++k) {
-          r[prevs[k].prev_src_covered][prevs[k].prev_trg_covered] = true;
-          int src_delta = i - prevs[k].prev_src_covered;
-          edges[prevs[k].prev_src_covered][prevs[k].prev_trg_covered][src_delta][j - prevs[k].prev_trg_covered] = true;
-          short &msd = max_src_delta[prevs[k].prev_src_covered][prevs[k].prev_trg_covered];
-          if (src_delta > msd) msd = src_delta;
-//          b[prevs[k].prev_src_covered][prevs[k].prev_trg_covered].push_back(nstate);
-        }
-      }
-    }
-    assert(!edges[0][0][1][0]);
-    assert(!edges[0][0][0][1]);
-    assert(!edges[0][0][0][0]);
-    cerr << "  MAX SRC DELTA[0][0] = " << max_src_delta[0][0] << endl;
-    assert(max_src_delta[0][0] > 0);
-    //cerr << "First cell contains " << b[0][0].size() << " forward pointers\n";
-    //for (int i = 0; i < b[0][0].size(); ++i) {
-    //  cerr << "  -> (" << b[0][0][i].next_src_covered << "," << b[0][0][i].next_trg_covered << ")\n";
-    //}
-  }
-};
-
-ostream& operator<<(ostream& os, const FSTState& q);
-struct FSTState {
-  explicit FSTState(int src_size) :
-      trg_covered_(),
-      src_covered_(),
-      src_coverage_(src_size) {}
-
-  FSTState(short trg_covered, short src_covered, const vector<bool>& src_coverage, const vector<short>& src_prefix) :
-      trg_covered_(trg_covered),
-      src_covered_(src_covered),
-      src_coverage_(src_coverage),
-      src_prefix_(src_prefix) {
-    if (src_coverage_.size() == src_covered) {
-      assert(src_prefix.size() == 0);
-    }
-  }
-
-  // if we extend by the word at src_position, what are
-  // the next states that are reachable and lie on a valid
-  // path to the final state?
-  vector<FSTState> Extensions(int src_position, int src_len, int trg_len, const Reachability& r) const {
-    assert(src_position < src_coverage_.size());
-    if (src_coverage_[src_position]) {
-      cerr << "Trying to extend " << *this << " with position " << src_position << endl;
-      abort();
-    }
-    vector<bool> ncvg = src_coverage_;
-    ncvg[src_position] = true;
-
-    vector<FSTState> res;
-    const int trg_remaining = trg_len - trg_covered_;
-    if (trg_remaining <= 0) {
-      cerr << "Target appears to have been covered: " << *this << " (trg_len=" << trg_len << ",trg_covered=" << trg_covered_ << ")" << endl;
-      abort();
-    }
-    const int src_remaining = src_len - src_covered_;
-    if (src_remaining <= 0) {
-      cerr << "Source appears to have been covered: " << *this << endl;
-      abort();
-    }
-
-    for (int tc = 1; tc <= kMAX_TRG_PHRASE; ++tc) {
-      if (r.edges[src_covered_][trg_covered_][src_prefix_.size() + 1][tc]) {
-        int nc = src_prefix_.size() + 1 + src_covered_;
-        res.push_back(FSTState(trg_covered_ + tc, nc, ncvg, vector<short>()));
-      }
-    }
-
-    if ((src_prefix_.size() + 1) < r.max_src_delta[src_covered_][trg_covered_]) {
-      vector<short> nsp = src_prefix_;
-      nsp.push_back(src_position);
-      res.push_back(FSTState(trg_covered_, src_covered_, ncvg, nsp));
-    }
-
-    if (res.size() == 0) {
-      cerr << *this << " can't be extended!\n";
-      abort();
-    }
-    return res;
-  }
-
-  short trg_covered_, src_covered_;
-  vector<bool> src_coverage_;
-  vector<short> src_prefix_;
-};
-bool operator<(const FSTState& q, const FSTState& r) {
-  if (q.trg_covered_ != r.trg_covered_) return q.trg_covered_ < r.trg_covered_;
-  if (q.src_covered_!= r.src_covered_) return q.src_covered_ < r.src_covered_;
-  if (q.src_coverage_ != r.src_coverage_) return q.src_coverage_ < r.src_coverage_;
-  return q.src_prefix_ < r.src_prefix_;
-}
-
-ostream& operator<<(ostream& os, const FSTState& q) {
-  os << "[" << q.trg_covered_ << " : ";
-  for (int i = 0; i < q.src_coverage_.size(); ++i)
-    os << q.src_coverage_[i];
-  os << " : <";
-  for (int i = 0; i < q.src_prefix_.size(); ++i) {
-    if (i != 0) os << ' ';
-    os << q.src_prefix_[i];
-  }
-  return os << ">]";
-}
-
-struct MyModel {
-  MyModel(ConditionalBase& rcp0) : rp0(rcp0) {}
-  typedef unordered_map<vector<WordID>, CCRP_NoTable<TRule>, boost::hash<vector<WordID> > > SrcToRuleCRPMap;
-
-  void DecrementRule(const TRule& rule) {
-    SrcToRuleCRPMap::iterator it = rules.find(rule.f_);
-    assert(it != rules.end());
-    it->second.decrement(rule);
-    if (it->second.num_customers() == 0) rules.erase(it);
-  }
-
-  void IncrementRule(const TRule& rule) {
-    SrcToRuleCRPMap::iterator it = rules.find(rule.f_);
-    if (it == rules.end()) {
-      CCRP_NoTable<TRule> crp(1,1);
-      it = rules.insert(make_pair(rule.f_, crp)).first;
-    }
-    it->second.increment(rule);
-  }
-
-  // conditioned on rule.f_
-  prob_t RuleConditionalProbability(const TRule& rule) const {
-    const prob_t base = rp0(rule);
-    SrcToRuleCRPMap::const_iterator it = rules.find(rule.f_);
-    if (it == rules.end()) {
-      return base;
-    } else {
-      const double lp = it->second.logprob(rule, log(base));
-      prob_t q; q.logeq(lp);
-      return q;
-    }
-  }
-
-  const ConditionalBase& rp0;
-  SrcToRuleCRPMap rules;
-};
-
-struct MyFST : public WFST {
-  MyFST(const vector<WordID>& ssrc, const vector<WordID>& strg, MyModel* m) :
-      src(ssrc), trg(strg),
-      r(src.size(),trg.size(),kMAX_SRC_PHRASE, kMAX_TRG_PHRASE),
-      model(m) {
-    FSTState in(src.size());
-    cerr << " INIT: " << in << endl;
-    init = GetNode(in);
-    for (int i = 0; i < in.src_coverage_.size(); ++i) in.src_coverage_[i] = true;
-    in.src_covered_ = src.size();
-    in.trg_covered_ = trg.size();
-    cerr << "FINAL: " << in << endl;
-    final = GetNode(in);
-  }
-  virtual const WFSTNode* Final() const;
-  virtual const WFSTNode* Initial() const;
-
-  const WFSTNode* GetNode(const FSTState& q);
-  map<FSTState, boost::shared_ptr<WFSTNode> > m;
-  const vector<WordID>& src;
-  const vector<WordID>& trg;
-  Reachability r;
-  const WFSTNode* init;
-  const WFSTNode* final;
-  MyModel* model;
-};
-
-struct MyNode : public WFSTNode {
-  MyNode(const FSTState& q, MyFST* fst) : state(q), container(fst) {}
-  virtual vector<pair<const WFSTNode*, TRulePtr> > ExtendInput(unsigned srcindex) const;
-  const FSTState state;
-  mutable MyFST* container;
-};
-
-vector<pair<const WFSTNode*, TRulePtr> > MyNode::ExtendInput(unsigned srcindex) const {
-  cerr << "EXTEND " << state << " with " << srcindex << endl;
-  vector<FSTState> ext = state.Extensions(srcindex, container->src.size(), container->trg.size(), container->r);
-  vector<pair<const WFSTNode*,TRulePtr> > res(ext.size());
-  for (unsigned i = 0; i < ext.size(); ++i) {
-    res[i].first = container->GetNode(ext[i]);
-    if (ext[i].src_prefix_.size() == 0) {
-      const unsigned trg_from = state.trg_covered_;
-      const unsigned trg_to = ext[i].trg_covered_;
-      const unsigned prev_prfx_size = state.src_prefix_.size();
-      res[i].second.reset(new TRule);
-      res[i].second->lhs_ = -TD::Convert("X");
-      vector<WordID>& src = res[i].second->f_;
-      vector<WordID>& trg = res[i].second->e_;
-      src.resize(prev_prfx_size + 1);
-      for (unsigned j = 0; j < prev_prfx_size; ++j)
-        src[j] = container->src[state.src_prefix_[j]];
-      src[prev_prfx_size] = container->src[srcindex];
-      for (unsigned j = trg_from; j < trg_to; ++j)
-        trg.push_back(container->trg[j]);
-      res[i].second->scores_.set_value(FD::Convert("Proposal"), log(container->model->RuleConditionalProbability(*res[i].second)));
-    }
-  }
-  return res;
-}
-
-const WFSTNode* MyFST::GetNode(const FSTState& q) {
-  boost::shared_ptr<WFSTNode>& res = m[q];
-  if (!res) {
-    res.reset(new MyNode(q, this));
-  }
-  return &*res;
-}
-
-const WFSTNode* MyFST::Final() const {
-  return final;
-}
-
-const WFSTNode* MyFST::Initial() const {
-  return init;
-}
-
-int main(int argc, char** argv) {
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  kMAX_TRG_PHRASE = conf["max_trg_phrase"].as<unsigned>();
-  kMAX_SRC_PHRASE = conf["max_src_phrase"].as<unsigned>();
-
-  if (!conf.count("model1")) {
-    cerr << argv[0] << "Please use --model1 to specify model 1 parameters\n";
-    return 1;
-  }
-  boost::shared_ptr<MT19937> prng;
-  if (conf.count("random_seed"))
-    prng.reset(new MT19937(conf["random_seed"].as<uint32_t>()));
-  else
-    prng.reset(new MT19937);
-  MT19937& rng = *prng;
-
-  vector<vector<int> > corpuse, corpusf;
-  set<int> vocabe, vocabf;
-  ReadParallelCorpus(conf["input"].as<string>(), &corpusf, &corpuse, &vocabf, &vocabe);
-  cerr << "f-Corpus size: " << corpusf.size() << " sentences\n";
-  cerr << "f-Vocabulary size: " << vocabf.size() << " types\n";
-  cerr << "f-Corpus size: " << corpuse.size() << " sentences\n";
-  cerr << "f-Vocabulary size: " << vocabe.size() << " types\n";
-  assert(corpusf.size() == corpuse.size());
-
-  ConditionalBase lp0(conf["model1_interpolation_weight"].as<double>(),
-                      vocabe.size(),
-                      conf["model1"].as<string>());
-  MyModel m(lp0);
-
-  TRule x("[X] ||| kAnwntR myN ||| at the convent ||| 0");
-  m.IncrementRule(x);
-  TRule y("[X] ||| nY dyN ||| gave ||| 0");
-  m.IncrementRule(y);
-
-
-  MyFST fst(corpusf[0], corpuse[0], &m);
-  ifstream in("./kimura.g");
-  assert(in);
-  CFG_WFSTComposer comp(fst);
-  Hypergraph hg;
-  bool succeed = comp.Compose(&in, &hg);
-  hg.PrintGraphviz();
-  if (succeed) { cerr << "SUCCESS.\n"; } else { cerr << "FAILURE REPORTED.\n"; }
-
-#if 0
-  ifstream in2("./amnabooks.g");
-  assert(in2);
-  MyFST fst2(corpusf[1], corpuse[1], &m);
-  CFG_WFSTComposer comp2(fst2);
-  Hypergraph hg2;
-  bool succeed2 = comp2.Compose(&in2, &hg2);
-  if (succeed2) { cerr << "SUCCESS.\n"; } else { cerr << "FAILURE REPORTED.\n"; }
-#endif
-
-  SparseVector<double> w; w.set_value(FD::Convert("Proposal"), 1.0);
-  hg.Reweight(w);
-  cerr << ViterbiFTree(hg) << endl;
-  return 0;
-}
-