Merge pull request #27 from pks/master

Tidying (soft) syntax features; loo for C++ extractor; updates for dtrain 

13 files changed, 189 insertions, 26 deletions

diff --git a/extractor/grammar_extractor.cc b/extractor/grammar_extractor.cc
index 8050ce7b..1fbdee5b 100644
--- a/extractor/grammar_extractor.cc
+++ b/extractor/grammar_extractor.cc
@@ -3,11 +3,13 @@
 #include <iterator>
 #include <sstream>
 #include <vector>
+#include <unordered_set>
 
 #include "grammar.h"
 #include "rule.h"
 #include "rule_factory.h"
 #include "vocabulary.h"
+#include "data_array.h"
 
 using namespace std;
 
@@ -32,10 +34,10 @@ GrammarExtractor::GrammarExtractor(
     vocabulary(vocabulary),
     rule_factory(rule_factory) {}
 
-Grammar GrammarExtractor::GetGrammar(const string& sentence) {
+Grammar GrammarExtractor::GetGrammar(const string& sentence, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) {
   vector<string> words = TokenizeSentence(sentence);
   vector<int> word_ids = AnnotateWords(words);
-  return rule_factory->GetGrammar(word_ids);
+  return rule_factory->GetGrammar(word_ids, blacklisted_sentence_ids, source_data_array);
 }
 
 vector<string> GrammarExtractor::TokenizeSentence(const string& sentence) {
diff --git a/extractor/grammar_extractor.h b/extractor/grammar_extractor.h
index b36ceeb9..6c0aafbf 100644
--- a/extractor/grammar_extractor.h
+++ b/extractor/grammar_extractor.h
@@ -4,6 +4,7 @@
 #include <memory>
 #include <string>
 #include <vector>
+#include <unordered_set>
 
 using namespace std;
 
@@ -44,7 +45,7 @@ class GrammarExtractor {
 
   // Converts the sentence to a vector of word ids and uses the RuleFactory to
   // extract the SCFG rules which may be used to decode the sentence.
-  Grammar GetGrammar(const string& sentence);
+  Grammar GetGrammar(const string& sentence, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array);
 
  private:
   // Splits the sentence in a vector of words.
diff --git a/extractor/grammar_extractor_test.cc b/extractor/grammar_extractor_test.cc
index 823bb8b4..f32a9599 100644
--- a/extractor/grammar_extractor_test.cc
+++ b/extractor/grammar_extractor_test.cc
@@ -39,12 +39,15 @@ TEST(GrammarExtractorTest, TestAnnotatingWords) {
   vector<Rule> rules;
   vector<string> feature_names;
   Grammar grammar(rules, feature_names);
-  EXPECT_CALL(*factory, GetGrammar(word_ids))
+  unordered_set<int> blacklisted_sentence_ids;
+  shared_ptr<DataArray> source_data_array;
+  EXPECT_CALL(*factory, GetGrammar(word_ids, blacklisted_sentence_ids, source_data_array))
       .WillOnce(Return(grammar));
 
   GrammarExtractor extractor(vocabulary, factory);
   string sentence = "Anna has many many apples .";
-  extractor.GetGrammar(sentence);
+
+  extractor.GetGrammar(sentence, blacklisted_sentence_ids, source_data_array);
 }
 
 } // namespace
diff --git a/extractor/mocks/mock_rule_factory.h b/extractor/mocks/mock_rule_factory.h
index 7389b396..86a084b5 100644
--- a/extractor/mocks/mock_rule_factory.h
+++ b/extractor/mocks/mock_rule_factory.h
@@ -7,7 +7,7 @@ namespace extractor {
 
 class MockHieroCachingRuleFactory : public HieroCachingRuleFactory {
  public:
-  MOCK_METHOD1(GetGrammar, Grammar(const vector<int>& word_ids));
+  MOCK_METHOD3(GetGrammar, Grammar(const vector<int>& word_ids, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array));
 };
 
 } // namespace extractor
diff --git a/extractor/rule_factory.cc b/extractor/rule_factory.cc
index 8c30fb9e..e52019ae 100644
--- a/extractor/rule_factory.cc
+++ b/extractor/rule_factory.cc
@@ -17,6 +17,7 @@
 #include "suffix_array.h"
 #include "time_util.h"
 #include "vocabulary.h"
+#include "data_array.h"
 
 using namespace std;
 using namespace chrono;
@@ -100,7 +101,7 @@ HieroCachingRuleFactory::HieroCachingRuleFactory() {}
 
 HieroCachingRuleFactory::~HieroCachingRuleFactory() {}
 
-Grammar HieroCachingRuleFactory::GetGrammar(const vector<int>& word_ids) {
+Grammar HieroCachingRuleFactory::GetGrammar(const vector<int>& word_ids, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) {
   Clock::time_point start_time = Clock::now();
   double total_extract_time = 0;
   double total_intersect_time = 0;
@@ -192,7 +193,7 @@ Grammar HieroCachingRuleFactory::GetGrammar(const vector<int>& word_ids) {
       Clock::time_point extract_start = Clock::now();
       if (!state.starts_with_x) {
         // Extract rules for the sampled set of occurrences.
-        PhraseLocation sample = sampler->Sample(next_node->matchings);
+        PhraseLocation sample = sampler->Sample(next_node->matchings, blacklisted_sentence_ids, source_data_array);
         vector<Rule> new_rules =
             rule_extractor->ExtractRules(next_phrase, sample);
         rules.insert(rules.end(), new_rules.begin(), new_rules.end());
diff --git a/extractor/rule_factory.h b/extractor/rule_factory.h
index 52e8712a..c7332720 100644
--- a/extractor/rule_factory.h
+++ b/extractor/rule_factory.h
@@ -3,6 +3,7 @@
 
 #include <memory>
 #include <vector>
+#include <unordered_set>
 
 #include "matchings_trie.h"
 
@@ -71,7 +72,7 @@ class HieroCachingRuleFactory {
 
   // Constructs SCFG rules for a given sentence.
   // (See class description for more details.)
-  virtual Grammar GetGrammar(const vector<int>& word_ids);
+  virtual Grammar GetGrammar(const vector<int>& word_ids, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array);
 
  protected:
   HieroCachingRuleFactory();
diff --git a/extractor/rule_factory_test.cc b/extractor/rule_factory_test.cc
index 08af3dcd..f26cc567 100644
--- a/extractor/rule_factory_test.cc
+++ b/extractor/rule_factory_test.cc
@@ -76,7 +76,9 @@ TEST_F(RuleFactoryTest, TestGetGrammarDifferentWords) {
       .WillRepeatedly(Return(PhraseLocation(0, 1)));
 
   vector<int> word_ids = {2, 3, 4};
-  Grammar grammar = factory->GetGrammar(word_ids);
+  unordered_set<int> blacklisted_sentence_ids;
+  shared_ptr<DataArray> source_data_array;
+  Grammar grammar = factory->GetGrammar(word_ids, blacklisted_sentence_ids, source_data_array);
   EXPECT_EQ(feature_names, grammar.GetFeatureNames());
   EXPECT_EQ(7, grammar.GetRules().size());
 }
@@ -94,7 +96,9 @@ TEST_F(RuleFactoryTest, TestGetGrammarRepeatingWords) {
       .WillRepeatedly(Return(PhraseLocation(0, 1)));
 
   vector<int> word_ids = {2, 3, 4, 2, 3};
-  Grammar grammar = factory->GetGrammar(word_ids);
+  unordered_set<int> blacklisted_sentence_ids;
+  shared_ptr<DataArray> source_data_array;
+  Grammar grammar = factory->GetGrammar(word_ids, blacklisted_sentence_ids, source_data_array);
   EXPECT_EQ(feature_names, grammar.GetFeatureNames());
   EXPECT_EQ(28, grammar.GetRules().size());
 }
diff --git a/extractor/run_extractor.cc b/extractor/run_extractor.cc
index 8a9ca89d..6eb55073 100644
--- a/extractor/run_extractor.cc
+++ b/extractor/run_extractor.cc
@@ -75,7 +75,9 @@ int main(int argc, char** argv) {
     ("max_samples", po::value<int>()->default_value(300),
         "Maximum number of samples")
     ("tight_phrases", po::value<bool>()->default_value(true),
-        "False if phrases may be loose (better, but slower)");
+        "False if phrases may be loose (better, but slower)")
+    ("leave_one_out", po::value<bool>()->zero_tokens(),
+        "do leave-one-out estimation of grammars (e.g. for extracting grammars for the training set");
 
   po::variables_map vm;
   po::store(po::parse_command_line(argc, argv, desc), vm);
@@ -96,6 +98,11 @@ int main(int argc, char** argv) {
     return 1;
   }
 
+  bool leave_one_out = false;
+  if (vm.count("leave_one_out")) {
+    leave_one_out = true;
+  }
+
   int num_threads = vm["threads"].as<int>();
   cerr << "Grammar extraction will use " << num_threads << " threads." << endl;
 
@@ -223,7 +230,9 @@ int main(int argc, char** argv) {
     }
     suffixes[i] = suffix;
 
-    Grammar grammar = extractor.GetGrammar(sentences[i]);
+    unordered_set<int> blacklisted_sentence_ids;
+    if (leave_one_out) blacklisted_sentence_ids.insert(i);
+    Grammar grammar = extractor.GetGrammar(sentences[i], blacklisted_sentence_ids, source_data_array);
     ofstream output(GetGrammarFilePath(grammar_path, i).c_str());
     output << grammar;
   }
diff --git a/extractor/sample_source.txt b/extractor/sample_source.txt
new file mode 100644
index 00000000..971baf6d
--- /dev/null
+++ b/extractor/sample_source.txt
@@ -0,0 +1,2 @@
+ana are mere .
+ana bea mult lapte .
diff --git a/extractor/sampler.cc b/extractor/sampler.cc
index d81956b5..d332dd90 100644
--- a/extractor/sampler.cc
+++ b/extractor/sampler.cc
@@ -12,7 +12,7 @@ Sampler::Sampler() {}
 
 Sampler::~Sampler() {}
 
-PhraseLocation Sampler::Sample(const PhraseLocation& location) const {
+PhraseLocation Sampler::Sample(const PhraseLocation& location, unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) const {
   vector<int> sample;
   int num_subpatterns;
   if (location.matchings == NULL) {
@@ -20,8 +20,37 @@ PhraseLocation Sampler::Sample(const PhraseLocation& location) const {
     num_subpatterns = 1;
     int low = location.sa_low, high = location.sa_high;
     double step = max(1.0, (double) (high - low) / max_samples);
-    for (double i = low; i < high && sample.size() < max_samples; i += step) {
-      sample.push_back(suffix_array->GetSuffix(Round(i)));
+    double i = low, last = i;
+    bool found;
+    while (sample.size() < max_samples && i < high) {
+      int x = suffix_array->GetSuffix(Round(i));
+      int id = source_data_array->GetSentenceId(x);
+      if (find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) != blacklisted_sentence_ids.end()) {
+        found = false;
+        double backoff_step = 1;
+        while (true) {
+          if ((double)backoff_step >= step) break;
+          double j = i - backoff_step;
+          x = suffix_array->GetSuffix(Round(j));
+          id = source_data_array->GetSentenceId(x);
+          if (x >= 0 && j > last && find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) == blacklisted_sentence_ids.end()) {
+            found = true; last = i; break;
+          }
+          double k = i + backoff_step;
+          x = suffix_array->GetSuffix(Round(k));
+          id = source_data_array->GetSentenceId(x);
+          if (k < min(i+step, (double)high) && find(blacklisted_sentence_ids.begin(), blacklisted_sentence_ids.end(), id) == blacklisted_sentence_ids.end()) {
+            found = true; last = k; break;
+          }
+          if (j <= last && k >= high) break;
+          backoff_step++;
+        }
+      } else {
+        found = true;
+        last = i;
+      }
+      if (found) sample.push_back(x);
+      i += step;
     }
   } else {
     // Sample vector of occurrences.
diff --git a/extractor/sampler.h b/extractor/sampler.h
index be4aa1bb..30e747fd 100644
--- a/extractor/sampler.h
+++ b/extractor/sampler.h
@@ -2,6 +2,9 @@
 #define _SAMPLER_H_
 
 #include <memory>
+#include <unordered_set>
+
+#include "data_array.h"
 
 using namespace std;
 
@@ -20,7 +23,7 @@ class Sampler {
   virtual ~Sampler();
 
   // Samples uniformly at most max_samples phrase occurrences.
-  virtual PhraseLocation Sample(const PhraseLocation& location) const;
+  virtual PhraseLocation Sample(const PhraseLocation& location, const unordered_set<int> blacklisted_sentence_ids, const shared_ptr<DataArray> source_data_array) const;
 
  protected:
   Sampler();
diff --git a/extractor/sampler_test.cc b/extractor/sampler_test.cc
index e9abebfa..965567ba 100644
--- a/extractor/sampler_test.cc
+++ b/extractor/sampler_test.cc
@@ -3,6 +3,7 @@
 #include <memory>
 
 #include "mocks/mock_suffix_array.h"
+#include "mocks/mock_data_array.h"
 #include "phrase_location.h"
 #include "sampler.h"
 
@@ -15,6 +16,8 @@ namespace {
 class SamplerTest : public Test {
  protected:
   virtual void SetUp() {
+    source_data_array = make_shared<MockDataArray>();
+    EXPECT_CALL(*source_data_array, GetSentenceId(_)).WillRepeatedly(Return(9999));
     suffix_array = make_shared<MockSuffixArray>();
     for (int i = 0; i < 10; ++i) {
       EXPECT_CALL(*suffix_array, GetSuffix(i)).WillRepeatedly(Return(i));
@@ -23,51 +26,54 @@ class SamplerTest : public Test {
 
   shared_ptr<MockSuffixArray> suffix_array;
   shared_ptr<Sampler> sampler;
+  shared_ptr<MockDataArray> source_data_array;
 };
 
 TEST_F(SamplerTest, TestSuffixArrayRange) {
   PhraseLocation location(0, 10);
+  unordered_set<int> blacklist;
 
   sampler = make_shared<Sampler>(suffix_array, 1);
   vector<int> expected_locations = {0};
-  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
 
   sampler = make_shared<Sampler>(suffix_array, 2);
   expected_locations = {0, 5};
-  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
 
   sampler = make_shared<Sampler>(suffix_array, 3);
   expected_locations = {0, 3, 7};
-  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
 
   sampler = make_shared<Sampler>(suffix_array, 4);
   expected_locations = {0, 3, 5, 8};
-  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
 
   sampler = make_shared<Sampler>(suffix_array, 100);
   expected_locations = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
-  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
 }
 
 TEST_F(SamplerTest, TestSubstringsSample) {
   vector<int> locations = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+  unordered_set<int> blacklist;
   PhraseLocation location(locations, 2);
 
   sampler = make_shared<Sampler>(suffix_array, 1);
   vector<int> expected_locations = {0, 1};
-  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location, blacklist, source_data_array));
 
   sampler = make_shared<Sampler>(suffix_array, 2);
   expected_locations = {0, 1, 6, 7};
-  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location, blacklist, source_data_array));
 
   sampler = make_shared<Sampler>(suffix_array, 3);
   expected_locations = {0, 1, 4, 5, 6, 7};
-  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location, blacklist, source_data_array));
 
   sampler = make_shared<Sampler>(suffix_array, 7);
   expected_locations = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
-  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location));
+  EXPECT_EQ(PhraseLocation(expected_locations, 2), sampler->Sample(location, blacklist, source_data_array));
 }
 
 } // namespace
diff --git a/extractor/sampler_test_blacklist.cc b/extractor/sampler_test_blacklist.cc
new file mode 100644
index 00000000..3305b990
--- /dev/null
+++ b/extractor/sampler_test_blacklist.cc
@@ -0,0 +1,102 @@
+#include <gtest/gtest.h>
+
+#include <memory>
+
+#include "mocks/mock_suffix_array.h"
+#include "mocks/mock_data_array.h"
+#include "phrase_location.h"
+#include "sampler.h"
+
+using namespace std;
+using namespace ::testing;
+
+namespace extractor {
+namespace {
+
+class SamplerTestBlacklist : public Test {
+ protected:
+  virtual void SetUp() {
+    source_data_array = make_shared<MockDataArray>();
+    for (int i = 0; i < 10; ++i) {
+      EXPECT_CALL(*source_data_array, GetSentenceId(i)).WillRepeatedly(Return(i));
+    }
+    for (int i = -10; i < 0; ++i) {
+      EXPECT_CALL(*source_data_array, GetSentenceId(i)).WillRepeatedly(Return(0));
+    }
+    suffix_array = make_shared<MockSuffixArray>();
+    for (int i = -10; i < 10; ++i) {
+      EXPECT_CALL(*suffix_array, GetSuffix(i)).WillRepeatedly(Return(i));
+    }
+  }
+
+  shared_ptr<MockSuffixArray> suffix_array;
+  shared_ptr<Sampler> sampler;
+  shared_ptr<MockDataArray> source_data_array;
+};
+
+TEST_F(SamplerTestBlacklist, TestSuffixArrayRange) {
+  PhraseLocation location(0, 10);
+  unordered_set<int> blacklist;
+  vector<int> expected_locations;
+   
+  blacklist.insert(0);
+  sampler = make_shared<Sampler>(suffix_array, 1);
+  expected_locations = {1};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+  blacklist.clear();
+  
+  for (int i = 0; i < 9; i++) {
+    blacklist.insert(i);
+  }
+  sampler = make_shared<Sampler>(suffix_array, 1);
+  expected_locations = {9};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+  blacklist.clear();
+
+  blacklist.insert(0);
+  blacklist.insert(5);
+  sampler = make_shared<Sampler>(suffix_array, 2);
+  expected_locations = {1, 4};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+  blacklist.clear();
+
+  blacklist.insert(0);
+  blacklist.insert(1);
+  blacklist.insert(2);
+  blacklist.insert(3);
+  sampler = make_shared<Sampler>(suffix_array, 2);
+  expected_locations = {4, 5};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+  blacklist.clear();
+
+  blacklist.insert(0);
+  blacklist.insert(3);
+  blacklist.insert(7);
+  sampler = make_shared<Sampler>(suffix_array, 3);
+  expected_locations = {1, 2, 6};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+  blacklist.clear();
+
+  blacklist.insert(0);
+  blacklist.insert(3);
+  blacklist.insert(5);
+  blacklist.insert(8);
+  sampler = make_shared<Sampler>(suffix_array, 4);
+  expected_locations = {1, 2, 4, 7};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+  blacklist.clear();
+  
+  blacklist.insert(0);
+  sampler = make_shared<Sampler>(suffix_array, 100);
+  expected_locations = {1, 2, 3, 4, 5, 6, 7, 8, 9};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+  blacklist.clear();
+ 
+  blacklist.insert(9);
+  sampler = make_shared<Sampler>(suffix_array, 100);
+  expected_locations = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+  EXPECT_EQ(PhraseLocation(expected_locations, 1), sampler->Sample(location, blacklist, source_data_array));
+}
+
+} // namespace
+} // namespace extractor