Compile count-based bilex table for online grammar extraction.

8 files changed, 902 insertions, 729 deletions

diff --git a/python/cdec/sa/__init__.py b/python/cdec/sa/__init__.py
index 14ba5ecb..0c132cb9 100644
--- a/python/cdec/sa/__init__.py
+++ b/python/cdec/sa/__init__.py
@@ -3,6 +3,7 @@ from cdec.sa._sa import make_lattice, decode_lattice, decode_sentence,\
         SuffixArray, DataArray, LCP, Precomputation, Alignment, BiLex,\
         HieroCachingRuleFactory, Sampler, Scorer
 from cdec.sa.extractor import GrammarExtractor
+import online
 
 _SA_FEATURES = []
 _SA_ANNOTATORS = {}
diff --git a/python/cdec/sa/_sa.cpp b/python/cdec/sa/_sa.cpp
index c59fa22b..6e8b0a6f 100644
--- a/python/cdec/sa/_sa.cpp
+++ b/python/cdec/sa/_sa.cpp
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.19.2 on Mon Mar  3 08:00:58 2014 */
+/* Generated by Cython 0.19.2 on Thu Mar  6 14:00:22 2014 */
 
 #define PY_SSIZE_T_CLEAN
 #ifndef CYTHON_USE_PYLONG_INTERNALS
@@ -710,7 +710,7 @@ struct __pyx_obj_4cdec_2sa_3_sa___pyx_scope_struct_4_make_lattice {
 };
 
 
-/* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2144
+/* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2149
  * 
  *     # Rule string from rule
  *     def fmt_rule(self, f, e, a):             # <<<<<<<<<<<<<<
@@ -863,7 +863,7 @@ struct __pyx_obj_4cdec_2sa_3_sa___pyx_scope_struct_29_genexpr {
 };
 
 
-/* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2163
+/* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2168
  *     # (Used for EGivenFCoherent)
  *     # Return set of (fphrase, lex_i, lex_j)
  *     def get_f_phrases(self, f_words):             # <<<<<<<<<<<<<<
@@ -1019,7 +1019,7 @@ struct __pyx_obj_4cdec_2sa_3_sa___pyx_scope_struct_13_decode_words {
 };
 
 
-/* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2140
+/* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2145
  *         f = Phrase(f_sym)
  *         e = Phrase(e_sym)
  *         a = tuple(self.alignment.link(i, j) for i, j in links)             # <<<<<<<<<<<<<<
@@ -1281,7 +1281,7 @@ struct __pyx_obj_4cdec_2sa_3_sa___pyx_scope_struct_11_encode_words {
 };
 
 
-/* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2145
+/* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2150
  *     # Rule string from rule
  *     def fmt_rule(self, f, e, a):
  *         a_str = ' '.join('{0}-{1}'.format(*self.alignment.unlink(packed)) for packed in a)             # <<<<<<<<<<<<<<
@@ -1332,7 +1332,7 @@ struct __pyx_obj_4cdec_2sa_3_sa___pyx_scope_struct_6_genexpr {
 };
 
 
-/* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2079
+/* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2084
  * 
  *     # Create a rule from source, target, non-terminals, and alignments
  *     def form_rule(self, f_i, e_i, f_span, e_span, nt, al):             # <<<<<<<<<<<<<<
@@ -61846,6 +61846,7 @@ static PyObject *__pyx_pf_4cdec_2sa_3_sa_23HieroCachingRuleFactory_25add_instanc
   PyObject *__pyx_v_e_ph = NULL;
   PyObject *__pyx_v_aligned_fe = NULL;
   PyObject *__pyx_v_aligned_ef = NULL;
+  int __pyx_v_null_word;
   PyObject *__pyx_v_i = NULL;
   PyObject *__pyx_v_j = NULL;
   PyObject *__pyx_v_e_i_aligned = NULL;
@@ -61871,6 +61872,7 @@ static PyObject *__pyx_pf_4cdec_2sa_3_sa_23HieroCachingRuleFactory_25add_instanc
   Py_ssize_t __pyx_t_14;
   PyObject *(*__pyx_t_15)(PyObject *);
   PyObject *__pyx_t_16 = NULL;
+  int __pyx_t_17;
   int __pyx_lineno = 0;
   const char *__pyx_filename = NULL;
   int __pyx_clineno = 0;
@@ -62925,7 +62927,7 @@ static PyObject *__pyx_pf_4cdec_2sa_3_sa_23HieroCachingRuleFactory_25add_instanc
  *         # Update Bilexical counts
  *         aligned_fe = [list() for _ in range(len(f_words))]             # <<<<<<<<<<<<<<
  *         aligned_ef = [list() for _ in range(len(e_words))]
- *         for (i, j) in alignment:
+ *         null_word = sym_fromstring('NULL', True)
  */
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@@ -62993,8 +62995,8 @@ static PyObject *__pyx_pf_4cdec_2sa_3_sa_23HieroCachingRuleFactory_25add_instanc
  *         # Update Bilexical counts
  *         aligned_fe = [list() for _ in range(len(f_words))]
  *         aligned_ef = [list() for _ in range(len(e_words))]             # <<<<<<<<<<<<<<
+ *         null_word = sym_fromstring('NULL', True)
  *         for (i, j) in alignment:
- *             aligned_fe[i].append(j)
  */
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@@ -63061,6 +63063,15 @@ static PyObject *__pyx_pf_4cdec_2sa_3_sa_23HieroCachingRuleFactory_25add_instanc
   /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2060
  *         aligned_fe = [list() for _ in range(len(f_words))]
  *         aligned_ef = [list() for _ in range(len(e_words))]
+ *         null_word = sym_fromstring('NULL', True)             # <<<<<<<<<<<<<<
+ *         for (i, j) in alignment:
+ *             aligned_fe[i].append(j)
+ */
+  __pyx_v_null_word = __pyx_f_4cdec_2sa_3_sa_sym_fromstring(__pyx_k__NULL, 1);
+
+  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2061
+ *         aligned_ef = [list() for _ in range(len(e_words))]
+ *         null_word = sym_fromstring('NULL', True)
  *         for (i, j) in alignment:             # <<<<<<<<<<<<<<
  *             aligned_fe[i].append(j)
  *             aligned_ef[j].append(i)
@@ -63069,7 +63080,7 @@ static PyObject *__pyx_pf_4cdec_2sa_3_sa_23HieroCachingRuleFactory_25add_instanc
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+      __pyx_t_3 = PySequence_ITEM(__pyx_t_4, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2061; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-          else {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2060; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -63109,7 +63120,7 @@ static PyObject *__pyx_pf_4cdec_2sa_3_sa_23HieroCachingRuleFactory_25add_instanc
       if (unlikely(size != 2)) {
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-        {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2060; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+        {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2061; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -63122,16 +63133,16 @@ static PyObject *__pyx_pf_4cdec_2sa_3_sa_23HieroCachingRuleFactory_25add_instanc
       __Pyx_INCREF(__pyx_t_6);
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+      __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2061; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+      __pyx_t_7 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2061; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -63139,7 +63150,7 @@ static PyObject *__pyx_pf_4cdec_2sa_3_sa_23HieroCachingRuleFactory_25add_instanc
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@@ -63147,7 +63158,7 @@ static PyObject *__pyx_pf_4cdec_2sa_3_sa_23HieroCachingRuleFactory_25add_instanc
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-      {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2060; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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-    /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2061
- *         aligned_ef = [list() for _ in range(len(e_words))]
+    /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2062
+ *         null_word = sym_fromstring('NULL', True)
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  *             aligned_fe[i].append(j)             # <<<<<<<<<<<<<<
  *             aligned_ef[j].append(i)
  *         for f_i in range(len(f_words)):
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-    /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2062
+    /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2063
  *         for (i, j) in alignment:
  *             aligned_fe[i].append(j)
  *             aligned_ef[j].append(i)             # <<<<<<<<<<<<<<
  *         for f_i in range(len(f_words)):
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  *             aligned_ef[j].append(i)
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-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2138
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+          __Pyx_RaiseArgtupleInvalid("fmt_rule", 1, 3, 3, 2); {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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-/* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2145
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-    /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2171
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-      /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2190
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-        /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2191
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-      /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2193
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 }
 
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-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2165
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-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2166
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-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2168
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-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2196
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-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2199
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-    /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2202
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-/* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2220
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-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2222
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-    /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2224
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-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2083
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-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2093
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-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2168
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+  __pyx_k_tuple_153 = PyTuple_Pack(10, ((PyObject *)__pyx_n_s__f_i), ((PyObject *)__pyx_n_s__f_j), ((PyObject *)__pyx_n_s__lex_i), ((PyObject *)__pyx_n_s__lex_j), ((PyObject *)__pyx_n_s__wc), ((PyObject *)__pyx_n_s__ntc), ((PyObject *)__pyx_n_s__syms), ((PyObject *)__pyx_n_s__f), ((PyObject *)__pyx_n_s__new_lex_i), ((PyObject *)__pyx_n_s__new_lex_j)); if (unlikely(!__pyx_k_tuple_153)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_153));
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+  __pyx_k_codeobj_154 = (PyObject*)__Pyx_PyCode_New(7, 0, 10, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_153, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_144, __pyx_n_s__extract, 2173, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_154)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
   /* "cdec/sa/_sa.pyx":5
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-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2206
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+  __pyx_k_tuple_177 = PyTuple_Pack(4, ((PyObject *)__pyx_n_s__vec), ((PyObject *)__pyx_n_s__i), ((PyObject *)__pyx_n_s__j), ((PyObject *)__pyx_n_s__k)); if (unlikely(!__pyx_k_tuple_177)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_k_codeobj_178 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_177, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_144, __pyx_n_s__span_check, 2211, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_178)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2214
+  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2219
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-  __pyx_k_tuple_179 = PyTuple_Pack(4, ((PyObject *)__pyx_n_s__vec), ((PyObject *)__pyx_n_s__i), ((PyObject *)__pyx_n_s__j), ((PyObject *)__pyx_n_s__k)); if (unlikely(!__pyx_k_tuple_179)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_179 = PyTuple_Pack(4, ((PyObject *)__pyx_n_s__vec), ((PyObject *)__pyx_n_s__i), ((PyObject *)__pyx_n_s__j), ((PyObject *)__pyx_n_s__k)); if (unlikely(!__pyx_k_tuple_179)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+  __pyx_k_codeobj_180 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_179, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_144, __pyx_n_s__span_inc, 2219, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_180)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
 
-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2220
+  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2225
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-  __pyx_k_tuple_181 = PyTuple_Pack(4, ((PyObject *)__pyx_n_s__vec), ((PyObject *)__pyx_n_s__i), ((PyObject *)__pyx_n_s__j), ((PyObject *)__pyx_n_s__k)); if (unlikely(!__pyx_k_tuple_181)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_tuple_181 = PyTuple_Pack(4, ((PyObject *)__pyx_n_s__vec), ((PyObject *)__pyx_n_s__i), ((PyObject *)__pyx_n_s__j), ((PyObject *)__pyx_n_s__k)); if (unlikely(!__pyx_k_tuple_181)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_k_tuple_181);
   __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_181));
-  __pyx_k_codeobj_182 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_181, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_144, __pyx_n_s__span_dec, 2220, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_182)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_k_codeobj_182 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_181, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_144, __pyx_n_s__span_dec, 2225, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_182)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_RefNannyFinishContext();
   return 0;
   __pyx_L1_error:;
@@ -77278,7 +77343,7 @@ PyMODINIT_FUNC PyInit__sa(void)
   __pyx_ptype_4cdec_2sa_3_sa_SuffixArray = &__pyx_type_4cdec_2sa_3_sa_SuffixArray;
   if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_4_make_lattice) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_4cdec_2sa_3_sa___pyx_scope_struct_4_make_lattice = &__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_4_make_lattice;
-  if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_24_fmt_rule) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_24_fmt_rule) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_4cdec_2sa_3_sa___pyx_scope_struct_24_fmt_rule = &__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_24_fmt_rule;
   if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa_LCP) < 0) {__pyx_filename = __pyx_f[9]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__Pyx_SetAttrString(__pyx_m, "LCP", (PyObject *)&__pyx_type_4cdec_2sa_3_sa_LCP) < 0) {__pyx_filename = __pyx_f[9]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -77316,7 +77381,7 @@ PyMODINIT_FUNC PyInit__sa(void)
   __pyx_ptype_4cdec_2sa_3_sa___pyx_scope_struct_1_read_bitext = &__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_1_read_bitext;
   if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_29_genexpr) < 0) {__pyx_filename = __pyx_f[13]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_4cdec_2sa_3_sa___pyx_scope_struct_29_genexpr = &__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_29_genexpr;
-  if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_26_get_f_phrases) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_26_get_f_phrases) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_4cdec_2sa_3_sa___pyx_scope_struct_26_get_f_phrases = &__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_26_get_f_phrases;
   __pyx_type_4cdec_2sa_3_sa_ExtendedTrieNode.tp_base = __pyx_ptype_4cdec_2sa_3_sa_TrieNode;
   if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa_ExtendedTrieNode) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -77334,7 +77399,7 @@ PyMODINIT_FUNC PyInit__sa(void)
   __pyx_ptype_4cdec_2sa_3_sa___pyx_scope_struct_19_input = &__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_19_input;
   if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_13_decode_words) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_4cdec_2sa_3_sa___pyx_scope_struct_13_decode_words = &__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_13_decode_words;
-  if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_23_genexpr) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_23_genexpr) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_4cdec_2sa_3_sa___pyx_scope_struct_23_genexpr = &__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_23_genexpr;
   if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa_Rule) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   if (__Pyx_SetAttrString(__pyx_m, "Rule", (PyObject *)&__pyx_type_4cdec_2sa_3_sa_Rule) < 0) {__pyx_filename = __pyx_f[7]; __pyx_lineno = 158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -77390,13 +77455,13 @@ PyMODINIT_FUNC PyInit__sa(void)
   __pyx_ptype_4cdec_2sa_3_sa_TrieTable = &__pyx_type_4cdec_2sa_3_sa_TrieTable;
   if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_11_encode_words) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_4cdec_2sa_3_sa___pyx_scope_struct_11_encode_words = &__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_11_encode_words;
-  if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_25_genexpr) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_25_genexpr) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_4cdec_2sa_3_sa___pyx_scope_struct_25_genexpr = &__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_25_genexpr;
   if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_12_genexpr) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_4cdec_2sa_3_sa___pyx_scope_struct_12_genexpr = &__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_12_genexpr;
   if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_6_genexpr) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_4cdec_2sa_3_sa___pyx_scope_struct_6_genexpr = &__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_6_genexpr;
-  if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_22_form_rule) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2079; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_22_form_rule) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_4cdec_2sa_3_sa___pyx_scope_struct_22_form_rule = &__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_22_form_rule;
   if (PyType_Ready(&__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_10_genexpr) < 0) {__pyx_filename = __pyx_f[10]; __pyx_lineno = 119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __pyx_ptype_4cdec_2sa_3_sa___pyx_scope_struct_10_genexpr = &__pyx_type_4cdec_2sa_3_sa___pyx_scope_struct_10_genexpr;
@@ -77964,40 +78029,40 @@ PyMODINIT_FUNC PyInit__sa(void)
   __Pyx_GIVEREF(__pyx_t_3);
   __pyx_t_3 = 0;
 
-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2206
+  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2211
  * 
  * # Spans are _inclusive_ on both ends [i, j]
  * def span_check(vec, i, j):             # <<<<<<<<<<<<<<
  *     k = i
  *     while k <= j:
  */
-  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_4cdec_2sa_3_sa_17span_check, NULL, __pyx_n_s_102); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_4cdec_2sa_3_sa_17span_check, NULL, __pyx_n_s_102); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  if (PyDict_SetItem(__pyx_d, __pyx_n_s__span_check, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_d, __pyx_n_s__span_check, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2214
+  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2219
  *     return True
  * 
  * def span_inc(vec, i, j):             # <<<<<<<<<<<<<<
  *     k = i
  *     while k <= j:
  */
-  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_4cdec_2sa_3_sa_19span_inc, NULL, __pyx_n_s_102); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_4cdec_2sa_3_sa_19span_inc, NULL, __pyx_n_s_102); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  if (PyDict_SetItem(__pyx_d, __pyx_n_s__span_inc, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_d, __pyx_n_s__span_inc, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
-  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2220
+  /* "/home/mdenkows/cdec/python/cdec/sa/rulefactory.pxi":2225
  *         k += 1
  * 
  * def span_dec(vec, i, j):             # <<<<<<<<<<<<<<
  *     k = i
  *     while k <= j:
  */
-  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_4cdec_2sa_3_sa_21span_dec, NULL, __pyx_n_s_102); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  __pyx_t_3 = PyCFunction_NewEx(&__pyx_mdef_4cdec_2sa_3_sa_21span_dec, NULL, __pyx_n_s_102); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_GOTREF(__pyx_t_3);
-  if (PyDict_SetItem(__pyx_d, __pyx_n_s__span_dec, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+  if (PyDict_SetItem(__pyx_d, __pyx_n_s__span_dec, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[8]; __pyx_lineno = 2225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
 
   /* "/home/mdenkows/cdec/python/cdec/sa/features.pxi":1
diff --git a/python/cdec/sa/compile.py b/python/cdec/sa/compile.py
index caa93f8b..3cdf212f 100644
--- a/python/cdec/sa/compile.py
+++ b/python/cdec/sa/compile.py
@@ -54,6 +54,8 @@ def main():
                         help='Bitext word alignment')
     parser.add_argument('-o', '--output', required=True,
                         help='Output path')
+    parser.add_argument('--online', action='store_true',
+                        help='Compile data for online grammar extraction')
     args = parser.parse_args()
 
     if not ((args.source and args.target) or args.bitext):
@@ -74,6 +76,8 @@ def main():
     precomp_bin = os.path.join(args.output, precomp_file)
     a_bin = os.path.join(args.output, 'a.bin')
     lex_bin = os.path.join(args.output, 'lex.bin')
+    # online only
+    bilex_file = os.path.join(args.output, 'bilex.gz')
 
     config = cdec.configobj.ConfigObj(args.config, unrepr=True)
     config['f_sa_file'] = os.path.abspath(f_sa_bin)
@@ -81,6 +85,8 @@ def main():
     config['a_file'] = os.path.abspath(a_bin)
     config['lex_file'] = os.path.abspath(lex_bin)
     config['precompute_file'] = os.path.abspath(precomp_bin)
+    if args.online:
+        config['bilex_file'] = os.path.abspath(bilex_file)
 
     start_time = monitor_cpu()
     logger.info('Compiling source suffix array')
@@ -122,6 +128,17 @@ def main():
     stop_time = monitor_cpu()
     logger.info('Compiling bilexical dictionary took %f seconds', stop_time - start_time)
 
+    if args.online:
+        start_time = monitor_cpu()
+        logger.info('Compiling online bilexical dictionary')
+        if args.bitext:
+            bilex = cdec.sa.online.Bilex(alignment_f=args.alignment, text_f=args.bitext)
+        else:
+            bilex = cdec.sa.online.Bilex(alignment_f=args.alignment, text_f=args.source, text_target_f=args.target)
+        bilex.write(bilex_file)
+        stop_time = monitor_cpu()
+        logger.info('Compiling online bilexical dictionary took %f seconds', stop_time - start_time)
+
     # Write configuration
     for name, value in zip(param_names, params):
         config[name] = value
diff --git a/python/cdec/sa/extract.py b/python/cdec/sa/extract.py
index d8f14b11..b6502c52 100644
--- a/python/cdec/sa/extract.py
+++ b/python/cdec/sa/extract.py
@@ -12,13 +12,12 @@ from cdec.sa._sa import monitor_cpu
 
 extractor, prefix = None, None
 online, compress = False, False
-vocab = None
 
 def make_extractor(args):
     global extractor, prefix, online, compress
     signal.signal(signal.SIGINT, signal.SIG_IGN) # Let parent process catch Ctrl+C
     load_features(args.features)
-    extractor = cdec.sa.GrammarExtractor(args.config, online, vocab)
+    extractor = cdec.sa.GrammarExtractor(args.config, online)
     prefix = args.grammars
     online = args.online
     compress = args.compress
@@ -64,7 +63,7 @@ def extract(inp):
     return '<seg grammar="{}" id="{}">{}</seg>{}'.format(grammar_file, i, sentence, suffix)
 
 def main():
-    global online, vocab
+    global online
     logging.basicConfig(level=logging.INFO)
     parser = argparse.ArgumentParser(description='Extract grammars from a compiled corpus.')
     parser.add_argument('-c', '--config', required=True,
@@ -79,8 +78,6 @@ def main():
                         help='additional feature definitions')
     parser.add_argument('-o', '--online', action='store_true',
                         help='online grammar extraction')
-    parser.add_argument('-e', '--except-vocab', default=None,
-                        help='add LM and Lex except features (use with -o, pass vocab.gz)')
     parser.add_argument('-z', '--compress', action='store_true',
                         help='compress grammars with gzip')
     args = parser.parse_args()
@@ -94,7 +91,6 @@ def main():
             sys.exit(1)
 
     online = args.online
-    vocab = args.except_vocab
 
     start_time = monitor_cpu()
     if args.jobs > 1:
diff --git a/python/cdec/sa/extractor.py b/python/cdec/sa/extractor.py
index 244f84be..25313cc3 100644
--- a/python/cdec/sa/extractor.py
+++ b/python/cdec/sa/extractor.py
@@ -4,14 +4,14 @@ import cdec.configobj
 from cdec.sa._sa import gzip_or_text
 from cdec.sa.features import EgivenFCoherent, SampleCountF, CountEF,\
         MaxLexEgivenF, MaxLexFgivenE, IsSingletonF, IsSingletonFE,\
-        IsSupportedOnline, CountExceptLM, CountExceptLex
+        IsSupportedOnline, CountExceptLM
 import cdec.sa
 
 # maximum span of a grammar rule in TEST DATA
 MAX_INITIAL_SIZE = 15
 
 class GrammarExtractor:
-    def __init__(self, config, online=False, vocab=None, features=None):
+    def __init__(self, config, online=False, features=None):
         if isinstance(config, basestring):
             if not os.path.exists(config):
                 raise IOError('cannot read configuration from {0}'.format(config))
@@ -60,13 +60,13 @@ class GrammarExtractor:
         tt = cdec.sa.BiLex(from_binary=config['lex_file'])
 
         # TODO: clean this up
+        # Load data and add features for online grammar extraction
         extended_features = []
         if online:
             extended_features.append(IsSupportedOnline)
-        if vocab:
+            vocab_file = config['vocab_file']
             vcb_set = set(line.strip() for line in gzip_or_text(vocab))
             extended_features.append(CountExceptLM(vcb_set))
-            extended_features.append(CountExceptLex(tt))
             
         # TODO: use @cdec.sa.features decorator for standard features too
         # + add a mask to disable features
diff --git a/python/cdec/sa/features.py b/python/cdec/sa/features.py
index dcc60401..3e6af859 100644
--- a/python/cdec/sa/features.py
+++ b/python/cdec/sa/features.py
@@ -145,9 +145,3 @@ def CountExceptLM(vocab):
     def CountExceptLM(ctx): # Word count in bitext (inc online data) but NOT mono text
         return sum(1 for e in ctx.ephrase.words if e not in vocab)
     return CountExceptLM
-
-def CountExceptLex(ttable):
-    def CountExceptLex(ctx): # Word count in online data but NOT aligned in original bitext
-        # TODO: Check that online data actually contains aligned word when rulefactory TODO is addressed.
-        return sum(1 for e in ctx.ephrase.words if not ttable.contains_e_word(e))
-    return CountExceptLex
diff --git a/python/cdec/sa/online.py b/python/cdec/sa/online.py
new file mode 100644
index 00000000..92f6eae2
--- /dev/null
+++ b/python/cdec/sa/online.py
@@ -0,0 +1,95 @@
+from __future__ import division
+
+import collections
+import gzip
+import itertools
+
+from cdec.sa._sa import gzip_or_text
+
+# Same as Cython implementation.  Collisions with NULL in bitext?
+NULL_WORD = 'NULL'
+
+def learn_vocab(text_f):
+    vocab = set()
+    for line in gzip_or_text(text_f):
+        for word in line.strip().split():
+            vocab.add(word)
+    return vocab
+
+def write_vocab(vocab, out_f):
+    with gzip.open(out_f, 'wb') as out:
+        for word in sorted(vocab):
+            out.write('{}\n'.format(word))
+
+def read_vocab(in_f):
+    return set(line.strip() for line in gzip_or_text(in_f))
+
+class Bilex:
+
+    def __init__(self, in_f=None, alignment_f=None, text_f=None, target_text_f=None):
+        self.f = collections.defaultdict(int)
+        self.e = collections.defaultdict(int)
+        self.fe = collections.defaultdict(lambda: collections.defaultdict(int))
+        self.ef = collections.defaultdict(lambda: collections.defaultdict(int))
+
+        # Read from file
+        if in_f:
+            self.read(in_f)
+        # Build from aligned bitext
+        elif alignment_f:
+            # Allow one or two args for bitext
+            if target_text_f:
+                t = itertools.izip((line.strip() for line in gzip_or_text(text_f)), (line.strip() for line in gzip_or_text(target_text_f)))
+            else:
+                t = (line.strip().split(' ||| ') for line in gzip_or_text(text_f))
+            a = (line.strip() for line in gzip_or_text(alignment_f))
+            for (source, target) in t:
+                links = sorted(tuple(int(link) for link in link_str.split('-')) for link_str in a.next().split())
+                self.update(source.split(), target.split(), links)
+
+    # Add bilex counts from new aligned sentence pair
+    def update(self, f_words, e_words, links):
+        aligned_fe = [list() for _ in range(len(f_words))]
+        aligned_ef = [list() for _ in range(len(e_words))]
+        for (i, j) in links:
+            aligned_fe[i].append(j)
+            aligned_ef[j].append(i)
+        for f_i in range(len(f_words)):
+            self.f[f_words[f_i]] += 1
+            e_i_aligned = aligned_fe[f_i]
+            lc = len(e_i_aligned)
+            if lc > 0:
+                for e_i in e_i_aligned:
+                    self.fe[f_words[f_i]][e_words[e_i]] += (1 / lc)
+            else:
+                self.fe[f_words[f_i]][NULL_WORD] += 1
+        for e_i in range(len(e_words)):
+            self.e[e_words[e_i]] += 1
+            f_i_aligned = aligned_ef[e_i]
+            lc = len(f_i_aligned)
+            if lc > 0:
+                for f_i in f_i_aligned:
+                    self.ef[e_words[e_i]][f_words[f_i]] += (1 / lc)
+            else:
+                self.ef[e_words[e_i]][NULL_WORD] += 1
+
+    def write(self, out_f):
+        fv = sorted(self.f)
+        ev = sorted(self.e)
+        with gzip.open(out_f, 'wb') as out:
+            for f in fv:
+                out.write('{} {}\n'.format(f, self.f[f]))
+            out.write('\n')
+            for e in ev:
+                out.write('{} {}\n'.format(e, self.e[e]))
+            out.write('\n')
+            for f in fv:
+                for (e, c) in sorted(self.fe[f].iteritems()):
+                    out.write('{} {} {}\n'.format(f, e, c))
+            for e in ev:
+                for (f, c) in sorted(self.ef[e].iteritems()):
+                    out.write('{} {} {}\n'.format(e, f, c))
+
+    def read(self, in_f):
+        with gzip_or_text(in_f) as inp:
+            pass
diff --git a/python/cdec/sa/rulefactory.pxi b/python/cdec/sa/rulefactory.pxi
index 044a78c8..86b994b9 100644
--- a/python/cdec/sa/rulefactory.pxi
+++ b/python/cdec/sa/rulefactory.pxi
@@ -2057,23 +2057,28 @@ cdef class HieroCachingRuleFactory:
         # Update Bilexical counts
         aligned_fe = [list() for _ in range(len(f_words))]
         aligned_ef = [list() for _ in range(len(e_words))]
+        null_word = sym_fromstring('NULL', True)
         for (i, j) in alignment:
             aligned_fe[i].append(j)
             aligned_ef[j].append(i)
         for f_i in range(len(f_words)):
+            stats.bilex_f[f_words[f_i]] += 1
             e_i_aligned = aligned_fe[f_i]
             lc = len(e_i_aligned)
             if lc > 0:
-                stats.bilex_f[f_words[f_i]] += 1
                 for e_i in e_i_aligned:
                     stats.bilex_fe[f_words[f_i]][e_words[e_i]] += (1.0) / lc
+            else:
+                stats.bilex_fe[f_words[f_i]][null_word] += 1
         for e_i in range(len(e_words)):
+            stats.bilex_e[e_words[e_i]] += 1
             f_i_aligned = aligned_ef[e_i]
             lc = len(f_i_aligned)
             if lc > 0:
-                stats.bilex_e[e_words[e_i]] += 1
                 for f_i in f_i_aligned:
                     stats.bilex_ef[e_words[e_i]][f_words[f_i]] += (1.0) / lc
+            else:
+                stats.bilex_ef[e_words[e_i]][null_word] += 1
 
     # Create a rule from source, target, non-terminals, and alignments
     def form_rule(self, f_i, e_i, f_span, e_span, nt, al):