* Tmp commit of ner code

spacy/ner/_state.pxd

@@ -6,6 +6,7 @@ cdef int begin_entity(State* s, label) except -1
 cdef int end_entity(State* s) except -1
 
 cdef State* init_state(Pool mem, int sent_length) except NULL
+cdef int copy_state(Pool mem, State* dest, State* source) except -1
 
 cdef bint entity_is_open(State *s) except -1
 

spacy/ner/_state.pyx

@@ -1,44 +1,50 @@
-from .bilou_moves cimport BEGIN, UNIT
+cdef void begin_entity(State* s, label):
-
-
-cdef int begin_entity(State* s, label) except -1:
-    s.curr.start = s.i
-    s.curr.label = label
-
-
-cdef int end_entity(State* s) except -1:
-    s.curr.end = s.i
-    s.ents[s.j] = s.curr
     s.j += 1
-    s.curr.start = 0
+    s.ents[s.j].start = s.i
-    s.curr.label = -1
+    s.ents[s.j].tag = label
-    s.curr.end = 0
+    s.ents[s.j].end = s.i + 1
+
+
+cdef void end_entity(State* s):
+    s.ents[s.j].end = s.i + 1
 
 
 cdef State* init_state(Pool mem, int sent_length) except NULL:
     s = <State*>mem.alloc(1, sizeof(State))
-    s.j = 0
     s.ents = <Entity*>mem.alloc(sent_length, sizeof(Entity))
-    for i in range(sent_length):
-        s.ents[i].label = -1
-    s.curr.label = -1
     s.tags = <int*>mem.alloc(sent_length, sizeof(int))
     s.length = sent_length
-    return s
 
 
-cdef bint entity_is_open(State *s) except -1:
+cdef bint entity_is_open(State *s):
-    return s.curr.label != -1
+    return s.ents[s.j].start != 0
 
 
-cdef bint entity_is_sunk(State *s, Move* golds) except -1:
+cdef bint entity_is_sunk(State *s, Move* golds):
     if not entity_is_open(s):
         return False
 
-    cdef Move* gold = &golds[s.curr.start]
+    cdef Entity* ent = &s.ents[s.j]
+    cdef Move* gold = &golds[ent.start]
     if gold.action != BEGIN and gold.action != UNIT:
         return True
-    elif gold.label != s.curr.label:
+    elif gold.label != ent.label:
         return True
     else:
         return False
+
+
+cdef int copy_state(Pool mem, State* dest, State* source) except -1:
+    '''Copy state source into state dest.'''
+    if source.length > dest.length:
+        dest.ents = <Entity*>mem.realloc(dest.ents, source.length * sizeof(Entity))
+        dest.tags = <int*>mem.realloc(dest.tags, source.length * sizeof(int))
+    memcpy(dest.ents, source.ents, source.length * sizeof(Entity))
+    memcpy(dest.tags, source.tags, source.length * sizeof(int))
+    dest.length = source.length
+    dest.i = source.i
+    dest.j = source.j
+    dest.curr = source.curr
+
+
+

spacy/ner/greedy_parser.pyx

@@ -1,6 +1,3 @@
-from __future__ import division
-from __future__ import unicode_literals
-
 cimport cython
 import random
 import os
@@ -10,56 +7,14 @@ import json
 
 from thinc.features cimport ConjFeat
 
-from .context cimport fill_context
+from ..context cimport fill_context
-from .context cimport N_FIELDS
+from ..context cimport N_FIELDS
-from .structs cimport Move, State
+from .moves cimport Move
-from .io_moves cimport fill_moves, transition, best_accepted
+from .moves cimport fill_moves, transition, best_accepted
-from .io_moves cimport set_accept_if_valid, set_accept_if_oracle
+from .moves cimport set_accept_if_valid, set_accept_if_oracle
-from .io_moves import get_n_moves
+from .moves import get_n_moves
+from ._state cimport State
 from ._state cimport init_state
-from ._state cimport entity_is_open
-from ._state cimport end_entity
-from .annot cimport NERAnnotation
-
-
-def setup_model_dir(entity_types, templates, model_dir):
-    if path.exists(model_dir):
-        shutil.rmtree(model_dir)
-    os.mkdir(model_dir)
-    config = {
-        'templates': templates,
-        'entity_types': entity_types,
-    }
-    with open(path.join(model_dir, 'config.json'), 'w') as file_:
-        json.dump(config, file_)
-
-
-def train(train_sents, model_dir, nr_iter=10):
-    cdef Tokens tokens
-    cdef NERAnnotation gold_ner
-    parser = NERParser(model_dir)
-    for _ in range(nr_iter):
-        tp = 0
-        fp = 0
-        fn = 0
-        for i, (tokens, gold_ner) in enumerate(train_sents):
-            #print [tokens[i].string for i in range(tokens.length)]
-            test_ents = set(parser.train(tokens, gold_ner))
-            #print 'Test', test_ents
-            gold_ents = set(gold_ner.entities)
-            #print 'Gold', set(gold_ner.entities)
-            tp += len(gold_ents.intersection(test_ents))
-            fp += len(test_ents - gold_ents)
-            fn += len(gold_ents - test_ents)
-        p = tp / (tp + fp)
-        r = tp / (tp + fn)
-        f = 2 * ((p * r) / (p + r))
-        print 'P: %.3f' % p,
-        print 'R: %.3f' % r,
-        print 'F: %.3f' % f
-        random.shuffle(train_sents)
-    parser.model.end_training()
-    parser.model.dump(path.join(model_dir, 'model'))
 
 
 cdef class NERParser:
@@ -67,12 +22,12 @@ cdef class NERParser:
         self.mem = Pool()
         cfg = json.load(open(path.join(model_dir, 'config.json')))
         templates = cfg['templates']
-        self.extractor = Extractor(templates, [ConjFeat] * len(templates))
         self.entity_types = cfg['entity_types']
+        self.extractor = Extractor(templates, [ConjFeat] * len(templates))
         self.n_classes = get_n_moves(len(self.entity_types))
         self._moves = <Move*>self.mem.alloc(self.n_classes, sizeof(Move))
-        fill_moves(self._moves, self.n_classes, self.entity_types)
+        fill_moves(self._moves, len(self.entity_types))
-        self.model = LinearModel(self.n_classes)
+        self.model = LinearModel(len(self.tag_names))
         if path.exists(path.join(model_dir, 'model')):
             self.model.load(path.join(model_dir, 'model'))
 
@@ -81,59 +36,46 @@ cdef class NERParser:
         self._values = <weight_t*>self.mem.alloc(self.extractor.n+1, sizeof(weight_t))
         self._scores = <weight_t*>self.mem.alloc(self.model.nr_class, sizeof(weight_t))
 
-    cpdef list train(self, Tokens tokens, NERAnnotation annot):
+    cpdef int train(self, Tokens tokens, gold_classes):
         cdef Pool mem = Pool()
         cdef State* s = init_state(mem, tokens.length)
+        cdef Move* golds = <Move*>mem.alloc(len(gold_classes), sizeof(Move))
+        for i, clas in enumerate(gold_classes):
+            golds[i] = self.moves[clas - 1]
+            assert golds[i].id == clas
         cdef Move* guess
-        cdef Move* oracle_move
-        n_correct = 0
-        cdef int f = 0
         while s.i < tokens.length:
-            fill_context(self._context, s, tokens)
+            fill_context(self._context, s.i, tokens)
             self.extractor.extract(self._feats, self._values, self._context, NULL)
             self.model.score(self._scores, self._feats, self._values)
             
             set_accept_if_valid(self._moves, self.n_classes, s)
             guess = best_accepted(self._moves, self._scores, self.n_classes)
-            assert guess.clas != 0
+
-            set_accept_if_oracle(self._moves, self.n_classes, s,
+            set_accept_if_oracle(self._moves, golds, self.n_classes, s) # TODO
-                                 annot.starts, annot.ends, annot.labels)
+            gold = best_accepted(self._moves, self._scores, self.n_classes)
-            oracle_move = best_accepted(self._moves, self._scores, self.n_classes)
+
-            assert oracle_move.clas != 0
+            if guess.clas == gold.clas:
-            if guess.clas == oracle_move.clas:
+                self.model.update({})
-                counts = {}
+                return 0
-                n_correct += 1
+
-            else:
+            counts = {guess.clas: {}, gold.clas: {}}
-                counts = {guess.clas: {}, oracle_move.clas: {}}
+            self.extractor.count(counts[gold.clas], self._feats, 1)
-                self.extractor.count(counts[oracle_move.clas], self._feats, 1)
             self.extractor.count(counts[guess.clas], self._feats, -1)
             self.model.update(counts)
+
             transition(s, guess)
             tokens.ner[s.i-1] = s.tags[s.i-1]
-        if entity_is_open(s):
-            s.curr.label = annot.labels[s.curr.start]
-            end_entity(s)
-        entities = []
-        for i in range(s.j):
-            entities.append((s.ents[i].start, s.ents[i].end, s.ents[i].label))
-        return entities
 
-    cpdef list set_tags(self, Tokens tokens):
+    cpdef int set_tags(self, Tokens tokens) except -1:
         cdef Pool mem = Pool()
         cdef State* s = init_state(mem, tokens.length)
         cdef Move* move
         while s.i < tokens.length:
-            fill_context(self._context, s, tokens)
+            fill_context(self._context, s.i, tokens)
             self.extractor.extract(self._feats, self._values, self._context, NULL)
             self.model.score(self._scores, self._feats, self._values)
             set_accept_if_valid(self._moves, self.n_classes, s)
             move = best_accepted(self._moves, self._scores, self.n_classes)
             transition(s, move)
             tokens.ner[s.i-1] = s.tags[s.i-1]
-        if entity_is_open(s):
-            s.curr.label = move.label
-            end_entity(s)
-        entities = []
-        for i in range(s.j):
-            entities.append((s.ents[i].start, s.ents[i].end, s.ents[i].label))
-        return entities

spacy/ner/io_moves.pyx

@@ -77,11 +77,16 @@ cdef int set_accept_if_valid(Move* moves, int n, State* s) except 0:
     moves[0].accept = False
     for i in range(1, n):
         if moves[i].action == SHIFT:
-            moves[i].accept = moves[i].label == s.curr.label or not entity_is_open(s)
+            if s.i >= s.length:
+                moves[i].accept = False
+            elif open_ent and moves[i].label != s.curr.label:
+                moves[i].accept = False
+            else:
+                moves[i].accept = True
         elif moves[i].action == REDUCE:
             moves[i].accept = open_ent
         elif moves[i].action == OUT:
-            moves[i].accept = not open_ent
+            moves[i].accept = s.i < s.length and not open_ent
         n_accept += moves[i].accept
     return n_accept
 
@@ -150,3 +155,7 @@ cdef int fill_moves(Move* moves, int n, list entity_types) except -1:
     moves[i].clas = i
     moves[i].label = 0
     i += 1
+
+
+cdef bint is_final(State* s):
+    return s.i == s.length and not entity_is_open(s)