# cython: profile=True import re import random import numpy import tempfile import shutil import itertools from pathlib import Path import srsly import warnings from .syntax import nonproj from .tokens import Doc, Span from .errors import Errors, AlignmentError, Warnings from . import util punct_re = re.compile(r"\W") def tags_to_entities(tags): entities = [] start = None for i, tag in enumerate(tags): if tag is None: continue if tag.startswith("O"): # TODO: We shouldn't be getting these malformed inputs. Fix this. if start is not None: start = None continue elif tag == "-": continue elif tag.startswith("I"): if start is None: raise ValueError(Errors.E067.format(tags=tags[:i + 1])) continue if tag.startswith("U"): entities.append((tag[2:], i, i)) elif tag.startswith("B"): start = i elif tag.startswith("L"): entities.append((tag[2:], start, i)) start = None else: raise ValueError(Errors.E068.format(tag=tag)) return entities def merge_sents(sents): m_deps = [[], [], [], [], [], []] m_cats = {} m_brackets = [] i = 0 for (ids, words, tags, heads, labels, ner), (cats, brackets) in sents: m_deps[0].extend(id_ + i for id_ in ids) m_deps[1].extend(words) m_deps[2].extend(tags) m_deps[3].extend(head + i for head in heads) m_deps[4].extend(labels) m_deps[5].extend(ner) m_brackets.extend((b["first"] + i, b["last"] + i, b["label"]) for b in brackets) m_cats.update(cats) i += len(ids) return [(m_deps, (m_cats, m_brackets))] def _normalize_for_alignment(tokens): return [w.replace(" ", "").lower() for w in tokens] def align(tokens_a, tokens_b): """Calculate alignment tables between two tokenizations. tokens_a (List[str]): The candidate tokenization. tokens_b (List[str]): The reference tokenization. RETURNS: (tuple): A 5-tuple consisting of the following information: * cost (int): The number of misaligned tokens. * a2b (List[int]): Mapping of indices in `tokens_a` to indices in `tokens_b`. For instance, if `a2b[4] == 6`, that means that `tokens_a[4]` aligns to `tokens_b[6]`. If there's no one-to-one alignment for a token, it has the value -1. * b2a (List[int]): The same as `a2b`, but mapping the other direction. * a2b_multi (Dict[int, int]): A dictionary mapping indices in `tokens_a` to indices in `tokens_b`, where multiple tokens of `tokens_a` align to the same token of `tokens_b`. * b2a_multi (Dict[int, int]): As with `a2b_multi`, but mapping the other direction. """ tokens_a = _normalize_for_alignment(tokens_a) tokens_b = _normalize_for_alignment(tokens_b) cost = 0 a2b = numpy.empty(len(tokens_a), dtype="i") b2a = numpy.empty(len(tokens_b), dtype="i") a2b.fill(-1) b2a.fill(-1) a2b_multi = {} b2a_multi = {} i = 0 j = 0 offset_a = 0 offset_b = 0 while i < len(tokens_a) and j < len(tokens_b): a = tokens_a[i][offset_a:] b = tokens_b[j][offset_b:] if a == b: if offset_a == offset_b == 0: a2b[i] = j b2a[j] = i elif offset_a == 0: cost += 2 a2b_multi[i] = j elif offset_b == 0: cost += 2 b2a_multi[j] = i offset_a = offset_b = 0 i += 1 j += 1 elif a == "": assert offset_a == 0 cost += 1 i += 1 elif b == "": assert offset_b == 0 cost += 1 j += 1 elif b.startswith(a): cost += 1 if offset_a == 0: a2b_multi[i] = j i += 1 offset_a = 0 offset_b += len(a) elif a.startswith(b): cost += 1 if offset_b == 0: b2a_multi[j] = i j += 1 offset_b = 0 offset_a += len(b) else: assert "".join(tokens_a) != "".join(tokens_b) raise AlignmentError(Errors.E186.format(tok_a=tokens_a, tok_b=tokens_b)) return cost, a2b, b2a, a2b_multi, b2a_multi class GoldCorpus(object): """An annotated corpus, using the JSON file format. Manages annotations for tagging, dependency parsing and NER. DOCS: https://spacy.io/api/goldcorpus """ def __init__(self, train, dev, gold_preproc=False, limit=None): """Create a GoldCorpus. train (unicode or Path): File or directory of training data. dev (unicode or Path): File or directory of development data. RETURNS (GoldCorpus): The newly created object. """ self.limit = limit if isinstance(train, str) or isinstance(train, Path): train = self.read_examples(self.walk_corpus(train)) dev = self.read_examples(self.walk_corpus(dev)) # Write temp directory with one doc per file, so we can shuffle and stream self.tmp_dir = Path(tempfile.mkdtemp()) self.write_msgpack(self.tmp_dir / "train", train, limit=self.limit) self.write_msgpack(self.tmp_dir / "dev", dev, limit=self.limit) def __del__(self): shutil.rmtree(self.tmp_dir) @staticmethod def write_msgpack(directory, examples, limit=0): if not directory.exists(): directory.mkdir() n = 0 for i, example in enumerate(examples): ex_dict = example.to_dict() text = example.text srsly.write_msgpack(directory / f"{i}.msg", (text, ex_dict)) n += 1 if limit and n >= limit: break @staticmethod def walk_corpus(path): path = util.ensure_path(path) if not path.is_dir(): return [path] paths = [path] locs = [] seen = set() for path in paths: if str(path) in seen: continue seen.add(str(path)) if path.parts[-1].startswith("."): continue elif path.is_dir(): paths.extend(path.iterdir()) elif path.parts[-1].endswith((".json", ".jsonl")): locs.append(path) return locs @staticmethod def read_examples(locs, limit=0): """ Yield training examples """ i = 0 for loc in locs: loc = util.ensure_path(loc) file_name = loc.parts[-1] if file_name.endswith("json"): examples = read_json_file(loc) elif file_name.endswith("jsonl"): gold_tuples = srsly.read_jsonl(loc) first_gold_tuple = next(gold_tuples) gold_tuples = itertools.chain([first_gold_tuple], gold_tuples) # TODO: proper format checks with schemas if isinstance(first_gold_tuple, dict): if first_gold_tuple.get("paragraphs", None): examples = read_json_object(gold_tuples) elif first_gold_tuple.get("doc_annotation", None): examples = [] for ex_dict in gold_tuples: doc = ex_dict.get("doc", None) if doc is None: doc = ex_dict.get("text", None) if not (doc is None or isinstance(doc, Doc) or isinstance(doc, str)): raise ValueError(Errors.E987.format(type=type(doc))) examples.append(Example.from_dict(ex_dict, doc=doc)) elif file_name.endswith("msg"): text, ex_dict = srsly.read_msgpack(loc) examples = [Example.from_dict(ex_dict, doc=text)] else: supported = ("json", "jsonl", "msg") raise ValueError(Errors.E124.format(path=loc, formats=supported)) try: for example in examples: yield example i += 1 if limit and i >= limit: return except KeyError as e: msg = "Missing key {}".format(e) raise KeyError(Errors.E996.format(file=file_name, msg=msg)) except UnboundLocalError as e: msg = "Unexpected document structure" raise ValueError(Errors.E996.format(file=file_name, msg=msg)) @property def dev_examples(self): locs = (self.tmp_dir / "dev").iterdir() yield from self.read_examples(locs, limit=self.limit) @property def train_examples(self): locs = (self.tmp_dir / "train").iterdir() yield from self.read_examples(locs, limit=self.limit) def count_train(self): """Returns count of words in train examples""" n = 0 i = 0 for example in self.train_examples: n += len(example.token_annotation.words) if self.limit and i >= self.limit: break i += 1 return n def train_dataset(self, nlp, gold_preproc=False, max_length=None, noise_level=0.0, orth_variant_level=0.0, ignore_misaligned=False): locs = list((self.tmp_dir / 'train').iterdir()) random.shuffle(locs) train_examples = self.read_examples(locs, limit=self.limit) gold_examples = self.iter_gold_docs(nlp, train_examples, gold_preproc, max_length=max_length, noise_level=noise_level, orth_variant_level=orth_variant_level, make_projective=True, ignore_misaligned=ignore_misaligned) yield from gold_examples def train_dataset_without_preprocessing(self, nlp, gold_preproc=False, ignore_misaligned=False): examples = self.iter_gold_docs(nlp, self.train_examples, gold_preproc=gold_preproc, ignore_misaligned=ignore_misaligned) yield from examples def dev_dataset(self, nlp, gold_preproc=False, ignore_misaligned=False): examples = self.iter_gold_docs(nlp, self.dev_examples, gold_preproc=gold_preproc, ignore_misaligned=ignore_misaligned) yield from examples @classmethod def iter_gold_docs(cls, nlp, examples, gold_preproc, max_length=None, noise_level=0.0, orth_variant_level=0.0, make_projective=False, ignore_misaligned=False): """ Setting gold_preproc will result in creating a doc per sentence """ for example in examples: if gold_preproc: split_examples = example.split_sents() example_golds = [] for split_example in split_examples: split_example_docs = cls._make_docs(nlp, split_example, gold_preproc, noise_level=noise_level, orth_variant_level=orth_variant_level) split_example_golds = cls._make_golds(split_example_docs, vocab=nlp.vocab, make_projective=make_projective, ignore_misaligned=ignore_misaligned) example_golds.extend(split_example_golds) else: example_docs = cls._make_docs(nlp, example, gold_preproc, noise_level=noise_level, orth_variant_level=orth_variant_level) example_golds = cls._make_golds(example_docs, vocab=nlp.vocab, make_projective=make_projective, ignore_misaligned=ignore_misaligned) for ex in example_golds: if ex.goldparse is not None: if (not max_length) or len(ex.doc) < max_length: yield ex @classmethod def _make_docs(cls, nlp, example, gold_preproc, noise_level=0.0, orth_variant_level=0.0): var_example = make_orth_variants(nlp, example, orth_variant_level=orth_variant_level) # gold_preproc is not used ?! if example.text is not None: var_text = add_noise(var_example.text, noise_level) var_doc = nlp.make_doc(var_text) var_example.doc = var_doc else: var_doc = Doc(nlp.vocab, words=add_noise(var_example.token_annotation.words, noise_level)) var_example.doc = var_doc return [var_example] @classmethod def _make_golds(cls, examples, vocab=None, make_projective=False, ignore_misaligned=False): filtered_examples = [] for example in examples: gold_parses = example.get_gold_parses(vocab=vocab, make_projective=make_projective, ignore_misaligned=ignore_misaligned) assert len(gold_parses) == 1 doc, gold = gold_parses[0] if doc: assert doc == example.doc example.goldparse = gold filtered_examples.append(example) return filtered_examples def make_orth_variants(nlp, example, orth_variant_level=0.0): if random.random() >= orth_variant_level: return example if not example.token_annotation: return example raw = example.text if random.random() >= 0.5: lower = True if raw is not None: raw = raw.lower() ndsv = nlp.Defaults.single_orth_variants ndpv = nlp.Defaults.paired_orth_variants # modify words in paragraph_tuples variant_example = Example(doc=raw) token_annotation = example.token_annotation words = token_annotation.words tags = token_annotation.tags if not words or not tags: # add the unmodified annotation token_dict = token_annotation.to_dict() variant_example.set_token_annotation(**token_dict) else: if lower: words = [w.lower() for w in words] # single variants punct_choices = [random.choice(x["variants"]) for x in ndsv] for word_idx in range(len(words)): for punct_idx in range(len(ndsv)): if tags[word_idx] in ndsv[punct_idx]["tags"] \ and words[word_idx] in ndsv[punct_idx]["variants"]: words[word_idx] = punct_choices[punct_idx] # paired variants punct_choices = [random.choice(x["variants"]) for x in ndpv] for word_idx in range(len(words)): for punct_idx in range(len(ndpv)): if tags[word_idx] in ndpv[punct_idx]["tags"] \ and words[word_idx] in itertools.chain.from_iterable(ndpv[punct_idx]["variants"]): # backup option: random left vs. right from pair pair_idx = random.choice([0, 1]) # best option: rely on paired POS tags like `` / '' if len(ndpv[punct_idx]["tags"]) == 2: pair_idx = ndpv[punct_idx]["tags"].index(tags[word_idx]) # next best option: rely on position in variants # (may not be unambiguous, so order of variants matters) else: for pair in ndpv[punct_idx]["variants"]: if words[word_idx] in pair: pair_idx = pair.index(words[word_idx]) words[word_idx] = punct_choices[punct_idx][pair_idx] token_dict = token_annotation.to_dict() token_dict["words"] = words token_dict["tags"] = tags variant_example.set_token_annotation(**token_dict) # modify raw to match variant_paragraph_tuples if raw is not None: variants = [] for single_variants in ndsv: variants.extend(single_variants["variants"]) for paired_variants in ndpv: variants.extend(list(itertools.chain.from_iterable(paired_variants["variants"]))) # store variants in reverse length order to be able to prioritize # longer matches (e.g., "---" before "--") variants = sorted(variants, key=lambda x: len(x)) variants.reverse() variant_raw = "" raw_idx = 0 # add initial whitespace while raw_idx < len(raw) and re.match("\s", raw[raw_idx]): variant_raw += raw[raw_idx] raw_idx += 1 for word in variant_example.token_annotation.words: match_found = False # add identical word if word not in variants and raw[raw_idx:].startswith(word): variant_raw += word raw_idx += len(word) match_found = True # add variant word else: for variant in variants: if not match_found and \ raw[raw_idx:].startswith(variant): raw_idx += len(variant) variant_raw += word match_found = True # something went wrong, abort # (add a warning message?) if not match_found: return example # add following whitespace while raw_idx < len(raw) and re.match("\s", raw[raw_idx]): variant_raw += raw[raw_idx] raw_idx += 1 variant_example.doc = variant_raw return variant_example return variant_example def add_noise(orig, noise_level): if random.random() >= noise_level: return orig elif type(orig) == list: corrupted = [_corrupt(word, noise_level) for word in orig] corrupted = [w for w in corrupted if w] return corrupted else: return "".join(_corrupt(c, noise_level) for c in orig) def _corrupt(c, noise_level): if random.random() >= noise_level: return c elif c in [".", "'", "!", "?", ","]: return "\n" else: return c.lower() def read_json_object(json_corpus_section): """Take a list of JSON-formatted documents (e.g. from an already loaded training data file) and yield annotations in the GoldParse format. json_corpus_section (list): The data. YIELDS (Example): The reformatted data - one training example per paragraph """ for json_doc in json_corpus_section: examples = json_to_examples(json_doc) for ex in examples: yield ex def json_to_examples(doc): """Convert an item in the JSON-formatted training data to the format used by GoldParse. doc (dict): One entry in the training data. YIELDS (Example): The reformatted data - one training example per paragraph """ paragraphs = [] for paragraph in doc["paragraphs"]: example = Example(doc=paragraph.get("raw", None)) words = [] ids = [] tags = [] pos = [] morphs = [] lemmas = [] heads = [] labels = [] ner = [] sent_starts = [] brackets = [] for sent in paragraph["sentences"]: sent_start_i = len(words) for i, token in enumerate(sent["tokens"]): words.append(token["orth"]) ids.append(token.get('id', sent_start_i + i)) tags.append(token.get('tag', "-")) pos.append(token.get("pos", "")) morphs.append(token.get("morph", "")) lemmas.append(token.get("lemma", "")) heads.append(token.get("head", 0) + sent_start_i + i) labels.append(token.get("dep", "")) # Ensure ROOT label is case-insensitive if labels[-1].lower() == "root": labels[-1] = "ROOT" ner.append(token.get("ner", "-")) if i == 0: sent_starts.append(1) else: sent_starts.append(0) if "brackets" in sent: brackets.extend((b["first"] + sent_start_i, b["last"] + sent_start_i, b["label"]) for b in sent["brackets"]) cats = {} for cat in paragraph.get("cats", {}): cats[cat["label"]] = cat["value"] example.set_token_annotation(ids=ids, words=words, tags=tags, pos=pos, morphs=morphs, lemmas=lemmas, heads=heads, deps=labels, entities=ner, sent_starts=sent_starts, brackets=brackets) example.set_doc_annotation(cats=cats) yield example def read_json_file(loc, docs_filter=None, limit=None): loc = util.ensure_path(loc) if loc.is_dir(): for filename in loc.iterdir(): yield from read_json_file(loc / filename, limit=limit) else: for doc in _json_iterate(loc): if docs_filter is not None and not docs_filter(doc): continue for json_data in json_to_examples(doc): yield json_data def _json_iterate(loc): # We should've made these files jsonl...But since we didn't, parse out # the docs one-by-one to reduce memory usage. # It's okay to read in the whole file -- just don't parse it into JSON. cdef bytes py_raw loc = util.ensure_path(loc) with loc.open("rb") as file_: py_raw = file_.read() cdef long file_length = len(py_raw) if file_length > 2 ** 30: warnings.warn(Warnings.W027.format(size=file_length)) raw = py_raw cdef int square_depth = 0 cdef int curly_depth = 0 cdef int inside_string = 0 cdef int escape = 0 cdef long start = -1 cdef char c cdef char quote = ord('"') cdef char backslash = ord("\\") cdef char open_square = ord("[") cdef char close_square = ord("]") cdef char open_curly = ord("{") cdef char close_curly = ord("}") for i in range(file_length): c = raw[i] if escape: escape = False continue if c == backslash: escape = True continue if c == quote: inside_string = not inside_string continue if inside_string: continue if c == open_square: square_depth += 1 elif c == close_square: square_depth -= 1 elif c == open_curly: if square_depth == 1 and curly_depth == 0: start = i curly_depth += 1 elif c == close_curly: curly_depth -= 1 if square_depth == 1 and curly_depth == 0: py_str = py_raw[start : i + 1].decode("utf8") try: yield srsly.json_loads(py_str) except Exception: print(py_str) raise start = -1 def iob_to_biluo(tags): out = [] tags = list(tags) while tags: out.extend(_consume_os(tags)) out.extend(_consume_ent(tags)) return out def biluo_to_iob(tags): out = [] for tag in tags: tag = tag.replace("U-", "B-", 1).replace("L-", "I-", 1) out.append(tag) return out def _consume_os(tags): while tags and tags[0] == "O": yield tags.pop(0) def _consume_ent(tags): if not tags: return [] tag = tags.pop(0) target_in = "I" + tag[1:] target_last = "L" + tag[1:] length = 1 while tags and tags[0] in {target_in, target_last}: length += 1 tags.pop(0) label = tag[2:] if length == 1: if len(label) == 0: raise ValueError(Errors.E177.format(tag=tag)) return ["U-" + label] else: start = "B-" + label end = "L-" + label middle = [f"I-{label}" for _ in range(1, length - 1)] return [start] + middle + [end] cdef class TokenAnnotation: def __init__(self, ids=None, words=None, tags=None, pos=None, morphs=None, lemmas=None, heads=None, deps=None, entities=None, sent_starts=None, brackets=None): self.ids = ids if ids else [] self.words = words if words else [] self.tags = tags if tags else [] self.pos = pos if pos else [] self.morphs = morphs if morphs else [] self.lemmas = lemmas if lemmas else [] self.heads = heads if heads else [] self.deps = deps if deps else [] self.entities = entities if entities else [] self.sent_starts = sent_starts if sent_starts else [] self.brackets_by_start = {} if brackets: for b_start, b_end, b_label in brackets: self.brackets_by_start.setdefault(b_start, []).append((b_end, b_label)) @property def brackets(self): brackets = [] for start, ends_labels in self.brackets_by_start.items(): for end, label in ends_labels: brackets.append((start, end, label)) return brackets @classmethod def from_dict(cls, token_dict): return cls(ids=token_dict.get("ids", None), words=token_dict.get("words", None), tags=token_dict.get("tags", None), pos=token_dict.get("pos", None), morphs=token_dict.get("morphs", None), lemmas=token_dict.get("lemmas", None), heads=token_dict.get("heads", None), deps=token_dict.get("deps", None), entities=token_dict.get("entities", None), sent_starts=token_dict.get("sent_starts", None), brackets=token_dict.get("brackets", None)) def to_dict(self): return {"ids": self.ids, "words": self.words, "tags": self.tags, "pos": self.pos, "morphs": self.morphs, "lemmas": self.lemmas, "heads": self.heads, "deps": self.deps, "entities": self.entities, "sent_starts": self.sent_starts, "brackets": self.brackets} def get_id(self, i): return self.ids[i] if i < len(self.ids) else i def get_word(self, i): return self.words[i] if i < len(self.words) else "" def get_tag(self, i): return self.tags[i] if i < len(self.tags) else "-" def get_pos(self, i): return self.pos[i] if i < len(self.pos) else "" def get_morph(self, i): return self.morphs[i] if i < len(self.morphs) else "" def get_lemma(self, i): return self.lemmas[i] if i < len(self.lemmas) else "" def get_head(self, i): return self.heads[i] if i < len(self.heads) else i def get_dep(self, i): return self.deps[i] if i < len(self.deps) else "" def get_entity(self, i): return self.entities[i] if i < len(self.entities) else "-" def get_sent_start(self, i): return self.sent_starts[i] if i < len(self.sent_starts) else None def __str__(self): return str(self.to_dict()) def __repr__(self): return self.__str__() cdef class DocAnnotation: def __init__(self, cats=None, links=None): self.cats = cats if cats else {} self.links = links if links else {} @classmethod def from_dict(cls, doc_dict): return cls(cats=doc_dict.get("cats", None), links=doc_dict.get("links", None)) def to_dict(self): return {"cats": self.cats, "links": self.links} def __str__(self): return str(self.to_dict()) def __repr__(self): return self.__str__() cdef class Example: def __init__(self, doc_annotation=None, token_annotation=None, doc=None, goldparse=None): """ Doc can either be text, or an actual Doc """ self.doc = doc self.doc_annotation = doc_annotation if doc_annotation else DocAnnotation() self.token_annotation = token_annotation if token_annotation else TokenAnnotation() self.goldparse = goldparse @classmethod def from_gold(cls, goldparse, doc=None): doc_annotation = DocAnnotation(cats=goldparse.cats, links=goldparse.links) token_annotation = goldparse.get_token_annotation() return cls(doc_annotation, token_annotation, doc) @classmethod def from_dict(cls, example_dict, doc=None): token_dict = example_dict.get("token_annotation", {}) token_annotation = TokenAnnotation.from_dict(token_dict) doc_dict = example_dict.get("doc_annotation", {}) doc_annotation = DocAnnotation.from_dict(doc_dict) return cls(doc_annotation, token_annotation, doc) def to_dict(self): """ Note that this method does NOT export the doc, only the annotations ! """ token_dict = self.token_annotation.to_dict() doc_dict = self.doc_annotation.to_dict() return {"token_annotation": token_dict, "doc_annotation": doc_dict} @property def text(self): if self.doc is None: return None if isinstance(self.doc, Doc): return self.doc.text return self.doc @property def gold(self): if self.goldparse is None: doc, gold = self.get_gold_parses()[0] self.goldparse = gold return self.goldparse def set_token_annotation(self, ids=None, words=None, tags=None, pos=None, morphs=None, lemmas=None, heads=None, deps=None, entities=None, sent_starts=None, brackets=None): self.token_annotation = TokenAnnotation(ids=ids, words=words, tags=tags, pos=pos, morphs=morphs, lemmas=lemmas, heads=heads, deps=deps, entities=entities, sent_starts=sent_starts, brackets=brackets) def set_doc_annotation(self, cats=None, links=None): if cats: self.doc_annotation.cats = cats if links: self.doc_annotation.links = links def split_sents(self): """ Split the token annotations into multiple Examples based on sent_starts and return a list of the new Examples""" if not self.token_annotation.words: return [self] s_example = Example(doc=None, doc_annotation=self.doc_annotation) s_ids, s_words, s_tags, s_pos, s_morphs = [], [], [], [], [] s_lemmas, s_heads, s_deps, s_ents, s_sent_starts = [], [], [], [], [] s_brackets = [] sent_start_i = 0 cdef TokenAnnotation t = self.token_annotation split_examples = [] cdef int b_start, b_end cdef unicode b_label for i in range(len(t.words)): if i > 0 and t.sent_starts[i] == 1: s_example.set_token_annotation(ids=s_ids, words=s_words, tags=s_tags, pos=s_pos, morphs=s_morphs, lemmas=s_lemmas, heads=s_heads, deps=s_deps, entities=s_ents, sent_starts=s_sent_starts, brackets=s_brackets) split_examples.append(s_example) s_example = Example(doc=None, doc_annotation=self.doc_annotation) s_ids, s_words, s_tags, s_pos, s_heads = [], [], [], [], [] s_deps, s_ents, s_morphs, s_lemmas = [], [], [], [] s_sent_starts, s_brackets = [], [] sent_start_i = i s_ids.append(t.get_id(i)) s_words.append(t.get_word(i)) s_tags.append(t.get_tag(i)) s_pos.append(t.get_pos(i)) s_morphs.append(t.get_morph(i)) s_lemmas.append(t.get_lemma(i)) s_heads.append(t.get_head(i) - sent_start_i) s_deps.append(t.get_dep(i)) s_ents.append(t.get_entity(i)) s_sent_starts.append(t.get_sent_start(i)) for b_end, b_label in t.brackets_by_start.get(i, []): s_brackets.append( (i - sent_start_i, b_end - sent_start_i, b_label) ) i += 1 s_example.set_token_annotation(ids=s_ids, words=s_words, tags=s_tags, pos=s_pos, morphs=s_morphs, lemmas=s_lemmas, heads=s_heads, deps=s_deps, entities=s_ents, sent_starts=s_sent_starts, brackets=s_brackets) split_examples.append(s_example) return split_examples def get_gold_parses(self, merge=True, vocab=None, make_projective=False, ignore_misaligned=False): """Return a list of (doc, GoldParse) objects. If merge is set to True, keep all Token annotations as one big list.""" d = self.doc_annotation # merge == do not modify Example if merge: t = self.token_annotation doc = self.doc if doc is None or not isinstance(doc, Doc): if not vocab: raise ValueError(Errors.E998) doc = Doc(vocab, words=t.words) try: gp = GoldParse.from_annotation(doc, d, t, make_projective=make_projective) except AlignmentError: if ignore_misaligned: gp = None else: raise return [(doc, gp)] # not merging: one GoldParse per sentence, defining docs with the words # from each sentence else: parses = [] split_examples = self.split_sents() for split_example in split_examples: if not vocab: raise ValueError(Errors.E998) split_doc = Doc(vocab, words=split_example.token_annotation.words) try: gp = GoldParse.from_annotation(split_doc, d, split_example.token_annotation, make_projective=make_projective) except AlignmentError: if ignore_misaligned: gp = None else: raise if gp is not None: parses.append((split_doc, gp)) return parses @classmethod def to_example_objects(cls, examples, make_doc=None, keep_raw_text=False): """ Return a list of Example objects, from a variety of input formats. make_doc needs to be provided when the examples contain text strings and keep_raw_text=False """ if isinstance(examples, Example): return [examples] if isinstance(examples, tuple): examples = [examples] converted_examples = [] for ex in examples: if isinstance(ex, Example): converted_examples.append(ex) # convert string to Doc to Example elif isinstance(ex, str): if keep_raw_text: converted_examples.append(Example(doc=ex)) else: doc = make_doc(ex) converted_examples.append(Example(doc=doc)) # convert Doc to Example elif isinstance(ex, Doc): converted_examples.append(Example(doc=ex)) # convert tuples to Example elif isinstance(ex, tuple) and len(ex) == 2: doc, gold = ex gold_dict = {} # convert string to Doc if isinstance(doc, str) and not keep_raw_text: doc = make_doc(doc) # convert dict to GoldParse if isinstance(gold, dict): gold_dict = gold if doc is not None or gold.get("words", None) is not None: gold = GoldParse(doc, **gold) else: gold = None if gold is not None: converted_examples.append(Example.from_gold(goldparse=gold, doc=doc)) else: raise ValueError(Errors.E999.format(gold_dict=gold_dict)) else: converted_examples.append(ex) return converted_examples cdef class GoldParse: """Collection for training annotations. DOCS: https://spacy.io/api/goldparse """ @classmethod def from_annotation(cls, doc, doc_annotation, token_annotation, make_projective=False): return cls(doc, words=token_annotation.words, tags=token_annotation.tags, pos=token_annotation.pos, morphs=token_annotation.morphs, lemmas=token_annotation.lemmas, heads=token_annotation.heads, deps=token_annotation.deps, entities=token_annotation.entities, sent_starts=token_annotation.sent_starts, cats=doc_annotation.cats, links=doc_annotation.links, make_projective=make_projective) def get_token_annotation(self): ids = None if self.words: ids = list(range(len(self.words))) return TokenAnnotation(ids=ids, words=self.words, tags=self.tags, pos=self.pos, morphs=self.morphs, lemmas=self.lemmas, heads=self.heads, deps=self.labels, entities=self.ner, sent_starts=self.sent_starts) def __init__(self, doc, words=None, tags=None, pos=None, morphs=None, lemmas=None, heads=None, deps=None, entities=None, sent_starts=None, make_projective=False, cats=None, links=None): """Create a GoldParse. The fields will not be initialized if len(doc) is zero. doc (Doc): The document the annotations refer to. words (iterable): A sequence of unicode word strings. tags (iterable): A sequence of strings, representing tag annotations. pos (iterable): A sequence of strings, representing UPOS annotations. morphs (iterable): A sequence of strings, representing morph annotations. lemmas (iterable): A sequence of strings, representing lemma annotations. heads (iterable): A sequence of integers, representing syntactic head offsets. deps (iterable): A sequence of strings, representing the syntactic relation types. entities (iterable): A sequence of named entity annotations, either as BILUO tag strings, or as `(start_char, end_char, label)` tuples, representing the entity positions. sent_starts (iterable): A sequence of sentence position tags, 1 for the first word in a sentence, 0 for all others. cats (dict): Labels for text classification. Each key in the dictionary may be a string or an int, or a `(start_char, end_char, label)` tuple, indicating that the label is applied to only part of the document (usually a sentence). Unlike entity annotations, label annotations can overlap, i.e. a single word can be covered by multiple labelled spans. The TextCategorizer component expects true examples of a label to have the value 1.0, and negative examples of a label to have the value 0.0. Labels not in the dictionary are treated as missing - the gradient for those labels will be zero. links (dict): A dict with `(start_char, end_char)` keys, and the values being dicts with kb_id:value entries, representing the external IDs in a knowledge base (KB) mapped to either 1.0 or 0.0, indicating positive and negative examples respectively. RETURNS (GoldParse): The newly constructed object. """ self.mem = Pool() self.loss = 0 self.length = len(doc) self.cats = {} if cats is None else dict(cats) self.links = {} if links is None else dict(links) # temporary doc for aligning entity annotation entdoc = None # avoid allocating memory if the doc does not contain any tokens if self.length == 0: self.words = [] self.tags = [] self.heads = [] self.labels = [] self.ner = [] self.morphs = [] # set a minimal orig so that the scorer can score an empty doc self.orig = TokenAnnotation(ids=[]) else: if not words: words = [token.text for token in doc] if not tags: tags = [None for _ in words] if not pos: pos = [None for _ in words] if not morphs: morphs = [None for _ in words] if not lemmas: lemmas = [None for _ in words] if not heads: heads = [None for _ in words] if not deps: deps = [None for _ in words] if not sent_starts: sent_starts = [None for _ in words] if entities is None: entities = ["-" for _ in words] elif len(entities) == 0: entities = ["O" for _ in words] else: # Translate the None values to '-', to make processing easier. # See Issue #2603 entities = [(ent if ent is not None else "-") for ent in entities] if not isinstance(entities[0], str): # Assume we have entities specified by character offset. # Create a temporary Doc corresponding to provided words # (to preserve gold tokenization) and text (to preserve # character offsets). entdoc_words, entdoc_spaces = util.get_words_and_spaces(words, doc.text) entdoc = Doc(doc.vocab, words=entdoc_words, spaces=entdoc_spaces) entdoc_entities = biluo_tags_from_offsets(entdoc, entities) # There may be some additional whitespace tokens in the # temporary doc, so check that the annotations align with # the provided words while building a list of BILUO labels. entities = [] words_offset = 0 for i in range(len(entdoc_words)): if words[i + words_offset] == entdoc_words[i]: entities.append(entdoc_entities[i]) else: words_offset -= 1 if len(entities) != len(words): warnings.warn(Warnings.W029.format(text=doc.text)) entities = ["-" for _ in words] # These are filled by the tagger/parser/entity recogniser self.c.tags = self.mem.alloc(len(doc), sizeof(int)) self.c.heads = self.mem.alloc(len(doc), sizeof(int)) self.c.labels = self.mem.alloc(len(doc), sizeof(attr_t)) self.c.has_dep = self.mem.alloc(len(doc), sizeof(int)) self.c.sent_start = self.mem.alloc(len(doc), sizeof(int)) self.c.ner = self.mem.alloc(len(doc), sizeof(Transition)) self.words = [None] * len(doc) self.tags = [None] * len(doc) self.pos = [None] * len(doc) self.morphs = [None] * len(doc) self.lemmas = [None] * len(doc) self.heads = [None] * len(doc) self.labels = [None] * len(doc) self.ner = [None] * len(doc) self.sent_starts = [None] * len(doc) # This needs to be done before we align the words if make_projective and any(heads) and any(deps) : heads, deps = nonproj.projectivize(heads, deps) # Do many-to-one alignment for misaligned tokens. # If we over-segment, we'll have one gold word that covers a sequence # of predicted words # If we under-segment, we'll have one predicted word that covers a # sequence of gold words. # If we "mis-segment", we'll have a sequence of predicted words covering # a sequence of gold words. That's many-to-many -- we don't do that # except for NER spans where the start and end can be aligned. cost, i2j, j2i, i2j_multi, j2i_multi = align([t.orth_ for t in doc], words) self.cand_to_gold = [(j if j >= 0 else None) for j in i2j] self.gold_to_cand = [(i if i >= 0 else None) for i in j2i] self.orig = TokenAnnotation(ids=list(range(len(words))), words=words, tags=tags, pos=pos, morphs=morphs, lemmas=lemmas, heads=heads, deps=deps, entities=entities, sent_starts=sent_starts, brackets=[]) for i, gold_i in enumerate(self.cand_to_gold): if doc[i].text.isspace(): self.words[i] = doc[i].text self.tags[i] = "_SP" self.pos[i] = "SPACE" self.morphs[i] = None self.lemmas[i] = None self.heads[i] = None self.labels[i] = None self.ner[i] = None self.sent_starts[i] = 0 if gold_i is None: if i in i2j_multi: self.words[i] = words[i2j_multi[i]] self.tags[i] = tags[i2j_multi[i]] self.pos[i] = pos[i2j_multi[i]] self.morphs[i] = morphs[i2j_multi[i]] self.lemmas[i] = lemmas[i2j_multi[i]] self.sent_starts[i] = sent_starts[i2j_multi[i]] is_last = i2j_multi[i] != i2j_multi.get(i+1) # Set next word in multi-token span as head, until last if not is_last: self.heads[i] = i+1 self.labels[i] = "subtok" else: head_i = heads[i2j_multi[i]] if head_i: self.heads[i] = self.gold_to_cand[head_i] self.labels[i] = deps[i2j_multi[i]] ner_tag = entities[i2j_multi[i]] # Assign O/- for many-to-one O/- NER tags if ner_tag in ("O", "-"): self.ner[i] = ner_tag else: self.words[i] = words[gold_i] self.tags[i] = tags[gold_i] self.pos[i] = pos[gold_i] self.morphs[i] = morphs[gold_i] self.lemmas[i] = lemmas[gold_i] self.sent_starts[i] = sent_starts[gold_i] if heads[gold_i] is None: self.heads[i] = None else: self.heads[i] = self.gold_to_cand[heads[gold_i]] self.labels[i] = deps[gold_i] self.ner[i] = entities[gold_i] # Assign O/- for one-to-many O/- NER tags for j, cand_j in enumerate(self.gold_to_cand): if cand_j is None: if j in j2i_multi: i = j2i_multi[j] ner_tag = entities[j] if ner_tag in ("O", "-"): self.ner[i] = ner_tag # If there is entity annotation and some tokens remain unaligned, # align all entities at the character level to account for all # possible token misalignments within the entity spans if any([e not in ("O", "-") for e in entities]) and None in self.ner: # If the temporary entdoc wasn't created above, initialize it if not entdoc: entdoc_words, entdoc_spaces = util.get_words_and_spaces(words, doc.text) entdoc = Doc(doc.vocab, words=entdoc_words, spaces=entdoc_spaces) # Get offsets based on gold words and BILUO entities entdoc_offsets = offsets_from_biluo_tags(entdoc, entities) aligned_offsets = [] aligned_spans = [] # Filter offsets to identify those that align with doc tokens for offset in entdoc_offsets: span = doc.char_span(offset[0], offset[1]) if span and not span.text.isspace(): aligned_offsets.append(offset) aligned_spans.append(span) # Convert back to BILUO for doc tokens and assign NER for all # aligned spans biluo_tags = biluo_tags_from_offsets(doc, aligned_offsets, missing=None) for span in aligned_spans: for i in range(span.start, span.end): self.ner[i] = biluo_tags[i] # Prevent whitespace that isn't within entities from being tagged as # an entity. for i in range(len(self.ner)): if self.tags[i] == "_SP": prev_ner = self.ner[i-1] if i >= 1 else None next_ner = self.ner[i+1] if (i+1) < len(self.ner) else None if prev_ner == "O" or next_ner == "O": self.ner[i] = "O" cycle = nonproj.contains_cycle(self.heads) if cycle is not None: raise ValueError(Errors.E069.format(cycle=cycle, cycle_tokens=" ".join([f"'{self.words[tok_id]}'" for tok_id in cycle]), doc_tokens=" ".join(words[:50]))) def __len__(self): """Get the number of gold-standard tokens. RETURNS (int): The number of gold-standard tokens. """ return self.length @property def is_projective(self): """Whether the provided syntactic annotations form a projective dependency tree. """ return not nonproj.is_nonproj_tree(self.heads) def docs_to_json(docs, id=0, ner_missing_tag="O"): """Convert a list of Doc objects into the JSON-serializable format used by the spacy train command. docs (iterable / Doc): The Doc object(s) to convert. id (int): Id for the JSON. RETURNS (dict): The data in spaCy's JSON format - each input doc will be treated as a paragraph in the output doc """ if isinstance(docs, Doc): docs = [docs] json_doc = {"id": id, "paragraphs": []} for i, doc in enumerate(docs): json_para = {'raw': doc.text, "sentences": [], "cats": []} for cat, val in doc.cats.items(): json_cat = {"label": cat, "value": val} json_para["cats"].append(json_cat) ent_offsets = [(e.start_char, e.end_char, e.label_) for e in doc.ents] biluo_tags = biluo_tags_from_offsets(doc, ent_offsets, missing=ner_missing_tag) for j, sent in enumerate(doc.sents): json_sent = {"tokens": [], "brackets": []} for token in sent: json_token = {"id": token.i, "orth": token.text} if doc.is_tagged: json_token["tag"] = token.tag_ json_token["pos"] = token.pos_ json_token["morph"] = token.morph_ json_token["lemma"] = token.lemma_ if doc.is_parsed: json_token["head"] = token.head.i-token.i json_token["dep"] = token.dep_ json_token["ner"] = biluo_tags[token.i] json_sent["tokens"].append(json_token) json_para["sentences"].append(json_sent) json_doc["paragraphs"].append(json_para) return json_doc def biluo_tags_from_offsets(doc, entities, missing="O"): """Encode labelled spans into per-token tags, using the Begin/In/Last/Unit/Out scheme (BILUO). doc (Doc): The document that the entity offsets refer to. The output tags will refer to the token boundaries within the document. entities (iterable): A sequence of `(start, end, label)` triples. `start` and `end` should be character-offset integers denoting the slice into the original string. RETURNS (list): A list of unicode strings, describing the tags. Each tag string will be of the form either "", "O" or "{action}-{label}", where action is one of "B", "I", "L", "U". The string "-" is used where the entity offsets don't align with the tokenization in the `Doc` object. The training algorithm will view these as missing values. "O" denotes a non-entity token. "B" denotes the beginning of a multi-token entity, "I" the inside of an entity of three or more tokens, and "L" the end of an entity of two or more tokens. "U" denotes a single-token entity. EXAMPLE: >>> text = 'I like London.' >>> entities = [(len('I like '), len('I like London'), 'LOC')] >>> doc = nlp.tokenizer(text) >>> tags = biluo_tags_from_offsets(doc, entities) >>> assert tags == ["O", "O", 'U-LOC', "O"] """ # Ensure no overlapping entity labels exist tokens_in_ents = {} starts = {token.idx: token.i for token in doc} ends = {token.idx + len(token): token.i for token in doc} biluo = ["-" for _ in doc] # Handle entity cases for start_char, end_char, label in entities: for token_index in range(start_char, end_char): if token_index in tokens_in_ents.keys(): raise ValueError(Errors.E103.format( span1=(tokens_in_ents[token_index][0], tokens_in_ents[token_index][1], tokens_in_ents[token_index][2]), span2=(start_char, end_char, label))) tokens_in_ents[token_index] = (start_char, end_char, label) start_token = starts.get(start_char) end_token = ends.get(end_char) # Only interested if the tokenization is correct if start_token is not None and end_token is not None: if start_token == end_token: biluo[start_token] = f"U-{label}" else: biluo[start_token] = f"B-{label}" for i in range(start_token+1, end_token): biluo[i] = f"I-{label}" biluo[end_token] = f"L-{label}" # Now distinguish the O cases from ones where we miss the tokenization entity_chars = set() for start_char, end_char, label in entities: for i in range(start_char, end_char): entity_chars.add(i) for token in doc: for i in range(token.idx, token.idx + len(token)): if i in entity_chars: break else: biluo[token.i] = missing if "-" in biluo: ent_str = str(entities) warnings.warn(Warnings.W030.format( text=doc.text[:50] + "..." if len(doc.text) > 50 else doc.text, entities=ent_str[:50] + "..." if len(ent_str) > 50 else ent_str )) return biluo def spans_from_biluo_tags(doc, tags): """Encode per-token tags following the BILUO scheme into Span object, e.g. to overwrite the doc.ents. doc (Doc): The document that the BILUO tags refer to. entities (iterable): A sequence of BILUO tags with each tag describing one token. Each tags string will be of the form of either "", "O" or "{action}-{label}", where action is one of "B", "I", "L", "U". RETURNS (list): A sequence of Span objects. """ token_offsets = tags_to_entities(tags) spans = [] for label, start_idx, end_idx in token_offsets: span = Span(doc, start_idx, end_idx + 1, label=label) spans.append(span) return spans def offsets_from_biluo_tags(doc, tags): """Encode per-token tags following the BILUO scheme into entity offsets. doc (Doc): The document that the BILUO tags refer to. entities (iterable): A sequence of BILUO tags with each tag describing one token. Each tags string will be of the form of either "", "O" or "{action}-{label}", where action is one of "B", "I", "L", "U". RETURNS (list): A sequence of `(start, end, label)` triples. `start` and `end` will be character-offset integers denoting the slice into the original string. """ spans = spans_from_biluo_tags(doc, tags) return [(span.start_char, span.end_char, span.label_) for span in spans] def is_punct_label(label): return label == "P" or label.lower() == "punct"