import warnings import numpy from ..tokens.doc cimport Doc from ..tokens.span cimport Span from ..tokens.span import Span from ..attrs import IDS from .align import Alignment from .iob_utils import biluo_to_iob, biluo_tags_from_offsets, biluo_tags_from_doc from .iob_utils import spans_from_biluo_tags from ..errors import Errors, Warnings from ..syntax import nonproj cpdef Doc annotations2doc(vocab, tok_annot, doc_annot): """ Create a Doc from dictionaries with token and doc annotations. """ attrs, array = _annot2array(vocab, tok_annot, doc_annot) output = Doc(vocab, words=tok_annot["ORTH"], spaces=tok_annot["SPACY"]) if "entities" in doc_annot: _add_entities_to_doc(output, doc_annot["entities"]) if array.size: output = output.from_array(attrs, array) # links are currently added with ENT_KB_ID on the token level output.cats.update(doc_annot.get("cats", {})) return output cdef class Example: def __init__(self, Doc predicted, Doc reference, *, alignment=None): """ Doc can either be text, or an actual Doc """ if predicted is None: raise TypeError(Errors.E972.format(arg="predicted")) if reference is None: raise TypeError(Errors.E972.format(arg="reference")) self.x = predicted self.y = reference self._alignment = alignment property predicted: def __get__(self): return self.x def __set__(self, doc): self.x = doc property reference: def __get__(self): return self.y def __set__(self, doc): self.y = doc def copy(self): return Example( self.x.copy(), self.y.copy() ) @classmethod def from_dict(cls, Doc predicted, dict example_dict): if example_dict is None: raise ValueError(Errors.E976) if not isinstance(predicted, Doc): raise TypeError(Errors.E975.format(type=type(predicted))) example_dict = _fix_legacy_dict_data(example_dict) tok_dict, doc_dict = _parse_example_dict_data(example_dict) if "ORTH" not in tok_dict: tok_dict["ORTH"] = [tok.text for tok in predicted] tok_dict["SPACY"] = [tok.whitespace_ for tok in predicted] if not _has_field(tok_dict, "SPACY"): spaces = _guess_spaces(predicted.text, tok_dict["ORTH"]) return Example( predicted, annotations2doc(predicted.vocab, tok_dict, doc_dict) ) @property def alignment(self): if self._alignment is None: spacy_words = [token.orth_ for token in self.predicted] gold_words = [token.orth_ for token in self.reference] if gold_words == []: gold_words = spacy_words self._alignment = Alignment.from_strings(spacy_words, gold_words) return self._alignment def get_aligned(self, field, as_string=False): """Return an aligned array for a token attribute.""" align = self.alignment.x2y vocab = self.reference.vocab gold_values = self.reference.to_array([field]) output = [None] * len(self.predicted) for token in self.predicted: if token.is_space: output[token.i] = None else: values = gold_values[align[token.i].dataXd] values = values.ravel() if len(values) == 0: output[token.i] = None elif len(values) == 1: output[token.i] = values[0] elif len(set(list(values))) == 1: # If all aligned tokens have the same value, use it. output[token.i] = values[0] else: output[token.i] = None if as_string and field not in ["ENT_IOB", "SENT_START"]: output = [vocab.strings[o] if o is not None else o for o in output] return output def get_aligned_parse(self, projectivize=True): cand_to_gold = self.alignment.x2y gold_to_cand = self.alignment.y2x aligned_heads = [None] * self.x.length aligned_deps = [None] * self.x.length heads = [token.head.i for token in self.y] deps = [token.dep_ for token in self.y] if projectivize: heads, deps = nonproj.projectivize(heads, deps) for cand_i in range(self.x.length): if cand_to_gold.lengths[cand_i] == 1: gold_i = cand_to_gold[cand_i].dataXd[0, 0] if gold_to_cand.lengths[heads[gold_i]] == 1: aligned_heads[cand_i] = int(gold_to_cand[heads[gold_i]].dataXd[0, 0]) aligned_deps[cand_i] = deps[gold_i] return aligned_heads, aligned_deps def get_aligned_spans_x2y(self, x_spans): return self._get_aligned_spans(self.y, x_spans, self.alignment.x2y) def get_aligned_spans_y2x(self, y_spans): return self._get_aligned_spans(self.x, y_spans, self.alignment.y2x) def _get_aligned_spans(self, doc, spans, align): seen = set() output = [] for span in spans: indices = align[span.start : span.end].data.ravel() indices = [idx for idx in indices if idx not in seen] if len(indices) >= 1: aligned_span = Span(doc, indices[0], indices[-1] + 1, label=span.label) target_text = span.text.lower().strip().replace(" ", "") our_text = aligned_span.text.lower().strip().replace(" ", "") if our_text == target_text: output.append(aligned_span) seen.update(indices) return output def get_aligned_ner(self): if not self.y.is_nered: return [None] * len(self.x) # should this be 'missing' instead of 'None' ? x_ents = self.get_aligned_spans_y2x(self.y.ents) # Default to 'None' for missing values x_tags = biluo_tags_from_offsets( self.x, [(e.start_char, e.end_char, e.label_) for e in x_ents], missing=None ) # Now fill the tokens we can align to O. O = 2 # I=1, O=2, B=3 for i, ent_iob in enumerate(self.get_aligned("ENT_IOB")): if x_tags[i] is None: if ent_iob == O: x_tags[i] = "O" elif self.x[i].is_space: x_tags[i] = "O" return x_tags def to_dict(self): return { "doc_annotation": { "cats": dict(self.reference.cats), "entities": biluo_tags_from_doc(self.reference), "links": self._links_to_dict() }, "token_annotation": { "ids": [t.i+1 for t in self.reference], "words": [t.text for t in self.reference], "tags": [t.tag_ for t in self.reference], "lemmas": [t.lemma_ for t in self.reference], "pos": [t.pos_ for t in self.reference], "morphs": [t.morph_ for t in self.reference], "heads": [t.head.i for t in self.reference], "deps": [t.dep_ for t in self.reference], "sent_starts": [int(bool(t.is_sent_start)) for t in self.reference] } } def _links_to_dict(self): links = {} for ent in self.reference.ents: if ent.kb_id_: links[(ent.start_char, ent.end_char)] = {ent.kb_id_: 1.0} return 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.reference.is_sentenced: return [self] align = self.alignment.y2x seen_indices = set() output = [] for y_sent in self.reference.sents: indices = align[y_sent.start : y_sent.end].data.ravel() indices = [idx for idx in indices if idx not in seen_indices] if indices: x_sent = self.predicted[indices[0] : indices[-1] + 1] output.append(Example(x_sent.as_doc(), y_sent.as_doc())) seen_indices.update(indices) return output property text: def __get__(self): return self.x.text def __str__(self): return str(self.to_dict()) def __repr__(self): return str(self.to_dict()) def _annot2array(vocab, tok_annot, doc_annot): attrs = [] values = [] for key, value in doc_annot.items(): if value: if key == "entities": pass elif key == "links": ent_kb_ids = _parse_links(vocab, tok_annot["ORTH"], tok_annot["SPACY"], value) tok_annot["ENT_KB_ID"] = ent_kb_ids elif key == "cats": pass else: raise ValueError(Errors.E974.format(obj="doc", key=key)) for key, value in tok_annot.items(): if key not in IDS: raise ValueError(Errors.E974.format(obj="token", key=key)) elif key in ["ORTH", "SPACY"]: pass elif key == "HEAD": attrs.append(key) values.append([h-i for i, h in enumerate(value)]) elif key == "SENT_START": attrs.append(key) values.append(value) elif key == "MORPH": attrs.append(key) values.append([vocab.morphology.add(v) for v in value]) else: attrs.append(key) values.append([vocab.strings.add(v) for v in value]) array = numpy.asarray(values, dtype="uint64") return attrs, array.T def _add_entities_to_doc(doc, ner_data): if ner_data is None: return elif ner_data == []: doc.ents = [] elif isinstance(ner_data[0], tuple): return _add_entities_to_doc( doc, biluo_tags_from_offsets(doc, ner_data) ) elif isinstance(ner_data[0], str) or ner_data[0] is None: return _add_entities_to_doc( doc, spans_from_biluo_tags(doc, ner_data) ) elif isinstance(ner_data[0], Span): # Ugh, this is super messy. Really hard to set O entities doc.ents = ner_data doc.ents = [span for span in ner_data if span.label_] else: raise ValueError(Errors.E973) def _parse_example_dict_data(example_dict): return ( example_dict["token_annotation"], example_dict["doc_annotation"] ) def _fix_legacy_dict_data(example_dict): token_dict = example_dict.get("token_annotation", {}) doc_dict = example_dict.get("doc_annotation", {}) for key, value in example_dict.items(): if value: if key in ("token_annotation", "doc_annotation"): pass elif key == "ids": pass elif key in ("cats", "links"): doc_dict[key] = value elif key in ("ner", "entities"): doc_dict["entities"] = value else: token_dict[key] = value # Remap keys remapping = { "words": "ORTH", "tags": "TAG", "pos": "POS", "lemmas": "LEMMA", "deps": "DEP", "heads": "HEAD", "sent_starts": "SENT_START", "morphs": "MORPH", "spaces": "SPACY", } old_token_dict = token_dict token_dict = {} for key, value in old_token_dict.items(): if key in ("text", "ids", "brackets"): pass elif key in remapping: token_dict[remapping[key]] = value else: raise KeyError(Errors.E983.format(key=key, dict="token_annotation", keys=remapping.keys())) text = example_dict.get("text", example_dict.get("raw")) if _has_field(token_dict, "ORTH") and not _has_field(token_dict, "SPACY"): token_dict["SPACY"] = _guess_spaces(text, token_dict["ORTH"]) if "HEAD" in token_dict and "SENT_START" in token_dict: # If heads are set, we don't also redundantly specify SENT_START. token_dict.pop("SENT_START") warnings.warn(Warnings.W092) return { "token_annotation": token_dict, "doc_annotation": doc_dict } def _has_field(annot, field): if field not in annot: return False elif annot[field] is None: return False elif len(annot[field]) == 0: return False elif all([value is None for value in annot[field]]): return False else: return True def _parse_ner_tags(biluo_or_offsets, vocab, words, spaces): if isinstance(biluo_or_offsets[0], (list, tuple)): # Convert to biluo if necessary # This is annoying but to convert the offsets we need a Doc # that has the target tokenization. reference = Doc(vocab, words=words, spaces=spaces) biluo = biluo_tags_from_offsets(reference, biluo_or_offsets) else: biluo = biluo_or_offsets ent_iobs = [] ent_types = [] for iob_tag in biluo_to_iob(biluo): if iob_tag in (None, "-"): ent_iobs.append("") ent_types.append("") else: ent_iobs.append(iob_tag.split("-")[0]) if iob_tag.startswith("I") or iob_tag.startswith("B"): ent_types.append(iob_tag.split("-", 1)[1]) else: ent_types.append("") return ent_iobs, ent_types def _parse_links(vocab, words, spaces, links): reference = Doc(vocab, words=words, spaces=spaces) starts = {token.idx: token.i for token in reference} ends = {token.idx + len(token): token.i for token in reference} ent_kb_ids = ["" for _ in reference] for index, annot_dict in links.items(): true_kb_ids = [] for key, value in annot_dict.items(): if value == 1.0: true_kb_ids.append(key) if len(true_kb_ids) > 1: raise ValueError(Errors.E980) if len(true_kb_ids) == 1: start_char, end_char = index start_token = starts.get(start_char) end_token = ends.get(end_char) if start_token is None or end_token is None: raise ValueError(Errors.E981) for i in range(start_token, end_token+1): ent_kb_ids[i] = true_kb_ids[0] return ent_kb_ids def _guess_spaces(text, words): if text is None: return None spaces = [] text_pos = 0 # align words with text for word in words: try: word_start = text[text_pos:].index(word) except ValueError: spaces.append(True) continue text_pos += word_start + len(word) if text_pos < len(text) and text[text_pos] == " ": spaces.append(True) else: spaces.append(False) return spaces