mirror of
https://github.com/explosion/spaCy.git
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312 lines
14 KiB
Cython
312 lines
14 KiB
Cython
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# cython: profile=True
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import re
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import random
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import numpy
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import tempfile
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import shutil
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import itertools
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from pathlib import Path
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import srsly
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import warnings
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from .. import util
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from ..syntax import nonproj
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from ..tokens import Doc, Span
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from ..errors import Errors, AlignmentError, Warnings
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from .iob_utils import offsets_from_biluo_tags
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from .align import align
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punct_re = re.compile(r"\W")
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def is_punct_label(label):
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return label == "P" or label.lower() == "punct"
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cdef class GoldParse:
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"""Collection for training annotations.
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DOCS: https://spacy.io/api/goldparse
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"""
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@classmethod
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def from_annotation(cls, doc, doc_annotation, token_annotation, make_projective=False):
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return cls(doc, words=token_annotation.words,
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tags=token_annotation.tags,
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pos=token_annotation.pos,
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morphs=token_annotation.morphs,
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lemmas=token_annotation.lemmas,
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heads=token_annotation.heads,
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deps=token_annotation.deps,
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entities=token_annotation.entities,
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sent_starts=token_annotation.sent_starts,
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cats=doc_annotation.cats,
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links=doc_annotation.links,
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make_projective=make_projective)
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def get_token_annotation(self):
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ids = None
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if self.words:
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ids = list(range(len(self.words)))
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return TokenAnnotation(ids=ids, words=self.words, tags=self.tags,
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pos=self.pos, morphs=self.morphs,
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lemmas=self.lemmas, heads=self.heads,
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deps=self.labels, entities=self.ner,
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sent_starts=self.sent_starts)
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def __init__(self, doc, words=None, tags=None, pos=None, morphs=None,
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lemmas=None, heads=None, deps=None, entities=None,
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sent_starts=None, make_projective=False, cats=None,
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links=None):
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"""Create a GoldParse. The fields will not be initialized if len(doc) is zero.
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doc (Doc): The document the annotations refer to.
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words (iterable): A sequence of unicode word strings.
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tags (iterable): A sequence of strings, representing tag annotations.
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pos (iterable): A sequence of strings, representing UPOS annotations.
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morphs (iterable): A sequence of strings, representing morph
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annotations.
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lemmas (iterable): A sequence of strings, representing lemma
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annotations.
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heads (iterable): A sequence of integers, representing syntactic
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head offsets.
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deps (iterable): A sequence of strings, representing the syntactic
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relation types.
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entities (iterable): A sequence of named entity annotations, either as
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BILUO tag strings, or as `(start_char, end_char, label)` tuples,
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representing the entity positions.
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sent_starts (iterable): A sequence of sentence position tags, 1 for
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the first word in a sentence, 0 for all others.
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cats (dict): Labels for text classification. Each key in the dictionary
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may be a string or an int, or a `(start_char, end_char, label)`
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tuple, indicating that the label is applied to only part of the
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document (usually a sentence). Unlike entity annotations, label
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annotations can overlap, i.e. a single word can be covered by
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multiple labelled spans. The TextCategorizer component expects
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true examples of a label to have the value 1.0, and negative
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examples of a label to have the value 0.0. Labels not in the
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dictionary are treated as missing - the gradient for those labels
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will be zero.
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links (dict): A dict with `(start_char, end_char)` keys,
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and the values being dicts with kb_id:value entries,
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representing the external IDs in a knowledge base (KB)
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mapped to either 1.0 or 0.0, indicating positive and
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negative examples respectively.
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RETURNS (GoldParse): The newly constructed object.
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"""
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self.mem = Pool()
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self.loss = 0
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self.length = len(doc)
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self.cats = {} if cats is None else dict(cats)
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self.links = {} if links is None else dict(links)
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# temporary doc for aligning entity annotation
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entdoc = None
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# avoid allocating memory if the doc does not contain any tokens
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if self.length == 0:
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self.words = []
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self.tags = []
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self.heads = []
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self.labels = []
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self.ner = []
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self.morphs = []
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# set a minimal orig so that the scorer can score an empty doc
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self.orig = TokenAnnotation(ids=[])
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else:
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if not words:
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words = [token.text for token in doc]
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if not tags:
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tags = [None for _ in words]
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if not pos:
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pos = [None for _ in words]
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if not morphs:
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morphs = [None for _ in words]
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if not lemmas:
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lemmas = [None for _ in words]
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if not heads:
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heads = [None for _ in words]
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if not deps:
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deps = [None for _ in words]
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if not sent_starts:
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sent_starts = [None for _ in words]
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if entities is None:
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entities = ["-" for _ in words]
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elif len(entities) == 0:
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entities = ["O" for _ in words]
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else:
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# Translate the None values to '-', to make processing easier.
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# See Issue #2603
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entities = [(ent if ent is not None else "-") for ent in entities]
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if not isinstance(entities[0], str):
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# Assume we have entities specified by character offset.
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# Create a temporary Doc corresponding to provided words
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# (to preserve gold tokenization) and text (to preserve
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# character offsets).
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entdoc_words, entdoc_spaces = util.get_words_and_spaces(words, doc.text)
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entdoc = Doc(doc.vocab, words=entdoc_words, spaces=entdoc_spaces)
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entdoc_entities = biluo_tags_from_offsets(entdoc, entities)
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# There may be some additional whitespace tokens in the
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# temporary doc, so check that the annotations align with
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# the provided words while building a list of BILUO labels.
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entities = []
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words_offset = 0
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for i in range(len(entdoc_words)):
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if words[i + words_offset] == entdoc_words[i]:
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entities.append(entdoc_entities[i])
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else:
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words_offset -= 1
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if len(entities) != len(words):
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warnings.warn(Warnings.W029.format(text=doc.text))
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entities = ["-" for _ in words]
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# These are filled by the tagger/parser/entity recogniser
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self.c.tags = <int*>self.mem.alloc(len(doc), sizeof(int))
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self.c.heads = <int*>self.mem.alloc(len(doc), sizeof(int))
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self.c.labels = <attr_t*>self.mem.alloc(len(doc), sizeof(attr_t))
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self.c.has_dep = <int*>self.mem.alloc(len(doc), sizeof(int))
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self.c.sent_start = <int*>self.mem.alloc(len(doc), sizeof(int))
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self.c.ner = <Transition*>self.mem.alloc(len(doc), sizeof(Transition))
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self.words = [None] * len(doc)
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self.tags = [None] * len(doc)
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self.pos = [None] * len(doc)
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self.morphs = [None] * len(doc)
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self.lemmas = [None] * len(doc)
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self.heads = [None] * len(doc)
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self.labels = [None] * len(doc)
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self.ner = [None] * len(doc)
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self.sent_starts = [None] * len(doc)
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# This needs to be done before we align the words
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if make_projective and any(heads) and any(deps) :
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heads, deps = nonproj.projectivize(heads, deps)
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# Do many-to-one alignment for misaligned tokens.
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# If we over-segment, we'll have one gold word that covers a sequence
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# of predicted words
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# If we under-segment, we'll have one predicted word that covers a
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# sequence of gold words.
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# If we "mis-segment", we'll have a sequence of predicted words covering
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# a sequence of gold words. That's many-to-many -- we don't do that
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# except for NER spans where the start and end can be aligned.
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cost, i2j, j2i, i2j_multi, j2i_multi = align([t.orth_ for t in doc], words)
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self.cand_to_gold = [(j if j >= 0 else None) for j in i2j]
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self.gold_to_cand = [(i if i >= 0 else None) for i in j2i]
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self.orig = TokenAnnotation(ids=list(range(len(words))),
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words=words, tags=tags, pos=pos, morphs=morphs,
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lemmas=lemmas, heads=heads, deps=deps, entities=entities,
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sent_starts=sent_starts, brackets=[])
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for i, gold_i in enumerate(self.cand_to_gold):
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if doc[i].text.isspace():
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self.words[i] = doc[i].text
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self.tags[i] = "_SP"
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self.pos[i] = "SPACE"
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self.morphs[i] = None
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self.lemmas[i] = None
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self.heads[i] = None
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self.labels[i] = None
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self.ner[i] = None
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self.sent_starts[i] = 0
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if gold_i is None:
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if i in i2j_multi:
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self.words[i] = words[i2j_multi[i]]
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self.tags[i] = tags[i2j_multi[i]]
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self.pos[i] = pos[i2j_multi[i]]
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self.morphs[i] = morphs[i2j_multi[i]]
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self.lemmas[i] = lemmas[i2j_multi[i]]
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self.sent_starts[i] = sent_starts[i2j_multi[i]]
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is_last = i2j_multi[i] != i2j_multi.get(i+1)
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# Set next word in multi-token span as head, until last
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if not is_last:
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self.heads[i] = i+1
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self.labels[i] = "subtok"
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else:
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head_i = heads[i2j_multi[i]]
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if head_i:
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self.heads[i] = self.gold_to_cand[head_i]
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self.labels[i] = deps[i2j_multi[i]]
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ner_tag = entities[i2j_multi[i]]
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# Assign O/- for many-to-one O/- NER tags
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if ner_tag in ("O", "-"):
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self.ner[i] = ner_tag
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else:
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self.words[i] = words[gold_i]
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self.tags[i] = tags[gold_i]
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self.pos[i] = pos[gold_i]
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self.morphs[i] = morphs[gold_i]
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self.lemmas[i] = lemmas[gold_i]
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self.sent_starts[i] = sent_starts[gold_i]
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if heads[gold_i] is None:
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self.heads[i] = None
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else:
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self.heads[i] = self.gold_to_cand[heads[gold_i]]
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self.labels[i] = deps[gold_i]
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self.ner[i] = entities[gold_i]
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# Assign O/- for one-to-many O/- NER tags
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for j, cand_j in enumerate(self.gold_to_cand):
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if cand_j is None:
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if j in j2i_multi:
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i = j2i_multi[j]
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ner_tag = entities[j]
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if ner_tag in ("O", "-"):
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self.ner[i] = ner_tag
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# If there is entity annotation and some tokens remain unaligned,
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# align all entities at the character level to account for all
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# possible token misalignments within the entity spans
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if any([e not in ("O", "-") for e in entities]) and None in self.ner:
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# If the temporary entdoc wasn't created above, initialize it
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if not entdoc:
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entdoc_words, entdoc_spaces = util.get_words_and_spaces(words, doc.text)
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entdoc = Doc(doc.vocab, words=entdoc_words, spaces=entdoc_spaces)
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# Get offsets based on gold words and BILUO entities
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entdoc_offsets = offsets_from_biluo_tags(entdoc, entities)
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aligned_offsets = []
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aligned_spans = []
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# Filter offsets to identify those that align with doc tokens
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for offset in entdoc_offsets:
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span = doc.char_span(offset[0], offset[1])
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if span and not span.text.isspace():
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aligned_offsets.append(offset)
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aligned_spans.append(span)
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# Convert back to BILUO for doc tokens and assign NER for all
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# aligned spans
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biluo_tags = biluo_tags_from_offsets(doc, aligned_offsets, missing=None)
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for span in aligned_spans:
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for i in range(span.start, span.end):
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self.ner[i] = biluo_tags[i]
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# Prevent whitespace that isn't within entities from being tagged as
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# an entity.
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for i in range(len(self.ner)):
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if self.tags[i] == "_SP":
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prev_ner = self.ner[i-1] if i >= 1 else None
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next_ner = self.ner[i+1] if (i+1) < len(self.ner) else None
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if prev_ner == "O" or next_ner == "O":
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self.ner[i] = "O"
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cycle = nonproj.contains_cycle(self.heads)
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if cycle is not None:
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raise ValueError(Errors.E069.format(cycle=cycle,
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cycle_tokens=" ".join([f"'{self.words[tok_id]}'" for tok_id in cycle]),
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doc_tokens=" ".join(words[:50])))
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def __len__(self):
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"""Get the number of gold-standard tokens.
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RETURNS (int): The number of gold-standard tokens.
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"""
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return self.length
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@property
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def is_projective(self):
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"""Whether the provided syntactic annotations form a projective
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dependency tree.
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"""
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return not nonproj.is_nonproj_tree(self.heads)
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