mirror of
https://github.com/explosion/spaCy.git
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1707 lines
68 KiB
Cython
1707 lines
68 KiB
Cython
# cython: infer_types=True, bounds_check=False, profile=True
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cimport cython
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cimport numpy as np
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from libc.string cimport memcpy
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from libc.math cimport sqrt
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from libc.stdint cimport int32_t, uint64_t
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import copy
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from collections import Counter
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from enum import Enum
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import itertools
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import numpy
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import srsly
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from thinc.api import get_array_module
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from thinc.util import copy_array
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import warnings
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from .span cimport Span
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from .token cimport MISSING_DEP
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from ._dict_proxies import SpanGroups
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from .token cimport Token
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from ..lexeme cimport Lexeme, EMPTY_LEXEME
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from ..typedefs cimport attr_t, flags_t
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from ..attrs cimport attr_id_t
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from ..attrs cimport LENGTH, POS, LEMMA, TAG, MORPH, DEP, HEAD, SPACY, ENT_IOB
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from ..attrs cimport ENT_TYPE, ENT_ID, ENT_KB_ID, SENT_START, IDX, NORM
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from ..attrs import intify_attr, IDS
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from ..compat import copy_reg, pickle
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from ..errors import Errors, Warnings
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from ..morphology import Morphology
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from .. import util
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from .underscore import Underscore, get_ext_args
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from ._retokenize import Retokenizer
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from ._serialize import ALL_ATTRS as DOCBIN_ALL_ATTRS
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DEF PADDING = 5
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cdef int bounds_check(int i, int length, int padding) except -1:
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if (i + padding) < 0:
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raise IndexError(Errors.E026.format(i=i, length=length))
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if (i - padding) >= length:
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raise IndexError(Errors.E026.format(i=i, length=length))
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cdef attr_t get_token_attr(const TokenC* token, attr_id_t feat_name) nogil:
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if feat_name == LEMMA:
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return token.lemma
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elif feat_name == NORM:
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if not token.norm:
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return token.lex.norm
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return token.norm
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elif feat_name == POS:
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return token.pos
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elif feat_name == TAG:
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return token.tag
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elif feat_name == MORPH:
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return token.morph
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elif feat_name == DEP:
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return token.dep
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elif feat_name == HEAD:
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return token.head
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elif feat_name == SENT_START:
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return token.sent_start
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elif feat_name == SPACY:
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return token.spacy
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elif feat_name == ENT_IOB:
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return token.ent_iob
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elif feat_name == ENT_TYPE:
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return token.ent_type
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elif feat_name == ENT_ID:
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return token.ent_id
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elif feat_name == ENT_KB_ID:
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return token.ent_kb_id
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elif feat_name == IDX:
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return token.idx
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else:
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return Lexeme.get_struct_attr(token.lex, feat_name)
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cdef attr_t get_token_attr_for_matcher(const TokenC* token, attr_id_t feat_name) nogil:
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if feat_name == SENT_START:
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if token.sent_start == 1:
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return True
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else:
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return False
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else:
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return get_token_attr(token, feat_name)
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class SetEntsDefault(str, Enum):
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blocked = "blocked"
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missing = "missing"
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outside = "outside"
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unmodified = "unmodified"
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@classmethod
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def values(cls):
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return list(cls.__members__.keys())
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cdef class Doc:
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"""A sequence of Token objects. Access sentences and named entities, export
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annotations to numpy arrays, losslessly serialize to compressed binary
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strings. The `Doc` object holds an array of `TokenC` structs. The
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Python-level `Token` and `Span` objects are views of this array, i.e.
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they don't own the data themselves.
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EXAMPLE:
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Construction 1
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>>> doc = nlp(u'Some text')
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Construction 2
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>>> from spacy.tokens import Doc
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>>> doc = Doc(nlp.vocab, words=["hello", "world", "!"], spaces=[True, False, False])
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DOCS: https://nightly.spacy.io/api/doc
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"""
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@classmethod
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def set_extension(cls, name, **kwargs):
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"""Define a custom attribute which becomes available as `Doc._`.
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name (str): Name of the attribute to set.
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default: Optional default value of the attribute.
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getter (callable): Optional getter function.
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setter (callable): Optional setter function.
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method (callable): Optional method for method extension.
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force (bool): Force overwriting existing attribute.
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DOCS: https://nightly.spacy.io/api/doc#set_extension
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USAGE: https://nightly.spacy.io/usage/processing-pipelines#custom-components-attributes
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"""
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if cls.has_extension(name) and not kwargs.get("force", False):
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raise ValueError(Errors.E090.format(name=name, obj="Doc"))
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Underscore.doc_extensions[name] = get_ext_args(**kwargs)
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@classmethod
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def get_extension(cls, name):
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"""Look up a previously registered extension by name.
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name (str): Name of the extension.
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RETURNS (tuple): A `(default, method, getter, setter)` tuple.
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DOCS: https://nightly.spacy.io/api/doc#get_extension
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"""
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return Underscore.doc_extensions.get(name)
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@classmethod
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def has_extension(cls, name):
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"""Check whether an extension has been registered.
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name (str): Name of the extension.
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RETURNS (bool): Whether the extension has been registered.
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DOCS: https://nightly.spacy.io/api/doc#has_extension
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"""
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return name in Underscore.doc_extensions
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@classmethod
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def remove_extension(cls, name):
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"""Remove a previously registered extension.
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name (str): Name of the extension.
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RETURNS (tuple): A `(default, method, getter, setter)` tuple of the
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removed extension.
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DOCS: https://nightly.spacy.io/api/doc#remove_extension
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"""
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if not cls.has_extension(name):
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raise ValueError(Errors.E046.format(name=name))
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return Underscore.doc_extensions.pop(name)
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def __init__(
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self,
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Vocab vocab,
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words=None,
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spaces=None,
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*,
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user_data=None,
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tags=None,
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pos=None,
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morphs=None,
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lemmas=None,
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heads=None,
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deps=None,
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sent_starts=None,
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ents=None,
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):
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"""Create a Doc object.
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vocab (Vocab): A vocabulary object, which must match any models you
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want to use (e.g. tokenizer, parser, entity recognizer).
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words (Optional[List[str]]): A list of unicode strings to add to the document
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as words. If `None`, defaults to empty list.
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spaces (Optional[List[bool]]): A list of boolean values, of the same length as
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words. True means that the word is followed by a space, False means
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it is not. If `None`, defaults to `[True]*len(words)`
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user_data (dict or None): Optional extra data to attach to the Doc.
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tags (Optional[List[str]]): A list of unicode strings, of the same
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length as words, to assign as token.tag. Defaults to None.
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pos (Optional[List[str]]): A list of unicode strings, of the same
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length as words, to assign as token.pos. Defaults to None.
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morphs (Optional[List[str]]): A list of unicode strings, of the same
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length as words, to assign as token.morph. Defaults to None.
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lemmas (Optional[List[str]]): A list of unicode strings, of the same
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length as words, to assign as token.lemma. Defaults to None.
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heads (Optional[List[int]]): A list of values, of the same length as
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words, to assign as heads. Head indices are the position of the
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head in the doc. Defaults to None.
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deps (Optional[List[str]]): A list of unicode strings, of the same
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length as words, to assign as token.dep. Defaults to None.
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sent_starts (Optional[List[Union[bool, None]]]): A list of values, of
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the same length as words, to assign as token.is_sent_start. Will be
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overridden by heads if heads is provided. Defaults to None.
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ents (Optional[List[str]]): A list of unicode strings, of the same
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length as words, as IOB tags to assign as token.ent_iob and
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token.ent_type. Defaults to None.
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DOCS: https://nightly.spacy.io/api/doc#init
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"""
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self.vocab = vocab
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size = max(20, (len(words) if words is not None else 0))
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self.mem = Pool()
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self.spans = SpanGroups(self)
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# Guarantee self.lex[i-x], for any i >= 0 and x < padding is in bounds
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# However, we need to remember the true starting places, so that we can
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# realloc.
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assert size + (PADDING*2) > 0
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data_start = <TokenC*>self.mem.alloc(size + (PADDING*2), sizeof(TokenC))
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cdef int i
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for i in range(size + (PADDING*2)):
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data_start[i].lex = &EMPTY_LEXEME
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data_start[i].l_edge = i
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data_start[i].r_edge = i
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self.c = data_start + PADDING
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self.max_length = size
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self.length = 0
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self.sentiment = 0.0
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self.cats = {}
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self.user_hooks = {}
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self.user_token_hooks = {}
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self.user_span_hooks = {}
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self.tensor = numpy.zeros((0,), dtype="float32")
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self.user_data = {} if user_data is None else user_data
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self._vector = None
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self.noun_chunks_iterator = self.vocab.get_noun_chunks
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cdef bint has_space
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if words is None and spaces is not None:
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raise ValueError(Errors.E908)
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elif spaces is None and words is not None:
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self.has_unknown_spaces = True
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else:
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self.has_unknown_spaces = False
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words = words if words is not None else []
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spaces = spaces if spaces is not None else ([True] * len(words))
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if len(spaces) != len(words):
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raise ValueError(Errors.E027)
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cdef const LexemeC* lexeme
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for word, has_space in zip(words, spaces):
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if isinstance(word, unicode):
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lexeme = self.vocab.get(self.mem, word)
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elif isinstance(word, bytes):
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raise ValueError(Errors.E028.format(value=word))
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else:
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lexeme = self.vocab.get_by_orth(self.mem, word)
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self.push_back(lexeme, has_space)
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if heads is not None:
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heads = [head - i if head is not None else 0 for i, head in enumerate(heads)]
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if deps is not None:
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MISSING_DEP_ = self.vocab.strings[MISSING_DEP]
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deps = [dep if dep is not None else MISSING_DEP_ for dep in deps]
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if deps and not heads:
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heads = [0] * len(deps)
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if sent_starts is not None:
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for i in range(len(sent_starts)):
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if sent_starts[i] is True:
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sent_starts[i] = 1
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elif sent_starts[i] is False:
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sent_starts[i] = -1
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elif sent_starts[i] is None or sent_starts[i] not in [-1, 0, 1]:
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sent_starts[i] = 0
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ent_iobs = None
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ent_types = None
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if ents is not None:
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iob_strings = Token.iob_strings()
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# make valid IOB2 out of IOB1 or IOB2
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for i, ent in enumerate(ents):
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if ent is "":
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ents[i] = None
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elif ent is not None and not isinstance(ent, str):
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raise ValueError(Errors.E177.format(tag=ent))
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if i < len(ents) - 1:
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# OI -> OB
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if (ent is None or ent.startswith("O")) and \
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(ents[i+1] is not None and ents[i+1].startswith("I")):
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ents[i+1] = "B" + ents[i+1][1:]
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# B-TYPE1 I-TYPE2 or I-TYPE1 I-TYPE2 -> B/I-TYPE1 B-TYPE2
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if ent is not None and ents[i+1] is not None and \
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(ent.startswith("B") or ent.startswith("I")) and \
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ents[i+1].startswith("I") and \
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ent[1:] != ents[i+1][1:]:
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ents[i+1] = "B" + ents[i+1][1:]
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ent_iobs = []
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ent_types = []
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for ent in ents:
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if ent is None:
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ent_iobs.append(iob_strings.index(""))
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ent_types.append("")
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elif ent == "O":
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ent_iobs.append(iob_strings.index(ent))
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ent_types.append("")
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else:
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if len(ent) < 3 or ent[1] != "-":
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raise ValueError(Errors.E177.format(tag=ent))
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ent_iob, ent_type = ent.split("-", 1)
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if ent_iob not in iob_strings:
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raise ValueError(Errors.E177.format(tag=ent))
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ent_iob = iob_strings.index(ent_iob)
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ent_iobs.append(ent_iob)
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ent_types.append(ent_type)
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headings = []
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values = []
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annotations = [pos, heads, deps, lemmas, tags, morphs, sent_starts, ent_iobs, ent_types]
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possible_headings = [POS, HEAD, DEP, LEMMA, TAG, MORPH, SENT_START, ENT_IOB, ENT_TYPE]
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for a, annot in enumerate(annotations):
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if annot is not None:
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if len(annot) != len(words):
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raise ValueError(Errors.E189)
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headings.append(possible_headings[a])
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if annot is not heads and annot is not sent_starts and annot is not ent_iobs:
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values.extend(annot)
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for value in values:
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if value is not None:
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self.vocab.strings.add(value)
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# if there are any other annotations, set them
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if headings:
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attrs = self.to_array(headings)
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j = 0
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for annot in annotations:
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if annot:
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if annot is heads or annot is sent_starts or annot is ent_iobs:
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for i in range(len(words)):
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if attrs.ndim == 1:
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attrs[i] = annot[i]
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else:
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attrs[i, j] = annot[i]
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elif annot is morphs:
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for i in range(len(words)):
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morph_key = vocab.morphology.add(morphs[i])
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if attrs.ndim == 1:
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attrs[i] = morph_key
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else:
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attrs[i, j] = morph_key
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else:
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for i in range(len(words)):
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if attrs.ndim == 1:
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attrs[i] = self.vocab.strings[annot[i]]
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else:
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attrs[i, j] = self.vocab.strings[annot[i]]
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j += 1
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self.from_array(headings, attrs)
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@property
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def _(self):
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"""Custom extension attributes registered via `set_extension`."""
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return Underscore(Underscore.doc_extensions, self)
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@property
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def is_tagged(self):
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warnings.warn(Warnings.W107.format(prop="is_tagged", attr="TAG"), DeprecationWarning)
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return self.has_annotation("TAG")
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@property
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def is_parsed(self):
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warnings.warn(Warnings.W107.format(prop="is_parsed", attr="DEP"), DeprecationWarning)
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return self.has_annotation("DEP")
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@property
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def is_nered(self):
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warnings.warn(Warnings.W107.format(prop="is_nered", attr="ENT_IOB"), DeprecationWarning)
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return self.has_annotation("ENT_IOB")
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@property
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def is_sentenced(self):
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warnings.warn(Warnings.W107.format(prop="is_sentenced", attr="SENT_START"), DeprecationWarning)
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return self.has_annotation("SENT_START")
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def has_annotation(self, attr, *, require_complete=False):
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"""Check whether the doc contains annotation on a token attribute.
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attr (Union[int, str]): The attribute string name or int ID.
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require_complete (bool): Whether to check that the attribute is set on
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every token in the doc.
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RETURNS (bool): Whether annotation is present.
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DOCS: https://nightly.spacy.io/api/doc#has_annotation
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"""
|
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# empty docs are always annotated
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if self.length == 0:
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return True
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cdef int i
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cdef int range_start = 0
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if attr == "IS_SENT_START" or attr == self.vocab.strings["IS_SENT_START"]:
|
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attr = SENT_START
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attr = intify_attr(attr)
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# adjust attributes
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if attr == HEAD:
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# HEAD does not have an unset state, so rely on DEP
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attr = DEP
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# special cases for sentence boundaries
|
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if attr == SENT_START:
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if "sents" in self.user_hooks:
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return True
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# docs of length 1 always have sentence boundaries
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if self.length == 1:
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return True
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range_start = 1
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if require_complete:
|
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return all(Token.get_struct_attr(&self.c[i], attr) for i in range(range_start, self.length))
|
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else:
|
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return any(Token.get_struct_attr(&self.c[i], attr) for i in range(range_start, self.length))
|
||
|
||
def __getitem__(self, object i):
|
||
"""Get a `Token` or `Span` object.
|
||
|
||
i (int or tuple) The index of the token, or the slice of the document
|
||
to get.
|
||
RETURNS (Token or Span): The token at `doc[i]]`, or the span at
|
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`doc[start : end]`.
|
||
|
||
EXAMPLE:
|
||
>>> doc[i]
|
||
Get the `Token` object at position `i`, where `i` is an integer.
|
||
Negative indexing is supported, and follows the usual Python
|
||
semantics, i.e. `doc[-2]` is `doc[len(doc) - 2]`.
|
||
|
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>>> doc[start : end]]
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Get a `Span` object, starting at position `start` and ending at
|
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position `end`, where `start` and `end` are token indices. For
|
||
instance, `doc[2:5]` produces a span consisting of tokens 2, 3 and
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||
4. Stepped slices (e.g. `doc[start : end : step]`) are not
|
||
supported, as `Span` objects must be contiguous (cannot have gaps).
|
||
You can use negative indices and open-ended ranges, which have
|
||
their normal Python semantics.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#getitem
|
||
"""
|
||
if isinstance(i, slice):
|
||
start, stop = util.normalize_slice(len(self), i.start, i.stop, i.step)
|
||
return Span(self, start, stop, label=0)
|
||
if i < 0:
|
||
i = self.length + i
|
||
bounds_check(i, self.length, PADDING)
|
||
return Token.cinit(self.vocab, &self.c[i], i, self)
|
||
|
||
def __iter__(self):
|
||
"""Iterate over `Token` objects, from which the annotations can be
|
||
easily accessed. This is the main way of accessing `Token` objects,
|
||
which are the main way annotations are accessed from Python. If faster-
|
||
than-Python speeds are required, you can instead access the annotations
|
||
as a numpy array, or access the underlying C data directly from Cython.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#iter
|
||
"""
|
||
cdef int i
|
||
for i in range(self.length):
|
||
yield Token.cinit(self.vocab, &self.c[i], i, self)
|
||
|
||
def __len__(self):
|
||
"""The number of tokens in the document.
|
||
|
||
RETURNS (int): The number of tokens in the document.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#len
|
||
"""
|
||
return self.length
|
||
|
||
def __unicode__(self):
|
||
return "".join([t.text_with_ws for t in self])
|
||
|
||
def __bytes__(self):
|
||
return "".join([t.text_with_ws for t in self]).encode("utf-8")
|
||
|
||
def __str__(self):
|
||
return self.__unicode__()
|
||
|
||
def __repr__(self):
|
||
return self.__str__()
|
||
|
||
@property
|
||
def doc(self):
|
||
return self
|
||
|
||
def char_span(self, int start_idx, int end_idx, label=0, kb_id=0, vector=None, alignment_mode="strict"):
|
||
"""Create a `Span` object from the slice
|
||
`doc.text[start_idx : end_idx]`. Returns None if no valid `Span` can be
|
||
created.
|
||
|
||
doc (Doc): The parent document.
|
||
start_idx (int): The index of the first character of the span.
|
||
end_idx (int): The index of the first character after the span.
|
||
label (uint64 or string): A label to attach to the Span, e.g. for
|
||
named entities.
|
||
kb_id (uint64 or string): An ID from a KB to capture the meaning of a
|
||
named entity.
|
||
vector (ndarray[ndim=1, dtype='float32']): A meaning representation of
|
||
the span.
|
||
alignment_mode (str): How character indices are aligned to token
|
||
boundaries. Options: "strict" (character indices must be aligned
|
||
with token boundaries), "contract" (span of all tokens completely
|
||
within the character span), "expand" (span of all tokens at least
|
||
partially covered by the character span). Defaults to "strict".
|
||
RETURNS (Span): The newly constructed object.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#char_span
|
||
"""
|
||
if not isinstance(label, int):
|
||
label = self.vocab.strings.add(label)
|
||
if not isinstance(kb_id, int):
|
||
kb_id = self.vocab.strings.add(kb_id)
|
||
if alignment_mode not in ("strict", "contract", "expand"):
|
||
alignment_mode = "strict"
|
||
cdef int start = token_by_char(self.c, self.length, start_idx)
|
||
if start < 0 or (alignment_mode == "strict" and start_idx != self[start].idx):
|
||
return None
|
||
# end_idx is exclusive, so find the token at one char before
|
||
cdef int end = token_by_char(self.c, self.length, end_idx - 1)
|
||
if end < 0 or (alignment_mode == "strict" and end_idx != self[end].idx + len(self[end])):
|
||
return None
|
||
# Adjust start and end by alignment_mode
|
||
if alignment_mode == "contract":
|
||
if self[start].idx < start_idx:
|
||
start += 1
|
||
if end_idx < self[end].idx + len(self[end]):
|
||
end -= 1
|
||
# if no tokens are completely within the span, return None
|
||
if end < start:
|
||
return None
|
||
elif alignment_mode == "expand":
|
||
# Don't consider the trailing whitespace to be part of the previous
|
||
# token
|
||
if start_idx == self[start].idx + len(self[start]):
|
||
start += 1
|
||
# Currently we have the token index, we want the range-end index
|
||
end += 1
|
||
cdef Span span = Span(self, start, end, label=label, kb_id=kb_id, vector=vector)
|
||
return span
|
||
|
||
def similarity(self, other):
|
||
"""Make a semantic similarity estimate. The default estimate is cosine
|
||
similarity using an average of word vectors.
|
||
|
||
other (object): The object to compare with. By default, accepts `Doc`,
|
||
`Span`, `Token` and `Lexeme` objects.
|
||
RETURNS (float): A scalar similarity score. Higher is more similar.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#similarity
|
||
"""
|
||
if "similarity" in self.user_hooks:
|
||
return self.user_hooks["similarity"](self, other)
|
||
if isinstance(other, (Lexeme, Token)) and self.length == 1:
|
||
if self.c[0].lex.orth == other.orth:
|
||
return 1.0
|
||
elif isinstance(other, (Span, Doc)) and len(self) == len(other):
|
||
similar = True
|
||
for i in range(self.length):
|
||
if self[i].orth != other[i].orth:
|
||
similar = False
|
||
break
|
||
if similar:
|
||
return 1.0
|
||
if self.vocab.vectors.n_keys == 0:
|
||
warnings.warn(Warnings.W007.format(obj="Doc"))
|
||
if self.vector_norm == 0 or other.vector_norm == 0:
|
||
warnings.warn(Warnings.W008.format(obj="Doc"))
|
||
return 0.0
|
||
vector = self.vector
|
||
xp = get_array_module(vector)
|
||
result = xp.dot(vector, other.vector) / (self.vector_norm * other.vector_norm)
|
||
# ensure we get a scalar back (numpy does this automatically but cupy doesn't)
|
||
return result.item()
|
||
|
||
@property
|
||
def has_vector(self):
|
||
"""A boolean value indicating whether a word vector is associated with
|
||
the object.
|
||
|
||
RETURNS (bool): Whether a word vector is associated with the object.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#has_vector
|
||
"""
|
||
if "has_vector" in self.user_hooks:
|
||
return self.user_hooks["has_vector"](self)
|
||
elif self.vocab.vectors.data.size:
|
||
return True
|
||
elif self.tensor.size:
|
||
return True
|
||
else:
|
||
return False
|
||
|
||
property vector:
|
||
"""A real-valued meaning representation. Defaults to an average of the
|
||
token vectors.
|
||
|
||
RETURNS (numpy.ndarray[ndim=1, dtype='float32']): A 1D numpy array
|
||
representing the document's semantics.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#vector
|
||
"""
|
||
def __get__(self):
|
||
if "vector" in self.user_hooks:
|
||
return self.user_hooks["vector"](self)
|
||
if self._vector is not None:
|
||
return self._vector
|
||
xp = get_array_module(self.vocab.vectors.data)
|
||
if not len(self):
|
||
self._vector = xp.zeros((self.vocab.vectors_length,), dtype="f")
|
||
return self._vector
|
||
elif self.vocab.vectors.data.size > 0:
|
||
self._vector = sum(t.vector for t in self) / len(self)
|
||
return self._vector
|
||
elif self.tensor.size > 0:
|
||
self._vector = self.tensor.mean(axis=0)
|
||
return self._vector
|
||
else:
|
||
return xp.zeros((self.vocab.vectors_length,), dtype="float32")
|
||
|
||
def __set__(self, value):
|
||
self._vector = value
|
||
|
||
property vector_norm:
|
||
"""The L2 norm of the document's vector representation.
|
||
|
||
RETURNS (float): The L2 norm of the vector representation.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#vector_norm
|
||
"""
|
||
def __get__(self):
|
||
if "vector_norm" in self.user_hooks:
|
||
return self.user_hooks["vector_norm"](self)
|
||
cdef float value
|
||
cdef double norm = 0
|
||
if self._vector_norm is None:
|
||
norm = 0.0
|
||
for value in self.vector:
|
||
norm += value * value
|
||
self._vector_norm = sqrt(norm) if norm != 0 else 0
|
||
return self._vector_norm
|
||
|
||
def __set__(self, value):
|
||
self._vector_norm = value
|
||
|
||
@property
|
||
def text(self):
|
||
"""A unicode representation of the document text.
|
||
|
||
RETURNS (str): The original verbatim text of the document.
|
||
"""
|
||
return "".join(t.text_with_ws for t in self)
|
||
|
||
@property
|
||
def text_with_ws(self):
|
||
"""An alias of `Doc.text`, provided for duck-type compatibility with
|
||
`Span` and `Token`.
|
||
|
||
RETURNS (str): The original verbatim text of the document.
|
||
"""
|
||
return self.text
|
||
|
||
property ents:
|
||
"""The named entities in the document. Returns a tuple of named entity
|
||
`Span` objects, if the entity recognizer has been applied.
|
||
|
||
RETURNS (tuple): Entities in the document, one `Span` per entity.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#ents
|
||
"""
|
||
def __get__(self):
|
||
cdef int i
|
||
cdef const TokenC* token
|
||
cdef int start = -1
|
||
cdef attr_t label = 0
|
||
cdef attr_t kb_id = 0
|
||
output = []
|
||
for i in range(self.length):
|
||
token = &self.c[i]
|
||
if token.ent_iob == 1:
|
||
if start == -1:
|
||
seq = [f"{t.text}|{t.ent_iob_}" for t in self[i-5:i+5]]
|
||
raise ValueError(Errors.E093.format(seq=" ".join(seq)))
|
||
elif token.ent_iob == 2 or token.ent_iob == 0 or \
|
||
(token.ent_iob == 3 and token.ent_type == 0):
|
||
if start != -1:
|
||
output.append(Span(self, start, i, label=label, kb_id=kb_id))
|
||
start = -1
|
||
label = 0
|
||
kb_id = 0
|
||
elif token.ent_iob == 3:
|
||
if start != -1:
|
||
output.append(Span(self, start, i, label=label, kb_id=kb_id))
|
||
start = i
|
||
label = token.ent_type
|
||
kb_id = token.ent_kb_id
|
||
if start != -1:
|
||
output.append(Span(self, start, self.length, label=label, kb_id=kb_id))
|
||
# remove empty-label spans
|
||
output = [o for o in output if o.label_ != ""]
|
||
return tuple(output)
|
||
|
||
def __set__(self, ents):
|
||
# TODO:
|
||
# 1. Test basic data-driven ORTH gazetteer
|
||
# 2. Test more nuanced date and currency regex
|
||
cdef attr_t entity_type, kb_id
|
||
cdef int ent_start, ent_end
|
||
ent_spans = []
|
||
for ent_info in ents:
|
||
entity_type_, kb_id, ent_start, ent_end = get_entity_info(ent_info)
|
||
if isinstance(entity_type_, str):
|
||
self.vocab.strings.add(entity_type_)
|
||
span = Span(self, ent_start, ent_end, label=entity_type_, kb_id=kb_id)
|
||
ent_spans.append(span)
|
||
self.set_ents(ent_spans, default=SetEntsDefault.outside)
|
||
|
||
def set_ents(self, entities, *, blocked=None, missing=None, outside=None, default=SetEntsDefault.outside):
|
||
"""Set entity annotation.
|
||
|
||
entities (List[Span]): Spans with labels to set as entities.
|
||
blocked (Optional[List[Span]]): Spans to set as 'blocked' (never an
|
||
entity) for spacy's built-in NER component. Other components may
|
||
ignore this setting.
|
||
missing (Optional[List[Span]]): Spans with missing/unknown entity
|
||
information.
|
||
outside (Optional[List[Span]]): Spans outside of entities (O in IOB).
|
||
default (str): How to set entity annotation for tokens outside of any
|
||
provided spans. Options: "blocked", "missing", "outside" and
|
||
"unmodified" (preserve current state). Defaults to "outside".
|
||
"""
|
||
if default not in SetEntsDefault.values():
|
||
raise ValueError(Errors.E1011.format(default=default, modes=", ".join(SetEntsDefault)))
|
||
|
||
# Ignore spans with missing labels
|
||
entities = [ent for ent in entities if ent.label > 0]
|
||
|
||
if blocked is None:
|
||
blocked = tuple()
|
||
if missing is None:
|
||
missing = tuple()
|
||
if outside is None:
|
||
outside = tuple()
|
||
|
||
# Find all tokens covered by spans and check that none are overlapping
|
||
cdef int i
|
||
seen_tokens = set()
|
||
for span in itertools.chain.from_iterable([entities, blocked, missing, outside]):
|
||
if not isinstance(span, Span):
|
||
raise ValueError(Errors.E1012.format(span=span))
|
||
for i in range(span.start, span.end):
|
||
if i in seen_tokens:
|
||
raise ValueError(Errors.E1010.format(i=i))
|
||
seen_tokens.add(i)
|
||
|
||
# Set all specified entity information
|
||
for span in entities:
|
||
for i in range(span.start, span.end):
|
||
if i == span.start:
|
||
self.c[i].ent_iob = 3
|
||
else:
|
||
self.c[i].ent_iob = 1
|
||
self.c[i].ent_type = span.label
|
||
self.c[i].ent_kb_id = span.kb_id
|
||
for span in blocked:
|
||
for i in range(span.start, span.end):
|
||
self.c[i].ent_iob = 3
|
||
self.c[i].ent_type = 0
|
||
for span in missing:
|
||
for i in range(span.start, span.end):
|
||
self.c[i].ent_iob = 0
|
||
self.c[i].ent_type = 0
|
||
for span in outside:
|
||
for i in range(span.start, span.end):
|
||
self.c[i].ent_iob = 2
|
||
self.c[i].ent_type = 0
|
||
|
||
# Set tokens outside of all provided spans
|
||
if default != SetEntsDefault.unmodified:
|
||
for i in range(self.length):
|
||
if i not in seen_tokens:
|
||
self.c[i].ent_type = 0
|
||
if default == SetEntsDefault.outside:
|
||
self.c[i].ent_iob = 2
|
||
elif default == SetEntsDefault.missing:
|
||
self.c[i].ent_iob = 0
|
||
elif default == SetEntsDefault.blocked:
|
||
self.c[i].ent_iob = 3
|
||
|
||
# Fix any resulting inconsistent annotation
|
||
for i in range(self.length - 1):
|
||
# I must follow B or I: convert I to B
|
||
if (self.c[i].ent_iob == 0 or self.c[i].ent_iob == 2) and \
|
||
self.c[i+1].ent_iob == 1:
|
||
self.c[i+1].ent_iob = 3
|
||
# Change of type with BI or II: convert second I to B
|
||
if self.c[i].ent_type != self.c[i+1].ent_type and \
|
||
(self.c[i].ent_iob == 3 or self.c[i].ent_iob == 1) and \
|
||
self.c[i+1].ent_iob == 1:
|
||
self.c[i+1].ent_iob = 3
|
||
|
||
@property
|
||
def noun_chunks(self):
|
||
"""Iterate over the base noun phrases in the document. Yields base
|
||
noun-phrase #[code Span] objects, if the document has been
|
||
syntactically parsed. A base noun phrase, or "NP chunk", is a noun
|
||
phrase that does not permit other NPs to be nested within it – so no
|
||
NP-level coordination, no prepositional phrases, and no relative
|
||
clauses.
|
||
|
||
YIELDS (Span): Noun chunks in the document.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#noun_chunks
|
||
"""
|
||
|
||
# Accumulate the result before beginning to iterate over it. This
|
||
# prevents the tokenisation from being changed out from under us
|
||
# during the iteration. The tricky thing here is that Span accepts
|
||
# its tokenisation changing, so it's okay once we have the Span
|
||
# objects. See Issue #375.
|
||
spans = []
|
||
if self.noun_chunks_iterator is not None:
|
||
for start, end, label in self.noun_chunks_iterator(self):
|
||
spans.append(Span(self, start, end, label=label))
|
||
for span in spans:
|
||
yield span
|
||
|
||
@property
|
||
def sents(self):
|
||
"""Iterate over the sentences in the document. Yields sentence `Span`
|
||
objects. Sentence spans have no label.
|
||
|
||
YIELDS (Span): Sentences in the document.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#sents
|
||
"""
|
||
if not self.has_annotation("SENT_START"):
|
||
raise ValueError(Errors.E030)
|
||
if "sents" in self.user_hooks:
|
||
yield from self.user_hooks["sents"](self)
|
||
else:
|
||
start = 0
|
||
for i in range(1, self.length):
|
||
if self.c[i].sent_start == 1:
|
||
yield Span(self, start, i)
|
||
start = i
|
||
if start != self.length:
|
||
yield Span(self, start, self.length)
|
||
|
||
@property
|
||
def lang(self):
|
||
"""RETURNS (uint64): ID of the language of the doc's vocabulary."""
|
||
return self.vocab.strings[self.vocab.lang]
|
||
|
||
@property
|
||
def lang_(self):
|
||
"""RETURNS (str): Language of the doc's vocabulary, e.g. 'en'."""
|
||
return self.vocab.lang
|
||
|
||
cdef int push_back(self, LexemeOrToken lex_or_tok, bint has_space) except -1:
|
||
if self.length == self.max_length:
|
||
self._realloc(self.length * 2)
|
||
cdef TokenC* t = &self.c[self.length]
|
||
if LexemeOrToken is const_TokenC_ptr:
|
||
t[0] = lex_or_tok[0]
|
||
else:
|
||
t.lex = lex_or_tok
|
||
if self.length == 0:
|
||
t.idx = 0
|
||
else:
|
||
t.idx = (t-1).idx + (t-1).lex.length + (t-1).spacy
|
||
t.l_edge = self.length
|
||
t.r_edge = self.length
|
||
if t.lex.orth == 0:
|
||
raise ValueError(Errors.E031.format(i=self.length))
|
||
t.spacy = has_space
|
||
self.length += 1
|
||
if self.length == 1:
|
||
# Set token.sent_start to 1 for first token. See issue #2869
|
||
self.c[0].sent_start = 1
|
||
return t.idx + t.lex.length + t.spacy
|
||
|
||
@cython.boundscheck(False)
|
||
cpdef np.ndarray to_array(self, object py_attr_ids):
|
||
"""Export given token attributes to a numpy `ndarray`.
|
||
If `attr_ids` is a sequence of M attributes, the output array will be
|
||
of shape `(N, M)`, where N is the length of the `Doc` (in tokens). If
|
||
`attr_ids` is a single attribute, the output shape will be (N,). You
|
||
can specify attributes by integer ID (e.g. spacy.attrs.LEMMA) or
|
||
string name (e.g. 'LEMMA' or 'lemma').
|
||
|
||
attr_ids (list[]): A list of attributes (int IDs or string names).
|
||
RETURNS (numpy.ndarray[long, ndim=2]): A feature matrix, with one row
|
||
per word, and one column per attribute indicated in the input
|
||
`attr_ids`.
|
||
|
||
EXAMPLE:
|
||
>>> from spacy.attrs import LOWER, POS, ENT_TYPE, IS_ALPHA
|
||
>>> doc = nlp(text)
|
||
>>> # All strings mapped to integers, for easy export to numpy
|
||
>>> np_array = doc.to_array([LOWER, POS, ENT_TYPE, IS_ALPHA])
|
||
"""
|
||
cdef int i, j
|
||
cdef attr_id_t feature
|
||
cdef np.ndarray[attr_t, ndim=2] output
|
||
# Handle scalar/list inputs of strings/ints for py_attr_ids
|
||
# See also #3064
|
||
if isinstance(py_attr_ids, str):
|
||
# Handle inputs like doc.to_array('ORTH')
|
||
py_attr_ids = [py_attr_ids]
|
||
elif not hasattr(py_attr_ids, "__iter__"):
|
||
# Handle inputs like doc.to_array(ORTH)
|
||
py_attr_ids = [py_attr_ids]
|
||
# Allow strings, e.g. 'lemma' or 'LEMMA'
|
||
try:
|
||
py_attr_ids = [(IDS[id_.upper()] if hasattr(id_, "upper") else id_)
|
||
for id_ in py_attr_ids]
|
||
except KeyError as msg:
|
||
keys = [k for k in IDS.keys() if not k.startswith("FLAG")]
|
||
raise KeyError(Errors.E983.format(dict="IDS", key=msg, keys=keys)) from None
|
||
# Make an array from the attributes --- otherwise our inner loop is
|
||
# Python dict iteration.
|
||
cdef np.ndarray attr_ids = numpy.asarray(py_attr_ids, dtype="i")
|
||
output = numpy.ndarray(shape=(self.length, len(attr_ids)), dtype=numpy.uint64)
|
||
c_output = <attr_t*>output.data
|
||
c_attr_ids = <attr_id_t*>attr_ids.data
|
||
cdef TokenC* token
|
||
cdef int nr_attr = attr_ids.shape[0]
|
||
for i in range(self.length):
|
||
token = &self.c[i]
|
||
for j in range(nr_attr):
|
||
c_output[i*nr_attr + j] = get_token_attr(token, c_attr_ids[j])
|
||
# Handle 1d case
|
||
return output if len(attr_ids) >= 2 else output.reshape((self.length,))
|
||
|
||
def count_by(self, attr_id_t attr_id, exclude=None, object counts=None):
|
||
"""Count the frequencies of a given attribute. Produces a dict of
|
||
`{attribute (int): count (ints)}` frequencies, keyed by the values of
|
||
the given attribute ID.
|
||
|
||
attr_id (int): The attribute ID to key the counts.
|
||
RETURNS (dict): A dictionary mapping attributes to integer counts.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#count_by
|
||
"""
|
||
cdef int i
|
||
cdef attr_t attr
|
||
cdef size_t count
|
||
|
||
if counts is None:
|
||
counts = Counter()
|
||
output_dict = True
|
||
else:
|
||
output_dict = False
|
||
# Take this check out of the loop, for a bit of extra speed
|
||
if exclude is None:
|
||
for i in range(self.length):
|
||
counts[get_token_attr(&self.c[i], attr_id)] += 1
|
||
else:
|
||
for i in range(self.length):
|
||
if not exclude(self[i]):
|
||
counts[get_token_attr(&self.c[i], attr_id)] += 1
|
||
if output_dict:
|
||
return dict(counts)
|
||
|
||
def _realloc(self, new_size):
|
||
if new_size < self.max_length:
|
||
return
|
||
self.max_length = new_size
|
||
n = new_size + (PADDING * 2)
|
||
# What we're storing is a "padded" array. We've jumped forward PADDING
|
||
# places, and are storing the pointer to that. This way, we can access
|
||
# words out-of-bounds, and get out-of-bounds markers.
|
||
# Now that we want to realloc, we need the address of the true start,
|
||
# so we jump the pointer back PADDING places.
|
||
cdef TokenC* data_start = self.c - PADDING
|
||
data_start = <TokenC*>self.mem.realloc(data_start, n * sizeof(TokenC))
|
||
self.c = data_start + PADDING
|
||
cdef int i
|
||
for i in range(self.length, self.max_length + PADDING):
|
||
self.c[i].lex = &EMPTY_LEXEME
|
||
|
||
def from_array(self, attrs, array):
|
||
"""Load attributes from a numpy array. Write to a `Doc` object, from an
|
||
`(M, N)` array of attributes.
|
||
|
||
attrs (list) A list of attribute ID ints.
|
||
array (numpy.ndarray[ndim=2, dtype='int32']): The attribute values.
|
||
RETURNS (Doc): Itself.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#from_array
|
||
"""
|
||
# Handle scalar/list inputs of strings/ints for py_attr_ids
|
||
# See also #3064
|
||
if isinstance(attrs, str):
|
||
# Handle inputs like doc.to_array('ORTH')
|
||
attrs = [attrs]
|
||
elif not hasattr(attrs, "__iter__"):
|
||
# Handle inputs like doc.to_array(ORTH)
|
||
attrs = [attrs]
|
||
# Allow strings, e.g. 'lemma' or 'LEMMA'
|
||
attrs = [(IDS[id_.upper()] if hasattr(id_, "upper") else id_)
|
||
for id_ in attrs]
|
||
if array.dtype != numpy.uint64:
|
||
warnings.warn(Warnings.W028.format(type=array.dtype))
|
||
|
||
cdef int i, col
|
||
cdef int32_t abs_head_index
|
||
cdef attr_id_t attr_id
|
||
cdef TokenC* tokens = self.c
|
||
cdef int length = len(array)
|
||
if length != len(self):
|
||
raise ValueError(Errors.E971.format(array_length=length, doc_length=len(self)))
|
||
|
||
# Get set up for fast loading
|
||
cdef Pool mem = Pool()
|
||
cdef int n_attrs = len(attrs)
|
||
# attrs should not be empty, but make sure to avoid zero-length mem alloc
|
||
assert n_attrs > 0
|
||
attr_ids = <attr_id_t*>mem.alloc(n_attrs, sizeof(attr_id_t))
|
||
for i, attr_id in enumerate(attrs):
|
||
attr_ids[i] = attr_id
|
||
if len(array.shape) == 1:
|
||
array = array.reshape((array.size, 1))
|
||
cdef np.ndarray transposed_array = numpy.ascontiguousarray(array.T)
|
||
values = <const uint64_t*>transposed_array.data
|
||
stride = transposed_array.shape[1]
|
||
# Check that all heads are within the document bounds
|
||
if HEAD in attrs:
|
||
col = attrs.index(HEAD)
|
||
for i in range(length):
|
||
# cast index to signed int
|
||
abs_head_index = <int32_t>values[col * stride + i]
|
||
abs_head_index += i
|
||
if abs_head_index < 0 or abs_head_index >= length:
|
||
raise ValueError(
|
||
Errors.E190.format(
|
||
index=i,
|
||
value=array[i, col],
|
||
rel_head_index=abs_head_index-i
|
||
)
|
||
)
|
||
# Verify ENT_IOB are proper integers
|
||
if ENT_IOB in attrs:
|
||
iob_strings = Token.iob_strings()
|
||
col = attrs.index(ENT_IOB)
|
||
n_iob_strings = len(iob_strings)
|
||
for i in range(length):
|
||
value = values[col * stride + i]
|
||
if value < 0 or value >= n_iob_strings:
|
||
raise ValueError(
|
||
Errors.E982.format(
|
||
values=iob_strings,
|
||
value=value
|
||
)
|
||
)
|
||
# Now load the data
|
||
for i in range(length):
|
||
token = &self.c[i]
|
||
for j in range(n_attrs):
|
||
value = values[j * stride + i]
|
||
if attr_ids[j] == MORPH:
|
||
# add morph to morphology table
|
||
self.vocab.morphology.add(self.vocab.strings[value])
|
||
Token.set_struct_attr(token, attr_ids[j], value)
|
||
# If document is parsed, set children and sentence boundaries
|
||
if HEAD in attrs and DEP in attrs:
|
||
col = attrs.index(DEP)
|
||
if array[:, col].any():
|
||
set_children_from_heads(self.c, 0, length)
|
||
return self
|
||
|
||
@staticmethod
|
||
def from_docs(docs, ensure_whitespace=True, attrs=None):
|
||
"""Concatenate multiple Doc objects to form a new one. Raises an error
|
||
if the `Doc` objects do not all share the same `Vocab`.
|
||
|
||
docs (list): A list of Doc objects.
|
||
ensure_whitespace (bool): Insert a space between two adjacent docs whenever the first doc does not end in whitespace.
|
||
attrs (list): Optional list of attribute ID ints or attribute name strings.
|
||
RETURNS (Doc): A doc that contains the concatenated docs, or None if no docs were given.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#from_docs
|
||
"""
|
||
if not docs:
|
||
return None
|
||
|
||
vocab = {doc.vocab for doc in docs}
|
||
if len(vocab) > 1:
|
||
raise ValueError(Errors.E999)
|
||
(vocab,) = vocab
|
||
|
||
if attrs is None:
|
||
attrs = list(Doc._get_array_attrs())
|
||
else:
|
||
if any(isinstance(attr, str) for attr in attrs): # resolve attribute names
|
||
attrs = [intify_attr(attr) for attr in attrs] # intify_attr returns None for invalid attrs
|
||
attrs = list(attr for attr in set(attrs) if attr) # filter duplicates, remove None if present
|
||
if SPACY not in attrs:
|
||
attrs.append(SPACY)
|
||
|
||
concat_words = []
|
||
concat_spaces = []
|
||
concat_user_data = {}
|
||
char_offset = 0
|
||
for doc in docs:
|
||
concat_words.extend(t.text for t in doc)
|
||
concat_spaces.extend(bool(t.whitespace_) for t in doc)
|
||
|
||
for key, value in doc.user_data.items():
|
||
if isinstance(key, tuple) and len(key) == 4:
|
||
data_type, name, start, end = key
|
||
if start is not None or end is not None:
|
||
start += char_offset
|
||
if end is not None:
|
||
end += char_offset
|
||
concat_user_data[(data_type, name, start, end)] = copy.copy(value)
|
||
else:
|
||
warnings.warn(Warnings.W101.format(name=name))
|
||
else:
|
||
warnings.warn(Warnings.W102.format(key=key, value=value))
|
||
char_offset += len(doc.text)
|
||
if ensure_whitespace and not (len(doc) > 0 and doc[-1].is_space):
|
||
char_offset += 1
|
||
|
||
arrays = [doc.to_array(attrs) for doc in docs]
|
||
|
||
if ensure_whitespace:
|
||
spacy_index = attrs.index(SPACY)
|
||
for i, array in enumerate(arrays[:-1]):
|
||
if len(array) > 0 and not docs[i][-1].is_space:
|
||
array[-1][spacy_index] = 1
|
||
token_offset = -1
|
||
for doc in docs[:-1]:
|
||
token_offset += len(doc)
|
||
if not (len(doc) > 0 and doc[-1].is_space):
|
||
concat_spaces[token_offset] = True
|
||
|
||
concat_array = numpy.concatenate(arrays)
|
||
|
||
concat_doc = Doc(vocab, words=concat_words, spaces=concat_spaces, user_data=concat_user_data)
|
||
|
||
concat_doc.from_array(attrs, concat_array)
|
||
|
||
return concat_doc
|
||
|
||
def get_lca_matrix(self):
|
||
"""Calculates a matrix of Lowest Common Ancestors (LCA) for a given
|
||
`Doc`, where LCA[i, j] is the index of the lowest common ancestor among
|
||
token i and j.
|
||
|
||
RETURNS (np.array[ndim=2, dtype=numpy.int32]): LCA matrix with shape
|
||
(n, n), where n = len(self).
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#get_lca_matrix
|
||
"""
|
||
return numpy.asarray(_get_lca_matrix(self, 0, len(self)))
|
||
|
||
def copy(self):
|
||
cdef Doc other = Doc(self.vocab)
|
||
other._vector = copy.deepcopy(self._vector)
|
||
other._vector_norm = copy.deepcopy(self._vector_norm)
|
||
other.tensor = copy.deepcopy(self.tensor)
|
||
other.cats = copy.deepcopy(self.cats)
|
||
other.user_data = copy.deepcopy(self.user_data)
|
||
other.sentiment = self.sentiment
|
||
other.has_unknown_spaces = self.has_unknown_spaces
|
||
other.user_hooks = dict(self.user_hooks)
|
||
other.user_token_hooks = dict(self.user_token_hooks)
|
||
other.user_span_hooks = dict(self.user_span_hooks)
|
||
other.length = self.length
|
||
other.max_length = self.max_length
|
||
buff_size = other.max_length + (PADDING*2)
|
||
assert buff_size > 0
|
||
tokens = <TokenC*>other.mem.alloc(buff_size, sizeof(TokenC))
|
||
memcpy(tokens, self.c - PADDING, buff_size * sizeof(TokenC))
|
||
other.c = &tokens[PADDING]
|
||
return other
|
||
|
||
def to_disk(self, path, *, exclude=tuple()):
|
||
"""Save the current state to a directory.
|
||
|
||
path (str / Path): A path to a directory, which will be created if
|
||
it doesn't exist. Paths may be either strings or Path-like objects.
|
||
exclude (Iterable[str]): String names of serialization fields to exclude.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#to_disk
|
||
"""
|
||
path = util.ensure_path(path)
|
||
with path.open("wb") as file_:
|
||
file_.write(self.to_bytes(exclude=exclude))
|
||
|
||
def from_disk(self, path, *, exclude=tuple()):
|
||
"""Loads state from a directory. Modifies the object in place and
|
||
returns it.
|
||
|
||
path (str / Path): A path to a directory. Paths may be either
|
||
strings or `Path`-like objects.
|
||
exclude (list): String names of serialization fields to exclude.
|
||
RETURNS (Doc): The modified `Doc` object.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#from_disk
|
||
"""
|
||
path = util.ensure_path(path)
|
||
with path.open("rb") as file_:
|
||
bytes_data = file_.read()
|
||
return self.from_bytes(bytes_data, exclude=exclude)
|
||
|
||
def to_bytes(self, *, exclude=tuple()):
|
||
"""Serialize, i.e. export the document contents to a binary string.
|
||
|
||
exclude (list): String names of serialization fields to exclude.
|
||
RETURNS (bytes): A losslessly serialized copy of the `Doc`, including
|
||
all annotations.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#to_bytes
|
||
"""
|
||
return srsly.msgpack_dumps(self.to_dict(exclude=exclude))
|
||
|
||
def from_bytes(self, bytes_data, *, exclude=tuple()):
|
||
"""Deserialize, i.e. import the document contents from a binary string.
|
||
|
||
data (bytes): The string to load from.
|
||
exclude (list): String names of serialization fields to exclude.
|
||
RETURNS (Doc): Itself.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#from_bytes
|
||
"""
|
||
return self.from_dict(srsly.msgpack_loads(bytes_data), exclude=exclude)
|
||
|
||
def to_dict(self, *, exclude=tuple()):
|
||
"""Export the document contents to a dictionary for serialization.
|
||
|
||
exclude (list): String names of serialization fields to exclude.
|
||
RETURNS (bytes): A losslessly serialized copy of the `Doc`, including
|
||
all annotations.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#to_bytes
|
||
"""
|
||
array_head = Doc._get_array_attrs()
|
||
strings = set()
|
||
for token in self:
|
||
strings.add(token.tag_)
|
||
strings.add(token.lemma_)
|
||
strings.add(str(token.morph))
|
||
strings.add(token.dep_)
|
||
strings.add(token.ent_type_)
|
||
strings.add(token.ent_kb_id_)
|
||
strings.add(token.ent_id_)
|
||
strings.add(token.norm_)
|
||
for group in self.spans.values():
|
||
for span in group:
|
||
strings.add(span.label_)
|
||
# Msgpack doesn't distinguish between lists and tuples, which is
|
||
# vexing for user data. As a best guess, we *know* that within
|
||
# keys, we must have tuples. In values we just have to hope
|
||
# users don't mind getting a list instead of a tuple.
|
||
serializers = {
|
||
"text": lambda: self.text,
|
||
"array_head": lambda: array_head,
|
||
"array_body": lambda: self.to_array(array_head),
|
||
"sentiment": lambda: self.sentiment,
|
||
"tensor": lambda: self.tensor,
|
||
"cats": lambda: self.cats,
|
||
"spans": lambda: self.spans.to_bytes(),
|
||
"strings": lambda: list(strings),
|
||
"has_unknown_spaces": lambda: self.has_unknown_spaces
|
||
}
|
||
if "user_data" not in exclude and self.user_data:
|
||
user_data_keys, user_data_values = list(zip(*self.user_data.items()))
|
||
if "user_data_keys" not in exclude:
|
||
serializers["user_data_keys"] = lambda: srsly.msgpack_dumps(user_data_keys)
|
||
if "user_data_values" not in exclude:
|
||
serializers["user_data_values"] = lambda: srsly.msgpack_dumps(user_data_values)
|
||
if "user_hooks" not in exclude and any((self.user_hooks, self.user_token_hooks, self.user_span_hooks)):
|
||
util.logger.warning(Warnings.W109)
|
||
return util.to_dict(serializers, exclude)
|
||
|
||
def from_dict(self, msg, *, exclude=tuple()):
|
||
"""Deserialize, i.e. import the document contents from a binary string.
|
||
|
||
data (bytes): The string to load from.
|
||
exclude (list): String names of serialization fields to exclude.
|
||
RETURNS (Doc): Itself.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#from_dict
|
||
"""
|
||
if self.length != 0:
|
||
raise ValueError(Errors.E033.format(length=self.length))
|
||
# Msgpack doesn't distinguish between lists and tuples, which is
|
||
# vexing for user data. As a best guess, we *know* that within
|
||
# keys, we must have tuples. In values we just have to hope
|
||
# users don't mind getting a list instead of a tuple.
|
||
if "user_data" not in exclude and "user_data_keys" in msg:
|
||
user_data_keys = srsly.msgpack_loads(msg["user_data_keys"], use_list=False)
|
||
user_data_values = srsly.msgpack_loads(msg["user_data_values"])
|
||
for key, value in zip(user_data_keys, user_data_values):
|
||
self.user_data[key] = value
|
||
cdef int i, start, end, has_space
|
||
if "sentiment" not in exclude and "sentiment" in msg:
|
||
self.sentiment = msg["sentiment"]
|
||
if "tensor" not in exclude and "tensor" in msg:
|
||
self.tensor = msg["tensor"]
|
||
if "cats" not in exclude and "cats" in msg:
|
||
self.cats = msg["cats"]
|
||
if "strings" not in exclude and "strings" in msg:
|
||
for s in msg["strings"]:
|
||
self.vocab.strings.add(s)
|
||
if "has_unknown_spaces" not in exclude and "has_unknown_spaces" in msg:
|
||
self.has_unknown_spaces = msg["has_unknown_spaces"]
|
||
start = 0
|
||
cdef const LexemeC* lex
|
||
cdef unicode orth_
|
||
text = msg["text"]
|
||
attrs = msg["array_body"]
|
||
for i in range(attrs.shape[0]):
|
||
end = start + attrs[i, 0]
|
||
has_space = attrs[i, 1]
|
||
orth_ = text[start:end]
|
||
lex = self.vocab.get(self.mem, orth_)
|
||
self.push_back(lex, has_space)
|
||
start = end + has_space
|
||
self.from_array(msg["array_head"][2:], attrs[:, 2:])
|
||
if "spans" in msg:
|
||
self.spans.from_bytes(msg["spans"])
|
||
else:
|
||
self.spans.clear()
|
||
return self
|
||
|
||
def extend_tensor(self, tensor):
|
||
"""Concatenate a new tensor onto the doc.tensor object.
|
||
|
||
The doc.tensor attribute holds dense feature vectors
|
||
computed by the models in the pipeline. Let's say a
|
||
document with 30 words has a tensor with 128 dimensions
|
||
per word. doc.tensor.shape will be (30, 128). After
|
||
calling doc.extend_tensor with an array of shape (30, 64),
|
||
doc.tensor == (30, 192).
|
||
"""
|
||
xp = get_array_module(self.tensor)
|
||
if self.tensor.size == 0:
|
||
self.tensor.resize(tensor.shape, refcheck=False)
|
||
copy_array(self.tensor, tensor)
|
||
else:
|
||
self.tensor = xp.hstack((self.tensor, tensor))
|
||
|
||
def retokenize(self):
|
||
"""Context manager to handle retokenization of the Doc.
|
||
Modifications to the Doc's tokenization are stored, and then
|
||
made all at once when the context manager exits. This is
|
||
much more efficient, and less error-prone.
|
||
|
||
All views of the Doc (Span and Token) created before the
|
||
retokenization are invalidated, although they may accidentally
|
||
continue to work.
|
||
|
||
DOCS: https://nightly.spacy.io/api/doc#retokenize
|
||
USAGE: https://nightly.spacy.io/usage/linguistic-features#retokenization
|
||
"""
|
||
return Retokenizer(self)
|
||
|
||
def _bulk_merge(self, spans, attributes):
|
||
"""Retokenize the document, such that the spans given as arguments
|
||
are merged into single tokens. The spans need to be in document
|
||
order, and no span intersection is allowed.
|
||
|
||
spans (Span[]): Spans to merge, in document order, with all span
|
||
intersections empty. Cannot be empty.
|
||
attributes (Dictionary[]): Attributes to assign to the merged tokens. By default,
|
||
must be the same length as spans, empty dictionaries are allowed.
|
||
attributes are inherited from the syntactic root of the span.
|
||
RETURNS (Token): The first newly merged token.
|
||
"""
|
||
cdef unicode tag, lemma, ent_type
|
||
attr_len = len(attributes)
|
||
span_len = len(spans)
|
||
if not attr_len == span_len:
|
||
raise ValueError(Errors.E121.format(attr_len=attr_len, span_len=span_len))
|
||
with self.retokenize() as retokenizer:
|
||
for i, span in enumerate(spans):
|
||
fix_attributes(self, attributes[i])
|
||
remove_label_if_necessary(attributes[i])
|
||
retokenizer.merge(span, attributes[i])
|
||
|
||
def to_json(self, underscore=None):
|
||
"""Convert a Doc to JSON.
|
||
|
||
underscore (list): Optional list of string names of custom doc._.
|
||
attributes. Attribute values need to be JSON-serializable. Values will
|
||
be added to an "_" key in the data, e.g. "_": {"foo": "bar"}.
|
||
RETURNS (dict): The data in spaCy's JSON format.
|
||
"""
|
||
data = {"text": self.text}
|
||
if self.has_annotation("ENT_IOB"):
|
||
data["ents"] = [{"start": ent.start_char, "end": ent.end_char,
|
||
"label": ent.label_} for ent in self.ents]
|
||
if self.has_annotation("SENT_START"):
|
||
sents = list(self.sents)
|
||
data["sents"] = [{"start": sent.start_char, "end": sent.end_char}
|
||
for sent in sents]
|
||
if self.cats:
|
||
data["cats"] = self.cats
|
||
data["tokens"] = []
|
||
attrs = ["TAG", "MORPH", "POS", "LEMMA", "DEP"]
|
||
include_annotation = {attr: self.has_annotation(attr) for attr in attrs}
|
||
for token in self:
|
||
token_data = {"id": token.i, "start": token.idx, "end": token.idx + len(token)}
|
||
if include_annotation["TAG"]:
|
||
token_data["tag"] = token.tag_
|
||
if include_annotation["POS"]:
|
||
token_data["pos"] = token.pos_
|
||
if include_annotation["MORPH"]:
|
||
token_data["morph"] = token.morph.to_json()
|
||
if include_annotation["LEMMA"]:
|
||
token_data["lemma"] = token.lemma_
|
||
if include_annotation["DEP"]:
|
||
token_data["dep"] = token.dep_
|
||
token_data["head"] = token.head.i
|
||
data["tokens"].append(token_data)
|
||
if underscore:
|
||
data["_"] = {}
|
||
for attr in underscore:
|
||
if not self.has_extension(attr):
|
||
raise ValueError(Errors.E106.format(attr=attr, opts=underscore))
|
||
value = self._.get(attr)
|
||
if not srsly.is_json_serializable(value):
|
||
raise ValueError(Errors.E107.format(attr=attr, value=repr(value)))
|
||
data["_"][attr] = value
|
||
return data
|
||
|
||
def to_utf8_array(self, int nr_char=-1):
|
||
"""Encode word strings to utf8, and export to a fixed-width array
|
||
of characters. Characters are placed into the array in the order:
|
||
0, -1, 1, -2, etc
|
||
For example, if the array is sliced array[:, :8], the array will
|
||
contain the first 4 characters and last 4 characters of each word ---
|
||
with the middle characters clipped out. The value 255 is used as a pad
|
||
value.
|
||
"""
|
||
byte_strings = [token.orth_.encode('utf8') for token in self]
|
||
if nr_char == -1:
|
||
nr_char = max(len(bs) for bs in byte_strings)
|
||
cdef np.ndarray output = numpy.zeros((len(byte_strings), nr_char), dtype='uint8')
|
||
output.fill(255)
|
||
cdef int i, j, start_idx, end_idx
|
||
cdef bytes byte_string
|
||
cdef unsigned char utf8_char
|
||
for i, byte_string in enumerate(byte_strings):
|
||
j = 0
|
||
start_idx = 0
|
||
end_idx = len(byte_string) - 1
|
||
while j < nr_char and start_idx <= end_idx:
|
||
output[i, j] = <unsigned char>byte_string[start_idx]
|
||
start_idx += 1
|
||
j += 1
|
||
if j < nr_char and start_idx <= end_idx:
|
||
output[i, j] = <unsigned char>byte_string[end_idx]
|
||
end_idx -= 1
|
||
j += 1
|
||
return output
|
||
|
||
@staticmethod
|
||
def _get_array_attrs():
|
||
attrs = [LENGTH, SPACY]
|
||
attrs.extend(intify_attr(x) for x in DOCBIN_ALL_ATTRS)
|
||
return tuple(attrs)
|
||
|
||
|
||
cdef int token_by_start(const TokenC* tokens, int length, int start_char) except -2:
|
||
cdef int i = token_by_char(tokens, length, start_char)
|
||
if i >= 0 and tokens[i].idx == start_char:
|
||
return i
|
||
else:
|
||
return -1
|
||
|
||
|
||
cdef int token_by_end(const TokenC* tokens, int length, int end_char) except -2:
|
||
# end_char is exclusive, so find the token at one char before
|
||
cdef int i = token_by_char(tokens, length, end_char - 1)
|
||
if i >= 0 and tokens[i].idx + tokens[i].lex.length == end_char:
|
||
return i
|
||
else:
|
||
return -1
|
||
|
||
|
||
cdef int token_by_char(const TokenC* tokens, int length, int char_idx) except -2:
|
||
cdef int start = 0, mid, end = length - 1
|
||
while start <= end:
|
||
mid = (start + end) / 2
|
||
if char_idx < tokens[mid].idx:
|
||
end = mid - 1
|
||
elif char_idx >= tokens[mid].idx + tokens[mid].lex.length + tokens[mid].spacy:
|
||
start = mid + 1
|
||
else:
|
||
return mid
|
||
return -1
|
||
|
||
cdef int set_children_from_heads(TokenC* tokens, int start, int end) except -1:
|
||
# note: end is exclusive
|
||
cdef TokenC* head
|
||
cdef TokenC* child
|
||
cdef int i
|
||
# Set number of left/right children to 0. We'll increment it in the loops.
|
||
for i in range(start, end):
|
||
tokens[i].l_kids = 0
|
||
tokens[i].r_kids = 0
|
||
tokens[i].l_edge = i
|
||
tokens[i].r_edge = i
|
||
cdef int loop_count = 0
|
||
cdef bint heads_within_sents = False
|
||
# Try up to 10 iterations of adjusting lr_kids and lr_edges in order to
|
||
# handle non-projective dependency parses, stopping when all heads are
|
||
# within their respective sentence boundaries. We have documented cases
|
||
# that need at least 4 iterations, so this is to be on the safe side
|
||
# without risking getting stuck in an infinite loop if something is
|
||
# terribly malformed.
|
||
while not heads_within_sents:
|
||
heads_within_sents = _set_lr_kids_and_edges(tokens, start, end, loop_count)
|
||
if loop_count > 10:
|
||
util.logger.debug(Warnings.W026)
|
||
break
|
||
loop_count += 1
|
||
# Set sentence starts
|
||
for i in range(start, end):
|
||
tokens[i].sent_start = -1
|
||
for i in range(start, end):
|
||
if tokens[i].head == 0 and not Token.missing_head(&tokens[i]):
|
||
tokens[tokens[i].l_edge].sent_start = 1
|
||
|
||
|
||
cdef int _set_lr_kids_and_edges(TokenC* tokens, int start, int end, int loop_count) except -1:
|
||
# May be called multiple times due to non-projectivity. See issues #3170
|
||
# and #4688.
|
||
# Set left edges
|
||
cdef TokenC* head
|
||
cdef TokenC* child
|
||
cdef int i, j
|
||
for i in range(start, end):
|
||
child = &tokens[i]
|
||
head = &tokens[i + child.head]
|
||
if loop_count == 0 and child < head:
|
||
head.l_kids += 1
|
||
if child.l_edge < head.l_edge:
|
||
head.l_edge = child.l_edge
|
||
if child.r_edge > head.r_edge:
|
||
head.r_edge = child.r_edge
|
||
# Set right edges - same as above, but iterate in reverse
|
||
for i in range(end-1, start-1, -1):
|
||
child = &tokens[i]
|
||
head = &tokens[i + child.head]
|
||
if loop_count == 0 and child > head:
|
||
head.r_kids += 1
|
||
if child.r_edge > head.r_edge:
|
||
head.r_edge = child.r_edge
|
||
if child.l_edge < head.l_edge:
|
||
head.l_edge = child.l_edge
|
||
# Get sentence start positions according to current state
|
||
sent_starts = set()
|
||
for i in range(start, end):
|
||
if tokens[i].head == 0:
|
||
sent_starts.add(tokens[i].l_edge)
|
||
cdef int curr_sent_start = 0
|
||
cdef int curr_sent_end = 0
|
||
# Check whether any heads are not within the current sentence
|
||
for i in range(start, end):
|
||
if (i > 0 and i in sent_starts) or i == end - 1:
|
||
curr_sent_end = i
|
||
for j in range(curr_sent_start, curr_sent_end):
|
||
if tokens[j].head + j < curr_sent_start or tokens[j].head + j >= curr_sent_end + 1:
|
||
return False
|
||
curr_sent_start = i
|
||
return True
|
||
|
||
|
||
cdef int _get_tokens_lca(Token token_j, Token token_k):
|
||
"""Given two tokens, returns the index of the lowest common ancestor
|
||
(LCA) among the two. If they have no common ancestor, -1 is returned.
|
||
|
||
token_j (Token): a token.
|
||
token_k (Token): another token.
|
||
RETURNS (int): index of lowest common ancestor, or -1 if the tokens
|
||
have no common ancestor.
|
||
"""
|
||
if token_j == token_k:
|
||
return token_j.i
|
||
elif token_j.head == token_k:
|
||
return token_k.i
|
||
elif token_k.head == token_j:
|
||
return token_j.i
|
||
token_j_ancestors = set(token_j.ancestors)
|
||
if token_k in token_j_ancestors:
|
||
return token_k.i
|
||
for token_k_ancestor in token_k.ancestors:
|
||
if token_k_ancestor == token_j:
|
||
return token_j.i
|
||
if token_k_ancestor in token_j_ancestors:
|
||
return token_k_ancestor.i
|
||
return -1
|
||
|
||
|
||
cdef int [:,:] _get_lca_matrix(Doc doc, int start, int end):
|
||
"""Given a doc and a start and end position defining a set of contiguous
|
||
tokens within it, returns a matrix of Lowest Common Ancestors (LCA), where
|
||
LCA[i, j] is the index of the lowest common ancestor among token i and j.
|
||
If the tokens have no common ancestor within the specified span,
|
||
LCA[i, j] will be -1.
|
||
|
||
doc (Doc): The index of the token, or the slice of the document
|
||
start (int): First token to be included in the LCA matrix.
|
||
end (int): Position of next to last token included in the LCA matrix.
|
||
RETURNS (int [:, :]): memoryview of numpy.array[ndim=2, dtype=numpy.int32],
|
||
with shape (n, n), where n = len(doc).
|
||
"""
|
||
cdef int [:,:] lca_matrix
|
||
cdef int j, k
|
||
n_tokens= end - start
|
||
lca_mat = numpy.empty((n_tokens, n_tokens), dtype=numpy.int32)
|
||
lca_mat.fill(-1)
|
||
lca_matrix = lca_mat
|
||
for j in range(n_tokens):
|
||
token_j = doc[start + j]
|
||
# the common ancestor of token and itself is itself:
|
||
lca_matrix[j, j] = j
|
||
# we will only iterate through tokens in the same sentence
|
||
sent = token_j.sent
|
||
sent_start = sent.start
|
||
j_idx_in_sent = start + j - sent_start
|
||
n_missing_tokens_in_sent = len(sent) - j_idx_in_sent
|
||
# make sure we do not go past `end`, in cases where `end` < sent.end
|
||
max_range = min(j + n_missing_tokens_in_sent, end)
|
||
for k in range(j + 1, max_range):
|
||
lca = _get_tokens_lca(token_j, doc[start + k])
|
||
# if lca is outside of span, we set it to -1
|
||
if not start <= lca < end:
|
||
lca_matrix[j, k] = -1
|
||
lca_matrix[k, j] = -1
|
||
else:
|
||
lca_matrix[j, k] = lca - start
|
||
lca_matrix[k, j] = lca - start
|
||
return lca_matrix
|
||
|
||
|
||
def pickle_doc(doc):
|
||
bytes_data = doc.to_bytes(exclude=["vocab", "user_data", "user_hooks"])
|
||
hooks_and_data = (doc.user_data, doc.user_hooks, doc.user_span_hooks,
|
||
doc.user_token_hooks)
|
||
return (unpickle_doc, (doc.vocab, srsly.pickle_dumps(hooks_and_data), bytes_data))
|
||
|
||
|
||
def unpickle_doc(vocab, hooks_and_data, bytes_data):
|
||
user_data, doc_hooks, span_hooks, token_hooks = srsly.pickle_loads(hooks_and_data)
|
||
|
||
doc = Doc(vocab, user_data=user_data).from_bytes(bytes_data, exclude=["user_data"])
|
||
doc.user_hooks.update(doc_hooks)
|
||
doc.user_span_hooks.update(span_hooks)
|
||
doc.user_token_hooks.update(token_hooks)
|
||
return doc
|
||
|
||
|
||
copy_reg.pickle(Doc, pickle_doc, unpickle_doc)
|
||
|
||
|
||
def remove_label_if_necessary(attributes):
|
||
# More deprecated attribute handling =/
|
||
if "label" in attributes:
|
||
attributes["ent_type"] = attributes.pop("label")
|
||
|
||
|
||
def fix_attributes(doc, attributes):
|
||
if "label" in attributes and "ent_type" not in attributes:
|
||
if isinstance(attributes["label"], int):
|
||
attributes[ENT_TYPE] = attributes["label"]
|
||
else:
|
||
attributes[ENT_TYPE] = doc.vocab.strings[attributes["label"]]
|
||
if "ent_type" in attributes:
|
||
attributes[ENT_TYPE] = attributes["ent_type"]
|
||
|
||
|
||
def get_entity_info(ent_info):
|
||
if isinstance(ent_info, Span):
|
||
ent_type = ent_info.label
|
||
ent_kb_id = ent_info.kb_id
|
||
start = ent_info.start
|
||
end = ent_info.end
|
||
elif len(ent_info) == 3:
|
||
ent_type, start, end = ent_info
|
||
ent_kb_id = 0
|
||
elif len(ent_info) == 4:
|
||
ent_type, ent_kb_id, start, end = ent_info
|
||
else:
|
||
ent_id, ent_kb_id, ent_type, start, end = ent_info
|
||
return ent_type, ent_kb_id, start, end
|