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spaCy/spacy/tokens/doc.pyx

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# coding: utf8
# cython: infer_types=True
# cython: bounds_check=False
# cython: profile=True
from __future__ import unicode_literals
cimport cython
cimport numpy as np
from libc.string cimport memcpy, memset
from libc.math cimport sqrt
from collections import Counter
import numpy
import numpy.linalg
import struct
import srsly
from thinc.neural.util import get_array_module, copy_array
from .span cimport Span
from .token cimport Token
from ..lexeme cimport Lexeme, EMPTY_LEXEME
from ..typedefs cimport attr_t, flags_t
from ..attrs cimport ID, ORTH, NORM, LOWER, SHAPE, PREFIX, SUFFIX, CLUSTER
from ..attrs cimport LENGTH, POS, LEMMA, TAG, DEP, HEAD, SPACY, ENT_IOB
from ..attrs cimport ENT_TYPE, ENT_KB_ID, SENT_START, attr_id_t
from ..parts_of_speech cimport CCONJ, PUNCT, NOUN, univ_pos_t
from ..attrs import intify_attrs, IDS
from ..util import normalize_slice
from ..compat import is_config, copy_reg, pickle, basestring_
from ..errors import deprecation_warning, models_warning, user_warning
from ..errors import Errors, Warnings
from .. import util
from .underscore import Underscore, get_ext_args
from ._retokenize import Retokenizer
DEF PADDING = 5
cdef int bounds_check(int i, int length, int padding) except -1:
if (i + padding) < 0:
raise IndexError(Errors.E026.format(i=i, length=length))
if (i - padding) >= length:
raise IndexError(Errors.E026.format(i=i, length=length))
cdef attr_t get_token_attr(const TokenC* token, attr_id_t feat_name) nogil:
if feat_name == LEMMA:
return token.lemma
elif feat_name == NORM:
if not token.norm:
return token.lex.norm
return token.norm
elif feat_name == POS:
return token.pos
elif feat_name == TAG:
return token.tag
elif feat_name == DEP:
return token.dep
elif feat_name == HEAD:
return token.head
elif feat_name == SENT_START:
return token.sent_start
elif feat_name == SPACY:
return token.spacy
elif feat_name == ENT_IOB:
return token.ent_iob
elif feat_name == ENT_TYPE:
return token.ent_type
elif feat_name == ENT_KB_ID:
return token.ent_kb_id
else:
return Lexeme.get_struct_attr(token.lex, feat_name)
def _get_chunker(lang):
try:
cls = util.get_lang_class(lang)
except ImportError:
return None
except KeyError:
return None
return cls.Defaults.syntax_iterators.get("noun_chunks")
cdef class Doc:
"""A sequence of Token objects. Access sentences and named entities, export
annotations to numpy arrays, losslessly serialize to compressed binary
strings. The `Doc` object holds an array of `TokenC` structs. The
Python-level `Token` and `Span` objects are views of this array, i.e.
they don't own the data themselves.
EXAMPLE:
Construction 1
>>> doc = nlp(u'Some text')
Construction 2
>>> from spacy.tokens import Doc
>>> doc = Doc(nlp.vocab, words=[u'hello', u'world', u'!'],
>>> spaces=[True, False, False])
DOCS: https://spacy.io/api/doc
"""
@classmethod
def set_extension(cls, name, **kwargs):
"""Define a custom attribute which becomes available as `Doc._`.
name (unicode): Name of the attribute to set.
default: Optional default value of the attribute.
getter (callable): Optional getter function.
setter (callable): Optional setter function.
method (callable): Optional method for method extension.
force (bool): Force overwriting existing attribute.
DOCS: https://spacy.io/api/doc#set_extension
USAGE: https://spacy.io/usage/processing-pipelines#custom-components-attributes
"""
if cls.has_extension(name) and not kwargs.get("force", False):
raise ValueError(Errors.E090.format(name=name, obj="Doc"))
Underscore.doc_extensions[name] = get_ext_args(**kwargs)
@classmethod
def get_extension(cls, name):
"""Look up a previously registered extension by name.
name (unicode): Name of the extension.
RETURNS (tuple): A `(default, method, getter, setter)` tuple.
DOCS: https://spacy.io/api/doc#get_extension
"""
return Underscore.doc_extensions.get(name)
@classmethod
def has_extension(cls, name):
"""Check whether an extension has been registered.
name (unicode): Name of the extension.
RETURNS (bool): Whether the extension has been registered.
DOCS: https://spacy.io/api/doc#has_extension
"""
return name in Underscore.doc_extensions
@classmethod
def remove_extension(cls, name):
"""Remove a previously registered extension.
name (unicode): Name of the extension.
RETURNS (tuple): A `(default, method, getter, setter)` tuple of the
removed extension.
DOCS: https://spacy.io/api/doc#remove_extension
"""
if not cls.has_extension(name):
raise ValueError(Errors.E046.format(name=name))
return Underscore.doc_extensions.pop(name)
def __init__(self, Vocab vocab, words=None, spaces=None, user_data=None,
orths_and_spaces=None):
"""Create a Doc object.
vocab (Vocab): A vocabulary object, which must match any models you
want to use (e.g. tokenizer, parser, entity recognizer).
words (list or None): A list of unicode strings to add to the document
as words. If `None`, defaults to empty list.
spaces (list or None): A list of boolean values, of the same length as
words. True means that the word is followed by a space, False means
it is not. If `None`, defaults to `[True]*len(words)`
user_data (dict or None): Optional extra data to attach to the Doc.
RETURNS (Doc): The newly constructed object.
DOCS: https://spacy.io/api/doc#init
"""
self.vocab = vocab
size = 20
self.mem = Pool()
# Guarantee self.lex[i-x], for any i >= 0 and x < padding is in bounds
# However, we need to remember the true starting places, so that we can
# realloc.
data_start = <TokenC*>self.mem.alloc(size + (PADDING*2), sizeof(TokenC))
cdef int i
for i in range(size + (PADDING*2)):
data_start[i].lex = &EMPTY_LEXEME
data_start[i].l_edge = i
data_start[i].r_edge = i
self.c = data_start + PADDING
self.max_length = size
self.length = 0
self.is_tagged = False
self.is_parsed = False
self.sentiment = 0.0
self.cats = {}
self.user_hooks = {}
self.user_token_hooks = {}
self.user_span_hooks = {}
self.tensor = numpy.zeros((0,), dtype="float32")
self.user_data = {} if user_data is None else user_data
self._vector = None
self.noun_chunks_iterator = _get_chunker(self.vocab.lang)
cdef unicode orth
cdef bint has_space
if orths_and_spaces is None and words is not None:
if spaces is None:
spaces = [True] * len(words)
elif len(spaces) != len(words):
raise ValueError(Errors.E027)
orths_and_spaces = zip(words, spaces)
if orths_and_spaces is not None:
for orth_space in orths_and_spaces:
if isinstance(orth_space, unicode):
orth = orth_space
has_space = True
elif isinstance(orth_space, bytes):
raise ValueError(Errors.E028.format(value=orth_space))
else:
orth, has_space = orth_space
# Note that we pass self.mem here --- we have ownership, if LexemeC
# must be created.
self.push_back(
<const LexemeC*>self.vocab.get(self.mem, orth), has_space)
# Tough to decide on policy for this. Is an empty doc tagged and parsed?
# There's no information we'd like to add to it, so I guess so?
if self.length == 0:
self.is_tagged = True
self.is_parsed = True
@property
def _(self):
"""Custom extension attributes registered via `set_extension`."""
return Underscore(Underscore.doc_extensions, self)
@property
def is_sentenced(self):
"""Check if the document has sentence boundaries assigned. This is
defined as having at least one of the following:
a) An entry "sents" in doc.user_hooks";
b) Doc.is_parsed is set to True;
c) At least one token other than the first where sent_start is not None.
"""
if "sents" in self.user_hooks:
return True
if self.is_parsed:
return True
if len(self) < 2:
return True
for i in range(1, self.length):
if self.c[i].sent_start == -1 or self.c[i].sent_start == 1:
return True
return False
@property
def is_nered(self):
"""Check if the document has named entities set. Will return True if
*any* of the tokens has a named entity tag set (even if the others are
uknown values).
"""
if len(self) == 0:
return True
for i in range(self.length):
if self.c[i].ent_iob != 0:
return True
return False
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
`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]`.
>>> doc[start : end]]
Get a `Span` object, starting at position `start` and ending at
position `end`, where `start` and `end` are token indices. For
instance, `doc[2:5]` produces a span consisting of tokens 2, 3 and
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://spacy.io/api/doc#getitem
"""
if isinstance(i, slice):
start, stop = 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://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://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):
if is_config(python3=True):
return self.__unicode__()
return self.__bytes__()
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):
"""Create a `Span` object from the slice `doc.text[start : end]`.
doc (Doc): The parent document.
start (int): The index of the first character of the span.
end (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.
RETURNS (Span): The newly constructed object.
DOCS: https://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)
cdef int start = token_by_start(self.c, self.length, start_idx)
if start == -1:
return None
cdef int end = token_by_end(self.c, self.length, end_idx)
if end == -1:
return None
# 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://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)):
if len(self) == len(other):
for i in range(self.length):
if self[i].orth != other[i].orth:
break
else:
return 1.0
if self.vocab.vectors.n_keys == 0:
models_warning(Warnings.W007.format(obj="Doc"))
if self.vector_norm == 0 or other.vector_norm == 0:
user_warning(Warnings.W008.format(obj="Doc"))
return 0.0
vector = self.vector
xp = get_array_module(vector)
return xp.dot(vector, other.vector) / (self.vector_norm * other.vector_norm)
@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://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://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://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 (unicode): 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 (unicode): 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://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 = ["%s|%s" % (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:
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))
return tuple(output)
def __set__(self, ents):
# TODO:
# 1. Allow negative matches
# 2. Ensure pre-set NERs are not over-written during statistical
# prediction
# 3. Test basic data-driven ORTH gazetteer
# 4. Test more nuanced date and currency regex
tokens_in_ents = {}
cdef attr_t entity_type
cdef int ent_start, ent_end
for ent_info in ents:
entity_type, ent_start, ent_end = get_entity_info(ent_info)
for token_index in range(ent_start, ent_end):
if token_index in tokens_in_ents.keys():
raise ValueError(Errors.E103.format(
span1=(tokens_in_ents[token_index][0],
tokens_in_ents[token_index][1],
self.vocab.strings[tokens_in_ents[token_index][2]]),
span2=(ent_start, ent_end, self.vocab.strings[entity_type])))
tokens_in_ents[token_index] = (ent_start, ent_end, entity_type)
cdef int i
for i in range(self.length):
self.c[i].ent_type = 0
self.c[i].ent_kb_id = 0
self.c[i].ent_iob = 0 # Means missing.
cdef attr_t ent_type
cdef int start, end
for ent_info in ents:
ent_type, start, end = get_entity_info(ent_info)
if ent_type is None or ent_type < 0:
# Mark as O
for i in range(start, end):
self.c[i].ent_type = 0
self.c[i].ent_iob = 2
else:
# Mark (inside) as I
for i in range(start, end):
self.c[i].ent_type = ent_type
self.c[i].ent_iob = 1
# Set start as B
self.c[start].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://spacy.io/api/doc#noun_chunks
"""
if not self.is_parsed:
raise ValueError(Errors.E029)
# 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. To improve accuracy on informal
texts, spaCy calculates sentence boundaries from the syntactic
dependency parse. If the parser is disabled, the `sents` iterator will
be unavailable.
YIELDS (Span): Sentences in the document.
DOCS: https://spacy.io/api/doc#sents
"""
if not self.is_sentenced:
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 (unicode): 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 == 0:
# Flip these to false when we see the first token.
self.is_tagged = False
self.is_parsed = False
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, basestring_):
# 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'
py_attr_ids = [(IDS[id_.upper()] if hasattr(id_, "upper") else id_)
for id_ in py_attr_ids]
# 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://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):
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
cdef void set_parse(self, const TokenC* parsed) nogil:
# TODO: This method is fairly misleading atm. It's used by Parser
# to actually apply the parse calculated. Need to rethink this.
# Probably we should use from_array?
self.is_parsed = True
for i in range(self.length):
self.c[i] = parsed[i]
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://spacy.io/api/doc#from_array
"""
# Handle scalar/list inputs of strings/ints for py_attr_ids
# See also #3064
if isinstance(attrs, basestring_):
# 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 SENT_START in attrs and HEAD in attrs:
raise ValueError(Errors.E032)
cdef int i, col
cdef attr_id_t attr_id
cdef TokenC* tokens = self.c
cdef int length = len(array)
# Get set up for fast loading
cdef Pool mem = Pool()
cdef int n_attrs = len(attrs)
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))
# Do TAG first. This lets subsequent loop override stuff like POS, LEMMA
if TAG in attrs:
col = attrs.index(TAG)
for i in range(length):
if array[i, col] != 0:
self.vocab.morphology.assign_tag(&tokens[i], array[i, col])
# Now load the data
for i in range(length):
token = &self.c[i]
for j in range(n_attrs):
if attr_ids[j] != TAG:
Token.set_struct_attr(token, attr_ids[j], array[i, j])
# Set flags
self.is_parsed = bool(self.is_parsed or HEAD in attrs or DEP in attrs)
self.is_tagged = bool(self.is_tagged or TAG in attrs or POS in attrs)
# If document is parsed, set children
if self.is_parsed:
set_children_from_heads(self.c, length)
return self
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://spacy.io/api/doc#get_lca_matrix
"""
return numpy.asarray(_get_lca_matrix(self, 0, len(self)))
def to_disk(self, path, **kwargs):
"""Save the current state to a directory.
path (unicode or 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 (list): String names of serialization fields to exclude.
DOCS: https://spacy.io/api/doc#to_disk
"""
path = util.ensure_path(path)
with path.open("wb") as file_:
file_.write(self.to_bytes(**kwargs))
def from_disk(self, path, **kwargs):
"""Loads state from a directory. Modifies the object in place and
returns it.
path (unicode or 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://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, **kwargs)
def to_bytes(self, exclude=tuple(), **kwargs):
"""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://spacy.io/api/doc#to_bytes
"""
array_head = [LENGTH, SPACY, LEMMA, ENT_IOB, ENT_TYPE] # TODO: ENT_KB_ID ?
if self.is_tagged:
array_head.extend([TAG, POS])
# If doc parsed add head and dep attribute
if self.is_parsed:
array_head.extend([HEAD, DEP])
# Otherwise add sent_start
else:
array_head.append(SENT_START)
# 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,
}
for key in kwargs:
if key in serializers or key in ("user_data", "user_data_keys", "user_data_values"):
raise ValueError(Errors.E128.format(arg=key))
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)
return util.to_bytes(serializers, exclude)
def from_bytes(self, bytes_data, exclude=tuple(), **kwargs):
"""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://spacy.io/api/doc#from_bytes
"""
if self.length != 0:
raise ValueError(Errors.E033.format(length=self.length))
deserializers = {
"text": lambda b: None,
"array_head": lambda b: None,
"array_body": lambda b: None,
"sentiment": lambda b: None,
"tensor": lambda b: None,
"user_data_keys": lambda b: None,
"user_data_values": lambda b: None,
}
for key in kwargs:
if key in deserializers or key in ("user_data",):
raise ValueError(Errors.E128.format(arg=key))
msg = util.from_bytes(bytes_data, deserializers, exclude)
# 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"]
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:])
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://spacy.io/api/doc#retokenize
USAGE: https://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 emty.
attributes (Dictionary[]): Attributes to assign to the merged tokens. By default,
must be the same lenghth as spans, emty 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 merge(self, int start_idx, int end_idx, *args, **attributes):
"""Retokenize the document, such that the span at
`doc.text[start_idx : end_idx]` is merged into a single token. If
`start_idx` and `end_idx `do not mark start and end token boundaries,
the document remains unchanged.
start_idx (int): Character index of the start of the slice to merge.
end_idx (int): Character index after the end of the slice to merge.
**attributes: Attributes to assign to the merged token. By default,
attributes are inherited from the syntactic root of the span.
RETURNS (Token): The newly merged token, or `None` if the start and end
indices did not fall at token boundaries.
"""
cdef unicode tag, lemma, ent_type
deprecation_warning(Warnings.W013.format(obj="Doc"))
# TODO: ENT_KB_ID ?
if len(args) == 3:
deprecation_warning(Warnings.W003)
tag, lemma, ent_type = args
attributes[TAG] = tag
attributes[LEMMA] = lemma
attributes[ENT_TYPE] = ent_type
elif not args:
fix_attributes(self, attributes)
elif args:
raise ValueError(Errors.E034.format(n_args=len(args), args=repr(args),
kwargs=repr(attributes)))
remove_label_if_necessary(attributes)
attributes = intify_attrs(attributes, strings_map=self.vocab.strings)
cdef int start = token_by_start(self.c, self.length, start_idx)
if start == -1:
return None
cdef int end = token_by_end(self.c, self.length, end_idx)
if end == -1:
return None
# Currently we have the token index, we want the range-end index
end += 1
with self.retokenize() as retokenizer:
retokenizer.merge(self[start:end], attrs=attributes)
return self[start]
def print_tree(self, light=False, flat=False):
raise ValueError(Errors.E105)
def to_json(self, underscore=None):
"""Convert a Doc to JSON. The format it produces will be the new format
for the `spacy train` command (not implemented yet).
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.
DOCS: https://spacy.io/api/doc#to_json
"""
data = {"text": self.text}
if self.is_nered:
data["ents"] = [{"start": ent.start_char, "end": ent.end_char,
"label": ent.label_} for ent in self.ents]
if self.is_sentenced:
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"] = []
for token in self:
token_data = {"id": token.i, "start": token.idx, "end": token.idx + len(token)}
if self.is_tagged:
token_data["pos"] = token.pos_
token_data["tag"] = token.tag_
if self.is_parsed:
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
cdef int token_by_start(const TokenC* tokens, int length, int start_char) except -2:
cdef int i
for i in range(length):
if 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:
cdef int i
for i in range(length):
if tokens[i].idx + tokens[i].lex.length == end_char:
return i
else:
return -1
cdef int set_children_from_heads(TokenC* tokens, int length) except -1:
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(length):
tokens[i].l_kids = 0
tokens[i].r_kids = 0
tokens[i].l_edge = i
tokens[i].r_edge = i
# Three times, for non-projectivity. See issue #3170. This isn't a very
# satisfying fix, but I think it's sufficient.
for loop_count in range(3):
# Set left edges
for i in range(length):
child = &tokens[i]
head = &tokens[i + child.head]
if child < head and loop_count == 0:
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(length-1, -1, -1):
child = &tokens[i]
head = &tokens[i + child.head]
if child > head and loop_count == 0:
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
# Set sentence starts
for i in range(length):
if tokens[i].head == 0 and tokens[i].dep != 0:
tokens[tokens[i].l_edge].sent_start = 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
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"])
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
start = ent_info.start
end = ent_info.end
elif len(ent_info) == 3:
ent_type, start, end = ent_info
else:
ent_id, ent_type, start, end = ent_info
return ent_type, start, end
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