spaCy/spacy/training/example.pyx
Matthew Honnibal 7b3f0c6f1b
Questionable fix for parser training bug with misaligned sentences (#6694)
* Questionable fix for parser training bug with misaligned sentences

* Fix

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2021-01-15 14:18:24 +01:00

521 lines
19 KiB
Cython

from collections.abc import Iterable as IterableInstance
import warnings
import numpy
from murmurhash.mrmr cimport hash64
from ..tokens.doc cimport Doc
from ..tokens.span cimport Span
from ..tokens.span import Span
from ..attrs import IDS
from .alignment import Alignment
from .iob_utils import biluo_to_iob, offsets_to_biluo_tags, doc_to_biluo_tags
from .iob_utils import biluo_tags_to_spans
from ..errors import Errors, Warnings
from ..pipeline._parser_internals import nonproj
from ..tokens.token cimport MISSING_DEP
from ..util import logger
cpdef Doc annotations_to_doc(vocab, tok_annot, doc_annot):
""" Create a Doc from dictionaries with token and doc annotations. """
attrs, array = _annot2array(vocab, tok_annot, doc_annot)
output = Doc(vocab, words=tok_annot["ORTH"], spaces=tok_annot["SPACY"])
if "entities" in doc_annot:
_add_entities_to_doc(output, doc_annot["entities"])
if array.size:
output = output.from_array(attrs, array)
# links are currently added with ENT_KB_ID on the token level
output.cats.update(doc_annot.get("cats", {}))
return output
def validate_examples(examples, method):
"""Check that a batch of examples received during processing is valid.
This function lives here to prevent circular imports.
examples (Iterable[Examples]): A batch of examples.
method (str): The method name to show in error messages.
"""
if not isinstance(examples, IterableInstance):
err = Errors.E978.format(name=method, types=type(examples))
raise TypeError(err)
wrong = set([type(eg) for eg in examples if not isinstance(eg, Example)])
if wrong:
err = Errors.E978.format(name=method, types=wrong)
raise TypeError(err)
def validate_get_examples(get_examples, method):
"""Check that a generator of a batch of examples received during processing is valid:
the callable produces a non-empty list of Example objects.
This function lives here to prevent circular imports.
get_examples (Callable[[], Iterable[Example]]): A function that produces a batch of examples.
method (str): The method name to show in error messages.
"""
if get_examples is None or not hasattr(get_examples, "__call__"):
err = Errors.E930.format(method=method, obj=type(get_examples))
raise TypeError(err)
examples = get_examples()
if not examples:
err = Errors.E930.format(method=method, obj=examples)
raise TypeError(err)
validate_examples(examples, method)
cdef class Example:
def __init__(self, Doc predicted, Doc reference, *, alignment=None):
if predicted is None:
raise TypeError(Errors.E972.format(arg="predicted"))
if reference is None:
raise TypeError(Errors.E972.format(arg="reference"))
self.predicted = predicted
self.reference = reference
self._cached_alignment = alignment
def __len__(self):
return len(self.predicted)
property predicted:
def __get__(self):
return self.x
def __set__(self, doc):
self.x = doc
self._cached_alignment = None
self._cached_words_x = [t.text for t in doc]
property reference:
def __get__(self):
return self.y
def __set__(self, doc):
self.y = doc
self._cached_alignment = None
self._cached_words_y = [t.text for t in doc]
def copy(self):
return Example(
self.x.copy(),
self.y.copy()
)
@classmethod
def from_dict(cls, Doc predicted, dict example_dict):
if predicted is None:
raise ValueError(Errors.E976.format(n="first", type="Doc"))
if example_dict is None:
raise ValueError(Errors.E976.format(n="second", type="dict"))
example_dict = _fix_legacy_dict_data(example_dict)
tok_dict, doc_dict = _parse_example_dict_data(example_dict)
if "ORTH" not in tok_dict:
tok_dict["ORTH"] = [tok.text for tok in predicted]
tok_dict["SPACY"] = [tok.whitespace_ for tok in predicted]
return Example(
predicted,
annotations_to_doc(predicted.vocab, tok_dict, doc_dict)
)
@property
def alignment(self):
x_sig = hash64(self.x.c, sizeof(self.x.c[0]) * self.x.length, 0)
y_sig = hash64(self.y.c, sizeof(self.y.c[0]) * self.y.length, 0)
if self._cached_alignment is None:
words_x = [token.text for token in self.x]
words_y = [token.text for token in self.y]
self._x_sig = x_sig
self._y_sig = y_sig
self._cached_words_x = words_x
self._cached_words_y = words_y
self._cached_alignment = Alignment.from_strings(words_x, words_y)
return self._cached_alignment
elif self._x_sig == x_sig and self._y_sig == y_sig:
# If we have a cached alignment, check whether the cache is invalid
# due to retokenization. To make this check fast in loops, we first
# check a hash of the TokenC arrays.
return self._cached_alignment
else:
words_x = [token.text for token in self.x]
words_y = [token.text for token in self.y]
if words_x == self._cached_words_x and words_y == self._cached_words_y:
self._x_sig = x_sig
self._y_sig = y_sig
return self._cached_alignment
else:
self._cached_alignment = Alignment.from_strings(words_x, words_y)
self._cached_words_x = words_x
self._cached_words_y = words_y
self._x_sig = x_sig
self._y_sig = y_sig
return self._cached_alignment
def get_aligned(self, field, as_string=False):
"""Return an aligned array for a token attribute."""
align = self.alignment.x2y
vocab = self.reference.vocab
gold_values = self.reference.to_array([field])
output = [None] * len(self.predicted)
for token in self.predicted:
if token.is_space:
output[token.i] = None
else:
values = gold_values[align[token.i].dataXd]
values = values.ravel()
if len(values) == 0:
output[token.i] = None
elif len(values) == 1:
output[token.i] = values[0]
elif len(set(list(values))) == 1:
# If all aligned tokens have the same value, use it.
output[token.i] = values[0]
else:
output[token.i] = None
if as_string and field not in ["ENT_IOB", "SENT_START"]:
output = [vocab.strings[o] if o is not None else o for o in output]
return output
def get_aligned_parse(self, projectivize=True):
cand_to_gold = self.alignment.x2y
gold_to_cand = self.alignment.y2x
aligned_heads = [None] * self.x.length
aligned_deps = [None] * self.x.length
has_deps = [token.has_dep() for token in self.y]
has_heads = [token.has_head() for token in self.y]
heads = [token.head.i for token in self.y]
deps = [token.dep_ for token in self.y]
if projectivize:
proj_heads, proj_deps = nonproj.projectivize(heads, deps)
# ensure that missing data remains missing
heads = [h if has_heads[i] else heads[i] for i, h in enumerate(proj_heads)]
deps = [d if has_deps[i] else deps[i] for i, d in enumerate(proj_deps)]
for cand_i in range(self.x.length):
if cand_to_gold.lengths[cand_i] == 1:
gold_i = cand_to_gold[cand_i].dataXd[0, 0]
if gold_to_cand.lengths[heads[gold_i]] == 1:
aligned_heads[cand_i] = int(gold_to_cand[heads[gold_i]].dataXd[0, 0])
aligned_deps[cand_i] = deps[gold_i]
return aligned_heads, aligned_deps
def get_aligned_sent_starts(self):
"""Get list of SENT_START attributes aligned to the predicted tokenization.
If the reference has not sentence starts, return a list of None values.
"""
if self.y.has_annotation("SENT_START"):
align = self.alignment.y2x
sent_starts = [False] * len(self.x)
for y_sent in self.y.sents:
x_start = int(align[y_sent.start].dataXd[0])
sent_starts[x_start] = True
return sent_starts
else:
return [None] * len(self.x)
def get_aligned_spans_x2y(self, x_spans):
return self._get_aligned_spans(self.y, x_spans, self.alignment.x2y)
def get_aligned_spans_y2x(self, y_spans):
return self._get_aligned_spans(self.x, y_spans, self.alignment.y2x)
def _get_aligned_spans(self, doc, spans, align):
seen = set()
output = []
for span in spans:
indices = align[span.start : span.end].data.ravel()
indices = [idx for idx in indices if idx not in seen]
if len(indices) >= 1:
aligned_span = Span(doc, indices[0], indices[-1] + 1, label=span.label)
target_text = span.text.lower().strip().replace(" ", "")
our_text = aligned_span.text.lower().strip().replace(" ", "")
if our_text == target_text:
output.append(aligned_span)
seen.update(indices)
return output
def get_aligned_ner(self):
if not self.y.has_annotation("ENT_IOB"):
return [None] * len(self.x) # should this be 'missing' instead of 'None' ?
x_ents = self.get_aligned_spans_y2x(self.y.ents)
# Default to 'None' for missing values
x_tags = offsets_to_biluo_tags(
self.x,
[(e.start_char, e.end_char, e.label_) for e in x_ents],
missing=None
)
# Now fill the tokens we can align to O.
O = 2 # I=1, O=2, B=3
for i, ent_iob in enumerate(self.get_aligned("ENT_IOB")):
if x_tags[i] is None:
if ent_iob == O:
x_tags[i] = "O"
elif self.x[i].is_space:
x_tags[i] = "O"
return x_tags
def to_dict(self):
return {
"doc_annotation": {
"cats": dict(self.reference.cats),
"entities": doc_to_biluo_tags(self.reference),
"links": self._links_to_dict()
},
"token_annotation": {
"ORTH": [t.text for t in self.reference],
"SPACY": [bool(t.whitespace_) for t in self.reference],
"TAG": [t.tag_ for t in self.reference],
"LEMMA": [t.lemma_ for t in self.reference],
"POS": [t.pos_ for t in self.reference],
"MORPH": [str(t.morph) for t in self.reference],
"HEAD": [t.head.i for t in self.reference],
"DEP": [t.dep_ for t in self.reference],
"SENT_START": [int(bool(t.is_sent_start)) for t in self.reference]
}
}
def _links_to_dict(self):
links = {}
for ent in self.reference.ents:
if ent.kb_id_:
links[(ent.start_char, ent.end_char)] = {ent.kb_id_: 1.0}
return links
def split_sents(self):
""" Split the token annotations into multiple Examples based on
sent_starts and return a list of the new Examples"""
if not self.reference.has_annotation("SENT_START"):
return [self]
align = self.alignment.y2x
seen_indices = set()
output = []
for y_sent in self.reference.sents:
indices = align[y_sent.start : y_sent.end].data.ravel()
indices = [idx for idx in indices if idx not in seen_indices]
if indices:
x_sent = self.predicted[indices[0] : indices[-1] + 1]
output.append(Example(x_sent.as_doc(), y_sent.as_doc()))
seen_indices.update(indices)
return output
property text:
def __get__(self):
return self.x.text
def __str__(self):
return str(self.to_dict())
def __repr__(self):
return str(self.to_dict())
def _annot2array(vocab, tok_annot, doc_annot):
attrs = []
values = []
for key, value in doc_annot.items():
if value:
if key == "entities":
pass
elif key == "links":
ent_kb_ids = _parse_links(vocab, tok_annot["ORTH"], tok_annot["SPACY"], value)
tok_annot["ENT_KB_ID"] = ent_kb_ids
elif key == "cats":
pass
else:
raise ValueError(Errors.E974.format(obj="doc", key=key))
for key, value in tok_annot.items():
if key not in IDS:
raise ValueError(Errors.E974.format(obj="token", key=key))
elif key in ["ORTH", "SPACY"]:
pass
elif key == "HEAD":
attrs.append(key)
values.append([h-i if h is not None else 0 for i, h in enumerate(value)])
elif key == "DEP":
attrs.append(key)
values.append([vocab.strings.add(h) if h is not None else MISSING_DEP for h in value])
elif key == "SENT_START":
attrs.append(key)
values.append(value)
elif key == "MORPH":
attrs.append(key)
values.append([vocab.morphology.add(v) for v in value])
else:
attrs.append(key)
if not all(isinstance(v, str) for v in value):
types = set([type(v) for v in value])
raise TypeError(Errors.E969.format(field=key, types=types)) from None
values.append([vocab.strings.add(v) for v in value])
array = numpy.asarray(values, dtype="uint64")
return attrs, array.T
def _add_entities_to_doc(doc, ner_data):
if ner_data is None:
return
elif ner_data == []:
doc.ents = []
elif isinstance(ner_data[0], tuple):
return _add_entities_to_doc(
doc,
offsets_to_biluo_tags(doc, ner_data)
)
elif isinstance(ner_data[0], str) or ner_data[0] is None:
return _add_entities_to_doc(
doc,
biluo_tags_to_spans(doc, ner_data)
)
elif isinstance(ner_data[0], Span):
entities = []
missing = []
for span in ner_data:
if span.label:
entities.append(span)
else:
missing.append(span)
doc.set_ents(entities, missing=missing)
else:
raise ValueError(Errors.E973)
def _parse_example_dict_data(example_dict):
return (
example_dict["token_annotation"],
example_dict["doc_annotation"]
)
def _fix_legacy_dict_data(example_dict):
token_dict = example_dict.get("token_annotation", {})
doc_dict = example_dict.get("doc_annotation", {})
for key, value in example_dict.items():
if value:
if key in ("token_annotation", "doc_annotation"):
pass
elif key == "ids":
pass
elif key in ("cats", "links"):
doc_dict[key] = value
elif key in ("ner", "entities"):
doc_dict["entities"] = value
else:
token_dict[key] = value
# Remap keys
remapping = {
"words": "ORTH",
"tags": "TAG",
"pos": "POS",
"lemmas": "LEMMA",
"deps": "DEP",
"heads": "HEAD",
"sent_starts": "SENT_START",
"morphs": "MORPH",
"spaces": "SPACY",
}
old_token_dict = token_dict
token_dict = {}
for key, value in old_token_dict.items():
if key in ("text", "ids", "brackets"):
pass
elif key in remapping.values():
token_dict[key] = value
elif key.lower() in remapping:
token_dict[remapping[key.lower()]] = value
else:
all_keys = set(remapping.values())
all_keys.update(remapping.keys())
raise KeyError(Errors.E983.format(key=key, dict="token_annotation", keys=all_keys))
text = example_dict.get("text", example_dict.get("raw"))
if _has_field(token_dict, "ORTH") and not _has_field(token_dict, "SPACY"):
token_dict["SPACY"] = _guess_spaces(text, token_dict["ORTH"])
if "HEAD" in token_dict and "SENT_START" in token_dict:
# If heads are set, we don't also redundantly specify SENT_START.
token_dict.pop("SENT_START")
logger.debug(Warnings.W092)
return {
"token_annotation": token_dict,
"doc_annotation": doc_dict
}
def _has_field(annot, field):
if field not in annot:
return False
elif annot[field] is None:
return False
elif len(annot[field]) == 0:
return False
elif all([value is None for value in annot[field]]):
return False
else:
return True
def _parse_ner_tags(biluo_or_offsets, vocab, words, spaces):
if isinstance(biluo_or_offsets[0], (list, tuple)):
# Convert to biluo if necessary
# This is annoying but to convert the offsets we need a Doc
# that has the target tokenization.
reference = Doc(vocab, words=words, spaces=spaces)
biluo = offsets_to_biluo_tags(reference, biluo_or_offsets)
else:
biluo = biluo_or_offsets
ent_iobs = []
ent_types = []
for iob_tag in biluo_to_iob(biluo):
if iob_tag in (None, "-"):
ent_iobs.append("")
ent_types.append("")
else:
ent_iobs.append(iob_tag.split("-")[0])
if iob_tag.startswith("I") or iob_tag.startswith("B"):
ent_types.append(iob_tag.split("-", 1)[1])
else:
ent_types.append("")
return ent_iobs, ent_types
def _parse_links(vocab, words, spaces, links):
reference = Doc(vocab, words=words, spaces=spaces)
starts = {token.idx: token.i for token in reference}
ends = {token.idx + len(token): token.i for token in reference}
ent_kb_ids = ["" for _ in reference]
for index, annot_dict in links.items():
true_kb_ids = []
for key, value in annot_dict.items():
if value == 1.0:
true_kb_ids.append(key)
if len(true_kb_ids) > 1:
raise ValueError(Errors.E980)
if len(true_kb_ids) == 1:
start_char, end_char = index
start_token = starts.get(start_char)
end_token = ends.get(end_char)
if start_token is None or end_token is None:
raise ValueError(Errors.E981)
for i in range(start_token, end_token+1):
ent_kb_ids[i] = true_kb_ids[0]
return ent_kb_ids
def _guess_spaces(text, words):
if text is None:
return None
spaces = []
text_pos = 0
# align words with text
for word in words:
try:
word_start = text[text_pos:].index(word)
except ValueError:
spaces.append(True)
continue
text_pos += word_start + len(word)
if text_pos < len(text) and text[text_pos] == " ":
spaces.append(True)
else:
spaces.append(False)
return spaces