mirror of https://github.com/explosion/spaCy.git
1637 lines
63 KiB
Cython
1637 lines
63 KiB
Cython
# cython: infer_types=True, profile=True
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import numpy
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import srsly
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import random
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from ast import literal_eval
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from thinc.api import CosineDistance, to_categorical, get_array_module
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from thinc.api import set_dropout_rate, SequenceCategoricalCrossentropy
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import warnings
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from ..tokens.doc cimport Doc
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from ..syntax.nn_parser cimport Parser
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from ..syntax.ner cimport BiluoPushDown
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from ..syntax.arc_eager cimport ArcEager
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from ..morphology cimport Morphology
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from ..vocab cimport Vocab
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from .defaults import default_tagger, default_parser, default_ner, default_textcat
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from .defaults import default_nel, default_senter
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from .functions import merge_subtokens
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from ..language import Language, component
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from ..syntax import nonproj
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from ..gold import Example
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from ..attrs import POS, ID
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from ..util import link_vectors_to_models, create_default_optimizer
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from ..parts_of_speech import X
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from ..kb import KnowledgeBase
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from ..errors import Errors, TempErrors, Warnings
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from .. import util
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def _load_cfg(path):
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if path.exists():
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return srsly.read_json(path)
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else:
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return {}
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class Pipe(object):
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"""This class is not instantiated directly. Components inherit from it, and
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it defines the interface that components should follow to function as
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components in a spaCy analysis pipeline.
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"""
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name = None
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@classmethod
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def from_nlp(cls, nlp, model, **cfg):
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return cls(nlp.vocab, model, **cfg)
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def _get_doc(self, example):
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""" Use this method if the `example` can be both a Doc or an Example """
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if isinstance(example, Doc):
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return example
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return example.doc
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def __init__(self, vocab, model, **cfg):
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"""Create a new pipe instance."""
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raise NotImplementedError
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def __call__(self, example):
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"""Apply the pipe to one document. The document is
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modified in-place, and returned.
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Both __call__ and pipe should delegate to the `predict()`
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and `set_annotations()` methods.
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"""
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doc = self._get_doc(example)
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predictions = self.predict([doc])
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if isinstance(predictions, tuple) and len(predictions) == 2:
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scores, tensors = predictions
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self.set_annotations([doc], scores, tensors=tensors)
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else:
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self.set_annotations([doc], predictions)
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if isinstance(example, Example):
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example.doc = doc
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return example
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return doc
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def pipe(self, stream, batch_size=128, n_threads=-1, as_example=False):
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"""Apply the pipe to a stream of documents.
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Both __call__ and pipe should delegate to the `predict()`
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and `set_annotations()` methods.
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"""
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for examples in util.minibatch(stream, size=batch_size):
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docs = [self._get_doc(ex) for ex in examples]
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predictions = self.predict(docs)
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if isinstance(predictions, tuple) and len(tuple) == 2:
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scores, tensors = predictions
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self.set_annotations(docs, scores, tensors=tensors)
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else:
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self.set_annotations(docs, predictions)
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if as_example:
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for ex, doc in zip(examples, docs):
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ex.doc = doc
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yield ex
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else:
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yield from docs
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def predict(self, docs):
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"""Apply the pipeline's model to a batch of docs, without
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modifying them.
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"""
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raise NotImplementedError
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def set_annotations(self, docs, scores, tensors=None):
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"""Modify a batch of documents, using pre-computed scores."""
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raise NotImplementedError
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def update(self, examples, set_annotations=False, drop=0.0, sgd=None, losses=None):
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"""Learn from a batch of documents and gold-standard information,
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updating the pipe's model.
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Delegates to predict() and get_loss().
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"""
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if set_annotations:
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docs = (self._get_doc(ex) for ex in examples)
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docs = list(self.pipe(docs))
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def rehearse(self, examples, sgd=None, losses=None, **config):
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pass
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def get_loss(self, examples, scores):
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"""Find the loss and gradient of loss for the batch of
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examples (with embedded docs) and their predicted scores."""
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raise NotImplementedError
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def add_label(self, label):
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"""Add an output label, to be predicted by the model.
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It's possible to extend pretrained models with new labels,
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but care should be taken to avoid the "catastrophic forgetting"
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problem.
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"""
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raise NotImplementedError
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def create_optimizer(self):
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return create_default_optimizer()
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def begin_training(
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self, get_examples=lambda: [], pipeline=None, sgd=None, **kwargs
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):
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"""Initialize the pipe for training, using data exampes if available.
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If no model has been initialized yet, the model is added."""
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self.model.initialize()
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if hasattr(self, "vocab"):
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link_vectors_to_models(self.vocab)
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if sgd is None:
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sgd = self.create_optimizer()
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return sgd
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def set_output(self, nO):
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if self.model.has_dim("nO") is not False:
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self.model.set_dim("nO", nO)
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if self.model.has_ref("output_layer"):
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self.model.get_ref("output_layer").set_dim("nO", nO)
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def get_gradients(self):
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"""Get non-zero gradients of the model's parameters, as a dictionary
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keyed by the parameter ID. The values are (weights, gradients) tuples.
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"""
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gradients = {}
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queue = [self.model]
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seen = set()
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for node in queue:
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if node.id in seen:
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continue
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seen.add(node.id)
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if hasattr(node, "_mem") and node._mem.gradient.any():
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gradients[node.id] = [node._mem.weights, node._mem.gradient]
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if hasattr(node, "_layers"):
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queue.extend(node._layers)
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return gradients
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def use_params(self, params):
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"""Modify the pipe's model, to use the given parameter values."""
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with self.model.use_params(params):
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yield
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def to_bytes(self, exclude=tuple(), **kwargs):
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"""Serialize the pipe to a bytestring.
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exclude (list): String names of serialization fields to exclude.
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RETURNS (bytes): The serialized object.
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"""
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serialize = {}
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serialize["cfg"] = lambda: srsly.json_dumps(self.cfg)
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serialize["model"] = self.model.to_bytes
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if hasattr(self, "vocab"):
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serialize["vocab"] = self.vocab.to_bytes
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exclude = util.get_serialization_exclude(serialize, exclude, kwargs)
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return util.to_bytes(serialize, exclude)
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def from_bytes(self, bytes_data, exclude=tuple(), **kwargs):
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"""Load the pipe from a bytestring."""
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def load_model(b):
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try:
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self.model.from_bytes(b)
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except AttributeError:
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raise ValueError(Errors.E149)
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deserialize = {}
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if hasattr(self, "vocab"):
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deserialize["vocab"] = lambda b: self.vocab.from_bytes(b)
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deserialize["cfg"] = lambda b: self.cfg.update(srsly.json_loads(b))
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deserialize["model"] = load_model
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exclude = util.get_serialization_exclude(deserialize, exclude, kwargs)
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util.from_bytes(bytes_data, deserialize, exclude)
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return self
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def to_disk(self, path, exclude=tuple(), **kwargs):
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"""Serialize the pipe to disk."""
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serialize = {}
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serialize["cfg"] = lambda p: srsly.write_json(p, self.cfg)
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serialize["vocab"] = lambda p: self.vocab.to_disk(p)
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serialize["model"] = lambda p: self.model.to_disk(p)
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exclude = util.get_serialization_exclude(serialize, exclude, kwargs)
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util.to_disk(path, serialize, exclude)
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def from_disk(self, path, exclude=tuple(), **kwargs):
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"""Load the pipe from disk."""
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def load_model(p):
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try:
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self.model.from_bytes(p.open("rb").read())
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except AttributeError:
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raise ValueError(Errors.E149)
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deserialize = {}
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deserialize["vocab"] = lambda p: self.vocab.from_disk(p)
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deserialize["cfg"] = lambda p: self.cfg.update(_load_cfg(p))
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deserialize["model"] = load_model
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exclude = util.get_serialization_exclude(deserialize, exclude, kwargs)
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util.from_disk(path, deserialize, exclude)
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return self
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@component("tagger", assigns=["token.tag", "token.pos", "token.lemma"], default_model=default_tagger)
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class Tagger(Pipe):
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"""Pipeline component for part-of-speech tagging.
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DOCS: https://spacy.io/api/tagger
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"""
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def __init__(self, vocab, model, **cfg):
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self.vocab = vocab
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self.model = model
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self._rehearsal_model = None
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self.cfg = dict(sorted(cfg.items()))
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@property
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def labels(self):
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return tuple(self.vocab.morphology.tag_names)
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def __call__(self, example):
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doc = self._get_doc(example)
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tags = self.predict([doc])
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self.set_annotations([doc], tags)
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if isinstance(example, Example):
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example.doc = doc
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return example
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return doc
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def pipe(self, stream, batch_size=128, n_threads=-1, as_example=False):
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for examples in util.minibatch(stream, size=batch_size):
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docs = [self._get_doc(ex) for ex in examples]
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tag_ids = self.predict(docs)
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assert len(docs) == len(examples)
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assert len(tag_ids) == len(examples)
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self.set_annotations(docs, tag_ids)
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if as_example:
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for ex, doc in zip(examples, docs):
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ex.doc = doc
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yield ex
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else:
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yield from docs
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def predict(self, docs):
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if not any(len(doc) for doc in docs):
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# Handle cases where there are no tokens in any docs.
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n_labels = len(self.labels)
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guesses = [self.model.ops.alloc((0, n_labels)) for doc in docs]
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assert len(guesses) == len(docs)
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return guesses
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scores = self.model.predict(docs)
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assert len(scores) == len(docs), (len(scores), len(docs))
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guesses = self._scores2guesses(scores)
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assert len(guesses) == len(docs)
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return guesses
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def _scores2guesses(self, scores):
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guesses = []
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for doc_scores in scores:
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doc_guesses = doc_scores.argmax(axis=1)
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if not isinstance(doc_guesses, numpy.ndarray):
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doc_guesses = doc_guesses.get()
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guesses.append(doc_guesses)
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return guesses
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def set_annotations(self, docs, batch_tag_ids):
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if isinstance(docs, Doc):
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docs = [docs]
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cdef Doc doc
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cdef int idx = 0
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cdef Vocab vocab = self.vocab
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assign_morphology = self.cfg.get("set_morphology", True)
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for i, doc in enumerate(docs):
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doc_tag_ids = batch_tag_ids[i]
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if hasattr(doc_tag_ids, "get"):
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doc_tag_ids = doc_tag_ids.get()
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for j, tag_id in enumerate(doc_tag_ids):
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# Don't clobber preset POS tags
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if doc.c[j].tag == 0:
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if doc.c[j].pos == 0 and assign_morphology:
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# Don't clobber preset lemmas
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lemma = doc.c[j].lemma
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vocab.morphology.assign_tag_id(&doc.c[j], tag_id)
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if lemma != 0 and lemma != doc.c[j].lex.orth:
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doc.c[j].lemma = lemma
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else:
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doc.c[j].tag = self.vocab.strings[self.labels[tag_id]]
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idx += 1
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doc.is_tagged = True
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def update(self, examples, drop=0., sgd=None, losses=None, set_annotations=False):
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examples = Example.to_example_objects(examples)
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if losses is not None and self.name not in losses:
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losses[self.name] = 0.
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if not any(len(ex.doc) if ex.doc else 0 for ex in examples):
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# Handle cases where there are no tokens in any docs.
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return
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set_dropout_rate(self.model, drop)
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tag_scores, bp_tag_scores = self.model.begin_update([ex.doc for ex in examples])
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for sc in tag_scores:
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if self.model.ops.xp.isnan(sc.sum()):
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raise ValueError("nan value in scores")
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loss, d_tag_scores = self.get_loss(examples, tag_scores)
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bp_tag_scores(d_tag_scores)
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if sgd not in (None, False):
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self.model.finish_update(sgd)
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if losses is not None:
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losses[self.name] += loss
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if set_annotations:
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docs = [ex.doc for ex in examples]
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self.set_annotations(docs, self._scores2guesses(tag_scores))
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def rehearse(self, examples, drop=0., sgd=None, losses=None):
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"""Perform a 'rehearsal' update, where we try to match the output of
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an initial model.
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"""
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if self._rehearsal_model is None:
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return
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examples = Example.to_example_objects(examples)
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docs = [ex.doc for ex in examples]
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if not any(len(doc) for doc in docs):
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# Handle cases where there are no tokens in any docs.
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return
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set_dropout_rate(self.model, drop)
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guesses, backprop = self.model.begin_update(docs)
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target = self._rehearsal_model(examples)
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gradient = guesses - target
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backprop(gradient)
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self.model.finish_update(sgd)
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if losses is not None:
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losses.setdefault(self.name, 0.0)
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losses[self.name] += (gradient**2).sum()
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def get_loss(self, examples, scores):
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loss_func = SequenceCategoricalCrossentropy(names=self.labels)
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truths = [eg.gold.tags for eg in examples]
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d_scores, loss = loss_func(scores, truths)
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if self.model.ops.xp.isnan(loss):
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raise ValueError("nan value when computing loss")
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return float(loss), d_scores
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def begin_training(self, get_examples=lambda: [], pipeline=None, sgd=None,
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**kwargs):
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lemma_tables = ["lemma_rules", "lemma_index", "lemma_exc", "lemma_lookup"]
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if not any(table in self.vocab.lookups for table in lemma_tables):
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warnings.warn(Warnings.W022)
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if len(self.vocab.lookups.get_table("lexeme_norm", {})) == 0:
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warnings.warn(Warnings.W033.format(model="part-of-speech tagger"))
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orig_tag_map = dict(self.vocab.morphology.tag_map)
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new_tag_map = {}
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for example in get_examples():
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for tag in example.token_annotation.tags:
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if tag in orig_tag_map:
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new_tag_map[tag] = orig_tag_map[tag]
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else:
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new_tag_map[tag] = {POS: X}
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# TODO: do we still need this?
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if "_SP" in orig_tag_map:
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new_tag_map["_SP"] = orig_tag_map["_SP"]
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cdef Vocab vocab = self.vocab
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if new_tag_map:
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vocab.morphology = Morphology(vocab.strings, new_tag_map,
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vocab.morphology.lemmatizer,
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exc=vocab.morphology.exc)
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self.set_output(len(self.labels))
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doc_sample = [Doc(self.vocab, words=["hello", "world"])]
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if pipeline is not None:
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for name, component in pipeline:
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if component is self:
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break
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if hasattr(component, "pipe"):
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doc_sample = list(component.pipe(doc_sample))
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else:
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doc_sample = [component(doc) for doc in doc_sample]
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self.model.initialize(X=doc_sample)
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# Get batch of example docs, example outputs to call begin_training().
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# This lets the model infer shapes.
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link_vectors_to_models(self.vocab)
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if sgd is None:
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sgd = self.create_optimizer()
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return sgd
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def add_label(self, label, values=None):
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if not isinstance(label, str):
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raise ValueError(Errors.E187)
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if label in self.labels:
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return 0
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if self.model.has_dim("nO"):
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# Here's how the model resizing will work, once the
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# neuron-to-tag mapping is no longer controlled by
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# the Morphology class, which sorts the tag names.
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# The sorting makes adding labels difficult.
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# smaller = self.model._layers[-1]
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# larger = Softmax(len(self.labels)+1, smaller.nI)
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# copy_array(larger.W[:smaller.nO], smaller.W)
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# copy_array(larger.b[:smaller.nO], smaller.b)
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# self.model._layers[-1] = larger
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raise ValueError(TempErrors.T003)
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tag_map = dict(self.vocab.morphology.tag_map)
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||
if values is None:
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||
values = {POS: "X"}
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tag_map[label] = values
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self.vocab.morphology = Morphology(
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self.vocab.strings, tag_map=tag_map,
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lemmatizer=self.vocab.morphology.lemmatizer,
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exc=self.vocab.morphology.exc)
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return 1
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||
def use_params(self, params):
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with self.model.use_params(params):
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yield
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||
def to_bytes(self, exclude=tuple(), **kwargs):
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||
serialize = {}
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||
serialize["model"] = self.model.to_bytes
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||
serialize["vocab"] = self.vocab.to_bytes
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||
serialize["cfg"] = lambda: srsly.json_dumps(self.cfg)
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||
tag_map = dict(sorted(self.vocab.morphology.tag_map.items()))
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||
serialize["tag_map"] = lambda: srsly.msgpack_dumps(tag_map)
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||
exclude = util.get_serialization_exclude(serialize, exclude, kwargs)
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||
return util.to_bytes(serialize, exclude)
|
||
|
||
def from_bytes(self, bytes_data, exclude=tuple(), **kwargs):
|
||
def load_model(b):
|
||
try:
|
||
self.model.from_bytes(b)
|
||
except AttributeError:
|
||
raise ValueError(Errors.E149)
|
||
|
||
def load_tag_map(b):
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||
tag_map = srsly.msgpack_loads(b)
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||
self.vocab.morphology = Morphology(
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||
self.vocab.strings, tag_map=tag_map,
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||
lemmatizer=self.vocab.morphology.lemmatizer,
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||
exc=self.vocab.morphology.exc)
|
||
|
||
deserialize = {
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||
"vocab": lambda b: self.vocab.from_bytes(b),
|
||
"tag_map": load_tag_map,
|
||
"cfg": lambda b: self.cfg.update(srsly.json_loads(b)),
|
||
"model": lambda b: load_model(b),
|
||
}
|
||
exclude = util.get_serialization_exclude(deserialize, exclude, kwargs)
|
||
util.from_bytes(bytes_data, deserialize, exclude)
|
||
return self
|
||
|
||
def to_disk(self, path, exclude=tuple(), **kwargs):
|
||
tag_map = dict(sorted(self.vocab.morphology.tag_map.items()))
|
||
serialize = {
|
||
"vocab": lambda p: self.vocab.to_disk(p),
|
||
"tag_map": lambda p: srsly.write_msgpack(p, tag_map),
|
||
"model": lambda p: self.model.to_disk(p),
|
||
"cfg": lambda p: srsly.write_json(p, self.cfg),
|
||
}
|
||
exclude = util.get_serialization_exclude(serialize, exclude, kwargs)
|
||
util.to_disk(path, serialize, exclude)
|
||
|
||
def from_disk(self, path, exclude=tuple(), **kwargs):
|
||
def load_model(p):
|
||
with p.open("rb") as file_:
|
||
try:
|
||
self.model.from_bytes(file_.read())
|
||
except AttributeError:
|
||
raise ValueError(Errors.E149)
|
||
|
||
def load_tag_map(p):
|
||
tag_map = srsly.read_msgpack(p)
|
||
self.vocab.morphology = Morphology(
|
||
self.vocab.strings, tag_map=tag_map,
|
||
lemmatizer=self.vocab.morphology.lemmatizer,
|
||
exc=self.vocab.morphology.exc)
|
||
|
||
deserialize = {
|
||
"vocab": lambda p: self.vocab.from_disk(p),
|
||
"cfg": lambda p: self.cfg.update(_load_cfg(p)),
|
||
"tag_map": load_tag_map,
|
||
"model": load_model,
|
||
}
|
||
exclude = util.get_serialization_exclude(deserialize, exclude, kwargs)
|
||
util.from_disk(path, deserialize, exclude)
|
||
return self
|
||
|
||
|
||
@component("senter", assigns=["token.is_sent_start"], default_model=default_senter)
|
||
class SentenceRecognizer(Tagger):
|
||
"""Pipeline component for sentence segmentation.
|
||
|
||
DOCS: https://spacy.io/api/sentencerecognizer
|
||
"""
|
||
|
||
def __init__(self, vocab, model, **cfg):
|
||
self.vocab = vocab
|
||
self.model = model
|
||
self._rehearsal_model = None
|
||
self.cfg = dict(sorted(cfg.items()))
|
||
|
||
@property
|
||
def labels(self):
|
||
# labels are numbered by index internally, so this matches GoldParse
|
||
# and Example where the sentence-initial tag is 1 and other positions
|
||
# are 0
|
||
return tuple(["I", "S"])
|
||
|
||
def set_annotations(self, docs, batch_tag_ids):
|
||
if isinstance(docs, Doc):
|
||
docs = [docs]
|
||
cdef Doc doc
|
||
for i, doc in enumerate(docs):
|
||
doc_tag_ids = batch_tag_ids[i]
|
||
if hasattr(doc_tag_ids, "get"):
|
||
doc_tag_ids = doc_tag_ids.get()
|
||
for j, tag_id in enumerate(doc_tag_ids):
|
||
# Don't clobber existing sentence boundaries
|
||
if doc.c[j].sent_start == 0:
|
||
if tag_id == 1:
|
||
doc.c[j].sent_start = 1
|
||
else:
|
||
doc.c[j].sent_start = -1
|
||
|
||
def get_loss(self, examples, scores):
|
||
scores = self.model.ops.flatten(scores)
|
||
tag_index = range(len(self.labels))
|
||
cdef int idx = 0
|
||
correct = numpy.zeros((scores.shape[0],), dtype="i")
|
||
guesses = scores.argmax(axis=1)
|
||
known_labels = numpy.ones((scores.shape[0], 1), dtype="f")
|
||
for ex in examples:
|
||
gold = ex.gold
|
||
for sent_start in gold.sent_starts:
|
||
if sent_start is None:
|
||
correct[idx] = guesses[idx]
|
||
elif sent_start in tag_index:
|
||
correct[idx] = sent_start
|
||
else:
|
||
correct[idx] = 0
|
||
known_labels[idx] = 0.
|
||
idx += 1
|
||
correct = self.model.ops.xp.array(correct, dtype="i")
|
||
d_scores = scores - to_categorical(correct, n_classes=scores.shape[1])
|
||
d_scores *= self.model.ops.asarray(known_labels)
|
||
loss = (d_scores**2).sum()
|
||
docs = [ex.doc for ex in examples]
|
||
d_scores = self.model.ops.unflatten(d_scores, [len(d) for d in docs])
|
||
return float(loss), d_scores
|
||
|
||
def begin_training(self, get_examples=lambda: [], pipeline=None, sgd=None,
|
||
**kwargs):
|
||
self.set_output(len(self.labels))
|
||
self.model.initialize()
|
||
link_vectors_to_models(self.vocab)
|
||
if sgd is None:
|
||
sgd = self.create_optimizer()
|
||
return sgd
|
||
|
||
def add_label(self, label, values=None):
|
||
raise NotImplementedError
|
||
|
||
def to_bytes(self, exclude=tuple(), **kwargs):
|
||
serialize = {}
|
||
serialize["model"] = self.model.to_bytes
|
||
serialize["vocab"] = self.vocab.to_bytes
|
||
serialize["cfg"] = lambda: srsly.json_dumps(self.cfg)
|
||
exclude = util.get_serialization_exclude(serialize, exclude, kwargs)
|
||
return util.to_bytes(serialize, exclude)
|
||
|
||
def from_bytes(self, bytes_data, exclude=tuple(), **kwargs):
|
||
def load_model(b):
|
||
try:
|
||
self.model.from_bytes(b)
|
||
except AttributeError:
|
||
raise ValueError(Errors.E149)
|
||
|
||
deserialize = {
|
||
"vocab": lambda b: self.vocab.from_bytes(b),
|
||
"cfg": lambda b: self.cfg.update(srsly.json_loads(b)),
|
||
"model": lambda b: load_model(b),
|
||
}
|
||
exclude = util.get_serialization_exclude(deserialize, exclude, kwargs)
|
||
util.from_bytes(bytes_data, deserialize, exclude)
|
||
return self
|
||
|
||
def to_disk(self, path, exclude=tuple(), **kwargs):
|
||
serialize = {
|
||
"vocab": lambda p: self.vocab.to_disk(p),
|
||
"model": lambda p: p.open("wb").write(self.model.to_bytes()),
|
||
"cfg": lambda p: srsly.write_json(p, self.cfg),
|
||
}
|
||
exclude = util.get_serialization_exclude(serialize, exclude, kwargs)
|
||
util.to_disk(path, serialize, exclude)
|
||
|
||
def from_disk(self, path, exclude=tuple(), **kwargs):
|
||
def load_model(p):
|
||
with p.open("rb") as file_:
|
||
try:
|
||
self.model.from_bytes(file_.read())
|
||
except AttributeError:
|
||
raise ValueError(Errors.E149)
|
||
|
||
deserialize = {
|
||
"vocab": lambda p: self.vocab.from_disk(p),
|
||
"cfg": lambda p: self.cfg.update(_load_cfg(p)),
|
||
"model": load_model,
|
||
}
|
||
exclude = util.get_serialization_exclude(deserialize, exclude, kwargs)
|
||
util.from_disk(path, deserialize, exclude)
|
||
return self
|
||
|
||
|
||
@component("nn_labeller")
|
||
class MultitaskObjective(Tagger):
|
||
"""Experimental: Assist training of a parser or tagger, by training a
|
||
side-objective.
|
||
"""
|
||
|
||
def __init__(self, vocab, model, **cfg):
|
||
self.vocab = vocab
|
||
self.model = model
|
||
target = cfg["target"] # default: 'dep_tag_offset'
|
||
if target == "dep":
|
||
self.make_label = self.make_dep
|
||
elif target == "tag":
|
||
self.make_label = self.make_tag
|
||
elif target == "ent":
|
||
self.make_label = self.make_ent
|
||
elif target == "dep_tag_offset":
|
||
self.make_label = self.make_dep_tag_offset
|
||
elif target == "ent_tag":
|
||
self.make_label = self.make_ent_tag
|
||
elif target == "sent_start":
|
||
self.make_label = self.make_sent_start
|
||
elif hasattr(target, "__call__"):
|
||
self.make_label = target
|
||
else:
|
||
raise ValueError(Errors.E016)
|
||
self.cfg = dict(cfg)
|
||
|
||
@property
|
||
def labels(self):
|
||
return self.cfg.setdefault("labels", {})
|
||
|
||
@labels.setter
|
||
def labels(self, value):
|
||
self.cfg["labels"] = value
|
||
|
||
def set_annotations(self, docs, dep_ids, tensors=None):
|
||
pass
|
||
|
||
def begin_training(self, get_examples=lambda: [], pipeline=None,
|
||
sgd=None, **kwargs):
|
||
gold_examples = nonproj.preprocess_training_data(get_examples())
|
||
# for raw_text, doc_annot in gold_tuples:
|
||
for example in gold_examples:
|
||
for i in range(len(example.token_annotation.ids)):
|
||
label = self.make_label(i, example.token_annotation)
|
||
if label is not None and label not in self.labels:
|
||
self.labels[label] = len(self.labels)
|
||
self.model.initialize()
|
||
link_vectors_to_models(self.vocab)
|
||
if sgd is None:
|
||
sgd = self.create_optimizer()
|
||
return sgd
|
||
|
||
def predict(self, docs):
|
||
tokvecs = self.model.get_ref("tok2vec")(docs)
|
||
scores = self.model.get_ref("softmax")(tokvecs)
|
||
return tokvecs, scores
|
||
|
||
def get_loss(self, examples, scores):
|
||
cdef int idx = 0
|
||
correct = numpy.zeros((scores.shape[0],), dtype="i")
|
||
guesses = scores.argmax(axis=1)
|
||
golds = [ex.gold for ex in examples]
|
||
docs = [ex.doc for ex in examples]
|
||
for i, gold in enumerate(golds):
|
||
for j in range(len(docs[i])):
|
||
# Handels alignment for tokenization differences
|
||
token_annotation = gold.get_token_annotation()
|
||
label = self.make_label(j, token_annotation)
|
||
if label is None or label not in self.labels:
|
||
correct[idx] = guesses[idx]
|
||
else:
|
||
correct[idx] = self.labels[label]
|
||
idx += 1
|
||
correct = self.model.ops.xp.array(correct, dtype="i")
|
||
d_scores = scores - to_categorical(correct, n_classes=scores.shape[1])
|
||
loss = (d_scores**2).sum()
|
||
return float(loss), d_scores
|
||
|
||
@staticmethod
|
||
def make_dep(i, token_annotation):
|
||
if token_annotation.deps[i] is None or token_annotation.heads[i] is None:
|
||
return None
|
||
return token_annotation.deps[i]
|
||
|
||
@staticmethod
|
||
def make_tag(i, token_annotation):
|
||
return token_annotation.tags[i]
|
||
|
||
@staticmethod
|
||
def make_ent(i, token_annotation):
|
||
if token_annotation.entities is None:
|
||
return None
|
||
return token_annotation.entities[i]
|
||
|
||
@staticmethod
|
||
def make_dep_tag_offset(i, token_annotation):
|
||
if token_annotation.deps[i] is None or token_annotation.heads[i] is None:
|
||
return None
|
||
offset = token_annotation.heads[i] - i
|
||
offset = min(offset, 2)
|
||
offset = max(offset, -2)
|
||
return f"{token_annotation.deps[i]}-{token_annotation.tags[i]}:{offset}"
|
||
|
||
@staticmethod
|
||
def make_ent_tag(i, token_annotation):
|
||
if token_annotation.entities is None or token_annotation.entities[i] is None:
|
||
return None
|
||
else:
|
||
return f"{token_annotation.tags[i]}-{token_annotation.entities[i]}"
|
||
|
||
@staticmethod
|
||
def make_sent_start(target, token_annotation, cache=True, _cache={}):
|
||
"""A multi-task objective for representing sentence boundaries,
|
||
using BILU scheme. (O is impossible)
|
||
|
||
The implementation of this method uses an internal cache that relies
|
||
on the identity of the heads array, to avoid requiring a new piece
|
||
of gold data. You can pass cache=False if you know the cache will
|
||
do the wrong thing.
|
||
"""
|
||
words = token_annotation.words
|
||
heads = token_annotation.heads
|
||
assert len(words) == len(heads)
|
||
assert target < len(words), (target, len(words))
|
||
if cache:
|
||
if id(heads) in _cache:
|
||
return _cache[id(heads)][target]
|
||
else:
|
||
for key in list(_cache.keys()):
|
||
_cache.pop(key)
|
||
sent_tags = ["I-SENT"] * len(words)
|
||
_cache[id(heads)] = sent_tags
|
||
else:
|
||
sent_tags = ["I-SENT"] * len(words)
|
||
|
||
def _find_root(child):
|
||
seen = set([child])
|
||
while child is not None and heads[child] != child:
|
||
seen.add(child)
|
||
child = heads[child]
|
||
return child
|
||
|
||
sentences = {}
|
||
for i in range(len(words)):
|
||
root = _find_root(i)
|
||
if root is None:
|
||
sent_tags[i] = None
|
||
else:
|
||
sentences.setdefault(root, []).append(i)
|
||
for root, span in sorted(sentences.items()):
|
||
if len(span) == 1:
|
||
sent_tags[span[0]] = "U-SENT"
|
||
else:
|
||
sent_tags[span[0]] = "B-SENT"
|
||
sent_tags[span[-1]] = "L-SENT"
|
||
return sent_tags[target]
|
||
|
||
|
||
class ClozeMultitask(Pipe):
|
||
def __init__(self, vocab, model, **cfg):
|
||
self.vocab = vocab
|
||
self.model = model
|
||
self.cfg = cfg
|
||
self.distance = CosineDistance(ignore_zeros=True, normalize=False) # TODO: in config
|
||
|
||
def set_annotations(self, docs, dep_ids, tensors=None):
|
||
pass
|
||
|
||
def begin_training(self, get_examples=lambda: [], pipeline=None,
|
||
sgd=None, **kwargs):
|
||
link_vectors_to_models(self.vocab)
|
||
self.model.initialize()
|
||
X = self.model.ops.alloc((5, self.model.get_ref("tok2vec").get_dim("nO")))
|
||
self.model.output_layer.begin_training(X)
|
||
if sgd is None:
|
||
sgd = self.create_optimizer()
|
||
return sgd
|
||
|
||
def predict(self, docs):
|
||
tokvecs = self.model.get_ref("tok2vec")(docs)
|
||
vectors = self.model.get_ref("output_layer")(tokvecs)
|
||
return tokvecs, vectors
|
||
|
||
def get_loss(self, examples, vectors, prediction):
|
||
# The simplest way to implement this would be to vstack the
|
||
# token.vector values, but that's a bit inefficient, especially on GPU.
|
||
# Instead we fetch the index into the vectors table for each of our tokens,
|
||
# and look them up all at once. This prevents data copying.
|
||
ids = self.model.ops.flatten([ex.doc.to_array(ID).ravel() for ex in examples])
|
||
target = vectors[ids]
|
||
gradient = self.distance.get_grad(prediction, target)
|
||
loss = self.distance.get_loss(prediction, target)
|
||
return loss, gradient
|
||
|
||
def update(self, examples, drop=0., set_annotations=False, sgd=None, losses=None):
|
||
pass
|
||
|
||
def rehearse(self, examples, drop=0., sgd=None, losses=None):
|
||
examples = Example.to_example_objects(examples)
|
||
if losses is not None and self.name not in losses:
|
||
losses[self.name] = 0.
|
||
set_dropout_rate(self.model, drop)
|
||
predictions, bp_predictions = self.model.begin_update([ex.doc for ex in examples])
|
||
loss, d_predictions = self.get_loss(examples, self.vocab.vectors.data, predictions)
|
||
bp_predictions(d_predictions)
|
||
if sgd is not None:
|
||
self.model.finish_update(sgd)
|
||
|
||
if losses is not None:
|
||
losses[self.name] += loss
|
||
|
||
|
||
@component("textcat", assigns=["doc.cats"], default_model=default_textcat)
|
||
class TextCategorizer(Pipe):
|
||
"""Pipeline component for text classification.
|
||
|
||
DOCS: https://spacy.io/api/textcategorizer
|
||
"""
|
||
def __init__(self, vocab, model, **cfg):
|
||
self.vocab = vocab
|
||
self.model = model
|
||
self._rehearsal_model = None
|
||
self.cfg = dict(cfg)
|
||
|
||
@property
|
||
def labels(self):
|
||
return tuple(self.cfg.setdefault("labels", []))
|
||
|
||
def require_labels(self):
|
||
"""Raise an error if the component's model has no labels defined."""
|
||
if not self.labels:
|
||
raise ValueError(Errors.E143.format(name=self.name))
|
||
|
||
@labels.setter
|
||
def labels(self, value):
|
||
self.cfg["labels"] = tuple(value)
|
||
|
||
def pipe(self, stream, batch_size=128, n_threads=-1, as_example=False):
|
||
for examples in util.minibatch(stream, size=batch_size):
|
||
docs = [self._get_doc(ex) for ex in examples]
|
||
scores, tensors = self.predict(docs)
|
||
self.set_annotations(docs, scores, tensors=tensors)
|
||
|
||
if as_example:
|
||
for ex, doc in zip(examples, docs):
|
||
ex.doc = doc
|
||
yield ex
|
||
else:
|
||
yield from docs
|
||
|
||
def predict(self, docs):
|
||
tensors = [doc.tensor for doc in docs]
|
||
|
||
if not any(len(doc) for doc in docs):
|
||
# Handle cases where there are no tokens in any docs.
|
||
xp = get_array_module(tensors)
|
||
scores = xp.zeros((len(docs), len(self.labels)))
|
||
return scores, tensors
|
||
|
||
scores = self.model.predict(docs)
|
||
scores = self.model.ops.asarray(scores)
|
||
return scores, tensors
|
||
|
||
def set_annotations(self, docs, scores, tensors=None):
|
||
for i, doc in enumerate(docs):
|
||
for j, label in enumerate(self.labels):
|
||
doc.cats[label] = float(scores[i, j])
|
||
|
||
def update(self, examples, state=None, drop=0., set_annotations=False, sgd=None, losses=None):
|
||
examples = Example.to_example_objects(examples)
|
||
if not any(len(ex.doc) if ex.doc else 0 for ex in examples):
|
||
# Handle cases where there are no tokens in any docs.
|
||
return
|
||
set_dropout_rate(self.model, drop)
|
||
scores, bp_scores = self.model.begin_update([ex.doc for ex in examples])
|
||
loss, d_scores = self.get_loss(examples, scores)
|
||
bp_scores(d_scores)
|
||
if sgd is not None:
|
||
self.model.finish_update(sgd)
|
||
if losses is not None:
|
||
losses.setdefault(self.name, 0.0)
|
||
losses[self.name] += loss
|
||
if set_annotations:
|
||
docs = [ex.doc for ex in examples]
|
||
self.set_annotations(docs, scores=scores)
|
||
|
||
def rehearse(self, examples, drop=0., sgd=None, losses=None):
|
||
if self._rehearsal_model is None:
|
||
return
|
||
examples = Example.to_example_objects(examples)
|
||
docs=[ex.doc for ex in examples]
|
||
if not any(len(doc) for doc in docs):
|
||
# Handle cases where there are no tokens in any docs.
|
||
return
|
||
set_dropout_rate(self.model, drop)
|
||
scores, bp_scores = self.model.begin_update(docs)
|
||
target = self._rehearsal_model(examples)
|
||
gradient = scores - target
|
||
bp_scores(gradient)
|
||
if sgd is not None:
|
||
self.model.finish_update(sgd)
|
||
if losses is not None:
|
||
losses.setdefault(self.name, 0.0)
|
||
losses[self.name] += (gradient**2).sum()
|
||
|
||
def _examples_to_truth(self, examples):
|
||
gold_cats = [ex.doc_annotation.cats for ex in examples]
|
||
truths = numpy.zeros((len(gold_cats), len(self.labels)), dtype="f")
|
||
not_missing = numpy.ones((len(gold_cats), len(self.labels)), dtype="f")
|
||
for i, gold_cat in enumerate(gold_cats):
|
||
for j, label in enumerate(self.labels):
|
||
if label in gold_cat:
|
||
truths[i, j] = gold_cat[label]
|
||
else:
|
||
not_missing[i, j] = 0.
|
||
truths = self.model.ops.asarray(truths)
|
||
return truths, not_missing
|
||
|
||
def get_loss(self, examples, scores):
|
||
truths, not_missing = self._examples_to_truth(examples)
|
||
not_missing = self.model.ops.asarray(not_missing)
|
||
d_scores = (scores-truths) / scores.shape[0]
|
||
d_scores *= not_missing
|
||
mean_square_error = (d_scores**2).sum(axis=1).mean()
|
||
return float(mean_square_error), d_scores
|
||
|
||
def add_label(self, label):
|
||
if not isinstance(label, str):
|
||
raise ValueError(Errors.E187)
|
||
if label in self.labels:
|
||
return 0
|
||
if self.model.has_dim("nO"):
|
||
# This functionality was available previously, but was broken.
|
||
# The problem is that we resize the last layer, but the last layer
|
||
# is actually just an ensemble. We're not resizing the child layers
|
||
# - a huge problem.
|
||
raise ValueError(Errors.E116)
|
||
# smaller = self.model._layers[-1]
|
||
# larger = Linear(len(self.labels)+1, smaller.nI)
|
||
# copy_array(larger.W[:smaller.nO], smaller.W)
|
||
# copy_array(larger.b[:smaller.nO], smaller.b)
|
||
# self.model._layers[-1] = larger
|
||
self.labels = tuple(list(self.labels) + [label])
|
||
return 1
|
||
|
||
def begin_training(self, get_examples=lambda: [], pipeline=None, sgd=None, **kwargs):
|
||
# TODO: begin_training is not guaranteed to see all data / labels ?
|
||
examples = list(get_examples())
|
||
for example in examples:
|
||
for cat in example.doc_annotation.cats:
|
||
self.add_label(cat)
|
||
self.require_labels()
|
||
docs = [Doc(Vocab(), words=["hello"])]
|
||
truths, _ = self._examples_to_truth(examples)
|
||
self.set_output(len(self.labels))
|
||
link_vectors_to_models(self.vocab)
|
||
self.model.initialize(X=docs, Y=truths)
|
||
if sgd is None:
|
||
sgd = self.create_optimizer()
|
||
return sgd
|
||
|
||
|
||
cdef class DependencyParser(Parser):
|
||
"""Pipeline component for dependency parsing.
|
||
|
||
DOCS: https://spacy.io/api/dependencyparser
|
||
"""
|
||
# cdef classes can't have decorators, so we're defining this here
|
||
name = "parser"
|
||
factory = "parser"
|
||
assigns = ["token.dep", "token.is_sent_start", "doc.sents"]
|
||
requires = []
|
||
TransitionSystem = ArcEager
|
||
|
||
@property
|
||
def postprocesses(self):
|
||
output = [nonproj.deprojectivize]
|
||
if self.cfg.get("learn_tokens") is True:
|
||
output.append(merge_subtokens)
|
||
return tuple(output)
|
||
|
||
def add_multitask_objective(self, mt_component):
|
||
self._multitasks.append(mt_component)
|
||
|
||
def init_multitask_objectives(self, get_examples, pipeline, sgd=None, **cfg):
|
||
# TODO: transfer self.model.get_ref("tok2vec") to the multitask's model ?
|
||
for labeller in self._multitasks:
|
||
labeller.model.set_dim("nO", len(self.labels))
|
||
if labeller.model.has_ref("output_layer"):
|
||
labeller.model.get_ref("output_layer").set_dim("nO", len(self.labels))
|
||
labeller.begin_training(get_examples, pipeline=pipeline, sgd=sgd)
|
||
|
||
def __reduce__(self):
|
||
return (DependencyParser, (self.vocab, self.model), (self.moves, self.cfg))
|
||
|
||
def __getstate__(self):
|
||
return (self.moves, self.cfg)
|
||
|
||
def __setstate__(self, state):
|
||
moves, config = state
|
||
self.moves = moves
|
||
self.cfg = config
|
||
|
||
@property
|
||
def labels(self):
|
||
labels = set()
|
||
# Get the labels from the model by looking at the available moves
|
||
for move in self.move_names:
|
||
if "-" in move:
|
||
label = move.split("-")[1]
|
||
if "||" in label:
|
||
label = label.split("||")[1]
|
||
labels.add(label)
|
||
return tuple(sorted(labels))
|
||
|
||
|
||
cdef class EntityRecognizer(Parser):
|
||
"""Pipeline component for named entity recognition.
|
||
|
||
DOCS: https://spacy.io/api/entityrecognizer
|
||
"""
|
||
name = "ner"
|
||
factory = "ner"
|
||
assigns = ["doc.ents", "token.ent_iob", "token.ent_type"]
|
||
requires = []
|
||
TransitionSystem = BiluoPushDown
|
||
|
||
def add_multitask_objective(self, mt_component):
|
||
self._multitasks.append(mt_component)
|
||
|
||
def init_multitask_objectives(self, get_examples, pipeline, sgd=None, **cfg):
|
||
# TODO: transfer self.model.get_ref("tok2vec") to the multitask's model ?
|
||
for labeller in self._multitasks:
|
||
labeller.model.set_dim("nO", len(self.labels))
|
||
if labeller.model.has_ref("output_layer"):
|
||
labeller.model.get_ref("output_layer").set_dim("nO", len(self.labels))
|
||
labeller.begin_training(get_examples, pipeline=pipeline)
|
||
|
||
def __reduce__(self):
|
||
return (EntityRecognizer, (self.vocab, self.model), (self.moves, self.cfg))
|
||
|
||
def __getstate__(self):
|
||
return self.moves, self.cfg
|
||
|
||
def __setstate__(self, state):
|
||
moves, config = state
|
||
self.moves = moves
|
||
self.cfg = config
|
||
|
||
@property
|
||
def labels(self):
|
||
# Get the labels from the model by looking at the available moves, e.g.
|
||
# B-PERSON, I-PERSON, L-PERSON, U-PERSON
|
||
labels = set(move.split("-")[1] for move in self.move_names
|
||
if move[0] in ("B", "I", "L", "U"))
|
||
return tuple(sorted(labels))
|
||
|
||
|
||
@component(
|
||
"entity_linker",
|
||
requires=["doc.ents", "doc.sents", "token.ent_iob", "token.ent_type"],
|
||
assigns=["token.ent_kb_id"],
|
||
default_model=default_nel,
|
||
)
|
||
class EntityLinker(Pipe):
|
||
"""Pipeline component for named entity linking.
|
||
|
||
DOCS: https://spacy.io/api/entitylinker
|
||
"""
|
||
NIL = "NIL" # string used to refer to a non-existing link
|
||
|
||
def __init__(self, vocab, model, **cfg):
|
||
self.vocab = vocab
|
||
self.model = model
|
||
self.kb = None
|
||
self.kb = cfg.get("kb", None)
|
||
if self.kb is None:
|
||
# create an empty KB that should be filled by calling from_disk
|
||
self.kb = KnowledgeBase(vocab=vocab)
|
||
else:
|
||
del cfg["kb"] # we don't want to duplicate its serialization
|
||
if not isinstance(self.kb, KnowledgeBase):
|
||
raise ValueError(Errors.E990.format(type=type(self.kb)))
|
||
self.cfg = dict(cfg)
|
||
self.distance = CosineDistance(normalize=False)
|
||
# how many neightbour sentences to take into account
|
||
self.n_sents = cfg.get("n_sents", 0)
|
||
|
||
def set_kb(self, kb):
|
||
self.kb = kb
|
||
|
||
def require_model(self):
|
||
# Raise an error if the component's model is not initialized.
|
||
if getattr(self, "model", None) in (None, True, False):
|
||
raise ValueError(Errors.E109.format(name=self.name))
|
||
|
||
def require_kb(self):
|
||
# Raise an error if the knowledge base is not initialized.
|
||
if len(self.kb) == 0:
|
||
raise ValueError(Errors.E139.format(name=self.name))
|
||
|
||
def begin_training(self, get_examples=lambda: [], pipeline=None, sgd=None, **kwargs):
|
||
self.require_kb()
|
||
nO = self.kb.entity_vector_length
|
||
self.set_output(nO)
|
||
self.model.initialize()
|
||
if sgd is None:
|
||
sgd = self.create_optimizer()
|
||
return sgd
|
||
|
||
def update(self, examples, state=None, set_annotations=False, drop=0.0, sgd=None, losses=None):
|
||
self.require_kb()
|
||
if losses is not None:
|
||
losses.setdefault(self.name, 0.0)
|
||
if not examples:
|
||
return 0
|
||
examples = Example.to_example_objects(examples)
|
||
sentence_docs = []
|
||
docs = [ex.doc for ex in examples]
|
||
if set_annotations:
|
||
# This seems simpler than other ways to get that exact output -- but
|
||
# it does run the model twice :(
|
||
predictions = self.model.predict(docs)
|
||
golds = [ex.gold for ex in examples]
|
||
|
||
for doc, gold in zip(docs, golds):
|
||
ents_by_offset = dict()
|
||
|
||
sentences = [s for s in doc.sents]
|
||
|
||
for ent in doc.ents:
|
||
ents_by_offset[(ent.start_char, ent.end_char)] = ent
|
||
|
||
for entity, kb_dict in gold.links.items():
|
||
if isinstance(entity, str):
|
||
entity = literal_eval(entity)
|
||
start, end = entity
|
||
mention = doc.text[start:end]
|
||
|
||
# the gold annotations should link to proper entities - if this fails, the dataset is likely corrupt
|
||
if not (start, end) in ents_by_offset:
|
||
raise RuntimeError(Errors.E188)
|
||
|
||
ent = ents_by_offset[(start, end)]
|
||
|
||
for kb_id, value in kb_dict.items():
|
||
# Currently only training on the positive instances - we assume there is at least 1 per doc/gold
|
||
if value:
|
||
try:
|
||
# find the sentence in the list of sentences.
|
||
sent_index = sentences.index(ent.sent)
|
||
|
||
except AttributeError:
|
||
# Catch the exception when ent.sent is None and provide a user-friendly warning
|
||
raise RuntimeError(Errors.E030)
|
||
|
||
# get n previous sentences, if there are any
|
||
start_sentence = max(0, sent_index - self.n_sents)
|
||
|
||
# get n posterior sentences, or as many < n as there are
|
||
end_sentence = min(len(sentences) -1, sent_index + self.n_sents)
|
||
|
||
# get token positions
|
||
start_token = sentences[start_sentence].start
|
||
end_token = sentences[end_sentence].end
|
||
|
||
# append that span as a doc to training
|
||
sent_doc = doc[start_token:end_token].as_doc()
|
||
sentence_docs.append(sent_doc)
|
||
|
||
sentence_encodings, bp_context = self.model.begin_update(sentence_docs, drop=drop)
|
||
loss, d_scores = self.get_similarity_loss(scores=sentence_encodings, golds=golds, docs=None)
|
||
bp_context(d_scores, sgd=sgd)
|
||
set_dropout_rate(self.model, drop)
|
||
sentence_encodings, bp_context = self.model.begin_update(sentence_docs)
|
||
loss, d_scores = self.get_similarity_loss(scores=sentence_encodings, golds=golds)
|
||
bp_context(d_scores)
|
||
if sgd is not None:
|
||
self.model.finish_update(sgd)
|
||
|
||
if losses is not None:
|
||
losses[self.name] += loss
|
||
if set_annotations:
|
||
self.set_annotations(docs, predictions)
|
||
return loss
|
||
|
||
def get_similarity_loss(self, golds, scores):
|
||
entity_encodings = []
|
||
for gold in golds:
|
||
for entity, kb_dict in gold.links.items():
|
||
for kb_id, value in kb_dict.items():
|
||
# this loss function assumes we're only using positive examples
|
||
if value:
|
||
entity_encoding = self.kb.get_vector(kb_id)
|
||
entity_encodings.append(entity_encoding)
|
||
|
||
entity_encodings = self.model.ops.asarray(entity_encodings, dtype="float32")
|
||
|
||
if scores.shape != entity_encodings.shape:
|
||
raise RuntimeError(Errors.E147.format(method="get_similarity_loss", msg="gold entities do not match up"))
|
||
|
||
gradients = self.distance.get_grad(scores, entity_encodings)
|
||
loss = self.distance.get_loss(scores, entity_encodings)
|
||
loss = loss / len(entity_encodings)
|
||
return loss, gradients
|
||
|
||
def get_loss(self, examples, scores):
|
||
cats = []
|
||
for ex in examples:
|
||
for entity, kb_dict in ex.gold.links.items():
|
||
for kb_id, value in kb_dict.items():
|
||
cats.append([value])
|
||
|
||
cats = self.model.ops.asarray(cats, dtype="float32")
|
||
if len(scores) != len(cats):
|
||
raise RuntimeError(Errors.E147.format(method="get_loss", msg="gold entities do not match up"))
|
||
|
||
d_scores = (scores - cats)
|
||
loss = (d_scores ** 2).sum()
|
||
loss = loss / len(cats)
|
||
return loss, d_scores
|
||
|
||
def __call__(self, example):
|
||
doc = self._get_doc(example)
|
||
kb_ids, tensors = self.predict([doc])
|
||
self.set_annotations([doc], kb_ids, tensors=tensors)
|
||
if isinstance(example, Example):
|
||
example.doc = doc
|
||
return example
|
||
return doc
|
||
|
||
def pipe(self, stream, batch_size=128, n_threads=-1, as_example=False):
|
||
for examples in util.minibatch(stream, size=batch_size):
|
||
docs = [self._get_doc(ex) for ex in examples]
|
||
kb_ids, tensors = self.predict(docs)
|
||
self.set_annotations(docs, kb_ids, tensors=tensors)
|
||
|
||
if as_example:
|
||
for ex, doc in zip(examples, docs):
|
||
ex.doc = doc
|
||
yield ex
|
||
else:
|
||
yield from docs
|
||
|
||
def predict(self, docs):
|
||
""" Return the KB IDs for each entity in each doc, including NIL if there is no prediction """
|
||
self.require_kb()
|
||
entity_count = 0
|
||
final_kb_ids = []
|
||
final_tensors = []
|
||
|
||
if not docs:
|
||
return final_kb_ids, final_tensors
|
||
|
||
if isinstance(docs, Doc):
|
||
docs = [docs]
|
||
|
||
|
||
for i, doc in enumerate(docs):
|
||
sentences = [s for s in doc.sents]
|
||
|
||
if len(doc) > 0:
|
||
# Looping through each sentence and each entity
|
||
# This may go wrong if there are entities across sentences - which shouldn't happen normally.
|
||
for sent in doc.sents:
|
||
sent_doc = sent.as_doc()
|
||
# currently, the context is the same for each entity in a sentence (should be refined)
|
||
sentence_encoding = self.model.predict([sent_doc])[0]
|
||
xp = get_array_module(sentence_encoding)
|
||
sentence_encoding_t = sentence_encoding.T
|
||
sentence_norm = xp.linalg.norm(sentence_encoding_t)
|
||
|
||
for ent in sent_doc.ents:
|
||
entity_count += 1
|
||
|
||
to_discard = self.cfg.get("labels_discard", [])
|
||
if to_discard and ent.label_ in to_discard:
|
||
# ignoring this entity - setting to NIL
|
||
final_kb_ids.append(self.NIL)
|
||
final_tensors.append(sentence_encoding)
|
||
|
||
else:
|
||
candidates = self.kb.get_candidates(ent.text)
|
||
if not candidates:
|
||
# no prediction possible for this entity - setting to NIL
|
||
final_kb_ids.append(self.NIL)
|
||
final_tensors.append(sentence_encoding)
|
||
|
||
sent_doc = doc[sent.start:sent.end].as_doc()
|
||
|
||
# currently, the context is the same for each entity in a sentence (should be refined)
|
||
sentence_encoding = self.model([sent_doc])[0]
|
||
xp = get_array_module(sentence_encoding)
|
||
sentence_encoding_t = sentence_encoding.T
|
||
sentence_norm = xp.linalg.norm(sentence_encoding_t)
|
||
|
||
for ent in sent.ents:
|
||
entity_count += 1
|
||
|
||
to_discard = self.cfg.get("labels_discard", [])
|
||
if to_discard and ent.label_ in to_discard:
|
||
# ignoring this entity - setting to NIL
|
||
final_kb_ids.append(self.NIL)
|
||
final_tensors.append(sentence_encoding)
|
||
|
||
else:
|
||
random.shuffle(candidates)
|
||
|
||
# this will set all prior probabilities to 0 if they should be excluded from the model
|
||
prior_probs = xp.asarray([c.prior_prob for c in candidates])
|
||
if not self.cfg.get("incl_prior", True):
|
||
prior_probs = xp.asarray([0.0 for c in candidates])
|
||
scores = prior_probs
|
||
|
||
# add in similarity from the context
|
||
if self.cfg.get("incl_context", True):
|
||
entity_encodings = xp.asarray([c.entity_vector for c in candidates])
|
||
entity_norm = xp.linalg.norm(entity_encodings, axis=1)
|
||
|
||
if len(entity_encodings) != len(prior_probs):
|
||
raise RuntimeError(Errors.E147.format(method="predict", msg="vectors not of equal length"))
|
||
|
||
# cosine similarity
|
||
sims = xp.dot(entity_encodings, sentence_encoding_t) / (sentence_norm * entity_norm)
|
||
if sims.shape != prior_probs.shape:
|
||
raise ValueError(Errors.E161)
|
||
scores = prior_probs + sims - (prior_probs*sims)
|
||
|
||
# TODO: thresholding
|
||
best_index = scores.argmax().item()
|
||
best_candidate = candidates[best_index]
|
||
final_kb_ids.append(best_candidate.entity_)
|
||
final_tensors.append(sentence_encoding)
|
||
|
||
if not (len(final_tensors) == len(final_kb_ids) == entity_count):
|
||
raise RuntimeError(Errors.E147.format(method="predict", msg="result variables not of equal length"))
|
||
|
||
return final_kb_ids, final_tensors
|
||
|
||
def set_annotations(self, docs, kb_ids, tensors=None):
|
||
count_ents = len([ent for doc in docs for ent in doc.ents])
|
||
if count_ents != len(kb_ids):
|
||
raise ValueError(Errors.E148.format(ents=count_ents, ids=len(kb_ids)))
|
||
|
||
i=0
|
||
for doc in docs:
|
||
for ent in doc.ents:
|
||
kb_id = kb_ids[i]
|
||
i += 1
|
||
for token in ent:
|
||
token.ent_kb_id_ = kb_id
|
||
|
||
def to_disk(self, path, exclude=tuple(), **kwargs):
|
||
serialize = {}
|
||
self.cfg["entity_width"] = self.kb.entity_vector_length
|
||
serialize["cfg"] = lambda p: srsly.write_json(p, self.cfg)
|
||
serialize["vocab"] = lambda p: self.vocab.to_disk(p)
|
||
serialize["kb"] = lambda p: self.kb.dump(p)
|
||
serialize["model"] = lambda p: self.model.to_disk(p)
|
||
exclude = util.get_serialization_exclude(serialize, exclude, kwargs)
|
||
util.to_disk(path, serialize, exclude)
|
||
|
||
def from_disk(self, path, exclude=tuple(), **kwargs):
|
||
def load_model(p):
|
||
try:
|
||
self.model.from_bytes(p.open("rb").read())
|
||
except AttributeError:
|
||
raise ValueError(Errors.E149)
|
||
|
||
def load_kb(p):
|
||
self.kb = KnowledgeBase(vocab=self.vocab, entity_vector_length=self.cfg["entity_width"])
|
||
self.kb.load_bulk(p)
|
||
|
||
deserialize = {}
|
||
deserialize["vocab"] = lambda p: self.vocab.from_disk(p)
|
||
deserialize["cfg"] = lambda p: self.cfg.update(_load_cfg(p))
|
||
deserialize["kb"] = load_kb
|
||
deserialize["model"] = load_model
|
||
exclude = util.get_serialization_exclude(deserialize, exclude, kwargs)
|
||
util.from_disk(path, deserialize, exclude)
|
||
return self
|
||
|
||
def rehearse(self, examples, sgd=None, losses=None, **config):
|
||
raise NotImplementedError
|
||
|
||
def add_label(self, label):
|
||
raise NotImplementedError
|
||
|
||
|
||
@component("sentencizer", assigns=["token.is_sent_start", "doc.sents"])
|
||
class Sentencizer(Pipe):
|
||
"""Segment the Doc into sentences using a rule-based strategy.
|
||
|
||
DOCS: https://spacy.io/api/sentencizer
|
||
"""
|
||
|
||
default_punct_chars = ['!', '.', '?', '։', '؟', '۔', '܀', '܁', '܂', '߹',
|
||
'।', '॥', '၊', '။', '።', '፧', '፨', '᙮', '᜵', '᜶', '᠃', '᠉', '᥄',
|
||
'᥅', '᪨', '᪩', '᪪', '᪫', '᭚', '᭛', '᭞', '᭟', '᰻', '᰼', '᱾', '᱿',
|
||
'‼', '‽', '⁇', '⁈', '⁉', '⸮', '⸼', '꓿', '꘎', '꘏', '꛳', '꛷', '꡶',
|
||
'꡷', '꣎', '꣏', '꤯', '꧈', '꧉', '꩝', '꩞', '꩟', '꫰', '꫱', '꯫', '﹒',
|
||
'﹖', '﹗', '！', '．', '？', '𐩖', '𐩗', '𑁇', '𑁈', '𑂾', '𑂿', '𑃀',
|
||
'𑃁', '𑅁', '𑅂', '𑅃', '𑇅', '𑇆', '𑇍', '𑇞', '𑇟', '𑈸', '𑈹', '𑈻', '𑈼',
|
||
'𑊩', '𑑋', '𑑌', '𑗂', '𑗃', '𑗉', '𑗊', '𑗋', '𑗌', '𑗍', '𑗎', '𑗏', '𑗐',
|
||
'𑗑', '𑗒', '𑗓', '𑗔', '𑗕', '𑗖', '𑗗', '𑙁', '𑙂', '𑜼', '𑜽', '𑜾', '𑩂',
|
||
'𑩃', '𑪛', '𑪜', '𑱁', '𑱂', '𖩮', '𖩯', '𖫵', '𖬷', '𖬸', '𖭄', '𛲟', '𝪈',
|
||
'｡', '。']
|
||
|
||
def __init__(self, punct_chars=None, **kwargs):
|
||
"""Initialize the sentencizer.
|
||
|
||
punct_chars (list): Punctuation characters to split on. Will be
|
||
serialized with the nlp object.
|
||
RETURNS (Sentencizer): The sentencizer component.
|
||
|
||
DOCS: https://spacy.io/api/sentencizer#init
|
||
"""
|
||
if punct_chars:
|
||
self.punct_chars = set(punct_chars)
|
||
else:
|
||
self.punct_chars = set(self.default_punct_chars)
|
||
|
||
@classmethod
|
||
def from_nlp(cls, nlp, model=None, **cfg):
|
||
return cls(**cfg)
|
||
|
||
def begin_training(
|
||
self, get_examples=lambda: [], pipeline=None, sgd=None, **kwargs
|
||
):
|
||
pass
|
||
|
||
def __call__(self, example):
|
||
"""Apply the sentencizer to a Doc and set Token.is_sent_start.
|
||
|
||
example (Doc or Example): The document to process.
|
||
RETURNS (Doc or Example): The processed Doc or Example.
|
||
|
||
DOCS: https://spacy.io/api/sentencizer#call
|
||
"""
|
||
doc = self._get_doc(example)
|
||
start = 0
|
||
seen_period = False
|
||
for i, token in enumerate(doc):
|
||
is_in_punct_chars = token.text in self.punct_chars
|
||
token.is_sent_start = i == 0
|
||
if seen_period and not token.is_punct and not is_in_punct_chars:
|
||
doc[start].is_sent_start = True
|
||
start = token.i
|
||
seen_period = False
|
||
elif is_in_punct_chars:
|
||
seen_period = True
|
||
if start < len(doc):
|
||
doc[start].is_sent_start = True
|
||
if isinstance(example, Example):
|
||
example.doc = doc
|
||
return example
|
||
return doc
|
||
|
||
def pipe(self, stream, batch_size=128, n_threads=-1, as_example=False):
|
||
for examples in util.minibatch(stream, size=batch_size):
|
||
docs = [self._get_doc(ex) for ex in examples]
|
||
predictions = self.predict(docs)
|
||
if isinstance(predictions, tuple) and len(tuple) == 2:
|
||
scores, tensors = predictions
|
||
self.set_annotations(docs, scores, tensors=tensors)
|
||
else:
|
||
self.set_annotations(docs, predictions)
|
||
if as_example:
|
||
for ex, doc in zip(examples, docs):
|
||
ex.doc = doc
|
||
yield ex
|
||
else:
|
||
yield from docs
|
||
|
||
def predict(self, docs):
|
||
"""Apply the pipeline's model to a batch of docs, without
|
||
modifying them.
|
||
"""
|
||
if not any(len(doc) for doc in docs):
|
||
# Handle cases where there are no tokens in any docs.
|
||
guesses = [[] for doc in docs]
|
||
return guesses
|
||
guesses = []
|
||
for doc in docs:
|
||
doc_guesses = [False] * len(doc)
|
||
if len(doc) > 0:
|
||
start = 0
|
||
seen_period = False
|
||
doc_guesses[0] = True
|
||
for i, token in enumerate(doc):
|
||
is_in_punct_chars = token.text in self.punct_chars
|
||
if seen_period and not token.is_punct and not is_in_punct_chars:
|
||
doc_guesses[start] = True
|
||
start = token.i
|
||
seen_period = False
|
||
elif is_in_punct_chars:
|
||
seen_period = True
|
||
if start < len(doc):
|
||
doc_guesses[start] = True
|
||
guesses.append(doc_guesses)
|
||
return guesses
|
||
|
||
def set_annotations(self, docs, batch_tag_ids, tensors=None):
|
||
if isinstance(docs, Doc):
|
||
docs = [docs]
|
||
cdef Doc doc
|
||
cdef int idx = 0
|
||
for i, doc in enumerate(docs):
|
||
doc_tag_ids = batch_tag_ids[i]
|
||
for j, tag_id in enumerate(doc_tag_ids):
|
||
# Don't clobber existing sentence boundaries
|
||
if doc.c[j].sent_start == 0:
|
||
if tag_id:
|
||
doc.c[j].sent_start = 1
|
||
else:
|
||
doc.c[j].sent_start = -1
|
||
|
||
def to_bytes(self, **kwargs):
|
||
"""Serialize the sentencizer to a bytestring.
|
||
|
||
RETURNS (bytes): The serialized object.
|
||
|
||
DOCS: https://spacy.io/api/sentencizer#to_bytes
|
||
"""
|
||
return srsly.msgpack_dumps({"punct_chars": list(self.punct_chars)})
|
||
|
||
def from_bytes(self, bytes_data, **kwargs):
|
||
"""Load the sentencizer from a bytestring.
|
||
|
||
bytes_data (bytes): The data to load.
|
||
returns (Sentencizer): The loaded object.
|
||
|
||
DOCS: https://spacy.io/api/sentencizer#from_bytes
|
||
"""
|
||
cfg = srsly.msgpack_loads(bytes_data)
|
||
self.punct_chars = set(cfg.get("punct_chars", self.default_punct_chars))
|
||
return self
|
||
|
||
def to_disk(self, path, exclude=tuple(), **kwargs):
|
||
"""Serialize the sentencizer to disk.
|
||
|
||
DOCS: https://spacy.io/api/sentencizer#to_disk
|
||
"""
|
||
path = util.ensure_path(path)
|
||
path = path.with_suffix(".json")
|
||
srsly.write_json(path, {"punct_chars": list(self.punct_chars)})
|
||
|
||
|
||
def from_disk(self, path, exclude=tuple(), **kwargs):
|
||
"""Load the sentencizer from disk.
|
||
|
||
DOCS: https://spacy.io/api/sentencizer#from_disk
|
||
"""
|
||
path = util.ensure_path(path)
|
||
path = path.with_suffix(".json")
|
||
cfg = srsly.read_json(path)
|
||
self.punct_chars = set(cfg.get("punct_chars", self.default_punct_chars))
|
||
return self
|
||
|
||
|
||
# Cython classes can't be decorated, so we need to add the factories here
|
||
Language.factories["parser"] = lambda nlp, model, **cfg: parser_factory(nlp, model, **cfg)
|
||
Language.factories["ner"] = lambda nlp, model, **cfg: ner_factory(nlp, model, **cfg)
|
||
|
||
def parser_factory(nlp, model, **cfg):
|
||
default_config = {"learn_tokens": False, "min_action_freq": 30, "beam_width": 1, "beam_update_prob": 1.0}
|
||
if model is None:
|
||
model = default_parser()
|
||
warnings.warn(Warnings.W098.format(name="parser"))
|
||
for key, value in default_config.items():
|
||
if key not in cfg:
|
||
cfg[key] = value
|
||
return DependencyParser.from_nlp(nlp, model, **cfg)
|
||
|
||
def ner_factory(nlp, model, **cfg):
|
||
default_config = {"learn_tokens": False, "min_action_freq": 30, "beam_width": 1, "beam_update_prob": 1.0}
|
||
if model is None:
|
||
model = default_ner()
|
||
warnings.warn(Warnings.W098.format(name="ner"))
|
||
for key, value in default_config.items():
|
||
if key not in cfg:
|
||
cfg[key] = value
|
||
return EntityRecognizer.from_nlp(nlp, model, **cfg)
|
||
|
||
__all__ = ["Tagger", "DependencyParser", "EntityRecognizer", "TextCategorizer", "EntityLinker", "Sentencizer", "SentenceRecognizer"]
|