mirror of
https://github.com/explosion/spaCy.git
synced 2024-11-13 13:17:06 +03:00
8c29268749
* Update errors * Remove beam for now (maybe) Remove beam_utils Update setup.py Remove beam * Remove GoldParse WIP on removing goldparse Get ArcEager compiling after GoldParse excise Update setup.py Get spacy.syntax compiling after removing GoldParse Rename NewExample -> Example and clean up Clean html files Start updating tests Update Morphologizer * fix error numbers * fix merge conflict * informative error when calling to_array with wrong field * fix error catching * fixing language and scoring tests * start testing get_aligned * additional tests for new get_aligned function * Draft create_gold_state for arc_eager oracle * Fix import * Fix import * Remove TokenAnnotation code from nonproj * fixing NER one-to-many alignment * Fix many-to-one IOB codes * fix test for misaligned * attempt to fix cases with weird spaces * fix spaces * test_gold_biluo_different_tokenization works * allow None as BILUO annotation * fixed some tests + WIP roundtrip unit test * add spaces to json output format * minibatch utiltiy can deal with strings, docs or examples * fix augment (needs further testing) * various fixes in scripts - needs to be further tested * fix test_cli * cleanup * correct silly typo * add support for MORPH in to/from_array, fix morphologizer overfitting test * fix tagger * fix entity linker * ensure test keeps working with non-linked entities * pipe() takes docs, not examples * small bug fix * textcat bugfix * throw informative error when running the components with the wrong type of objects * fix parser tests to work with example (most still failing) * fix BiluoPushDown parsing entities * small fixes * bugfix tok2vec * fix renames and simple_ner labels * various small fixes * prevent writing dummy values like deps because that could interfer with sent_start values * fix the fix * implement split_sent with aligned SENT_START attribute * test for split sentences with various alignment issues, works * Return ArcEagerGoldParse from ArcEager * Update parser and NER gold stuff * Draft new GoldCorpus class * add links to to_dict * clean up * fix test checking for variants * Fix oracles * Start updating converters * Move converters under spacy.gold * Move things around * Fix naming * Fix name * Update converter to produce DocBin * Update converters * Allow DocBin to take list of Doc objects. * Make spacy convert output docbin * Fix import * Fix docbin * Fix compile in ArcEager * Fix import * Serialize all attrs by default * Update converter * Remove jsonl converter * Add json2docs converter * Draft Corpus class for DocBin * Work on train script * Update Corpus * Update DocBin * Allocate Doc before starting to add words * Make doc.from_array several times faster * Update train.py * Fix Corpus * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests * Skip tests that cause crashes * Skip test causing segfault * Remove GoldCorpus * Update imports * Update after removing GoldCorpus * Fix module name of corpus * Fix mimport * Work on parser oracle * Update arc_eager oracle * Restore ArcEager.get_cost function * Update transition system * Update test_arc_eager_oracle * Remove beam test * Update test * Unskip * Unskip tests * add links to to_dict * clean up * fix test checking for variants * Allow DocBin to take list of Doc objects. * Fix compile in ArcEager * Serialize all attrs by default Move converters under spacy.gold Move things around Fix naming Fix name Update converter to produce DocBin Update converters Make spacy convert output docbin Fix import Fix docbin Fix import Update converter Remove jsonl converter Add json2docs converter * Allocate Doc before starting to add words * Make doc.from_array several times faster * Start updating converters * Work on train script * Draft Corpus class for DocBin Update Corpus Fix Corpus * Update DocBin Add missing strings when serializing * Update train.py * Fix parser model * Start debugging arc_eager oracle * Update header * Fix parser declaration * Xfail some tests Skip tests that cause crashes Skip test causing segfault * Remove GoldCorpus Update imports Update after removing GoldCorpus Fix module name of corpus Fix mimport * Work on parser oracle Update arc_eager oracle Restore ArcEager.get_cost function Update transition system * Update tests Remove beam test Update test Unskip Unskip tests * Add get_aligned_parse method in Example Fix Example.get_aligned_parse * Add kwargs to Corpus.dev_dataset to match train_dataset * Update nonproj * Use get_aligned_parse in ArcEager * Add another arc-eager oracle test * Remove Example.doc property Remove Example.doc Remove Example.doc Remove Example.doc Remove Example.doc * Update ArcEager oracle Fix Break oracle * Debugging * Fix Corpus * Fix eg.doc * Format * small fixes * limit arg for Corpus * fix test_roundtrip_docs_to_docbin * fix test_make_orth_variants * fix add_label test * Update tests * avoid writing temp dir in json2docs, fixing 4402 test * Update test * Add missing costs to NER oracle * Update test * Work on Example.get_aligned_ner method * Clean up debugging * Xfail tests * Remove prints * Remove print * Xfail some tests * Replace unseen labels for parser * Update test * Update test * Xfail test * Fix Corpus * fix imports * fix docs_to_json * various small fixes * cleanup * Support gold_preproc in Corpus * Support gold_preproc * Pass gold_preproc setting into corpus * Remove debugging * Fix gold_preproc * Fix json2docs converter * Fix convert command * Fix flake8 * Fix import * fix output_dir (converted to Path by typer) * fix var * bugfix: update states after creating golds to avoid out of bounds indexing * Improve efficiency of ArEager oracle * pull merge_sent into iob2docs to avoid Doc creation for each line * fix asserts * bugfix excl Span.end in iob2docs * Support max_length in Corpus * Fix arc_eager oracle * Filter out uannotated sentences in NER * Remove debugging in parser * Simplify NER alignment * Fix conversion of NER data * Fix NER init_gold_batch * Tweak efficiency of precomputable affine * Update onto-json default * Update gold test for NER * Fix parser test * Update test * Add NER data test * Fix convert for single file * Fix test * Hack scorer to avoid evaluating non-nered data * Fix handling of NER data in Example * Output unlabelled spans from O biluo tags in iob_utils * Fix unset variable * Return kept examples from init_gold_batch * Return examples from init_gold_batch * Dont return Example from init_gold_batch * Set spaces on gold doc after conversion * Add test * Fix spaces reading * Improve NER alignment * Improve handling of missing values in NER * Restore the 'cutting' in parser training * Add assertion * Print epochs * Restore random cuts in parser/ner training * Implement Doc.copy * Implement Example.copy * Copy examples at the start of Language.update * Don't unset example docs * Tweak parser model slightly * attempt to fix _guess_spaces * _add_entities_to_doc first, so that links don't get overwritten * fixing get_aligned_ner for one-to-many * fix indexing into x_text * small fix biluo_tags_from_offsets * Add onto-ner config * Simplify NER alignment * Fix NER scoring for partially annotated documents * fix indexing into x_text * fix test_cli failing tests by ignoring spans in doc.ents with empty label * Fix limit * Improve NER alignment * Fix count_train * Remove print statement * fix tests, we're not having nothing but None * fix clumsy fingers * Fix tests * Fix doc.ents * Remove empty docs in Corpus and improve limit * Update config Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
1535 lines
60 KiB
Cython
1535 lines
60 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 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.example 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 __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, Doc doc):
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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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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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return doc
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def pipe(self, stream, batch_size=128, n_threads=-1):
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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 docs in util.minibatch(stream, size=batch_size):
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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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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 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, doc):
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tags = self.predict([doc])
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self.set_annotations([doc], tags)
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return doc
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def pipe(self, stream, batch_size=128, n_threads=-1):
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for docs in util.minibatch(stream, size=batch_size):
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tag_ids = self.predict(docs)
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self.set_annotations(docs, tag_ids)
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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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if losses is not None and self.name not in losses:
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losses[self.name] = 0.
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try:
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if not any(len(eg.predicted) if eg.predicted else 0 for eg 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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except AttributeError:
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types = set([type(eg) for eg in examples])
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raise ValueError(Errors.E978.format(name="Tagger", method="update", types=types))
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set_dropout_rate(self.model, drop)
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tag_scores, bp_tag_scores = self.model.begin_update(
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[eg.predicted for eg 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 = [eg.predicted for eg 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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try:
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docs = [eg.predicted for eg in examples]
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except AttributeError:
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types = set([type(eg) for eg in examples])
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raise ValueError(Errors.E978.format(name="Tagger", method="rehearse", types=types))
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if self._rehearsal_model is None:
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return
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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.get_aligned("tag", as_string=True) 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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|
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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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try:
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y = example.y
|
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except AttributeError:
|
||
raise ValueError(Errors.E978.format(name="Tagger", method="begin_training", types=type(example)))
|
||
for token in y:
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tag = token.tag_
|
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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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|
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cdef Vocab vocab = self.vocab
|
||
if new_tag_map:
|
||
if "_SP" in orig_tag_map:
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||
new_tag_map["_SP"] = orig_tag_map["_SP"]
|
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vocab.morphology = Morphology(vocab.strings, new_tag_map,
|
||
vocab.morphology.lemmatizer,
|
||
exc=vocab.morphology.exc)
|
||
self.set_output(len(self.labels))
|
||
doc_sample = [Doc(self.vocab, words=["hello", "world"])]
|
||
if pipeline is not None:
|
||
for name, component in pipeline:
|
||
if component is self:
|
||
break
|
||
if hasattr(component, "pipe"):
|
||
doc_sample = list(component.pipe(doc_sample))
|
||
else:
|
||
doc_sample = [component(doc) for doc in doc_sample]
|
||
self.model.initialize(X=doc_sample)
|
||
# Get batch of example docs, example outputs to call begin_training().
|
||
# This lets the model infer shapes.
|
||
link_vectors_to_models(self.vocab)
|
||
if sgd is None:
|
||
sgd = self.create_optimizer()
|
||
return sgd
|
||
|
||
def add_label(self, label, values=None):
|
||
if not isinstance(label, str):
|
||
raise ValueError(Errors.E187)
|
||
if label in self.labels:
|
||
return 0
|
||
if self.model.has_dim("nO"):
|
||
# Here's how the model resizing will work, once the
|
||
# neuron-to-tag mapping is no longer controlled by
|
||
# the Morphology class, which sorts the tag names.
|
||
# The sorting makes adding labels difficult.
|
||
# smaller = self.model._layers[-1]
|
||
# larger = Softmax(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
|
||
raise ValueError(TempErrors.T003)
|
||
tag_map = dict(self.vocab.morphology.tag_map)
|
||
if values is None:
|
||
values = {POS: "X"}
|
||
tag_map[label] = values
|
||
self.vocab.morphology = Morphology(
|
||
self.vocab.strings, tag_map=tag_map,
|
||
lemmatizer=self.vocab.morphology.lemmatizer,
|
||
exc=self.vocab.morphology.exc)
|
||
return 1
|
||
|
||
def use_params(self, params):
|
||
with self.model.use_params(params):
|
||
yield
|
||
|
||
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)
|
||
tag_map = dict(sorted(self.vocab.morphology.tag_map.items()))
|
||
serialize["tag_map"] = lambda: srsly.msgpack_dumps(tag_map)
|
||
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)
|
||
|
||
def load_tag_map(b):
|
||
tag_map = srsly.msgpack_loads(b)
|
||
self.vocab.morphology = Morphology(
|
||
self.vocab.strings, tag_map=tag_map,
|
||
lemmatizer=self.vocab.morphology.lemmatizer,
|
||
exc=self.vocab.morphology.exc)
|
||
|
||
deserialize = {
|
||
"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 eg in examples:
|
||
sent_starts = eg.get_aligned("sent_start")
|
||
for sent_start in 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 = [eg.predicted for eg 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 token in example.y:
|
||
label = self.make_label(token)
|
||
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)
|
||
docs = [eg.predicted for eg in examples]
|
||
for i, eg in enumerate(examples):
|
||
# Handles alignment for tokenization differences
|
||
doc_annots = eg.get_aligned() # TODO
|
||
for j in range(len(eg.predicted)):
|
||
tok_annots = {key: values[j] for key, values in tok_annots.items()}
|
||
label = self.make_label(j, tok_annots)
|
||
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(token):
|
||
return token.dep_
|
||
|
||
@staticmethod
|
||
def make_tag(token):
|
||
return token.tag_
|
||
|
||
@staticmethod
|
||
def make_ent(token):
|
||
if token.ent_iob_ == "O":
|
||
return "O"
|
||
else:
|
||
return token.ent_iob_ + "-" + token.ent_type_
|
||
|
||
@staticmethod
|
||
def make_dep_tag_offset(token):
|
||
dep = token.dep_
|
||
tag = token.tag_
|
||
offset = token.head.i - token.i
|
||
offset = min(offset, 2)
|
||
offset = max(offset, -2)
|
||
return f"{dep}-{tag}:{offset}"
|
||
|
||
@staticmethod
|
||
def make_ent_tag(token):
|
||
if token.ent_iob_ == "O":
|
||
ent = "O"
|
||
else:
|
||
ent = token.ent_iob_ + "-" + token.ent_type_
|
||
tag = token.tag_
|
||
return f"{tag}-{ent}"
|
||
|
||
@staticmethod
|
||
def make_sent_start(token):
|
||
"""A multi-task objective for representing sentence boundaries,
|
||
using BILU scheme. (O is impossible)
|
||
"""
|
||
if token.is_sent_start and token.is_sent_end:
|
||
return "U-SENT"
|
||
elif token.is_sent_start:
|
||
return "B-SENT"
|
||
else:
|
||
return "I-SENT"
|
||
|
||
|
||
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([eg.predicted.to_array(ID).ravel() for eg 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):
|
||
if losses is not None and self.name not in losses:
|
||
losses[self.name] = 0.
|
||
set_dropout_rate(self.model, drop)
|
||
try:
|
||
predictions, bp_predictions = self.model.begin_update([eg.predicted for eg in examples])
|
||
except AttributeError:
|
||
types = set([type(eg) for eg in examples])
|
||
raise ValueError(Errors.E978.format(name="ClozeMultitask", method="rehearse", types=types))
|
||
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):
|
||
for docs in util.minibatch(stream, size=batch_size):
|
||
scores, tensors = self.predict(docs)
|
||
self.set_annotations(docs, scores, tensors=tensors)
|
||
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):
|
||
try:
|
||
if not any(len(eg.predicted) if eg.predicted else 0 for eg in examples):
|
||
# Handle cases where there are no tokens in any docs.
|
||
return
|
||
except AttributeError:
|
||
types = set([type(eg) for eg in examples])
|
||
raise ValueError(Errors.E978.format(name="TextCategorizer", method="update", types=types))
|
||
set_dropout_rate(self.model, drop)
|
||
scores, bp_scores = self.model.begin_update(
|
||
[eg.predicted for eg 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 = [eg.predicted for eg 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
|
||
try:
|
||
docs = [eg.predicted for eg in examples]
|
||
except AttributeError:
|
||
types = set([type(eg) for eg in examples])
|
||
raise ValueError(Errors.E978.format(name="TextCategorizer", method="rehearse", types=types))
|
||
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):
|
||
truths = numpy.zeros((len(examples), len(self.labels)), dtype="f")
|
||
not_missing = numpy.ones((len(examples), len(self.labels)), dtype="f")
|
||
for i, eg in enumerate(examples):
|
||
for j, label in enumerate(self.labels):
|
||
if label in eg.reference.cats:
|
||
truths[i, j] = eg.reference.cats[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:
|
||
try:
|
||
y = example.y
|
||
except AttributeError:
|
||
raise ValueError(Errors.E978.format(name="TextCategorizer", method="update", types=type(example)))
|
||
for cat in y.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 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
|
||
sentence_docs = []
|
||
try:
|
||
docs = [eg.predicted for eg in examples]
|
||
except AttributeError:
|
||
types = set([type(eg) for eg in examples])
|
||
raise ValueError(Errors.E978.format(name="EntityLinker", method="update", types=types))
|
||
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)
|
||
|
||
for eg in examples:
|
||
sentences = [s for s in eg.predicted.sents]
|
||
kb_ids = eg.get_aligned("ENT_KB_ID", as_string=True)
|
||
for ent in eg.predicted.ents:
|
||
kb_id = kb_ids[ent.start] # KB ID of the first token is the same as the whole span
|
||
if kb_id:
|
||
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 = eg.predicted[start_token:end_token].as_doc()
|
||
sentence_docs.append(sent_doc)
|
||
set_dropout_rate(self.model, drop)
|
||
if not sentence_docs:
|
||
warnings.warn(Warnings.W093.format(name="Entity Linker"))
|
||
return 0.0
|
||
sentence_encodings, bp_context = self.model.begin_update(sentence_docs)
|
||
loss, d_scores = self.get_similarity_loss(
|
||
scores=sentence_encodings,
|
||
examples=examples
|
||
)
|
||
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, examples, scores):
|
||
entity_encodings = []
|
||
for eg in examples:
|
||
kb_ids = eg.get_aligned("ENT_KB_ID", as_string=True)
|
||
for ent in eg.predicted.ents:
|
||
kb_id = kb_ids[ent.start]
|
||
if kb_id:
|
||
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 eg in examples:
|
||
kb_ids = eg.get_aligned("ENT_KB_ID", as_string=True)
|
||
for ent in eg.predicted.ents:
|
||
kb_id = kb_ids[ent.start]
|
||
if kb_id:
|
||
cats.append([1.0])
|
||
|
||
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, doc):
|
||
kb_ids, tensors = self.predict([doc])
|
||
self.set_annotations([doc], kb_ids, tensors=tensors)
|
||
return doc
|
||
|
||
def pipe(self, stream, batch_size=128, n_threads=-1):
|
||
for docs in util.minibatch(stream, size=batch_size):
|
||
kb_ids, tensors = self.predict(docs)
|
||
self.set_annotations(docs, kb_ids, tensors=tensors)
|
||
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_index, sent in enumerate(sentences):
|
||
if sent.ents:
|
||
# get n_neightbour sentences, clipped to the length of the document
|
||
start_sentence = max(0, sent_index - self.n_sents)
|
||
end_sentence = min(len(sentences) -1, sent_index + self.n_sents)
|
||
|
||
start_token = sentences[start_sentence].start
|
||
end_token = sentences[end_sentence].end
|
||
|
||
sent_doc = doc[start_token:end_token].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.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)
|
||
|
||
elif len(candidates) == 1:
|
||
# shortcut for efficiency reasons: take the 1 candidate
|
||
|
||
# TODO: thresholding
|
||
final_kb_ids.append(candidates[0].entity_)
|
||
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, doc):
|
||
"""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
|
||
"""
|
||
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
|
||
return doc
|
||
|
||
def pipe(self, stream, batch_size=128, n_threads=-1):
|
||
for docs in util.minibatch(stream, size=batch_size):
|
||
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)
|
||
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"]
|