explosion/spaCy
1
1
Fork 0
mirror of https://github.com/explosion/spaCy.git synced 2024-12-24 00:46:28 +03:00
Code Issues Packages Projects Releases Wiki Activity

Improve spacy.gold (no GoldParse, no json format!) (#5555)

Browse Source 
* 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>
This commit is contained in:
Matthew Honnibal 2020-06-26 19:34:12 +02:00 committed by GitHub
parent 01c394eb23
commit 8c29268749
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
93 changed files with 3820 additions and 3995 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

40
bin/ud/ud_train.py
View File

@ -14,7 +14,7 @@ import spacy
import spacy.util
from bin.ud import conll17_ud_eval
from spacy.tokens import Token, Doc
from spacy.gold import GoldParse, Example
from spacy.gold import Example
from spacy.util import compounding, minibatch, minibatch_by_words
from spacy.syntax.nonproj import projectivize
from spacy.matcher import Matcher
@ -83,11 +83,11 @@ def read_data(
sent["heads"].append(head)
sent["deps"].append("ROOT" if dep == "root" else dep)
sent["spaces"].append(space_after == "_")
sent["entities"] = ["-"] * len(sent["words"])
sent["entities"] = ["-"] * len(sent["words"]) # TODO: doc-level format
sent["heads"], sent["deps"] = projectivize(sent["heads"], sent["deps"])
if oracle_segments:
docs.append(Doc(nlp.vocab, words=sent["words"], spaces=sent["spaces"]))
golds.append(GoldParse(docs[-1], **sent))
golds.append(sent)
assert golds[-1].morphology is not None
sent_annots.append(sent)
@ -151,28 +151,27 @@ def read_conllu(file_):
def _make_gold(nlp, text, sent_annots, drop_deps=0.0):
# Flatten the conll annotations, and adjust the head indices
flat = defaultdict(list)
gold = defaultdict(list)
sent_starts = []
for sent in sent_annots:
flat["heads"].extend(len(flat["words"])+head for head in sent["heads"])
gold["heads"].extend(len(gold["words"])+head for head in sent["heads"])
for field in ["words", "tags", "deps", "morphology", "entities", "spaces"]:
flat[field].extend(sent[field])
gold[field].extend(sent[field])
sent_starts.append(True)
sent_starts.extend([False] * (len(sent["words"]) - 1))
# Construct text if necessary
assert len(flat["words"]) == len(flat["spaces"])
assert len(gold["words"]) == len(gold["spaces"])
if text is None:
text = "".join(
word + " " * space for word, space in zip(flat["words"], flat["spaces"])
word + " " * space for word, space in zip(gold["words"], gold["spaces"])
)
doc = nlp.make_doc(text)
flat.pop("spaces")
gold = GoldParse(doc, **flat)
gold.sent_starts = sent_starts
gold.pop("spaces")
gold["sent_starts"] = sent_starts
for i in range(len(gold.heads)):
if random.random() < drop_deps:
gold.heads[i] = None
gold.labels[i] = None
gold["heads"][i] = None
gold["labels"][i] = None
return doc, gold
@ -183,15 +182,10 @@ def _make_gold(nlp, text, sent_annots, drop_deps=0.0):
def golds_to_gold_data(docs, golds):
"""Get out the training data format used by begin_training, given the
GoldParse objects."""
"""Get out the training data format used by begin_training"""
data = []
for doc, gold in zip(docs, golds):
example = Example(doc=doc)
example.add_doc_annotation(cats=gold.cats)
token_annotation_dict = gold.orig.to_dict()
example.add_token_annotation(**token_annotation_dict)
example.goldparse = gold
example = Example.from_dict(doc, gold)
data.append(example)
return data
@ -359,8 +353,8 @@ def initialize_pipeline(nlp, examples, config, device):
nlp.parser.add_multitask_objective("tag")
if config.multitask_sent:
nlp.parser.add_multitask_objective("sent_start")
for ex in examples:
gold = ex.gold
for eg in examples:
gold = eg.gold
for tag in gold.tags:
if tag is not None:
nlp.tagger.add_label(tag)
@ -541,7 +535,7 @@ def main(
else:
batches = minibatch(examples, size=batch_sizes)
losses = {}
n_train_words = sum(len(ex.doc) for ex in examples)
n_train_words = sum(len(eg.doc) for eg in examples)
with tqdm.tqdm(total=n_train_words, leave=False) as pbar:
for batch in batches:
pbar.update(sum(len(ex.doc) for ex in batch))

38
examples/experiments/onto-joint/defaults.cfg
View File

@ -5,17 +5,16 @@
# data is passed in sentence-by-sentence via some prior preprocessing.
gold_preproc = false
# Limitations on training document length or number of examples.
max_length = 0
max_length = 5000
limit = 0
# Data augmentation
orth_variant_level = 0.0
noise_level = 0.0
dropout = 0.1
# Controls early-stopping. 0 or -1 mean unlimited.
patience = 1600
max_epochs = 0
max_steps = 20000
eval_frequency = 400
eval_frequency = 200
# Other settings
seed = 0
accumulate_gradient = 1
@ -30,7 +29,7 @@ omit_extra_lookups = false
[training.batch_size]
@schedules = "compounding.v1"
start = 1000
start = 100
stop = 1000
compound = 1.001
@ -58,15 +57,11 @@ vectors = null
[nlp.pipeline.tok2vec]
factory = "tok2vec"
[nlp.pipeline.senter]
factory = "senter"
[nlp.pipeline.ner]
factory = "ner"
learn_tokens = false
min_action_freq = 1
beam_width = 1
beam_update_prob = 1.0
[nlp.pipeline.tagger]
factory = "tagger"
@ -74,16 +69,7 @@ factory = "tagger"
[nlp.pipeline.parser]
factory = "parser"
learn_tokens = false
min_action_freq = 1
beam_width = 1
beam_update_prob = 1.0
[nlp.pipeline.senter.model]
@architectures = "spacy.Tagger.v1"
[nlp.pipeline.senter.model.tok2vec]
@architectures = "spacy.Tok2VecTensors.v1"
width = ${nlp.pipeline.tok2vec.model:width}
min_action_freq = 30
[nlp.pipeline.tagger.model]
@architectures = "spacy.Tagger.v1"
@ -96,8 +82,8 @@ width = ${nlp.pipeline.tok2vec.model:width}
@architectures = "spacy.TransitionBasedParser.v1"
nr_feature_tokens = 8
hidden_width = 128
maxout_pieces = 3
use_upper = false
maxout_pieces = 2
use_upper = true
[nlp.pipeline.parser.model.tok2vec]
@architectures = "spacy.Tok2VecTensors.v1"
@ -107,8 +93,8 @@ width = ${nlp.pipeline.tok2vec.model:width}
@architectures = "spacy.TransitionBasedParser.v1"
nr_feature_tokens = 3
hidden_width = 128
maxout_pieces = 3
use_upper = false
maxout_pieces = 2
use_upper = true
[nlp.pipeline.ner.model.tok2vec]
@architectures = "spacy.Tok2VecTensors.v1"
@ -117,10 +103,10 @@ width = ${nlp.pipeline.tok2vec.model:width}
[nlp.pipeline.tok2vec.model]
@architectures = "spacy.HashEmbedCNN.v1"
pretrained_vectors = ${nlp:vectors}
width = 256
depth = 6
width = 128
depth = 4
window_size = 1
embed_size = 10000
embed_size = 7000
maxout_pieces = 3
subword_features = true
dropout = null
dropout = ${training:dropout}

1
examples/experiments/onto-joint/pretrain.cfg
View File

@ -9,7 +9,6 @@ max_length = 0
limit = 0
# Data augmentation
orth_variant_level = 0.0
noise_level = 0.0
dropout = 0.1
# Controls early-stopping. 0 or -1 mean unlimited.
patience = 1600

80
examples/experiments/onto-ner.cfg Normal file
View File

@ -0,0 +1,80 @@
# Training hyper-parameters and additional features.
[training]
# Whether to train on sequences with 'gold standard' sentence boundaries
# and tokens. If you set this to true, take care to ensure your run-time
# data is passed in sentence-by-sentence via some prior preprocessing.
gold_preproc = false
# Limitations on training document length or number of examples.
max_length = 5000
limit = 0
# Data augmentation
orth_variant_level = 0.0
dropout = 0.2
# Controls early-stopping. 0 or -1 mean unlimited.
patience = 1600
max_epochs = 0
max_steps = 20000
eval_frequency = 500
# Other settings
seed = 0
accumulate_gradient = 1
use_pytorch_for_gpu_memory = false
# Control how scores are printed and checkpoints are evaluated.
scores = ["speed", "ents_p", "ents_r", "ents_f"]
score_weights = {"ents_f": 1.0}
# These settings are invalid for the transformer models.
init_tok2vec = null
discard_oversize = false
omit_extra_lookups = false
[training.batch_size]
@schedules = "compounding.v1"
start = 100
stop = 1000
compound = 1.001
[training.optimizer]
@optimizers = "Adam.v1"
beta1 = 0.9
beta2 = 0.999
L2_is_weight_decay = false
L2 = 1e-6
grad_clip = 1.0
use_averages = true
eps = 1e-8
learn_rate = 0.001
#[optimizer.learn_rate]
#@schedules = "warmup_linear.v1"
#warmup_steps = 250
#total_steps = 20000
#initial_rate = 0.001
[nlp]
lang = "en"
vectors = null
[nlp.pipeline.ner]
factory = "ner"
learn_tokens = false
min_action_freq = 1
beam_width = 1
beam_update_prob = 1.0
[nlp.pipeline.ner.model]
@architectures = "spacy.TransitionBasedParser.v1"
nr_feature_tokens = 3
hidden_width = 64
maxout_pieces = 2
use_upper = true
[nlp.pipeline.ner.model.tok2vec]
@architectures = "spacy.HashEmbedCNN.v1"
pretrained_vectors = ${nlp:vectors}
width = 96
depth = 4
window_size = 1
embed_size = 2000
maxout_pieces = 3
subword_features = true
dropout = ${training:dropout}

1
examples/experiments/ptb-joint-pos-dep/bilstm_tok2vec.cfg
View File

@ -6,7 +6,6 @@ init_tok2vec = null
vectors = null
max_epochs = 100
orth_variant_level = 0.0
noise_level = 0.0
gold_preproc = true
max_length = 0
use_gpu = 0

1
examples/experiments/ptb-joint-pos-dep/defaults.cfg
View File

@ -6,7 +6,6 @@ init_tok2vec = null
vectors = null
max_epochs = 100
orth_variant_level = 0.0
noise_level = 0.0
gold_preproc = true
max_length = 0
use_gpu = -1

66
examples/training/conllu.py
View File

@ -12,7 +12,7 @@ import tqdm
import spacy
import spacy.util
from spacy.tokens import Token, Doc
from spacy.gold import GoldParse, Example
from spacy.gold import Example
from spacy.syntax.nonproj import projectivize
from collections import defaultdict
from spacy.matcher import Matcher
@ -33,31 +33,6 @@ random.seed(0)
numpy.random.seed(0)
def minibatch_by_words(examples, size=5000):
random.shuffle(examples)
if isinstance(size, int):
size_ = itertools.repeat(size)
else:
size_ = size
examples = iter(examples)
while True:
batch_size = next(size_)
batch = []
while batch_size >= 0:
try:
example = next(examples)
except StopIteration:
if batch:
yield batch
return
batch_size -= len(example.doc)
batch.append(example)
if batch:
yield batch
else:
break
################
# Data reading #
################
@ -110,7 +85,7 @@ def read_data(
sent["heads"], sent["deps"] = projectivize(sent["heads"], sent["deps"])
if oracle_segments:
docs.append(Doc(nlp.vocab, words=sent["words"], spaces=sent["spaces"]))
golds.append(GoldParse(docs[-1], **sent))
golds.append(sent)
sent_annots.append(sent)
if raw_text and max_doc_length and len(sent_annots) >= max_doc_length:
@ -159,20 +134,19 @@ def read_conllu(file_):
def _make_gold(nlp, text, sent_annots):
# Flatten the conll annotations, and adjust the head indices
flat = defaultdict(list)
gold = defaultdict(list)
for sent in sent_annots:
flat["heads"].extend(len(flat["words"]) + head for head in sent["heads"])
gold["heads"].extend(len(gold["words"]) + head for head in sent["heads"])
for field in ["words", "tags", "deps", "entities", "spaces"]:
flat[field].extend(sent[field])
gold[field].extend(sent[field])
# Construct text if necessary
assert len(flat["words"]) == len(flat["spaces"])
assert len(gold["words"]) == len(gold["spaces"])
if text is None:
text = "".join(
word + " " * space for word, space in zip(flat["words"], flat["spaces"])
word + " " * space for word, space in zip(gold["words"], gold["spaces"])
)
doc = nlp.make_doc(text)
flat.pop("spaces")
gold = GoldParse(doc, **flat)
gold.pop("spaces")
return doc, gold
@ -182,15 +156,10 @@ def _make_gold(nlp, text, sent_annots):
def golds_to_gold_data(docs, golds):
"""Get out the training data format used by begin_training, given the
GoldParse objects."""
"""Get out the training data format used by begin_training."""
data = []
for doc, gold in zip(docs, golds):
example = Example(doc=doc)
example.add_doc_annotation(cats=gold.cats)
token_annotation_dict = gold.orig.to_dict()
example.add_token_annotation(**token_annotation_dict)
example.goldparse = gold
example = Example.from_dict(doc, gold)
data.append(example)
return data
@ -313,15 +282,15 @@ def initialize_pipeline(nlp, examples, config):
nlp.parser.add_multitask_objective("sent_start")
nlp.parser.moves.add_action(2, "subtok")
nlp.add_pipe(nlp.create_pipe("tagger"))
for ex in examples:
for tag in ex.gold.tags:
for eg in examples:
for tag in eg.gold.tags:
if tag is not None:
nlp.tagger.add_label(tag)
# Replace labels that didn't make the frequency cutoff
actions = set(nlp.parser.labels)
label_set = set([act.split("-")[1] for act in actions if "-" in act])
for ex in examples:
gold = ex.gold
for eg in examples:
gold = eg.gold
for i, label in enumerate(gold.labels):
if label is not None and label not in label_set:
gold.labels[i] = label.split("||")[0]
@ -415,13 +384,12 @@ def main(ud_dir, parses_dir, config, corpus, limit=0):
optimizer = initialize_pipeline(nlp, examples, config)
for i in range(config.nr_epoch):
docs = [nlp.make_doc(example.doc.text) for example in examples]
batches = minibatch_by_words(examples, size=config.batch_size)
batches = spacy.minibatch_by_words(examples, size=config.batch_size)
losses = {}
n_train_words = sum(len(doc) for doc in docs)
n_train_words = sum(len(eg.reference.doc) for eg in examples)
with tqdm.tqdm(total=n_train_words, leave=False) as pbar:
for batch in batches:
pbar.update(sum(len(ex.doc) for ex in batch))
pbar.update(sum(len(eg.reference.doc) for eg in batch))
nlp.update(
examples=batch, sgd=optimizer, drop=config.dropout, losses=losses,
)

2
examples/training/create_kb.py
View File

@ -30,7 +30,7 @@ ENTITIES = {"Q2146908": ("American golfer", 342), "Q7381115": ("publisher", 17)}
model=("Model name, should have pretrained word embeddings", "positional", None, str),
output_dir=("Optional output directory", "option", "o", Path),
)
def main(model=None, output_dir=None):
def main(model, output_dir=None):
"""Load the model and create the KB with pre-defined entity encodings.
If an output_dir is provided, the KB will be stored there in a file 'kb'.
The updated vocab will also be written to a directory in the output_dir."""

32
examples/training/ner_multitask_objective.py
View File

@ -24,8 +24,10 @@ import random
import plac
import spacy
import os.path
from spacy.gold.example import Example
from spacy.tokens import Doc
from spacy.gold import read_json_file, GoldParse
from spacy.gold import read_json_file
random.seed(0)
@ -59,27 +61,25 @@ def main(n_iter=10):
print(nlp.pipeline)
print("Create data", len(TRAIN_DATA))
optimizer = nlp.begin_training(get_examples=lambda: TRAIN_DATA)
optimizer = nlp.begin_training()
for itn in range(n_iter):
random.shuffle(TRAIN_DATA)
losses = {}
for example in TRAIN_DATA:
for token_annotation in example.token_annotations:
doc = Doc(nlp.vocab, words=token_annotation.words)
gold = GoldParse.from_annotation(doc, example.doc_annotation, token_annotation)
nlp.update(
examples=[(doc, gold)], # 1 example
drop=0.2, # dropout - make it harder to memorise data
sgd=optimizer, # callable to update weights
losses=losses,
)
for example_dict in TRAIN_DATA:
doc = Doc(nlp.vocab, words=example_dict["words"])
example = Example.from_dict(doc, example_dict)
nlp.update(
examples=[example], # 1 example
drop=0.2, # dropout - make it harder to memorise data
sgd=optimizer, # callable to update weights
losses=losses,
)
print(losses.get("nn_labeller", 0.0), losses["ner"])
# test the trained model
for example in TRAIN_DATA:
if example.text is not None:
doc = nlp(example.text)
for example_dict in TRAIN_DATA:
if "text" in example_dict:
doc = nlp(example_dict["text"])
print("Entities", [(ent.text, ent.label_) for ent in doc.ents])
print("Tokens", [(t.text, t.ent_type_, t.ent_iob) for t in doc])

13
examples/training/rehearsal.py
View File

@ -4,9 +4,10 @@ import random
import warnings
import srsly
import spacy
from spacy.gold import GoldParse
from spacy.gold import Example
from spacy.util import minibatch, compounding
# TODO: further fix & test this script for v.3 ? (read_gold_data is never called)
LABEL = "ANIMAL"
TRAIN_DATA = [
@ -36,15 +37,13 @@ def read_raw_data(nlp, jsonl_loc):
def read_gold_data(nlp, gold_loc):
docs = []
golds = []
examples = []
for json_obj in srsly.read_jsonl(gold_loc):
doc = nlp.make_doc(json_obj["text"])
ents = [(ent["start"], ent["end"], ent["label"]) for ent in json_obj["spans"]]
gold = GoldParse(doc, entities=ents)
docs.append(doc)
golds.append(gold)
return list(zip(docs, golds))
example = Example.from_dict(doc, {"entities": ents})
examples.append(example)
return examples
def main(model_name, unlabelled_loc):

7
examples/training/train_textcat.py
View File

@ -19,7 +19,7 @@ from ml_datasets import loaders
import spacy
from spacy import util
from spacy.util import minibatch, compounding
from spacy.gold import Example, GoldParse
from spacy.gold import Example
@plac.annotations(
@ -62,11 +62,10 @@ def main(config_path, output_dir=None, n_iter=20, n_texts=2000, init_tok2vec=Non
train_examples = []
for text, cats in zip(train_texts, train_cats):
doc = nlp.make_doc(text)
gold = GoldParse(doc, cats=cats)
example = Example.from_dict(doc, {"cats": cats})
for cat in cats:
textcat.add_label(cat)
ex = Example.from_gold(gold, doc=doc)
train_examples.append(ex)
train_examples.append(example)
with nlp.select_pipes(enable="textcat"): # only train textcat
optimizer = nlp.begin_training()

7
setup.py
View File

@ -23,6 +23,8 @@ Options.docstrings = True
PACKAGES = find_packages()
MOD_NAMES = [
"spacy.gold.align",
"spacy.gold.example",
"spacy.parts_of_speech",
"spacy.strings",
"spacy.lexeme",
@ -37,11 +39,10 @@ MOD_NAMES = [
"spacy.tokenizer",
"spacy.syntax.nn_parser",
"spacy.syntax._parser_model",
"spacy.syntax._beam_utils",
"spacy.syntax.nonproj",
"spacy.syntax.transition_system",
"spacy.syntax.arc_eager",
"spacy.gold",
"spacy.gold.gold_io",
"spacy.tokens.doc",
"spacy.tokens.span",
"spacy.tokens.token",
@ -120,7 +121,7 @@ class build_ext_subclass(build_ext, build_ext_options):
def clean(path):
for path in path.glob("**/*"):
if path.is_file() and path.suffix in (".so", ".cpp"):
if path.is_file() and path.suffix in (".so", ".cpp", ".html"):
print(f"Deleting {path.name}")
path.unlink()

2
spacy/about.py
View File

@ -1,6 +1,6 @@
# fmt: off
__title__ = "spacy"
__version__ = "3.0.0.dev9"
__version__ = "3.0.0"
__release__ = True
__download_url__ = "https://github.com/explosion/spacy-models/releases/download"
__compatibility__ = "https://raw.githubusercontent.com/explosion/spacy-models/master/compatibility.json"

2
spacy/cli/__init__.py
View File

@ -8,7 +8,7 @@ from .download import download # noqa: F401
from .info import info # noqa: F401
from .package import package # noqa: F401
from .profile import profile # noqa: F401
from .train_from_config import train # noqa: F401
from .train import train_cli # noqa: F401
from .pretrain import pretrain # noqa: F401
from .debug_data import debug_data # noqa: F401
from .evaluate import evaluate # noqa: F401

268
spacy/cli/convert.py
View File

@ -4,53 +4,56 @@ from pathlib import Path
from wasabi import Printer
import srsly
import re
import sys
from ._app import app, Arg, Opt
from .converters import conllu2json, iob2json, conll_ner2json
from .converters import ner_jsonl2json
from ..gold import docs_to_json
from ..tokens import DocBin
from ..gold.converters import iob2docs, conll_ner2docs, json2docs
# Converters are matched by file extension except for ner/iob, which are
# matched by file extension and content. To add a converter, add a new
# entry to this dict with the file extension mapped to the converter function
# imported from /converters.
CONVERTERS = {
"conllubio": conllu2json,
"conllu": conllu2json,
"conll": conllu2json,
"ner": conll_ner2json,
"iob": iob2json,
"jsonl": ner_jsonl2json,
# "conllubio": conllu2docs, TODO
# "conllu": conllu2docs, TODO
# "conll": conllu2docs, TODO
"ner": conll_ner2docs,
"iob": iob2docs,
"json": json2docs,
}
# File types
FILE_TYPES_STDOUT = ("json", "jsonl")
# File types that can be written to stdout
FILE_TYPES_STDOUT = ("json")
class FileTypes(str, Enum):
json = "json"
jsonl = "jsonl"
msg = "msg"
spacy = "spacy"
@app.command("convert")
def convert_cli(
# fmt: off
input_file: str = Arg(..., help="Input file", exists=True),
input_path: str = Arg(..., help="Input file or directory", exists=True),
output_dir: Path = Arg("-", help="Output directory. '-' for stdout.", allow_dash=True, exists=True),
file_type: FileTypes = Opt(FileTypes.json.value, "--file-type", "-t", help="Type of data to produce"),
file_type: FileTypes = Opt("spacy", "--file-type", "-t", help="Type of data to produce"),
n_sents: int = Opt(1, "--n-sents", "-n", help="Number of sentences per doc (0 to disable)"),
seg_sents: bool = Opt(False, "--seg-sents", "-s", help="Segment sentences (for -c ner)"),
model: Optional[str] = Opt(None, "--model", "-b", help="Model for sentence segmentation (for -s)"),
morphology: bool = Opt(False, "--morphology", "-m", help="Enable appending morphology to tags"),
merge_subtokens: bool = Opt(False, "--merge-subtokens", "-T", help="Merge CoNLL-U subtokens"),
converter: str = Opt("auto", "--converter", "-c", help=f"Converter: {tuple(CONVERTERS.keys())}"),
ner_map_path: Optional[Path] = Opt(None, "--ner-map-path", "-N", help="NER tag mapping (as JSON-encoded dict of entity types)", exists=True),
ner_map: Optional[Path] = Opt(None, "--ner-map", "-N", help="NER tag mapping (as JSON-encoded dict of entity types)", exists=True),
lang: Optional[str] = Opt(None, "--lang", "-l", help="Language (if tokenizer required)"),
# fmt: on
):
"""
Convert files into JSON format for use with train command and other
Convert files into json or DocBin format for use with train command and other
experiment management functions. If no output_dir is specified, the data
is written to stdout, so you can pipe them forward to a JSON file:
$ spacy convert some_file.conllu > some_file.json
@ -58,9 +61,15 @@ def convert_cli(
if isinstance(file_type, FileTypes):
# We get an instance of the FileTypes from the CLI so we need its string value
file_type = file_type.value
input_path = Path(input_path)
output_dir = "-" if output_dir == Path("-") else output_dir
cli_args = locals()
silent = output_dir == "-"
msg = Printer(no_print=silent)
verify_cli_args(msg, **cli_args)
converter = _get_converter(msg, converter, input_path)
convert(
input_file,
input_path,
output_dir,
file_type=file_type,
n_sents=n_sents,
@ -69,92 +78,78 @@ def convert_cli(
morphology=morphology,
merge_subtokens=merge_subtokens,
converter=converter,
ner_map_path=ner_map_path,
ner_map=ner_map,
lang=lang,
silent=silent,
msg=msg,
)
def convert(
input_file: Path,
output_dir: Path,
*,
file_type: str = "json",
n_sents: int = 1,
seg_sents: bool = False,
model: Optional[str] = None,
morphology: bool = False,
merge_subtokens: bool = False,
converter: str = "auto",
ner_map_path: Optional[Path] = None,
lang: Optional[str] = None,
silent: bool = True,
input_path: Path,
output_dir: Path,
*,
file_type: str = "json",
n_sents: int = 1,
seg_sents: bool = False,
model: Optional[str] = None,
morphology: bool = False,
merge_subtokens: bool = False,
converter: str = "auto",
ner_map: Optional[Path] = None,
lang: Optional[str] = None,
silent: bool = True,
msg: Optional[Path] = None,
) -> None:
msg = Printer(no_print=silent, pretty=not silent)
input_path = Path(input_file)
if file_type not in FILE_TYPES_STDOUT and output_dir == "-":
# TODO: support msgpack via stdout in srsly?
msg.fail(
f"Can't write .{file_type} data to stdout",
"Please specify an output directory.",
exits=1,
)
if not input_path.exists():
msg.fail("Input file not found", input_path, exits=1)
if output_dir != "-" and not Path(output_dir).exists():
msg.fail("Output directory not found", output_dir, exits=1)
input_data = input_path.open("r", encoding="utf-8").read()
if converter == "auto":
converter = input_path.suffix[1:]
if converter == "ner" or converter == "iob":
converter_autodetect = autodetect_ner_format(input_data)
if converter_autodetect == "ner":
msg.info("Auto-detected token-per-line NER format")
converter = converter_autodetect
elif converter_autodetect == "iob":
msg.info("Auto-detected sentence-per-line NER format")
converter = converter_autodetect
else:
msg.warn(
"Can't automatically detect NER format. Conversion may not "
"succeed. See https://spacy.io/api/cli#convert"
)
if converter not in CONVERTERS:
msg.fail(f"Can't find converter for {converter}", exits=1)
ner_map = None
if ner_map_path is not None:
ner_map = srsly.read_json(ner_map_path)
# Use converter function to convert data
func = CONVERTERS[converter]
data = func(
input_data,
n_sents=n_sents,
seg_sents=seg_sents,
append_morphology=morphology,
merge_subtokens=merge_subtokens,
lang=lang,
model=model,
no_print=silent,
ner_map=ner_map,
)
if output_dir != "-":
# Export data to a file
suffix = f".{file_type}"
output_file = Path(output_dir) / Path(input_path.parts[-1]).with_suffix(suffix)
if file_type == "json":
srsly.write_json(output_file, data)
elif file_type == "jsonl":
srsly.write_jsonl(output_file, data)
elif file_type == "msg":
srsly.write_msgpack(output_file, data)
msg.good(f"Generated output file ({len(data)} documents): {output_file}")
else:
# Print to stdout
if file_type == "json":
srsly.write_json("-", data)
elif file_type == "jsonl":
srsly.write_jsonl("-", data)
if not msg:
msg = Printer(no_print=silent)
ner_map = srsly.read_json(ner_map) if ner_map is not None else None
for input_loc in walk_directory(input_path):
input_data = input_loc.open("r", encoding="utf-8").read()
# Use converter function to convert data
func = CONVERTERS[converter]
docs = func(
input_data,
n_sents=n_sents,
seg_sents=seg_sents,
append_morphology=morphology,
merge_subtokens=merge_subtokens,
lang=lang,
model=model,
no_print=silent,
ner_map=ner_map,
)
if output_dir == "-":
_print_docs_to_stdout(docs, file_type)
else:
if input_loc != input_path:
subpath = input_loc.relative_to(input_path)
output_file = Path(output_dir) / subpath.with_suffix(f".{file_type}")
else:
output_file = Path(output_dir) / input_loc.parts[-1]
output_file = output_file.with_suffix(f".{file_type}")
_write_docs_to_file(docs, output_file, file_type)
msg.good(f"Generated output file ({len(docs)} documents): {output_file}")
def _print_docs_to_stdout(docs, output_type):
if output_type == "json":
srsly.write_json("-", docs_to_json(docs))
else:
sys.stdout.buffer.write(DocBin(docs=docs).to_bytes())
def _write_docs_to_file(docs, output_file, output_type):
if not output_file.parent.exists():
output_file.parent.mkdir(parents=True)
if output_type == "json":
srsly.write_json(output_file, docs_to_json(docs))
else:
data = DocBin(docs=docs).to_bytes()
with output_file.open("wb") as file_:
file_.write(data)
def autodetect_ner_format(input_data: str) -> str:
# guess format from the first 20 lines
@ -173,3 +168,86 @@ def autodetect_ner_format(input_data: str) -> str:
if format_guesses["ner"] == 0 and format_guesses["iob"] > 0:
return "iob"
return None
def walk_directory(path):
if not path.is_dir():
return [path]
paths = [path]
locs = []
seen = set()
for path in paths:
if str(path) in seen:
continue
seen.add(str(path))
if path.parts[-1].startswith("."):
continue
elif path.is_dir():
paths.extend(path.iterdir())
else:
locs.append(path)
return locs
def verify_cli_args(
msg,
input_path,
output_dir,
file_type,
n_sents,
seg_sents,
model,
morphology,
merge_subtokens,
converter,
ner_map,
lang,
):
input_path = Path(input_path)
if file_type not in FILE_TYPES_STDOUT and output_dir == "-":
# TODO: support msgpack via stdout in srsly?
msg.fail(
f"Can't write .{file_type} data to stdout",
"Please specify an output directory.",
exits=1,
)
if not input_path.exists():
msg.fail("Input file not found", input_path, exits=1)
if output_dir != "-" and not Path(output_dir).exists():
msg.fail("Output directory not found", output_dir, exits=1)
if input_path.is_dir():
input_locs = walk_directory(input_path)
if len(input_locs) == 0:
msg.fail("No input files in directory", input_path, exits=1)
file_types = list(set([loc.suffix[1:] for loc in input_locs]))
if len(file_types) >= 2:
file_types = ",".join(file_types)
msg.fail("All input files must be same type", file_types, exits=1)
converter = _get_converter(msg, converter, input_path)
if converter not in CONVERTERS:
msg.fail(f"Can't find converter for {converter}", exits=1)
return converter
def _get_converter(msg, converter, input_path):
if input_path.is_dir():
input_path = walk_directory(input_path)[0]
if converter == "auto":
converter = input_path.suffix[1:]
if converter == "ner" or converter == "iob":
with input_path.open() as file_:
input_data = file_.read()
converter_autodetect = autodetect_ner_format(input_data)
if converter_autodetect == "ner":
msg.info("Auto-detected token-per-line NER format")
converter = converter_autodetect
elif converter_autodetect == "iob":
msg.info("Auto-detected sentence-per-line NER format")
converter = converter_autodetect
else:
msg.warn(
"Can't automatically detect NER format. "
"Conversion may not succeed. "
"See https://spacy.io/api/cli#convert"
)
return converter

4
spacy/cli/converters/__init__.py
View File

@ -1,4 +0,0 @@
from .conllu2json import conllu2json # noqa: F401
from .iob2json import iob2json # noqa: F401
from .conll_ner2json import conll_ner2json # noqa: F401
from .jsonl2json import ner_jsonl2json # noqa: F401

65
spacy/cli/converters/iob2json.py
View File

@ -1,65 +0,0 @@
from wasabi import Printer
from ...gold import iob_to_biluo
from ...util import minibatch
from .conll_ner2json import n_sents_info
def iob2json(input_data, n_sents=10, no_print=False, *args, **kwargs):
"""
Convert IOB files with one sentence per line and tags separated with '|'
into JSON format for use with train cli. IOB and IOB2 are accepted.
Sample formats:
I|O like|O London|I-GPE and|O New|B-GPE York|I-GPE City|I-GPE .|O
I|O like|O London|B-GPE and|O New|B-GPE York|I-GPE City|I-GPE .|O
I|PRP|O like|VBP|O London|NNP|I-GPE and|CC|O New|NNP|B-GPE York|NNP|I-GPE City|NNP|I-GPE .|.|O
I|PRP|O like|VBP|O London|NNP|B-GPE and|CC|O New|NNP|B-GPE York|NNP|I-GPE City|NNP|I-GPE .|.|O
"""
msg = Printer(no_print=no_print)
docs = read_iob(input_data.split("\n"))
if n_sents > 0:
n_sents_info(msg, n_sents)
docs = merge_sentences(docs, n_sents)
return docs
def read_iob(raw_sents):
sentences = []
for line in raw_sents:
if not line.strip():
continue
tokens = [t.split("|") for t in line.split()]
if len(tokens[0]) == 3:
words, pos, iob = zip(*tokens)
elif len(tokens[0]) == 2:
words, iob = zip(*tokens)
pos = ["-"] * len(words)
else:
raise ValueError(
"The sentence-per-line IOB/IOB2 file is not formatted correctly. Try checking whitespace and delimiters. See https://spacy.io/api/cli#convert"
)
biluo = iob_to_biluo(iob)
sentences.append(
[
{"orth": w, "tag": p, "ner": ent}
for (w, p, ent) in zip(words, pos, biluo)
]
)
sentences = [{"tokens": sent} for sent in sentences]
paragraphs = [{"sentences": [sent]} for sent in sentences]
docs = [{"id": i, "paragraphs": [para]} for i, para in enumerate(paragraphs)]
return docs
def merge_sentences(docs, n_sents):
merged = []
for group in minibatch(docs, size=n_sents):
group = list(group)
first = group.pop(0)
to_extend = first["paragraphs"][0]["sentences"]
for sent in group:
to_extend.extend(sent["paragraphs"][0]["sentences"])
merged.append(first)
return merged

50
spacy/cli/converters/jsonl2json.py
View File

@ -1,50 +0,0 @@
import srsly
from ...gold import docs_to_json
from ...util import get_lang_class, minibatch
def ner_jsonl2json(input_data, lang=None, n_sents=10, use_morphology=False, **_):
if lang is None:
raise ValueError("No --lang specified, but tokenization required")
json_docs = []
input_examples = [srsly.json_loads(line) for line in input_data.strip().split("\n")]
nlp = get_lang_class(lang)()
sentencizer = nlp.create_pipe("sentencizer")
for i, batch in enumerate(minibatch(input_examples, size=n_sents)):
docs = []
for record in batch:
raw_text = record["text"]
if "entities" in record:
ents = record["entities"]
else:
ents = record["spans"]
ents = [(e["start"], e["end"], e["label"]) for e in ents]
doc = nlp.make_doc(raw_text)
sentencizer(doc)
spans = [doc.char_span(s, e, label=L) for s, e, L in ents]
doc.ents = _cleanup_spans(spans)
docs.append(doc)
json_docs.append(docs_to_json(docs, id=i))
return json_docs
def _cleanup_spans(spans):
output = []
seen = set()
for span in spans:
if span is not None:
# Trim whitespace
while len(span) and span[0].is_space:
span = span[1:]
while len(span) and span[-1].is_space:
span = span[:-1]
if not len(span):
continue
for i in range(span.start, span.end):
if i in seen:
break
else:
output.append(span)
seen.update(range(span.start, span.end))
return output

16
spacy/cli/debug_data.py
View File

@ -6,7 +6,7 @@ import srsly
from wasabi import Printer, MESSAGES
from ._app import app, Arg, Opt
from ..gold import GoldCorpus, Example
from ..gold import Corpus, Example
from ..syntax import nonproj
from ..language import Language
from ..util import load_model, get_lang_class
@ -99,7 +99,7 @@ def debug_data(
loading_train_error_message = ""
loading_dev_error_message = ""
with msg.loading("Loading corpus..."):
corpus = GoldCorpus(train_path, dev_path)
corpus = Corpus(train_path, dev_path)
try:
train_dataset = list(corpus.train_dataset(nlp))
train_dataset_unpreprocessed = list(
@ -518,12 +518,12 @@ def _compile_gold(
"texts": set(),
}
for example in examples:
gold = example.gold
doc = example.doc
valid_words = [x for x in gold.words if x is not None]
gold = example.reference
doc = example.predicted
valid_words = [x for x in gold if x is not None]
data["words"].update(valid_words)
data["n_words"] += len(valid_words)
data["n_misaligned_words"] += len(gold.words) - len(valid_words)
data["n_misaligned_words"] += len(gold) - len(valid_words)
data["texts"].add(doc.text)
if len(nlp.vocab.vectors):
for word in valid_words:
@ -578,10 +578,10 @@ def _format_labels(labels: List[Tuple[str, int]], counts: bool = False) -> str:
def _get_examples_without_label(data: Sequence[Example], label: str) -> int:
count = 0
for ex in data:
for eg in data:
labels = [
label.split("-")[1]
for label in ex.gold.ner
for label in eg.gold.ner
if label not in ("O", "-", None)
]
if label not in labels:

15
spacy/cli/evaluate.py
View File

@ -3,10 +3,10 @@ from timeit import default_timer as timer
from wasabi import Printer
from pathlib import Path
from ._app import app, Arg, Opt
from ..gold import Corpus
from ..tokens import Doc
from ._app import app, Arg, Opt
from ..scorer import Scorer
from ..gold import GoldCorpus
from .. import util
from .. import displacy
@ -20,7 +20,9 @@ def evaluate_cli(
gold_preproc: bool = Opt(False, "--gold-preproc", "-G", help="Use gold preprocessing"),
displacy_path: Optional[Path] = Opt(None, "--displacy-path", "-dp", help="Directory to output rendered parses as HTML", exists=True, file_okay=False),
displacy_limit: int = Opt(25, "--displacy-limit", "-dl", help="Limit of parses to render as HTML"),
# fmt: on
return_scores: bool = Opt(False, "--return-scores", "-R", help="Return dict containing model scores"),
# fmt: on
):
"""
Evaluate a model. To render a sample of parses in a HTML file, set an
@ -34,6 +36,7 @@ def evaluate_cli(
displacy_path=displacy_path,
displacy_limit=displacy_limit,
silent=False,
return_scores=return_scores,
)
@ -45,6 +48,7 @@ def evaluate(
displacy_path: Optional[Path] = None,
displacy_limit: int = 25,
silent: bool = True,
return_scores: bool = False,
) -> Scorer:
msg = Printer(no_print=silent, pretty=not silent)
util.fix_random_seed()
@ -57,7 +61,7 @@ def evaluate(
msg.fail("Evaluation data not found", data_path, exits=1)
if displacy_path and not displacy_path.exists():
msg.fail("Visualization output directory not found", displacy_path, exits=1)
corpus = GoldCorpus(data_path, data_path)
corpus = Corpus(data_path, data_path)
if model.startswith("blank:"):
nlp = util.get_lang_class(model.replace("blank:", ""))()
else:
@ -101,7 +105,8 @@ def evaluate(
ents=render_ents,
)
msg.good(f"Generated {displacy_limit} parses as HTML", displacy_path)
return scorer.scores
if return_scores:
return scorer.scores
def render_parses(

3
spacy/cli/pretrain.py
View File

@ -179,8 +179,7 @@ def pretrain(
skip_counter = 0
loss_func = pretrain_config["loss_func"]
for epoch in range(epoch_resume, pretrain_config["max_epochs"]):
examples = [Example(doc=text) for text in texts]
batches = util.minibatch_by_words(examples, size=pretrain_config["batch_size"])
batches = util.minibatch_by_words(texts, size=pretrain_config["batch_size"])
for batch_id, batch in enumerate(batches):
docs, count = make_docs(
nlp,

278
spacy/cli/train_from_config.py → spacy/cli/train.py
View File

@ -1,16 +1,18 @@
from typing import Optional, Dict
from typing import Optional, Dict, List, Union, Sequence
from timeit import default_timer as timer
import srsly
import tqdm
from pydantic import BaseModel, FilePath
from pathlib import Path
from wasabi import msg
import thinc
import thinc.schedules
from thinc.api import use_pytorch_for_gpu_memory
from thinc.api import Model, use_pytorch_for_gpu_memory
import random
from ._app import app, Arg, Opt
from ..gold import GoldCorpus
from ..gold import Corpus
from ..lookups import Lookups
from .. import util
from ..errors import Errors
@ -82,6 +84,41 @@ subword_features = true
"""
class PipelineComponent(BaseModel):
factory: str
model: Model
class Config:
arbitrary_types_allowed = True
class ConfigSchema(BaseModel):
optimizer: Optional["Optimizer"]
class training(BaseModel):
patience: int = 10
eval_frequency: int = 100
dropout: float = 0.2
init_tok2vec: Optional[FilePath] = None
max_epochs: int = 100
orth_variant_level: float = 0.0
gold_preproc: bool = False
max_length: int = 0
use_gpu: int = 0
scores: List[str] = ["ents_p", "ents_r", "ents_f"]
score_weights: Dict[str, Union[int, float]] = {"ents_f": 1.0}
limit: int = 0
batch_size: Union[Sequence[int], int]
class nlp(BaseModel):
lang: str
vectors: Optional[str]
pipeline: Optional[Dict[str, PipelineComponent]]
class Config:
extra = "allow"
@app.command("train")
def train_cli(
# fmt: off
@ -104,33 +141,8 @@ def train_cli(
command.
"""
util.set_env_log(verbose)
verify_cli_args(**locals())
# Make sure all files and paths exists if they are needed
if not config_path or not config_path.exists():
msg.fail("Config file not found", config_path, exits=1)
if not train_path or not train_path.exists():
msg.fail("Training data not found", train_path, exits=1)
if not dev_path or not dev_path.exists():
msg.fail("Development data not found", dev_path, exits=1)
if output_path is not None:
if not output_path.exists():
output_path.mkdir()
msg.good(f"Created output directory: {output_path}")
elif output_path.exists() and [p for p in output_path.iterdir() if p.is_dir()]:
msg.warn(
"Output directory is not empty.",
"This can lead to unintended side effects when saving the model. "
"Please use an empty directory or a different path instead. If "
"the specified output path doesn't exist, the directory will be "
"created for you.",
)
if code_path is not None:
if not code_path.exists():
msg.fail("Path to Python code not found", code_path, exits=1)
try:
util.import_file("python_code", code_path)
except Exception as e:
msg.fail(f"Couldn't load Python code: {code_path}", e, exits=1)
if raw_text is not None:
raw_text = list(srsly.read_jsonl(raw_text))
tag_map = {}
@ -139,8 +151,6 @@ def train_cli(
weights_data = None
if init_tok2vec is not None:
if not init_tok2vec.exists():
msg.fail("Can't find pretrained tok2vec", init_tok2vec, exits=1)
with init_tok2vec.open("rb") as file_:
weights_data = file_.read()
@ -184,71 +194,20 @@ def train(
nlp = util.load_model_from_config(nlp_config)
optimizer = training["optimizer"]
limit = training["limit"]
msg.info("Loading training corpus")
corpus = GoldCorpus(data_paths["train"], data_paths["dev"], limit=limit)
# verify textcat config
corpus = Corpus(data_paths["train"], data_paths["dev"], limit=limit)
if "textcat" in nlp_config["pipeline"]:
textcat_labels = set(nlp.get_pipe("textcat").labels)
textcat_multilabel = not nlp_config["pipeline"]["textcat"]["model"][
"exclusive_classes"
]
# check whether the setting 'exclusive_classes' corresponds to the provided training data
if textcat_multilabel:
multilabel_found = False
for ex in corpus.train_examples:
cats = ex.doc_annotation.cats
textcat_labels.update(cats.keys())
if list(cats.values()).count(1.0) != 1:
multilabel_found = True
if not multilabel_found:
msg.warn(
"The textcat training instances look like they have "
"mutually exclusive classes. Set 'exclusive_classes' "
"to 'true' in the config to train a classifier with "
"mutually exclusive classes more accurately."
)
else:
for ex in corpus.train_examples:
cats = ex.doc_annotation.cats
textcat_labels.update(cats.keys())
if list(cats.values()).count(1.0) != 1:
msg.fail(
"Some textcat training instances do not have exactly "
"one positive label. Set 'exclusive_classes' "
"to 'false' in the config to train a classifier with classes "
"that are not mutually exclusive."
)
msg.info(
f"Initialized textcat component for {len(textcat_labels)} unique labels"
)
nlp.get_pipe("textcat").labels = tuple(textcat_labels)
# if 'positive_label' is provided: double check whether it's in the data and the task is binary
if nlp_config["pipeline"]["textcat"].get("positive_label", None):
textcat_labels = nlp.get_pipe("textcat").cfg.get("labels", [])
pos_label = nlp_config["pipeline"]["textcat"]["positive_label"]
if pos_label not in textcat_labels:
msg.fail(
f"The textcat's 'positive_label' config setting '{pos_label}' "
f"does not match any label in the training data.",
exits=1,
)
if len(textcat_labels) != 2:
msg.fail(
f"A textcat 'positive_label' '{pos_label}' was "
f"provided for training data that does not appear to be a "
f"binary classification problem with two labels.",
exits=1,
)
verify_textcat_config(nlp, nlp_config)
if training.get("resume", False):
msg.info("Resuming training")
nlp.resume_training()
else:
msg.info(f"Initializing the nlp pipeline: {nlp.pipe_names}")
nlp.begin_training(lambda: corpus.train_examples)
train_examples = list(corpus.train_dataset(
nlp,
shuffle=False,
gold_preproc=training["gold_preproc"]
))
nlp.begin_training(lambda: train_examples)
# Update tag map with provided mapping
nlp.vocab.morphology.tag_map.update(tag_map)
@ -279,6 +238,7 @@ def train(
)
tok2vec.from_bytes(weights_data)
msg.info("Loading training corpus")
train_batches = create_train_batches(nlp, corpus, training)
evaluate = create_evaluation_callback(nlp, optimizer, corpus, training)
@ -311,18 +271,15 @@ def train(
update_meta(training, nlp, info)
nlp.to_disk(output_path / "model-best")
progress = tqdm.tqdm(total=training["eval_frequency"], leave=False)
# Clean up the objects to faciliate garbage collection.
for eg in batch:
eg.doc = None
eg.goldparse = None
eg.doc_annotation = None
eg.token_annotation = None
except Exception as e:
msg.warn(
f"Aborting and saving the final best model. "
f"Encountered exception: {str(e)}",
exits=1,
)
if output_path is not None:
msg.warn(
f"Aborting and saving the final best model. "
f"Encountered exception: {str(e)}",
exits=1,
)
else:
raise e
finally:
if output_path is not None:
final_model_path = output_path / "model-final"
@ -335,21 +292,19 @@ def train(
def create_train_batches(nlp, corpus, cfg):
epochs_todo = cfg.get("max_epochs", 0)
max_epochs = cfg.get("max_epochs", 0)
train_examples = list(corpus.train_dataset(
nlp,
shuffle=True,
gold_preproc=cfg["gold_preproc"],
max_length=cfg["max_length"]
))
epoch = 0
while True:
train_examples = list(
corpus.train_dataset(
nlp,
noise_level=0.0, # I think this is deprecated?
orth_variant_level=cfg["orth_variant_level"],
gold_preproc=cfg["gold_preproc"],
max_length=cfg["max_length"],
ignore_misaligned=True,
)
)
if len(train_examples) == 0:
raise ValueError(Errors.E988)
random.shuffle(train_examples)
epoch += 1
batches = util.minibatch_by_words(
train_examples,
size=cfg["batch_size"],
@ -358,15 +313,12 @@ def create_train_batches(nlp, corpus, cfg):
# make sure the minibatch_by_words result is not empty, or we'll have an infinite training loop
try:
first = next(batches)
yield first
yield epoch, first
except StopIteration:
raise ValueError(Errors.E986)
for batch in batches:
yield batch
epochs_todo -= 1
# We intentionally compare exactly to 0 here, so that max_epochs < 1
# will not break.
if epochs_todo == 0:
yield epoch, batch
if max_epochs >= 1 and epoch >= max_epochs:
break
@ -377,7 +329,8 @@ def create_evaluation_callback(nlp, optimizer, corpus, cfg):
nlp, gold_preproc=cfg["gold_preproc"], ignore_misaligned=True
)
)
n_words = sum(len(ex.doc) for ex in dev_examples)
n_words = sum(len(ex.predicted) for ex in dev_examples)
start_time = timer()
if optimizer.averages:
@ -395,7 +348,7 @@ def create_evaluation_callback(nlp, optimizer, corpus, cfg):
except KeyError as e:
raise KeyError(
Errors.E983.format(
dict_name="score_weights", key=str(e), keys=list(scores.keys())
dict="score_weights", key=str(e), keys=list(scores.keys())
)
)
@ -438,7 +391,7 @@ def train_while_improving(
Every iteration, the function yields out a tuple with:
* batch: A zipped sequence of Tuple[Doc, GoldParse] pairs.
* batch: A list of Example objects.
* info: A dict with various information about the last update (see below).
* is_best_checkpoint: A value in None, False, True, indicating whether this
was the best evaluation so far. You should use this to save the model
@ -470,7 +423,7 @@ def train_while_improving(
(nlp.make_doc(rt["text"]) for rt in raw_text), size=8
)
for step, batch in enumerate(train_data):
for step, (epoch, batch) in enumerate(train_data):
dropout = next(dropouts)
with nlp.select_pipes(enable=to_enable):
for subbatch in subdivide_batch(batch, accumulate_gradient):
@ -492,6 +445,7 @@ def train_while_improving(
score, other_scores = (None, None)
is_best_checkpoint = None
info = {
"epoch": epoch,
"step": step,
"score": score,
"other_scores": other_scores,
@ -512,7 +466,7 @@ def train_while_improving(
def subdivide_batch(batch, accumulate_gradient):
batch = list(batch)
batch.sort(key=lambda eg: len(eg.doc))
batch.sort(key=lambda eg: len(eg.predicted))
sub_len = len(batch) // accumulate_gradient
start = 0
for i in range(accumulate_gradient):
@ -530,9 +484,9 @@ def setup_printer(training, nlp):
score_widths = [max(len(col), 6) for col in score_cols]
loss_cols = [f"Loss {pipe}" for pipe in nlp.pipe_names]
loss_widths = [max(len(col), 8) for col in loss_cols]
table_header = ["#"] + loss_cols + score_cols + ["Score"]
table_header = ["E", "#"] + loss_cols + score_cols + ["Score"]
table_header = [col.upper() for col in table_header]
table_widths = [6] + loss_widths + score_widths + [6]
table_widths = [3, 6] + loss_widths + score_widths + [6]
table_aligns = ["r" for _ in table_widths]
msg.row(table_header, widths=table_widths)
@ -547,9 +501,7 @@ def setup_printer(training, nlp):
except KeyError as e:
raise KeyError(
Errors.E983.format(
dict_name="scores (losses)",
key=str(e),
keys=list(info["losses"].keys()),
dict="scores (losses)", key=str(e), keys=list(info["losses"].keys())
)
)
@ -560,13 +512,13 @@ def setup_printer(training, nlp):
except KeyError as e:
raise KeyError(
Errors.E983.format(
dict_name="scores (other)",
dict="scores (other)",
key=str(e),
keys=list(info["other_scores"].keys()),
)
)
data = (
[info["step"]] + losses + scores + ["{0:.2f}".format(float(info["score"]))]
[info["epoch"], info["step"]] + losses + scores + ["{0:.2f}".format(float(info["score"]))]
)
msg.row(data, widths=table_widths, aligns=table_aligns)
@ -580,3 +532,67 @@ def update_meta(training, nlp, info):
nlp.meta["performance"][metric] = info["other_scores"][metric]
for pipe_name in nlp.pipe_names:
nlp.meta["performance"][f"{pipe_name}_loss"] = info["losses"][pipe_name]
def verify_cli_args(
train_path,
dev_path,
config_path,
output_path=None,
code_path=None,
init_tok2vec=None,
raw_text=None,
verbose=False,
use_gpu=-1,
tag_map_path=None,
omit_extra_lookups=False,
):
# Make sure all files and paths exists if they are needed
if not config_path or not config_path.exists():
msg.fail("Config file not found", config_path, exits=1)
if not train_path or not train_path.exists():
msg.fail("Training data not found", train_path, exits=1)
if not dev_path or not dev_path.exists():
msg.fail("Development data not found", dev_path, exits=1)
if output_path is not None:
if not output_path.exists():
output_path.mkdir()
msg.good(f"Created output directory: {output_path}")
elif output_path.exists() and [p for p in output_path.iterdir() if p.is_dir()]:
msg.warn(
"Output directory is not empty.",
"This can lead to unintended side effects when saving the model. "
"Please use an empty directory or a different path instead. If "
"the specified output path doesn't exist, the directory will be "
"created for you.",
)
if code_path is not None:
if not code_path.exists():
msg.fail("Path to Python code not found", code_path, exits=1)
try:
util.import_file("python_code", code_path)
except Exception as e:
msg.fail(f"Couldn't load Python code: {code_path}", e, exits=1)
if init_tok2vec is not None and not init_tok2vec.exists():
msg.fail("Can't find pretrained tok2vec", init_tok2vec, exits=1)
def verify_textcat_config(nlp, nlp_config):
# if 'positive_label' is provided: double check whether it's in the data and
# the task is binary
if nlp_config["pipeline"]["textcat"].get("positive_label", None):
textcat_labels = nlp.get_pipe("textcat").cfg.get("labels", [])
pos_label = nlp_config["pipeline"]["textcat"]["positive_label"]
if pos_label not in textcat_labels:
msg.fail(
f"The textcat's 'positive_label' config setting '{pos_label}' "
f"does not match any label in the training data.",
exits=1,
)
if len(textcat_labels) != 2:
msg.fail(
f"A textcat 'positive_label' '{pos_label}' was "
f"provided for training data that does not appear to be a "
f"binary classification problem with two labels.",
exits=1,
)

24
spacy/errors.py
View File

@ -132,6 +132,8 @@ class Warnings(object):
"are currently: da, de, el, en, id, lb, pt, ru, sr, ta, th.")
# TODO: fix numbering after merging develop into master
W093 = ("Could not find any data to train the {name} on. Is your "
"input data correctly formatted ?")
W094 = ("Model '{model}' ({model_version}) specifies an under-constrained "
"spaCy version requirement: {version}. This can lead to compatibility "
"problems with older versions, or as new spaCy versions are "
@ -575,9 +577,6 @@ class Errors(object):
"{obj}.{attr}\nAttribute '{attr}' does not exist on {obj}.")
E186 = ("'{tok_a}' and '{tok_b}' are different texts.")
E187 = ("Only unicode strings are supported as labels.")
E188 = ("Could not match the gold entity links to entities in the doc - "
"make sure the gold EL data refers to valid results of the "
"named entity recognizer in the `nlp` pipeline.")
E189 = ("Each argument to `get_doc` should be of equal length.")
E190 = ("Token head out of range in `Doc.from_array()` for token index "
"'{index}' with value '{value}' (equivalent to relative head "
@ -602,10 +601,17 @@ class Errors(object):
"can not be combined with adding a pretrained Tok2Vec layer.")
# TODO: fix numbering after merging develop into master
E983 = ("Invalid key for '{dict_name}': {key}. Available keys: "
E978 = ("The {method} method of component {name} takes a list of Example objects, "
"but found {types} instead.")
E979 = ("Cannot convert {type} to an Example object.")
E980 = ("Each link annotation should refer to a dictionary with at most one "
"identifier mapping to 1.0, and all others to 0.0.")
E981 = ("The offsets of the annotations for 'links' need to refer exactly "
"to the offsets of the 'entities' annotations.")
E982 = ("The 'ent_iob' attribute of a Token should be an integer indexing "
"into {values}, but found {value}.")
E983 = ("Invalid key for '{dict}': {key}. Available keys: "
"{keys}")
E984 = ("Could not parse the {input} - double check the data is written "
"in the correct format as expected by spaCy.")
E985 = ("The pipeline component '{component}' is already available in the base "
"model. The settings in the component block in the config file are "
"being ignored. If you want to replace this component instead, set "
@ -637,11 +643,7 @@ class Errors(object):
E997 = ("Tokenizer special cases are not allowed to modify the text. "
"This would map '{chunk}' to '{orth}' given token attributes "
"'{token_attrs}'.")
E998 = ("To create GoldParse objects from Example objects without a "
"Doc, get_gold_parses() should be called with a Vocab object.")
E999 = ("Encountered an unexpected format for the dictionary holding "
"gold annotations: {gold_dict}")
@add_codes
class TempErrors(object):

68
spacy/gold.pxd
View File

@ -1,68 +0,0 @@
from cymem.cymem cimport Pool
from .typedefs cimport attr_t
from .syntax.transition_system cimport Transition
from .tokens import Doc
cdef struct GoldParseC:
int* tags
int* heads
int* has_dep
int* sent_start
attr_t* labels
int** brackets
Transition* ner
cdef class GoldParse:
cdef Pool mem
cdef GoldParseC c
cdef readonly TokenAnnotation orig
cdef int length
cdef public int loss
cdef public list words
cdef public list tags
cdef public list pos
cdef public list morphs
cdef public list lemmas
cdef public list sent_starts
cdef public list heads
cdef public list labels
cdef public dict orths
cdef public list ner
cdef public dict brackets
cdef public dict cats
cdef public dict links
cdef readonly list cand_to_gold
cdef readonly list gold_to_cand
cdef class TokenAnnotation:
cdef public list ids
cdef public list words
cdef public list tags
cdef public list pos
cdef public list morphs
cdef public list lemmas
cdef public list heads
cdef public list deps
cdef public list entities
cdef public list sent_starts
cdef public dict brackets_by_start
cdef class DocAnnotation:
cdef public object cats
cdef public object links
cdef class Example:
cdef public object doc
cdef public TokenAnnotation token_annotation
cdef public DocAnnotation doc_annotation
cdef public object goldparse

1420
spacy/gold.pyx
View File

File diff suppressed because it is too large Load Diff

0
spacy/gold/__init__.pxd Normal file
View File

11
spacy/gold/__init__.py Normal file
View File

@ -0,0 +1,11 @@
from .corpus import Corpus
from .example import Example
from .align import align
from .iob_utils import iob_to_biluo, biluo_to_iob
from .iob_utils import biluo_tags_from_offsets, offsets_from_biluo_tags
from .iob_utils import spans_from_biluo_tags
from .iob_utils import tags_to_entities
from .gold_io import docs_to_json
from .gold_io import read_json_file

8
spacy/gold/align.pxd Normal file
View File

@ -0,0 +1,8 @@
cdef class Alignment:
cdef public object cost
cdef public object i2j
cdef public object j2i
cdef public object i2j_multi
cdef public object j2i_multi
cdef public object cand_to_gold
cdef public object gold_to_cand

101
spacy/gold/align.pyx Normal file
View File

@ -0,0 +1,101 @@
import numpy
from ..errors import Errors, AlignmentError
cdef class Alignment:
def __init__(self, spacy_words, gold_words):
# Do many-to-one alignment for misaligned tokens.
# If we over-segment, we'll have one gold word that covers a sequence
# of predicted words
# If we under-segment, we'll have one predicted word that covers a
# sequence of gold words.
# If we "mis-segment", we'll have a sequence of predicted words covering
# a sequence of gold words. That's many-to-many -- we don't do that
# except for NER spans where the start and end can be aligned.
cost, i2j, j2i, i2j_multi, j2i_multi = align(spacy_words, gold_words)
self.cost = cost
self.i2j = i2j
self.j2i = j2i
self.i2j_multi = i2j_multi
self.j2i_multi = j2i_multi
self.cand_to_gold = [(j if j >= 0 else None) for j in i2j]
self.gold_to_cand = [(i if i >= 0 else None) for i in j2i]
def align(tokens_a, tokens_b):
"""Calculate alignment tables between two tokenizations.
tokens_a (List[str]): The candidate tokenization.
tokens_b (List[str]): The reference tokenization.
RETURNS: (tuple): A 5-tuple consisting of the following information:
* cost (int): The number of misaligned tokens.
* a2b (List[int]): Mapping of indices in `tokens_a` to indices in `tokens_b`.
For instance, if `a2b[4] == 6`, that means that `tokens_a[4]` aligns
to `tokens_b[6]`. If there's no one-to-one alignment for a token,
it has the value -1.
* b2a (List[int]): The same as `a2b`, but mapping the other direction.
* a2b_multi (Dict[int, int]): A dictionary mapping indices in `tokens_a`
to indices in `tokens_b`, where multiple tokens of `tokens_a` align to
the same token of `tokens_b`.
* b2a_multi (Dict[int, int]): As with `a2b_multi`, but mapping the other
direction.
"""
tokens_a = _normalize_for_alignment(tokens_a)
tokens_b = _normalize_for_alignment(tokens_b)
cost = 0
a2b = numpy.empty(len(tokens_a), dtype="i")
b2a = numpy.empty(len(tokens_b), dtype="i")
a2b.fill(-1)
b2a.fill(-1)
a2b_multi = {}
b2a_multi = {}
i = 0
j = 0
offset_a = 0
offset_b = 0
while i < len(tokens_a) and j < len(tokens_b):
a = tokens_a[i][offset_a:]
b = tokens_b[j][offset_b:]
if a == b:
if offset_a == offset_b == 0:
a2b[i] = j
b2a[j] = i
elif offset_a == 0:
cost += 2
a2b_multi[i] = j
elif offset_b == 0:
cost += 2
b2a_multi[j] = i
offset_a = offset_b = 0
i += 1
j += 1
elif a == "":
assert offset_a == 0
cost += 1
i += 1
elif b == "":
assert offset_b == 0
cost += 1
j += 1
elif b.startswith(a):
cost += 1
if offset_a == 0:
a2b_multi[i] = j
i += 1
offset_a = 0
offset_b += len(a)
elif a.startswith(b):
cost += 1
if offset_b == 0:
b2a_multi[j] = i
j += 1
offset_b = 0
offset_a += len(b)
else:
assert "".join(tokens_a) != "".join(tokens_b)
raise AlignmentError(Errors.E186.format(tok_a=tokens_a, tok_b=tokens_b))
return cost, a2b, b2a, a2b_multi, b2a_multi
def _normalize_for_alignment(tokens):
return [w.replace(" ", "").lower() for w in tokens]

111
spacy/gold/augment.py Normal file
View File

@ -0,0 +1,111 @@
import random
import itertools
def make_orth_variants_example(nlp, example, orth_variant_level=0.0): # TODO: naming
raw_text = example.text
orig_dict = example.to_dict()
variant_text, variant_token_annot = make_orth_variants(
nlp, raw_text, orig_dict["token_annotation"], orth_variant_level
)
doc = nlp.make_doc(variant_text)
orig_dict["token_annotation"] = variant_token_annot
return example.from_dict(doc, orig_dict)
def make_orth_variants(nlp, raw_text, orig_token_dict, orth_variant_level=0.0):
if random.random() >= orth_variant_level:
return raw_text, orig_token_dict
if not orig_token_dict:
return raw_text, orig_token_dict
raw = raw_text
token_dict = orig_token_dict
lower = False
if random.random() >= 0.5:
lower = True
if raw is not None:
raw = raw.lower()
ndsv = nlp.Defaults.single_orth_variants
ndpv = nlp.Defaults.paired_orth_variants
words = token_dict.get("words", [])
tags = token_dict.get("tags", [])
# keep unmodified if words or tags are not defined
if words and tags:
if lower:
words = [w.lower() for w in words]
# single variants
punct_choices = [random.choice(x["variants"]) for x in ndsv]
for word_idx in range(len(words)):
for punct_idx in range(len(ndsv)):
if (
tags[word_idx] in ndsv[punct_idx]["tags"]
and words[word_idx] in ndsv[punct_idx]["variants"]
):
words[word_idx] = punct_choices[punct_idx]
# paired variants
punct_choices = [random.choice(x["variants"]) for x in ndpv]
for word_idx in range(len(words)):
for punct_idx in range(len(ndpv)):
if tags[word_idx] in ndpv[punct_idx]["tags"] and words[
word_idx
] in itertools.chain.from_iterable(ndpv[punct_idx]["variants"]):
# backup option: random left vs. right from pair
pair_idx = random.choice([0, 1])
# best option: rely on paired POS tags like `` / ''
if len(ndpv[punct_idx]["tags"]) == 2:
pair_idx = ndpv[punct_idx]["tags"].index(tags[word_idx])
# next best option: rely on position in variants
# (may not be unambiguous, so order of variants matters)
else:
for pair in ndpv[punct_idx]["variants"]:
if words[word_idx] in pair:
pair_idx = pair.index(words[word_idx])
words[word_idx] = punct_choices[punct_idx][pair_idx]
token_dict["words"] = words
token_dict["tags"] = tags
# modify raw
if raw is not None:
variants = []
for single_variants in ndsv:
variants.extend(single_variants["variants"])
for paired_variants in ndpv:
variants.extend(
list(itertools.chain.from_iterable(paired_variants["variants"]))
)
# store variants in reverse length order to be able to prioritize
# longer matches (e.g., "---" before "--")
variants = sorted(variants, key=lambda x: len(x))
variants.reverse()
variant_raw = ""
raw_idx = 0
# add initial whitespace
while raw_idx < len(raw) and raw[raw_idx].isspace():
variant_raw += raw[raw_idx]
raw_idx += 1
for word in words:
match_found = False
# skip whitespace words
if word.isspace():
match_found = True
# add identical word
elif word not in variants and raw[raw_idx:].startswith(word):
variant_raw += word
raw_idx += len(word)
match_found = True
# add variant word
else:
for variant in variants:
if not match_found and raw[raw_idx:].startswith(variant):
raw_idx += len(variant)
variant_raw += word
match_found = True
# something went wrong, abort
# (add a warning message?)
if not match_found:
return raw_text, orig_token_dict
# add following whitespace
while raw_idx < len(raw) and raw[raw_idx].isspace():
variant_raw += raw[raw_idx]
raw_idx += 1
raw = variant_raw
return raw, token_dict

6
spacy/gold/converters/__init__.py Normal file
View File

@ -0,0 +1,6 @@
from .iob2docs import iob2docs # noqa: F401
from .conll_ner2docs import conll_ner2docs # noqa: F401
from .json2docs import json2docs
# TODO: Update this one
# from .conllu2docs import conllu2docs # noqa: F401

63
spacy/cli/converters/conll_ner2json.py → spacy/gold/converters/conll_ner2docs.py
View File

@ -1,17 +1,18 @@
from wasabi import Printer
from .. import tags_to_entities
from ...gold import iob_to_biluo
from ...lang.xx import MultiLanguage
from ...tokens.doc import Doc
from ...tokens import Doc, Span
from ...util import load_model
def conll_ner2json(
def conll_ner2docs(
input_data, n_sents=10, seg_sents=False, model=None, no_print=False, **kwargs
):
"""
Convert files in the CoNLL-2003 NER format and similar
whitespace-separated columns into JSON format for use with train cli.
whitespace-separated columns into Doc objects.
The first column is the tokens, the final column is the IOB tags. If an
additional second column is present, the second column is the tags.
@ -81,17 +82,25 @@ def conll_ner2json(
"No document delimiters found. Use `-n` to automatically group "
"sentences into documents."
)
if model:
nlp = load_model(model)
else:
nlp = MultiLanguage()
output_docs = []
for doc in input_data.strip().split(doc_delimiter):
doc = doc.strip()
if not doc:
for conll_doc in input_data.strip().split(doc_delimiter):
conll_doc = conll_doc.strip()
if not conll_doc:
continue
output_doc = []
for sent in doc.split("\n\n"):
sent = sent.strip()
if not sent:
words = []
sent_starts = []
pos_tags = []
biluo_tags = []
for conll_sent in conll_doc.split("\n\n"):
conll_sent = conll_sent.strip()
if not conll_sent:
continue
lines = [line.strip() for line in sent.split("\n") if line.strip()]
lines = [line.strip() for line in conll_sent.split("\n") if line.strip()]
cols = list(zip(*[line.split() for line in lines]))
if len(cols) < 2:
raise ValueError(
@ -99,25 +108,19 @@ def conll_ner2json(
"Try checking whitespace and delimiters. See "
"https://spacy.io/api/cli#convert"
)
words = cols[0]
iob_ents = cols[-1]
if len(cols) > 2:
tags = cols[1]
else:
tags = ["-"] * len(words)
biluo_ents = iob_to_biluo(iob_ents)
output_doc.append(
{
"tokens": [
{"orth": w, "tag": tag, "ner": ent}
for (w, tag, ent) in zip(words, tags, biluo_ents)
]
}
)
output_docs.append(
{"id": len(output_docs), "paragraphs": [{"sentences": output_doc}]}
)
output_doc = []
length = len(cols[0])
words.extend(cols[0])
sent_starts.extend([True] + [False] * (length - 1))
biluo_tags.extend(iob_to_biluo(cols[-1]))
pos_tags.extend(cols[1] if len(cols) > 2 else ["-"] * length)
doc = Doc(nlp.vocab, words=words)
for i, token in enumerate(doc):
token.tag_ = pos_tags[i]
token.is_sent_start = sent_starts[i]
entities = tags_to_entities(biluo_tags)
doc.ents = [Span(doc, start=s, end=e + 1, label=L) for L, s, e in entities]
output_docs.append(doc)
return output_docs

72
spacy/cli/converters/conllu2json.py → spacy/gold/converters/conllu2json.py
View File

@ -1,10 +1,10 @@
import re
from .conll_ner2docs import n_sents_info
from ...gold import Example
from ...gold import iob_to_biluo, spans_from_biluo_tags, biluo_tags_from_offsets
from ...gold import iob_to_biluo, spans_from_biluo_tags
from ...language import Language
from ...tokens import Doc, Token
from .conll_ner2json import n_sents_info
from wasabi import Printer
@ -12,7 +12,6 @@ def conllu2json(
input_data,
n_sents=10,
append_morphology=False,
lang=None,
ner_map=None,
merge_subtokens=False,
no_print=False,
@ -44,10 +43,7 @@ def conllu2json(
raw += example.text
sentences.append(
generate_sentence(
example.token_annotation,
has_ner_tags,
MISC_NER_PATTERN,
ner_map=ner_map,
example.to_dict(), has_ner_tags, MISC_NER_PATTERN, ner_map=ner_map,
)
)
# Real-sized documents could be extracted using the comments on the
@ -145,21 +141,22 @@ def get_entities(lines, tag_pattern, ner_map=None):
return iob_to_biluo(iob)
def generate_sentence(token_annotation, has_ner_tags, tag_pattern, ner_map=None):
def generate_sentence(example_dict, has_ner_tags, tag_pattern, ner_map=None):
sentence = {}
tokens = []
for i, id_ in enumerate(token_annotation.ids):
token_annotation = example_dict["token_annotation"]
for i, id_ in enumerate(token_annotation["ids"]):
token = {}
token["id"] = id_
token["orth"] = token_annotation.get_word(i)
token["tag"] = token_annotation.get_tag(i)
token["pos"] = token_annotation.get_pos(i)
token["lemma"] = token_annotation.get_lemma(i)
token["morph"] = token_annotation.get_morph(i)
token["head"] = token_annotation.get_head(i) - id_
token["dep"] = token_annotation.get_dep(i)
token["orth"] = token_annotation["words"][i]
token["tag"] = token_annotation["tags"][i]
token["pos"] = token_annotation["pos"][i]
token["lemma"] = token_annotation["lemmas"][i]
token["morph"] = token_annotation["morphs"][i]
token["head"] = token_annotation["heads"][i] - i
token["dep"] = token_annotation["deps"][i]
if has_ner_tags:
token["ner"] = token_annotation.get_entity(i)
token["ner"] = example_dict["doc_annotation"]["entities"][i]
tokens.append(token)
sentence["tokens"] = tokens
return sentence
@ -267,40 +264,25 @@ def example_from_conllu_sentence(
doc = merge_conllu_subtokens(lines, doc)
# create Example from custom Doc annotation
ids, words, tags, heads, deps = [], [], [], [], []
pos, lemmas, morphs, spaces = [], [], [], []
words, spaces, tags, morphs, lemmas = [], [], [], [], []
for i, t in enumerate(doc):
ids.append(i)
words.append(t._.merged_orth)
lemmas.append(t._.merged_lemma)
spaces.append(t._.merged_spaceafter)
morphs.append(t._.merged_morph)
if append_morphology and t._.merged_morph:
tags.append(t.tag_ + "__" + t._.merged_morph)
else:
tags.append(t.tag_)
pos.append(t.pos_)
morphs.append(t._.merged_morph)
lemmas.append(t._.merged_lemma)
heads.append(t.head.i)
deps.append(t.dep_)
spaces.append(t._.merged_spaceafter)
ent_offsets = [(e.start_char, e.end_char, e.label_) for e in doc.ents]
ents = biluo_tags_from_offsets(doc, ent_offsets)
raw = ""
for word, space in zip(words, spaces):
raw += word
if space:
raw += " "
example = Example(doc=raw)
example.set_token_annotation(
ids=ids,
words=words,
tags=tags,
pos=pos,
morphs=morphs,
lemmas=lemmas,
heads=heads,
deps=deps,
entities=ents,
)
doc_x = Doc(vocab, words=words, spaces=spaces)
ref_dict = Example(doc_x, reference=doc).to_dict()
ref_dict["words"] = words
ref_dict["lemmas"] = lemmas
ref_dict["spaces"] = spaces
ref_dict["tags"] = tags
ref_dict["morphs"] = morphs
example = Example.from_dict(doc_x, ref_dict)
return example

64
spacy/gold/converters/iob2docs.py Normal file
View File

@ -0,0 +1,64 @@
from wasabi import Printer
from .conll_ner2docs import n_sents_info
from ...gold import iob_to_biluo, tags_to_entities
from ...tokens import Doc, Span
from ...util import minibatch
def iob2docs(input_data, vocab, n_sents=10, no_print=False, *args, **kwargs):
"""
Convert IOB files with one sentence per line and tags separated with '|'
into Doc objects so they can be saved. IOB and IOB2 are accepted.
Sample formats:
I|O like|O London|I-GPE and|O New|B-GPE York|I-GPE City|I-GPE .|O
I|O like|O London|B-GPE and|O New|B-GPE York|I-GPE City|I-GPE .|O
I|PRP|O like|VBP|O London|NNP|I-GPE and|CC|O New|NNP|B-GPE York|NNP|I-GPE City|NNP|I-GPE .|.|O
I|PRP|O like|VBP|O London|NNP|B-GPE and|CC|O New|NNP|B-GPE York|NNP|I-GPE City|NNP|I-GPE .|.|O
"""
msg = Printer(no_print=no_print)
if n_sents > 0:
n_sents_info(msg, n_sents)
docs = read_iob(input_data.split("\n"), vocab, n_sents)
return docs
def read_iob(raw_sents, vocab, n_sents):
docs = []
for group in minibatch(raw_sents, size=n_sents):
tokens = []
words = []
tags = []
iob = []
sent_starts = []
for line in group:
if not line.strip():
continue
sent_tokens = [t.split("|") for t in line.split()]
if len(sent_tokens[0]) == 3:
sent_words, sent_tags, sent_iob = zip(*sent_tokens)
elif len(sent_tokens[0]) == 2:
sent_words, sent_iob = zip(*sent_tokens)
sent_tags = ["-"] * len(sent_words)
else:
raise ValueError(
"The sentence-per-line IOB/IOB2 file is not formatted correctly. Try checking whitespace and delimiters. See https://spacy.io/api/cli#convert"
)
words.extend(sent_words)
tags.extend(sent_tags)
iob.extend(sent_iob)
tokens.extend(sent_tokens)
sent_starts.append(True)
sent_starts.extend([False for _ in sent_words[1:]])
doc = Doc(vocab, words=words)
for i, tag in enumerate(tags):
doc[i].tag_ = tag
for i, sent_start in enumerate(sent_starts):
doc[i].is_sent_start = sent_start
biluo = iob_to_biluo(iob)
entities = tags_to_entities(biluo)
doc.ents = [Span(doc, start=s, end=e+1, label=L) for (L, s, e) in entities]
docs.append(doc)
return docs

24
spacy/gold/converters/json2docs.py Normal file
View File

@ -0,0 +1,24 @@
import srsly
from ..gold_io import json_iterate, json_to_annotations
from ..example import annotations2doc
from ..example import _fix_legacy_dict_data, _parse_example_dict_data
from ...util import load_model
from ...lang.xx import MultiLanguage
def json2docs(input_data, model=None, **kwargs):
nlp = load_model(model) if model is not None else MultiLanguage()
if not isinstance(input_data, bytes):
if not isinstance(input_data, str):
input_data = srsly.json_dumps(input_data)
input_data = input_data.encode("utf8")
docs = []
for json_doc in json_iterate(input_data):
for json_para in json_to_annotations(json_doc):
example_dict = _fix_legacy_dict_data(json_para)
tok_dict, doc_dict = _parse_example_dict_data(example_dict)
if json_para.get("raw"):
assert tok_dict.get("SPACY")
doc = annotations2doc(nlp.vocab, tok_dict, doc_dict)
docs.append(doc)
return docs

122
spacy/gold/corpus.py Normal file
View File

@ -0,0 +1,122 @@
import random
from .. import util
from .example import Example
from ..tokens import DocBin, Doc
class Corpus:
"""An annotated corpus, reading train and dev datasets from
the DocBin (.spacy) format.
DOCS: https://spacy.io/api/goldcorpus
"""
def __init__(self, train_loc, dev_loc, limit=0):
"""Create a Corpus.
train (str / Path): File or directory of training data.
dev (str / Path): File or directory of development data.
limit (int): Max. number of examples returned
RETURNS (Corpus): The newly created object.
"""
self.train_loc = train_loc
self.dev_loc = dev_loc
self.limit = limit
@staticmethod
def walk_corpus(path):
path = util.ensure_path(path)
if not path.is_dir():
return [path]
paths = [path]
locs = []
seen = set()
for path in paths:
if str(path) in seen:
continue
seen.add(str(path))
if path.parts[-1].startswith("."):
continue
elif path.is_dir():
paths.extend(path.iterdir())
elif path.parts[-1].endswith(".spacy"):
locs.append(path)
return locs
def make_examples(self, nlp, reference_docs, max_length=0):
for reference in reference_docs:
if max_length >= 1 and len(reference) >= max_length:
if reference.is_sentenced:
for ref_sent in reference.sents:
yield Example(
nlp.make_doc(ref_sent.text),
ref_sent.as_doc()
)
else:
yield Example(
nlp.make_doc(reference.text),
reference
)
def make_examples_gold_preproc(self, nlp, reference_docs):
for reference in reference_docs:
if reference.is_sentenced:
ref_sents = [sent.as_doc() for sent in reference.sents]
else:
ref_sents = [reference]
for ref_sent in ref_sents:
yield Example(
Doc(
nlp.vocab,
words=[w.text for w in ref_sent],
spaces=[bool(w.whitespace_) for w in ref_sent]
),
ref_sent
)
def read_docbin(self, vocab, locs):
""" Yield training examples as example dicts """
i = 0
for loc in locs:
loc = util.ensure_path(loc)
if loc.parts[-1].endswith(".spacy"):
with loc.open("rb") as file_:
doc_bin = DocBin().from_bytes(file_.read())
docs = doc_bin.get_docs(vocab)
for doc in docs:
if len(doc):
yield doc
i += 1
if self.limit >= 1 and i >= self.limit:
break
def count_train(self, nlp):
"""Returns count of words in train examples"""
n = 0
i = 0
for example in self.train_dataset(nlp):
n += len(example.predicted)
if self.limit >= 0 and i >= self.limit:
break
i += 1
return n
def train_dataset(self, nlp, *, shuffle=True, gold_preproc=False,
max_length=0, **kwargs):
ref_docs = self.read_docbin(nlp.vocab, self.walk_corpus(self.train_loc))
if gold_preproc:
examples = self.make_examples_gold_preproc(nlp, ref_docs)
else:
examples = self.make_examples(nlp, ref_docs, max_length)
if shuffle:
examples = list(examples)
random.shuffle(examples)
yield from examples
def dev_dataset(self, nlp, *, gold_preproc=False, **kwargs):
ref_docs = self.read_docbin(nlp.vocab, self.walk_corpus(self.dev_loc))
if gold_preproc:
examples = self.make_examples_gold_preproc(nlp, ref_docs)
else:
examples = self.make_examples(nlp, ref_docs, max_length=0)
yield from examples

8
spacy/gold/example.pxd Normal file
View File

@ -0,0 +1,8 @@
from ..tokens.doc cimport Doc
from .align cimport Alignment
cdef class Example:
cdef readonly Doc x
cdef readonly Doc y
cdef readonly Alignment _alignment

432
spacy/gold/example.pyx Normal file
View File

@ -0,0 +1,432 @@
import warnings
import numpy
from ..tokens import Token
from ..tokens.doc cimport Doc
from ..tokens.span cimport Span
from ..tokens.span import Span
from ..attrs import IDS
from .align cimport Alignment
from .iob_utils import biluo_to_iob, biluo_tags_from_offsets, biluo_tags_from_doc
from .iob_utils import spans_from_biluo_tags
from .align import Alignment
from ..errors import Errors, AlignmentError
from ..syntax import nonproj
from ..util import get_words_and_spaces
cpdef Doc annotations2doc(vocab, tok_annot, doc_annot):
""" Create a Doc from dictionaries with token and doc annotations. Assumes ORTH & SPACY are set. """
attrs, array = _annot2array(vocab, tok_annot, doc_annot)
output = Doc(vocab, words=tok_annot["ORTH"], spaces=tok_annot["SPACY"])
if "entities" in doc_annot:
_add_entities_to_doc(output, doc_annot["entities"])
if array.size:
output = output.from_array(attrs, array)
# links are currently added with ENT_KB_ID on the token level
output.cats.update(doc_annot.get("cats", {}))
return output
cdef class Example:
def __init__(self, Doc predicted, Doc reference, *, Alignment alignment=None):
""" Doc can either be text, or an actual Doc """
msg = "Example.__init__ got None for '{arg}'. Requires Doc."
if predicted is None:
raise TypeError(msg.format(arg="predicted"))
if reference is None:
raise TypeError(msg.format(arg="reference"))
self.x = predicted
self.y = reference
self._alignment = alignment
property predicted:
def __get__(self):
return self.x
def __set__(self, doc):
self.x = doc
property reference:
def __get__(self):
return self.y
def __set__(self, doc):
self.y = doc
def copy(self):
return Example(
self.x.copy(),
self.y.copy()
)
@classmethod
def from_dict(cls, Doc predicted, dict example_dict):
if example_dict is None:
raise ValueError("Example.from_dict expected dict, received None")
if not isinstance(predicted, Doc):
raise TypeError(f"Argument 1 should be Doc. Got {type(predicted)}")
example_dict = _fix_legacy_dict_data(example_dict)
tok_dict, doc_dict = _parse_example_dict_data(example_dict)
if "ORTH" not in tok_dict:
tok_dict["ORTH"] = [tok.text for tok in predicted]
tok_dict["SPACY"] = [tok.whitespace_ for tok in predicted]
if not _has_field(tok_dict, "SPACY"):
tok_dict["SPACY"] = _guess_spaces(predicted.text, tok_dict["ORTH"])
return Example(
predicted,
annotations2doc(predicted.vocab, tok_dict, doc_dict)
)
@property
def alignment(self):
if self._alignment is None:
spacy_words = [token.orth_ for token in self.predicted]
gold_words = [token.orth_ for token in self.reference]
if gold_words == []:
gold_words = spacy_words
self._alignment = Alignment(spacy_words, gold_words)
return self._alignment
def get_aligned(self, field, as_string=False):
"""Return an aligned array for a token attribute."""
i2j_multi = self.alignment.i2j_multi
cand_to_gold = self.alignment.cand_to_gold
vocab = self.reference.vocab
gold_values = self.reference.to_array([field])
output = [None] * len(self.predicted)
for i, gold_i in enumerate(cand_to_gold):
if self.predicted[i].text.isspace():
output[i] = None
if gold_i is None:
if i in i2j_multi:
output[i] = gold_values[i2j_multi[i]]
else:
output[i] = None
else:
output[i] = gold_values[gold_i]
if as_string and field not in ["ENT_IOB", "SENT_START"]:
output = [vocab.strings[o] if o is not None else o for o in output]
return output
def get_aligned_parse(self, projectivize=True):
cand_to_gold = self.alignment.cand_to_gold
gold_to_cand = self.alignment.gold_to_cand
aligned_heads = [None] * self.x.length
aligned_deps = [None] * self.x.length
heads = [token.head.i for token in self.y]
deps = [token.dep_ for token in self.y]
heads, deps = nonproj.projectivize(heads, deps)
for cand_i in range(self.x.length):
gold_i = cand_to_gold[cand_i]
if gold_i is not None: # Alignment found
gold_head = gold_to_cand[heads[gold_i]]
if gold_head is not None:
aligned_heads[cand_i] = gold_head
aligned_deps[cand_i] = deps[gold_i]
return aligned_heads, aligned_deps
def get_aligned_ner(self):
if not self.y.is_nered:
return [None] * len(self.x) # should this be 'missing' instead of 'None' ?
x_text = self.x.text
# Get a list of entities, and make spans for non-entity tokens.
# We then work through the spans in order, trying to find them in
# the text and using that to get the offset. Any token that doesn't
# get a tag set this way is tagged None.
# This could maybe be improved? It at least feels easy to reason about.
y_spans = list(self.y.ents)
y_spans.sort()
x_text_offset = 0
x_spans = []
for y_span in y_spans:
if x_text.count(y_span.text) >= 1:
start_char = x_text.index(y_span.text) + x_text_offset
end_char = start_char + len(y_span.text)
x_span = self.x.char_span(start_char, end_char, label=y_span.label)
if x_span is not None:
x_spans.append(x_span)
x_text = self.x.text[end_char:]
x_text_offset = end_char
x_tags = biluo_tags_from_offsets(
self.x,
[(e.start_char, e.end_char, e.label_) for e in x_spans],
missing=None
)
gold_to_cand = self.alignment.gold_to_cand
for token in self.y:
if token.ent_iob_ == "O":
cand_i = gold_to_cand[token.i]
if cand_i is not None and x_tags[cand_i] is None:
x_tags[cand_i] = "O"
i2j_multi = self.alignment.i2j_multi
for i, tag in enumerate(x_tags):
if tag is None and i in i2j_multi:
gold_i = i2j_multi[i]
if gold_i is not None and self.y[gold_i].ent_iob_ == "O":
x_tags[i] = "O"
return x_tags
def to_dict(self):
return {
"doc_annotation": {
"cats": dict(self.reference.cats),
"entities": biluo_tags_from_doc(self.reference),
"links": self._links_to_dict()
},
"token_annotation": {
"ids": [t.i+1 for t in self.reference],
"words": [t.text for t in self.reference],
"tags": [t.tag_ for t in self.reference],
"lemmas": [t.lemma_ for t in self.reference],
"pos": [t.pos_ for t in self.reference],
"morphs": [t.morph_ for t in self.reference],
"heads": [t.head.i for t in self.reference],
"deps": [t.dep_ for t in self.reference],
"sent_starts": [int(bool(t.is_sent_start)) for t in self.reference]
}
}
def _links_to_dict(self):
links = {}
for ent in self.reference.ents:
if ent.kb_id_:
links[(ent.start_char, ent.end_char)] = {ent.kb_id_: 1.0}
return links
def split_sents(self):
""" Split the token annotations into multiple Examples based on
sent_starts and return a list of the new Examples"""
if not self.reference.is_sentenced:
return [self]
sent_starts = self.get_aligned("SENT_START")
sent_starts.append(1) # appending virtual start of a next sentence to facilitate search
output = []
pred_start = 0
for sent in self.reference.sents:
new_ref = sent.as_doc()
pred_end = sent_starts.index(1, pred_start+1) # find where the next sentence starts
new_pred = self.predicted[pred_start : pred_end].as_doc()
output.append(Example(new_pred, new_ref))
pred_start = pred_end
return output
property text:
def __get__(self):
return self.x.text
def __str__(self):
return str(self.to_dict())
def __repr__(self):
return str(self.to_dict())
def _annot2array(vocab, tok_annot, doc_annot):
attrs = []
values = []
for key, value in doc_annot.items():
if value:
if key == "entities":
pass
elif key == "links":
entities = doc_annot.get("entities", {})
if not entities:
raise ValueError(Errors.E981)
ent_kb_ids = _parse_links(vocab, tok_annot["ORTH"], value, entities)
tok_annot["ENT_KB_ID"] = ent_kb_ids
elif key == "cats":
pass
else:
raise ValueError(f"Unknown doc attribute: {key}")
for key, value in tok_annot.items():
if key not in IDS:
raise ValueError(f"Unknown token attribute: {key}")
elif key in ["ORTH", "SPACY"]:
pass
elif key == "HEAD":
attrs.append(key)
values.append([h-i for i, h in enumerate(value)])
elif key == "SENT_START":
attrs.append(key)
values.append(value)
elif key == "MORPH":
attrs.append(key)
values.append([vocab.morphology.add(v) for v in value])
else:
attrs.append(key)
values.append([vocab.strings.add(v) for v in value])
array = numpy.asarray(values, dtype="uint64")
return attrs, array.T
def _add_entities_to_doc(doc, ner_data):
if ner_data is None:
return
elif ner_data == []:
doc.ents = []
elif isinstance(ner_data[0], tuple):
return _add_entities_to_doc(
doc,
biluo_tags_from_offsets(doc, ner_data)
)
elif isinstance(ner_data[0], str) or ner_data[0] is None:
return _add_entities_to_doc(
doc,
spans_from_biluo_tags(doc, ner_data)
)
elif isinstance(ner_data[0], Span):
# Ugh, this is super messy. Really hard to set O entities
doc.ents = ner_data
doc.ents = [span for span in ner_data if span.label_]
else:
raise ValueError("Unexpected type for NER data")
def _parse_example_dict_data(example_dict):
return (
example_dict["token_annotation"],
example_dict["doc_annotation"]
)
def _fix_legacy_dict_data(example_dict):
token_dict = example_dict.get("token_annotation", {})
doc_dict = example_dict.get("doc_annotation", {})
for key, value in example_dict.items():
if value:
if key in ("token_annotation", "doc_annotation"):
pass
elif key == "ids":
pass
elif key in ("cats", "links"):
doc_dict[key] = value
elif key in ("ner", "entities"):
doc_dict["entities"] = value
else:
token_dict[key] = value
# Remap keys
remapping = {
"words": "ORTH",
"tags": "TAG",
"pos": "POS",
"lemmas": "LEMMA",
"deps": "DEP",
"heads": "HEAD",
"sent_starts": "SENT_START",
"morphs": "MORPH",
"spaces": "SPACY",
}
old_token_dict = token_dict
token_dict = {}
for key, value in old_token_dict.items():
if key in ("text", "ids", "brackets"):
pass
elif key in remapping:
token_dict[remapping[key]] = value
else:
raise KeyError(Errors.E983.format(key=key, dict="token_annotation", keys=remapping.keys()))
text = example_dict.get("text", example_dict.get("raw"))
if "HEAD" in token_dict and "SENT_START" in token_dict:
# If heads are set, we don't also redundantly specify SENT_START.
token_dict.pop("SENT_START")
warnings.warn("Ignoring annotations for sentence starts, as dependency heads are set")
return {
"token_annotation": token_dict,
"doc_annotation": doc_dict
}
def _has_field(annot, field):
if field not in annot:
return False
elif annot[field] is None:
return False
elif len(annot[field]) == 0:
return False
elif all([value is None for value in annot[field]]):
return False
else:
return True
def _parse_ner_tags(biluo_or_offsets, vocab, words, spaces):
if isinstance(biluo_or_offsets[0], (list, tuple)):
# Convert to biluo if necessary
# This is annoying but to convert the offsets we need a Doc
# that has the target tokenization.
reference = Doc(vocab, words=words, spaces=spaces)
biluo = biluo_tags_from_offsets(reference, biluo_or_offsets)
else:
biluo = biluo_or_offsets
ent_iobs = []
ent_types = []
for iob_tag in biluo_to_iob(biluo):
if iob_tag in (None, "-"):
ent_iobs.append("")
ent_types.append("")
else:
ent_iobs.append(iob_tag.split("-")[0])
if iob_tag.startswith("I") or iob_tag.startswith("B"):
ent_types.append(iob_tag.split("-", 1)[1])
else:
ent_types.append("")
return ent_iobs, ent_types
def _parse_links(vocab, words, links, entities):
reference = Doc(vocab, words=words)
starts = {token.idx: token.i for token in reference}
ends = {token.idx + len(token): token.i for token in reference}
ent_kb_ids = ["" for _ in reference]
entity_map = [(ent[0], ent[1]) for ent in entities]
# links annotations need to refer 1-1 to entity annotations - throw error otherwise
for index, annot_dict in links.items():
start_char, end_char = index
if (start_char, end_char) not in entity_map:
raise ValueError(Errors.E981)
for index, annot_dict in links.items():
true_kb_ids = []
for key, value in annot_dict.items():
if value == 1.0:
true_kb_ids.append(key)
if len(true_kb_ids) > 1:
raise ValueError(Errors.E980)
if len(true_kb_ids) == 1:
start_char, end_char = index
start_token = starts.get(start_char)
end_token = ends.get(end_char)
for i in range(start_token, end_token+1):
ent_kb_ids[i] = true_kb_ids[0]
return ent_kb_ids
def _guess_spaces(text, words):
if text is None:
return [True] * len(words)
spaces = []
text_pos = 0
# align words with text
for word in words:
try:
word_start = text[text_pos:].index(word)
except ValueError:
spaces.append(True)
continue
text_pos += word_start + len(word)
if text_pos < len(text) and text[text_pos] == " ":
spaces.append(True)
else:
spaces.append(False)
return spaces

199
spacy/gold/gold_io.pyx Normal file
View File

@ -0,0 +1,199 @@
import warnings
import srsly
from .. import util
from ..errors import Warnings
from ..tokens import Doc
from .iob_utils import biluo_tags_from_offsets, tags_to_entities
import json
def docs_to_json(docs, doc_id=0, ner_missing_tag="O"):
"""Convert a list of Doc objects into the JSON-serializable format used by
the spacy train command.
docs (iterable / Doc): The Doc object(s) to convert.
doc_id (int): Id for the JSON.
RETURNS (dict): The data in spaCy's JSON format
- each input doc will be treated as a paragraph in the output doc
"""
if isinstance(docs, Doc):
docs = [docs]
json_doc = {"id": doc_id, "paragraphs": []}
for i, doc in enumerate(docs):
json_para = {'raw': doc.text, "sentences": [], "cats": [], "entities": [], "links": []}
for cat, val in doc.cats.items():
json_cat = {"label": cat, "value": val}
json_para["cats"].append(json_cat)
for ent in doc.ents:
ent_tuple = (ent.start_char, ent.end_char, ent.label_)
json_para["entities"].append(ent_tuple)
if ent.kb_id_:
link_dict = {(ent.start_char, ent.end_char): {ent.kb_id_: 1.0}}
json_para["links"].append(link_dict)
ent_offsets = [(e.start_char, e.end_char, e.label_) for e in doc.ents]
biluo_tags = biluo_tags_from_offsets(doc, ent_offsets, missing=ner_missing_tag)
for j, sent in enumerate(doc.sents):
json_sent = {"tokens": [], "brackets": []}
for token in sent:
json_token = {"id": token.i, "orth": token.text, "space": token.whitespace_}
if doc.is_tagged:
json_token["tag"] = token.tag_
json_token["pos"] = token.pos_
json_token["morph"] = token.morph_
json_token["lemma"] = token.lemma_
if doc.is_parsed:
json_token["head"] = token.head.i-token.i
json_token["dep"] = token.dep_
json_sent["tokens"].append(json_token)
json_para["sentences"].append(json_sent)
json_doc["paragraphs"].append(json_para)
return json_doc
def read_json_file(loc, docs_filter=None, limit=None):
"""Read Example dictionaries from a json file or directory."""
loc = util.ensure_path(loc)
if loc.is_dir():
for filename in loc.iterdir():
yield from read_json_file(loc / filename, limit=limit)
else:
with loc.open("rb") as file_:
utf8_str = file_.read()
for json_doc in json_iterate(utf8_str):
if docs_filter is not None and not docs_filter(json_doc):
continue
for json_paragraph in json_to_annotations(json_doc):
yield json_paragraph
def json_to_annotations(doc):
"""Convert an item in the JSON-formatted training data to the format
used by Example.
doc (dict): One entry in the training data.
YIELDS (tuple): The reformatted data - one training example per paragraph
"""
for paragraph in doc["paragraphs"]:
example = {"text": paragraph.get("raw", None)}
words = []
spaces = []
ids = []
tags = []
ner_tags = []
pos = []
morphs = []
lemmas = []
heads = []
labels = []
sent_starts = []
brackets = []
for sent in paragraph["sentences"]:
sent_start_i = len(words)
for i, token in enumerate(sent["tokens"]):
words.append(token["orth"])
spaces.append(token.get("space", None))
ids.append(token.get('id', sent_start_i + i))
tags.append(token.get("tag", None))
pos.append(token.get("pos", None))
morphs.append(token.get("morph", None))
lemmas.append(token.get("lemma", None))
if "head" in token:
heads.append(token["head"] + sent_start_i + i)
else:
heads.append(None)
if "dep" in token:
labels.append(token["dep"])
# Ensure ROOT label is case-insensitive
if labels[-1].lower() == "root":
labels[-1] = "ROOT"
else:
labels.append(None)
ner_tags.append(token.get("ner", None))
if i == 0:
sent_starts.append(1)
else:
sent_starts.append(0)
if "brackets" in sent:
brackets.extend((b["first"] + sent_start_i,
b["last"] + sent_start_i, b["label"])
for b in sent["brackets"])
example["token_annotation"] = dict(
ids=ids,
words=words,
spaces=spaces,
sent_starts=sent_starts,
brackets=brackets
)
# avoid including dummy values that looks like gold info was present
if any(tags):
example["token_annotation"]["tags"] = tags
if any(pos):
example["token_annotation"]["pos"] = pos
if any(morphs):
example["token_annotation"]["morphs"] = morphs
if any(lemmas):
example["token_annotation"]["lemmas"] = lemmas
if any(head is not None for head in heads):
example["token_annotation"]["heads"] = heads
if any(labels):
example["token_annotation"]["deps"] = labels
cats = {}
for cat in paragraph.get("cats", {}):
cats[cat["label"]] = cat["value"]
example["doc_annotation"] = dict(
cats=cats,
entities=ner_tags,
links=paragraph.get("links", []) # TODO: fix/test
)
yield example
def json_iterate(bytes utf8_str):
# We should've made these files jsonl...But since we didn't, parse out
# the docs one-by-one to reduce memory usage.
# It's okay to read in the whole file -- just don't parse it into JSON.
cdef long file_length = len(utf8_str)
if file_length > 2 ** 30:
warnings.warn(Warnings.W027.format(size=file_length))
raw = <char*>utf8_str
cdef int square_depth = 0
cdef int curly_depth = 0
cdef int inside_string = 0
cdef int escape = 0
cdef long start = -1
cdef char c
cdef char quote = ord('"')
cdef char backslash = ord("\\")
cdef char open_square = ord("[")
cdef char close_square = ord("]")
cdef char open_curly = ord("{")
cdef char close_curly = ord("}")
for i in range(file_length):
c = raw[i]
if escape:
escape = False
continue
if c == backslash:
escape = True
continue
if c == quote:
inside_string = not inside_string
continue
if inside_string:
continue
if c == open_square:
square_depth += 1
elif c == close_square:
square_depth -= 1
elif c == open_curly:
if square_depth == 1 and curly_depth == 0:
start = i
curly_depth += 1
elif c == close_curly:
curly_depth -= 1
if square_depth == 1 and curly_depth == 0:
substr = utf8_str[start : i + 1].decode("utf8")
yield srsly.json_loads(substr)
start = -1

209
spacy/gold/iob_utils.py Normal file
View File

@ -0,0 +1,209 @@
import warnings
from ..errors import Errors, Warnings
from ..tokens import Span
def iob_to_biluo(tags):
out = []
tags = list(tags)
while tags:
out.extend(_consume_os(tags))
out.extend(_consume_ent(tags))
return out
def biluo_to_iob(tags):
out = []
for tag in tags:
if tag is None:
out.append(tag)
else:
tag = tag.replace("U-", "B-", 1).replace("L-", "I-", 1)
out.append(tag)
return out
def _consume_os(tags):
while tags and tags[0] == "O":
yield tags.pop(0)
def _consume_ent(tags):
if not tags:
return []
tag = tags.pop(0)
target_in = "I" + tag[1:]
target_last = "L" + tag[1:]
length = 1
while tags and tags[0] in {target_in, target_last}:
length += 1
tags.pop(0)
label = tag[2:]
if length == 1:
if len(label) == 0:
raise ValueError(Errors.E177.format(tag=tag))
return ["U-" + label]
else:
start = "B-" + label
end = "L-" + label
middle = [f"I-{label}" for _ in range(1, length - 1)]
return [start] + middle + [end]
def biluo_tags_from_doc(doc, missing="O"):
return biluo_tags_from_offsets(
doc,
[(ent.start_char, ent.end_char, ent.label_) for ent in doc.ents],
missing=missing,
)
def biluo_tags_from_offsets(doc, entities, missing="O"):
"""Encode labelled spans into per-token tags, using the
Begin/In/Last/Unit/Out scheme (BILUO).
doc (Doc): The document that the entity offsets refer to. The output tags
will refer to the token boundaries within the document.
entities (iterable): A sequence of `(start, end, label)` triples. `start`
and `end` should be character-offset integers denoting the slice into
the original string.
RETURNS (list): A list of unicode strings, describing the tags. Each tag
string will be of the form either "", "O" or "{action}-{label}", where
action is one of "B", "I", "L", "U". The string "-" is used where the
entity offsets don't align with the tokenization in the `Doc` object.
The training algorithm will view these as missing values. "O" denotes a
non-entity token. "B" denotes the beginning of a multi-token entity,
"I" the inside of an entity of three or more tokens, and "L" the end
of an entity of two or more tokens. "U" denotes a single-token entity.
EXAMPLE:
>>> text = 'I like London.'
>>> entities = [(len('I like '), len('I like London'), 'LOC')]
>>> doc = nlp.tokenizer(text)
>>> tags = biluo_tags_from_offsets(doc, entities)
>>> assert tags == ["O", "O", 'U-LOC', "O"]
"""
# Ensure no overlapping entity labels exist
tokens_in_ents = {}
starts = {token.idx: token.i for token in doc}
ends = {token.idx + len(token): token.i for token in doc}
biluo = ["-" for _ in doc]
# Handle entity cases
for start_char, end_char, label in entities:
if not label:
for s in starts: # account for many-to-one
if s >= start_char and s < end_char:
biluo[starts[s]] = "O"
else:
for token_index in range(start_char, end_char):
if token_index in tokens_in_ents.keys():
raise ValueError(
Errors.E103.format(
span1=(
tokens_in_ents[token_index][0],
tokens_in_ents[token_index][1],
tokens_in_ents[token_index][2],
),
span2=(start_char, end_char, label),
)
)
tokens_in_ents[token_index] = (start_char, end_char, label)
start_token = starts.get(start_char)
end_token = ends.get(end_char)
# Only interested if the tokenization is correct
if start_token is not None and end_token is not None:
if start_token == end_token:
biluo[start_token] = f"U-{label}"
else:
biluo[start_token] = f"B-{label}"
for i in range(start_token + 1, end_token):
biluo[i] = f"I-{label}"
biluo[end_token] = f"L-{label}"
# Now distinguish the O cases from ones where we miss the tokenization
entity_chars = set()
for start_char, end_char, label in entities:
for i in range(start_char, end_char):
entity_chars.add(i)
for token in doc:
for i in range(token.idx, token.idx + len(token)):
if i in entity_chars:
break
else:
biluo[token.i] = missing
if "-" in biluo and missing != "-":
ent_str = str(entities)
warnings.warn(
Warnings.W030.format(
text=doc.text[:50] + "..." if len(doc.text) > 50 else doc.text,
entities=ent_str[:50] + "..." if len(ent_str) > 50 else ent_str,
)
)
return biluo
def spans_from_biluo_tags(doc, tags):
"""Encode per-token tags following the BILUO scheme into Span object, e.g.
to overwrite the doc.ents.
doc (Doc): The document that the BILUO tags refer to.
entities (iterable): A sequence of BILUO tags with each tag describing one
token. Each tags string will be of the form of either "", "O" or
"{action}-{label}", where action is one of "B", "I", "L", "U".
RETURNS (list): A sequence of Span objects.
"""
token_offsets = tags_to_entities(tags)
spans = []
for label, start_idx, end_idx in token_offsets:
span = Span(doc, start_idx, end_idx + 1, label=label)
spans.append(span)
return spans
def offsets_from_biluo_tags(doc, tags):
"""Encode per-token tags following the BILUO scheme into entity offsets.
doc (Doc): The document that the BILUO tags refer to.
entities (iterable): A sequence of BILUO tags with each tag describing one
token. Each tags string will be of the form of either "", "O" or
"{action}-{label}", where action is one of "B", "I", "L", "U".
RETURNS (list): A sequence of `(start, end, label)` triples. `start` and
`end` will be character-offset integers denoting the slice into the
original string.
"""
spans = spans_from_biluo_tags(doc, tags)
return [(span.start_char, span.end_char, span.label_) for span in spans]
def tags_to_entities(tags):
""" Note that the end index returned by this function is inclusive.
To use it for Span creation, increment the end by 1."""
entities = []
start = None
for i, tag in enumerate(tags):
if tag is None:
continue
if tag.startswith("O"):
# TODO: We shouldn't be getting these malformed inputs. Fix this.
if start is not None:
start = None
else:
entities.append(("", i, i))
continue
elif tag == "-":
continue
elif tag.startswith("I"):
if start is None:
raise ValueError(Errors.E067.format(tags=tags[: i + 1]))
continue
if tag.startswith("U"):
entities.append((tag[2:], i, i))
elif tag.startswith("B"):
start = i
elif tag.startswith("L"):
entities.append((tag[2:], start, i))
start = None
else:
raise ValueError(Errors.E068.format(tag=tag))
return entities

57
spacy/language.py
View File

@ -529,6 +529,22 @@ class Language(object):
def make_doc(self, text):
return self.tokenizer(text)
def _convert_examples(self, examples):
converted_examples = []
if isinstance(examples, tuple):
examples = [examples]
for eg in examples:
if isinstance(eg, Example):
converted_examples.append(eg.copy())
elif isinstance(eg, tuple):
doc, annot = eg
if isinstance(doc, str):
doc = self.make_doc(doc)
converted_examples.append(Example.from_dict(doc, annot))
else:
raise ValueError(Errors.E979.format(type=type(eg)))
return converted_examples
def update(
self,
examples,
@ -556,7 +572,7 @@ class Language(object):
if len(examples) == 0:
return
examples = Example.to_example_objects(examples, make_doc=self.make_doc)
examples = self._convert_examples(examples)
if sgd is None:
if self._optimizer is None:
@ -604,7 +620,7 @@ class Language(object):
# TODO: document
if len(examples) == 0:
return
examples = Example.to_example_objects(examples, make_doc=self.make_doc)
examples = self._convert_examples(examples)
if sgd is None:
if self._optimizer is None:
self._optimizer = create_default_optimizer()
@ -632,19 +648,6 @@ class Language(object):
sgd(W, dW, key=key)
return losses
def preprocess_gold(self, examples):
"""Can be called before training to pre-process gold data. By default,
it handles nonprojectivity and adds missing tags to the tag map.
examples (iterable): `Example` objects.
YIELDS (tuple): `Example` objects.
"""
for name, proc in self.pipeline:
if hasattr(proc, "preprocess_gold"):
examples = proc.preprocess_gold(examples)
for ex in examples:
yield ex
def begin_training(self, get_examples=None, sgd=None, component_cfg=None, **cfg):
"""Allocate models, pre-process training data and acquire a trainer and
optimizer. Used as a contextmanager.
@ -662,7 +665,7 @@ class Language(object):
# Populate vocab
else:
for example in get_examples():
for word in example.token_annotation.words:
for word in [t.text for t in example.reference]:
_ = self.vocab[word] # noqa: F841
if cfg.get("device", -1) >= 0:
@ -725,24 +728,26 @@ class Language(object):
DOCS: https://spacy.io/api/language#evaluate
"""
examples = Example.to_example_objects(examples, make_doc=self.make_doc)
examples = self._convert_examples(examples)
if scorer is None:
scorer = Scorer(pipeline=self.pipeline)
if component_cfg is None:
component_cfg = {}
docs = list(eg.predicted for eg in examples)
for name, pipe in self.pipeline:
kwargs = component_cfg.get(name, {})
kwargs.setdefault("batch_size", batch_size)
if not hasattr(pipe, "pipe"):
examples = _pipe(examples, pipe, kwargs)
docs = _pipe(docs, pipe, kwargs)
else:
examples = pipe.pipe(examples, as_example=True, **kwargs)
for ex in examples:
docs = pipe.pipe(docs, **kwargs)
for i, (doc, eg) in enumerate(zip(docs, examples)):
if verbose:
print(ex.doc)
print(doc)
eg.predicted = doc
kwargs = component_cfg.get("scorer", {})
kwargs.setdefault("verbose", verbose)
scorer.score(ex, **kwargs)
scorer.score(eg, **kwargs)
return scorer
@contextmanager
@ -787,7 +792,6 @@ class Language(object):
cleanup=False,
component_cfg=None,
n_process=1,
as_example=False,
):
"""Process texts as a stream, and yield `Doc` objects in order.
@ -821,7 +825,6 @@ class Language(object):
disable=disable,
n_process=n_process,
component_cfg=component_cfg,
as_example=as_example,
)
for doc, context in zip(docs, contexts):
yield (doc, context)
@ -1210,9 +1213,9 @@ def _pipe(examples, proc, kwargs):
for arg in ["n_threads", "batch_size"]:
if arg in kwargs:
kwargs.pop(arg)
for ex in examples:
ex = proc(ex, **kwargs)
yield ex
for eg in examples:
eg = proc(eg, **kwargs)
yield eg
def _apply_pipes(make_doc, pipes, receiver, sender, underscore_state):

3
spacy/ml/_biluo.py
View File

@ -80,13 +80,12 @@ def _get_transition_table(
B_start, B_end = (0, n_labels)
I_start, I_end = (B_end, B_end + n_labels)
L_start, L_end = (I_end, I_end + n_labels)
U_start, U_end = (L_end, L_end + n_labels)
U_start, _ = (L_end, L_end + n_labels)
# Using ranges allows us to set specific cells, which is necessary to express
# that only actions of the same label are valid continuations.
B_range = numpy.arange(B_start, B_end)
I_range = numpy.arange(I_start, I_end)
L_range = numpy.arange(L_start, L_end)
O_action = U_end
# If this is the last token and the previous action was B or I, only L
# of that label is valid
table[1, B_range, L_range] = 1

6
spacy/ml/_precomputable_affine.py
View File

@ -48,8 +48,7 @@ def forward(model, X, is_train):
model.inc_grad("b", dY.sum(axis=0))
dY = dY.reshape((dY.shape[0], nO * nP))
Wopfi = W.transpose((1, 2, 0, 3))
Wopfi = model.ops.xp.ascontiguousarray(Wopfi)
Wopfi = model.ops.as_contig(W.transpose((1, 2, 0, 3)))
Wopfi = Wopfi.reshape((nO * nP, nF * nI))
dXf = model.ops.gemm(dY.reshape((dY.shape[0], nO * nP)), Wopfi)
@ -59,7 +58,8 @@ def forward(model, X, is_train):
model.ops.gemm(dY, Xf, out=dWopfi, trans1=True)
dWopfi = dWopfi.reshape((nO, nP, nF, nI))
# (o, p, f, i) --> (f, o, p, i)
model.inc_grad("W", dWopfi.transpose((2, 0, 1, 3)))
dWopfi = model.ops.as_contig(dWopfi.transpose((2, 0, 1, 3)))
model.inc_grad("W", dWopfi)
return dXf.reshape((dXf.shape[0], nF, nI))
return Yf, backward

4
spacy/ml/models/multi_task.py
View File

@ -48,9 +48,7 @@ def build_masked_language_model(vocab, wrapped_model, mask_prob=0.15):
def mlm_forward(model, docs, is_train):
mask, docs = _apply_mask(docs, random_words, mask_prob=mask_prob)
mask = model.ops.asarray(mask).reshape((mask.shape[0], 1))
output, backprop = model.get_ref("wrapped-model").begin_update(
docs
) # drop=drop
output, backprop = model.get_ref("wrapped-model").begin_update(docs)
def mlm_backward(d_output):
d_output *= 1 - mask

7
spacy/ml/models/parser.py
View File

@ -1,5 +1,6 @@
from pydantic import StrictInt
from thinc.api import Model, chain, list2array, Linear, zero_init, use_ops, with_array
from thinc.api import LayerNorm, Maxout, Mish
from ...util import registry
from .._precomputable_affine import PrecomputableAffine
@ -16,7 +17,11 @@ def build_tb_parser_model(
nO=None,
):
t2v_width = tok2vec.get_dim("nO") if tok2vec.has_dim("nO") else None
tok2vec = chain(tok2vec, with_array(Linear(hidden_width, t2v_width)), list2array(),)
tok2vec = chain(
tok2vec,
list2array(),
Linear(hidden_width, t2v_width),
)
tok2vec.set_dim("nO", hidden_width)
lower = PrecomputableAffine(

32
spacy/ml/models/textcat.py
View File

@ -1,8 +1,30 @@
from thinc.api import Model, reduce_mean, Linear, list2ragged, Logistic
from thinc.api import ParametricAttention, chain, concatenate, clone, Dropout
from thinc.api import SparseLinear, Softmax, softmax_activation, Maxout
from thinc.api import reduce_sum, Relu, residual, expand_window, HashEmbed
from thinc.api import with_ragged, with_array, with_cpu, uniqued, FeatureExtractor
from thinc.api import (
Model,
reduce_mean,
Linear,
list2ragged,
Logistic,
ParametricAttention,
)
from thinc.api import chain, concatenate, clone, Dropout
from thinc.api import (
SparseLinear,
Softmax,
softmax_activation,
Maxout,
reduce_sum,
Relu,
residual,
expand_window,
)
from thinc.api import (
HashEmbed,
with_ragged,
with_array,
with_cpu,
uniqued,
FeatureExtractor,
)
from ..spacy_vectors import SpacyVectors
from ... import util

2
spacy/ml/models/tok2vec.py
View File

@ -147,7 +147,7 @@ def hash_char_embed_bilstm_v1(
@registry.architectures.register("spacy.LayerNormalizedMaxout.v1")
def LayerNormalizedMaxout(width, maxout_pieces):
return Maxout(nO=width, nP=maxout_pieces, dropout=0.0, normalize=True,)
return Maxout(nO=width, nP=maxout_pieces, dropout=0.0, normalize=True)
@registry.architectures.register("spacy.MultiHashEmbed.v1")

5
spacy/ml/tb_framework.py
View File

@ -38,8 +38,9 @@ def forward(model, X, is_train):
def init(model, X=None, Y=None):
tok2vec = model.get_ref("tok2vec").initialize(X=X)
lower = model.get_ref("lower").initialize()
model.get_ref("tok2vec").initialize(X=X)
lower = model.get_ref("lower")
lower.initialize()
if model.attrs["has_upper"]:
statevecs = model.ops.alloc2f(2, lower.get_dim("nO"))
model.get_ref("upper").initialize(X=statevecs)

19
spacy/pipeline/morphologizer.pyx
View File

@ -51,9 +51,9 @@ class Morphologizer(Tagger):
def begin_training(self, get_examples=lambda: [], pipeline=None, sgd=None,
**kwargs):
for example in get_examples():
for i, morph in enumerate(example.token_annotation.morphs):
pos = example.token_annotation.get_pos(i)
morph = Morphology.feats_to_dict(morph)
for i, token in enumerate(example.reference):
pos = token.pos_
morph = token.morph
norm_morph = self.vocab.strings[self.vocab.morphology.add(morph)]
if pos:
morph["POS"] = pos
@ -91,11 +91,12 @@ class Morphologizer(Tagger):
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 i in range(len(gold.morphs)):
pos = gold.pos[i] if i < len(gold.pos) else ""
morph = gold.morphs[i]
for eg in examples:
pos_tags = eg.get_aligned("POS", as_string=True)
morphs = eg.get_aligned("MORPH", as_string=True)
for i in range(len(morphs)):
pos = pos_tags[i]
morph = morphs[i]
feats = Morphology.feats_to_dict(morph)
if pos:
feats["POS"] = pos
@ -115,7 +116,7 @@ class Morphologizer(Tagger):
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]
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

410
spacy/pipeline/pipes.pyx
View File

@ -2,7 +2,6 @@
import numpy
import srsly
import random
from ast import literal_eval
from thinc.api import CosineDistance, to_categorical, get_array_module
from thinc.api import set_dropout_rate, SequenceCategoricalCrossentropy
@ -20,7 +19,7 @@ from .defaults import default_nel, default_senter
from .functions import merge_subtokens
from ..language import Language, component
from ..syntax import nonproj
from ..gold import Example
from ..gold.example import Example
from ..attrs import POS, ID
from ..util import link_vectors_to_models, create_default_optimizer
from ..parts_of_speech import X
@ -48,56 +47,39 @@ class Pipe(object):
def from_nlp(cls, nlp, model, **cfg):
return cls(nlp.vocab, model, **cfg)
def _get_doc(self, example):
""" Use this method if the `example` can be both a Doc or an Example """
if isinstance(example, Doc):
return example
return example.doc
def __init__(self, vocab, model, **cfg):
"""Create a new pipe instance."""
raise NotImplementedError
def __call__(self, example):
def __call__(self, Doc doc):
"""Apply the pipe to one document. The document is
modified in-place, and returned.
Both __call__ and pipe should delegate to the `predict()`
and `set_annotations()` methods.
"""
doc = self._get_doc(example)
predictions = self.predict([doc])
if isinstance(predictions, tuple) and len(predictions) == 2:
scores, tensors = predictions
self.set_annotations([doc], scores, tensors=tensors)
else:
self.set_annotations([doc], predictions)
if isinstance(example, Example):
example.doc = doc
return example
return doc
def pipe(self, stream, batch_size=128, n_threads=-1, as_example=False):
def pipe(self, stream, batch_size=128, n_threads=-1):
"""Apply the pipe to a stream of documents.
Both __call__ and pipe should delegate to the `predict()`
and `set_annotations()` methods.
"""
for examples in util.minibatch(stream, size=batch_size):
docs = [self._get_doc(ex) for ex in examples]
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)
if as_example:
for ex, doc in zip(examples, docs):
ex.doc = doc
yield ex
else:
yield from docs
yield from docs
def predict(self, docs):
"""Apply the pipeline's model to a batch of docs, without
@ -109,16 +91,6 @@ class Pipe(object):
"""Modify a batch of documents, using pre-computed scores."""
raise NotImplementedError
def update(self, examples, set_annotations=False, drop=0.0, sgd=None, losses=None):
"""Learn from a batch of documents and gold-standard information,
updating the pipe's model.
Delegates to predict() and get_loss().
"""
if set_annotations:
docs = (self._get_doc(ex) for ex in examples)
docs = list(self.pipe(docs))
def rehearse(self, examples, sgd=None, losses=None, **config):
pass
@ -255,29 +227,16 @@ class Tagger(Pipe):
def labels(self):
return tuple(self.vocab.morphology.tag_names)
def __call__(self, example):
doc = self._get_doc(example)
def __call__(self, doc):
tags = self.predict([doc])
self.set_annotations([doc], tags)
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]
def pipe(self, stream, batch_size=128, n_threads=-1):
for docs in util.minibatch(stream, size=batch_size):
tag_ids = self.predict(docs)
assert len(docs) == len(examples)
assert len(tag_ids) == len(examples)
self.set_annotations(docs, tag_ids)
if as_example:
for ex, doc in zip(examples, docs):
ex.doc = doc
yield ex
else:
yield from docs
yield from docs
def predict(self, docs):
if not any(len(doc) for doc in docs):
@ -327,15 +286,19 @@ class Tagger(Pipe):
doc.is_tagged = True
def update(self, examples, drop=0., sgd=None, losses=None, set_annotations=False):
examples = Example.to_example_objects(examples)
if losses is not None and self.name not in losses:
losses[self.name] = 0.
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
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="Tagger", method="update", types=types))
set_dropout_rate(self.model, drop)
tag_scores, bp_tag_scores = self.model.begin_update([ex.doc for ex in examples])
tag_scores, bp_tag_scores = self.model.begin_update(
[eg.predicted for eg in examples])
for sc in tag_scores:
if self.model.ops.xp.isnan(sc.sum()):
raise ValueError("nan value in scores")
@ -347,17 +310,20 @@ class Tagger(Pipe):
if losses is not None:
losses[self.name] += loss
if set_annotations:
docs = [ex.doc for ex in examples]
docs = [eg.predicted for eg in examples]
self.set_annotations(docs, self._scores2guesses(tag_scores))
def rehearse(self, examples, drop=0., sgd=None, losses=None):
"""Perform a 'rehearsal' update, where we try to match the output of
an initial model.
"""
try:
docs = [eg.predicted for eg in examples]
except AttributeError:
types = set([type(eg) for eg in examples])
raise ValueError(Errors.E978.format(name="Tagger", method="rehearse", types=types))
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
@ -373,7 +339,7 @@ class Tagger(Pipe):
def get_loss(self, examples, scores):
loss_func = SequenceCategoricalCrossentropy(names=self.labels)
truths = [eg.gold.tags for eg in examples]
truths = [eg.get_aligned("tag", as_string=True) for eg in examples]
d_scores, loss = loss_func(scores, truths)
if self.model.ops.xp.isnan(loss):
raise ValueError("nan value when computing loss")
@ -389,7 +355,12 @@ class Tagger(Pipe):
orig_tag_map = dict(self.vocab.morphology.tag_map)
new_tag_map = {}
for example in get_examples():
for tag in example.token_annotation.tags:
try:
y = example.y
except AttributeError:
raise ValueError(Errors.E978.format(name="Tagger", method="begin_training", types=type(example)))
for token in y:
tag = token.tag_
if tag in orig_tag_map:
new_tag_map[tag] = orig_tag_map[tag]
else:
@ -564,9 +535,9 @@ class SentenceRecognizer(Tagger):
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:
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:
@ -579,7 +550,7 @@ class SentenceRecognizer(Tagger):
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]
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
@ -690,8 +661,8 @@ class MultitaskObjective(Tagger):
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)
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()
@ -709,13 +680,13 @@ class MultitaskObjective(Tagger):
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)
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:
@ -727,83 +698,49 @@ class MultitaskObjective(Tagger):
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]
def make_dep(token):
return token.dep_
@staticmethod
def make_tag(i, token_annotation):
return token_annotation.tags[i]
def make_tag(token):
return token.tag_
@staticmethod
def make_ent(i, token_annotation):
if token_annotation.entities is None:
return None
return token_annotation.entities[i]
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(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
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"{token_annotation.deps[i]}-{token_annotation.tags[i]}:{offset}"
return f"{dep}-{tag}:{offset}"
@staticmethod
def make_ent_tag(i, token_annotation):
if token_annotation.entities is None or token_annotation.entities[i] is None:
return None
def make_ent_tag(token):
if token.ent_iob_ == "O":
ent = "O"
else:
return f"{token_annotation.tags[i]}-{token_annotation.entities[i]}"
ent = token.ent_iob_ + "-" + token.ent_type_
tag = token.tag_
return f"{tag}-{ent}"
@staticmethod
def make_sent_start(target, token_annotation, cache=True, _cache={}):
def make_sent_start(token):
"""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
if token.is_sent_start and token.is_sent_end:
return "U-SENT"
elif token.is_sent_start:
return "B-SENT"
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]
return "I-SENT"
class ClozeMultitask(Pipe):
@ -836,7 +773,7 @@ class ClozeMultitask(Pipe):
# 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])
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)
@ -846,11 +783,14 @@ class ClozeMultitask(Pipe):
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])
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:
@ -885,18 +825,11 @@ class TextCategorizer(Pipe):
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]
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)
if as_example:
for ex, doc in zip(examples, docs):
ex.doc = doc
yield ex
else:
yield from docs
yield from docs
def predict(self, docs):
tensors = [doc.tensor for doc in docs]
@ -917,12 +850,17 @@ class TextCategorizer(Pipe):
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
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([ex.doc for ex in examples])
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:
@ -931,14 +869,17 @@ class TextCategorizer(Pipe):
losses.setdefault(self.name, 0.0)
losses[self.name] += loss
if set_annotations:
docs = [ex.doc for ex in examples]
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
examples = Example.to_example_objects(examples)
docs=[ex.doc for ex in examples]
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
@ -954,13 +895,12 @@ class TextCategorizer(Pipe):
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):
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 gold_cat:
truths[i, j] = gold_cat[label]
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)
@ -997,7 +937,11 @@ class TextCategorizer(Pipe):
# 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:
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"])]
@ -1156,65 +1100,52 @@ class EntityLinker(Pipe):
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]
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)
golds = [ex.gold for ex in examples]
for doc, gold in zip(docs, golds):
ents_by_offset = dict()
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)
sentences = [s for s in doc.sents]
# get n posterior sentences, or as many < n as there are
end_sentence = min(len(sentences) -1, sent_index + self.n_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)
# 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, golds=golds)
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)
@ -1224,15 +1155,15 @@ class EntityLinker(Pipe):
self.set_annotations(docs, predictions)
return loss
def get_similarity_loss(self, golds, scores):
def get_similarity_loss(self, examples, 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)
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")
@ -1246,10 +1177,12 @@ class EntityLinker(Pipe):
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])
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):
@ -1260,27 +1193,16 @@ class EntityLinker(Pipe):
loss = loss / len(cats)
return loss, d_scores
def __call__(self, example):
doc = self._get_doc(example)
def __call__(self, doc):
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]
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)
if as_example:
for ex, doc in zip(examples, docs):
ex.doc = doc
yield ex
else:
yield from docs
yield from docs
def predict(self, docs):
""" Return the KB IDs for each entity in each doc, including NIL if there is no prediction """
@ -1466,7 +1388,7 @@ class Sentencizer(Pipe):
):
pass
def __call__(self, example):
def __call__(self, doc):
"""Apply the sentencizer to a Doc and set Token.is_sent_start.
example (Doc or Example): The document to process.
@ -1474,7 +1396,6 @@ class Sentencizer(Pipe):
DOCS: https://spacy.io/api/sentencizer#call
"""
doc = self._get_doc(example)
start = 0
seen_period = False
for i, token in enumerate(doc):
@ -1488,26 +1409,17 @@ class Sentencizer(Pipe):
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]
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)
if as_example:
for ex, doc in zip(examples, docs):
ex.doc = doc
yield ex
else:
yield from docs
yield from docs
def predict(self, docs):
"""Apply the pipeline's model to a batch of docs, without

8
spacy/pipeline/simple_ner.py
View File

@ -70,8 +70,7 @@ class SimpleNER(Pipe):
def update(self, examples, set_annotations=False, drop=0.0, sgd=None, losses=None):
if not any(_has_ner(eg) for eg in examples):
return 0
examples = Example.to_example_objects(examples)
docs = [ex.doc for ex in examples]
docs = [eg.doc for eg in examples]
set_dropout_rate(self.model, drop)
scores, bp_scores = self.model.begin_update(docs)
loss, d_scores = self.get_loss(examples, scores)
@ -140,8 +139,7 @@ def _has_ner(eg):
def _get_labels(examples):
labels = set()
for eg in examples:
for ner_tag in eg.token_annotation.entities:
for ner_tag in eg.get_aligned("ENT_TYPE", as_string=True):
if ner_tag != "O" and ner_tag != "-":
_, label = ner_tag.split("-", 1)
labels.add(label)
labels.add(ner_tag)
return list(sorted(labels))

17
spacy/pipeline/tok2vec.py
View File

@ -5,7 +5,7 @@ from ..gold import Example
from ..tokens import Doc
from ..vocab import Vocab
from ..language import component
from ..util import link_vectors_to_models, minibatch, eg2doc
from ..util import link_vectors_to_models, minibatch
from .defaults import default_tok2vec
@ -51,22 +51,18 @@ class Tok2Vec(Pipe):
self.set_annotations([doc], tokvecses)
return doc
def pipe(self, stream, batch_size=128, n_threads=-1, as_example=False):
def pipe(self, stream, batch_size=128, n_threads=-1):
"""Process `Doc` objects as a stream.
stream (iterator): A sequence of `Doc` objects to process.
batch_size (int): Number of `Doc` objects to group.
n_threads (int): Number of threads.
YIELDS (iterator): A sequence of `Doc` objects, in order of input.
"""
for batch in minibatch(stream, batch_size):
batch = list(batch)
if as_example:
docs = [eg2doc(doc) for doc in batch]
else:
docs = batch
for docs in minibatch(stream, batch_size):
docs = list(docs)
tokvecses = self.predict(docs)
self.set_annotations(docs, tokvecses)
yield from batch
yield from docs
def predict(self, docs):
"""Return a single tensor for a batch of documents.
@ -97,8 +93,7 @@ class Tok2Vec(Pipe):
"""
if losses is None:
losses = {}
examples = Example.to_example_objects(examples)
docs = [eg.doc for eg in examples]
docs = [eg.predicted for eg in examples]
if isinstance(docs, Doc):
docs = [docs]
set_dropout_rate(self.model, drop)

118
spacy/scorer.py
View File

@ -1,6 +1,5 @@
import numpy as np
from .gold import tags_to_entities, GoldParse, DocAnnotation
from .errors import Errors
@ -275,7 +274,7 @@ class Scorer(object):
}
def score(self, example, verbose=False, punct_labels=("p", "punct")):
"""Update the evaluation scores from a single Doc / GoldParse pair.
"""Update the evaluation scores from a single Example.
example (Example): The predicted annotations + correct annotations.
verbose (bool): Print debugging information.
@ -285,17 +284,9 @@ class Scorer(object):
DOCS: https://spacy.io/api/scorer#score
"""
if isinstance(example, tuple) and len(example) == 2:
doc, gold = example
else:
gold = example.gold
doc = example.doc
if len(doc) != len(gold):
doc_annotation = DocAnnotation(cats=gold.cats)
token_annotation = gold.orig
gold = GoldParse.from_annotation(doc, doc_annotation, token_annotation)
orig = gold.orig
doc = example.predicted
gold_doc = example.reference
align = example.alignment
gold_deps = set()
gold_deps_per_dep = {}
gold_tags = set()
@ -303,36 +294,28 @@ class Scorer(object):
gold_morphs = set()
gold_morphs_per_feat = {}
gold_sent_starts = set()
gold_ents = set(tags_to_entities(orig.entities))
for id_, tag, pos, morph, head, dep, sent_start in zip(
orig.ids,
orig.tags,
orig.pos,
orig.morphs,
orig.heads,
orig.deps,
orig.sent_starts,
):
gold_tags.add((id_, tag))
gold_pos.add((id_, pos))
gold_morphs.add((id_, morph))
if morph:
for feat in morph.split("|"):
for gold_i, token in enumerate(gold_doc):
gold_tags.add((gold_i, token.tag_))
gold_pos.add((gold_i, token.pos_))
gold_morphs.add((gold_i, token.morph_))
if token.morph_:
for feat in token.morph_.split("|"):
field, values = feat.split("=")
if field not in self.morphs_per_feat:
self.morphs_per_feat[field] = PRFScore()
if field not in gold_morphs_per_feat:
gold_morphs_per_feat[field] = set()
gold_morphs_per_feat[field].add((id_, feat))
if sent_start:
gold_sent_starts.add(id_)
if dep not in (None, "") and dep.lower() not in punct_labels:
gold_deps.add((id_, head, dep.lower()))
if dep.lower() not in self.labelled_per_dep:
self.labelled_per_dep[dep.lower()] = PRFScore()
if dep.lower() not in gold_deps_per_dep:
gold_deps_per_dep[dep.lower()] = set()
gold_deps_per_dep[dep.lower()].add((id_, head, dep.lower()))
gold_morphs_per_feat[field].add((gold_i, feat))
if token.sent_start:
gold_sent_starts.add(gold_i)
dep = token.dep_.lower()
if dep not in punct_labels:
gold_deps.add((gold_i, token.head.i, dep))
if dep not in self.labelled_per_dep:
self.labelled_per_dep[dep] = PRFScore()
if dep not in gold_deps_per_dep:
gold_deps_per_dep[dep] = set()
gold_deps_per_dep[dep].add((gold_i, token.head.i, dep))
cand_deps = set()
cand_deps_per_dep = {}
cand_tags = set()
@ -343,7 +326,7 @@ class Scorer(object):
for token in doc:
if token.orth_.isspace():
continue
gold_i = gold.cand_to_gold[token.i]
gold_i = align.cand_to_gold[token.i]
if gold_i is None:
self.tokens.fp += 1
else:
@ -362,7 +345,7 @@ class Scorer(object):
if token.is_sent_start:
cand_sent_starts.add(gold_i)
if token.dep_.lower() not in punct_labels and token.orth_.strip():
gold_head = gold.cand_to_gold[token.head.i]
gold_head = align.cand_to_gold[token.head.i]
# None is indistinct, so we can't just add it to the set
# Multiple (None, None) deps are possible
if gold_i is None or gold_head is None:
@ -377,23 +360,30 @@ class Scorer(object):
cand_deps_per_dep[token.dep_.lower()].add(
(gold_i, gold_head, token.dep_.lower())
)
if "-" not in [token[-1] for token in orig.entities]:
# Find all NER labels in gold and doc
ent_labels = set([x[0] for x in gold_ents] + [k.label_ for k in doc.ents])
# Set up all labels for per type scoring and prepare gold per type
gold_per_ents = {ent_label: set() for ent_label in ent_labels}
for ent_label in ent_labels:
if ent_label not in self.ner_per_ents:
self.ner_per_ents[ent_label] = PRFScore()
gold_per_ents[ent_label].update(
[x for x in gold_ents if x[0] == ent_label]
)
# Find all candidate labels, for all and per type
cand_ents = set()
# Find all NER labels in gold and doc
ent_labels = set(
[k.label_ for k in gold_doc.ents] + [k.label_ for k in doc.ents]
)
# Set up all labels for per type scoring and prepare gold per type
gold_per_ents = {ent_label: set() for ent_label in ent_labels}
for ent_label in ent_labels:
if ent_label not in self.ner_per_ents:
self.ner_per_ents[ent_label] = PRFScore()
# Find all candidate labels, for all and per type
gold_ents = set()
cand_ents = set()
# If we have missing values in the gold, we can't easily tell whether
# our NER predictions are true.
# It seems bad but it's what we've always done.
if all(token.ent_iob != 0 for token in gold_doc):
for ent in gold_doc.ents:
gold_ent = (ent.label_, ent.start, ent.end - 1)
gold_ents.add(gold_ent)
gold_per_ents[ent.label_].add((ent.label_, ent.start, ent.end - 1))
cand_per_ents = {ent_label: set() for ent_label in ent_labels}
for ent in doc.ents:
first = gold.cand_to_gold[ent.start]
last = gold.cand_to_gold[ent.end - 1]
first = align.cand_to_gold[ent.start]
last = align.cand_to_gold[ent.end - 1]
if first is None or last is None:
self.ner.fp += 1
self.ner_per_ents[ent.label_].fp += 1
@ -424,40 +414,40 @@ class Scorer(object):
set(item[:2] for item in cand_deps), set(item[:2] for item in gold_deps)
)
if (
len(gold.cats) > 0
len(gold_doc.cats) > 0
and set(self.textcat_f_per_cat)
== set(self.textcat_auc_per_cat)
== set(gold.cats)
and set(gold.cats) == set(doc.cats)
== set(gold_doc.cats)
and set(gold_doc.cats) == set(doc.cats)
):
goldcat = max(gold.cats, key=gold.cats.get)
goldcat = max(gold_doc.cats, key=gold_doc.cats.get)
candcat = max(doc.cats, key=doc.cats.get)
if self.textcat_positive_label:
self.textcat.score_set(
set([self.textcat_positive_label]) & set([candcat]),
set([self.textcat_positive_label]) & set([goldcat]),
)
for label in set(gold.cats):
for label in set(gold_doc.cats):
self.textcat_auc_per_cat[label].score_set(
doc.cats[label], gold.cats[label]
doc.cats[label], gold_doc.cats[label]
)
self.textcat_f_per_cat[label].score_set(
set([label]) & set([candcat]), set([label]) & set([goldcat])
)
elif len(self.textcat_f_per_cat) > 0:
model_labels = set(self.textcat_f_per_cat)
eval_labels = set(gold.cats)
eval_labels = set(gold_doc.cats)
raise ValueError(
Errors.E162.format(model_labels=model_labels, eval_labels=eval_labels)
)
elif len(self.textcat_auc_per_cat) > 0:
model_labels = set(self.textcat_auc_per_cat)
eval_labels = set(gold.cats)
eval_labels = set(gold_doc.cats)
raise ValueError(
Errors.E162.format(model_labels=model_labels, eval_labels=eval_labels)
)
if verbose:
gold_words = orig.words
gold_words = gold_doc.words
for w_id, h_id, dep in cand_deps - gold_deps:
print("F", gold_words[w_id], dep, gold_words[h_id])
for w_id, h_id, dep in gold_deps - cand_deps:

9
spacy/syntax/_beam_utils.pxd
View File

@ -1,9 +0,0 @@
from ..typedefs cimport hash_t, class_t
# These are passed as callbacks to thinc.search.Beam
cdef int transition_state(void* _dest, void* _src, class_t clas, void* _moves) except -1
cdef int check_final_state(void* _state, void* extra_args) except -1
cdef hash_t hash_state(void* _state, void* _) except 0

329
spacy/syntax/_beam_utils.pyx
View File

@ -1,329 +0,0 @@
# cython: infer_types=True, profile=True
cimport numpy as np
from cpython.ref cimport PyObject, Py_XDECREF
from thinc.extra.search cimport Beam
from thinc.extra.search cimport MaxViolation
from thinc.extra.search import MaxViolation
import numpy
from ..typedefs cimport hash_t, class_t
from .transition_system cimport TransitionSystem, Transition
from ..gold cimport GoldParse
from .stateclass cimport StateC, StateClass
from ..errors import Errors
# These are passed as callbacks to thinc.search.Beam
cdef int transition_state(void* _dest, void* _src, class_t clas, void* _moves) except -1:
dest = <StateC*>_dest
src = <StateC*>_src
moves = <const Transition*>_moves
dest.clone(src)
moves[clas].do(dest, moves[clas].label)
dest.push_hist(clas)
cdef int check_final_state(void* _state, void* extra_args) except -1:
state = <StateC*>_state
return state.is_final()
cdef hash_t hash_state(void* _state, void* _) except 0:
state = <StateC*>_state
if state.is_final():
return 1
else:
return state.hash()
def collect_states(beams):
cdef StateClass state
cdef Beam beam
states = []
for state_or_beam in beams:
if isinstance(state_or_beam, StateClass):
states.append(state_or_beam)
else:
beam = state_or_beam
state = StateClass.borrow(<StateC*>beam.at(0))
states.append(state)
return states
cdef class ParserBeam(object):
cdef public TransitionSystem moves
cdef public object states
cdef public object golds
cdef public object beams
cdef public object dones
def __init__(self, TransitionSystem moves, states, golds,
int width, float density=0.):
self.moves = moves
self.states = states
self.golds = golds
self.beams = []
cdef Beam beam
cdef StateClass state
cdef StateC* st
for state in states:
beam = Beam(self.moves.n_moves, width, min_density=density)
beam.initialize(self.moves.init_beam_state,
self.moves.del_beam_state, state.c.length,
state.c._sent)
for i in range(beam.width):
st = <StateC*>beam.at(i)
st.offset = state.c.offset
self.beams.append(beam)
self.dones = [False] * len(self.beams)
@property
def is_done(self):
return all(b.is_done or self.dones[i]
for i, b in enumerate(self.beams))
def __getitem__(self, i):
return self.beams[i]
def __len__(self):
return len(self.beams)
def advance(self, scores, follow_gold=False):
cdef Beam beam
for i, beam in enumerate(self.beams):
if beam.is_done or not scores[i].size or self.dones[i]:
continue
self._set_scores(beam, scores[i])
if self.golds is not None:
self._set_costs(beam, self.golds[i], follow_gold=follow_gold)
beam.advance(transition_state, hash_state, <void*>self.moves.c)
beam.check_done(check_final_state, NULL)
# This handles the non-monotonic stuff for the parser.
if beam.is_done and self.golds is not None:
for j in range(beam.size):
state = StateClass.borrow(<StateC*>beam.at(j))
if state.is_final():
try:
if self.moves.is_gold_parse(state, self.golds[i]):
beam._states[j].loss = 0.0
except NotImplementedError:
break
def _set_scores(self, Beam beam, float[:, ::1] scores):
cdef float* c_scores = &scores[0, 0]
cdef int nr_state = min(scores.shape[0], beam.size)
cdef int nr_class = scores.shape[1]
for i in range(nr_state):
state = <StateC*>beam.at(i)
if not state.is_final():
for j in range(nr_class):
beam.scores[i][j] = c_scores[i * nr_class + j]
self.moves.set_valid(beam.is_valid[i], state)
else:
for j in range(beam.nr_class):
beam.scores[i][j] = 0
beam.costs[i][j] = 0
def _set_costs(self, Beam beam, GoldParse gold, int follow_gold=False):
for i in range(beam.size):
state = StateClass.borrow(<StateC*>beam.at(i))
if not state.is_final():
self.moves.set_costs(beam.is_valid[i], beam.costs[i],
state, gold)
if follow_gold:
min_cost = 0
for j in range(beam.nr_class):
if beam.is_valid[i][j] and beam.costs[i][j] < min_cost:
min_cost = beam.costs[i][j]
for j in range(beam.nr_class):
if beam.costs[i][j] > min_cost:
beam.is_valid[i][j] = 0
def get_token_ids(states, int n_tokens):
cdef StateClass state
cdef np.ndarray ids = numpy.zeros((len(states), n_tokens),
dtype='int32', order='C')
c_ids = <int*>ids.data
for i, state in enumerate(states):
if not state.is_final():
state.c.set_context_tokens(c_ids, n_tokens)
else:
ids[i] = -1
c_ids += ids.shape[1]
return ids
nr_update = 0
def update_beam(TransitionSystem moves, int nr_feature, int max_steps,
states, golds,
state2vec, vec2scores,
int width, losses=None, drop=0.,
early_update=True, beam_density=0.0):
global nr_update
cdef MaxViolation violn
nr_update += 1
pbeam = ParserBeam(moves, states, golds, width=width, density=beam_density)
gbeam = ParserBeam(moves, states, golds, width=width, density=beam_density)
cdef StateClass state
beam_maps = []
backprops = []
violns = [MaxViolation() for _ in range(len(states))]
for t in range(max_steps):
if pbeam.is_done and gbeam.is_done:
break
# The beam maps let us find the right row in the flattened scores
# arrays for each state. States are identified by (example id,
# history). We keep a different beam map for each step (since we'll
# have a flat scores array for each step). The beam map will let us
# take the per-state losses, and compute the gradient for each (step,
# state, class).
beam_maps.append({})
# Gather all states from the two beams in a list. Some stats may occur
# in both beams. To figure out which beam each state belonged to,
# we keep two lists of indices, p_indices and g_indices
states, p_indices, g_indices = get_states(pbeam, gbeam, beam_maps[-1],
nr_update)
if not states:
break
# Now that we have our flat list of states, feed them through the model
token_ids = get_token_ids(states, nr_feature)
vectors, bp_vectors = state2vec.begin_update(token_ids, drop=drop)
scores, bp_scores = vec2scores.begin_update(vectors, drop=drop)
# Store the callbacks for the backward pass
backprops.append((token_ids, bp_vectors, bp_scores))
# Unpack the flat scores into lists for the two beams. The indices arrays
# tell us which example and state the scores-row refers to.
p_scores = [numpy.ascontiguousarray(scores[indices], dtype='f')
for indices in p_indices]
g_scores = [numpy.ascontiguousarray(scores[indices], dtype='f')
for indices in g_indices]
# Now advance the states in the beams. The gold beam is constrained to
# to follow only gold analyses.
pbeam.advance(p_scores)
gbeam.advance(g_scores, follow_gold=True)
# Track the "maximum violation", to use in the update.
for i, violn in enumerate(violns):
violn.check_crf(pbeam[i], gbeam[i])
histories = []
losses = []
for violn in violns:
if violn.p_hist:
histories.append(violn.p_hist + violn.g_hist)
losses.append(violn.p_probs + violn.g_probs)
else:
histories.append([])
losses.append([])
states_d_scores = get_gradient(moves.n_moves, beam_maps, histories, losses)
beams = list(pbeam.beams) + list(gbeam.beams)
return states_d_scores, backprops[:len(states_d_scores)], beams
def get_states(pbeams, gbeams, beam_map, nr_update):
seen = {}
states = []
p_indices = []
g_indices = []
cdef Beam pbeam, gbeam
if len(pbeams) != len(gbeams):
raise ValueError(Errors.E079.format(pbeams=len(pbeams), gbeams=len(gbeams)))
for eg_id, (pbeam, gbeam) in enumerate(zip(pbeams, gbeams)):
p_indices.append([])
g_indices.append([])
for i in range(pbeam.size):
state = StateClass.borrow(<StateC*>pbeam.at(i))
if not state.is_final():
key = tuple([eg_id] + pbeam.histories[i])
if key in seen:
raise ValueError(Errors.E080.format(key=key))
seen[key] = len(states)
p_indices[-1].append(len(states))
states.append(state)
beam_map.update(seen)
for i in range(gbeam.size):
state = StateClass.borrow(<StateC*>gbeam.at(i))
if not state.is_final():
key = tuple([eg_id] + gbeam.histories[i])
if key in seen:
g_indices[-1].append(seen[key])
else:
g_indices[-1].append(len(states))
beam_map[key] = len(states)
states.append(state)
p_idx = [numpy.asarray(idx, dtype='i') for idx in p_indices]
g_idx = [numpy.asarray(idx, dtype='i') for idx in g_indices]
return states, p_idx, g_idx
def get_gradient(nr_class, beam_maps, histories, losses):
"""The global model assigns a loss to each parse. The beam scores
are additive, so the same gradient is applied to each action
in the history. This gives the gradient of a single *action*
for a beam state -- so we have "the gradient of loss for taking
action i given history H."
Histories: Each hitory is a list of actions
Each candidate has a history
Each beam has multiple candidates
Each batch has multiple beams
So history is list of lists of lists of ints
"""
grads = []
nr_steps = []
for eg_id, hists in enumerate(histories):
nr_step = 0
for loss, hist in zip(losses[eg_id], hists):
if loss != 0.0 and not numpy.isnan(loss):
nr_step = max(nr_step, len(hist))
nr_steps.append(nr_step)
for i in range(max(nr_steps)):
grads.append(numpy.zeros((max(beam_maps[i].values())+1, nr_class),
dtype='f'))
if len(histories) != len(losses):
raise ValueError(Errors.E081.format(n_hist=len(histories), losses=len(losses)))
for eg_id, hists in enumerate(histories):
for loss, hist in zip(losses[eg_id], hists):
if loss == 0.0 or numpy.isnan(loss):
continue
key = tuple([eg_id])
# Adjust loss for length
# We need to do this because each state in a short path is scored
# multiple times, as we add in the average cost when we run out
# of actions.
avg_loss = loss / len(hist)
loss += avg_loss * (nr_steps[eg_id] - len(hist))
for j, clas in enumerate(hist):
i = beam_maps[j][key]
# In step j, at state i action clas
# resulted in loss
grads[j][i, clas] += loss
key = key + tuple([clas])
return grads
def cleanup_beam(Beam beam):
cdef StateC* state
# Once parsing has finished, states in beam may not be unique. Is this
# correct?
seen = set()
for i in range(beam.width):
addr = <size_t>beam._parents[i].content
if addr not in seen:
state = <StateC*>addr
del state
seen.add(addr)
else:
raise ValueError(Errors.E023.format(addr=addr, i=i))
addr = <size_t>beam._states[i].content
if addr not in seen:
state = <StateC*>addr
del state
seen.add(addr)
else:
raise ValueError(Errors.E023.format(addr=addr, i=i))

5
spacy/syntax/_parser_model.pyx
View File

@ -16,7 +16,6 @@ from thinc.api import Linear, Model, CupyOps, NumpyOps, use_ops, noop
from ..typedefs cimport weight_t, class_t, hash_t
from ..tokens.doc cimport Doc
from ..gold cimport GoldParse
from .stateclass cimport StateClass
from .transition_system cimport Transition
@ -24,7 +23,6 @@ from ..compat import copy_array
from ..errors import Errors, TempErrors
from ..util import link_vectors_to_models, create_default_optimizer
from .. import util
from . import _beam_utils
from . import nonproj
@ -261,8 +259,7 @@ class ParserStepModel(Model):
def mark_class_seen(self, class_):
self._class_mask[class_] = 1
def get_token_ids(self, batch):
states = _beam_utils.collect_states(batch)
def get_token_ids(self, states):
cdef StateClass state
states = [state for state in states if not state.is_final()]
cdef np.ndarray ids = numpy.zeros((len(states), self.state2vec.nF),

5
spacy/syntax/arc_eager.pxd
View File

@ -3,12 +3,11 @@ from cymem.cymem cimport Pool
from .stateclass cimport StateClass
from ..typedefs cimport weight_t, attr_t
from .transition_system cimport TransitionSystem, Transition
from ..gold cimport GoldParseC
cdef class ArcEager(TransitionSystem):
pass
cdef weight_t push_cost(StateClass stcls, const GoldParseC* gold, int target) nogil
cdef weight_t arc_cost(StateClass stcls, const GoldParseC* gold, int head, int child) nogil
cdef weight_t push_cost(StateClass stcls, const void* _gold, int target) nogil
cdef weight_t arc_cost(StateClass stcls, const void* _gold, int head, int child) nogil

642
spacy/syntax/arc_eager.pyx
View File

@ -1,19 +1,19 @@
# cython: profile=True, cdivision=True, infer_types=True
from cpython.ref cimport Py_INCREF
from cymem.cymem cimport Pool
from thinc.extra.search cimport Beam
from cymem.cymem cimport Pool, Address
from libc.stdint cimport int32_t
from collections import defaultdict, Counter
import json
from ..typedefs cimport hash_t, attr_t
from ..strings cimport hash_string
from ..gold cimport GoldParse, GoldParseC
from ..structs cimport TokenC
from ..tokens.doc cimport Doc, set_children_from_heads
from .stateclass cimport StateClass
from ._state cimport StateC
from .transition_system cimport move_cost_func_t, label_cost_func_t
from ..gold.example cimport Example
from ..errors import Errors
from .nonproj import is_nonproj_tree
@ -49,53 +49,232 @@ MOVE_NAMES[RIGHT] = 'R'
MOVE_NAMES[BREAK] = 'B'
cdef enum:
HEAD_IN_STACK = 0
HEAD_IN_BUFFER
HEAD_UNKNOWN
IS_SENT_START
SENT_START_UNKNOWN
cdef struct GoldParseStateC:
char* state_bits
int32_t* n_kids_in_buffer
int32_t* n_kids_in_stack
int32_t* heads
attr_t* labels
int32_t** kids
int32_t* n_kids
int32_t length
int32_t stride
cdef GoldParseStateC create_gold_state(Pool mem, StateClass stcls,
heads, labels, sent_starts) except *:
cdef GoldParseStateC gs
gs.length = len(heads)
gs.stride = 1
gs.labels = <attr_t*>mem.alloc(gs.length, sizeof(gs.labels[0]))
gs.heads = <int32_t*>mem.alloc(gs.length, sizeof(gs.heads[0]))
gs.n_kids = <int32_t*>mem.alloc(gs.length, sizeof(gs.n_kids[0]))
gs.state_bits = <char*>mem.alloc(gs.length, sizeof(gs.state_bits[0]))
gs.n_kids_in_buffer = <int32_t*>mem.alloc(gs.length, sizeof(gs.n_kids_in_buffer[0]))
gs.n_kids_in_stack = <int32_t*>mem.alloc(gs.length, sizeof(gs.n_kids_in_stack[0]))
for i, is_sent_start in enumerate(sent_starts):
if is_sent_start == True:
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
IS_SENT_START,
1
)
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
SENT_START_UNKNOWN,
0
)
elif is_sent_start is None:
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
SENT_START_UNKNOWN,
1
)
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
IS_SENT_START,
0
)
else:
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
SENT_START_UNKNOWN,
0
)
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
IS_SENT_START,
0
)
for i, (head, label) in enumerate(zip(heads, labels)):
if head is not None:
gs.heads[i] = head
gs.labels[i] = label
if i != head:
gs.n_kids[head] += 1
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
HEAD_UNKNOWN,
0
)
else:
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
HEAD_UNKNOWN,
1
)
# Make an array of pointers, pointing into the gs_kids_flat array.
gs.kids = <int32_t**>mem.alloc(gs.length, sizeof(int32_t*))
for i in range(gs.length):
if gs.n_kids[i] != 0:
gs.kids[i] = <int32_t*>mem.alloc(gs.n_kids[i], sizeof(int32_t))
# This is a temporary buffer
js_addr = Address(gs.length, sizeof(int32_t))
js = <int32_t*>js_addr.ptr
for i in range(gs.length):
if not is_head_unknown(&gs, i):
head = gs.heads[i]
if head != i:
gs.kids[head][js[head]] = i
js[head] += 1
return gs
cdef void update_gold_state(GoldParseStateC* gs, StateClass stcls) nogil:
for i in range(gs.length):
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
HEAD_IN_BUFFER,
0
)
gs.state_bits[i] = set_state_flag(
gs.state_bits[i],
HEAD_IN_STACK,
0
)
gs.n_kids_in_stack[i] = 0
gs.n_kids_in_buffer[i] = 0
for i in range(stcls.stack_depth()):
s_i = stcls.S(i)
if not is_head_unknown(gs, s_i):
gs.n_kids_in_stack[gs.heads[s_i]] += 1
for kid in gs.kids[s_i][:gs.n_kids[s_i]]:
gs.state_bits[kid] = set_state_flag(
gs.state_bits[kid],
HEAD_IN_STACK,
1
)
for i in range(stcls.buffer_length()):
b_i = stcls.B(i)
if not is_head_unknown(gs, b_i):
gs.n_kids_in_buffer[gs.heads[b_i]] += 1
for kid in gs.kids[b_i][:gs.n_kids[b_i]]:
gs.state_bits[kid] = set_state_flag(
gs.state_bits[kid],
HEAD_IN_BUFFER,
1
)
cdef class ArcEagerGold:
cdef GoldParseStateC c
cdef Pool mem
def __init__(self, ArcEager moves, StateClass stcls, Example example):
self.mem = Pool()
heads, labels = example.get_aligned_parse(projectivize=True)
labels = [label if label is not None else "" for label in labels]
labels = [example.x.vocab.strings.add(label) for label in labels]
sent_starts = example.get_aligned("SENT_START")
assert len(heads) == len(labels) == len(sent_starts)
self.c = create_gold_state(self.mem, stcls, heads, labels, sent_starts)
def update(self, StateClass stcls):
update_gold_state(&self.c, stcls)
cdef int check_state_gold(char state_bits, char flag) nogil:
cdef char one = 1
return state_bits & (one << flag)
cdef int set_state_flag(char state_bits, char flag, int value) nogil:
cdef char one = 1
if value:
return state_bits | (one << flag)
else:
return state_bits & ~(one << flag)
cdef int is_head_in_stack(const GoldParseStateC* gold, int i) nogil:
return check_state_gold(gold.state_bits[i], HEAD_IN_STACK)
cdef int is_head_in_buffer(const GoldParseStateC* gold, int i) nogil:
return check_state_gold(gold.state_bits[i], HEAD_IN_BUFFER)
cdef int is_head_unknown(const GoldParseStateC* gold, int i) nogil:
return check_state_gold(gold.state_bits[i], HEAD_UNKNOWN)
cdef int is_sent_start(const GoldParseStateC* gold, int i) nogil:
return check_state_gold(gold.state_bits[i], IS_SENT_START)
cdef int is_sent_start_unknown(const GoldParseStateC* gold, int i) nogil:
return check_state_gold(gold.state_bits[i], SENT_START_UNKNOWN)
# Helper functions for the arc-eager oracle
cdef weight_t push_cost(StateClass stcls, const GoldParseC* gold, int target) nogil:
cdef weight_t push_cost(StateClass stcls, const void* _gold, int target) nogil:
gold = <const GoldParseStateC*>_gold
cdef weight_t cost = 0
cdef int i, S_i
for i in range(stcls.stack_depth()):
S_i = stcls.S(i)
if gold.heads[target] == S_i:
cost += 1
if gold.heads[S_i] == target and (NON_MONOTONIC or not stcls.has_head(S_i)):
cost += 1
if BINARY_COSTS and cost >= 1:
return cost
cost += Break.is_valid(stcls.c, 0) and Break.move_cost(stcls, gold) == 0
return cost
cdef weight_t pop_cost(StateClass stcls, const GoldParseC* gold, int target) nogil:
cdef weight_t cost = 0
cdef int i, B_i
for i in range(stcls.buffer_length()):
B_i = stcls.B(i)
cost += gold.heads[B_i] == target
cost += gold.heads[target] == B_i
if gold.heads[B_i] == B_i or gold.heads[B_i] < target:
break
if BINARY_COSTS and cost >= 1:
return cost
if is_head_in_stack(gold, target):
cost += 1
cost += gold.n_kids_in_stack[target]
if Break.is_valid(stcls.c, 0) and Break.move_cost(stcls, gold) == 0:
cost += 1
return cost
cdef weight_t arc_cost(StateClass stcls, const GoldParseC* gold, int head, int child) nogil:
cdef weight_t pop_cost(StateClass stcls, const void* _gold, int target) nogil:
gold = <const GoldParseStateC*>_gold
cdef weight_t cost = 0
if is_head_in_buffer(gold, target):
cost += 1
cost += gold[0].n_kids_in_buffer[target]
if Break.is_valid(stcls.c, 0) and Break.move_cost(stcls, gold) == 0:
cost += 1
return cost
cdef weight_t arc_cost(StateClass stcls, const void* _gold, int head, int child) nogil:
gold = <const GoldParseStateC*>_gold
if arc_is_gold(gold, head, child):
return 0
elif stcls.H(child) == gold.heads[child]:
return 1
# Head in buffer
elif gold.heads[child] >= stcls.B(0) and stcls.B(1) != 0:
elif is_head_in_buffer(gold, child):
return 1
else:
return 0
cdef bint arc_is_gold(const GoldParseC* gold, int head, int child) nogil:
if not gold.has_dep[child]:
cdef bint arc_is_gold(const GoldParseStateC* gold, int head, int child) nogil:
if is_head_unknown(gold, child):
return True
elif gold.heads[child] == head:
return True
@ -103,8 +282,8 @@ cdef bint arc_is_gold(const GoldParseC* gold, int head, int child) nogil:
return False
cdef bint label_is_gold(const GoldParseC* gold, int head, int child, attr_t label) nogil:
if not gold.has_dep[child]:
cdef bint label_is_gold(const GoldParseStateC* gold, int head, int child, attr_t label) nogil:
if is_head_unknown(gold, child):
return True
elif label == 0:
return True
@ -114,8 +293,9 @@ cdef bint label_is_gold(const GoldParseC* gold, int head, int child, attr_t labe
return False
cdef bint _is_gold_root(const GoldParseC* gold, int word) nogil:
return gold.heads[word] == word or not gold.has_dep[word]
cdef bint _is_gold_root(const GoldParseStateC* gold, int word) nogil:
return gold.heads[word] == word or is_head_unknown(gold, word)
cdef class Shift:
@staticmethod
@ -129,15 +309,17 @@ cdef class Shift:
st.fast_forward()
@staticmethod
cdef weight_t cost(StateClass st, const GoldParseC* gold, attr_t label) nogil:
cdef weight_t cost(StateClass st, const void* _gold, attr_t label) nogil:
gold = <const GoldParseStateC*>_gold
return Shift.move_cost(st, gold) + Shift.label_cost(st, gold, label)
@staticmethod
cdef inline weight_t move_cost(StateClass s, const GoldParseC* gold) nogil:
cdef inline weight_t move_cost(StateClass s, const void* _gold) nogil:
gold = <const GoldParseStateC*>_gold
return push_cost(s, gold, s.B(0))
@staticmethod
cdef inline weight_t label_cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef inline weight_t label_cost(StateClass s, const void* _gold, attr_t label) nogil:
return 0
@ -155,26 +337,28 @@ cdef class Reduce:
st.fast_forward()
@staticmethod
cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef weight_t cost(StateClass s, const void* _gold, attr_t label) nogil:
gold = <const GoldParseStateC*>_gold
return Reduce.move_cost(s, gold) + Reduce.label_cost(s, gold, label)
@staticmethod
cdef inline weight_t move_cost(StateClass st, const GoldParseC* gold) nogil:
cost = pop_cost(st, gold, st.S(0))
if not st.has_head(st.S(0)):
# Decrement cost for the arcs e save
for i in range(1, st.stack_depth()):
S_i = st.S(i)
if gold.heads[st.S(0)] == S_i:
cost -= 1
if gold.heads[S_i] == st.S(0):
cost -= 1
cdef inline weight_t move_cost(StateClass st, const void* _gold) nogil:
gold = <const GoldParseStateC*>_gold
s0 = st.S(0)
cost = pop_cost(st, gold, s0)
return_to_buffer = not st.has_head(s0)
if return_to_buffer:
# Decrement cost for the arcs we save, as we'll be putting this
# back to the buffer
if is_head_in_stack(gold, s0):
cost -= 1
cost -= gold.n_kids_in_stack[s0]
if Break.is_valid(st.c, 0) and Break.move_cost(st, gold) == 0:
cost -= 1
return cost
@staticmethod
cdef inline weight_t label_cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef inline weight_t label_cost(StateClass s, const void* gold, attr_t label) nogil:
return 0
@ -193,25 +377,28 @@ cdef class LeftArc:
st.fast_forward()
@staticmethod
cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef inline weight_t cost(StateClass s, const void* _gold, attr_t label) nogil:
gold = <const GoldParseStateC*>_gold
return LeftArc.move_cost(s, gold) + LeftArc.label_cost(s, gold, label)
@staticmethod
cdef inline weight_t move_cost(StateClass s, const GoldParseC* gold) nogil:
cdef inline weight_t move_cost(StateClass s, const GoldParseStateC* gold) nogil:
cdef weight_t cost = 0
if arc_is_gold(gold, s.B(0), s.S(0)):
s0 = s.S(0)
b0 = s.B(0)
if arc_is_gold(gold, b0, s0):
# Have a negative cost if we 'recover' from the wrong dependency
return 0 if not s.has_head(s.S(0)) else -1
return 0 if not s.has_head(s0) else -1
else:
# Account for deps we might lose between S0 and stack
if not s.has_head(s.S(0)):
for i in range(1, s.stack_depth()):
cost += gold.heads[s.S(i)] == s.S(0)
cost += gold.heads[s.S(0)] == s.S(i)
if not s.has_head(s0):
cost += gold.n_kids_in_stack[s0]
if is_head_in_buffer(gold, s0):
cost += 1
return cost + pop_cost(s, gold, s.S(0)) + arc_cost(s, gold, s.B(0), s.S(0))
@staticmethod
cdef inline weight_t label_cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef inline weight_t label_cost(StateClass s, const GoldParseStateC* gold, attr_t label) nogil:
return arc_is_gold(gold, s.B(0), s.S(0)) and not label_is_gold(gold, s.B(0), s.S(0), label)
@ -223,7 +410,7 @@ cdef class RightArc:
return 0
sent_start = st._sent[st.B_(0).l_edge].sent_start
return sent_start != 1 and st.H(st.S(0)) != st.B(0)
@staticmethod
cdef int transition(StateC* st, attr_t label) nogil:
st.add_arc(st.S(0), st.B(0), label)
@ -231,11 +418,13 @@ cdef class RightArc:
st.fast_forward()
@staticmethod
cdef inline weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef inline weight_t cost(StateClass s, const void* _gold, attr_t label) nogil:
gold = <const GoldParseStateC*>_gold
return RightArc.move_cost(s, gold) + RightArc.label_cost(s, gold, label)
@staticmethod
cdef inline weight_t move_cost(StateClass s, const GoldParseC* gold) nogil:
cdef inline weight_t move_cost(StateClass s, const void* _gold) nogil:
gold = <const GoldParseStateC*>_gold
if arc_is_gold(gold, s.S(0), s.B(0)):
return 0
elif s.c.shifted[s.B(0)]:
@ -244,7 +433,8 @@ cdef class RightArc:
return push_cost(s, gold, s.B(0)) + arc_cost(s, gold, s.S(0), s.B(0))
@staticmethod
cdef weight_t label_cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef weight_t label_cost(StateClass s, const void* _gold, attr_t label) nogil:
gold = <const GoldParseStateC*>_gold
return arc_is_gold(gold, s.S(0), s.B(0)) and not label_is_gold(gold, s.S(0), s.B(0), label)
@ -271,23 +461,22 @@ cdef class Break:
st.fast_forward()
@staticmethod
cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef weight_t cost(StateClass s, const void* _gold, attr_t label) nogil:
gold = <const GoldParseStateC*>_gold
return Break.move_cost(s, gold) + Break.label_cost(s, gold, label)
@staticmethod
cdef inline weight_t move_cost(StateClass s, const GoldParseC* gold) nogil:
cdef weight_t cost = 0
cdef int i, j, S_i, B_i
cdef inline weight_t move_cost(StateClass s, const void* _gold) nogil:
gold = <const GoldParseStateC*>_gold
cost = 0
for i in range(s.stack_depth()):
S_i = s.S(i)
for j in range(s.buffer_length()):
B_i = s.B(j)
cost += gold.heads[S_i] == B_i
cost += gold.heads[B_i] == S_i
if cost != 0:
return cost
# Check for sentence boundary --- if it's here, we can't have any deps
# between stack and buffer, so rest of action is irrelevant.
cost += gold.n_kids_in_buffer[S_i]
if is_head_in_buffer(gold, S_i):
cost += 1
# It's weird not to check the gold sentence boundaries but if we do,
# we can't account for "sunk costs", i.e. situations where we're already
# wrong.
s0_root = _get_root(s.S(0), gold)
b0_root = _get_root(s.B(0), gold)
if s0_root != b0_root or s0_root == -1 or b0_root == -1:
@ -296,14 +485,16 @@ cdef class Break:
return cost + 1
@staticmethod
cdef inline weight_t label_cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef inline weight_t label_cost(StateClass s, const void* gold, attr_t label) nogil:
return 0
cdef int _get_root(int word, const GoldParseC* gold) nogil:
while gold.heads[word] != word and gold.has_dep[word] and word >= 0:
word = gold.heads[word]
if not gold.has_dep[word]:
cdef int _get_root(int word, const GoldParseStateC* gold) nogil:
if is_head_unknown(gold, word):
return -1
while gold.heads[word] != word and word >= 0:
word = gold.heads[word]
if is_head_unknown(gold, word):
return -1
else:
return word
@ -330,8 +521,6 @@ cdef int _del_state(Pool mem, void* state, void* x) except -1:
cdef class ArcEager(TransitionSystem):
def __init__(self, *args, **kwargs):
TransitionSystem.__init__(self, *args, **kwargs)
self.init_beam_state = _init_state
self.del_beam_state = _del_state
@classmethod
def get_actions(cls, **kwargs):
@ -345,10 +534,11 @@ cdef class ArcEager(TransitionSystem):
for label in kwargs.get('right_labels', []):
actions[RIGHT][label] = 1
actions[REDUCE][label] = 1
for example in kwargs.get('gold_parses', []):
heads, labels = nonproj.projectivize(example.token_annotation.heads,
example.token_annotation.deps)
for child, head, label in zip(example.token_annotation.ids, heads, labels):
for example in kwargs.get('examples', []):
heads, labels = example.get_aligned_parse(projectivize=True)
for child, (head, label) in enumerate(zip(heads, labels)):
if head is None or label is None:
continue
if label.upper() == 'ROOT' :
label = 'ROOT'
if head == child:
@ -378,102 +568,47 @@ cdef class ArcEager(TransitionSystem):
def action_types(self):
return (SHIFT, REDUCE, LEFT, RIGHT, BREAK)
def get_cost(self, StateClass state, GoldParse gold, action):
cdef Transition t = self.lookup_transition(action)
if not t.is_valid(state.c, t.label):
return 9000
else:
return t.get_cost(state, &gold.c, t.label)
def transition(self, StateClass state, action):
cdef Transition t = self.lookup_transition(action)
t.do(state.c, t.label)
return state
def is_gold_parse(self, StateClass state, GoldParse gold):
predicted = set()
truth = set()
for i in range(gold.length):
if gold.cand_to_gold[i] is None:
continue
if state.safe_get(i).dep:
predicted.add((i, state.H(i),
self.strings[state.safe_get(i).dep]))
else:
predicted.add((i, state.H(i), 'ROOT'))
id_ = gold.orig.ids[gold.cand_to_gold[i]]
head = gold.orig.heads[gold.cand_to_gold[i]]
dep = gold.orig.deps[gold.cand_to_gold[i]]
truth.add((id_, head, dep))
return truth == predicted
def is_gold_parse(self, StateClass state, gold):
raise NotImplementedError
def has_gold(self, GoldParse gold, start=0, end=None):
end = end or len(gold.heads)
if all([tag is None for tag in gold.heads[start:end]]):
return False
else:
return True
def preprocess_gold(self, GoldParse gold):
if not self.has_gold(gold):
return None
# Figure out whether we're using subtok
use_subtok = False
for action, labels in self.labels.items():
if SUBTOK_LABEL in labels:
use_subtok = True
break
for i, (head, dep) in enumerate(zip(gold.heads, gold.labels)):
# Missing values
if head is None or dep is None:
gold.c.heads[i] = i
gold.c.has_dep[i] = False
elif dep == SUBTOK_LABEL and not use_subtok:
# If we're not doing the joint tokenization and parsing,
# regard these subtok labels as missing
gold.c.heads[i] = i
gold.c.labels[i] = 0
gold.c.has_dep[i] = False
else:
if head > i:
action = LEFT
elif head < i:
action = RIGHT
else:
action = BREAK
if dep not in self.labels[action]:
if action == BREAK:
dep = 'ROOT'
elif nonproj.is_decorated(dep):
backoff = nonproj.decompose(dep)[0]
if backoff in self.labels[action]:
dep = backoff
else:
dep = 'dep'
else:
dep = 'dep'
gold.c.has_dep[i] = True
if dep.upper() == 'ROOT':
dep = 'ROOT'
gold.c.heads[i] = head
gold.c.labels[i] = self.strings.add(dep)
def init_gold(self, StateClass state, Example example):
gold = ArcEagerGold(self, state, example)
self._replace_unseen_labels(gold)
return gold
def get_beam_parses(self, Beam beam):
parses = []
probs = beam.probs
for i in range(beam.size):
state = <StateC*>beam.at(i)
if state.is_final():
self.finalize_state(state)
prob = probs[i]
parse = []
for j in range(state.length):
head = state.H(j)
label = self.strings[state._sent[j].dep]
parse.append((head, j, label))
parses.append((prob, parse))
return parses
def init_gold_batch(self, examples):
all_states = self.init_batch([eg.predicted for eg in examples])
golds = []
states = []
for state, eg in zip(all_states, examples):
if self.has_gold(eg) and not state.is_final():
golds.append(self.init_gold(state, eg))
states.append(state)
n_steps = sum([len(s.queue) for s in states])
return states, golds, n_steps
def _replace_unseen_labels(self, ArcEagerGold gold):
backoff_label = self.strings["dep"]
root_label = self.strings["ROOT"]
left_labels = self.labels[LEFT]
right_labels = self.labels[RIGHT]
break_labels = self.labels[BREAK]
for i in range(gold.c.length):
if not is_head_unknown(&gold.c, i):
head = gold.c.heads[i]
label = self.strings[gold.c.labels[i]]
if head > i and label not in left_labels:
gold.c.labels[i] = backoff_label
elif head < i and label not in right_labels:
gold.c.labels[i] = backoff_label
elif head == i and label not in break_labels:
gold.c.labels[i] = root_label
return gold
cdef Transition lookup_transition(self, object name_or_id) except *:
if isinstance(name_or_id, int):
@ -489,7 +624,7 @@ cdef class ArcEager(TransitionSystem):
for i in range(self.n_moves):
if self.c[i].move == move and self.c[i].label == label:
return self.c[i]
return Transition(clas=0, move=MISSING, label=0)
raise KeyError(f"Unknown transition: {name}")
def move_name(self, int move, attr_t label):
label_str = self.strings[label]
@ -554,6 +689,13 @@ cdef class ArcEager(TransitionSystem):
doc.is_parsed = True
set_children_from_heads(doc.c, doc.length)
def has_gold(self, Example eg, start=0, end=None):
for word in eg.y[start:end]:
if word.dep != 0:
return True
else:
return False
cdef int set_valid(self, int* output, const StateC* st) nogil:
cdef bint[N_MOVES] is_valid
is_valid[SHIFT] = Shift.is_valid(st, 0)
@ -567,68 +709,110 @@ cdef class ArcEager(TransitionSystem):
output[i] = self.c[i].is_valid(st, self.c[i].label)
else:
output[i] = is_valid[self.c[i].move]
def get_cost(self, StateClass stcls, gold, int i):
if not isinstance(gold, ArcEagerGold):
raise TypeError("Expected ArcEagerGold")
cdef ArcEagerGold gold_ = gold
gold_state = gold_.c
n_gold = 0
if self.c[i].is_valid(stcls.c, self.c[i].label):
cost = self.c[i].get_cost(stcls, &gold_state, self.c[i].label)
else:
cost = 9000
return cost
cdef int set_costs(self, int* is_valid, weight_t* costs,
StateClass stcls, GoldParse gold) except -1:
cdef int i, move
cdef attr_t label
cdef label_cost_func_t[N_MOVES] label_cost_funcs
cdef move_cost_func_t[N_MOVES] move_cost_funcs
cdef weight_t[N_MOVES] move_costs
for i in range(N_MOVES):
move_costs[i] = 9000
move_cost_funcs[SHIFT] = Shift.move_cost
move_cost_funcs[REDUCE] = Reduce.move_cost
move_cost_funcs[LEFT] = LeftArc.move_cost
move_cost_funcs[RIGHT] = RightArc.move_cost
move_cost_funcs[BREAK] = Break.move_cost
label_cost_funcs[SHIFT] = Shift.label_cost
label_cost_funcs[REDUCE] = Reduce.label_cost
label_cost_funcs[LEFT] = LeftArc.label_cost
label_cost_funcs[RIGHT] = RightArc.label_cost
label_cost_funcs[BREAK] = Break.label_cost
cdef attr_t* labels = gold.c.labels
cdef int* heads = gold.c.heads
StateClass stcls, gold) except -1:
if not isinstance(gold, ArcEagerGold):
raise TypeError("Expected ArcEagerGold")
cdef ArcEagerGold gold_ = gold
gold_.update(stcls)
gold_state = gold_.c
n_gold = 0
for i in range(self.n_moves):
if self.c[i].is_valid(stcls.c, self.c[i].label):
is_valid[i] = True
move = self.c[i].move
label = self.c[i].label
if move_costs[move] == 9000:
move_costs[move] = move_cost_funcs[move](stcls, &gold.c)
costs[i] = move_costs[move] + label_cost_funcs[move](stcls, &gold.c, label)
costs[i] = self.c[i].get_cost(stcls, &gold_state, self.c[i].label)
n_gold += costs[i] <= 0
else:
is_valid[i] = False
costs[i] = 9000
if n_gold < 1:
# Check projectivity --- leading cause
if is_nonproj_tree(gold.heads):
raise ValueError(Errors.E020)
else:
failure_state = stcls.print_state(gold.words)
raise ValueError(Errors.E021.format(n_actions=self.n_moves,
state=failure_state))
raise ValueError
def get_beam_annot(self, Beam beam):
length = (<StateC*>beam.at(0)).length
heads = [{} for _ in range(length)]
deps = [{} for _ in range(length)]
probs = beam.probs
for i in range(beam.size):
state = <StateC*>beam.at(i)
self.finalize_state(state)
if state.is_final():
prob = probs[i]
for j in range(state.length):
head = j + state._sent[j].head
dep = state._sent[j].dep
heads[j].setdefault(head, 0.0)
heads[j][head] += prob
deps[j].setdefault(dep, 0.0)
deps[j][dep] += prob
return heads, deps
def get_oracle_sequence(self, Example example):
cdef StateClass state
cdef ArcEagerGold gold
states, golds, n_steps = self.init_gold_batch([example])
if not golds:
return []
cdef Pool mem = Pool()
# n_moves should not be zero at this point, but make sure to avoid zero-length mem alloc
assert self.n_moves > 0
costs = <float*>mem.alloc(self.n_moves, sizeof(float))
is_valid = <int*>mem.alloc(self.n_moves, sizeof(int))
state = states[0]
gold = golds[0]
history = []
debug_log = []
failed = False
while not state.is_final():
try:
self.set_costs(is_valid, costs, state, gold)
except ValueError:
failed = True
break
for i in range(self.n_moves):
if is_valid[i] and costs[i] <= 0:
action = self.c[i]
history.append(i)
s0 = state.S(0)
b0 = state.B(0)
debug_log.append(" ".join((
self.get_class_name(i),
"S0=", (example.x[s0].text if s0 >= 0 else "__"),
"B0=", (example.x[b0].text if b0 >= 0 else "__"),
"S0 head?", str(state.has_head(state.S(0))),
)))
action.do(state.c, action.label)
break
else:
failed = False
break
if failed:
print("Actions")
for i in range(self.n_moves):
print(self.get_class_name(i))
print("Gold")
for token in example.y:
print(token.i, token.text, token.dep_, token.head.text)
aligned_heads, aligned_labels = example.get_aligned_parse()
print("Aligned heads")
for i, head in enumerate(aligned_heads):
print(example.x[i], example.x[head] if head is not None else "__")
print("Predicted tokens")
print([(w.i, w.text) for w in example.x])
s0 = state.S(0)
b0 = state.B(0)
debug_log.append(" ".join((
"?",
"S0=", (example.x[s0].text if s0 >= 0 else "-"),
"B0=", (example.x[b0].text if b0 >= 0 else "-"),
"S0 head?", str(state.has_head(state.S(0))),
)))
s0 = state.S(0)
b0 = state.B(0)
print("\n".join(debug_log))
print("Arc is gold B0, S0?", arc_is_gold(&gold.c, b0, s0))
print("Arc is gold S0, B0?", arc_is_gold(&gold.c, s0, b0))
print("is_head_unknown(s0)", is_head_unknown(&gold.c, s0))
print("is_head_unknown(b0)", is_head_unknown(&gold.c, b0))
print("b0", b0, "gold.heads[s0]", gold.c.heads[s0])
print("Stack", [example.x[i] for i in state.stack])
print("Buffer", [example.x[i] for i in state.queue])
raise ValueError(Errors.E024)
return history

1
spacy/syntax/ner.pxd
View File

@ -1,6 +1,5 @@
from .transition_system cimport TransitionSystem
from .transition_system cimport Transition
from ..gold cimport GoldParseC
from ..typedefs cimport attr_t

168
spacy/syntax/ner.pyx
View File

@ -1,15 +1,16 @@
from thinc.extra.search cimport Beam
from collections import Counter
from libc.stdint cimport int32_t
from cymem.cymem cimport Pool
from ..typedefs cimport weight_t
from .stateclass cimport StateClass
from ._state cimport StateC
from .transition_system cimport Transition
from .transition_system cimport do_func_t
from ..gold cimport GoldParseC, GoldParse
from ..lexeme cimport Lexeme
from ..attrs cimport IS_SPACE
from ..gold.iob_utils import biluo_tags_from_offsets
from ..gold.example cimport Example
from ..errors import Errors
@ -35,6 +36,43 @@ MOVE_NAMES[OUT] = 'O'
MOVE_NAMES[ISNT] = 'x'
cdef struct GoldNERStateC:
Transition* ner
int32_t length
cdef class BiluoGold:
cdef Pool mem
cdef GoldNERStateC c
def __init__(self, BiluoPushDown moves, StateClass stcls, Example example):
self.mem = Pool()
self.c = create_gold_state(self.mem, moves, stcls, example)
def update(self, StateClass stcls):
update_gold_state(&self.c, stcls)
cdef GoldNERStateC create_gold_state(
Pool mem,
BiluoPushDown moves,
StateClass stcls,
Example example
) except *:
cdef GoldNERStateC gs
gs.ner = <Transition*>mem.alloc(example.x.length, sizeof(Transition))
ner_tags = example.get_aligned_ner()
for i, ner_tag in enumerate(ner_tags):
gs.ner[i] = moves.lookup_transition(ner_tag)
return gs
cdef void update_gold_state(GoldNERStateC* gs, StateClass stcls) except *:
# We don't need to update each time, unlike the parser.
pass
cdef do_func_t[N_MOVES] do_funcs
@ -71,12 +109,12 @@ cdef class BiluoPushDown(TransitionSystem):
for action in (BEGIN, IN, LAST, UNIT):
actions[action][entity_type] = 1
moves = ('M', 'B', 'I', 'L', 'U')
for example in kwargs.get('gold_parses', []):
for i, ner_tag in enumerate(example.token_annotation.entities):
if ner_tag != 'O' and ner_tag != '-':
_, label = ner_tag.split('-', 1)
for example in kwargs.get('examples', []):
for token in example.y:
ent_type = token.ent_type_
if ent_type:
for action in (BEGIN, IN, LAST, UNIT):
actions[action][label] += 1
actions[action][ent_type] += 1
return actions
@property
@ -91,52 +129,16 @@ cdef class BiluoPushDown(TransitionSystem):
else:
return MOVE_NAMES[move] + '-' + self.strings[label]
def has_gold(self, GoldParse gold, start=0, end=None):
end = end or len(gold.ner)
if all([tag in ('-', None) for tag in gold.ner[start:end]]):
return False
else:
return True
def preprocess_gold(self, GoldParse gold):
if not self.has_gold(gold):
return None
for i in range(gold.length):
gold.c.ner[i] = self.lookup_transition(gold.ner[i])
return gold
def get_beam_annot(self, Beam beam):
entities = {}
probs = beam.probs
for i in range(beam.size):
state = <StateC*>beam.at(i)
if state.is_final():
self.finalize_state(state)
prob = probs[i]
for j in range(state._e_i):
start = state._ents[j].start
end = state._ents[j].end
label = state._ents[j].label
entities.setdefault((start, end, label), 0.0)
entities[(start, end, label)] += prob
return entities
def get_beam_parses(self, Beam beam):
parses = []
probs = beam.probs
for i in range(beam.size):
state = <StateC*>beam.at(i)
if state.is_final():
self.finalize_state(state)
prob = probs[i]
parse = []
for j in range(state._e_i):
start = state._ents[j].start
end = state._ents[j].end
label = state._ents[j].label
parse.append((start, end, self.strings[label]))
parses.append((prob, parse))
return parses
def init_gold_batch(self, examples):
all_states = self.init_batch([eg.predicted for eg in examples])
golds = []
states = []
for state, eg in zip(all_states, examples):
if self.has_gold(eg) and not state.is_final():
golds.append(self.init_gold(state, eg))
states.append(state)
n_steps = sum([len(s.queue) for s in states])
return states, golds, n_steps
cdef Transition lookup_transition(self, object name) except *:
cdef attr_t label
@ -237,6 +239,47 @@ cdef class BiluoPushDown(TransitionSystem):
self.add_action(UNIT, st._sent[i].ent_type)
self.add_action(LAST, st._sent[i].ent_type)
def init_gold(self, StateClass state, Example example):
return BiluoGold(self, state, example)
def has_gold(self, Example eg, start=0, end=None):
for word in eg.y[start:end]:
if word.ent_iob != 0:
return True
else:
return False
def get_cost(self, StateClass stcls, gold, int i):
if not isinstance(gold, BiluoGold):
raise TypeError("Expected BiluoGold")
cdef BiluoGold gold_ = gold
gold_state = gold_.c
n_gold = 0
if self.c[i].is_valid(stcls.c, self.c[i].label):
cost = self.c[i].get_cost(stcls, &gold_state, self.c[i].label)
else:
cost = 9000
return cost
cdef int set_costs(self, int* is_valid, weight_t* costs,
StateClass stcls, gold) except -1:
if not isinstance(gold, BiluoGold):
raise TypeError("Expected BiluoGold")
cdef BiluoGold gold_ = gold
gold_.update(stcls)
gold_state = gold_.c
n_gold = 0
for i in range(self.n_moves):
if self.c[i].is_valid(stcls.c, self.c[i].label):
is_valid[i] = 1
costs[i] = self.c[i].get_cost(stcls, &gold_state, self.c[i].label)
n_gold += costs[i] <= 0
else:
is_valid[i] = 0
costs[i] = 9000
if n_gold < 1:
raise ValueError
cdef class Missing:
@staticmethod
@ -248,7 +291,7 @@ cdef class Missing:
pass
@staticmethod
cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef weight_t cost(StateClass s, const void* _gold, attr_t label) nogil:
return 9000
@ -300,7 +343,8 @@ cdef class Begin:
st.pop()
@staticmethod
cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef weight_t cost(StateClass s, const void* _gold, attr_t label) nogil:
gold = <GoldNERStateC*>_gold
cdef int g_act = gold.ner[s.B(0)].move
cdef attr_t g_tag = gold.ner[s.B(0)].label
@ -363,7 +407,8 @@ cdef class In:
st.pop()
@staticmethod
cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef weight_t cost(StateClass s, const void* _gold, attr_t label) nogil:
gold = <GoldNERStateC*>_gold
move = IN
cdef int next_act = gold.ner[s.B(1)].move if s.B(1) >= 0 else OUT
cdef int g_act = gold.ner[s.B(0)].move
@ -429,7 +474,8 @@ cdef class Last:
st.pop()
@staticmethod
cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef weight_t cost(StateClass s, const void* _gold, attr_t label) nogil:
gold = <GoldNERStateC*>_gold
move = LAST
cdef int g_act = gold.ner[s.B(0)].move
@ -497,7 +543,8 @@ cdef class Unit:
st.pop()
@staticmethod
cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef weight_t cost(StateClass s, const void* _gold, attr_t label) nogil:
gold = <GoldNERStateC*>_gold
cdef int g_act = gold.ner[s.B(0)].move
cdef attr_t g_tag = gold.ner[s.B(0)].label
@ -537,7 +584,8 @@ cdef class Out:
st.pop()
@staticmethod
cdef weight_t cost(StateClass s, const GoldParseC* gold, attr_t label) nogil:
cdef weight_t cost(StateClass s, const void* _gold, attr_t label) nogil:
gold = <GoldNERStateC*>_gold
cdef int g_act = gold.ner[s.B(0)].move
cdef attr_t g_tag = gold.ner[s.B(0)].label

319
spacy/syntax/nn_parser.pyx
View File

@ -9,7 +9,6 @@ from libcpp.vector cimport vector
from libc.string cimport memset, memcpy
from libc.stdlib cimport calloc, free
from cymem.cymem cimport Pool
from thinc.extra.search cimport Beam
from thinc.backends.linalg cimport Vec, VecVec
from thinc.api import chain, clone, Linear, list2array, NumpyOps, CupyOps, use_ops
@ -21,7 +20,6 @@ import numpy
import warnings
from ..tokens.doc cimport Doc
from ..gold cimport GoldParse
from ..typedefs cimport weight_t, class_t, hash_t
from ._parser_model cimport alloc_activations, free_activations
from ._parser_model cimport predict_states, arg_max_if_valid
@ -30,14 +28,12 @@ from ._parser_model cimport get_c_weights, get_c_sizes
from .stateclass cimport StateClass
from ._state cimport StateC
from .transition_system cimport Transition
from . cimport _beam_utils
from ..gold.example cimport Example
from ..gold import Example
from ..util import link_vectors_to_models, create_default_optimizer, registry
from ..compat import copy_array
from ..errors import Errors, Warnings
from .. import util
from . import _beam_utils
from . import nonproj
@ -144,71 +140,46 @@ cdef class Parser:
'''
pass
def preprocess_gold(self, examples):
for ex in examples:
yield ex
def use_params(self, params):
# Can't decorate cdef class :(. Workaround.
with self.model.use_params(params):
yield
def __call__(self, Doc doc, beam_width=None):
def __call__(self, Doc doc):
"""Apply the parser or entity recognizer, setting the annotations onto
the `Doc` object.
doc (Doc): The document to be processed.
"""
if beam_width is None:
beam_width = self.cfg['beam_width']
beam_density = self.cfg.get('beam_density', 0.)
states = self.predict([doc], beam_width=beam_width,
beam_density=beam_density)
states = self.predict([doc])
self.set_annotations([doc], states, tensors=None)
return doc
def pipe(self, docs, int batch_size=256, int n_threads=-1, beam_width=None,
as_example=False):
def pipe(self, docs, int batch_size=256, int n_threads=-1):
"""Process a stream of documents.
stream: The sequence of documents to process.
batch_size (int): Number of documents to accumulate into a working set.
YIELDS (Doc): Documents, in order.
"""
if beam_width is None:
beam_width = self.cfg['beam_width']
beam_density = self.cfg.get('beam_density', 0.)
cdef Doc doc
for batch in util.minibatch(docs, size=batch_size):
batch_in_order = list(batch)
docs = [self._get_doc(ex) for ex in batch_in_order]
by_length = sorted(docs, key=lambda doc: len(doc))
by_length = sorted(batch, key=lambda doc: len(doc))
for subbatch in util.minibatch(by_length, size=max(batch_size//4, 2)):
subbatch = list(subbatch)
parse_states = self.predict(subbatch, beam_width=beam_width,
beam_density=beam_density)
parse_states = self.predict(subbatch)
self.set_annotations(subbatch, parse_states, tensors=None)
if as_example:
annotated_examples = []
for ex, doc in zip(batch_in_order, docs):
ex.doc = doc
annotated_examples.append(ex)
yield from annotated_examples
else:
yield from batch_in_order
yield from batch_in_order
def predict(self, docs, beam_width=1, beam_density=0.0, drop=0.):
def predict(self, docs):
if isinstance(docs, Doc):
docs = [docs]
if not any(len(doc) for doc in docs):
result = self.moves.init_batch(docs)
self._resize()
return result
if beam_width < 2:
return self.greedy_parse(docs, drop=drop)
else:
return self.beam_parse(docs, beam_width=beam_width,
beam_density=beam_density, drop=drop)
return self.greedy_parse(docs, drop=0.0)
def greedy_parse(self, docs, drop=0.):
cdef vector[StateC*] states
@ -230,44 +201,6 @@ cdef class Parser:
weights, sizes)
return batch
def beam_parse(self, docs, int beam_width, float drop=0., beam_density=0.):
cdef Beam beam
cdef Doc doc
cdef np.ndarray token_ids
set_dropout_rate(self.model, drop)
beams = self.moves.init_beams(docs, beam_width, beam_density=beam_density)
# This is pretty dirty, but the NER can resize itself in init_batch,
# if labels are missing. We therefore have to check whether we need to
# expand our model output.
self._resize()
cdef int nr_feature = self.model.get_ref("lower").get_dim("nF")
model = self.model.predict(docs)
token_ids = numpy.zeros((len(docs) * beam_width, nr_feature),
dtype='i', order='C')
cdef int* c_ids
cdef int n_states
model = self.model.predict(docs)
todo = [beam for beam in beams if not beam.is_done]
while todo:
token_ids.fill(-1)
c_ids = <int*>token_ids.data
n_states = 0
for beam in todo:
for i in range(beam.size):
state = <StateC*>beam.at(i)
# This way we avoid having to score finalized states
# We do have to take care to keep indexes aligned, though
if not state.is_final():
state.set_context_tokens(c_ids, nr_feature)
c_ids += nr_feature
n_states += 1
if n_states == 0:
break
vectors = model.state2vec.predict(token_ids[:n_states])
scores = model.vec2scores.predict(vectors)
todo = self.transition_beams(todo, scores)
return beams
cdef void _parseC(self, StateC** states,
WeightsC weights, SizesC sizes) nogil:
cdef int i, j
@ -288,20 +221,9 @@ cdef class Parser:
unfinished.clear()
free_activations(&activations)
def set_annotations(self, docs, states_or_beams, tensors=None):
def set_annotations(self, docs, states, tensors=None):
cdef StateClass state
cdef Beam beam
cdef Doc doc
states = []
beams = []
for state_or_beam in states_or_beams:
if isinstance(state_or_beam, StateClass):
states.append(state_or_beam)
else:
beam = state_or_beam
state = StateClass.borrow(<StateC*>beam.at(0))
states.append(state)
beams.append(beam)
for i, (state, doc) in enumerate(zip(states, docs)):
self.moves.finalize_state(state.c)
for j in range(doc.length):
@ -309,8 +231,6 @@ cdef class Parser:
self.moves.finalize_doc(doc)
for hook in self.postprocesses:
hook(doc)
for beam in beams:
_beam_utils.cleanup_beam(beam)
def transition_states(self, states, float[:, ::1] scores):
cdef StateClass state
@ -342,50 +262,25 @@ cdef class Parser:
states[i].push_hist(guess)
free(is_valid)
def transition_beams(self, beams, float[:, ::1] scores):
cdef Beam beam
cdef float* c_scores = &scores[0, 0]
for beam in beams:
for i in range(beam.size):
state = <StateC*>beam.at(i)
if not state.is_final():
self.moves.set_valid(beam.is_valid[i], state)
memcpy(beam.scores[i], c_scores, scores.shape[1] * sizeof(float))
c_scores += scores.shape[1]
beam.advance(_beam_utils.transition_state, _beam_utils.hash_state, <void*>self.moves.c)
beam.check_done(_beam_utils.check_final_state, NULL)
return [b for b in beams if not b.is_done]
def update(self, examples, drop=0., set_annotations=False, sgd=None, losses=None):
examples = Example.to_example_objects(examples)
if losses is None:
losses = {}
losses.setdefault(self.name, 0.)
for multitask in self._multitasks:
multitask.update(examples, drop=drop, sgd=sgd)
# The probability we use beam update, instead of falling back to
# a greedy update
beam_update_prob = self.cfg['beam_update_prob']
if self.cfg['beam_width'] >= 2 and numpy.random.random() < beam_update_prob:
return self.update_beam(examples, self.cfg['beam_width'],
drop=drop, sgd=sgd, losses=losses, set_annotations=set_annotations,
beam_density=self.cfg.get('beam_density', 0.001))
set_dropout_rate(self.model, drop)
cut_gold = True
if cut_gold:
# Chop sequences into lengths of this many transitions, to make the
# batch uniform length.
cut_gold = numpy.random.choice(range(20, 100))
states, golds, max_steps = self._init_gold_batch(examples, max_length=cut_gold)
else:
states, golds, max_steps = self._init_gold_batch_no_cut(examples)
states_golds = [(s, g) for (s, g) in zip(states, golds)
if not s.is_final() and g is not None]
# Prepare the stepwise model, and get the callback for finishing the batch
model, backprop_tok2vec = self.model.begin_update([ex.doc for ex in examples])
model, backprop_tok2vec = self.model.begin_update(
[eg.predicted for eg in examples])
# Chop sequences into lengths of this many transitions, to make the
# batch uniform length. We randomize this to overfit less.
cut_gold = numpy.random.choice(range(20, 100))
states, golds, max_steps = self._init_gold_batch(
examples,
max_length=cut_gold
)
all_states = list(states)
states_golds = zip(states, golds)
for _ in range(max_steps):
if not states_golds:
break
@ -395,18 +290,18 @@ cdef class Parser:
backprop(d_scores)
# Follow the predicted action
self.transition_states(states, scores)
states_golds = [eg for eg in states_golds if not eg[0].is_final()]
states_golds = [(s, g) for (s, g) in zip(states, golds) if not s.is_final()]
backprop_tok2vec(golds)
if sgd is not None:
if sgd not in (None, False):
self.model.finish_update(sgd)
if set_annotations:
docs = [ex.doc for ex in examples]
docs = [eg.predicted for eg in examples]
self.set_annotations(docs, all_states)
return losses
def rehearse(self, examples, sgd=None, losses=None, **cfg):
"""Perform a "rehearsal" update, to prevent catastrophic forgetting."""
examples = Example.to_example_objects(examples)
if losses is None:
losses = {}
for multitask in self._multitasks:
@ -416,7 +311,7 @@ cdef class Parser:
return None
losses.setdefault(self.name, 0.)
docs = [ex.doc for ex in examples]
docs = [eg.predicted for eg in examples]
states = self.moves.init_batch(docs)
# This is pretty dirty, but the NER can resize itself in init_batch,
# if labels are missing. We therefore have to check whether we need to
@ -448,52 +343,6 @@ cdef class Parser:
losses[self.name] += loss / n_scores
return losses
def update_beam(self, examples, width, drop=0., sgd=None, losses=None,
set_annotations=False, beam_density=0.0):
examples = Example.to_example_objects(examples)
docs = [ex.doc for ex in examples]
golds = [ex.gold for ex in examples]
new_golds = []
lengths = [len(d) for d in docs]
states = self.moves.init_batch(docs)
for gold in golds:
self.moves.preprocess_gold(gold)
new_golds.append(gold)
set_dropout_rate(self.model, drop)
model, backprop_tok2vec = self.model.begin_update(docs)
states_d_scores, backprops, beams = _beam_utils.update_beam(
self.moves,
self.model.get_ref("lower").get_dim("nF"),
10000,
states,
golds,
model.state2vec,
model.vec2scores,
width,
losses=losses,
beam_density=beam_density
)
for i, d_scores in enumerate(states_d_scores):
losses[self.name] += (d_scores**2).mean()
ids, bp_vectors, bp_scores = backprops[i]
d_vector = bp_scores(d_scores)
if isinstance(model.ops, CupyOps) \
and not isinstance(ids, model.state2vec.ops.xp.ndarray):
model.backprops.append((
util.get_async(model.cuda_stream, ids),
util.get_async(model.cuda_stream, d_vector),
bp_vectors))
else:
model.backprops.append((ids, d_vector, bp_vectors))
backprop_tok2vec(golds)
if sgd is not None:
self.model.finish_update(sgd)
if set_annotations:
self.set_annotations(docs, beams)
cdef Beam beam
for beam in beams:
_beam_utils.cleanup_beam(beam)
def get_gradients(self):
"""Get non-zero gradients of the model's parameters, as a dictionary
keyed by the parameter ID. The values are (weights, gradients) tuples.
@ -511,66 +360,8 @@ cdef class Parser:
queue.extend(node._layers)
return gradients
def _init_gold_batch_no_cut(self, whole_examples):
states = self.moves.init_batch([eg.doc for eg in whole_examples])
good_docs = []
good_golds = []
good_states = []
for i, eg in enumerate(whole_examples):
doc = eg.doc
gold = self.moves.preprocess_gold(eg.gold)
if gold is not None and self.moves.has_gold(gold):
good_docs.append(doc)
good_golds.append(gold)
good_states.append(states[i])
n_moves = []
for doc, gold in zip(good_docs, good_golds):
oracle_actions = self.moves.get_oracle_sequence(doc, gold)
n_moves.append(len(oracle_actions))
return good_states, good_golds, max(n_moves, default=0) * 2
def _init_gold_batch(self, whole_examples, min_length=5, max_length=500):
"""Make a square batch, of length equal to the shortest doc. A long
doc will get multiple states. Let's say we have a doc of length 2*N,
where N is the shortest doc. We'll make two states, one representing
long_doc[:N], and another representing long_doc[N:]."""
cdef:
StateClass state
Transition action
whole_docs = [ex.doc for ex in whole_examples]
whole_golds = [ex.gold for ex in whole_examples]
whole_states = self.moves.init_batch(whole_docs)
max_length = max(min_length, min(max_length, min([len(doc) for doc in whole_docs])))
max_moves = 0
states = []
golds = []
for doc, state, gold in zip(whole_docs, whole_states, whole_golds):
gold = self.moves.preprocess_gold(gold)
if gold is None:
continue
oracle_actions = self.moves.get_oracle_sequence(doc, gold)
start = 0
while start < len(doc):
state = state.copy()
n_moves = 0
while state.B(0) < start and not state.is_final():
action = self.moves.c[oracle_actions.pop(0)]
action.do(state.c, action.label)
state.c.push_hist(action.clas)
n_moves += 1
has_gold = self.moves.has_gold(gold, start=start,
end=start+max_length)
if not state.is_final() and has_gold:
states.append(state)
golds.append(gold)
max_moves = max(max_moves, n_moves)
start += min(max_length, len(doc)-start)
max_moves = max(max_moves, len(oracle_actions))
return states, golds, max_moves
def get_batch_loss(self, states, golds, float[:, ::1] scores, losses):
cdef StateClass state
cdef GoldParse gold
cdef Pool mem = Pool()
cdef int i
@ -613,9 +404,11 @@ cdef class Parser:
if not hasattr(get_examples, '__call__'):
gold_tuples = get_examples
get_examples = lambda: gold_tuples
actions = self.moves.get_actions(gold_parses=get_examples(),
min_freq=self.cfg['min_action_freq'],
learn_tokens=self.cfg["learn_tokens"])
actions = self.moves.get_actions(
examples=get_examples(),
min_freq=self.cfg['min_action_freq'],
learn_tokens=self.cfg["learn_tokens"]
)
for action, labels in self.moves.labels.items():
actions.setdefault(action, {})
for label, freq in labels.items():
@ -627,13 +420,8 @@ cdef class Parser:
if sgd is None:
sgd = self.create_optimizer()
doc_sample = []
gold_sample = []
for example in islice(get_examples(), 10):
parses = example.get_gold_parses(merge=False, vocab=self.vocab)
for doc, gold in parses:
if len(doc):
doc_sample.append(doc)
gold_sample.append(gold)
doc_sample.append(example.predicted)
if pipeline is not None:
for name, component in pipeline:
@ -652,12 +440,6 @@ cdef class Parser:
link_vectors_to_models(self.vocab)
return sgd
def _get_doc(self, example):
""" Use this method if the `example` can be both a Doc or an Example """
if isinstance(example, Doc):
return example
return example.doc
def to_disk(self, path, exclude=tuple(), **kwargs):
serializers = {
'model': lambda p: (self.model.to_disk(p) if self.model is not True else True),
@ -714,3 +496,42 @@ cdef class Parser:
except AttributeError:
raise ValueError(Errors.E149)
return self
def _init_gold_batch(self, examples, min_length=5, max_length=500):
"""Make a square batch, of length equal to the shortest doc. A long
doc will get multiple states. Let's say we have a doc of length 2*N,
where N is the shortest doc. We'll make two states, one representing
long_doc[:N], and another representing long_doc[N:]."""
cdef:
StateClass state
Transition action
all_states = self.moves.init_batch([eg.predicted for eg in examples])
kept = []
for state, eg in zip(all_states, examples):
if self.moves.has_gold(eg) and not state.is_final():
gold = self.moves.init_gold(state, eg)
kept.append((eg, state, gold))
max_length = max(min_length, min(max_length, min([len(eg.x) for eg in examples])))
max_moves = 0
states = []
golds = []
for eg, state, gold in kept:
oracle_actions = self.moves.get_oracle_sequence(eg)
start = 0
while start < len(eg.predicted):
state = state.copy()
n_moves = 0
while state.B(0) < start and not state.is_final():
action = self.moves.c[oracle_actions.pop(0)]
action.do(state.c, action.label)
state.c.push_hist(action.clas)
n_moves += 1
has_gold = self.moves.has_gold(eg, start=start,
end=start+max_length)
if not state.is_final() and has_gold:
states.append(state)
golds.append(gold)
max_moves = max(max_moves, n_moves)
start += min(max_length, len(eg.x)-start)
max_moves = max(max_moves, len(oracle_actions))
return states, golds, max_moves

57
spacy/syntax/nonproj.pyx
View File

@ -7,7 +7,6 @@ from copy import copy
from ..tokens.doc cimport Doc, set_children_from_heads
from ..gold import Example
from ..errors import Errors
@ -50,8 +49,12 @@ def is_nonproj_arc(tokenid, heads):
return False
elif head is None: # unattached tokens cannot be non-projective
return False
start, end = (head+1, tokenid) if head < tokenid else (tokenid+1, head)
cdef int start, end
if head < tokenid:
start, end = (head+1, tokenid)
else:
start, end = (tokenid+1, head)
for k in range(start, end):
for ancestor in ancestors(k, heads):
if ancestor is None: # for unattached tokens/subtrees
@ -78,8 +81,8 @@ def is_decorated(label):
def count_decorated_labels(gold_data):
freqs = {}
for example in gold_data:
proj_heads, deco_deps = projectivize(example.token_annotation.heads,
example.token_annotation.deps)
proj_heads, deco_deps = projectivize(example.get_aligned("HEAD"),
example.get_aligned("DEP"))
# set the label to ROOT for each root dependent
deco_deps = ['ROOT' if head == i else deco_deps[i]
for i, head in enumerate(proj_heads)]
@ -90,31 +93,6 @@ def count_decorated_labels(gold_data):
return freqs
def preprocess_training_data(gold_data, label_freq_cutoff=30):
preprocessed = []
freqs = {}
for example in gold_data:
new_example = Example(doc=example.doc)
proj_heads, deco_deps = projectivize(example.token_annotation.heads,
example.token_annotation.deps)
# set the label to ROOT for each root dependent
deco_deps = ['ROOT' if head == i else deco_deps[i]
for i, head in enumerate(proj_heads)]
# count label frequencies
if label_freq_cutoff > 0:
for label in deco_deps:
if is_decorated(label):
freqs[label] = freqs.get(label, 0) + 1
proj_token_dict = example.token_annotation.to_dict()
proj_token_dict["heads"] = proj_heads
proj_token_dict["deps"] = deco_deps
new_example.set_token_annotation(**proj_token_dict)
preprocessed.append(new_example)
if label_freq_cutoff > 0:
return _filter_labels(preprocessed, label_freq_cutoff, freqs)
return preprocessed
def projectivize(heads, labels):
# Use the algorithm by Nivre & Nilsson 2005. Assumes heads to be a proper
# tree, i.e. connected and cycle-free. Returns a new pair (heads, labels)
@ -200,22 +178,3 @@ def _find_new_head(token, headlabel):
next_queue.append(child)
queue = next_queue
return token.head
def _filter_labels(examples, cutoff, freqs):
# throw away infrequent decorated labels
# can't learn them reliably anyway and keeps label set smaller
filtered = []
for example in examples:
new_example = Example(doc=example.doc)
filtered_labels = []
for label in example.token_annotation.deps:
if is_decorated(label) and freqs.get(label, 0) < cutoff:
filtered_labels.append(decompose(label)[0])
else:
filtered_labels.append(label)
filtered_token_dict = example.token_annotation.to_dict()
filtered_token_dict["deps"] = filtered_labels
new_example.set_token_annotation(**filtered_token_dict)
filtered.append(new_example)
return filtered

15
spacy/syntax/transition_system.pxd
View File

@ -2,11 +2,10 @@ from cymem.cymem cimport Pool
from ..typedefs cimport attr_t, weight_t
from ..structs cimport TokenC
from ..gold cimport GoldParse
from ..gold cimport GoldParseC
from ..strings cimport StringStore
from .stateclass cimport StateClass
from ._state cimport StateC
from ..gold.example cimport Example
cdef struct Transition:
@ -17,14 +16,14 @@ cdef struct Transition:
weight_t score
bint (*is_valid)(const StateC* state, attr_t label) nogil
weight_t (*get_cost)(StateClass state, const GoldParseC* gold, attr_t label) nogil
weight_t (*get_cost)(StateClass state, const void* gold, attr_t label) nogil
int (*do)(StateC* state, attr_t label) nogil
ctypedef weight_t (*get_cost_func_t)(StateClass state, const GoldParseC* gold,
ctypedef weight_t (*get_cost_func_t)(StateClass state, const void* gold,
attr_tlabel) nogil
ctypedef weight_t (*move_cost_func_t)(StateClass state, const GoldParseC* gold) nogil
ctypedef weight_t (*label_cost_func_t)(StateClass state, const GoldParseC*
ctypedef weight_t (*move_cost_func_t)(StateClass state, const void* gold) nogil
ctypedef weight_t (*label_cost_func_t)(StateClass state, const void*
gold, attr_t label) nogil
ctypedef int (*do_func_t)(StateC* state, attr_t label) nogil
@ -41,8 +40,6 @@ cdef class TransitionSystem:
cdef int _size
cdef public attr_t root_label
cdef public freqs
cdef init_state_t init_beam_state
cdef del_state_t del_beam_state
cdef public object labels
cdef int initialize_state(self, StateC* state) nogil
@ -55,4 +52,4 @@ cdef class TransitionSystem:
cdef int set_valid(self, int* output, const StateC* st) nogil
cdef int set_costs(self, int* is_valid, weight_t* costs,
StateClass state, GoldParse gold) except -1
StateClass state, gold) except -1

84
spacy/syntax/transition_system.pyx
View File

@ -1,13 +1,12 @@
# cython: infer_types=True
from __future__ import print_function
from cpython.ref cimport Py_INCREF
from cymem.cymem cimport Pool
from thinc.extra.search cimport Beam
from collections import Counter
import srsly
from ..typedefs cimport weight_t
from . cimport _beam_utils
from ..tokens.doc cimport Doc
from ..structs cimport TokenC
from .stateclass cimport StateClass
@ -47,8 +46,6 @@ cdef class TransitionSystem:
if labels_by_action:
self.initialize_actions(labels_by_action, min_freq=min_freq)
self.root_label = self.strings.add('ROOT')
self.init_beam_state = _init_state
self.del_beam_state = _del_state
def __reduce__(self):
return (self.__class__, (self.strings, self.labels), None, None)
@ -64,48 +61,55 @@ cdef class TransitionSystem:
offset += len(doc)
return states
def init_beams(self, docs, beam_width, beam_density=0.):
cdef Doc doc
beams = []
cdef int offset = 0
# Doc objects might contain labels that we need to register actions for. We need to check for that
# *before* we create any Beam objects, because the Beam object needs the correct number of
# actions. It's sort of dumb, but the best way is to just call init_batch() -- that triggers the additions,
# and it doesn't matter that we create and discard the state objects.
self.init_batch(docs)
for doc in docs:
beam = Beam(self.n_moves, beam_width, min_density=beam_density)
beam.initialize(self.init_beam_state, self.del_beam_state,
doc.length, doc.c)
for i in range(beam.width):
state = <StateC*>beam.at(i)
state.offset = offset
offset += len(doc)
beam.check_done(_beam_utils.check_final_state, NULL)
beams.append(beam)
return beams
def get_oracle_sequence(self, doc, GoldParse gold):
def get_oracle_sequence(self, Example example, _debug=False):
cdef Pool mem = Pool()
# n_moves should not be zero at this point, but make sure to avoid zero-length mem alloc
assert self.n_moves > 0
costs = <float*>mem.alloc(self.n_moves, sizeof(float))
is_valid = <int*>mem.alloc(self.n_moves, sizeof(int))
cdef StateClass state = StateClass(doc, offset=0)
self.initialize_state(state.c)
cdef StateClass state
states, golds, n_steps = self.init_gold_batch([example])
if not states:
return []
state = states[0]
gold = golds[0]
history = []
debug_log = []
while not state.is_final():
self.set_costs(is_valid, costs, state, gold)
for i in range(self.n_moves):
if is_valid[i] and costs[i] <= 0:
action = self.c[i]
history.append(i)
s0 = state.S(0)
b0 = state.B(0)
if _debug:
debug_log.append(" ".join((
self.get_class_name(i),
"S0=", (example.x[s0].text if s0 >= 0 else "__"),
"B0=", (example.x[b0].text if b0 >= 0 else "__"),
"S0 head?", str(state.has_head(state.S(0))),
)))
action.do(state.c, action.label)
break
else:
if _debug:
print("Actions")
for i in range(self.n_moves):
print(self.get_class_name(i))
print("Gold")
for token in example.y:
print(token.text, token.dep_, token.head.text)
s0 = state.S(0)
b0 = state.B(0)
debug_log.append(" ".join((
"?",
"S0=", (example.x[s0].text if s0 >= 0 else "-"),
"B0=", (example.x[b0].text if b0 >= 0 else "-"),
"S0 head?", str(state.has_head(state.S(0))),
)))
print("\n".join(debug_log))
raise ValueError(Errors.E024)
return history
@ -124,12 +128,6 @@ cdef class TransitionSystem:
def finalize_doc(self, doc):
pass
def preprocess_gold(self, GoldParse gold):
raise NotImplementedError
def is_gold_parse(self, StateClass state, GoldParse gold):
raise NotImplementedError
cdef Transition lookup_transition(self, object name) except *:
raise NotImplementedError
@ -148,18 +146,8 @@ cdef class TransitionSystem:
is_valid[i] = self.c[i].is_valid(st, self.c[i].label)
cdef int set_costs(self, int* is_valid, weight_t* costs,
StateClass stcls, GoldParse gold) except -1:
cdef int i
self.set_valid(is_valid, stcls.c)
cdef int n_gold = 0
for i in range(self.n_moves):
if is_valid[i]:
costs[i] = self.c[i].get_cost(stcls, &gold.c, self.c[i].label)
n_gold += costs[i] <= 0
else:
costs[i] = 9000
if n_gold <= 0:
raise ValueError(Errors.E024)
StateClass stcls, gold) except -1:
raise NotImplementedError
def get_class_name(self, int clas):
act = self.c[clas]

16
spacy/tests/doc/test_array.py
View File

@ -1,6 +1,6 @@
import pytest
from spacy.tokens import Doc
from spacy.attrs import ORTH, SHAPE, POS, DEP
from spacy.attrs import ORTH, SHAPE, POS, DEP, MORPH
from ..util import get_doc
@ -44,6 +44,20 @@ def test_doc_array_tag(en_vocab):
assert feats_array[3][1] == doc[3].pos
def test_doc_array_morph(en_vocab):
words = ["Eat", "blue", "ham"]
morph = ["Feat=V", "Feat=J", "Feat=N"]
doc = get_doc(en_vocab, words=words, morphs=morph)
assert morph[0] == doc[0].morph_
assert morph[1] == doc[1].morph_
assert morph[2] == doc[2].morph_
feats_array = doc.to_array((ORTH, MORPH))
assert feats_array[0][1] == doc[0].morph.key
assert feats_array[1][1] == doc[1].morph.key
assert feats_array[2][1] == doc[2].morph.key
def test_doc_array_dep(en_vocab):
words = ["A", "nice", "sentence", "."]
deps = ["det", "amod", "ROOT", "punct"]

15
spacy/tests/parser/test_add_label.py
View File

@ -1,8 +1,9 @@
import pytest
from thinc.api import Adam
from spacy.attrs import NORM
from spacy.gold import GoldParse
from spacy.vocab import Vocab
from spacy.gold import Example
from spacy.pipeline.defaults import default_parser, default_ner
from spacy.tokens import Doc
from spacy.pipeline import DependencyParser, EntityRecognizer
@ -39,8 +40,9 @@ def _train_parser(parser):
for i in range(5):
losses = {}
doc = Doc(parser.vocab, words=["a", "b", "c", "d"])
gold = GoldParse(doc, heads=[1, 1, 3, 3], deps=["left", "ROOT", "left", "ROOT"])
parser.update((doc, gold), sgd=sgd, losses=losses)
gold = {"heads": [1, 1, 3, 3], "deps": ["left", "ROOT", "left", "ROOT"]}
example = Example.from_dict(doc, gold)
parser.update([example], sgd=sgd, losses=losses)
return parser
@ -51,10 +53,9 @@ def test_add_label(parser):
for i in range(100):
losses = {}
doc = Doc(parser.vocab, words=["a", "b", "c", "d"])
gold = GoldParse(
doc, heads=[1, 1, 3, 3], deps=["right", "ROOT", "left", "ROOT"]
)
parser.update((doc, gold), sgd=sgd, losses=losses)
gold = {"heads": [1, 1, 3, 3], "deps": ["right", "ROOT", "left", "ROOT"]}
example = Example.from_dict(doc, gold)
parser.update([example], sgd=sgd, losses=losses)
doc = Doc(parser.vocab, words=["a", "b", "c", "d"])
doc = parser(doc)
assert doc[0].dep_ == "right"

133
spacy/tests/parser/test_arc_eager_oracle.py
View File

@ -1,22 +1,23 @@
import pytest
from spacy.vocab import Vocab
from spacy.gold import Example
from spacy.pipeline.defaults import default_parser
from spacy.pipeline import DependencyParser
from spacy.tokens import Doc
from spacy.gold import GoldParse
from spacy.syntax.nonproj import projectivize
from spacy.syntax.stateclass import StateClass
from spacy.syntax.arc_eager import ArcEager
def get_sequence_costs(M, words, heads, deps, transitions):
doc = Doc(Vocab(), words=words)
gold = GoldParse(doc, heads=heads, deps=deps)
state = StateClass(doc)
M.preprocess_gold(gold)
example = Example.from_dict(doc, {"heads": heads, "deps": deps})
states, golds, _ = M.init_gold_batch([example])
state = states[0]
gold = golds[0]
cost_history = []
for gold_action in transitions:
gold.update(state)
state_costs = {}
for i in range(M.n_moves):
name = M.class_name(i)
@ -39,31 +40,13 @@ def arc_eager(vocab):
return moves
@pytest.fixture
def words():
return ["a", "b"]
@pytest.fixture
def doc(words, vocab):
if vocab is None:
vocab = Vocab()
return Doc(vocab, words=list(words))
@pytest.fixture
def gold(doc, words):
if len(words) == 2:
return GoldParse(doc, words=["a", "b"], heads=[0, 0], deps=["ROOT", "right"])
else:
raise NotImplementedError
@pytest.mark.xfail
def test_oracle_four_words(arc_eager, vocab):
words = ["a", "b", "c", "d"]
heads = [1, 1, 3, 3]
deps = ["left", "ROOT", "left", "ROOT"]
for dep in deps:
arc_eager.add_action(2, dep) # Left
arc_eager.add_action(3, dep) # Right
actions = ["L-left", "B-ROOT", "L-left"]
state, cost_history = get_sequence_costs(arc_eager, words, heads, deps, actions)
assert state.is_final()
@ -72,7 +55,7 @@ def test_oracle_four_words(arc_eager, vocab):
assert state_costs[actions[i]] == 0.0, actions[i]
for other_action, cost in state_costs.items():
if other_action != actions[i]:
assert cost >= 1
assert cost >= 1, (i, other_action)
annot_tuples = [
@ -140,7 +123,7 @@ def test_get_oracle_actions():
doc = Doc(Vocab(), words=[t[1] for t in annot_tuples])
config = {
"learn_tokens": False,
"min_action_freq": 30,
"min_action_freq": 0,
"beam_width": 1,
"beam_update_prob": 1.0,
}
@ -149,12 +132,98 @@ def test_get_oracle_actions():
parser.moves.add_action(1, "")
parser.moves.add_action(1, "")
parser.moves.add_action(4, "ROOT")
heads, deps = projectivize(heads, deps)
for i, (head, dep) in enumerate(zip(heads, deps)):
if head > i:
parser.moves.add_action(2, dep)
elif head < i:
parser.moves.add_action(3, dep)
heads, deps = projectivize(heads, deps)
gold = GoldParse(doc, words=words, tags=tags, heads=heads, deps=deps)
parser.moves.preprocess_gold(gold)
parser.moves.get_oracle_sequence(doc, gold)
example = Example.from_dict(
doc, {"words": words, "tags": tags, "heads": heads, "deps": deps}
)
parser.moves.get_oracle_sequence(example)
def test_oracle_dev_sentence(vocab, arc_eager):
words_deps_heads = """
Rolls-Royce nn Inc.
Motor nn Inc.
Cars nn Inc.
Inc. nsubj said
said ROOT said
it nsubj expects
expects ccomp said
its poss sales
U.S. nn sales
sales nsubj steady
to aux steady
remain cop steady
steady xcomp expects
at prep steady
about quantmod 1,200
1,200 num cars
cars pobj at
in prep steady
1990 pobj in
. punct said
"""
expected_transitions = [
"S", # Shift 'Motor'
"S", # Shift 'Cars'
"L-nn", # Attach 'Cars' to 'Inc.'
"L-nn", # Attach 'Motor' to 'Inc.'
"L-nn", # Attach 'Rolls-Royce' to 'Inc.', force shift
"L-nsubj", # Attach 'Inc.' to 'said'
"S", # Shift 'it'
"L-nsubj", # Attach 'it.' to 'expects'
"R-ccomp", # Attach 'expects' to 'said'
"S", # Shift 'its'
"S", # Shift 'U.S.'
"L-nn", # Attach 'U.S.' to 'sales'
"L-poss", # Attach 'its' to 'sales'
"S", # Shift 'sales'
"S", # Shift 'to'
"S", # Shift 'remain'
"L-cop", # Attach 'remain' to 'steady'
"L-aux", # Attach 'to' to 'steady'
"L-nsubj", # Attach 'sales' to 'steady'
"R-xcomp", # Attach 'steady' to 'expects'
"R-prep", # Attach 'at' to 'steady'
"S", # Shift 'about'
"L-quantmod", # Attach "about" to "1,200"
"S", # Shift "1,200"
"L-num", # Attach "1,200" to "cars"
"R-pobj", # Attach "cars" to "at"
"D", # Reduce "cars"
"D", # Reduce "at"
"R-prep", # Attach "in" to "steady"
"R-pobj", # Attach "1990" to "in"
"D", # Reduce "1990"
"D", # Reduce "in"
"D", # Reduce "steady"
"D", # Reduce "expects"
"R-punct", # Attach "." to "said"
]
gold_words = []
gold_deps = []
gold_heads = []
for line in words_deps_heads.strip().split("\n"):
line = line.strip()
if not line:
continue
word, dep, head = line.split()
gold_words.append(word)
gold_deps.append(dep)
gold_heads.append(head)
gold_heads = [gold_words.index(head) for head in gold_heads]
for dep in gold_deps:
arc_eager.add_action(2, dep) # Left
arc_eager.add_action(3, dep) # Right
doc = Doc(Vocab(), words=gold_words)
example = Example.from_dict(doc, {"heads": gold_heads, "deps": gold_deps})
ae_oracle_actions = arc_eager.get_oracle_sequence(example)
ae_oracle_actions = [arc_eager.get_class_name(i) for i in ae_oracle_actions]
assert ae_oracle_actions == expected_transitions

55
spacy/tests/parser/test_ner.py
View File

@ -1,4 +1,6 @@
import pytest
from spacy.attrs import ENT_IOB
from spacy import util
from spacy.lang.en import English
@ -8,12 +10,11 @@ from spacy.pipeline.defaults import default_ner
from spacy.pipeline import EntityRecognizer, EntityRuler
from spacy.vocab import Vocab
from spacy.syntax.ner import BiluoPushDown
from spacy.gold import GoldParse
from spacy.gold import Example
from spacy.tokens import Doc
from ..util import make_tempdir
TRAIN_DATA = [
("Who is Shaka Khan?", {"entities": [(7, 17, "PERSON")]}),
("I like London and Berlin.", {"entities": [(7, 13, "LOC"), (18, 24, "LOC")]}),
@ -52,51 +53,55 @@ def tsys(vocab, entity_types):
def test_get_oracle_moves(tsys, doc, entity_annots):
gold = GoldParse(doc, entities=entity_annots)
tsys.preprocess_gold(gold)
act_classes = tsys.get_oracle_sequence(doc, gold)
example = Example.from_dict(doc, {"entities": entity_annots})
act_classes = tsys.get_oracle_sequence(example)
names = [tsys.get_class_name(act) for act in act_classes]
assert names == ["U-PERSON", "O", "O", "B-GPE", "L-GPE", "O"]
def test_get_oracle_moves_negative_entities(tsys, doc, entity_annots):
entity_annots = [(s, e, "!" + label) for s, e, label in entity_annots]
gold = GoldParse(doc, entities=entity_annots)
for i, tag in enumerate(gold.ner):
example = Example.from_dict(doc, {"entities": entity_annots})
ex_dict = example.to_dict()
for i, tag in enumerate(ex_dict["doc_annotation"]["entities"]):
if tag == "L-!GPE":
gold.ner[i] = "-"
tsys.preprocess_gold(gold)
act_classes = tsys.get_oracle_sequence(doc, gold)
ex_dict["doc_annotation"]["entities"][i] = "-"
example = Example.from_dict(doc, ex_dict)
act_classes = tsys.get_oracle_sequence(example)
names = [tsys.get_class_name(act) for act in act_classes]
assert names
def test_get_oracle_moves_negative_entities2(tsys, vocab):
doc = Doc(vocab, words=["A", "B", "C", "D"])
gold = GoldParse(doc, entities=[])
gold.ner = ["B-!PERSON", "L-!PERSON", "B-!PERSON", "L-!PERSON"]
tsys.preprocess_gold(gold)
act_classes = tsys.get_oracle_sequence(doc, gold)
entity_annots = ["B-!PERSON", "L-!PERSON", "B-!PERSON", "L-!PERSON"]
example = Example.from_dict(doc, {"entities": entity_annots})
act_classes = tsys.get_oracle_sequence(example)
names = [tsys.get_class_name(act) for act in act_classes]
assert names
@pytest.mark.xfail(reason="Maybe outdated? Unsure")
def test_get_oracle_moves_negative_O(tsys, vocab):
doc = Doc(vocab, words=["A", "B", "C", "D"])
gold = GoldParse(doc, entities=[])
gold.ner = ["O", "!O", "O", "!O"]
tsys.preprocess_gold(gold)
act_classes = tsys.get_oracle_sequence(doc, gold)
entity_annots = ["O", "!O", "O", "!O"]
example = Example.from_dict(doc, {"entities": entity_annots})
act_classes = tsys.get_oracle_sequence(example)
names = [tsys.get_class_name(act) for act in act_classes]
assert names
# We can't easily represent this on a Doc object. Not sure what the best solution
# would be, but I don't think it's an important use case?
@pytest.mark.xfail(reason="No longer supported")
def test_oracle_moves_missing_B(en_vocab):
words = ["B", "52", "Bomber"]
biluo_tags = [None, None, "L-PRODUCT"]
doc = Doc(en_vocab, words=words)
gold = GoldParse(doc, words=words, entities=biluo_tags)
example = Example.from_dict(doc, {"words": words, "entities": biluo_tags})
moves = BiluoPushDown(en_vocab.strings)
move_types = ("M", "B", "I", "L", "U", "O")
@ -111,16 +116,17 @@ def test_oracle_moves_missing_B(en_vocab):
moves.add_action(move_types.index("I"), label)
moves.add_action(move_types.index("L"), label)
moves.add_action(move_types.index("U"), label)
moves.preprocess_gold(gold)
moves.get_oracle_sequence(doc, gold)
moves.get_oracle_sequence(example)
# We can't easily represent this on a Doc object. Not sure what the best solution
# would be, but I don't think it's an important use case?
@pytest.mark.xfail(reason="No longer supported")
def test_oracle_moves_whitespace(en_vocab):
words = ["production", "\n", "of", "Northrop", "\n", "Corp.", "\n", "'s", "radar"]
biluo_tags = ["O", "O", "O", "B-ORG", None, "I-ORG", "L-ORG", "O", "O"]
doc = Doc(en_vocab, words=words)
gold = GoldParse(doc, words=words, entities=biluo_tags)
example = Example.from_dict(doc, {"entities": biluo_tags})
moves = BiluoPushDown(en_vocab.strings)
move_types = ("M", "B", "I", "L", "U", "O")
@ -132,8 +138,7 @@ def test_oracle_moves_whitespace(en_vocab):
else:
action, label = tag.split("-")
moves.add_action(move_types.index(action), label)
moves.preprocess_gold(gold)
moves.get_oracle_sequence(doc, gold)
moves.get_oracle_sequence(example)
def test_accept_blocked_token():

8
spacy/tests/parser/test_neural_parser.py
View File

@ -1,10 +1,11 @@
import pytest
from spacy.gold import Example
from spacy.pipeline.defaults import default_parser, default_tok2vec
from spacy.vocab import Vocab
from spacy.syntax.arc_eager import ArcEager
from spacy.syntax.nn_parser import Parser
from spacy.tokens.doc import Doc
from spacy.gold import GoldParse
from thinc.api import Model
@ -52,7 +53,7 @@ def doc(vocab):
@pytest.fixture
def gold(doc):
return GoldParse(doc, heads=[1, 1, 1], deps=["L", "ROOT", "R"])
return {"heads": [1, 1, 1], "deps": ["L", "ROOT", "R"]}
def test_can_init_nn_parser(parser):
@ -77,7 +78,8 @@ def test_update_doc(parser, model, doc, gold):
weights -= 0.001 * gradient
return weights, gradient
parser.update((doc, gold), sgd=optimize)
example = Example.from_dict(doc, gold)
parser.update([example], sgd=optimize)
@pytest.mark.xfail

107
spacy/tests/parser/test_nn_beam.py
View File

@ -1,107 +0,0 @@
import pytest
import numpy
from spacy.vocab import Vocab
from spacy.language import Language
from spacy.pipeline.defaults import default_parser
from spacy.pipeline import DependencyParser
from spacy.syntax.arc_eager import ArcEager
from spacy.tokens import Doc
from spacy.syntax._beam_utils import ParserBeam
from spacy.syntax.stateclass import StateClass
from spacy.gold import GoldParse
@pytest.fixture
def vocab():
return Vocab()
@pytest.fixture
def moves(vocab):
aeager = ArcEager(vocab.strings, {})
aeager.add_action(2, "nsubj")
aeager.add_action(3, "dobj")
aeager.add_action(2, "aux")
return aeager
@pytest.fixture
def docs(vocab):
return [Doc(vocab, words=["Rats", "bite", "things"])]
@pytest.fixture
def states(docs):
return [StateClass(doc) for doc in docs]
@pytest.fixture
def tokvecs(docs, vector_size):
output = []
for doc in docs:
vec = numpy.random.uniform(-0.1, 0.1, (len(doc), vector_size))
output.append(numpy.asarray(vec))
return output
@pytest.fixture
def golds(docs):
return [GoldParse(doc) for doc in docs]
@pytest.fixture
def batch_size(docs):
return len(docs)
@pytest.fixture
def beam_width():
return 4
@pytest.fixture
def vector_size():
return 6
@pytest.fixture
def beam(moves, states, golds, beam_width):
return ParserBeam(moves, states, golds, width=beam_width, density=0.0)
@pytest.fixture
def scores(moves, batch_size, beam_width):
return [
numpy.asarray(
numpy.random.uniform(-0.1, 0.1, (batch_size, moves.n_moves)), dtype="f"
)
for _ in range(batch_size)
]
def test_create_beam(beam):
pass
def test_beam_advance(beam, scores):
beam.advance(scores)
def test_beam_advance_too_few_scores(beam, scores):
with pytest.raises(IndexError):
beam.advance(scores[:-1])
def test_beam_parse():
nlp = Language()
config = {
"learn_tokens": False,
"min_action_freq": 30,
"beam_width": 1,
"beam_update_prob": 1.0,
}
nlp.add_pipe(DependencyParser(nlp.vocab, default_parser(), **config), name="parser")
nlp.parser.add_label("nsubj")
nlp.parser.begin_training([], token_vector_width=8, hidden_width=8)
doc = nlp.make_doc("Australia is a country")
nlp.parser(doc, beam_width=2)

9
spacy/tests/parser/test_parse.py
View File

@ -33,7 +33,7 @@ def test_parser_root(en_tokenizer):
@pytest.mark.xfail
@pytest.mark.parametrize("text", ["Hello"])
# @pytest.mark.parametrize("text", ["Hello"])
def test_parser_parse_one_word_sentence(en_tokenizer, en_parser, text):
tokens = en_tokenizer(text)
doc = get_doc(
@ -46,7 +46,8 @@ def test_parser_parse_one_word_sentence(en_tokenizer, en_parser, text):
assert doc[0].dep != 0
@pytest.mark.xfail
# We removed the step_through API a while ago. we should bring it back though
@pytest.mark.xfail(reason="Unsupported")
def test_parser_initial(en_tokenizer, en_parser):
text = "I ate the pizza with anchovies."
# heads = [1, 0, 1, -2, -3, -1, -5]
@ -90,8 +91,8 @@ def test_parser_merge_pp(en_tokenizer):
assert doc[2].text == "another phrase"
assert doc[3].text == "occurs"
@pytest.mark.xfail
# We removed the step_through API a while ago. we should bring it back though
@pytest.mark.xfail(reason="Unsupported")
def test_parser_arc_eager_finalize_state(en_tokenizer, en_parser):
text = "a b c d e"

8
spacy/tests/parser/test_preset_sbd.py
View File

@ -1,9 +1,9 @@
import pytest
from thinc.api import Adam
from spacy.attrs import NORM
from spacy.gold import GoldParse
from spacy.vocab import Vocab
from spacy.gold import Example
from spacy.pipeline.defaults import default_parser
from spacy.tokens import Doc
from spacy.pipeline import DependencyParser
@ -33,8 +33,10 @@ def parser(vocab):
for i in range(10):
losses = {}
doc = Doc(vocab, words=["a", "b", "c", "d"])
gold = GoldParse(doc, heads=[1, 1, 3, 3], deps=["left", "ROOT", "left", "ROOT"])
parser.update((doc, gold), sgd=sgd, losses=losses)
example = Example.from_dict(
doc, {"heads": [1, 1, 3, 3], "deps": ["left", "ROOT", "left", "ROOT"]}
)
parser.update([example], sgd=sgd, losses=losses)
return parser

16
spacy/tests/pipeline/test_entity_linker.py
View File

@ -252,10 +252,18 @@ def test_preserving_links_ents_2(nlp):
# fmt: off
TRAIN_DATA = [
("Russ Cochran captured his first major title with his son as caddie.", {"links": {(0, 12): {"Q7381115": 0.0, "Q2146908": 1.0}}}),
("Russ Cochran his reprints include EC Comics.", {"links": {(0, 12): {"Q7381115": 1.0, "Q2146908": 0.0}}}),
("Russ Cochran has been publishing comic art.", {"links": {(0, 12): {"Q7381115": 1.0, "Q2146908": 0.0}}}),
("Russ Cochran was a member of University of Kentucky's golf team.", {"links": {(0, 12): {"Q7381115": 0.0, "Q2146908": 1.0}}}),
("Russ Cochran captured his first major title with his son as caddie.",
{"links": {(0, 12): {"Q7381115": 0.0, "Q2146908": 1.0}},
"entities": [(0, 12, "PERSON")]}),
("Russ Cochran his reprints include EC Comics.",
{"links": {(0, 12): {"Q7381115": 1.0, "Q2146908": 0.0}},
"entities": [(0, 12, "PERSON")]}),
("Russ Cochran has been publishing comic art.",
{"links": {(0, 12): {"Q7381115": 1.0, "Q2146908": 0.0}},
"entities": [(0, 12, "PERSON")]}),
("Russ Cochran was a member of University of Kentucky's golf team.",
{"links": {(0, 12): {"Q7381115": 0.0, "Q2146908": 1.0}},
"entities": [(0, 12, "PERSON"), (43, 51, "LOC")]}),
]
GOLD_entities = ["Q2146908", "Q7381115", "Q7381115", "Q2146908"]
# fmt: on

2
spacy/tests/pipeline/test_morphologizer.py
View File

@ -53,7 +53,7 @@ def test_overfitting_IO():
"Feat=J|POS=ADJ",
"Feat=N|POS=NOUN",
]
assert gold_morphs == [t.morph_ for t in doc]
assert [t.morph_ for t in doc] == gold_morphs
# Also test the results are still the same after IO
with make_tempdir() as tmp_dir:

2
spacy/tests/pipeline/test_sentencizer.py
View File

@ -26,7 +26,7 @@ def test_sentencizer_pipe():
sent_starts = [t.is_sent_start for t in doc]
assert sent_starts == [True, False, True, False, False, False, False]
assert len(list(doc.sents)) == 2
for ex in nlp.pipe(texts, as_example=True):
for ex in nlp.pipe(texts):
doc = ex.doc
assert doc.is_sentenced
sent_starts = [t.is_sent_start for t in doc]

15
spacy/tests/pipeline/test_textcat.py
View File

@ -7,11 +7,11 @@ from spacy.lang.en import English
from spacy.language import Language
from spacy.pipeline import TextCategorizer
from spacy.tokens import Doc
from spacy.gold import GoldParse
from spacy.util import fix_random_seed
from ..util import make_tempdir
from spacy.pipeline.defaults import default_tok2vec
from ...gold import Example
TRAIN_DATA = [
("I'm so happy.", {"cats": {"POSITIVE": 1.0, "NEGATIVE": 0.0}}),
@ -51,21 +51,20 @@ def test_textcat_learns_multilabel():
cats = {letter: float(w2 == letter) for letter in letters}
docs.append((Doc(nlp.vocab, words=["d"] * 3 + [w1, w2] + ["d"] * 3), cats))
random.shuffle(docs)
model = TextCategorizer(nlp.vocab, width=8)
textcat = TextCategorizer(nlp.vocab, width=8)
for letter in letters:
model.add_label(letter)
optimizer = model.begin_training()
textcat.add_label(letter)
optimizer = textcat.begin_training()
for i in range(30):
losses = {}
Ys = [GoldParse(doc, cats=cats) for doc, cats in docs]
Xs = [doc for doc, cats in docs]
model.update(Xs, Ys, sgd=optimizer, losses=losses)
examples = [Example.from_dict(doc, {"cats": cats}) for doc, cat in docs]
textcat.update(examples, sgd=optimizer, losses=losses)
random.shuffle(docs)
for w1 in letters:
for w2 in letters:
doc = Doc(nlp.vocab, words=["d"] * 3 + [w1, w2] + ["d"] * 3)
truth = {letter: w2 == letter for letter in letters}
model(doc)
textcat(doc)
for cat, score in doc.cats.items():
if not truth[cat]:
assert score < 0.5

15
spacy/tests/regression/test_issue1501-2000.py
View File

@ -277,11 +277,18 @@ def test_issue1967(label):
"beam_update_prob": 1.0,
}
ner = EntityRecognizer(Vocab(), default_ner(), **config)
example = Example(doc=None)
example.set_token_annotation(
ids=[0], words=["word"], tags=["tag"], heads=[0], deps=["dep"], entities=[label]
example = Example.from_dict(
Doc(ner.vocab, words=["word"]),
{
"ids": [0],
"words": ["word"],
"tags": ["tag"],
"heads": [0],
"deps": ["dep"],
"entities": [label],
},
)
ner.moves.get_actions(gold_parses=[example])
assert "JOB-NAME" in ner.moves.get_actions(examples=[example])[1]
def test_issue1971(en_vocab):

4
spacy/tests/regression/test_issue4313.py
View File

@ -1,5 +1,7 @@
from collections import defaultdict
import pytest
from spacy.pipeline.defaults import default_ner
from spacy.pipeline import EntityRecognizer
@ -7,6 +9,8 @@ from spacy.lang.en import English
from spacy.tokens import Span
# skipped after removing Beam stuff during the Example/GoldParse refactor
@pytest.mark.skip
def test_issue4313():
""" This should not crash or exit with some strange error code """
beam_width = 16

26
spacy/tests/regression/test_issue4402.py
View File

@ -1,24 +1,31 @@
import srsly
from spacy.gold import GoldCorpus
from spacy.gold import Corpus
from spacy.lang.en import English
from ..util import make_tempdir
from ...gold.converters import json2docs
from ...tokens import DocBin
def test_issue4402():
nlp = English()
with make_tempdir() as tmpdir:
json_path = tmpdir / "test4402.json"
srsly.write_json(json_path, json_data)
output_file = tmpdir / "test4402.spacy"
docs = json2docs([json_data])
data = DocBin(docs=docs, attrs =["ORTH", "SENT_START", "ENT_IOB", "ENT_TYPE"]).to_bytes()
with output_file.open("wb") as file_:
file_.write(data)
corpus = Corpus(train_loc=str(output_file), dev_loc=str(output_file))
corpus = GoldCorpus(str(json_path), str(json_path))
train_data = list(corpus.train_dataset(nlp))
assert len(train_data) == 2
train_data = list(corpus.train_dataset(nlp, gold_preproc=True, max_length=0))
# assert that the data got split into 4 sentences
assert len(train_data) == 4
split_train_data = []
for eg in train_data:
split_train_data.extend(eg.split_sents())
assert len(split_train_data) == 4
json_data = [
json_data =\
{
"id": 0,
"paragraphs": [
@ -89,4 +96,3 @@ json_data = [
},
],
}
]

5
spacy/tests/regression/test_issue4529.py
View File

@ -1,5 +1,6 @@
import pytest
from spacy.gold import GoldParse
from spacy.gold import Example
@pytest.mark.parametrize(
@ -7,4 +8,4 @@ from spacy.gold import GoldParse
)
def test_gold_misaligned(en_tokenizer, text, words):
doc = en_tokenizer(text)
GoldParse(doc, words=words)
Example.from_dict(doc, {"words": words})

10
spacy/tests/regression/test_issue4665.py
View File

@ -1,4 +1,7 @@
from spacy.cli.converters.conllu2json import conllu2json
import pytest
# TODO
# from spacy.gold.converters.conllu2docs import conllu2docs
input_data = """
1 [ _ PUNCT -LRB- _ _ punct _ _
@ -22,10 +25,11 @@ input_data = """
"""
@pytest.mark.xfail
def test_issue4665():
"""
conllu2json should not raise an exception if the HEAD column contains an
underscore
"""
conllu2json(input_data)
pass
# conllu2json(input_data)

44
spacy/tests/test_cli.py
View File

@ -1,9 +1,14 @@
import pytest
from spacy.gold import docs_to_json
from spacy.gold.converters import iob2docs, conll_ner2docs
from spacy.gold.converters.conllu2json import conllu2json
from spacy.lang.en import English
from spacy.cli.converters import conllu2json, iob2json, conll_ner2json
from spacy.cli.pretrain import make_docs
# TODO
# from spacy.gold.converters import conllu2docs
def test_cli_converters_conllu2json():
# from NorNE: https://github.com/ltgoslo/norne/blob/3d23274965f513f23aa48455b28b1878dad23c05/ud/nob/no_bokmaal-ud-dev.conllu
@ -109,7 +114,7 @@ def test_cli_converters_conllu2json_subtokens():
assert [t["ner"] for t in tokens] == ["O", "U-PER", "O", "O"]
def test_cli_converters_iob2json():
def test_cli_converters_iob2json(en_vocab):
lines = [
"I|O like|O London|I-GPE and|O New|B-GPE York|I-GPE City|I-GPE .|O",
"I|O like|O London|B-GPE and|O New|B-GPE York|I-GPE City|I-GPE .|O",
@ -117,19 +122,21 @@ def test_cli_converters_iob2json():
"I|PRP|O like|VBP|O London|NNP|B-GPE and|CC|O New|NNP|B-GPE York|NNP|I-GPE City|NNP|I-GPE .|.|O",
]
input_data = "\n".join(lines)
converted = iob2json(input_data, n_sents=10)
assert len(converted) == 1
assert converted[0]["id"] == 0
assert len(converted[0]["paragraphs"]) == 1
assert len(converted[0]["paragraphs"][0]["sentences"]) == 4
converted_docs = iob2docs(input_data, en_vocab, n_sents=10)
assert len(converted_docs) == 1
converted = docs_to_json(converted_docs)
assert converted["id"] == 0
assert len(converted["paragraphs"]) == 1
assert len(converted["paragraphs"][0]["sentences"]) == 4
for i in range(0, 4):
sent = converted[0]["paragraphs"][0]["sentences"][i]
sent = converted["paragraphs"][0]["sentences"][i]
assert len(sent["tokens"]) == 8
tokens = sent["tokens"]
# fmt: off
assert [t["orth"] for t in tokens] == ["I", "like", "London", "and", "New", "York", "City", "."]
assert [t["ner"] for t in tokens] == ["O", "O", "U-GPE", "O", "B-GPE", "I-GPE", "L-GPE", "O"]
# fmt: on
assert len(converted_docs[0].ents) == 8
for ent in converted_docs[0].ents:
assert(ent.text in ["New York City", "London"])
def test_cli_converters_conll_ner2json():
@ -182,19 +189,22 @@ def test_cli_converters_conll_ner2json():
".\t.\t_\tO",
]
input_data = "\n".join(lines)
converted = conll_ner2json(input_data, n_sents=10)
assert len(converted) == 1
assert converted[0]["id"] == 0
assert len(converted[0]["paragraphs"]) == 1
assert len(converted[0]["paragraphs"][0]["sentences"]) == 5
converted_docs = conll_ner2docs(input_data, n_sents=10)
assert len(converted_docs) == 1
converted = docs_to_json(converted_docs)
assert converted["id"] == 0
assert len(converted["paragraphs"]) == 1
assert len(converted["paragraphs"][0]["sentences"]) == 5
for i in range(0, 5):
sent = converted[0]["paragraphs"][0]["sentences"][i]
sent = converted["paragraphs"][0]["sentences"][i]
assert len(sent["tokens"]) == 8
tokens = sent["tokens"]
# fmt: off
assert [t["orth"] for t in tokens] == ["I", "like", "London", "and", "New", "York", "City", "."]
assert [t["ner"] for t in tokens] == ["O", "O", "U-GPE", "O", "B-GPE", "I-GPE", "L-GPE", "O"]
# fmt: on
assert len(converted_docs[0].ents) == 10
for ent in converted_docs[0].ents:
assert (ent.text in ["New York City", "London"])
def test_pretrain_make_docs():

520
spacy/tests/test_gold.py
View File

@ -1,15 +1,18 @@
from spacy.errors import AlignmentError
from spacy.gold import biluo_tags_from_offsets, offsets_from_biluo_tags
from spacy.gold import spans_from_biluo_tags, GoldParse, iob_to_biluo, align
from spacy.gold import GoldCorpus, docs_to_json, Example, DocAnnotation
from spacy.gold import spans_from_biluo_tags, iob_to_biluo, align
from spacy.gold import Corpus, docs_to_json
from spacy.gold.example import Example
from spacy.gold.converters import json2docs
from spacy.lang.en import English
from spacy.syntax.nonproj import is_nonproj_tree
from spacy.tokens import Doc
from spacy.tokens import Doc, DocBin
from spacy.util import get_words_and_spaces, compounding, minibatch
import pytest
import srsly
from .util import make_tempdir
from ..gold.augment import make_orth_variants_example
@pytest.fixture
@ -89,11 +92,18 @@ def merged_dict():
return {
"ids": [1, 2, 3, 4, 5, 6, 7],
"words": ["Hi", "there", "everyone", "It", "is", "just", "me"],
"spaces": [True, True, True, True, True, True, False],
"tags": ["INTJ", "ADV", "PRON", "PRON", "AUX", "ADV", "PRON"],
"sent_starts": [1, 0, 0, 1, 0, 0, 0, 0],
"sent_starts": [1, 0, 0, 1, 0, 0, 0],
}
@pytest.fixture
def vocab():
nlp = English()
return nlp.vocab
def test_gold_biluo_U(en_vocab):
words = ["I", "flew", "to", "London", "."]
spaces = [True, True, True, False, True]
@ -143,38 +153,182 @@ def test_gold_biluo_misalign(en_vocab):
assert tags == ["O", "O", "O", "-", "-", "-"]
def test_example_from_dict_no_ner(en_vocab):
words = ["a", "b", "c", "d"]
spaces = [True, True, False, True]
predicted = Doc(en_vocab, words=words, spaces=spaces)
example = Example.from_dict(predicted, {"words": words})
ner_tags = example.get_aligned_ner()
assert ner_tags == [None, None, None, None]
def test_example_from_dict_some_ner(en_vocab):
words = ["a", "b", "c", "d"]
spaces = [True, True, False, True]
predicted = Doc(en_vocab, words=words, spaces=spaces)
example = Example.from_dict(
predicted,
{
"words": words,
"entities": ["U-LOC", None, None, None]
}
)
ner_tags = example.get_aligned_ner()
assert ner_tags == ["U-LOC", None, None, None]
def test_json2docs_no_ner(en_vocab):
data = [{
"id":1,
"paragraphs":[
{
"sentences":[
{
"tokens":[
{
"dep":"nn",
"head":1,
"tag":"NNP",
"orth":"Ms."
},
{
"dep":"nsubj",
"head":1,
"tag":"NNP",
"orth":"Haag"
},
{
"dep":"ROOT",
"head":0,
"tag":"VBZ",
"orth":"plays"
},
{
"dep":"dobj",
"head":-1,
"tag":"NNP",
"orth":"Elianti"
},
{
"dep":"punct",
"head":-2,
"tag":".",
"orth":"."
}
]
}
]
}
]
}]
docs = json2docs(data)
assert len(docs) == 1
for doc in docs:
assert not doc.is_nered
for token in doc:
assert token.ent_iob == 0
eg = Example(
Doc(
doc.vocab,
words=[w.text for w in doc],
spaces=[bool(w.whitespace_) for w in doc]
),
doc
)
ner_tags = eg.get_aligned_ner()
assert ner_tags == [None, None, None, None, None]
def test_split_sentences(en_vocab):
words = ["I", "flew", "to", "San Francisco Valley", "had", "loads of fun"]
doc = Doc(en_vocab, words=words)
gold_words = [
"I",
"flew",
"to",
"San",
"Francisco",
"Valley",
"had",
"loads",
"of",
"fun",
]
sent_starts = [True, False, False, False, False, False, True, False, False, False]
example = Example.from_dict(doc, {"words": gold_words, "sent_starts": sent_starts})
assert example.text == "I flew to San Francisco Valley had loads of fun "
split_examples = example.split_sents()
assert len(split_examples) == 2
assert split_examples[0].text == "I flew to San Francisco Valley "
assert split_examples[1].text == "had loads of fun "
words = ["I", "flew", "to", "San", "Francisco", "Valley", "had", "loads", "of fun"]
doc = Doc(en_vocab, words=words)
gold_words = [
"I",
"flew",
"to",
"San Francisco",
"Valley",
"had",
"loads of",
"fun",
]
sent_starts = [True, False, False, False, False, True, False, False]
example = Example.from_dict(doc, {"words": gold_words, "sent_starts": sent_starts})
assert example.text == "I flew to San Francisco Valley had loads of fun "
split_examples = example.split_sents()
assert len(split_examples) == 2
assert split_examples[0].text == "I flew to San Francisco Valley "
assert split_examples[1].text == "had loads of fun "
def test_gold_biluo_different_tokenization(en_vocab, en_tokenizer):
# one-to-many
words = ["I", "flew to", "San Francisco Valley", "."]
spaces = [True, True, False, False]
doc = Doc(en_vocab, words=words, spaces=spaces)
entities = [(len("I flew to "), len("I flew to San Francisco Valley"), "LOC")]
gp = GoldParse(
doc,
words=["I", "flew", "to", "San", "Francisco", "Valley", "."],
entities=entities,
)
assert gp.ner == ["O", "O", "U-LOC", "O"]
gold_words = ["I", "flew", "to", "San", "Francisco", "Valley", "."]
example = Example.from_dict(doc, {"words": gold_words, "entities": entities})
ner_tags = example.get_aligned_ner()
assert ner_tags == ["O", None, "U-LOC", "O"]
# many-to-one
words = ["I", "flew", "to", "San", "Francisco", "Valley", "."]
spaces = [True, True, True, True, True, False, False]
doc = Doc(en_vocab, words=words, spaces=spaces)
entities = [(len("I flew to "), len("I flew to San Francisco Valley"), "LOC")]
gp = GoldParse(
doc, words=["I", "flew to", "San Francisco Valley", "."], entities=entities
)
assert gp.ner == ["O", "O", "O", "B-LOC", "I-LOC", "L-LOC", "O"]
gold_words = ["I", "flew to", "San Francisco Valley", "."]
example = Example.from_dict(doc, {"words": gold_words, "entities": entities})
ner_tags = example.get_aligned_ner()
assert ner_tags == ["O", "O", "O", "B-LOC", "I-LOC", "L-LOC", "O"]
# misaligned
words = ["I flew", "to", "San Francisco", "Valley", "."]
spaces = [True, True, True, False, False]
doc = Doc(en_vocab, words=words, spaces=spaces)
entities = [(len("I flew to "), len("I flew to San Francisco Valley"), "LOC")]
gp = GoldParse(
doc, words=["I", "flew to", "San", "Francisco Valley", "."], entities=entities,
offset_start = len("I flew to ")
offset_end = len("I flew to San Francisco Valley")
entities = [(offset_start, offset_end, "LOC")]
links = {(offset_start, offset_end): {"Q816843": 1.0}}
gold_words = ["I", "flew to", "San", "Francisco Valley", "."]
example = Example.from_dict(
doc, {"words": gold_words, "entities": entities, "links": links}
)
assert gp.ner == ["O", "O", "B-LOC", "L-LOC", "O"]
ner_tags = example.get_aligned_ner()
assert ner_tags == [None, "O", "B-LOC", "L-LOC", "O"]
#assert example.get_aligned("ENT_KB_ID", as_string=True) == [
# "",
# "",
# "Q816843",
# "Q816843",
# "",
#]
#assert example.to_dict()["doc_annotation"]["links"][(offset_start, offset_end)] == {
# "Q816843": 1.0
#}
# additional whitespace tokens in GoldParse words
words, spaces = get_words_and_spaces(
@ -183,33 +337,34 @@ def test_gold_biluo_different_tokenization(en_vocab, en_tokenizer):
)
doc = Doc(en_vocab, words=words, spaces=spaces)
entities = [(len("I flew to "), len("I flew to San Francisco Valley"), "LOC")]
gp = GoldParse(
doc,
words=["I", "flew", " ", "to", "San Francisco Valley", "."],
entities=entities,
gold_words = ["I", "flew", " ", "to", "San Francisco Valley", "."]
gold_spaces = [True, True, False, True, False, False]
example = Example.from_dict(
doc, {"words": gold_words, "spaces": gold_spaces, "entities": entities}
)
assert gp.ner == ["O", "O", "O", "O", "B-LOC", "L-LOC", "O"]
ner_tags = example.get_aligned_ner()
assert ner_tags == ["O", "O", "O", "O", "B-LOC", "L-LOC", "O"]
# from issue #4791
data = (
"I'll return the ₹54 amount",
{
"words": ["I", "'ll", "return", "the", "₹", "54", "amount"],
"entities": [(16, 19, "MONEY")],
},
doc = en_tokenizer("I'll return the ₹54 amount")
gold_words = ["I", "'ll", "return", "the", "₹", "54", "amount"]
gold_spaces = [False, True, True, True, False, True, False]
entities = [(16, 19, "MONEY")]
example = Example.from_dict(
doc, {"words": gold_words, "spaces": gold_spaces, "entities": entities}
)
gp = GoldParse(en_tokenizer(data[0]), **data[1])
assert gp.ner == ["O", "O", "O", "O", "U-MONEY", "O"]
ner_tags = example.get_aligned_ner()
assert ner_tags == ["O", "O", "O", "O", "U-MONEY", "O"]
data = (
"I'll return the $54 amount",
{
"words": ["I", "'ll", "return", "the", "$", "54", "amount"],
"entities": [(16, 19, "MONEY")],
},
doc = en_tokenizer("I'll return the $54 amount")
gold_words = ["I", "'ll", "return", "the", "$", "54", "amount"]
gold_spaces = [False, True, True, True, False, True, False]
entities = [(16, 19, "MONEY")]
example = Example.from_dict(
doc, {"words": gold_words, "spaces": gold_spaces, "entities": entities}
)
gp = GoldParse(en_tokenizer(data[0]), **data[1])
assert gp.ner == ["O", "O", "O", "O", "B-MONEY", "L-MONEY", "O"]
ner_tags = example.get_aligned_ner()
assert ner_tags == ["O", "O", "O", "O", "B-MONEY", "L-MONEY", "O"]
def test_roundtrip_offsets_biluo_conversion(en_tokenizer):
@ -220,6 +375,7 @@ def test_roundtrip_offsets_biluo_conversion(en_tokenizer):
biluo_tags_converted = biluo_tags_from_offsets(doc, offsets)
assert biluo_tags_converted == biluo_tags
offsets_converted = offsets_from_biluo_tags(doc, biluo_tags)
offsets_converted = [ent for ent in offsets if ent[2]]
assert offsets_converted == offsets
@ -227,6 +383,7 @@ def test_biluo_spans(en_tokenizer):
doc = en_tokenizer("I flew to Silicon Valley via London.")
biluo_tags = ["O", "O", "O", "B-LOC", "L-LOC", "O", "U-GPE", "O"]
spans = spans_from_biluo_tags(doc, biluo_tags)
spans = [span for span in spans if span.label_]
assert len(spans) == 2
assert spans[0].text == "Silicon Valley"
assert spans[0].label_ == "LOC"
@ -237,7 +394,8 @@ def test_biluo_spans(en_tokenizer):
def test_gold_ner_missing_tags(en_tokenizer):
doc = en_tokenizer("I flew to Silicon Valley via London.")
biluo_tags = [None, "O", "O", "B-LOC", "L-LOC", "O", "U-GPE", "O"]
gold = GoldParse(doc, entities=biluo_tags) # noqa: F841
example = Example.from_dict(doc, {"entities": biluo_tags})
assert example.get_aligned("ENT_IOB") == [0, 2, 2, 3, 1, 2, 3, 2]
def test_iob_to_biluo():
@ -250,159 +408,98 @@ def test_iob_to_biluo():
iob_to_biluo(bad_iob)
def test_roundtrip_docs_to_json(doc):
def test_roundtrip_docs_to_docbin(doc):
nlp = English()
text = doc.text
idx = [t.idx for t in doc]
tags = [t.tag_ for t in doc]
pos = [t.pos_ for t in doc]
morphs = [t.morph_ for t in doc]
lemmas = [t.lemma_ for t in doc]
deps = [t.dep_ for t in doc]
heads = [t.head.i for t in doc]
biluo_tags = iob_to_biluo(
[t.ent_iob_ + "-" + t.ent_type_ if t.ent_type_ else "O" for t in doc]
)
cats = doc.cats
ents = [(e.start_char, e.end_char, e.label_) for e in doc.ents]
# roundtrip to JSON
# roundtrip to DocBin
with make_tempdir() as tmpdir:
json_file = tmpdir / "roundtrip.json"
srsly.write_json(json_file, [docs_to_json(doc)])
goldcorpus = GoldCorpus(train=str(json_file), dev=str(json_file))
reloaded_example = next(goldcorpus.dev_dataset(nlp))
goldparse = reloaded_example.gold
assert len(doc) == goldcorpus.count_train()
assert text == reloaded_example.text
assert tags == goldparse.tags
assert pos == goldparse.pos
assert morphs == goldparse.morphs
assert lemmas == goldparse.lemmas
assert deps == goldparse.labels
assert heads == goldparse.heads
assert biluo_tags == goldparse.ner
assert "TRAVEL" in goldparse.cats
assert "BAKING" in goldparse.cats
assert cats["TRAVEL"] == goldparse.cats["TRAVEL"]
assert cats["BAKING"] == goldparse.cats["BAKING"]
# roundtrip to JSONL train dicts
with make_tempdir() as tmpdir:
jsonl_file = tmpdir / "roundtrip.jsonl"
srsly.write_jsonl(jsonl_file, [docs_to_json(doc)])
goldcorpus = GoldCorpus(str(jsonl_file), str(jsonl_file))
reloaded_example = next(goldcorpus.dev_dataset(nlp))
goldparse = reloaded_example.gold
assert len(doc) == goldcorpus.count_train()
assert text == reloaded_example.text
assert tags == goldparse.tags
assert pos == goldparse.pos
assert morphs == goldparse.morphs
assert lemmas == goldparse.lemmas
assert deps == goldparse.labels
assert heads == goldparse.heads
assert biluo_tags == goldparse.ner
assert "TRAVEL" in goldparse.cats
assert "BAKING" in goldparse.cats
assert cats["TRAVEL"] == goldparse.cats["TRAVEL"]
assert cats["BAKING"] == goldparse.cats["BAKING"]
# roundtrip to JSONL tuples
with make_tempdir() as tmpdir:
jsonl_file = tmpdir / "roundtrip.jsonl"
# write to JSONL train dicts
srsly.write_jsonl(jsonl_file, [docs_to_json(doc)])
goldcorpus = GoldCorpus(str(jsonl_file), str(jsonl_file))
# load and rewrite as JSONL tuples
srsly.write_jsonl(jsonl_file, goldcorpus.train_examples)
goldcorpus = GoldCorpus(str(jsonl_file), str(jsonl_file))
reloaded_example = next(goldcorpus.dev_dataset(nlp))
goldparse = reloaded_example.gold
assert len(doc) == goldcorpus.count_train()
assert text == reloaded_example.text
assert tags == goldparse.tags
assert deps == goldparse.labels
assert heads == goldparse.heads
assert lemmas == goldparse.lemmas
assert biluo_tags == goldparse.ner
assert "TRAVEL" in goldparse.cats
assert "BAKING" in goldparse.cats
assert cats["TRAVEL"] == goldparse.cats["TRAVEL"]
assert cats["BAKING"] == goldparse.cats["BAKING"]
def test_projective_train_vs_nonprojective_dev(doc):
nlp = English()
deps = [t.dep_ for t in doc]
heads = [t.head.i for t in doc]
with make_tempdir() as tmpdir:
jsonl_file = tmpdir / "test.jsonl"
# write to JSONL train dicts
srsly.write_jsonl(jsonl_file, [docs_to_json(doc)])
goldcorpus = GoldCorpus(str(jsonl_file), str(jsonl_file))
train_reloaded_example = next(goldcorpus.train_dataset(nlp))
train_goldparse = train_reloaded_example.gold
dev_reloaded_example = next(goldcorpus.dev_dataset(nlp))
dev_goldparse = dev_reloaded_example.gold
assert is_nonproj_tree([t.head.i for t in doc]) is True
assert is_nonproj_tree(train_goldparse.heads) is False
assert heads[:-1] == train_goldparse.heads[:-1]
assert heads[-1] != train_goldparse.heads[-1]
assert deps[:-1] == train_goldparse.labels[:-1]
assert deps[-1] != train_goldparse.labels[-1]
assert heads == dev_goldparse.heads
assert deps == dev_goldparse.labels
goldcorpus = Corpus(str(json_file), str(json_file))
output_file = tmpdir / "roundtrip.spacy"
data = DocBin(docs=[doc]).to_bytes()
with output_file.open("wb") as file_:
file_.write(data)
goldcorpus = Corpus(train_loc=str(output_file), dev_loc=str(output_file))
reloaded_example = next(goldcorpus.dev_dataset(nlp=nlp))
assert len(doc) == goldcorpus.count_train(nlp)
assert text == reloaded_example.reference.text
assert idx == [t.idx for t in reloaded_example.reference]
assert tags == [t.tag_ for t in reloaded_example.reference]
assert pos == [t.pos_ for t in reloaded_example.reference]
assert morphs == [t.morph_ for t in reloaded_example.reference]
assert lemmas == [t.lemma_ for t in reloaded_example.reference]
assert deps == [t.dep_ for t in reloaded_example.reference]
assert heads == [t.head.i for t in reloaded_example.reference]
assert ents == [
(e.start_char, e.end_char, e.label_) for e in reloaded_example.reference.ents
]
assert "TRAVEL" in reloaded_example.reference.cats
assert "BAKING" in reloaded_example.reference.cats
assert cats["TRAVEL"] == reloaded_example.reference.cats["TRAVEL"]
assert cats["BAKING"] == reloaded_example.reference.cats["BAKING"]
# Hm, not sure where misalignment check would be handled? In the components too?
# I guess that does make sense. A text categorizer doesn't care if it's
# misaligned...
@pytest.mark.xfail(reason="Outdated")
def test_ignore_misaligned(doc):
nlp = English()
text = doc.text
with make_tempdir() as tmpdir:
jsonl_file = tmpdir / "test.jsonl"
json_file = tmpdir / "test.json"
data = [docs_to_json(doc)]
data[0]["paragraphs"][0]["raw"] = text.replace("Sarah", "Jane")
# write to JSONL train dicts
srsly.write_jsonl(jsonl_file, data)
goldcorpus = GoldCorpus(str(jsonl_file), str(jsonl_file))
# write to JSON train dicts
srsly.write_json(json_file, data)
goldcorpus = Corpus(str(json_file), str(json_file))
with pytest.raises(AlignmentError):
train_reloaded_example = next(goldcorpus.train_dataset(nlp))
with pytest.raises(AlignmentError):
train_reloaded_example = next(goldcorpus.train_dataset(nlp))
with make_tempdir() as tmpdir:
jsonl_file = tmpdir / "test.jsonl"
json_file = tmpdir / "test.json"
data = [docs_to_json(doc)]
data[0]["paragraphs"][0]["raw"] = text.replace("Sarah", "Jane")
# write to JSONL train dicts
srsly.write_jsonl(jsonl_file, data)
goldcorpus = GoldCorpus(str(jsonl_file), str(jsonl_file))
# write to JSON train dicts
srsly.write_json(json_file, data)
goldcorpus = Corpus(str(json_file), str(json_file))
# doesn't raise an AlignmentError, but there is nothing to iterate over
# because the only example can't be aligned
train_reloaded_example = list(goldcorpus.train_dataset(nlp, ignore_misaligned=True))
assert len(train_reloaded_example) == 0
# doesn't raise an AlignmentError, but there is nothing to iterate over
# because the only example can't be aligned
train_reloaded_example = list(
goldcorpus.train_dataset(nlp, ignore_misaligned=True)
)
assert len(train_reloaded_example) == 0
# We probably want the orth variant logic back, but this test won't be quite
# right -- we need to go from DocBin.
def test_make_orth_variants(doc):
nlp = English()
with make_tempdir() as tmpdir:
jsonl_file = tmpdir / "test.jsonl"
# write to JSONL train dicts
srsly.write_jsonl(jsonl_file, [docs_to_json(doc)])
goldcorpus = GoldCorpus(str(jsonl_file), str(jsonl_file))
output_file = tmpdir / "roundtrip.spacy"
data = DocBin(docs=[doc]).to_bytes()
with output_file.open("wb") as file_:
file_.write(data)
goldcorpus = Corpus(train_loc=str(output_file), dev_loc=str(output_file))
# due to randomness, test only that this runs with no errors for now
train_reloaded_example = next(goldcorpus.train_dataset(nlp, orth_variant_level=0.2))
train_goldparse = train_reloaded_example.gold # noqa: F841
# due to randomness, test only that this runs with no errors for now
train_example = next(goldcorpus.train_dataset(nlp))
variant_example = make_orth_variants_example(
nlp, train_example, orth_variant_level=0.2
)
@pytest.mark.parametrize(
@ -439,39 +536,35 @@ def test_align(tokens_a, tokens_b, expected):
def test_goldparse_startswith_space(en_tokenizer):
text = " a"
doc = en_tokenizer(text)
g = GoldParse(doc, words=["a"], entities=["U-DATE"], deps=["ROOT"], heads=[0])
assert g.words == [" ", "a"]
assert g.ner == [None, "U-DATE"]
assert g.labels == [None, "ROOT"]
gold_words = ["a"]
entities = ["U-DATE"]
deps = ["ROOT"]
heads = [0]
example = Example.from_dict(
doc, {"words": gold_words, "entities": entities, "deps": deps, "heads": heads}
)
ner_tags = example.get_aligned_ner()
assert ner_tags == [None, "U-DATE"]
assert example.get_aligned("DEP", as_string=True) == [None, "ROOT"]
def test_gold_constructor():
"""Test that the GoldParse constructor works fine"""
"""Test that the Example constructor works fine"""
nlp = English()
doc = nlp("This is a sentence")
gold = GoldParse(doc, cats={"cat1": 1.0, "cat2": 0.0})
assert gold.cats["cat1"]
assert not gold.cats["cat2"]
assert gold.words == ["This", "is", "a", "sentence"]
def test_gold_orig_annot():
nlp = English()
doc = nlp("This is a sentence")
gold = GoldParse(doc, cats={"cat1": 1.0, "cat2": 0.0})
assert gold.orig.words == ["This", "is", "a", "sentence"]
assert gold.cats["cat1"]
doc_annotation = DocAnnotation(cats={"cat1": 0.0, "cat2": 1.0})
gold2 = GoldParse.from_annotation(doc, doc_annotation, gold.orig)
assert gold2.orig.words == ["This", "is", "a", "sentence"]
assert not gold2.cats["cat1"]
example = Example.from_dict(doc, {"cats": {"cat1": 1.0, "cat2": 0.0}})
assert example.get_aligned("ORTH", as_string=True) == [
"This",
"is",
"a",
"sentence",
]
assert example.reference.cats["cat1"]
assert not example.reference.cats["cat2"]
def test_tuple_format_implicit():
"""Test tuple format with implicit GoldParse creation"""
"""Test tuple format"""
train_data = [
("Uber blew through $1 million a week", {"entities": [(0, 4, "ORG")]}),
@ -486,7 +579,7 @@ def test_tuple_format_implicit():
def test_tuple_format_implicit_invalid():
"""Test that an error is thrown for an implicit invalid GoldParse field"""
"""Test that an error is thrown for an implicit invalid field"""
train_data = [
("Uber blew through $1 million a week", {"frumble": [(0, 4, "ORG")]}),
@ -497,10 +590,11 @@ def test_tuple_format_implicit_invalid():
("Google rebrands its business apps", {"entities": [(0, 6, "ORG")]}),
]
with pytest.raises(TypeError):
with pytest.raises(KeyError):
_train(train_data)
def _train(train_data):
nlp = English()
ner = nlp.create_pipe("ner")
@ -518,43 +612,23 @@ def _train(train_data):
def test_split_sents(merged_dict):
nlp = English()
example = Example()
example.set_token_annotation(**merged_dict)
assert len(example.get_gold_parses(merge=False, vocab=nlp.vocab)) == 2
assert len(example.get_gold_parses(merge=True, vocab=nlp.vocab)) == 1
example = Example.from_dict(
Doc(nlp.vocab, words=merged_dict["words"], spaces=merged_dict["spaces"]),
merged_dict,
)
assert example.text == "Hi there everyone It is just me"
split_examples = example.split_sents()
assert len(split_examples) == 2
assert split_examples[0].text == "Hi there everyone "
assert split_examples[1].text == "It is just me"
token_annotation_1 = split_examples[0].token_annotation
assert token_annotation_1.ids == [1, 2, 3]
assert token_annotation_1.words == ["Hi", "there", "everyone"]
assert token_annotation_1.tags == ["INTJ", "ADV", "PRON"]
assert token_annotation_1.sent_starts == [1, 0, 0]
token_annotation_1 = split_examples[0].to_dict()["token_annotation"]
assert token_annotation_1["words"] == ["Hi", "there", "everyone"]
assert token_annotation_1["tags"] == ["INTJ", "ADV", "PRON"]
assert token_annotation_1["sent_starts"] == [1, 0, 0]
token_annotation_2 = split_examples[1].token_annotation
assert token_annotation_2.ids == [4, 5, 6, 7]
assert token_annotation_2.words == ["It", "is", "just", "me"]
assert token_annotation_2.tags == ["PRON", "AUX", "ADV", "PRON"]
assert token_annotation_2.sent_starts == [1, 0, 0, 0]
def test_tuples_to_example(merged_dict):
ex = Example()
ex.set_token_annotation(**merged_dict)
cats = {"TRAVEL": 1.0, "BAKING": 0.0}
ex.set_doc_annotation(cats=cats)
ex_dict = ex.to_dict()
assert ex_dict["token_annotation"]["ids"] == merged_dict["ids"]
assert ex_dict["token_annotation"]["words"] == merged_dict["words"]
assert ex_dict["token_annotation"]["tags"] == merged_dict["tags"]
assert ex_dict["token_annotation"]["sent_starts"] == merged_dict["sent_starts"]
assert ex_dict["doc_annotation"]["cats"] == cats
def test_empty_example_goldparse():
nlp = English()
doc = nlp("")
example = Example(doc=doc)
assert len(example.get_gold_parses()) == 1
token_annotation_2 = split_examples[1].to_dict()["token_annotation"]
assert token_annotation_2["words"] == ["It", "is", "just", "me"]
assert token_annotation_2["tags"] == ["PRON", "AUX", "ADV", "PRON"]
assert token_annotation_2["sent_starts"] == [1, 0, 0, 0]

20
spacy/tests/test_language.py
View File

@ -1,6 +1,5 @@
import itertools
import pytest
from spacy.gold import GoldParse
from spacy.language import Language
from spacy.tokens import Doc, Span
from spacy.vocab import Vocab
@ -24,40 +23,27 @@ def test_language_update(nlp):
annots = {"cats": {"POSITIVE": 1.0, "NEGATIVE": 0.0}}
wrongkeyannots = {"LABEL": True}
doc = Doc(nlp.vocab, words=text.split(" "))
gold = GoldParse(doc, **annots)
# Update with doc and gold objects
nlp.update((doc, gold))
# Update with text and dict
nlp.update((text, annots))
# Update with doc object and dict
nlp.update((doc, annots))
# Update with text and gold object
nlp.update((text, gold))
# Update with empty doc and gold object
nlp.update((None, gold))
# Update badly
with pytest.raises(ValueError):
nlp.update((doc, None))
with pytest.raises(TypeError):
with pytest.raises(KeyError):
nlp.update((text, wrongkeyannots))
def test_language_evaluate(nlp):
text = "hello world"
annots = {"cats": {"POSITIVE": 1.0, "NEGATIVE": 0.0}}
annots = {"doc_annotation": {"cats": {"POSITIVE": 1.0, "NEGATIVE": 0.0}}}
doc = Doc(nlp.vocab, words=text.split(" "))
gold = GoldParse(doc, **annots)
# Evaluate with doc and gold objects
nlp.evaluate([(doc, gold)])
# Evaluate with text and dict
nlp.evaluate([(text, annots)])
# Evaluate with doc object and dict
nlp.evaluate([(doc, annots)])
# Evaluate with text and gold object
nlp.evaluate([(text, gold)])
# Evaluate badly
with pytest.raises(Exception):
nlp.evaluate([text, gold])
nlp.evaluate([text, annots])
def test_evaluate_no_pipe(nlp):

242
spacy/tests/test_new_example.py Normal file
View File

@ -0,0 +1,242 @@
import pytest
from spacy.gold.example import Example
from spacy.tokens import Doc
from spacy.vocab import Vocab
def test_Example_init_requires_doc_objects():
vocab = Vocab()
with pytest.raises(TypeError):
example = Example(None, None)
with pytest.raises(TypeError):
example = Example(Doc(vocab, words=["hi"]), None)
with pytest.raises(TypeError):
example = Example(None, Doc(vocab, words=["hi"]))
def test_Example_from_dict_basic():
example = Example.from_dict(
Doc(Vocab(), words=["hello", "world"]), {"words": ["hello", "world"]}
)
assert isinstance(example.x, Doc)
assert isinstance(example.y, Doc)
@pytest.mark.parametrize(
"annots", [{"words": ["ice", "cream"], "weirdannots": ["something", "such"]}]
)
def test_Example_from_dict_invalid(annots):
vocab = Vocab()
predicted = Doc(vocab, words=annots["words"])
with pytest.raises(KeyError):
Example.from_dict(predicted, annots)
@pytest.mark.parametrize(
"pred_words", [["ice", "cream"], ["icecream"], ["i", "ce", "cream"]]
)
@pytest.mark.parametrize("annots", [{"words": ["icecream"], "tags": ["NN"]}])
def test_Example_from_dict_with_tags(pred_words, annots):
vocab = Vocab()
predicted = Doc(vocab, words=pred_words)
example = Example.from_dict(predicted, annots)
for i, token in enumerate(example.reference):
assert token.tag_ == annots["tags"][i]
aligned_tags = example.get_aligned("tag", as_string=True)
assert aligned_tags == ["NN" for _ in predicted]
def test_aligned_tags():
pred_words = ["Apply", "some", "sunscreen", "unless", "you", "can", "not"]
gold_words = ["Apply", "some", "sun", "screen", "unless", "you", "cannot"]
gold_tags = ["VERB", "DET", "NOUN", "NOUN", "SCONJ", "PRON", "VERB"]
annots = {"words": gold_words, "tags": gold_tags}
vocab = Vocab()
predicted = Doc(vocab, words=pred_words)
example = Example.from_dict(predicted, annots)
aligned_tags = example.get_aligned("tag", as_string=True)
assert aligned_tags == ["VERB", "DET", None, "SCONJ", "PRON", "VERB", "VERB"]
def test_aligned_tags_multi():
pred_words = ["Applysome", "sunscreen", "unless", "you", "can", "not"]
gold_words = ["Apply", "somesun", "screen", "unless", "you", "cannot"]
gold_tags = ["VERB", "DET", "NOUN", "SCONJ", "PRON", "VERB"]
annots = {"words": gold_words, "tags": gold_tags}
vocab = Vocab()
predicted = Doc(vocab, words=pred_words)
example = Example.from_dict(predicted, annots)
aligned_tags = example.get_aligned("tag", as_string=True)
assert aligned_tags == [None, None, "SCONJ", "PRON", "VERB", "VERB"]
@pytest.mark.parametrize(
"annots",
[
{
"words": ["I", "like", "London", "and", "Berlin", "."],
"deps": ["nsubj", "ROOT", "dobj", "cc", "conj", "punct"],
"heads": [1, 1, 1, 2, 2, 1],
}
],
)
def test_Example_from_dict_with_parse(annots):
vocab = Vocab()
predicted = Doc(vocab, words=annots["words"])
example = Example.from_dict(predicted, annots)
for i, token in enumerate(example.reference):
assert token.dep_ == annots["deps"][i]
assert token.head.i == annots["heads"][i]
@pytest.mark.parametrize(
"annots",
[
{
"words": ["Sarah", "'s", "sister", "flew"],
"morphs": [
"NounType=prop|Number=sing",
"Poss=yes",
"Number=sing",
"Tense=past|VerbForm=fin",
],
}
],
)
def test_Example_from_dict_with_morphology(annots):
vocab = Vocab()
predicted = Doc(vocab, words=annots["words"])
example = Example.from_dict(predicted, annots)
for i, token in enumerate(example.reference):
assert token.morph_ == annots["morphs"][i]
@pytest.mark.parametrize(
"annots",
[
{
"words": ["This", "is", "one", "sentence", "this", "is", "another"],
"sent_starts": [1, 0, 0, 0, 1, 0, 0],
}
],
)
def test_Example_from_dict_with_sent_start(annots):
vocab = Vocab()
predicted = Doc(vocab, words=annots["words"])
example = Example.from_dict(predicted, annots)
assert len(list(example.reference.sents)) == 2
for i, token in enumerate(example.reference):
assert bool(token.is_sent_start) == bool(annots["sent_starts"][i])
@pytest.mark.parametrize(
"annots",
[
{
"words": ["This", "is", "a", "sentence"],
"cats": {"cat1": 1.0, "cat2": 0.0, "cat3": 0.5},
}
],
)
def test_Example_from_dict_with_cats(annots):
vocab = Vocab()
predicted = Doc(vocab, words=annots["words"])
example = Example.from_dict(predicted, annots)
assert len(list(example.reference.cats)) == 3
assert example.reference.cats["cat1"] == 1.0
assert example.reference.cats["cat2"] == 0.0
assert example.reference.cats["cat3"] == 0.5
@pytest.mark.parametrize(
"annots",
[
{
"words": ["I", "like", "New", "York", "and", "Berlin", "."],
"entities": [(7, 15, "LOC"), (20, 26, "LOC")],
}
],
)
def test_Example_from_dict_with_entities(annots):
vocab = Vocab()
predicted = Doc(vocab, words=annots["words"])
example = Example.from_dict(predicted, annots)
assert len(list(example.reference.ents)) == 2
assert [example.reference[i].ent_iob_ for i in range(7)] == [
"O",
"O",
"B",
"I",
"O",
"B",
"O",
]
assert example.get_aligned("ENT_IOB") == [2, 2, 3, 1, 2, 3, 2]
assert example.reference[2].ent_type_ == "LOC"
assert example.reference[3].ent_type_ == "LOC"
assert example.reference[5].ent_type_ == "LOC"
@pytest.mark.parametrize(
"annots",
[
{
"words": ["I", "like", "New", "York", "and", "Berlin", "."],
"entities": [
(0, 4, "LOC"),
(21, 27, "LOC"),
], # not aligned to token boundaries
}
],
)
def test_Example_from_dict_with_entities_invalid(annots):
vocab = Vocab()
predicted = Doc(vocab, words=annots["words"])
example = Example.from_dict(predicted, annots)
# TODO: shouldn't this throw some sort of warning ?
assert len(list(example.reference.ents)) == 0
@pytest.mark.parametrize(
"annots",
[
{
"words": ["I", "like", "New", "York", "and", "Berlin", "."],
"entities": [(7, 15, "LOC"), (20, 26, "LOC")],
"links": {
(7, 15): {"Q60": 1.0, "Q64": 0.0},
(20, 26): {"Q60": 0.0, "Q64": 1.0},
},
}
],
)
def test_Example_from_dict_with_links(annots):
vocab = Vocab()
predicted = Doc(vocab, words=annots["words"])
example = Example.from_dict(predicted, annots)
assert example.reference[0].ent_kb_id_ == ""
assert example.reference[1].ent_kb_id_ == ""
assert example.reference[2].ent_kb_id_ == "Q60"
assert example.reference[3].ent_kb_id_ == "Q60"
assert example.reference[4].ent_kb_id_ == ""
assert example.reference[5].ent_kb_id_ == "Q64"
assert example.reference[6].ent_kb_id_ == ""
@pytest.mark.parametrize(
"annots",
[
{
"words": ["I", "like", "New", "York", "and", "Berlin", "."],
"entities": [(7, 15, "LOC"), (20, 26, "LOC")],
"links": {(0, 1): {"Q7381115": 1.0, "Q2146908": 0.0}},
}
],
)
def test_Example_from_dict_with_links_invalid(annots):
vocab = Vocab()
predicted = Doc(vocab, words=annots["words"])
with pytest.raises(ValueError):
Example.from_dict(predicted, annots)

41
spacy/tests/test_scorer.py
View File

@ -1,12 +1,14 @@
from numpy.testing import assert_almost_equal, assert_array_almost_equal
import pytest
from pytest import approx
from spacy.gold import Example, GoldParse
from spacy.gold import Example
from spacy.gold.iob_utils import biluo_tags_from_offsets
from spacy.scorer import Scorer, ROCAUCScore
from spacy.scorer import _roc_auc_score, _roc_curve
from .util import get_doc
from spacy.lang.en import English
test_las_apple = [
[
"Apple is looking at buying U.K. startup for $ 1 billion",
@ -89,8 +91,9 @@ def test_las_per_type(en_vocab):
heads=([h - i for i, h in enumerate(annot["heads"])]),
deps=annot["deps"],
)
gold = GoldParse(doc, heads=annot["heads"], deps=annot["deps"])
scorer.score((doc, gold))
gold = {"heads": annot["heads"], "deps": annot["deps"]}
example = Example.from_dict(doc, gold)
scorer.score(example)
results = scorer.scores
assert results["uas"] == 100
@ -111,9 +114,10 @@ def test_las_per_type(en_vocab):
heads=([h - i for i, h in enumerate(annot["heads"])]),
deps=annot["deps"],
)
gold = GoldParse(doc, heads=annot["heads"], deps=annot["deps"])
gold = {"heads": annot["heads"], "deps": annot["deps"]}
doc[0].dep_ = "compound"
scorer.score((doc, gold))
example = Example.from_dict(doc, gold)
scorer.score(example)
results = scorer.scores
assert results["uas"] == 100
@ -135,8 +139,8 @@ def test_ner_per_type(en_vocab):
words=input_.split(" "),
ents=[[0, 1, "CARDINAL"], [2, 3, "CARDINAL"]],
)
ex = Example(doc=doc)
ex.set_token_annotation(entities=annot["entities"])
entities = biluo_tags_from_offsets(doc, annot["entities"])
ex = Example.from_dict(doc, {"entities": entities})
scorer.score(ex)
results = scorer.scores
@ -156,8 +160,8 @@ def test_ner_per_type(en_vocab):
words=input_.split(" "),
ents=[[0, 1, "ORG"], [5, 6, "GPE"], [6, 7, "ORG"]],
)
ex = Example(doc=doc)
ex.set_token_annotation(entities=annot["entities"])
entities = biluo_tags_from_offsets(doc, annot["entities"])
ex = Example.from_dict(doc, {"entities": entities})
scorer.score(ex)
results = scorer.scores
@ -181,13 +185,13 @@ def test_ner_per_type(en_vocab):
def test_tag_score(tagged_doc):
# Gold and Doc are identical
scorer = Scorer()
gold = GoldParse(
tagged_doc,
tags=[t.tag_ for t in tagged_doc],
pos=[t.pos_ for t in tagged_doc],
morphs=[t.morph_ for t in tagged_doc],
)
scorer.score((tagged_doc, gold))
gold = {
"tags": [t.tag_ for t in tagged_doc],
"pos": [t.pos_ for t in tagged_doc],
"morphs": [t.morph_ for t in tagged_doc],
}
example = Example.from_dict(tagged_doc, gold)
scorer.score(example)
results = scorer.scores
assert results["tags_acc"] == 100
@ -204,8 +208,9 @@ def test_tag_score(tagged_doc):
morphs = [t.morph_ for t in tagged_doc]
morphs[1] = "Number=sing"
morphs[2] = "Number=plur"
gold = GoldParse(tagged_doc, tags=tags, pos=pos, morphs=morphs)
scorer.score((tagged_doc, gold))
gold = {"tags": tags, "pos": pos, "morphs": morphs}
example = Example.from_dict(tagged_doc, gold)
scorer.score(example)
results = scorer.scores
assert results["tags_acc"] == 90

13
spacy/tests/test_util.py
View File

@ -1,5 +1,4 @@
import pytest
from spacy.gold import Example
from .util import get_random_doc
@ -25,19 +24,16 @@ from spacy.util import minibatch_by_words
)
def test_util_minibatch(doc_sizes, expected_batches):
docs = [get_random_doc(doc_size) for doc_size in doc_sizes]
examples = [Example(doc=doc) for doc in docs]
tol = 0.2
batch_size = 1000
batches = list(
minibatch_by_words(
examples=examples, size=batch_size, tolerance=tol, discard_oversize=True
)
minibatch_by_words(docs, size=batch_size, tolerance=tol, discard_oversize=True)
)
assert [len(batch) for batch in batches] == expected_batches
max_size = batch_size + batch_size * tol
for batch in batches:
assert sum([len(example.doc) for example in batch]) < max_size
assert sum([len(doc) for doc in batch]) < max_size
@pytest.mark.parametrize(
@ -54,12 +50,9 @@ def test_util_minibatch(doc_sizes, expected_batches):
def test_util_minibatch_oversize(doc_sizes, expected_batches):
""" Test that oversized documents are returned in their own batch"""
docs = [get_random_doc(doc_size) for doc_size in doc_sizes]
examples = [Example(doc=doc) for doc in docs]
tol = 0.2
batch_size = 1000
batches = list(
minibatch_by_words(
examples=examples, size=batch_size, tolerance=tol, discard_oversize=False
)
minibatch_by_words(docs, size=batch_size, tolerance=tol, discard_oversize=False)
)
assert [len(batch) for batch in batches] == expected_batches

23
spacy/tests/util.py
View File

@ -7,7 +7,7 @@ from pathlib import Path
from spacy import Errors
from spacy.tokens import Doc, Span
from spacy.attrs import POS, TAG, HEAD, DEP, LEMMA
from spacy.attrs import POS, TAG, HEAD, DEP, LEMMA, MORPH
from spacy.vocab import Vocab
@ -27,15 +27,23 @@ def make_tempdir():
def get_doc(
vocab, words=[], pos=None, heads=None, deps=None, tags=None, ents=None, lemmas=None
vocab,
words=[],
pos=None,
heads=None,
deps=None,
tags=None,
ents=None,
lemmas=None,
morphs=None,
):
"""Create Doc object from given vocab, words and annotations."""
if deps and not heads:
heads = [0] * len(deps)
headings = []
values = []
annotations = [pos, heads, deps, lemmas, tags]
possible_headings = [POS, HEAD, DEP, LEMMA, TAG]
annotations = [pos, heads, deps, lemmas, tags, morphs]
possible_headings = [POS, HEAD, DEP, LEMMA, TAG, MORPH]
for a, annot in enumerate(annotations):
if annot is not None:
if len(annot) != len(words):
@ -61,6 +69,13 @@ def get_doc(
attrs[i] = heads[i]
else:
attrs[i, j] = heads[i]
elif annot is morphs:
for i in range(len(words)):
morph_key = vocab.morphology.add(morphs[i])
if attrs.ndim == 1:
attrs[i] = morph_key
else:
attrs[i, j] = morph_key
else:
for i in range(len(words)):
if attrs.ndim == 1:

2
spacy/tokenizer.pyx
View File

@ -218,7 +218,7 @@ cdef class Tokenizer:
doc.c[doc.length - 1].spacy = string[-1] == " " and not in_ws
return doc
def pipe(self, texts, batch_size=1000, n_threads=-1, as_example=False):
def pipe(self, texts, batch_size=1000, n_threads=-1):
"""Tokenize a stream of texts.
texts: A sequence of unicode texts.

18
spacy/tokens/_serialize.py
View File

@ -9,6 +9,9 @@ from ..attrs import SPACY, ORTH, intify_attr
from ..errors import Errors
ALL_ATTRS = ("ORTH", "TAG", "HEAD", "DEP", "ENT_IOB", "ENT_TYPE", "LEMMA", "MORPH")
class DocBin(object):
"""Pack Doc objects for binary serialization.
@ -39,7 +42,7 @@ class DocBin(object):
document from the DocBin.
"""
def __init__(self, attrs=None, store_user_data=False):
def __init__(self, attrs=ALL_ATTRS, store_user_data=False, docs=[]):
"""Create a DocBin object to hold serialized annotations.
attrs (list): List of attributes to serialize. 'orth' and 'spacy' are
@ -49,7 +52,6 @@ class DocBin(object):
DOCS: https://spacy.io/api/docbin#init
"""
attrs = attrs or []
attrs = sorted([intify_attr(attr) for attr in attrs])
self.attrs = [attr for attr in attrs if attr != ORTH and attr != SPACY]
self.attrs.insert(0, ORTH) # Ensure ORTH is always attrs[0]
@ -59,6 +61,8 @@ class DocBin(object):
self.user_data = []
self.strings = set()
self.store_user_data = store_user_data
for doc in docs:
self.add(doc)
def __len__(self):
"""RETURNS: The number of Doc objects added to the DocBin."""
@ -79,7 +83,12 @@ class DocBin(object):
assert array.shape[0] == spaces.shape[0] # this should never happen
spaces = spaces.reshape((spaces.shape[0], 1))
self.spaces.append(numpy.asarray(spaces, dtype=bool))
self.strings.update(w.text for w in doc)
for token in doc:
self.strings.add(token.text)
self.strings.add(token.tag_)
self.strings.add(token.lemma_)
self.strings.add(token.dep_)
self.strings.add(token.ent_type_)
self.cats.append(doc.cats)
if self.store_user_data:
self.user_data.append(srsly.msgpack_dumps(doc.user_data))
@ -98,8 +107,7 @@ class DocBin(object):
for i in range(len(self.tokens)):
tokens = self.tokens[i]
spaces = self.spaces[i]
words = [vocab.strings[orth] for orth in tokens[:, orth_col]]
doc = Doc(vocab, words=words, spaces=spaces)
doc = Doc(vocab, words=tokens[:, orth_col], spaces=spaces)
doc = doc.from_array(self.attrs, tokens)
doc.cats = self.cats[i]
if self.store_user_data:

133
spacy/tokens/doc.pyx
View File

@ -3,6 +3,7 @@ cimport cython
cimport numpy as np
from libc.string cimport memcpy, memset
from libc.math cimport sqrt
from libc.stdint cimport int32_t, uint64_t
from collections import Counter
import numpy
@ -12,13 +13,14 @@ import srsly
from thinc.api import get_array_module
from thinc.util import copy_array
import warnings
import copy
from .span cimport Span
from .token cimport Token
from ..lexeme cimport Lexeme, EMPTY_LEXEME
from ..typedefs cimport attr_t, flags_t
from ..attrs cimport ID, ORTH, NORM, LOWER, SHAPE, PREFIX, SUFFIX, CLUSTER
from ..attrs cimport LENGTH, POS, LEMMA, TAG, DEP, HEAD, SPACY, ENT_IOB
from ..attrs cimport LENGTH, POS, LEMMA, TAG, MORPH, DEP, HEAD, SPACY, ENT_IOB
from ..attrs cimport ENT_TYPE, ENT_ID, ENT_KB_ID, SENT_START, IDX, attr_id_t
from ..parts_of_speech cimport CCONJ, PUNCT, NOUN, univ_pos_t
@ -52,6 +54,8 @@ cdef attr_t get_token_attr(const TokenC* token, attr_id_t feat_name) nogil:
return token.pos
elif feat_name == TAG:
return token.tag
elif feat_name == MORPH:
return token.morph
elif feat_name == DEP:
return token.dep
elif feat_name == HEAD:
@ -184,7 +188,7 @@ cdef class Doc:
DOCS: https://spacy.io/api/doc#init
"""
self.vocab = vocab
size = 20
size = max(20, (len(words) if words is not None else 0))
self.mem = Pool()
# Guarantee self.lex[i-x], for any i >= 0 and x < padding is in bounds
# However, we need to remember the true starting places, so that we can
@ -209,7 +213,6 @@ cdef class Doc:
self.user_data = {} if user_data is None else user_data
self._vector = None
self.noun_chunks_iterator = _get_chunker(self.vocab.lang)
cdef unicode orth
cdef bint has_space
if orths_and_spaces is None and words is not None:
if spaces is None:
@ -217,19 +220,22 @@ cdef class Doc:
elif len(spaces) != len(words):
raise ValueError(Errors.E027)
orths_and_spaces = zip(words, spaces)
cdef const LexemeC* lexeme
if orths_and_spaces is not None:
orths_and_spaces = list(orths_and_spaces)
for orth_space in orths_and_spaces:
if isinstance(orth_space, unicode):
orth = orth_space
lexeme = self.vocab.get(self.mem, orth_space)
has_space = True
elif isinstance(orth_space, bytes):
raise ValueError(Errors.E028.format(value=orth_space))
elif isinstance(orth_space[0], unicode):
lexeme = self.vocab.get(self.mem, orth_space[0])
has_space = orth_space[1]
else:
orth, has_space = orth_space
# Note that we pass self.mem here --- we have ownership, if LexemeC
# must be created.
self.push_back(
<const LexemeC*>self.vocab.get(self.mem, orth), has_space)
lexeme = self.vocab.get_by_orth(self.mem, orth_space[0])
has_space = orth_space[1]
self.push_back(lexeme, has_space)
# Tough to decide on policy for this. Is an empty doc tagged and parsed?
# There's no information we'd like to add to it, so I guess so?
if self.length == 0:
@ -517,7 +523,8 @@ cdef class Doc:
if start == -1:
seq = [f"{t.text}|{t.ent_iob_}" for t in self[i-5:i+5]]
raise ValueError(Errors.E093.format(seq=" ".join(seq)))
elif token.ent_iob == 2 or token.ent_iob == 0:
elif token.ent_iob == 2 or token.ent_iob == 0 or \
(token.ent_iob == 3 and token.ent_type == 0):
if start != -1:
output.append(Span(self, start, i, label=label, kb_id=kb_id))
start = -1
@ -531,6 +538,8 @@ cdef class Doc:
kb_id = token.ent_kb_id
if start != -1:
output.append(Span(self, start, self.length, label=label, kb_id=kb_id))
# remove empty-label spans
output = [o for o in output if o.label_ != ""]
return tuple(output)
def __set__(self, ents):
@ -699,8 +708,12 @@ cdef class Doc:
# Handle inputs like doc.to_array(ORTH)
py_attr_ids = [py_attr_ids]
# Allow strings, e.g. 'lemma' or 'LEMMA'
py_attr_ids = [(IDS[id_.upper()] if hasattr(id_, "upper") else id_)
try:
py_attr_ids = [(IDS[id_.upper()] if hasattr(id_, "upper") else id_)
for id_ in py_attr_ids]
except KeyError as msg:
keys = [k for k in IDS.keys() if not k.startswith("FLAG")]
raise KeyError(Errors.E983.format(dict="IDS", key=msg, keys=keys))
# Make an array from the attributes --- otherwise our inner loop is
# Python dict iteration.
cdef np.ndarray attr_ids = numpy.asarray(py_attr_ids, dtype="i")
@ -747,6 +760,8 @@ cdef class Doc:
return dict(counts)
def _realloc(self, new_size):
if new_size < self.max_length:
return
self.max_length = new_size
n = new_size + (PADDING * 2)
# What we're storing is a "padded" array. We've jumped forward PADDING
@ -795,10 +810,14 @@ cdef class Doc:
if SENT_START in attrs and HEAD in attrs:
raise ValueError(Errors.E032)
cdef int i, col, abs_head_index
cdef int i, col
cdef int32_t abs_head_index
cdef attr_id_t attr_id
cdef TokenC* tokens = self.c
cdef int length = len(array)
if length != len(self):
raise ValueError("Cannot set array values longer than the document.")
# Get set up for fast loading
cdef Pool mem = Pool()
cdef int n_attrs = len(attrs)
@ -809,26 +828,52 @@ cdef class Doc:
attr_ids[i] = attr_id
if len(array.shape) == 1:
array = array.reshape((array.size, 1))
cdef np.ndarray transposed_array = numpy.ascontiguousarray(array.T)
values = <const uint64_t*>transposed_array.data
stride = transposed_array.shape[1]
# Check that all heads are within the document bounds
if HEAD in attrs:
col = attrs.index(HEAD)
for i in range(length):
# cast index to signed int
abs_head_index = numpy.int32(array[i, col]) + i
abs_head_index = <int32_t>values[col * stride + i]
abs_head_index += i
if abs_head_index < 0 or abs_head_index >= length:
raise ValueError(Errors.E190.format(index=i, value=array[i, col], rel_head_index=numpy.int32(array[i, col])))
raise ValueError(
Errors.E190.format(
index=i,
value=array[i, col],
rel_head_index=abs_head_index-i
)
)
# Do TAG first. This lets subsequent loop override stuff like POS, LEMMA
if TAG in attrs:
col = attrs.index(TAG)
for i in range(length):
if array[i, col] != 0:
self.vocab.morphology.assign_tag(&tokens[i], array[i, col])
value = values[col * stride + i]
if value != 0:
self.vocab.morphology.assign_tag(&tokens[i], value)
# Verify ENT_IOB are proper integers
if ENT_IOB in attrs:
iob_strings = Token.iob_strings()
col = attrs.index(ENT_IOB)
n_iob_strings = len(iob_strings)
for i in range(length):
value = values[col * stride + i]
if value < 0 or value >= n_iob_strings:
raise ValueError(
Errors.E982.format(
values=iob_strings,
value=value
)
)
# Now load the data
for i in range(length):
token = &self.c[i]
for j in range(n_attrs):
if attr_ids[j] != TAG:
Token.set_struct_attr(token, attr_ids[j], array[i, j])
value = values[j * stride + i]
Token.set_struct_attr(token, attr_ids[j], value)
# Set flags
self.is_parsed = bool(self.is_parsed or HEAD in attrs)
self.is_tagged = bool(self.is_tagged or TAG in attrs or POS in attrs)
@ -849,6 +894,28 @@ cdef class Doc:
"""
return numpy.asarray(_get_lca_matrix(self, 0, len(self)))
def copy(self):
cdef Doc other = Doc(self.vocab)
other._vector = copy.deepcopy(self._vector)
other._vector_norm = copy.deepcopy(self._vector_norm)
other.tensor = copy.deepcopy(self.tensor)
other.cats = copy.deepcopy(self.cats)
other.user_data = copy.deepcopy(self.user_data)
other.is_tagged = self.is_tagged
other.is_parsed = self.is_parsed
other.is_morphed = self.is_morphed
other.sentiment = self.sentiment
other.user_hooks = dict(self.user_hooks)
other.user_token_hooks = dict(self.user_token_hooks)
other.user_span_hooks = dict(self.user_span_hooks)
other.length = self.length
other.max_length = self.max_length
buff_size = other.max_length + (PADDING*2)
tokens = <TokenC*>other.mem.alloc(buff_size, sizeof(TokenC))
memcpy(tokens, self.c - PADDING, buff_size * sizeof(TokenC))
other.c = &tokens[PADDING]
return other
def to_disk(self, path, **kwargs):
"""Save the current state to a directory.
@ -881,6 +948,32 @@ cdef class Doc:
def to_bytes(self, exclude=tuple(), **kwargs):
"""Serialize, i.e. export the document contents to a binary string.
exclude (list): String names of serialization fields to exclude.
RETURNS (bytes): A losslessly serialized copy of the `Doc`, including
all annotations.
DOCS: https://spacy.io/api/doc#to_bytes
"""
return srsly.msgpack_dumps(self.to_dict(exclude=exclude, **kwargs))
def from_bytes(self, bytes_data, exclude=tuple(), **kwargs):
"""Deserialize, i.e. import the document contents from a binary string.
data (bytes): The string to load from.
exclude (list): String names of serialization fields to exclude.
RETURNS (Doc): Itself.
DOCS: https://spacy.io/api/doc#from_bytes
"""
return self.from_dict(
srsly.msgpack_loads(bytes_data),
exclude=exclude,
**kwargs
)
def to_dict(self, exclude=tuple(), **kwargs):
"""Export the document contents to a dictionary for serialization.
exclude (list): String names of serialization fields to exclude.
RETURNS (bytes): A losslessly serialized copy of the `Doc`, including
all annotations.
@ -917,9 +1010,9 @@ cdef class Doc:
serializers["user_data_keys"] = lambda: srsly.msgpack_dumps(user_data_keys)
if "user_data_values" not in exclude:
serializers["user_data_values"] = lambda: srsly.msgpack_dumps(user_data_values)
return util.to_bytes(serializers, exclude)
return util.to_dict(serializers, exclude)
def from_bytes(self, bytes_data, exclude=tuple(), **kwargs):
def from_dict(self, msg, exclude=tuple(), **kwargs):
"""Deserialize, i.e. import the document contents from a binary string.
data (bytes): The string to load from.
@ -943,7 +1036,6 @@ cdef class Doc:
for key in kwargs:
if key in deserializers or key in ("user_data",):
raise ValueError(Errors.E128.format(arg=key))
msg = util.from_bytes(bytes_data, deserializers, exclude)
# Msgpack doesn't distinguish between lists and tuples, which is
# vexing for user data. As a best guess, we *know* that within
# keys, we must have tuples. In values we just have to hope
@ -975,6 +1067,7 @@ cdef class Doc:
self.from_array(msg["array_head"][2:], attrs[:, 2:])
return self
def extend_tensor(self, tensor):
"""Concatenate a new tensor onto the doc.tensor object.

7
spacy/tokens/token.pyx
View File

@ -778,6 +778,10 @@ cdef class Token:
"""
return self.c.ent_iob
@classmethod
def iob_strings(cls):
return ("", "I", "O", "B")
@property
def ent_iob_(self):
"""IOB code of named entity tag. "B" means the token begins an entity,
@ -787,8 +791,7 @@ cdef class Token:
RETURNS (str): IOB code of named entity tag.
"""
iob_strings = ("", "I", "O", "B")
return iob_strings[self.c.ent_iob]
return self.iob_strings()[self.c.ent_iob]
property ent_id:
"""RETURNS (uint64): ID of the entity the token is an instance of,

51
spacy/util.py
View File

@ -499,14 +499,6 @@ def get_async(stream, numpy_array):
return array
def eg2doc(example):
"""Get a Doc object from an Example (or if it's a Doc, use it directly)"""
# Put the import here to avoid circular import problems
from .tokens.doc import Doc
return example if isinstance(example, Doc) else example.doc
def env_opt(name, default=None):
if type(default) is float:
type_convert = float
@ -725,12 +717,13 @@ def decaying(start, stop, decay):
curr -= decay
def minibatch_by_words(
examples, size, count_words=len, tolerance=0.2, discard_oversize=False
):
def minibatch_by_words(docs, size, tolerance=0.2, discard_oversize=False):
"""Create minibatches of roughly a given number of words. If any examples
are longer than the specified batch length, they will appear in a batch by
themselves, or be discarded if discard_oversize=True."""
themselves, or be discarded if discard_oversize=True.
The argument 'docs' can be a list of strings, Doc's or Example's. """
from .gold import Example
if isinstance(size, int):
size_ = itertools.repeat(size)
elif isinstance(size, List):
@ -745,22 +738,27 @@ def minibatch_by_words(
batch_size = 0
overflow_size = 0
for example in examples:
n_words = count_words(example.doc)
for doc in docs:
if isinstance(doc, Example):
n_words = len(doc.reference)
elif isinstance(doc, str):
n_words = len(doc.split())
else:
n_words = len(doc)
# if the current example exceeds the maximum batch size, it is returned separately
# but only if discard_oversize=False.
if n_words > target_size + tol_size:
if not discard_oversize:
yield [example]
yield [doc]
# add the example to the current batch if there's no overflow yet and it still fits
elif overflow_size == 0 and (batch_size + n_words) <= target_size:
batch.append(example)
batch.append(doc)
batch_size += n_words
# add the example to the overflow buffer if it fits in the tolerance margin
elif (batch_size + overflow_size + n_words) <= (target_size + tol_size):
overflow.append(example)
overflow.append(doc)
overflow_size += n_words
# yield the previous batch and start a new one. The new one gets the overflow examples.
@ -775,12 +773,12 @@ def minibatch_by_words(
# this example still fits
if (batch_size + n_words) <= target_size:
batch.append(example)
batch.append(doc)
batch_size += n_words
# this example fits in overflow
elif (batch_size + n_words) <= (target_size + tol_size):
overflow.append(example)
overflow.append(doc)
overflow_size += n_words
# this example does not fit with the previous overflow: start another new batch
@ -788,7 +786,7 @@ def minibatch_by_words(
yield batch
target_size = next(size_)
tol_size = target_size * tolerance
batch = [example]
batch = [doc]
batch_size = n_words
# yield the final batch
@ -849,16 +847,23 @@ def filter_spans(spans):
def to_bytes(getters, exclude):
return srsly.msgpack_dumps(to_dict(getters, exclude))
def from_bytes(bytes_data, setters, exclude):
return from_dict(srsly.msgpack_loads(bytes_data), setters, exclude)
def to_dict(getters, exclude):
serialized = {}
for key, getter in getters.items():
# Split to support file names like meta.json
if key.split(".")[0] not in exclude:
serialized[key] = getter()
return srsly.msgpack_dumps(serialized)
return serialized
def from_bytes(bytes_data, setters, exclude):
msg = srsly.msgpack_loads(bytes_data)
def from_dict(msg, setters, exclude):
for key, setter in setters.items():
# Split to support file names like meta.json
if key.split(".")[0] not in exclude and key in msg: