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spaCy/spacy/cli/debug_data.py

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from typing import List, Sequence, Dict, Any, Tuple, Optional
from pathlib import Path
from collections import Counter
import sys
import srsly
from wasabi import Printer, MESSAGES, msg
import typer
from ._util import app, Arg, Opt, show_validation_error, parse_config_overrides
from ._util import import_code, debug_cli
from ..training import Example
from ..training.initialize import get_sourced_components
from ..schemas import ConfigSchemaTraining
from ..pipeline._parser_internals import nonproj
from ..language import Language
from ..util import registry, resolve_dot_names
from .. import util
# Minimum number of expected occurrences of NER label in data to train new label
NEW_LABEL_THRESHOLD = 50
# Minimum number of expected occurrences of dependency labels
DEP_LABEL_THRESHOLD = 20
# Minimum number of expected examples to train a new pipeline
BLANK_MODEL_MIN_THRESHOLD = 100
BLANK_MODEL_THRESHOLD = 2000
@debug_cli.command(
"data", context_settings={"allow_extra_args": True, "ignore_unknown_options": True}
)
@app.command(
"debug-data",
context_settings={"allow_extra_args": True, "ignore_unknown_options": True},
hidden=True, # hide this from main CLI help but still allow it to work with warning
)
def debug_data_cli(
# fmt: off
ctx: typer.Context, # This is only used to read additional arguments
config_path: Path = Arg(..., help="Path to config file", exists=True, allow_dash=True),
code_path: Optional[Path] = Opt(None, "--code-path", "-c", help="Path to Python file with additional code (registered functions) to be imported"),
ignore_warnings: bool = Opt(False, "--ignore-warnings", "-IW", help="Ignore warnings, only show stats and errors"),
verbose: bool = Opt(False, "--verbose", "-V", help="Print additional information and explanations"),
no_format: bool = Opt(False, "--no-format", "-NF", help="Don't pretty-print the results"),
# fmt: on
):
"""
Analyze, debug and validate your training and development data. Outputs
useful stats, and can help you find problems like invalid entity annotations,
cyclic dependencies, low data labels and more.
DOCS: https://nightly.spacy.io/api/cli#debug-data
"""
if ctx.command.name == "debug-data":
msg.warn(
"The debug-data command is now available via the 'debug data' "
"subcommand (without the hyphen). You can run python -m spacy debug "
"--help for an overview of the other available debugging commands."
)
overrides = parse_config_overrides(ctx.args)
import_code(code_path)
debug_data(
config_path,
config_overrides=overrides,
ignore_warnings=ignore_warnings,
verbose=verbose,
no_format=no_format,
silent=False,
)
def debug_data(
config_path: Path,
*,
config_overrides: Dict[str, Any] = {},
ignore_warnings: bool = False,
verbose: bool = False,
no_format: bool = True,
silent: bool = True,
):
msg = Printer(
no_print=silent, pretty=not no_format, ignore_warnings=ignore_warnings
)
# Make sure all files and paths exists if they are needed
with show_validation_error(config_path):
cfg = util.load_config(config_path, overrides=config_overrides)
nlp = util.load_model_from_config(cfg)
config = nlp.config.interpolate()
T = registry.resolve(config["training"], schema=ConfigSchemaTraining)
# Use original config here, not resolved version
sourced_components = get_sourced_components(cfg)
frozen_components = T["frozen_components"]
resume_components = [p for p in sourced_components if p not in frozen_components]
pipeline = nlp.pipe_names
factory_names = [nlp.get_pipe_meta(pipe).factory for pipe in nlp.pipe_names]
msg.divider("Data file validation")
# Create the gold corpus to be able to better analyze data
dot_names = [T["train_corpus"], T["dev_corpus"]]
train_corpus, dev_corpus = resolve_dot_names(config, dot_names)
train_dataset = list(train_corpus(nlp))
dev_dataset = list(dev_corpus(nlp))
msg.good("Corpus is loadable")
nlp.initialize(lambda: train_dataset)
msg.good("Pipeline can be initialized with data")
# Create all gold data here to avoid iterating over the train_dataset constantly
gold_train_data = _compile_gold(train_dataset, factory_names, nlp, make_proj=True)
gold_train_unpreprocessed_data = _compile_gold(
train_dataset, factory_names, nlp, make_proj=False
)
gold_dev_data = _compile_gold(dev_dataset, factory_names, nlp, make_proj=True)
train_texts = gold_train_data["texts"]
dev_texts = gold_dev_data["texts"]
frozen_components = T["frozen_components"]
msg.divider("Training stats")
msg.text(f"Language: {nlp.lang}")
msg.text(f"Training pipeline: {', '.join(pipeline)}")
if resume_components:
msg.text(f"Components from other pipelines: {', '.join(resume_components)}")
if frozen_components:
msg.text(f"Frozen components: {', '.join(frozen_components)}")
msg.text(f"{len(train_dataset)} training docs")
msg.text(f"{len(dev_dataset)} evaluation docs")
if not len(gold_dev_data):
msg.fail("No evaluation docs")
overlap = len(train_texts.intersection(dev_texts))
if overlap:
msg.warn(f"{overlap} training examples also in evaluation data")
else:
msg.good("No overlap between training and evaluation data")
# TODO: make this feedback more fine-grained and report on updated
# components vs. blank components
if not resume_components and len(train_dataset) < BLANK_MODEL_THRESHOLD:
text = f"Low number of examples to train a new pipeline ({len(train_dataset)})"
if len(train_dataset) < BLANK_MODEL_MIN_THRESHOLD:
msg.fail(text)
else:
msg.warn(text)
msg.text(
f"It's recommended to use at least {BLANK_MODEL_THRESHOLD} examples "
f"(minimum {BLANK_MODEL_MIN_THRESHOLD})",
show=verbose,
)
msg.divider("Vocab & Vectors")
n_words = gold_train_data["n_words"]
msg.info(
f"{n_words} total word(s) in the data ({len(gold_train_data['words'])} unique)"
)
if gold_train_data["n_misaligned_words"] > 0:
n_misaligned = gold_train_data["n_misaligned_words"]
msg.warn(f"{n_misaligned} misaligned tokens in the training data")
if gold_dev_data["n_misaligned_words"] > 0:
n_misaligned = gold_dev_data["n_misaligned_words"]
msg.warn(f"{n_misaligned} misaligned tokens in the dev data")
most_common_words = gold_train_data["words"].most_common(10)
msg.text(
f"10 most common words: {_format_labels(most_common_words, counts=True)}",
show=verbose,
)
if len(nlp.vocab.vectors):
msg.info(
f"{len(nlp.vocab.vectors)} vectors ({nlp.vocab.vectors.n_keys} "
f"unique keys, {nlp.vocab.vectors_length} dimensions)"
)
n_missing_vectors = sum(gold_train_data["words_missing_vectors"].values())
msg.warn(
"{} words in training data without vectors ({:0.2f}%)".format(
n_missing_vectors, n_missing_vectors / gold_train_data["n_words"]
),
)
msg.text(
"10 most common words without vectors: {}".format(
_format_labels(
gold_train_data["words_missing_vectors"].most_common(10),
counts=True,
)
),
show=verbose,
)
else:
msg.info("No word vectors present in the package")
if "ner" in factory_names:
# Get all unique NER labels present in the data
labels = set(
label for label in gold_train_data["ner"] if label not in ("O", "-", None)
)
label_counts = gold_train_data["ner"]
model_labels = _get_labels_from_model(nlp, "ner")
new_labels = [l for l in labels if l not in model_labels]
existing_labels = [l for l in labels if l in model_labels]
has_low_data_warning = False
has_no_neg_warning = False
has_ws_ents_error = False
has_punct_ents_warning = False
msg.divider("Named Entity Recognition")
msg.info(
f"{len(new_labels)} new label(s), {len(existing_labels)} existing label(s)"
)
missing_values = label_counts["-"]
msg.text(f"{missing_values} missing value(s) (tokens with '-' label)")
for label in new_labels:
if len(label) == 0:
msg.fail("Empty label found in new labels")
if new_labels:
labels_with_counts = [
(label, count)
for label, count in label_counts.most_common()
if label != "-"
]
labels_with_counts = _format_labels(labels_with_counts, counts=True)
msg.text(f"New: {labels_with_counts}", show=verbose)
if existing_labels:
msg.text(f"Existing: {_format_labels(existing_labels)}", show=verbose)
if gold_train_data["ws_ents"]:
msg.fail(f"{gold_train_data['ws_ents']} invalid whitespace entity spans")
has_ws_ents_error = True
if gold_train_data["punct_ents"]:
msg.warn(f"{gold_train_data['punct_ents']} entity span(s) with punctuation")
has_punct_ents_warning = True
for label in new_labels:
if label_counts[label] <= NEW_LABEL_THRESHOLD:
msg.warn(
f"Low number of examples for new label '{label}' ({label_counts[label]})"
)
has_low_data_warning = True
with msg.loading("Analyzing label distribution..."):
neg_docs = _get_examples_without_label(train_dataset, label)
if neg_docs == 0:
msg.warn(f"No examples for texts WITHOUT new label '{label}'")
has_no_neg_warning = True
if not has_low_data_warning:
msg.good("Good amount of examples for all labels")
if not has_no_neg_warning:
msg.good("Examples without occurrences available for all labels")
if not has_ws_ents_error:
msg.good("No entities consisting of or starting/ending with whitespace")
if not has_punct_ents_warning:
msg.good("No entities consisting of or starting/ending with punctuation")
if has_low_data_warning:
msg.text(
f"To train a new entity type, your data should include at "
f"least {NEW_LABEL_THRESHOLD} instances of the new label",
show=verbose,
)
if has_no_neg_warning:
msg.text(
"Training data should always include examples of entities "
"in context, as well as examples without a given entity "
"type.",
show=verbose,
)
if has_ws_ents_error:
msg.text(
"As of spaCy v2.1.0, entity spans consisting of or starting/ending "
"with whitespace characters are considered invalid."
)
if has_punct_ents_warning:
msg.text(
"Entity spans consisting of or starting/ending "
"with punctuation can not be trained with a noise level > 0."
)
if "textcat" in factory_names:
msg.divider("Text Classification")
labels = [label for label in gold_train_data["cats"]]
model_labels = _get_labels_from_model(nlp, "textcat")
new_labels = [l for l in labels if l not in model_labels]
existing_labels = [l for l in labels if l in model_labels]
msg.info(
f"Text Classification: {len(new_labels)} new label(s), "
f"{len(existing_labels)} existing label(s)"
)
if new_labels:
labels_with_counts = _format_labels(
gold_train_data["cats"].most_common(), counts=True
)
msg.text(f"New: {labels_with_counts}", show=verbose)
if existing_labels:
msg.text(f"Existing: {_format_labels(existing_labels)}", show=verbose)
if set(gold_train_data["cats"]) != set(gold_dev_data["cats"]):
msg.fail(
f"The train and dev labels are not the same. "
f"Train labels: {_format_labels(gold_train_data['cats'])}. "
f"Dev labels: {_format_labels(gold_dev_data['cats'])}."
)
if gold_train_data["n_cats_multilabel"] > 0:
msg.info(
"The train data contains instances without "
"mutually-exclusive classes. Use '--textcat-multilabel' "
"when training."
)
if gold_dev_data["n_cats_multilabel"] == 0:
msg.warn(
"Potential train/dev mismatch: the train data contains "
"instances without mutually-exclusive classes while the "
"dev data does not."
)
else:
msg.info(
"The train data contains only instances with "
"mutually-exclusive classes."
)
if gold_dev_data["n_cats_multilabel"] > 0:
msg.fail(
"Train/dev mismatch: the dev data contains instances "
"without mutually-exclusive classes while the train data "
"contains only instances with mutually-exclusive classes."
)
if "tagger" in factory_names:
msg.divider("Part-of-speech Tagging")
labels = [label for label in gold_train_data["tags"]]
# TODO: does this need to be updated?
msg.info(f"{len(labels)} label(s) in data")
labels_with_counts = _format_labels(
gold_train_data["tags"].most_common(), counts=True
)
msg.text(labels_with_counts, show=verbose)
if "parser" in factory_names:
has_low_data_warning = False
msg.divider("Dependency Parsing")
# profile sentence length
msg.info(
f"Found {gold_train_data['n_sents']} sentence(s) with an average "
f"length of {gold_train_data['n_words'] / gold_train_data['n_sents']:.1f} words."
)
# check for documents with multiple sentences
sents_per_doc = gold_train_data["n_sents"] / len(gold_train_data["texts"])
if sents_per_doc < 1.1:
msg.warn(
f"The training data contains {sents_per_doc:.2f} sentences per "
f"document. When there are very few documents containing more "
f"than one sentence, the parser will not learn how to segment "
f"longer texts into sentences."
)
# profile labels
labels_train = [label for label in gold_train_data["deps"]]
labels_train_unpreprocessed = [
label for label in gold_train_unpreprocessed_data["deps"]
]
labels_dev = [label for label in gold_dev_data["deps"]]
if gold_train_unpreprocessed_data["n_nonproj"] > 0:
n_nonproj = gold_train_unpreprocessed_data["n_nonproj"]
msg.info(f"Found {n_nonproj} nonprojective train sentence(s)")
if gold_dev_data["n_nonproj"] > 0:
n_nonproj = gold_dev_data["n_nonproj"]
msg.info(f"Found {n_nonproj} nonprojective dev sentence(s)")
msg.info(f"{len(labels_train_unpreprocessed)} label(s) in train data")
msg.info(f"{len(labels_train)} label(s) in projectivized train data")
labels_with_counts = _format_labels(
gold_train_unpreprocessed_data["deps"].most_common(), counts=True
)
msg.text(labels_with_counts, show=verbose)
# rare labels in train
for label in gold_train_unpreprocessed_data["deps"]:
if gold_train_unpreprocessed_data["deps"][label] <= DEP_LABEL_THRESHOLD:
msg.warn(
f"Low number of examples for label '{label}' "
f"({gold_train_unpreprocessed_data['deps'][label]})"
)
has_low_data_warning = True
# rare labels in projectivized train
rare_projectivized_labels = []
for label in gold_train_data["deps"]:
if gold_train_data["deps"][label] <= DEP_LABEL_THRESHOLD and "||" in label:
rare_projectivized_labels.append(
f"{label}: {gold_train_data['deps'][label]}"
)
if len(rare_projectivized_labels) > 0:
msg.warn(
f"Low number of examples for {len(rare_projectivized_labels)} "
"label(s) in the projectivized dependency trees used for "
"training. You may want to projectivize labels such as punct "
"before training in order to improve parser performance."
)
msg.warn(
f"Projectivized labels with low numbers of examples: ",
", ".join(rare_projectivized_labels),
show=verbose,
)
has_low_data_warning = True
# labels only in train
if set(labels_train) - set(labels_dev):
msg.warn(
"The following labels were found only in the train data:",
", ".join(set(labels_train) - set(labels_dev)),
show=verbose,
)
# labels only in dev
if set(labels_dev) - set(labels_train):
msg.warn(
"The following labels were found only in the dev data:",
", ".join(set(labels_dev) - set(labels_train)),
show=verbose,
)
if has_low_data_warning:
msg.text(
f"To train a parser, your data should include at "
f"least {DEP_LABEL_THRESHOLD} instances of each label.",
show=verbose,
)
# multiple root labels
if len(gold_train_unpreprocessed_data["roots"]) > 1:
msg.warn(
f"Multiple root labels "
f"({', '.join(gold_train_unpreprocessed_data['roots'])}) "
f"found in training data. spaCy's parser uses a single root "
f"label ROOT so this distinction will not be available."
)
# these should not happen, but just in case
if gold_train_data["n_nonproj"] > 0:
msg.fail(
f"Found {gold_train_data['n_nonproj']} nonprojective "
f"projectivized train sentence(s)"
)
if gold_train_data["n_cycles"] > 0:
msg.fail(
f"Found {gold_train_data['n_cycles']} projectivized train sentence(s) with cycles"
)
msg.divider("Summary")
good_counts = msg.counts[MESSAGES.GOOD]
warn_counts = msg.counts[MESSAGES.WARN]
fail_counts = msg.counts[MESSAGES.FAIL]
if good_counts:
msg.good(f"{good_counts} {'check' if good_counts == 1 else 'checks'} passed")
if warn_counts:
msg.warn(f"{warn_counts} {'warning' if warn_counts == 1 else 'warnings'}")
if fail_counts:
msg.fail(f"{fail_counts} {'error' if fail_counts == 1 else 'errors'}")
sys.exit(1)
def _load_file(file_path: Path, msg: Printer) -> None:
file_name = file_path.parts[-1]
if file_path.suffix == ".json":
with msg.loading(f"Loading {file_name}..."):
data = srsly.read_json(file_path)
msg.good(f"Loaded {file_name}")
return data
elif file_path.suffix == ".jsonl":
with msg.loading(f"Loading {file_name}..."):
data = srsly.read_jsonl(file_path)
msg.good(f"Loaded {file_name}")
return data
msg.fail(
f"Can't load file extension {file_path.suffix}",
"Expected .json or .jsonl",
exits=1,
)
def _compile_gold(
examples: Sequence[Example],
factory_names: List[str],
nlp: Language,
make_proj: bool,
) -> Dict[str, Any]:
data = {
"ner": Counter(),
"cats": Counter(),
"tags": Counter(),
"deps": Counter(),
"words": Counter(),
"roots": Counter(),
"ws_ents": 0,
"punct_ents": 0,
"n_words": 0,
"n_misaligned_words": 0,
"words_missing_vectors": Counter(),
"n_sents": 0,
"n_nonproj": 0,
"n_cycles": 0,
"n_cats_multilabel": 0,
"texts": set(),
}
for eg in examples:
gold = eg.reference
doc = eg.predicted
valid_words = [x.text for x in gold]
data["words"].update(valid_words)
data["n_words"] += len(valid_words)
align = eg.alignment
for token in doc:
if token.orth_.isspace():
continue
if align.x2y.lengths[token.i] != 1:
data["n_misaligned_words"] += 1
data["texts"].add(doc.text)
if len(nlp.vocab.vectors):
for word in [t.text for t in doc]:
if nlp.vocab.strings[word] not in nlp.vocab.vectors:
data["words_missing_vectors"].update([word])
if "ner" in factory_names:
for i, label in enumerate(eg.get_aligned_ner()):
if label is None:
continue
if label.startswith(("B-", "U-", "L-")) and doc[i].is_space:
# "Illegal" whitespace entity
data["ws_ents"] += 1
if label.startswith(("B-", "U-", "L-")) and doc[i].text in [
".",
"'",
"!",
"?",
",",
]:
# punctuation entity: could be replaced by whitespace when training with noise,
# so add a warning to alert the user to this unexpected side effect.
data["punct_ents"] += 1
if label.startswith(("B-", "U-")):
combined_label = label.split("-")[1]
data["ner"][combined_label] += 1
elif label == "-":
data["ner"]["-"] += 1
if "textcat" in factory_names:
data["cats"].update(gold.cats)
if list(gold.cats.values()).count(1.0) != 1:
data["n_cats_multilabel"] += 1
if "tagger" in factory_names:
tags = eg.get_aligned("TAG", as_string=True)
data["tags"].update([x for x in tags if x is not None])
if "parser" in factory_names:
aligned_heads, aligned_deps = eg.get_aligned_parse(projectivize=make_proj)
data["deps"].update([x for x in aligned_deps if x is not None])
for i, (dep, head) in enumerate(zip(aligned_deps, aligned_heads)):
if head == i:
data["roots"].update([dep])
data["n_sents"] += 1
if nonproj.is_nonproj_tree(aligned_heads):
data["n_nonproj"] += 1
if nonproj.contains_cycle(aligned_heads):
data["n_cycles"] += 1
return data
def _format_labels(labels: List[Tuple[str, int]], counts: bool = False) -> str:
if counts:
return ", ".join([f"'{l}' ({c})" for l, c in labels])
return ", ".join([f"'{l}'" for l in labels])
def _get_examples_without_label(data: Sequence[Example], label: str) -> int:
count = 0
for eg in data:
labels = [
label.split("-")[1]
for label in eg.get_aligned_ner()
if label not in ("O", "-", None)
]
if label not in labels:
count += 1
return count
def _get_labels_from_model(nlp: Language, pipe_name: str) -> Sequence[str]:
if pipe_name not in nlp.pipe_names:
return set()
pipe = nlp.get_pipe(pipe_name)
return pipe.labels
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