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spaCy/spacy/cli/find_threshold.py

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Python
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import functools
import logging
import operator
from pathlib import Path
from typing import Any, Dict, List, Optional, Tuple
import numpy
import wasabi.tables
from .. import util
from ..errors import Errors
from ..pipeline import MultiLabel_TextCategorizer, TextCategorizer
from ..training import Corpus
from ._util import Arg, Opt, app, import_code, setup_gpu
_DEFAULTS = {
"n_trials": 11,
"use_gpu": -1,
"gold_preproc": False,
}
@app.command(
"find-threshold",
context_settings={"allow_extra_args": False, "ignore_unknown_options": True},
)
def find_threshold_cli(
# fmt: off
model: str = Arg(..., help="Model name or path"),
data_path: Path = Arg(..., help="Location of binary evaluation data in .spacy format", exists=True),
pipe_name: str = Arg(..., help="Name of pipe to examine thresholds for"),
threshold_key: str = Arg(..., help="Key of threshold attribute in component's configuration"),
scores_key: str = Arg(..., help="Metric to optimize"),
n_trials: int = Opt(_DEFAULTS["n_trials"], "--n_trials", "-n", help="Number of trials to determine optimal thresholds"),
code_path: Optional[Path] = Opt(None, "--code", "-c", help="Path to Python file with additional code (registered functions) to be imported"),
use_gpu: int = Opt(_DEFAULTS["use_gpu"], "--gpu-id", "-g", help="GPU ID or -1 for CPU"),
gold_preproc: bool = Opt(_DEFAULTS["gold_preproc"], "--gold-preproc", "-G", help="Use gold preprocessing"),
verbose: bool = Opt(False, "--verbose", "-V", "-VV", help="Display more information for debugging purposes"),
# fmt: on
):
"""
Runs prediction trials for a trained model with varying thresholds to maximize
the specified metric. The search space for the threshold is traversed linearly
from 0 to 1 in `n_trials` steps. Results are displayed in a table on `stdout`
(the corresponding API call to `spacy.cli.find_threshold.find_threshold()`
returns all results).
This is applicable only for components whose predictions are influenced by
thresholds - e.g. `textcat_multilabel` and `spancat`, but not `textcat`. Note
that the full path to the corresponding threshold attribute in the config has to
be provided.
DOCS: https://spacy.io/api/cli#find-threshold
"""
if verbose:
util.logger.setLevel(logging.DEBUG)
import_code(code_path)
find_threshold(
model=model,
data_path=data_path,
pipe_name=pipe_name,
threshold_key=threshold_key,
scores_key=scores_key,
n_trials=n_trials,
use_gpu=use_gpu,
gold_preproc=gold_preproc,
silent=False,
)
def find_threshold(
model: str,
data_path: Path,
pipe_name: str,
threshold_key: str,
scores_key: str,
*,
n_trials: int = _DEFAULTS["n_trials"], # type: ignore
use_gpu: int = _DEFAULTS["use_gpu"], # type: ignore
gold_preproc: bool = _DEFAULTS["gold_preproc"], # type: ignore
silent: bool = True,
) -> Tuple[float, float, Dict[float, float]]:
"""
Runs prediction trials for models with varying thresholds to maximize the specified metric.
model (Union[str, Path]): Pipeline to evaluate. Can be a package or a path to a data directory.
data_path (Path): Path to file with DocBin with docs to use for threshold search.
pipe_name (str): Name of pipe to examine thresholds for.
threshold_key (str): Key of threshold attribute in component's configuration.
scores_key (str): Name of score to metric to optimize.
n_trials (int): Number of trials to determine optimal thresholds.
use_gpu (int): GPU ID or -1 for CPU.
gold_preproc (bool): Whether to use gold preprocessing. Gold preprocessing helps the annotations align to the
tokenization, and may result in sequences of more consistent length. However, it may reduce runtime accuracy due
to train/test skew.
silent (bool): Whether to print non-error-related output to stdout.
RETURNS (Tuple[float, float, Dict[float, float]]): Best found threshold, the corresponding score, scores for all
evaluated thresholds.
"""
setup_gpu(use_gpu, silent=silent)
data_path = util.ensure_path(data_path)
if not data_path.exists():
wasabi.msg.fail("Evaluation data not found", data_path, exits=1)
nlp = util.load_model(model)
if pipe_name not in nlp.component_names:
raise AttributeError(
Errors.E001.format(name=pipe_name, opts=nlp.component_names)
)
pipe = nlp.get_pipe(pipe_name)
if not hasattr(pipe, "scorer"):
raise AttributeError(Errors.E1045)
if type(pipe) == TextCategorizer:
wasabi.msg.warn(
"The `textcat` component doesn't use a threshold as it's not applicable to the concept of "
"exclusive classes. All thresholds will yield the same results."
)
if not silent:
wasabi.msg.info(
title=f"Optimizing for {scores_key} for component '{pipe_name}' with {n_trials} "
f"trials."
)
# Load evaluation corpus.
corpus = Corpus(data_path, gold_preproc=gold_preproc)
dev_dataset = list(corpus(nlp))
config_keys = threshold_key.split(".")
def set_nested_item(
config: Dict[str, Any], keys: List[str], value: float
) -> Dict[str, Any]:
"""Set item in nested dictionary. Adapted from https://stackoverflow.com/a/54138200.
config (Dict[str, Any]): Configuration dictionary.
keys (List[Any]): Path to value to set.
value (float): Value to set.
RETURNS (Dict[str, Any]): Updated dictionary.
"""
functools.reduce(operator.getitem, keys[:-1], config)[keys[-1]] = value
return config
def filter_config(
config: Dict[str, Any], keys: List[str], full_key: str
) -> Dict[str, Any]:
"""Filters provided config dictionary so that only the specified keys path remains.
config (Dict[str, Any]): Configuration dictionary.
keys (List[Any]): Path to value to set.
full_key (str): Full user-specified key.
RETURNS (Dict[str, Any]): Filtered dictionary.
"""
if keys[0] not in config:
wasabi.msg.fail(
title=f"Failed to look up `{full_key}` in config: sub-key {[keys[0]]} not found.",
text=f"Make sure you specified {[keys[0]]} correctly. The following sub-keys are available instead: "
f"{list(config.keys())}",
exits=1,
)
return {
keys[0]: filter_config(config[keys[0]], keys[1:], full_key)
if len(keys) > 1
else config[keys[0]]
}
# Evaluate with varying threshold values.
scores: Dict[float, float] = {}
config_keys_full = ["components", pipe_name, *config_keys]
table_col_widths = (10, 10)
thresholds = numpy.linspace(0, 1, n_trials)
print(wasabi.tables.row(["Threshold", f"{scores_key}"], widths=table_col_widths))
for threshold in thresholds:
# Reload pipeline with overrides specifying the new threshold.
nlp = util.load_model(
model,
config=set_nested_item(
filter_config(
nlp.config, config_keys_full, ".".join(config_keys_full)
).copy(),
config_keys_full,
threshold,
),
)
if hasattr(pipe, "cfg"):
setattr(
nlp.get_pipe(pipe_name),
"cfg",
set_nested_item(getattr(pipe, "cfg"), config_keys, threshold),
)
eval_scores = nlp.evaluate(dev_dataset)
if scores_key not in eval_scores:
wasabi.msg.fail(
title=f"Failed to look up score `{scores_key}` in evaluation results.",
text=f"Make sure you specified the correct value for `scores_key`. The following scores are "
f"available: {list(eval_scores.keys())}",
exits=1,
)
scores[threshold] = eval_scores[scores_key]
if not isinstance(scores[threshold], (float, int)):
wasabi.msg.fail(
f"Returned score for key '{scores_key}' is not numeric. Threshold optimization only works for numeric "
f"scores.",
exits=1,
)
print(
wasabi.row(
[round(threshold, 3), round(scores[threshold], 3)],
widths=table_col_widths,
)
)
best_threshold = max(scores.keys(), key=(lambda key: scores[key]))
# If all scores are identical, emit warning.
if len(set(scores.values())) == 1:
wasabi.msg.warn(
title="All scores are identical. Verify that all settings are correct.",
text=""
if (
not isinstance(pipe, MultiLabel_TextCategorizer)
or scores_key in ("cats_macro_f", "cats_micro_f")
)
else "Use `cats_macro_f` or `cats_micro_f` when optimizing the threshold for `textcat_multilabel`.",
)
else:
if not silent:
print(
f"\nBest threshold: {round(best_threshold, ndigits=4)} with {scores_key} value of {scores[best_threshold]}."
)
return best_threshold, scores[best_threshold], scores
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