spaCy/website/docs/api/spanruler.md
Adriane Boyd a322d6d5f2
Add SpanRuler component (#9880)
* Add SpanRuler component

Add a `SpanRuler` component similar to `EntityRuler` that saves a list
of matched spans to `Doc.spans[spans_key]`. The matches from the token
and phrase matchers are deduplicated and sorted before assignment but
are not otherwise filtered.

* Update spacy/pipeline/span_ruler.py

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Fix cast

* Add self.key property

* Use number of patterns as length

* Remove patterns kwarg from init

* Update spacy/tests/pipeline/test_span_ruler.py

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Add options for spans filter and setting to ents

* Add `spans_filter` option as a registered function'
* Make `spans_key` optional and if `None`, set to `doc.ents` instead of
`doc.spans[spans_key]`.

* Update and generalize tests

* Add test for setting doc.ents, fix key property type

* Fix typing

* Allow independent doc.spans and doc.ents

* If `spans_key` is set, set `doc.spans` with `spans_filter`.
* If `annotate_ents` is set, set `doc.ents` with `ents_fitler`.
  * Use `util.filter_spans` by default as `ents_filter`.
  * Use a custom warning if the filter does not work for `doc.ents`.

* Enable use of SpanC.id in Span

* Support id in SpanRuler as Span.id

* Update types

* `id` can only be provided as string (already by `PatternType`
definition)

* Update all uses of Span.id/ent_id in Doc

* Rename Span id kwarg to span_id

* Update types and docs

* Add ents filter to mimic EntityRuler overwrite_ents

* Refactor `ents_filter` to take `entities, spans` args for more
  filtering options
* Give registered filters more descriptive names
* Allow registered `filter_spans` filter
  (`spacy.first_longest_spans_filter.v1`) to take any number of
  `Iterable[Span]` objects as args so it can be used for spans filter
  or ents filter

* Implement future entity ruler as span ruler

Implement a compatible `entity_ruler` as `future_entity_ruler` using
`SpanRuler` as the underlying component:
* Add `sort_key` and `sort_reverse` to allow the sorting behavior to be
  customized. (Necessary for the same sorting/filtering as in
  `EntityRuler`.)
* Implement `overwrite_overlapping_ents_filter` and
  `preserve_existing_ents_filter` to support
  `EntityRuler.overwrite_ents` settings.
* Add `remove_by_id` to support `EntityRuler.remove` functionality.
* Refactor `entity_ruler` tests to parametrize all tests to test both
  `entity_ruler` and `future_entity_ruler`
* Implement `SpanRuler.token_patterns` and `SpanRuler.phrase_patterns`
  properties.

Additional changes:

* Move all config settings to top-level attributes to avoid duplicating
  settings in the config vs. `span_ruler/cfg`. (Also avoids a lot of
  casting.)

* Format

* Fix filter make method name

* Refactor to use same error for removing by label or ID

* Also provide existing spans to spans filter

* Support ids property

* Remove token_patterns and phrase_patterns

* Update docstrings

* Add span ruler docs

* Fix types

* Apply suggestions from code review

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Move sorting into filters

* Check for all tokens in seen tokens in entity ruler filters

* Remove registered sort key

* Set Token.ent_id in a backwards-compatible way in Doc.set_ents

* Remove sort options from API docs

* Update docstrings

* Rename entity ruler filters

* Fix and parameterize scoring

* Add id to Span API docs

* Fix typo in API docs

* Include explicit labeled=True for scorer

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2022-06-02 13:12:53 +02:00

17 KiB

title tag source new teaser api_string_name api_trainable
SpanRuler class spacy/pipeline/span_ruler.py 3.3 Pipeline component for rule-based span and named entity recognition span_ruler false

The span ruler lets you add spans to Doc.spans and/or Doc.ents using token-based rules or exact phrase matches. For usage examples, see the docs on rule-based span matching.

Assigned Attributes

Matches will be saved to Doc.spans[spans_key] as a SpanGroup and/or to Doc.ents, where the annotation is saved in the Token.ent_type and Token.ent_iob fields.

Location Value
Doc.spans[spans_key] The annotated spans. SpanGroup
Doc.ents The annotated spans. Tuple[Span]
Token.ent_iob An enum encoding of the IOB part of the named entity tag. int
Token.ent_iob_ The IOB part of the named entity tag. str
Token.ent_type The label part of the named entity tag (hash). int
Token.ent_type_ The label part of the named entity tag. str

Config and implementation

The default config is defined by the pipeline component factory and describes how the component should be configured. You can override its settings via the config argument on nlp.add_pipe or in your config.cfg.

Example

config = {
   "spans_key": "my_spans",
   "validate": True,
   "overwrite": False,
}
nlp.add_pipe("span_ruler", config=config)
Setting Description
spans_key The spans key to save the spans under. If None, no spans are saved. Defaults to "ruler". Optional[str]
spans_filter The optional method to filter spans before they are assigned to doc.spans. Defaults to None. Optional[CallableIterable[Span], Iterable[Span, List[Span]]]
annotate_ents Whether to save spans to doc.ents. Defaults to False. bool
ents_filter The method to filter spans before they are assigned to doc.ents. Defaults to util.filter_chain_spans. CallableIterable[Span], Iterable[Span, List[Span]]
phrase_matcher_attr Token attribute to match on, passed to the internal PhraseMatcher as attr. Defaults to None. Optional[Union[int, str]]
validate Whether patterns should be validated, passed to Matcher and PhraseMatcher as validate. Defaults to False. bool
overwrite Whether to remove any existing spans under Doc.spans[spans key] if spans_key is set, or to remove any ents under Doc.ents if annotate_ents is set. Defaults to True. bool
scorer The scoring method. Defaults to Scorer.score_spans for Doc.spans[spans_key] with overlapping spans allowed. Optional[Callable]
%%GITHUB_SPACY/spacy/pipeline/span_ruler.py

SpanRuler.__init__

Initialize the span ruler. If patterns are supplied here, they need to be a list of dictionaries with a "label" and "pattern" key. A pattern can either be a token pattern (list) or a phrase pattern (string). For example: {"label": "ORG", "pattern": "Apple"}.

Example

# Construction via add_pipe
ruler = nlp.add_pipe("span_ruler")

# Construction from class
from spacy.pipeline import SpanRuler
ruler = SpanRuler(nlp, overwrite=True)
Name Description
nlp The shared nlp object to pass the vocab to the matchers and process phrase patterns. Language
name Instance name of the current pipeline component. Typically passed in automatically from the factory when the component is added. Used to disable the current span ruler while creating phrase patterns with the nlp object. str
keyword-only
spans_key The spans key to save the spans under. If None, no spans are saved. Defaults to "ruler". Optional[str]
spans_filter The optional method to filter spans before they are assigned to doc.spans. Defaults to None. Optional[CallableIterable[Span], Iterable[Span, List[Span]]]
annotate_ents Whether to save spans to doc.ents. Defaults to False. bool
ents_filter The method to filter spans before they are assigned to doc.ents. Defaults to util.filter_chain_spans. CallableIterable[Span], Iterable[Span, List[Span]]
phrase_matcher_attr Token attribute to match on, passed to the internal PhraseMatcher as attr. Defaults to None. Optional[Union[int, str]]
validate Whether patterns should be validated, passed to Matcher and PhraseMatcher as validate. Defaults to False. bool
overwrite Whether to remove any existing spans under Doc.spans[spans key] if spans_key is set, or to remove any ents under Doc.ents if annotate_ents is set. Defaults to True. bool
scorer The scoring method. Defaults to Scorer.score_spans for Doc.spans[spans_key] with overlapping spans allowed. Optional[Callable]

SpanRuler.initialize

Initialize the component with data and used before training to load in rules from a pattern file. This method is typically called by Language.initialize and lets you customize arguments it receives via the [initialize.components] block in the config. Any existing patterns are removed on initialization.

Example

span_ruler = nlp.add_pipe("span_ruler")
span_ruler.initialize(lambda: [], nlp=nlp, patterns=patterns)
### config.cfg
[initialize.components.span_ruler]

[initialize.components.span_ruler.patterns]
@readers = "srsly.read_jsonl.v1"
path = "corpus/span_ruler_patterns.jsonl
Name Description
get_examples Function that returns gold-standard annotations in the form of Example objects. Not used by the SpanRuler. Callable], Iterable[Example
keyword-only
nlp The current nlp object. Defaults to None. Optional[Language]
patterns The list of patterns. Defaults to None. Optional[Sequence[Dict[str, Union[str, List[Dict[str, Any]]]]]]

SpanRuler._\len__

The number of all patterns added to the span ruler.

Example

ruler = nlp.add_pipe("span_ruler")
assert len(ruler) == 0
ruler.add_patterns([{"label": "ORG", "pattern": "Apple"}])
assert len(ruler) == 1
Name Description
RETURNS The number of patterns. int

SpanRuler.__contains__

Whether a label is present in the patterns.

Example

ruler = nlp.add_pipe("span_ruler")
ruler.add_patterns([{"label": "ORG", "pattern": "Apple"}])
assert "ORG" in ruler
assert not "PERSON" in ruler
Name Description
label The label to check. str
RETURNS Whether the span ruler contains the label. bool

SpanRuler.__call__

Find matches in the Doc and add them to doc.spans[span_key] and/or doc.ents. Typically, this happens automatically after the component has been added to the pipeline using nlp.add_pipe. If the span ruler was initialized with overwrite=True, existing spans and entities will be removed.

Example

ruler = nlp.add_pipe("span_ruler")
ruler.add_patterns([{"label": "ORG", "pattern": "Apple"}])

doc = nlp("A text about Apple.")
spans = [(span.text, span.label_) for span in doc.spans["ruler"]]
assert spans == [("Apple", "ORG")]
Name Description
doc The Doc object to process, e.g. the Doc in the pipeline. Doc
RETURNS The modified Doc with added spans/entities. Doc

SpanRuler.add_patterns

Add patterns to the span ruler. A pattern can either be a token pattern (list of dicts) or a phrase pattern (string). For more details, see the usage guide on rule-based matching.

Example

patterns = [
    {"label": "ORG", "pattern": "Apple"},
    {"label": "GPE", "pattern": [{"lower": "san"}, {"lower": "francisco"}]}
]
ruler = nlp.add_pipe("span_ruler")
ruler.add_patterns(patterns)
Name Description
patterns The patterns to add. List[Dict[str, Union[str, List[dict]]]]

SpanRuler.remove

Remove patterns by label from the span ruler. A ValueError is raised if the label does not exist in any patterns.

Example

patterns = [{"label": "ORG", "pattern": "Apple", "id": "apple"}]
ruler = nlp.add_pipe("span_ruler")
ruler.add_patterns(patterns)
ruler.remove("ORG")
Name Description
label The label of the pattern rule. str

SpanRuler.remove_by_id

Remove patterns by ID from the span ruler. A ValueError is raised if the ID does not exist in any patterns.

Example

patterns = [{"label": "ORG", "pattern": "Apple", "id": "apple"}]
ruler = nlp.add_pipe("span_ruler")
ruler.add_patterns(patterns)
ruler.remove_by_id("apple")
Name Description
pattern_id The ID of the pattern rule. str

SpanRuler.clear

Remove all patterns the span ruler.

Example

patterns = [{"label": "ORG", "pattern": "Apple", "id": "apple"}]
ruler = nlp.add_pipe("span_ruler")
ruler.add_patterns(patterns)
ruler.clear()

SpanRuler.to_disk

Save the span ruler patterns to a directory. The patterns will be saved as newline-delimited JSON (JSONL).

Example

ruler = nlp.add_pipe("span_ruler")
ruler.to_disk("/path/to/span_ruler")
Name Description
path A path to a directory, which will be created if it doesn't exist. Paths may be either strings or Path-like objects. Union[str, Path]

SpanRuler.from_disk

Load the span ruler from a path.

Example

ruler = nlp.add_pipe("span_ruler")
ruler.from_disk("/path/to/span_ruler")
Name Description
path A path to a directory. Paths may be either strings or Path-like objects. Union[str, Path]
RETURNS The modified SpanRuler object. SpanRuler

SpanRuler.to_bytes

Serialize the span ruler to a bytestring.

Example

ruler = nlp.add_pipe("span_ruler")
ruler_bytes = ruler.to_bytes()
Name Description
RETURNS The serialized patterns. bytes

SpanRuler.from_bytes

Load the pipe from a bytestring. Modifies the object in place and returns it.

Example

ruler_bytes = ruler.to_bytes()
ruler = nlp.add_pipe("span_ruler")
ruler.from_bytes(ruler_bytes)
Name Description
bytes_data The bytestring to load. bytes
RETURNS The modified SpanRuler object. SpanRuler

SpanRuler.labels

All labels present in the match patterns.

Name Description
RETURNS The string labels. Tuple[str, ...]

SpanRuler.ids

All IDs present in the id property of the match patterns.

Name Description
RETURNS The string IDs. Tuple[str, ...]

SpanRuler.patterns

All patterns that were added to the span ruler.

Name Description
RETURNS The original patterns, one dictionary per pattern. List[Dict[str, Union[str, dict]]]

Attributes

Name Description
key The spans key that spans are saved under. Optional[str]
matcher The underlying matcher used to process token patterns. Matcher
phrase_matcher The underlying phrase matcher used to process phrase patterns. PhraseMatcher