spaCy/spacy/tokens/doc_bin.py

from typing import List, Dict, Set, Iterable, Iterator, Union, Optional
from pathlib import Path
import numpy
from numpy import ndarray
import zlib
import srsly
from thinc.api import NumpyOps

from .doc import Doc
from ..vocab import Vocab
from ..compat import copy_reg
from ..attrs import SPACY, ORTH, intify_attr, IDS
from ..errors import Errors
from ..util import ensure_path, SimpleFrozenList
from .span_groups import SpanGroups

# fmt: off
ALL_ATTRS = ("ORTH", "NORM", "TAG", "HEAD", "DEP", "ENT_IOB", "ENT_TYPE", "ENT_KB_ID", "ENT_ID", "LEMMA", "MORPH", "POS", "SENT_START")
# fmt: on


class DocBin:
    """Pack Doc objects for binary serialization.

    The DocBin class lets you efficiently serialize the information from a
    collection of Doc objects. You can control which information is serialized
    by passing a list of attribute IDs, and optionally also specify whether the
    user data is serialized. The DocBin is faster and produces smaller data
    sizes than pickle, and allows you to deserialize without executing arbitrary
    Python code.

    The serialization format is gzipped msgpack, where the msgpack object has
    the following structure:

    {
        "attrs": List[uint64], # e.g. [TAG, HEAD, ENT_IOB, ENT_TYPE]
        "tokens": bytes, # Serialized numpy uint64 array with the token data
        "spans": List[Dict[str, bytes]], # SpanGroups data for each doc
        "spaces": bytes, # Serialized numpy boolean array with spaces data
        "lengths": bytes, # Serialized numpy int32 array with the doc lengths
        "strings": List[str] # List of unique strings in the token data
        "version": str, # DocBin version number
    }

    Strings for the words, tags, labels etc are represented by 64-bit hashes in
    the token data, and every string that occurs at least once is passed via the
    strings object. This means the storage is more efficient if you pack more
    documents together, because you have less duplication in the strings.

    A notable downside to this format is that you can't easily extract just one
    document from the DocBin.
    """

    def __init__(
        self,
        attrs: Iterable[str] = ALL_ATTRS,
        store_user_data: bool = False,
        docs: Iterable[Doc] = SimpleFrozenList(),
    ) -> None:
        """Create a DocBin object to hold serialized annotations.

        attrs (Iterable[str]): List of attributes to serialize. 'orth' and
            'spacy' are always serialized, so they're not required.
        store_user_data (bool): Whether to write the `Doc.user_data` to bytes/file.
        docs (Iterable[Doc]): Docs to add.

        DOCS: https://spacy.io/api/docbin#init
        """
        int_attrs = [intify_attr(attr) for attr in attrs]
        if None in int_attrs:
            non_valid = [attr for attr in attrs if intify_attr(attr) is None]
            raise KeyError(
                Errors.E983.format(dict="attrs", key=non_valid, keys=IDS.keys())
            ) from None
        attrs = sorted(int_attrs)
        self.version = "0.1"
        self.attrs = [attr for attr in attrs if attr != ORTH and attr != SPACY]
        self.attrs.insert(0, ORTH)  # Ensure ORTH is always attrs[0]
        self.tokens: List[ndarray] = []
        self.spaces: List[ndarray] = []
        self.cats: List[Dict] = []
        self.span_groups: List[bytes] = []
        self.user_data: List[Optional[bytes]] = []
        self.flags: List[Dict] = []
        self.strings: Set[str] = set()
        self.store_user_data = store_user_data
        for doc in docs:
            self.add(doc)

    def __len__(self) -> int:
        """RETURNS: The number of Doc objects added to the DocBin."""
        return len(self.tokens)

    def add(self, doc: Doc) -> None:
        """Add a Doc's annotations to the DocBin for serialization.

        doc (Doc): The Doc object to add.

        DOCS: https://spacy.io/api/docbin#add
        """
        array = doc.to_array(self.attrs)
        if len(array.shape) == 1:
            array = array.reshape((array.shape[0], 1))
        self.tokens.append(array)
        spaces = doc.to_array(SPACY)
        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.flags.append({"has_unknown_spaces": doc.has_unknown_spaces})
        for token in doc:
            self.strings.add(token.text)
            self.strings.add(token.tag_)
            self.strings.add(token.lemma_)
            self.strings.add(token.norm_)
            self.strings.add(str(token.morph))
            self.strings.add(token.dep_)
            self.strings.add(token.ent_type_)
            self.strings.add(token.ent_kb_id_)
            self.strings.add(token.ent_id_)
        self.cats.append(doc.cats)
        if self.store_user_data:
            self.user_data.append(srsly.msgpack_dumps(doc.user_data))
        self.span_groups.append(doc.spans.to_bytes())
        for key, group in doc.spans.items():
            for span in group:
                self.strings.add(span.label_)

    def get_docs(self, vocab: Vocab) -> Iterator[Doc]:
        """Recover Doc objects from the annotations, using the given vocab.
        Note that the user data of each doc will be read (if available) and returned,
        regardless of the setting of 'self.store_user_data'.

        vocab (Vocab): The shared vocab.
        YIELDS (Doc): The Doc objects.

        DOCS: https://spacy.io/api/docbin#get_docs
        """
        for string in self.strings:
            vocab[string]
        orth_col = self.attrs.index(ORTH)
        for i in range(len(self.tokens)):
            flags = self.flags[i]
            tokens = self.tokens[i]
            spaces: Optional[ndarray] = self.spaces[i]
            if flags.get("has_unknown_spaces"):
                spaces = None
            doc = Doc(vocab, words=tokens[:, orth_col], spaces=spaces)  # type: ignore
            doc = doc.from_array(self.attrs, tokens)  # type: ignore
            doc.cats = self.cats[i]
            # backwards-compatibility: may be b'' or serialized empty list
            if self.span_groups[i] and self.span_groups[i] != SpanGroups._EMPTY_BYTES:
                doc.spans.from_bytes(self.span_groups[i])
            else:
                doc.spans.clear()
            if i < len(self.user_data) and self.user_data[i] is not None:
                user_data = srsly.msgpack_loads(self.user_data[i], use_list=False)
                doc.user_data.update(user_data)
            yield doc

    def merge(self, other: "DocBin") -> None:
        """Extend the annotations of this DocBin with the annotations from
        another. Will raise an error if the pre-defined attrs of the two
        DocBins don't match, or if they differ in whether or not to store
        user data.

        other (DocBin): The DocBin to merge into the current bin.

        DOCS: https://spacy.io/api/docbin#merge
        """
        if self.attrs != other.attrs:
            raise ValueError(
                Errors.E166.format(param="attrs", current=self.attrs, other=other.attrs)
            )
        if self.store_user_data != other.store_user_data:
            raise ValueError(
                Errors.E166.format(
                    param="store_user_data",
                    current=self.store_user_data,
                    other=other.store_user_data,
                )
            )
        self.tokens.extend(other.tokens)
        self.spaces.extend(other.spaces)
        self.strings.update(other.strings)
        self.cats.extend(other.cats)
        self.span_groups.extend(other.span_groups)
        self.flags.extend(other.flags)
        self.user_data.extend(other.user_data)

    def to_bytes(self) -> bytes:
        """Serialize the DocBin's annotations to a bytestring.

        RETURNS (bytes): The serialized DocBin.

        DOCS: https://spacy.io/api/docbin#to_bytes
        """
        for tokens in self.tokens:
            assert len(tokens.shape) == 2, tokens.shape  # this should never happen
        lengths = [len(tokens) for tokens in self.tokens]
        tokens = numpy.vstack(self.tokens) if self.tokens else numpy.asarray([])
        spaces = numpy.vstack(self.spaces) if self.spaces else numpy.asarray([])
        msg = {
            "version": self.version,
            "attrs": self.attrs,
            "tokens": tokens.tobytes("C"),
            "spaces": spaces.tobytes("C"),
            "lengths": numpy.asarray(lengths, dtype="int32").tobytes("C"),
            "strings": list(sorted(self.strings)),
            "cats": self.cats,
            "flags": self.flags,
            "span_groups": self.span_groups,
        }
        if self.store_user_data:
            msg["user_data"] = self.user_data
        return zlib.compress(srsly.msgpack_dumps(msg))

    def from_bytes(self, bytes_data: bytes) -> "DocBin":
        """Deserialize the DocBin's annotations from a bytestring.

        bytes_data (bytes): The data to load from.
        RETURNS (DocBin): The loaded DocBin.

        DOCS: https://spacy.io/api/docbin#from_bytes
        """
        try:
            msg = srsly.msgpack_loads(zlib.decompress(bytes_data))
        except zlib.error:
            raise ValueError(Errors.E1014)
        self.attrs = msg["attrs"]
        self.strings = set(msg["strings"])
        lengths = numpy.frombuffer(msg["lengths"], dtype="int32")
        flat_spaces = numpy.frombuffer(msg["spaces"], dtype=bool)
        flat_tokens = numpy.frombuffer(msg["tokens"], dtype="uint64")
        shape = (flat_tokens.size // len(self.attrs), len(self.attrs))
        flat_tokens = flat_tokens.reshape(shape)
        flat_spaces = flat_spaces.reshape((flat_spaces.size, 1))
        self.tokens = NumpyOps().unflatten(flat_tokens, lengths)
        self.spaces = NumpyOps().unflatten(flat_spaces, lengths)
        self.cats = msg["cats"]
        self.span_groups = msg.get("span_groups", [b"" for _ in lengths])
        self.flags = msg.get("flags", [{} for _ in lengths])
        if "user_data" in msg:
            self.user_data = list(msg["user_data"])
        else:
            self.user_data = [None] * len(self)
        for tokens in self.tokens:
            assert len(tokens.shape) == 2, tokens.shape  # this should never happen
        return self

    def to_disk(self, path: Union[str, Path]) -> None:
        """Save the DocBin to a file (typically called .spacy).

        path (str / Path): The file path.

        DOCS: https://spacy.io/api/docbin#to_disk
        """
        path = ensure_path(path)
        with path.open("wb") as file_:
            try:
                file_.write(self.to_bytes())
            except ValueError:
                raise ValueError(Errors.E870)

    def from_disk(self, path: Union[str, Path]) -> "DocBin":
        """Load the DocBin from a file (typically called .spacy).

        path (str / Path): The file path.
        RETURNS (DocBin): The loaded DocBin.

        DOCS: https://spacy.io/api/docbin#to_disk
        """
        path = ensure_path(path)
        with path.open("rb") as file_:
            self.from_bytes(file_.read())
        return self


def merge_bins(bins):
    merged = None
    for byte_string in bins:
        if byte_string is not None:
            doc_bin = DocBin(store_user_data=True).from_bytes(byte_string)
            if merged is None:
                merged = doc_bin
            else:
                merged.merge(doc_bin)
    if merged is not None:
        return merged.to_bytes()
    else:
        return b""


def pickle_bin(doc_bin):
    return (unpickle_bin, (doc_bin.to_bytes(),))


def unpickle_bin(byte_string):
    return DocBin().from_bytes(byte_string)


copy_reg.pickle(DocBin, pickle_bin, unpickle_bin)
# Compatibility, as we had named it this previously.
Binder = DocBin

__all__ = ["DocBin"]