[DRIVERS-2926] [PYTHON-4577] BSON Binary Vector Subtype Support (#1813)

Co-authored-by: Steven Silvester <[email protected]>
Co-authored-by: Steven Silvester <[email protected]>

.evergreen/resync-specs.sh

@@ -76,6 +76,9 @@ do
  atlas-data-lake-testing|data_lake)
  cpjson atlas-data-lake-testing/tests/ data_lake
  ;;
+ bson-binary-vector|bson_binary_vector)
+ cpjson bson-binary-vector/tests/ bson_binary_vector
+ ;;
  bson-corpus|bson_corpus)
  cpjson bson-corpus/tests/ bson_corpus
  ;;

bson/binary.py

@@ -13,7 +13,10 @@
 # limitations under the License.
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Tuple, Type, Union
+import struct
+from dataclasses import dataclass
+from enum import Enum
+from typing import TYPE_CHECKING, Any, Sequence, Tuple, Type, Union
 from uuid import UUID
 
 """Tools for representing BSON binary data.
@@ -191,21 +194,75 @@ class UuidRepresentation:
 """
 
 
+VECTOR_SUBTYPE = 9
+"""**(BETA)** BSON binary subtype for densely packed vector data.
+
+.. versionadded:: 4.10
+"""
+
+
 USER_DEFINED_SUBTYPE = 128
 """BSON binary subtype for any user defined structure.
 """
 
 
+class BinaryVectorDtype(Enum):
+ """**(BETA)** Datatypes of vector subtype.
+
+ :param FLOAT32: (0x27) Pack list of :class:`float` as float32
+ :param INT8: (0x03) Pack list of :class:`int` in [-128, 127] as signed int8
+ :param PACKED_BIT: (0x10) Pack list of :class:`int` in [0, 255] as unsigned uint8
+
+ The `PACKED_BIT` value represents a special case where vector values themselves
+ can only be of two values (0 or 1) but these are packed together into groups of 8,
+ a byte. In Python, these are displayed as ints in range [0, 255]
+
+ Each value is of type bytes with a length of one.
+
+ .. versionadded:: 4.10
+ """
+
+ INT8 = b"\x03"
+ FLOAT32 = b"\x27"
+ PACKED_BIT = b"\x10"
+
+
+@dataclass
+class BinaryVector:
+ """**(BETA)** Vector of numbers along with metadata for binary interoperability.
+ .. versionadded:: 4.10
+ """
+
+ __slots__ = ("data", "dtype", "padding")
+
+ def __init__(self, data: Sequence[float | int], dtype: BinaryVectorDtype, padding: int = 0):
+ """
+ :param data: Sequence of numbers representing the mathematical vector.
+ :param dtype: The data type stored in binary
+ :param padding: The number of bits in the final byte that are to be ignored
+ when a vector element's size is less than a byte
+ and the length of the vector is not a multiple of 8.
+ """
+ self.data = data
+ self.dtype = dtype
+ self.padding = padding
+
+
 class Binary(bytes):
  """Representation of BSON binary data.
 
- This is necessary because we want to represent Python strings as
- the BSON string type. We need to wrap binary data so we can tell
+ We want to represent Python strings as the BSON string type.
+ We need to wrap binary data so that we can tell
  the difference between what should be considered binary data and
  what should be considered a string when we encode to BSON.
 
- Raises TypeError if `data` is not an instance of :class:`bytes`
- or `subtype` is not an instance of :class:`int`.
+ **(BETA)** Subtype 9 provides a space-efficient representation of 1-dimensional vector data.
+ Its data is prepended with two bytes of metadata.
+ The first (dtype) describes its data type, such as float32 or int8.
+ The second (padding) prescribes the number of bits to ignore in the final byte.
+ This is relevant when the element size of the dtype is not a multiple of 8.
+
+ Raises TypeError if `subtype` is not an instance of :class:`int`.
  Raises ValueError if `subtype` is not in [0, 256).
 
  .. note::
@@ -218,7 +275,10 @@ class Binary(bytes):
  to use
 
  .. versionchanged:: 3.9
- Support any bytes-like type that implements the buffer protocol.
+ Support any bytes-like type that implements the buffer protocol.
+
+ .. versionchanged:: 4.10
+ **(BETA)** Addition of vector subtype.
  """
 
  _type_marker = 5
@@ -337,6 +397,86 @@ def as_uuid(self, uuid_representation: int = UuidRepresentation.STANDARD) -> UUI
  f"cannot decode subtype {self.subtype} to {UUID_REPRESENTATION_NAMES[uuid_representation]}"
  )
 
+ @classmethod
+ def from_vector(
+ cls: Type[Binary],
+ vector: list[int, float],
+ dtype: BinaryVectorDtype,
+ padding: int = 0,
+ ) -> Binary:
+ """**(BETA)** Create a BSON :class:`~bson.binary.Binary` of Vector subtype from a list of Numbers.
+
+ To interpret the representation of the numbers, a data type must be included.
+ See :class:`~bson.binary.BinaryVectorDtype` for available types and descriptions.
+
+ The dtype and padding are prepended to the binary data's value.
+
+ :param vector: List of values
+ :param dtype: Data type of the values
+ :param padding: For fractional bytes, number of bits to ignore at end of vector.
+ :return: Binary packed data identified by dtype and padding.
+
+ .. versionadded:: 4.10
+ """
+ if dtype == BinaryVectorDtype.INT8: # pack ints in [-128, 127] as signed int8
+ format_str = "b"
+ if padding:
+ raise ValueError(f"padding does not apply to {dtype=}")
+ elif dtype == BinaryVectorDtype.PACKED_BIT: # pack ints in [0, 255] as unsigned uint8
+ format_str = "B"
+ elif dtype == BinaryVectorDtype.FLOAT32: # pack floats as float32
+ format_str = "f"
+ if padding:
+ raise ValueError(f"padding does not apply to {dtype=}")
+ else:
+ raise NotImplementedError("%s not yet supported" % dtype)
+
+ metadata = struct.pack("<sB", dtype.value, padding)
+ data = struct.pack(f"{len(vector)}{format_str}", *vector)
+ return cls(metadata + data, subtype=VECTOR_SUBTYPE)
+
+ def as_vector(self) -> BinaryVector:
+ """**(BETA)** From the Binary, create a list of numbers, along with dtype and padding.
+
+ :return: BinaryVector
+
+ .. versionadded:: 4.10
+ """
+
+ if self.subtype != VECTOR_SUBTYPE:
+ raise ValueError(f"Cannot decode subtype {self.subtype} as a vector.")
+
+ position = 0
+ dtype, padding = struct.unpack_from("<sB", self, position)
+ position += 2
+ dtype = BinaryVectorDtype(dtype)
+ n_values = len(self) - position
+
+ if dtype == BinaryVectorDtype.INT8:
+ dtype_format = "b"
+ format_string = f"{n_values}{dtype_format}"
+ vector = list(struct.unpack_from(format_string, self, position))
+ return BinaryVector(vector, dtype, padding)
+
+ elif dtype == BinaryVectorDtype.FLOAT32:
+ n_bytes = len(self) - position
+ n_values = n_bytes // 4
+ if n_bytes % 4:
+ raise ValueError(
+ "Corrupt data. N bytes for a float32 vector must be a multiple of 4."
+ )
+ vector = list(struct.unpack_from(f"{n_values}f", self, position))
+ return BinaryVector(vector, dtype, padding)
+
+ elif dtype == BinaryVectorDtype.PACKED_BIT:
+ # data packed as uint8
+ dtype_format = "B"
+ unpacked_uint8s = list(struct.unpack_from(f"{n_values}{dtype_format}", self, position))
+ return BinaryVector(unpacked_uint8s, dtype, padding)
+
+ else:
+ raise NotImplementedError("Binary Vector dtype %s not yet supported" % dtype.name)
+
  @property
  def subtype(self) -> int:
  """Subtype of this binary data."""

doc/api/bson/binary.rst

@@ -21,6 +21,14 @@
  .. autoclass:: UuidRepresentation
  :members:
 
+ .. autoclass:: BinaryVectorDtype
+ :members:
+ :show-inheritance:
+
+ .. autoclass:: BinaryVector
+ :members:
+
+
  .. autoclass:: Binary(data, subtype=BINARY_SUBTYPE)
  :members:
  :show-inheritance:

doc/changelog.rst

@@ -19,7 +19,6 @@ in this release.
 
 .. _PyMongo 4.10 release notes in JIRA: https://jira.mongodb.org/secure/ReleaseNote.jspa?projectId=10004&version=40553
 
-
 Changes in Version 4.9.0
 -------------------------
 

test/bson_binary_vector/float32.json

@@ -0,0 +1,42 @@
+{
+ "description": "Tests of Binary subtype 9, Vectors, with dtype FLOAT32",
+ "test_key": "vector",
+ "tests": [
+ {
+ "description": "Simple Vector FLOAT32",
+ "valid": true,
+ "vector": [127.0, 7.0],
+ "dtype_hex": "0x27",
+ "dtype_alias": "FLOAT32",
+ "padding": 0,
+ "canonical_bson": "1C00000005766563746F72000A0000000927000000FE420000E04000"
+ },
+ {
+ "description": "Empty Vector FLOAT32",
+ "valid": true,
+ "vector": [],
+ "dtype_hex": "0x27",
+ "dtype_alias": "FLOAT32",
+ "padding": 0,
+ "canonical_bson": "1400000005766563746F72000200000009270000"
+ },
+ {
+ "description": "Infinity Vector FLOAT32",
+ "valid": true,
+ "vector": ["-inf", 0.0, "inf"],
+ "dtype_hex": "0x27",
+ "dtype_alias": "FLOAT32",
+ "padding": 0,
+ "canonical_bson": "2000000005766563746F72000E000000092700000080FF000000000000807F00"
+ },
+ {
+ "description": "FLOAT32 with padding",
+ "valid": false,
+ "vector": [127.0, 7.0],
+ "dtype_hex": "0x27",
+ "dtype_alias": "FLOAT32",
+ "padding": 3
+ }
+ ]
+}
+

test/bson_binary_vector/int8.json

@@ -0,0 +1,57 @@
+{
+ "description": "Tests of Binary subtype 9, Vectors, with dtype INT8",
+ "test_key": "vector",
+ "tests": [
+ {
+ "description": "Simple Vector INT8",
+ "valid": true,
+ "vector": [127, 7],
+ "dtype_hex": "0x03",
+ "dtype_alias": "INT8",
+ "padding": 0,
+ "canonical_bson": "1600000005766563746F7200040000000903007F0700"
+ },
+ {
+ "description": "Empty Vector INT8",
+ "valid": true,
+ "vector": [],
+ "dtype_hex": "0x03",
+ "dtype_alias": "INT8",
+ "padding": 0,
+ "canonical_bson": "1400000005766563746F72000200000009030000"
+ },
+ {
+ "description": "Overflow Vector INT8",
+ "valid": false,
+ "vector": [128],
+ "dtype_hex": "0x03",
+ "dtype_alias": "INT8",
+ "padding": 0
+ },
+ {
+ "description": "Underflow Vector INT8",
+ "valid": false,
+ "vector": [-129],
+ "dtype_hex": "0x03",
+ "dtype_alias": "INT8",
+ "padding": 0
+ },
+ {
+ "description": "INT8 with padding",
+ "valid": false,
+ "vector": [127, 7],
+ "dtype_hex": "0x03",
+ "dtype_alias": "INT8",
+ "padding": 3
+ },
+ {
+ "description": "INT8 with float inputs",
+ "valid": false,
+ "vector": [127.77, 7.77],
+ "dtype_hex": "0x03",
+ "dtype_alias": "INT8",
+ "padding": 0
+ }
+ ]
+}
+

test/bson_binary_vector/packed_bit.json

@@ -0,0 +1,50 @@
+{
+ "description": "Tests of Binary subtype 9, Vectors, with dtype PACKED_BIT",
+ "test_key": "vector",
+ "tests": [
+ {
+ "description": "Simple Vector PACKED_BIT",
+ "valid": true,
+ "vector": [127, 7],
+ "dtype_hex": "0x10",
+ "dtype_alias": "PACKED_BIT",
+ "padding": 0,
+ "canonical_bson": "1600000005766563746F7200040000000910007F0700"
+ },
+ {
+ "description": "Empty Vector PACKED_BIT",
+ "valid": true,
+ "vector": [],
+ "dtype_hex": "0x10",
+ "dtype_alias": "PACKED_BIT",
+ "padding": 0,
+ "canonical_bson": "1400000005766563746F72000200000009100000"
+ },
+ {
+ "description": "PACKED_BIT with padding",
+ "valid": true,
+ "vector": [127, 7],
+ "dtype_hex": "0x10",
+ "dtype_alias": "PACKED_BIT",
+ "padding": 3,
+ "canonical_bson": "1600000005766563746F7200040000000910037F0700"
+ },
+ {
+ "description": "Overflow Vector PACKED_BIT",
+ "valid": false,
+ "vector": [256],
+ "dtype_hex": "0x10",
+ "dtype_alias": "PACKED_BIT",
+ "padding": 0
+ },
+ {
+ "description": "Underflow Vector PACKED_BIT",
+ "valid": false,
+ "vector": [-1],
+ "dtype_hex": "0x10",
+ "dtype_alias": "PACKED_BIT",
+ "padding": 0
+ }
+ ]
+}
+