biotite 1.1.0__cp313-cp313-win_amd64.whl

biotite/structure/io/pdbx/encoding.pyx

@@ -0,0 +1,1031 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+"""
+This module contains data encodings for BinaryCIF files.
+"""
+
+__name__ = "biotite.structure.io.pdbx"
+__author__ = "Patrick Kunzmann"
+__all__ = ["ByteArrayEncoding", "FixedPointEncoding",
+           "IntervalQuantizationEncoding", "RunLengthEncoding",
+           "DeltaEncoding", "IntegerPackingEncoding", "StringArrayEncoding",
+           "TypeCode"]
+
+cimport cython
+cimport numpy as np
+
+from dataclasses import dataclass
+from abc import ABCMeta, abstractmethod
+from numbers import Integral
+from enum import IntEnum
+import re
+import numpy as np
+from .component import _Component
+from ....file import InvalidFileError
+
+ctypedef np.int8_t int8
+ctypedef np.int16_t int16
+ctypedef np.int32_t int32
+ctypedef np.uint8_t uint8
+ctypedef np.uint16_t uint16
+ctypedef np.uint32_t uint32
+ctypedef np.float32_t float32
+ctypedef np.float64_t float64
+
+ctypedef fused Integer:
+    uint8
+    uint16
+    uint32
+    int8
+    int16
+    int32
+
+# Used to create cartesian product of type combinations
+# in run-length encoding
+ctypedef fused OutputInteger:
+    uint8
+    uint16
+    uint32
+    int8
+    int16
+    int32
+
+ctypedef fused Float:
+    float32
+    float64
+
+
+CAMEL_CASE_PATTERN = re.compile(r"(?<!^)(?=[A-Z])")
+
+
+class TypeCode(IntEnum):
+    """
+    This enum type represents integers that represent data types in
+    *BinaryCIF*.
+    """
+    INT8 = 1
+    INT16 = 2
+    INT32 = 3
+    UINT8 = 4
+    UINT16 = 5
+    UINT32 = 6
+    FLOAT32 = 32
+    FLOAT64 = 33
+
+    @staticmethod
+    def from_dtype(dtype):
+        """
+        Convert a *NumPy* dtype to a *BinaryCIF* type code.
+
+        Parameters
+        ----------
+        dtype : dtype or int or TypeCode
+            The data type to be converted.
+            If already a type code, it is simply returned.
+
+        Returns
+        -------
+        type_code : TypeCode
+            The corresponding type code.
+        """
+        if isinstance(dtype, Integral):
+            # Already a type code
+            return TypeCode(dtype)
+        else:
+            dtype = np.dtype(dtype)
+            # Find the closest dtype supported by the format
+            if np.issubdtype(dtype, np.integer):
+                # int64 is not supported by format
+                if dtype == np.int64:
+                    supported_dtype = np.int32
+                elif dtype == np.uint64:
+                    supported_dtype = np.uint32
+                else:
+                    supported_dtype = dtype
+            elif np.issubdtype(dtype, np.floating):
+                if dtype == np.float16:
+                    supported_dtype = np.float32
+                # float128 is not available on all architectures
+                elif hasattr(np, "float128") and dtype == np.float128:
+                    supported_dtype = np.float64
+                else:
+                    supported_dtype = dtype
+            else:
+                raise ValueError(
+                    f"dtype '{dtype}' is not supported by BinaryCIF"
+                )
+            return _DTYPE_TO_TYPE_CODE[
+                np.dtype(supported_dtype).newbyteorder("<").str
+            ]
+
+    def to_dtype(self):
+        """
+        Convert this type code to a *NumPy* dtype.
+
+        Returns
+        -------
+        dtype : dtype
+            The corresponding data type.
+        """
+        return _TYPE_CODE_TO_DTYPE[self]
+
+# Converts BCIF integers representing the type to an actual NumPy dtype
+_TYPE_CODE_TO_DTYPE = {
+    # All data types are little-endian
+    TypeCode.INT8: "|i1",
+    TypeCode.INT16: "<i2",
+    TypeCode.INT32: "<i4",
+    TypeCode.UINT8: "|u1",
+    TypeCode.UINT16: "<u2",
+    TypeCode.UINT32: "<u4",
+    TypeCode.FLOAT32: "<f4",
+    TypeCode.FLOAT64: "<f8"
+}
+_DTYPE_TO_TYPE_CODE = {val: key for key, val in _TYPE_CODE_TO_DTYPE.items()}
+
+
+class Encoding(_Component, metaclass=ABCMeta):
+    """
+    Abstract base class for *BinaryCIF* data encodings.
+
+    Notes
+    -----
+    The encoding classes do not omit bound checks for decoding,
+    since the file content may be invalid/malicious.
+    """
+
+    @classmethod
+    def deserialize(cls, content):
+        params = {
+            _camel_to_snake_case(param): value
+            for param, value in content.items()
+        }
+        # 'kind' is no parameter, but indicates the class itself
+        params.pop("kind")
+        try:
+            encoding = cls(**params)
+        except TypeError as e:
+            raise InvalidFileError(
+                f"Invalid encoding parameters for {cls.__name__}"
+            )
+        except ValueError:
+            raise InvalidFileError(
+                f"Missing encoding parameters for {cls.__name__}"
+            )
+        return encoding
+
+    def serialize(self):
+        for param in self.__annotations__:
+            if getattr(self, param) is None:
+                raise ValueError(
+                    f"'{param}' must be explicitly given or needs to be "
+                    "determined from first encoding pass, before it is "
+                    "serialized"
+                )
+
+        serialized = {
+            _snake_to_camel_case(param): getattr(self, param)
+            for param in self.__annotations__
+        }
+        serialized.update({
+            "kind": _encoding_classes_kinds[type(self).__name__]
+        })
+        return serialized
+
+    @abstractmethod
+    def encode(self, data):
+        """
+        Apply this encoding to the given data.
+
+        Parameters
+        ----------
+        data : ndarray
+            The data to be encoded.
+
+        Returns
+        -------
+        encoded_data : ndarray or bytes
+            The encoded data.
+        """
+        raise NotImplementedError()
+
+    @abstractmethod
+    def decode(self, data):
+        """
+        Apply the inverse of this encoding to the given data.
+
+        Parameters
+        ----------
+        data : ndarray or bytes
+            The data to be decoded.
+
+        Returns
+        -------
+        decoded_data : ndarray
+            The decoded data.
+        """
+        # Important: Do not omit bound checks for decoding,
+        # since the file content may be invalid/malicious.
+        raise NotImplementedError()
+
+
+@dataclass
+class ByteArrayEncoding(Encoding):
+    r"""
+    Encoding that encodes an array into bytes.
+
+    Parameters
+    ----------
+    type : dytpe or TypeCode, optional
+        The data type of the array to be encoded.
+        Either a NumPy dtype or a *BinaryCIF* type code is accepted.
+        If omitted, the data type is taken from the data the
+        first time :meth:`encode()` is called.
+
+    Attributes
+    ----------
+    type : TypeCode
+
+    Examples
+    --------
+
+    >>> data = np.arange(3)
+    >>> print(data)
+    [0 1 2]
+    >>> print(ByteArrayEncoding().encode(data))
+    b'\x00\x00\x00\x00\x01\x00\x00\x00\x02\x00\x00\x00'
+    """
+    type: ... = None
+
+    def __post_init__(self):
+        if self.type is not None:
+            self.type = TypeCode.from_dtype(self.type)
+
+    def encode(self, data):
+        if self.type is None:
+            self.type = TypeCode.from_dtype(data.dtype)
+        return _safe_cast(data, self.type.to_dtype()).tobytes()
+
+    def decode(self, data):
+        # Data is raw bytes in this case
+        return np.frombuffer(data, dtype=self.type.to_dtype())
+
+
+@dataclass
+class FixedPointEncoding(Encoding):
+    """
+    Lossy encoding that multiplies floating point values with a given
+    factor and subsequently rounds them to the nearest integer.
+
+    Parameters
+    ----------
+    factor : float
+        The factor by which the data is multiplied before rounding.
+    src_type : dtype or TypeCode, optional
+        The data type of the array to be encoded.
+        Either a NumPy dtype or a *BinaryCIF* type code is accepted.
+        The dtype must be a float type.
+        If omitted, the data type is taken from the data the
+        first time :meth:`encode()` is called.
+
+    Attributes
+    ----------
+    factor : float
+    src_type : TypeCode
+
+    Examples
+    --------
+
+    >>> data = np.array([9.87, 6.543])
+    >>> print(data)
+    [9.870 6.543]
+    >>> print(FixedPointEncoding(factor=100).encode(data))
+    [987 654]
+    """
+    factor: ...
+    src_type: ... = None
+
+    def __post_init__(self):
+        if self.src_type is not None:
+            self.src_type = TypeCode.from_dtype(self.src_type)
+            if self.src_type not in (TypeCode.FLOAT32, TypeCode.FLOAT64):
+                raise ValueError(
+                    "Only floating point types are supported"
+                )
+
+    def encode(self, data):
+        # If not given in constructor, it is determined from the data
+        if self.src_type is None:
+            self.src_type = TypeCode.from_dtype(data.dtype)
+            if self.src_type not in (TypeCode.FLOAT32, TypeCode.FLOAT64):
+                raise ValueError(
+                    "Only floating point types are supported"
+                )
+
+        # Round to avoid wrong values due to floating point inaccuracies
+        return np.round(data * self.factor).astype(np.int32)
+
+    def decode(self, data):
+        return (data / self.factor).astype(
+            dtype=self.src_type.to_dtype(), copy=False
+        )
+
+
+@dataclass
+class IntervalQuantizationEncoding(Encoding):
+    """
+    Lossy encoding that sorts floating point values into bins.
+    Each bin is represented by an integer
+
+    Parameters
+    ----------
+    min, max : float
+        The minimum and maximum value the bins comprise.
+    num_steps : int
+        The number of bins.
+    src_type : dtype or TypeCode, optional
+        The data type of the array to be encoded.
+        Either a NumPy dtype or a *BinaryCIF* type code is accepted.
+        The dtype must be a float type.
+        If omitted, the data type is taken from the data the
+        first time :meth:`encode()` is called.
+
+    Attributes
+    ----------
+    min, max : float
+    num_steps : int
+    src_type : TypeCode
+
+    Examples
+    --------
+
+    >>> data = np.linspace(11, 12, 6)
+    >>> print(data)
+    [11.0 11.2 11.4 11.6 11.8 12.0]
+    >>> # Use 0.5 as step size
+    >>> encoding = IntervalQuantizationEncoding(min=10, max=20, num_steps=21)
+    >>> # The encoding is lossy, as different values are mapped to the same bin
+    >>> encoded = encoding.encode(data)
+    >>> print(encoded)
+    [2 3 3 4 4 4]
+    >>> decoded = encoding.decode(encoded)
+    >>> print(decoded)
+    [11.0 11.5 11.5 12.0 12.0 12.0]
+    """
+    min: ...
+    max: ...
+    num_steps: ...
+    src_type: ... = None
+
+    def __post_init__(self):
+        if self.src_type is not None:
+            self.src_type = TypeCode.from_dtype(self.src_type)
+
+    def encode(self, data):
+        # If not given in constructor, it is determined from the data
+        if self.src_type is None:
+            self.src_type = TypeCode.from_dtype(data.dtype)
+
+        steps = np.linspace(
+            self.min, self.max, self.num_steps, dtype=data.dtype
+        )
+        indices = np.searchsorted(steps, data, side="left")
+        return indices.astype(np.int32, copy=False)
+
+    def decode(self, data):
+        output = data * (self.max - self.min) / (self.num_steps - 1)
+        output = output.astype(self.src_type.to_dtype(), copy=False)
+        output += self.min
+        return output
+
+
+@dataclass
+class RunLengthEncoding(Encoding):
+    """
+    Encoding that compresses runs of equal values into pairs of
+    (value, run length).
+
+    Parameters
+    ----------
+    src_size : int, optional
+        The size of the array to be encoded.
+        If omitted, the size is determined from the data the
+        first time :meth:`encode()` is called.
+    src_type : dtype or TypeCode, optional
+        The data type of the array to be encoded.
+        Either a NumPy dtype or a *BinaryCIF* type code is accepted.
+        The dtype must be a integer type.
+        If omitted, the data type is taken from the data the
+        first time :meth:`encode()` is called.
+
+    Attributes
+    ----------
+    src_size : int
+    src_type : TypeCode
+
+    Examples
+    --------
+
+    >>> data = np.array([1, 1, 1, 5, 3, 3])
+    >>> print(data)
+    [1 1 1 5 3 3]
+    >>> encoded = RunLengthEncoding().encode(data)
+    >>> print(encoded)
+    [1 3 5 1 3 2]
+    >>> # Emphasize the the pairs
+    >>> print(encoded.reshape(-1, 2))
+    [[1 3]
+     [5 1]
+     [3 2]]
+    """
+    src_size: ... = None
+    src_type: ... = None
+
+    def __post_init__(self):
+        if self.src_type is not None:
+            self.src_type = TypeCode.from_dtype(self.src_type)
+
+    def encode(self, data):
+        # If not given in constructor, it is determined from the data
+        if self.src_type is None:
+            self.src_type = TypeCode.from_dtype(data.dtype)
+        if self.src_size is None:
+            self.src_size = data.shape[0]
+        elif self.src_size != data.shape[0]:
+            raise IndexError(
+                "Given source size does not match actual data size"
+            )
+        return self._encode(_safe_cast(data, self.src_type.to_dtype()))
+
+    def decode(self, data):
+        return self._decode(
+            data, np.empty(0, dtype=self.src_type.to_dtype())
+        )
+
+    def _encode(self, const Integer[:] data):
+        # Pessimistic allocation of output array
+        # -> Run length is 1 for every element
+        cdef int32[:] output = np.zeros(data.shape[0] * 2, dtype=np.int32)
+        cdef int i=0, j=0
+        cdef int val = data[0]
+        cdef int run_length = 0
+        cdef int curr_val
+        for i in range(data.shape[0]):
+            curr_val = data[i]
+            if curr_val == val:
+                run_length += 1
+            else:
+                # New element -> Write element with run-length
+                output[j] = val
+                output[j+1] = run_length
+                j += 2
+                val = curr_val
+                run_length = 1
+        # Write last element
+        output[j] = val
+        output[j+1] = run_length
+        j += 2
+        # Trim to correct size
+        return np.asarray(output)[:j]
+
+    def _decode(self, const Integer[:] data, OutputInteger[:] output_type):
+        """
+        `output_type` is merely a typed placeholder to allow for static
+        typing of output.
+        """
+        if data.shape[0] % 2 != 0:
+            raise ValueError("Invalid run-length encoded data")
+
+        cdef int length = 0
+        cdef int i, j
+        cdef int value, repeat
+
+        if self.src_size is None:
+            # Determine length of output array by summing run lengths
+            for i in range(1, data.shape[0], 2):
+                length += data[i]
+        else:
+            length = self.src_size
+
+        cdef OutputInteger[:] output = np.zeros(
+            length, dtype=np.asarray(output_type).dtype
+        )
+        # Fill output array
+        j = 0
+        for i in range(0, data.shape[0], 2):
+            value = data[i]
+            repeat = data[i+1]
+            output[j : j+repeat] = value
+            j += repeat
+        return np.asarray(output)
+
+
+@dataclass
+class DeltaEncoding(Encoding):
+    """
+    Encoding that encodes an array of integers into an array of
+    consecutive differences.
+
+    Parameters
+    ----------
+    src_type : dtype or TypeCode, optional
+        The data type of the array to be encoded.
+        Either a NumPy dtype or a *BinaryCIF* type code is accepted.
+        The dtype must be a integer type.
+        If omitted, the data type is taken from the data the
+        first time :meth:`encode()` is called.
+    origin : int, optional
+        The starting value from which the differences are calculated.
+        If omitted, the value is taken from the first array element the
+        first time :meth:`encode()` is called.
+
+    Attributes
+    ----------
+    src_type : TypeCode
+    origin : int
+
+    Examples
+    --------
+
+    >>> data = np.array([1, 1, 2, 3, 5, 8])
+    >>> encoding = DeltaEncoding()
+    >>> print(encoding.encode(data))
+    [0 0 1 1 2 3]
+    >>> print(encoding.origin)
+    1
+    """
+    src_type: ... = None
+    origin: ... = None
+
+    def __post_init__(self):
+        if self.src_type is not None:
+            self.src_type = TypeCode.from_dtype(self.src_type)
+
+    def encode(self, data):
+        # If not given in constructor, it is determined from the data
+        if self.src_type is None:
+            self.src_type = TypeCode.from_dtype(data.dtype)
+        if self.origin is None:
+            self.origin = data[0]
+
+        data = data - self.origin
+        return np.diff(data, prepend=0).astype(np.int32, copy=False)
+
+    def decode(self, data):
+        output = np.cumsum(data, dtype=self.src_type.to_dtype())
+        output += self.origin
+        return output
+
+
+@dataclass
+class IntegerPackingEncoding(Encoding):
+    """
+    Encoding that compresses an array of 32-bit integers into an array
+    of smaller sized integers.
+
+    If a value does not fit into smaller integer type,
+    the integer is represented by a sum of consecutive elements
+    in the compressed array.
+
+    Parameters
+    ----------
+    byte_count : int
+        The number of bytes the packed integers should occupy.
+        Supported values are 1 and 2 for 8-bit and 16-bit integers,
+        respectively.
+    src_size : int, optional
+        The size of the array to be encoded.
+        If omitted, the size is determined from the data the
+        first time :meth:`encode()` is called.
+    is_unsigned : bool, optional
+        Whether the values should be packed into signed or unsigned
+        integers.
+        If omitted, first time :meth:`encode()` is called, determines whether
+        the values fit into unsigned integers.
+
+    Attributes
+    ----------
+    byte_count : int
+    src_size : int
+    is_unsigned : bool
+
+    Examples
+    --------
+
+    >>> data = np.array([1, 2, -3, 128])
+    >>> print(data)
+    [  1   2  -3 128]
+    >>> print(IntegerPackingEncoding(byte_count=1).encode(data))
+    [  1   2  -3 127   1]
+    """
+    byte_count: ...
+    src_size: ... = None
+    is_unsigned: ... = None
+
+    def encode(self, data):
+        if self.src_size is None:
+            self.src_size = len(data)
+        elif self.src_size != len(data):
+            raise IndexError(
+                "Given source size does not match actual data size"
+            )
+        if self.is_unsigned is None:
+            # Only positive values -> use unsigned integers
+            self.is_unsigned = data.min().item() >= 0
+
+        data = data.astype(np.int32, copy=False)
+        return self._encode(
+            data, np.empty(0, dtype=self._determine_packed_dtype())
+        )
+
+    def decode(self, const Integer[:] data):
+        cdef int i, j
+        cdef int min_val, max_val
+        cdef int packed_val, unpacked_val
+        bounds = self._get_bounds(data)
+        min_val = bounds[0]
+        max_val = bounds[1]
+        # For signed integers, do not check lower bound (is always 0)
+        # -> Set lower bound to value that is never reached
+        if min_val == 0:
+            min_val = -1
+
+        cdef int32[:] output = np.zeros(self.src_size, dtype=np.int32)
+        j = 0
+        unpacked_val = 0
+        for i in range(data.shape[0]):
+            packed_val = data[i]
+            if packed_val == max_val or packed_val == min_val:
+                unpacked_val += packed_val
+            else:
+                unpacked_val += packed_val
+                output[j] = unpacked_val
+                unpacked_val = 0
+                j += 1
+        # Trim to correct size and return
+        return np.asarray(output)
+
+    def _determine_packed_dtype(self):
+        if self.byte_count == 1:
+            if self.is_unsigned:
+                return np.uint8
+            else:
+                return np.int8
+        elif self.byte_count == 2:
+            if self.is_unsigned:
+                return np.uint16
+            else:
+                return np.int16
+        else:
+            raise ValueError("Unsupported byte count")
+
+    @cython.cdivision(True)
+    def _encode(self, const Integer[:] data, OutputInteger[:] output_type):
+        """
+        `output_type` is merely a typed placeholder to allow for static
+        typing of output.
+        """
+        cdef int i=0, j=0
+
+        packed_type = np.asarray(output_type).dtype
+        cdef int min_val = np.iinfo(packed_type).min
+        cdef int max_val = np.iinfo(packed_type).max
+
+        # Get length of output array
+        # by summing up required length of each element
+        cdef int number
+        cdef long length = 0
+        for i in range(data.shape[0]):
+            number = data[i]
+            if number < 0:
+                if min_val == 0:
+                    raise ValueError(
+                        "Cannot pack negative numbers into unsigned type"
+                    )
+                # The required packed length for an element is the
+                # number of times min_val/max_val need to be repeated
+                length += number // min_val + 1
+            elif number > 0:
+                length += number // max_val + 1
+            else:
+                # number = 0
+                length += 1
+
+        # Fill output
+        cdef OutputInteger[:] output = np.zeros(length, dtype=packed_type)
+        cdef int remainder
+        j = 0
+        for i in range(data.shape[0]):
+            remainder = data[i]
+            if remainder < 0:
+                if min_val == 0:
+                    raise ValueError(
+                        "Cannot pack negative numbers into unsigned type"
+                    )
+                while remainder <= min_val:
+                    remainder -= min_val
+                    output[j] = min_val
+                    j += 1
+            elif remainder > 0:
+                while remainder >= max_val:
+                    remainder -= max_val
+                    output[j] = max_val
+                    j += 1
+            output[j] = remainder
+            j += 1
+        return np.asarray(output)
+
+    @staticmethod
+    def _get_bounds(const Integer[:] data):
+        if Integer is int8:
+            info = np.iinfo(np.int8)
+        elif Integer is int16:
+            info = np.iinfo(np.int16)
+        elif Integer is int32:
+            info = np.iinfo(np.int32)
+        elif Integer is uint8:
+            info = np.iinfo(np.uint8)
+        elif Integer is uint16:
+            info = np.iinfo(np.uint16)
+        elif Integer is uint32:
+            info = np.iinfo(np.uint32)
+        else:
+            raise ValueError("Unsupported integer type")
+        return info.min, info.max
+
+
+@dataclass
+class StringArrayEncoding(Encoding):
+    """
+    Encoding that compresses an array of strings into an array of
+    indices that point to the unique strings in that array.
+
+    The unique strings themselves are stored as part of the
+    :class:`StringArrayEncoding` as concatenated string.
+    The start index of each unique string in the concatenated string
+    is stored in an *offset* array.
+
+    Parameters
+    ----------
+    strings : ndarray, optional
+        The unique strings that are used for encoding.
+        If omitted, the unique strings are determined from the data the
+        first time :meth:`encode()` is called.
+    data_encoding : list of Encoding, optional
+        The encodings that are applied to the index array.
+        If omitted, the array is directly encoded into bytes without
+        further compression.
+    offset_encoding : list of Encoding, optional
+        The encodings that are applied to the offset array.
+        If omitted, the array is directly encoded into bytes without
+        further compression.
+
+    Attributes
+    ----------
+    strings : ndarray
+    data_encoding : list of Encoding
+    offset_encoding : list of Encoding
+
+    Examples
+    --------
+
+    >>> data = np.array(["apple", "banana", "cherry", "apple", "banana", "apple"])
+    >>> print(data)
+    ['apple' 'banana' 'cherry' 'apple' 'banana' 'apple']
+    >>> # By default the indices would directly be encoded into bytes
+    >>> # However, the indices should be printed here -> data_encoding=[]
+    >>> encoding = StringArrayEncoding(data_encoding=[])
+    >>> encoded = encoding.encode(data)
+    >>> print(encoding.strings)
+    ['apple' 'banana' 'cherry']
+    >>> print(encoded)
+    [0 1 2 0 1 0]
+    """
+
+    strings: ... = None
+    data_encoding: ... = None
+    offset_encoding: ... = None
+
+    def __init__(self, strings=None, data_encoding=None, offset_encoding=None):
+        self.strings = strings
+        if data_encoding is None:
+            data_encoding = [ByteArrayEncoding(TypeCode.INT32)]
+        self.data_encoding = data_encoding
+        if offset_encoding is None:
+            offset_encoding = [ByteArrayEncoding(TypeCode.INT32)]
+        self.offset_encoding = offset_encoding
+
+    @staticmethod
+    def deserialize(content):
+        data_encoding = [
+            deserialize_encoding(e) for e in content["dataEncoding"]
+        ]
+        offset_encoding = [
+            deserialize_encoding(e) for e in content["offsetEncoding"]
+        ]
+        cdef str concatenated_strings = content["stringData"]
+        cdef np.ndarray offsets = decode_stepwise(
+            content["offsets"], offset_encoding
+        )
+
+        strings = np.array([
+            concatenated_strings[offsets[i]:offsets[i+1]]
+            # The final offset is the exclusive stop index
+            for i in range(len(offsets)-1)
+        ], dtype="U")
+
+        return StringArrayEncoding(strings, data_encoding, offset_encoding)
+
+    def serialize(self):
+        if self.strings is None:
+            raise ValueError(
+                "'strings' must be explicitly given or needs to be "
+                "determined from first encoding pass, before it is serialized"
+            )
+
+        string_data = "".join(self.strings)
+        offsets = np.cumsum([0] + [len(s) for s in self.strings])
+
+        return {
+            "kind": "StringArray",
+            "dataEncoding": [e.serialize() for e in self.data_encoding],
+            "stringData": string_data,
+            "offsets": encode_stepwise(offsets, self.offset_encoding),
+            "offsetEncoding": [e.serialize() for e in self.offset_encoding],
+        }
+
+    def encode(self, data):
+        if not np.issubdtype(data.dtype, np.str_):
+            raise TypeError("Data must be of string type")
+
+        if self.strings is None:
+            # 'unique()' already sorts the strings, but this is not necessarily
+            # desired, as this makes efficient encoding of the indices more difficult
+            # -> Bring into the original order
+            _, unique_indices = np.unique(data, return_index=True)
+            self.strings = data[np.sort(unique_indices)]
+            check_present = False
+        else:
+            check_present = True
+
+        string_order = np.argsort(self.strings).astype(np.int32)
+        sorted_strings = self.strings[string_order]
+        sorted_indices = np.searchsorted(sorted_strings, data)
+        indices = string_order[sorted_indices]
+        if check_present and not np.all(self.strings[indices] == data):
+            raise ValueError("Data contains strings not present in 'strings'")
+        return encode_stepwise(indices, self.data_encoding)
+
+    def decode(self, data):
+        indices = decode_stepwise(data, self.data_encoding)
+        return self.strings[indices]
+
+    def __eq__(self, other):
+        if not isinstance(other, type(self)):
+            return False
+        if not np.array_equal(self.strings, other.strings):
+            return False
+        if self.data_encoding != other.data_encoding:
+            return False
+        if self.offset_encoding != other.offset_encoding:
+            return False
+        return True
+
+
+_encoding_classes = {
+    "ByteArray": ByteArrayEncoding,
+    "FixedPoint": FixedPointEncoding,
+    "IntervalQuantization": IntervalQuantizationEncoding,
+    "RunLength": RunLengthEncoding,
+    "Delta": DeltaEncoding,
+    "IntegerPacking": IntegerPackingEncoding,
+    "StringArray": StringArrayEncoding,
+}
+_encoding_classes_kinds = {
+    "ByteArrayEncoding": "ByteArray",
+    "FixedPointEncoding": "FixedPoint",
+    "IntervalQuantizationEncoding": "IntervalQuantization",
+    "RunLengthEncoding": "RunLength",
+    "DeltaEncoding": "Delta",
+    "IntegerPackingEncoding": "IntegerPacking",
+    "StringArrayEncoding": "StringArray",
+}
+
+
+def deserialize_encoding(content):
+    """
+    Create a :class:`Encoding` by deserializing the given *BinaryCIF* content.
+
+    Parameters
+    ----------
+    content : dict
+        The encoding represenet as *BinaryCIF* dictionary.
+
+    Returns
+    -------
+    encoding : Encoding
+        The deserialized encoding.
+    """
+    try:
+        encoding_class = _encoding_classes[content["kind"]]
+    except KeyError:
+        raise ValueError(
+            f"Unknown encoding kind '{content['kind']}'"
+        )
+    return encoding_class.deserialize(content)
+
+
+def create_uncompressed_encoding(array):
+    """
+    Create a simple encoding for the given array that does not compress the data.
+
+    Parameters
+    ----------
+    array : ndarray
+        The array to to create the encoding for.
+
+    Returns
+    -------
+    encoding : list of Encoding
+        The encoding for the data.
+    """
+    if np.issubdtype(array.dtype, np.str_):
+        return [StringArrayEncoding()]
+    else:
+        return [ByteArrayEncoding()]
+
+
+def encode_stepwise(data, encoding):
+    """
+    Apply a list of encodings stepwise to the given data.
+
+    Parameters
+    ----------
+    data : ndarray
+        The data to be encoded.
+    encoding : list of Encoding
+        The encodings to be applied.
+
+    Returns
+    -------
+    encoded_data : ndarray or bytes
+        The encoded data.
+    """
+    for encoding in encoding:
+        data = encoding.encode(data)
+    return data
+
+
+def decode_stepwise(data, encoding):
+    """
+    Apply a list of encodings stepwise to the given data.
+
+    Parameters
+    ----------
+    data : ndarray or bytes
+        The data to be decoded.
+    encoding : list of Encoding
+        The encodings to be applied.
+
+    Returns
+    -------
+    decoded_data : ndarray
+        The decoded data.
+    """
+    for enc in reversed(encoding):
+        data = enc.decode(data)
+    return data
+
+
+def _camel_to_snake_case(attribute_name):
+    return CAMEL_CASE_PATTERN.sub("_", attribute_name).lower()
+
+
+def _snake_to_camel_case(attribute_name):
+    attribute_name = "".join(
+        word.capitalize() for word in attribute_name.split("_")
+    )
+    return attribute_name[0].lower() + attribute_name[1:]
+
+
+def _safe_cast(array, dtype):
+    dtype = np.dtype(dtype)
+    if dtype == array.dtype:
+        return array
+    if np.issubdtype(dtype, np.integer):
+        if not np.issubdtype(array.dtype, np.integer):
+            raise ValueError("Cannot cast floating point to integer")
+        dtype_info = np.iinfo(dtype)
+        if np.any(array < dtype_info.min) or np.any(array > dtype_info.max):
+            raise ValueError("Integer values do not fit into the given dtype")
+    return array.astype(dtype)
+
+
+def _get_n_decimals(value, tolerance):
+    MAX_DECIMALS = 10
+    for n in range(MAX_DECIMALS):
+        if abs(value - round(value, n)) < tolerance:
+            return n
+    return MAX_DECIMALS