envs/kitoverlay/tifffile/_imagecodecs.py

# tifffile/_imagecodecs.py

# Copyright (c) 2008-2026, Christoph Gohlke
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"""Fallback imagecodecs codecs.

This module provides alternative, pure Python and NumPy implementations of
some functions of the `imagecodecs`_ package. The functions may raise
`NotImplementedError`.

.. _imagecodecs: https://github.com/cgohlke/imagecodecs

"""

from __future__ import annotations

__all__ = [
    'bitorder_decode',
    'delta_decode',
    'delta_encode',
    'float24_decode',
    'lzma_decode',
    'lzma_encode',
    'packbits_decode',
    'packints_decode',
    'packints_encode',
    'zlib_decode',
    'zlib_encode',
    'zstd_decode',
    'zstd_encode',
]

from typing import TYPE_CHECKING, overload

import numpy

if TYPE_CHECKING:
    from typing import Any, Literal

    from numpy.typing import ArrayLike, DTypeLike, NDArray

try:
    import lzma

    def lzma_encode(
        data: bytes | NDArray[Any],
        /,
        level: int | None = None,
        *,
        out: Any = None,
    ) -> bytes:
        """Compress LZMA.

        Parameters:
            data: Data to compress.
            level: Compression level (currently unused).
            out: Output buffer (currently unused).

        """
        del level, out  # unused
        if isinstance(data, numpy.ndarray):
            data = data.tobytes()
        return lzma.compress(data)

    def lzma_decode(data: bytes, /, *, out: Any = None) -> bytes:
        """Decompress LZMA.

        Parameters:
            data: Compressed data.
            out: Output buffer (currently unused).

        """
        del out  # unused
        return lzma.decompress(data)

except ImportError:
    # Python was built without lzma
    def lzma_encode(
        data: bytes | NDArray[Any],
        /,
        level: int | None = None,
        *,
        out: Any = None,
    ) -> bytes:
        """Raise ImportError."""
        del data, level, out  # unused
        import lzma  # noqa: F401

        return b''

    def lzma_decode(data: bytes, /, *, out: Any = None) -> bytes:
        """Raise ImportError."""
        del data, out  # unused
        import lzma  # noqa: F401

        return b''


try:
    import zlib

    def zlib_encode(
        data: bytes | NDArray[Any],
        /,
        level: int | None = None,
        *,
        out: Any = None,
    ) -> bytes:
        """Compress Zlib DEFLATE.

        Parameters:
            data: Data to compress.
            level: Compression level (0-9, default 6).
            out: Output buffer (currently unused).

        """
        del out  # unused
        if isinstance(data, numpy.ndarray):
            data = data.tobytes()
        return zlib.compress(data, 6 if level is None else level)

    def zlib_decode(data: bytes, /, *, out: Any = None) -> bytes:
        """Decompress Zlib DEFLATE.

        Parameters:
            data: Compressed data.
            out: Output buffer (currently unused).

        """
        del out  # unused
        return zlib.decompress(data)

except ImportError:
    # Python was built without zlib

    def zlib_encode(
        data: bytes | NDArray[Any],
        /,
        level: int | None = None,
        *,
        out: Any = None,
    ) -> bytes:
        """Raise ImportError."""
        del data, level, out  # unused
        import zlib  # noqa: F401

        return b''

    def zlib_decode(data: bytes, /, *, out: Any = None) -> bytes:
        """Raise ImportError."""
        del data, out  # unused
        import zlib  # noqa: F401

        return b''


try:
    from compression import zstd

    def zstd_encode(
        data: bytes | NDArray[Any],
        /,
        level: int | None = None,
        *,
        out: Any = None,
    ) -> bytes:
        """Compress ZSTD.

        Parameters:
            data: Data to compress.
            level: Compression level.
            out: Output buffer (currently unused).

        """
        del out  # unused
        if isinstance(data, numpy.ndarray):
            data = data.tobytes()
        return zstd.compress(data, level=level)

    def zstd_decode(data: bytes, /, *, out: Any = None) -> bytes:
        """Decompress ZSTD.

        Parameters:
            data: Compressed data.
            out: Output buffer (currently unused).

        """
        del out  # unused
        return zstd.decompress(data)

except ImportError:
    # Python was built without zstd
    def zstd_encode(
        data: bytes | NDArray[Any],
        /,
        level: int | None = None,
        *,
        out: Any = None,
    ) -> bytes:
        """Raise ImportError."""
        del data, level, out  # unused
        from compression import zstd  # noqa: F401

        return b''

    def zstd_decode(data: bytes, /, *, out: Any = None) -> bytes:
        """Raise ImportError."""
        del data, out  # unused
        from compression import zstd  # noqa: F401

        return b''


def packbits_decode(encoded: bytes, /, *, out: Any = None) -> bytes:
    r"""Decompress PackBits encoded byte string.

    Parameters:
        encoded: PackBits encoded byte string.
        out: Output buffer (currently unused).

    Returns:
        Decompressed byte string.

    Examples:
        >>> packbits_decode(b'\x80\x80')  # NOP
        b''
        >>> packbits_decode(b'\x02123')
        b'123'
        >>> packbits_decode(
        ...     b'\xfe\xaa\x02\x80\x00\x2a\xfd\xaa\x03\x80\x00\x2a\x22\xf7\xaa'
        ... )[:-5]
        b'\xaa\xaa\xaa\x80\x00*\xaa\xaa\xaa\xaa\x80\x00*"\xaa\xaa\xaa\xaa\xaa'

    """
    del out  # unused
    out = []
    out_extend = out.extend
    i = 0
    try:
        while True:
            n = ord(encoded[i : i + 1]) + 1
            i += 1
            if n > 129:
                # replicate
                out_extend(encoded[i : i + 1] * (258 - n))
                i += 1
            elif n < 129:
                # literal
                out_extend(encoded[i : i + n])
                i += n
    except TypeError:
        pass
    return bytes(out)


@overload
def delta_encode(
    data: bytes | bytearray,
    /,
    axis: int = -1,
    dist: int = 1,
    *,
    out: Any = None,
) -> bytes: ...


@overload
def delta_encode(
    data: NDArray[Any], /, axis: int = -1, dist: int = 1, *, out: Any = None
) -> NDArray[Any]: ...


def delta_encode(
    data: bytes | bytearray | NDArray[Any],
    /,
    axis: int = -1,
    dist: int = 1,
    *,
    out: Any = None,
) -> bytes | NDArray[Any]:
    """Encode Delta.

    Encode differences between consecutive samples along axis.

    Parameters:
        data: Data to encode.
        axis: Axis along which to compute differences (default -1).
        dist: Distance between samples (only dist=1 is supported).
        out: Output buffer (currently unused).

    Returns:
        Encoded data.
        Returns bytes for bytes/bytearray input, numpy array otherwise.

    """
    del out  # unused
    if dist != 1:
        msg = f"delta_encode with {dist=} requires the 'imagecodecs' package"
        raise NotImplementedError(msg)
    if isinstance(data, (bytes, bytearray)):
        data = numpy.frombuffer(data, dtype=numpy.uint8)
        diff = numpy.diff(data, axis=0)
        return numpy.insert(diff, 0, data[0]).tobytes()

    dtype = data.dtype
    if dtype.kind == 'f':
        data = data.view(f'{dtype.byteorder}u{dtype.itemsize}')
    diff = numpy.diff(data, axis=axis)
    key: list[int | slice] = [slice(None)] * data.ndim
    key[axis] = 0
    diff = numpy.insert(diff, 0, data[tuple(key)], axis=axis)
    if not data.dtype.isnative:
        diff = diff.byteswap(inplace=True)
        diff = diff.view(diff.dtype.newbyteorder())
    if dtype.kind == 'f':
        return diff.view(dtype)
    return diff


@overload
def delta_decode(
    data: bytes | bytearray, /, axis: int, dist: int, *, out: Any
) -> bytes: ...


@overload
def delta_decode(
    data: NDArray[Any], /, axis: int, dist: int, *, out: Any
) -> NDArray[Any]: ...


def delta_decode(
    data: bytes | bytearray | NDArray[Any],
    /,
    axis: int = -1,
    dist: int = 1,
    *,
    out: Any = None,
) -> bytes | NDArray[Any]:
    """Decode Delta.

    Decode delta-encoded data by computing cumulative sum along axis.

    Parameters:
        data: Encoded data.
        axis: Axis along which to compute cumulative sum (default -1).
        dist: Distance between samples (only dist=1 is supported).
        out: Output buffer for results.

    Returns:
        Decoded data.
        Returns bytes for bytes/bytearray input, numpy array otherwise.

    """
    if dist != 1:
        msg = f"delta_decode with {dist=} requires the 'imagecodecs' package"
        raise NotImplementedError(msg)
    if out is not None and not out.flags.writeable:
        out = None
    if isinstance(data, (bytes, bytearray)):
        data = numpy.frombuffer(data, dtype=numpy.uint8)
        return numpy.cumsum(  # type: ignore[no-any-return]
            data, axis=0, dtype=numpy.uint8, out=out
        ).tobytes()
    if data.dtype.kind == 'f':
        if not data.dtype.isnative:
            msg = (
                f'delta_decode with {data.dtype!r} '
                "requires the 'imagecodecs' package"
            )
            raise NotImplementedError(msg)
        view = data.view(f'{data.dtype.byteorder}u{data.dtype.itemsize}')
        view = numpy.cumsum(view, axis=axis, dtype=view.dtype)
        return view.view(data.dtype)
    return numpy.cumsum(  # type: ignore[no-any-return]
        data, axis=axis, dtype=data.dtype, out=out
    )


@overload
def bitorder_decode(
    data: bytearray,
    /,
    *,
    out: Any = None,
    _bitorder: list[Any] = [],  # noqa: B006
) -> bytearray: ...


@overload
def bitorder_decode(
    data: bytes,
    /,
    *,
    out: Any = None,
    _bitorder: list[Any] = [],  # noqa: B006
) -> bytes: ...


@overload
def bitorder_decode(
    data: NDArray[Any],
    /,
    *,
    out: Any = None,
    _bitorder: list[Any] = [],  # noqa: B006
) -> NDArray[Any]: ...


def bitorder_decode(
    data: bytes | bytearray | NDArray[Any],
    /,
    *,
    out: Any = None,
    _bitorder: list[Any] = [],  # noqa: B006
) -> bytes | bytearray | NDArray[Any]:
    r"""Reverse bits in each byte of bytes or numpy array.

    Decode data where pixels with lower column values are stored in the
    lower-order bits of the bytes (TIFF FillOrder is LSB2MSB).

    Parameters:
        data:
            Data to be bit-reversed.
            If bytes type, a new bit-reversed bytes is returned.
            NumPy arrays are bit-reversed in-place.
        out:
            Output buffer (currently unused).
        _bitorder:
            Internal caching parameter (not for public use).

    Examples:
        >>> bitorder_decode(b'\x01\x64')
        b'\x80&'
        >>> data = numpy.array([1, 666], dtype='uint16')
        >>> _ = bitorder_decode(data)
        >>> data
        array([  128, 16473], dtype=uint16)

    """
    del out  # unused
    if not _bitorder:
        _bitorder.append(
            b'\x00\x80@\xc0 \xa0`\xe0\x10\x90P\xd00\xb0p\xf0\x08\x88H'
            b'\xc8(\xa8h\xe8\x18\x98X\xd88\xb8x\xf8\x04\x84D\xc4$\xa4d'
            b'\xe4\x14\x94T\xd44\xb4t\xf4\x0c\x8cL\xcc,\xacl\xec\x1c\x9c'
            b'\\\xdc<\xbc|\xfc\x02\x82B\xc2"\xa2b\xe2\x12\x92R\xd22'
            b'\xb2r\xf2\n\x8aJ\xca*\xaaj\xea\x1a\x9aZ\xda:\xbaz\xfa'
            b'\x06\x86F\xc6&\xa6f\xe6\x16\x96V\xd66\xb6v\xf6\x0e\x8eN'
            b'\xce.\xaen\xee\x1e\x9e^\xde>\xbe~\xfe\x01\x81A\xc1!\xa1a'
            b'\xe1\x11\x91Q\xd11\xb1q\xf1\t\x89I\xc9)\xa9i\xe9\x19'
            b'\x99Y\xd99\xb9y\xf9\x05\x85E\xc5%\xa5e\xe5\x15\x95U\xd55'
            b'\xb5u\xf5\r\x8dM\xcd-\xadm\xed\x1d\x9d]\xdd=\xbd}\xfd'
            b'\x03\x83C\xc3#\xa3c\xe3\x13\x93S\xd33\xb3s\xf3\x0b\x8bK'
            b"\xcb+\xabk\xeb\x1b\x9b[\xdb;\xbb{\xfb\x07\x87G\xc7'\xa7g"
            b'\xe7\x17\x97W\xd77\xb7w\xf7\x0f\x8fO\xcf/\xafo\xef\x1f\x9f_'
            b'\xdf?\xbf\x7f\xff'
        )
        _bitorder.append(numpy.frombuffer(_bitorder[0], dtype=numpy.uint8))
    if isinstance(data, (bytes, bytearray)):
        return data.translate(_bitorder[0])
    try:
        view = data.view('uint8')
        numpy.take(_bitorder[1], view, out=view)
    except ValueError as exc:
        msg = "bitorder_decode of slices requires the 'imagecodecs' package"
        raise NotImplementedError(msg) from exc
    return data


def packints_decode(
    data: bytes,
    /,
    dtype: DTypeLike | None,
    bitspersample: int,
    runlen: int = 0,
    *,
    out: Any = None,
) -> NDArray[Any]:
    """Decompress bytes to array of integers.

    This implementation only handles itemsizes 1, 8, 16, 32, and 64 bits.
    Install the Imagecodecs package for decoding other integer sizes.

    Parameters:
        data:
            Data to decompress.
        dtype:
            Numpy boolean or integer type.
        bitspersample:
            Number of bits per integer.
        runlen:
            Number of consecutive integers after which to start at next byte.
        out:
            Output buffer (currently unused).

    Returns:
        Array of unpacked integers.

    Examples:
        >>> packints_decode(b'a', 'B', 1)
        array([0, 1, 1, 0, 0, 0, 0, 1], dtype=uint8)

    """
    del out  # unused
    if bitspersample == 1:  # bitarray
        data_array = numpy.frombuffer(data, '|B')
        data_array = numpy.unpackbits(data_array)
        if runlen > 0 and runlen % 8:
            data_array = data_array.reshape((-1, runlen + (8 - runlen % 8)))
            data_array = data_array[:, :runlen].reshape(-1)
        return data_array.astype(dtype)
    if bitspersample in (8, 16, 32, 64):
        return numpy.frombuffer(data, dtype)
    msg = (
        f'packints_decode of {bitspersample}-bit integers '
        "requires the 'imagecodecs' package"
    )
    raise NotImplementedError(msg)


def packints_encode(
    data: ArrayLike,
    bitspersample: int,
    /,
    *,
    axis: int = -1,
    out: Any = None,
) -> bytes | bytearray:
    """Tightly pack integers.

    Parameters:
        data: Array of integers to pack.
        bitspersample: Number of bits per integer.
        axis: Axis along which to pack.
        out: Output buffer.

    Returns:
        Packed byte string.

    """
    msg = "packints_encode requires the 'imagecodecs' package"
    raise NotImplementedError(msg)


def float24_decode(
    data: bytes, /, byteorder: Literal['>', '<']
) -> NDArray[Any]:
    """Return float32 array from float24.

    Parameters:
        data: Bytes containing float24 values.
        byteorder: Byte order, either '>' (big-endian) or '<' (little-endian).

    Returns:
        Array of float32 values.

    """
    msg = "float24_decode requires the 'imagecodecs' package"
    raise NotImplementedError(msg)