Skip to content

Commit

Permalink
Update tifffile/_imagecodecs.py
Browse files Browse the repository at this point in the history
  • Loading branch information
@cgohlke
cgohlke committed Sep 19, 2024
1 parent f45049c commit 412288c
Showing 1 changed file with 70 additions and 35 deletions.
105 changes: 70 additions & 35 deletions tifffile/_imagecodecs.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -55,36 +55,49 @@
'zlib_encode',
]

from typing import Any, Literal, overload
from typing import TYPE_CHECKING, overload

import numpy

if TYPE_CHECKING:
from typing import Any, Literal

from numpy.typing import DTypeLike, NDArray

try:
import lzma

def lzma_encode(
data: bytes | numpy.ndarray, /, level: int | None = None, *, out=None
data: bytes | NDArray[Any],
/,
level: int | None = None,
*,
out: Any = None,
) -> bytes:
"""Compress LZMA."""
if isinstance(data, numpy.ndarray):
data = data.tobytes()
return lzma.compress(data)

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

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

return b''

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

Expand All @@ -95,36 +108,44 @@ def lzma_decode(data: bytes, /, *, out=None) -> bytes:
import zlib

def zlib_encode(
data: bytes | numpy.ndarray, /, level: int | None = None, *, out=None
data: bytes | NDArray[Any],
/,
level: int | None = None,
*,
out: Any = None,
) -> bytes:
"""Compress Zlib DEFLATE."""
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=None) -> bytes:
def zlib_decode(data: bytes, /, *, out: Any = None) -> bytes:
"""Decompress Zlib DEFLATE."""
return zlib.decompress(data)

except ImportError:
# Python was built without zlib

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

return b''

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

return b''


def packbits_decode(encoded: bytes, /, *, out=None) -> bytes:
def packbits_decode(encoded: bytes, /, *, out: Any = None) -> bytes:
r"""Decompress PackBits encoded byte string.
>>> packbits_decode(b'\x80\x80') # NOP
Expand Down Expand Up @@ -159,24 +180,29 @@ def packbits_decode(encoded: bytes, /, *, out=None) -> bytes:

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


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


def delta_encode(
data: bytes | bytearray | numpy.ndarray,
data: bytes | bytearray | NDArray[Any],
/,
axis: int = -1,
dist: int = 1,
*,
out=None,
) -> bytes | numpy.ndarray:
out: Any = None,
) -> bytes | NDArray[Any]:
"""Encode Delta."""
if dist != 1:
raise NotImplementedError(
Expand Down Expand Up @@ -210,18 +236,18 @@ def delta_decode(

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


def delta_decode(
data: bytes | bytearray | numpy.ndarray,
data: bytes | bytearray | NDArray[Any],
/,
axis: int = -1,
dist: int = 1,
*,
out=None,
) -> bytes | numpy.ndarray:
out: Any = None,
) -> bytes | NDArray[Any]:
"""Decode Delta."""
if dist != 1:
raise NotImplementedError(
Expand All @@ -231,7 +257,9 @@ def delta_decode(
out = None
if isinstance(data, (bytes, bytearray)):
data = numpy.frombuffer(data, dtype=numpy.uint8)
return numpy.cumsum(data, axis=0, dtype=numpy.uint8, out=out).tobytes()
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:
raise NotImplementedError(
Expand All @@ -241,28 +269,30 @@ def delta_decode(
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(data, axis=axis, dtype=data.dtype, out=out)
return numpy.cumsum( # type: ignore[no-any-return]
data, axis=axis, dtype=data.dtype, out=out
)


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


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


def bitorder_decode(
data: bytes | bytearray | numpy.ndarray,
data: bytes | bytearray | NDArray[Any],
/,
*,
out=None,
out: Any = None,
_bitorder: list[Any] = [],
) -> bytes | numpy.ndarray:
) -> bytes | 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
Expand Down Expand Up @@ -310,18 +340,18 @@ def bitorder_decode(
raise NotImplementedError(
"bitorder_decode of slices requires the 'imagecodecs' package"
) from exc
return None
return None # type: ignore[unreachable]


def packints_decode(
data: bytes,
/,
dtype: numpy.dtype | str,
dtype: DTypeLike,
bitspersample: int,
runlen: int = 0,
*,
out=None,
) -> numpy.ndarray:
out: Any = None,
) -> NDArray[Any]:
"""Decompress bytes to array of integers.
This implementation only handles itemsizes 1, 8, 16, 32, and 64 bits.
Expand Down Expand Up @@ -358,7 +388,12 @@ def packints_decode(


def packints_encode(
data: numpy.ndarray, /, bitspersample: int, axis: int = -1, *, out=None
data: NDArray[Any],
/,
bitspersample: int,
axis: int = -1,
*,
out: Any = None,
) -> bytes:
"""Tightly pack integers."""
raise NotImplementedError(
Expand All @@ -368,7 +403,7 @@ def packints_encode(

def float24_decode(
data: bytes, /, byteorder: Literal['>', '<']
) -> numpy.ndarray:
) -> NDArray[Any]:
"""Return float32 array from float24."""
raise NotImplementedError(
"float24_decode requires the 'imagecodecs' package"
Expand Down

0 comments on commit 412288c

Please sign in to comment.