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33d1d58 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 | # tifffile/numcodecs.py
# Copyright (c) 2021-2026, Christoph Gohlke
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
"""TIFF codec for the Numcodecs package."""
from __future__ import annotations
__all__ = ['Tiff', 'register_codec']
from io import BytesIO
from typing import TYPE_CHECKING
from numcodecs import registry
from numcodecs.abc import Codec
from .tifffile import METADATA_DEFAULT, TiffFile, TiffWriter
if TYPE_CHECKING:
from collections.abc import Sequence
from typing import Any
from .tifffile import (
COMPRESSION,
EXTRASAMPLE,
PHOTOMETRIC,
PLANARCONFIG,
PREDICTOR,
ByteOrder,
TagTuple,
)
class Tiff(Codec): # type: ignore[misc]
"""TIFF codec for Numcodecs."""
codec_id = 'tifffile'
def __init__(
self,
# TiffFile.asarray
key: int | slice | Sequence[int] | None = None,
series: int | None = None,
level: int | None = None,
squeeze: bool | None = None,
buffersize: int | None = None,
# TiffWriter
bigtiff: bool = False,
byteorder: ByteOrder | None = None,
imagej: bool = False,
ome: bool | None = None,
# TiffWriter.write
photometric: PHOTOMETRIC | int | str | None = None,
planarconfig: PLANARCONFIG | int | str | None = None,
extrasamples: Sequence[EXTRASAMPLE | int | str] | None = None,
volumetric: bool = False,
tile: Sequence[int] | None = None,
rowsperstrip: int | None = None,
compression: COMPRESSION | int | str | None = None,
compressionargs: dict[str, Any] | None = None,
predictor: PREDICTOR | int | str | bool | None = None,
subsampling: tuple[int, int] | None = None,
metadata: dict[str, Any] | None = METADATA_DEFAULT,
extratags: Sequence[TagTuple] | None = None,
truncate: bool = False,
maxworkers: int | None = None,
) -> None:
self.key = key
self.series = series
self.level = level
self.squeeze = squeeze
self.buffersize = buffersize
self.bigtiff = bigtiff
self.byteorder = byteorder
self.imagej = imagej
self.ome = ome
self.photometric = photometric
self.planarconfig = planarconfig
self.extrasamples = extrasamples
self.volumetric = volumetric
self.tile = tile
self.rowsperstrip = rowsperstrip
self.compression = compression
self.compressionargs = compressionargs
self.predictor = predictor
self.subsampling = subsampling
self.metadata = metadata
self.extratags = extratags
self.truncate = truncate
self.maxworkers = maxworkers
def encode(self, buf: Any) -> bytes:
"""Return TIFF file as bytes."""
with BytesIO() as fh:
with TiffWriter(
fh,
bigtiff=self.bigtiff,
byteorder=self.byteorder,
imagej=self.imagej,
ome=self.ome,
) as tif:
tif.write(
buf,
photometric=self.photometric,
planarconfig=self.planarconfig,
extrasamples=self.extrasamples,
volumetric=self.volumetric,
tile=self.tile,
rowsperstrip=self.rowsperstrip,
compression=self.compression,
compressionargs=self.compressionargs,
predictor=self.predictor,
subsampling=self.subsampling,
metadata=self.metadata,
extratags=self.extratags,
truncate=self.truncate,
maxworkers=self.maxworkers,
)
return fh.getvalue()
def decode(self, buf: Any, out: Any = None) -> Any:
"""Return decoded image as NumPy array."""
with BytesIO(buf) as fh, TiffFile(fh) as tif:
return tif.asarray(
key=self.key,
series=self.series,
level=self.level,
squeeze=self.squeeze,
maxworkers=self.maxworkers,
buffersize=self.buffersize,
out=out,
)
def register_codec(
cls: type[Codec] = Tiff, codec_id: str | None = None
) -> None:
"""Register :py:class:`Tiff` codec with Numcodecs."""
registry.register_codec(cls, codec_id=codec_id)
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