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Merged
evamaxfield merged 6 commits into from
Feb 7, 2025
Merged

feature/parameterized-ome-tiff-writer-compression #88

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6d7d458
Move compression from hardcoded to ADOBE_DEFLATE to parametrized in O…
evamaxfield Jan 30, 2025
3a027bc
Update docstring
evamaxfield Jan 30, 2025
2580436
Open up access to all tifffile write kwargs, update docstring to prov…
evamaxfield Jan 31, 2025
c23774c
Remove enum import as no longer used for typing
evamaxfield Jan 31, 2025
8ea1feb
Lint and format and add smoke test for compression save
evamaxfield Jan 31, 2025
c653493
Merge branch 'main' into feature/parameterize-compression
evamaxfield Feb 7, 2025
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8 changes: 7 additions & 1 deletion bioio/writers/ome_tiff_writer.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-

import enum
import importlib.metadata
from typing import Any, Dict, List, Optional, Tuple, Union

Expand Down Expand Up @@ -46,6 +47,7 @@ def save(
Union[List[List[int]], List[Optional[List[List[int]]]]]
] = None,
fs_kwargs: Dict[str, Any] = {},
compression: enum.IntEnum = TIFF.COMPRESSION.ADOBE_DEFLATE,
**kwargs: Any,
) -> None:
"""
Expand Down Expand Up @@ -102,6 +104,10 @@ def save(
Any specific keyword arguments to pass down to the fsspec created
filesystem.
Default: {}
compression: enum.IntEnum
Which compression scheme to use during TIFF writing. See
tifffile.TIFF.COMPRESSION for all available options.
Default: "tifffile.TIFF.COMPRESSION.ADOBE_DEFLATE"

Raises
------
Expand Down Expand Up @@ -301,7 +307,7 @@ def save(
photometric=photometric,
metadata=None,
planarconfig=planarconfig,
compression=TIFF.COMPRESSION.ADOBE_DEFLATE,
compression=compression,
)

tif.close()
Expand Down