Bump tifffile from 2023.4.12 to 2023.9.18

[dependabot]

Bumps tifffile from 2023.4.12 to 2023.9.18.

Release notes

Sourced from tifffile's releases.

v2023.9.18

Tifffile is a Python library to

1. store NumPy arrays in TIFF (Tagged Image File Format) files, and
2. read image and metadata from TIFF-like files used in bioimaging.

Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, DNG, STK, LSM, SGI, NIHImage, ImageJ, MMStack, NDTiff, FluoView, ScanImage, SEQ, GEL, SVS, SCN, SIS, BIF, ZIF (Zoomable Image File Format), QPTIFF (QPI, PKI), NDPI, and GeoTIFF formatted files.

Image data can be read as NumPy arrays or Zarr arrays/groups from strips, tiles, pages (IFDs), SubIFDs, higher order series, and pyramidal levels.

Image data can be written to TIFF, BigTIFF, OME-TIFF, and ImageJ hyperstack compatible files in multi-page, volumetric, pyramidal, memory-mappable, tiled, predicted, or compressed form.

Many compression and predictor schemes are supported via the imagecodecs library, including LZW, PackBits, Deflate, PIXTIFF, LZMA, LERC, Zstd, JPEG (8 and 12-bit, lossless), JPEG 2000, JPEG XR, JPEG XL, WebP, PNG, EER, Jetraw, 24-bit floating-point, and horizontal differencing.

Tifffile can also be used to inspect TIFF structures, read image data from multi-dimensional file sequences, write fsspec ReferenceFileSystem for TIFF files and image file sequences, patch TIFF tag values, and parse many proprietary metadata formats.

v2023.8.30

Tifffile is a Python library to

1. store NumPy arrays in TIFF (Tagged Image File Format) files, and
2. read image and metadata from TIFF-like files used in bioimaging.

Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, DNG, STK, LSM, SGI, NIHImage, ImageJ, MMStack, NDTiff, FluoView, ScanImage, SEQ, GEL, SVS, SCN, SIS, BIF, ZIF (Zoomable Image File Format), QPTIFF (QPI, PKI), NDPI, and GeoTIFF formatted files.

Image data can be read as NumPy arrays or Zarr arrays/groups from strips, tiles, pages (IFDs), SubIFDs, higher order series, and pyramidal levels.

Image data can be written to TIFF, BigTIFF, OME-TIFF, and ImageJ hyperstack compatible files in multi-page, volumetric, pyramidal, memory-mappable, tiled, predicted, or compressed form.

Many compression and predictor schemes are supported via the imagecodecs library, including LZW, PackBits, Deflate, PIXTIFF, LZMA, LERC, Zstd, JPEG (8 and 12-bit, lossless), JPEG 2000, JPEG XR, JPEG XL, WebP, PNG, EER, Jetraw, 24-bit floating-point, and horizontal differencing.

Tifffile can also be used to inspect TIFF structures, read image data from multi-dimensional file sequences, write fsspec ReferenceFileSystem for TIFF files and image file sequences, patch TIFF tag values, and parse many proprietary metadata formats.

v2023.8.25

Tifffile is a Python library to

1. store NumPy arrays in TIFF (Tagged Image File Format) files, and
2. read image and metadata from TIFF-like files used in bioimaging.

Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, DNG, STK, LSM, SGI, NIHImage, ImageJ, MMStack, NDTiff, FluoView, ScanImage, SEQ, GEL, SVS, SCN, SIS, BIF, ZIF (Zoomable Image File Format), QPTIFF (QPI, PKI), NDPI, and GeoTIFF formatted files.

Image data can be read as NumPy arrays or Zarr arrays/groups from strips, tiles, pages (IFDs), SubIFDs, higher order series, and pyramidal levels.

Image data can be written to TIFF, BigTIFF, OME-TIFF, and ImageJ hyperstack compatible files in multi-page, volumetric, pyramidal, memory-mappable, tiled, predicted, or compressed form.

Many compression and predictor schemes are supported via the imagecodecs library, including LZW, PackBits, Deflate, PIXTIFF, LZMA, LERC, Zstd, JPEG (8 and 12-bit, lossless), JPEG 2000, JPEG XR, JPEG XL, WebP, PNG, EER, Jetraw, 24-bit floating-point, and horizontal differencing.

Tifffile can also be used to inspect TIFF structures, read image data from multi-dimensional file sequences, write fsspec ReferenceFileSystem for TIFF files and image file sequences, patch TIFF tag values, and parse many proprietary metadata formats.

v2023.8.12

Tifffile is a Python library to

... (truncated)

Changelog

Sourced from tifffile's changelog.

2023.9.18

• Pass 5025 tests.
• Raise exception when writing non-volume data with volumetric tiles (#225).
• Improve multi-threaded writing of compressed multi-page files.
• Fix fsspec reference for big-endian files with predictors.

2023.8.30

• Support exclusive file creation mode (#221, #223).

2023.8.25

• Verify shaped metadata is compatible with page shape.
• Support out parameter when returning selection from imread (#222).

2023.8.12

• Support decompressing EER frames.
• Facilitate filtering logged warnings (#216).
• Read more tags from UIC1Tag (#217).
• Fix premature closing of files in main (#218).
• Don't force matplotlib backend to tkagg in main (#219).
• Add py.typed marker.
• Drop support for imagecodecs < 2023.3.16.

2023.7.18

• Limit threading via TIFFFILE_NUM_THREADS environment variable (#215).
• Remove maxworkers parameter from tiff2fsspec (breaking).

2023.7.10

• Increase default strip size to 256 KB when writing with compression.
• Fix ZarrTiffStore with non-default chunkmode.

2023.7.4

• Add option to return selection from imread (#200).
• Fix reading OME series with missing trailing frames (#199).
• Fix fsspec reference for WebP compressed segments missing alpha channel.
• Fix linting issues.
• Detect files written by Agilent Technologies.
• Drop support for Python 3.8 and numpy < 1.21 (NEP29).

Commits

• 70a09c7 Release v2023.9.18
• d8843fe Update CHANGES.rst
• 6c394fb Update tifffile/tifffile.py
• 50213ac Update tests/test_tifffile.py
• 103b6a3 Release v2023.8.30
• d33b2fe Update CHANGES.rst
• b845f1f Update tifffile/tifffile.py
• 8508b7e Update examples/issue125.py
• 6115da6 Update examples/earthbigdata.py
• 50299c2 Update tests/conftest.py
• Additional commits viewable in compare view

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[dependabot]

Superseded by #818.