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OmicsML / dance

DANCE: a deep learning library and benchmark platform for single-cell analysis
https://pydance.readthedocs.io
BSD 2-Clause "Simplified" License
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build(deps): bump tifffile from 2024.2.12 to 2024.5.22 #449

Closed dependabot[bot] closed 2 months ago

dependabot[bot] commented 2 months ago

Bumps tifffile from 2024.2.12 to 2024.5.22.

Release notes

Sourced from tifffile's releases.

v2024.5.22

Read and write TIFF files

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, Philips DP, 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.

v2024.5.10

Read and write TIFF files

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, Philips DP, 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.

v2024.5.3

Read and write TIFF files

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, Philips DP, 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.

... (truncated)

Changelog

Sourced from tifffile's changelog.

2024.5.22

  • Pass 5084 tests.
  • Derive TiffPages, TiffPageSeries, FileSequence, StoredShape from Sequence.
  • Truncate circular IFD chain, do not raise TiffFileError (breaking).
  • Deprecate access to TiffPages.pages and FileSequence.files.
  • Enable DeprecationWarning for enums in TIFF namespace.
  • Remove some deprecated code (breaking).
  • Add iccprofile property to TiffPage and parameter to TiffWriter.write.
  • Do not detect VSI as SIS format.
  • Limit length of logged exception messages.
  • Work around GitHub not rendering docstring examples (#254, #255).

2024.5.10

  • Support reading JPEGXL compression in DNG 1.7.
  • Read invalid TIFF created by IDEAS software.

2024.5.3

  • Fix reading incompletely written LSM.
  • Fix reading Philips DP with extra rows of tiles (#253, breaking).

2024.4.24

  • Fix compatibility issue with numpy 2 (#252).

2024.4.18

  • Fix write_fsspec when last row of tiles is missing in Philips slide (#249).
  • Add option not to quote file names in write_fsspec.
  • Allow compress bilevel images with deflate, LZMA, and Zstd.
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dependabot[bot] commented 2 months ago

Superseded by #453.