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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 2024.7.24 #461

Closed dependabot[bot] closed 3 months ago

dependabot[bot] commented 4 months ago

Bumps tifffile from 2024.2.12 to 2024.7.24.

Release notes

Sourced from tifffile's releases.

v2024.7.24

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, GeoTIFF, Adobe DNG, ZIF (Zoomable Image File Format), MetaMorph STK, Zeiss LSM, ImageJ hyperstack, Micro-Manager MMStack and NDTiff, SGI, NIHImage, Olympus FluoView and SIS, ScanImage, Molecular Dynamics GEL, Aperio SVS, Leica SCN, Roche BIF, PerkinElmer QPTIFF (QPI, PKI), Hamamatsu NDPI, Argos AVS, and Philips DP 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.

v2024.7.21

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, GeoTIFF, Adobe DNG, ZIF (Zoomable Image File Format), MetaMorph STK, Zeiss LSM, ImageJ hyperstack, Micro-Manager MMStack and NDTiff, SGI, NIHImage, Olympus FluoView and SIS, ScanImage, Molecular Dynamics GEL, Aperio SVS, Leica SCN, Roche BIF, PerkinElmer QPTIFF (QPI, PKI), Hamamatsu NDPI, Argos AVS, and Philips DP 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.

v2024.7.2

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, GeoTIFF, Adobe DNG, ZIF (Zoomable Image File Format), MetaMorph STK, Zeiss LSM, ImageJ hyperstack, Micro-Manager MMStack and NDTiff, SGI, NIHImage, Olympus FluoView and SIS, ScanImage, Molecular Dynamics GEL, Aperio SVS, Leica SCN, Roche BIF, PerkinElmer QPTIFF (QPI, PKI), Hamamatsu NDPI, Argos AVS, and Philips DP 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.

2024.7.24

  • Pass 5092 tests.
  • Fix reading contiguous multi-page series via Zarr store (#67).

2024.7.21

  • Fix integer overflow in product function caused by numpy types.
  • Allow tag reader functions to fail.

2024.7.2

  • Enable memmap to create empty files with non-native byte order.
  • Deprecate Python 3.9, support Python 3.13.

2024.6.18

  • Ensure TiffPage.nodata is castable to dtype (breaking, #260).
  • Support Argos AVS slides.

2024.5.22

  • 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.
  • Fix docstring examples not correctly rendered on GitHub (#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.

... (truncated)

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dependabot[bot] commented 3 months ago

Superseded by #463.