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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 2023.7.10 to 2024.2.12 #418

Closed dependabot[bot] closed 6 months ago

dependabot[bot] commented 6 months ago

Bumps tifffile from 2023.7.10 to 2024.2.12.

Release notes

Sourced from tifffile's releases.

v2024.2.12

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, 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.

v2024.1.30

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, 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.

v2023.12.9

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, 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.

2024.2.12

  • Pass 5074 tests.
  • Deprecate dtype, add chunkdtype parameter in FileSequence.asarray.
  • Add imreadargs parameters passed to FileSequence.imread.

2024.1.30

  • Fix compatibility issue with numpy 2 (#238).
  • Enable DeprecationWarning for tuple compression argument.
  • Parse sequence of numbers in xml2dict.

2023.12.9

  • Read 32-bit Indica Labs TIFF as float32.
  • Fix UnboundLocalError reading big LSM files without time axis.
  • Use os.sched_getaffinity, if available, to get the number of CPUs (#231).
  • Limit the number of default worker threads to 32.

2023.9.26

  • Lazily convert dask array to ndarray when writing.
  • Allow to specify buffersize for reading and writing.
  • Fix IndexError reading some corrupted files with ZarrTiffStore (#227).

2023.9.18

  • 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.

... (truncated)

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RemyLau commented 6 months ago

@dependabot squash and merge