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Bump tifffile from 2023.4.12 to 2024.9.20 #1014

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Bumps tifffile from 2023.4.12 to 2024.9.20.

Release notes

Sourced from tifffile's releases.

v2024.9.20

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.

Changes

  • Fix writing colormap to ImageJ files (breaking).
  • Improve typing.
  • Remove support for Python 3.9.

v2024.8.30

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, 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.

v2024.8.28

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.

... (truncated)

Changelog

Sourced from tifffile's changelog.

2024.9.20

  • Pass 5107 tests.
  • Fix writing colormap to ImageJ files (breaking).
  • Improve typing.
  • Remove support for Python 3.9.

2024.8.30

  • Support writing OME Dataset and some StructuredAnnotations elements.

2024.8.28

  • Fix LSM scan types and dimension orders (#269, breaking).
  • Use IO[bytes] instead of BinaryIO for typing (#268).

2024.8.24

  • Do not remove trailing length-1 dimension writing non-shaped file (breaking).
  • Fix writing OME-TIFF with certain modulo axes orders.
  • Make imshow NaN aware.

2024.8.10

  • Relax bitspersample check for JPEG, JPEG2K, and JPEGXL compression (#265).

2024.7.24

  • 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.

... (truncated)

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Bumps [tifffile](https://github.com/cgohlke/tifffile) from 2023.4.12 to 2024.9.20.
- [Release notes](https://github.com/cgohlke/tifffile/releases)
- [Changelog](https://github.com/cgohlke/tifffile/blob/master/CHANGES.rst)
- [Commits](cgohlke/tifffile@v2023.4.12...v2024.9.20)

---
updated-dependencies:
- dependency-name: tifffile
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file major Add this label when bumping major version. python Pull requests that update Python code labels Sep 23, 2024
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