Bump tifffile from 2022.5.4 to 2022.7.28

[dependabot]

Bumps tifffile from 2022.5.4 to 2022.7.28.

Release notes

Sourced from tifffile's releases.

v2022.7.28

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, STK, LSM, SGI, NIHImage, ImageJ, MicroManager, FluoView, ScanImage, SEQ, GEL, SVS, SCN, SIS, BIF, ZIF (Zoomable Image File Format), QPTIFF (QPI), NDPI, and GeoTIFF 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.

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.

Changelog

Sourced from tifffile's changelog.

2022.7.28

• Pass 4906 tests.
• Rename FileSequence.labels attribute to dims (breaking).
• Rename tifffile_geodb module to geodb (breaking).
• Rename TiffFile._astuple method to astuple (breaking).
• Rename noplots command line argument to maxplots (breaking).
• Fix reading ImageJ hyperstacks with non-TZC order.
• Fix colorspace of JPEG segments encoded by Bio-Formats.
• Fix fei_metadata for HELIOS FIB-SEM (#141, needs test).
• Add xarray style properties to TiffPage (WIP).
• Add option to specify OME-XML for TiffFile.
• Add option to control multiscales in ZarrTiffStore.
• Support writing to uncompressed ZarrTiffStore.
• Support writing empty images with tiling.
• Support overwriting some tag values in NDPI (#137).
• Support Jetraw compression (experimental).
• Standardize resolution parameter and property.
• Deprecate third resolution argument on write (use resolutionunit).
• Deprecate tuple type compression argument on write (use compressionargs).
• Deprecate enums in TIFF namespace (use enums from module).
• Improve default number of threads to write compressed segments (#139).
• Parse metaseries time values as datetime objects (#143).
• Increase internal read and write buffers to 256 MB.
• Convert some warnings to debug messages.
• Declare all classes final.
• Add script to generate documentation via Sphinx.
• Convert docstrings to Google style with Sphinx directives.

Commits

• 619aa4d Release v2022.7.28
• fd99675 Update CHANGES.rst
• 6264cfe Update tifffile/tifffile.py
• ba0fba9 Update tests/test_tifffile.py
• a6852c2 Update tifffile/numcodecs.py
• 64ec32d Add tifffile/geodb.py
• e7865bc Update setup.py
• 12083bc Update tifffile/_imagecodecs.py
• 4e55ab2 Update tifffile/lsm2bin.py
• e5eabb6 Update tifffile/tiffcomment.py
• Additional commits viewable in compare view

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