Bump tifffile from 2022.2.9 to 2023.2.28

[dependabot]

Bumps tifffile from 2022.2.9 to 2023.2.28.

Release notes

Sourced from tifffile's releases.

v2023.3.27

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, Micro-Manager NDTiff, FluoView, ScanImage, SEQ, GEL, SVS, SCN, SIS, BIF, ZIF (Zoomable Image File Format), QPTIFF (QPI, PKI), 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.

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, 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.

v2023.2.3

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, MicroManager NDTiff, 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.

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, 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.

v2023.2.2

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, MicroManager NDTiff, 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.

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, Jetraw, 24-bit floating-point, and floating-point 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.

v2023.1.23

Tifffile is a Python library to

... (truncated)

Changelog

Sourced from tifffile's changelog.

2023.2.28

• Pass 4952 tests.
• Fix reading some Micro-Manager metadata from corrupted files.
• Speed up reading Micro-Manager indexmap for creation of OME series.

2023.2.27

• Pass 4952 tests.
• Use Micro-Manager indexmap offsets to create virtual TiffFrames.
• Fixes for future imagecodecs.

2023.2.3

• Fix overflow in calculation of databytecounts for large NDPI files.

2023.2.2

• Fix regression reading layered NDPI files.
• Add option to specify offset in FileHandle.read_array.

2023.1.23

• Support reading NDTiffStorage.
• Support reading PIXTIFF compression.
• Support LERC with Zstd or Deflate compression.
• Do not write duplicate and select extratags.
• Allow to write uncompressed image data beyond 4 GB in classic TIFF.
• Add option to specify chunkshape and dtype in FileSequence.asarray.
• Add option for imread to write to output in FileSequence.asarray (#172).
• Add function to read GDAL structural metadata.
• Add function to read NDTiff.index files.
• Fix IndexError accessing TiffFile.mdgel_metadata in non-MDGEL files.
• Fix unclosed file ResourceWarning in TiffWriter.
• Fix non-bool predictor arguments (#167).
• Relax detection of OME-XML (#173).
• Rename some TiffFrame parameters (breaking).
• Deprecate squeeze_axes (will change signature).
• Use defusexml in xml2dict.

2022.10.10

• Fix RecursionError in peek_iterator.
• Fix reading NDTiffv3 summary settings.
• Fix svs_description_metadata parsing (#149).
• Fix ImportError if Python was built without zlib or lzma.
• Fix bool of COMPRESSION and PREDICTOR instances.
• Deprecate non-sequence extrasamples arguments.
• Parse SCIFIO metadata as ImageJ.

... (truncated)

Commits

• deda2fc Release v2023.2.28
• 8dc90fb Update CHANGES.rst
• 58ad191 Update tifffile/tifffile.py
• 38c7d5e Update tests/test_tifffile.py
• 0d5c12f Release v2023.2.27
• 1ef68aa Update CHANGES.rst
• ab8d355 Update tifffile/tifffile.py
• 640b335 Update tests/test_tifffile.py
• 0c380b1 Release v2023.2.3
• 38d2c7d Update CHANGES.rst
• Additional commits viewable in compare view

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