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Abe404 / root_painter

RootPainter: Deep Learning Segmentation of Biological Images with Corrective Annotation
https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.18387
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Bump imagecodecs from 2021.8.26 to 2023.9.18 in /trainer #125

Open dependabot[bot] opened 1 year ago

dependabot[bot] commented 1 year ago

Bumps imagecodecs from 2021.8.26 to 2023.9.18.

Release notes

Sourced from imagecodecs's releases.

v2023.9.18

Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in Tifffile, Czifile, Zarr, kerchunk, and other scientific image input/output packages.

Decode and/or encode functions are implemented for Zlib (DEFLATE), GZIP, ZStandard (ZSTD), Blosc, Brotli, Snappy, LZMA, BZ2, LZ4, LZ4F, LZ4HC, LZ4H5, LZW, LZF, LZFSE, LZHAM, PGLZ (PostgreSQL LZ), RCOMP (Rice), ZFP, AEC, SZIP, LERC, EER, NPY, BCn, DDS, PNG, APNG, GIF, TIFF, WebP, QOI, JPEG 8 and 12-bit, Lossless JPEG (LJPEG, LJ92, JPEGLL), JPEG 2000 (JP2, J2K), JPEG LS, JPEG XL, JPEG XR (WDP, HD Photo), MOZJPEG, AVIF, HEIF, RGBE (HDR), Jetraw, PackBits, Packed Integers, Delta, XOR Delta, Floating Point Predictor, Bitorder reversal, Byteshuffle, Bitshuffle, Quantize (Scale, BitGroom, BitRound, GranularBR), Float24 (24-bit floating point), and CMS (color space transformations). Checksum functions are implemented for crc32, adler32, fletcher32, and Jenkins lookup3.

v2023.9.4

Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in Tifffile, Czifile, Zarr, kerchunk, and other scientific image input/output packages.

Decode and/or encode functions are implemented for Zlib (DEFLATE), GZIP, ZStandard (ZSTD), Blosc, Brotli, Snappy, LZMA, BZ2, LZ4, LZ4F, LZ4HC, LZ4H5, LZW, LZF, LZFSE, LZHAM, PGLZ (PostgreSQL LZ), RCOMP (Rice), ZFP, AEC, SZIP, LERC, EER, NPY, BCn, DDS, PNG, APNG, GIF, TIFF, WebP, QOI, JPEG 8 and 12-bit, Lossless JPEG (LJPEG, LJ92, JPEGLL), JPEG 2000 (JP2, J2K), JPEG LS, JPEG XL, JPEG XR (WDP, HD Photo), MOZJPEG, AVIF, HEIF, RGBE (HDR), Jetraw, PackBits, Packed Integers, Delta, XOR Delta, Floating Point Predictor, Bitorder reversal, Byteshuffle, Bitshuffle, Quantize (Scale, BitGroom, BitRound, GranularBR), Float24 (24-bit floating point), and CMS (color space transformations). Checksum functions are implemented for crc32, adler32, fletcher32, and Jenkins lookup3.

v2023.8.12

Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in Tifffile, Czifile, Zarr, kerchunk, and other scientific image input/output packages.

Decode and/or encode functions are implemented for Zlib (DEFLATE), GZIP, ZStandard (ZSTD), Blosc, Brotli, Snappy, LZMA, BZ2, LZ4, LZ4F, LZ4HC, LZW, LZF, LZFSE, LZHAM, PGLZ (PostgreSQL LZ), RCOMP (Rice), ZFP, AEC, SZIP, LERC, EER, NPY, BCn, DDS, PNG, APNG, GIF, TIFF, WebP, QOI, JPEG 8-bit, JPEG 12-bit, Lossless JPEG (LJPEG, LJ92, JPEGLL), JPEG 2000 (JP2, J2K), JPEG LS, JPEG XL, JPEG XR (WDP, HD Photo), MOZJPEG, AVIF, HEIF, RGBE (HDR), Jetraw, PackBits, Packed Integers, Delta, XOR Delta, Floating Point Predictor, Bitorder reversal, Byteshuffle, Bitshuffle, CMS (color space transformations), and Float24 (24-bit floating point). Checksum functions are implemented for crc32, adler32, fletcher32, and Jenkins lookup3.

v2023.7.10

Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in Tifffile, Czifile, Zarr, kerchunk, and other scientific image input/output packages.

Decode and/or encode functions are implemented for Zlib (DEFLATE), GZIP, ZStandard (ZSTD), Blosc, Brotli, Snappy, LZMA, BZ2, LZ4, LZ4F, LZ4HC, LZW, LZF, LZFSE, LZHAM, PGLZ (PostgreSQL LZ), RCOMP (Rice), ZFP, AEC, SZIP, LERC, NPY, BCn, DDS, PNG, APNG, GIF, TIFF, WebP, QOI, JPEG 8-bit, JPEG 12-bit, Lossless JPEG (LJPEG, LJ92, JPEGLL), JPEG 2000 (JP2, J2K), JPEG LS, JPEG XL, JPEG XR (WDP, HD Photo), MOZJPEG, AVIF, HEIF, RGBE (HDR), Jetraw, PackBits, Packed Integers, Delta, XOR Delta, Floating Point Predictor, Bitorder reversal, Byteshuffle, Bitshuffle, CMS (color space transformations), and Float24 (24-bit floating point).

v2023.7.4

Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in Tifffile, Czifile, Zarr, kerchunk, and other scientific image input/output packages.

Decode and/or encode functions are implemented for Zlib (DEFLATE), GZIP, ZStandard (ZSTD), Blosc, Brotli, Snappy, LZMA, BZ2, LZ4, LZ4F, LZ4HC, LZW, LZF, LZFSE, LZHAM, PGLZ (PostgreSQL LZ), RCOMP (Rice), ZFP, AEC, SZIP, LERC, NPY, BCn, DDS, PNG, APNG, GIF, TIFF, WebP, QOI, JPEG 8-bit, JPEG 12-bit, Lossless JPEG (LJPEG, LJ92, JPEGLL), JPEG 2000 (JP2, J2K), JPEG LS, JPEG XL, JPEG XR (WDP, HD Photo), MOZJPEG, AVIF, HEIF, RGBE (HDR), Jetraw, PackBits, Packed Integers, Delta, XOR Delta, Floating Point Predictor, Bitorder reversal, Byteshuffle, Bitshuffle, CMS (color space transformations), and Float24 (24-bit floating point).

v2023.3.16

Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in Tifffile, Czifile, Zarr, kerchunk, and other scientific image input/output packages.

Decode and/or encode functions are implemented for Zlib (DEFLATE), GZIP, ZStandard (ZSTD), Blosc, Brotli, Snappy, LZMA, BZ2, LZ4, LZ4F, LZ4HC, LZW, LZF, LZFSE, LZHAM, PGLZ (PostgreSQL LZ), RCOMP (Rice), ZFP, AEC, SZIP, LERC, NPY, PNG, APNG, GIF, TIFF, WebP, QOI, JPEG 8-bit, JPEG 12-bit, Lossless JPEG (LJPEG, LJ92, JPEGLL), JPEG 2000 (JP2, J2K), JPEG LS, JPEG XL, JPEG XR (WDP, HD Photo), MOZJPEG, AVIF, HEIF, RGBE (HDR), Jetraw, PackBits, Packed Integers, Delta, XOR Delta, Floating Point Predictor, Bitorder reversal, Byteshuffle, Bitshuffle, CMS (color space transformations), and Float24 (24-bit floating point).

v2023.1.23

Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in Tifffile, Czifile, Zarr, kerchunk, and other scientific image input/output packages.

Decode and/or encode functions are implemented for Zlib (DEFLATE), GZIP, ZStandard (ZSTD), Blosc, Brotli, Snappy, LZMA, BZ2, LZ4, LZ4F, LZ4HC, LZW, LZF, LZFSE, LZHAM, PGLZ (PostgreSQL LZ), RCOMP (Rice), ZFP, AEC, LERC, NPY, PNG, APNG, GIF, TIFF, WebP, QOI, JPEG 8-bit, JPEG 12-bit, Lossless JPEG (LJPEG, LJ92, JPEGLL, SOF3), JPEG 2000 (JP2, J2K), JPEG LS, JPEG XL, JPEG XR (WDP, HD Photo), MOZJPEG, AVIF, HEIF, RGBE (HDR), Jetraw, PackBits, Packed Integers, Delta, XOR Delta, Floating Point Predictor, Bitorder reversal, Byteshuffle, Bitshuffle, CMS (color space transformations), and Float24 (24-bit floating point).

v2022.12.24

Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in Tifffile, Czifile, Zarr, and other scientific image input/output packages.

Decode and/or encode functions are implemented for Zlib (DEFLATE), GZIP, ZStandard (ZSTD), Blosc, Brotli, Snappy, LZMA, BZ2, LZ4, LZ4F, LZ4HC, LZW, LZF, LZFSE, LZHAM, PGLZ (PostgreSQL LZ), RCOMP (Rice), ZFP, AEC, LERC, NPY, PNG, APNG, GIF, TIFF, WebP, QOI, JPEG 8-bit, JPEG 12-bit, Lossless JPEG (LJPEG, JPEGLL, SOF3), JPEG 2000 (JP2, J2K), JPEG LS, JPEG XR (WDP, HD Photo), JPEG XL, MOZJPEG, AVIF, HEIF, RGBE (HDR), Jetraw, PackBits, Packed Integers, Delta, XOR Delta, Floating Point Predictor, Bitorder reversal, Byteshuffle, Bitshuffle, CMS (color space transformations), and Float24 (24-bit floating point).

v2022.12.22

Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in Tifffile, Czifile, Zarr, and other scientific image input/output packages.

Decode and/or encode functions are implemented for Zlib (DEFLATE), GZIP, ZStandard (ZSTD), Blosc, Brotli, Snappy, LZMA, BZ2, LZ4, LZ4F, LZ4HC, LZW, LZF, LZFSE, LZHAM, PGLZ (PostgreSQL LZ), RCOMP (Rice), ZFP, AEC, LERC, NPY, PNG, APNG, GIF, TIFF, WebP, QOI, JPEG 8-bit, JPEG 12-bit, Lossless JPEG (LJPEG, JPEGLL, SOF3), JPEG 2000 (JP2, J2K), JPEG LS, JPEG XR (WDP, HD Photo), JPEG XL, MOZJPEG, AVIF, HEIF, RGBE (HDR), Jetraw, PackBits, Packed Integers, Delta, XOR Delta, Floating Point Predictor, Bitorder reversal, Byteshuffle, Bitshuffle, CMS (color space transformations), and Float24 (24-bit floating point).

v2022.9.26

Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in Tifffile, Czifile, Zarr, and other scientific image input/output packages.

Decode and/or encode functions are implemented for Zlib (DEFLATE), GZIP, ZStandard (ZSTD), Blosc, Brotli, Snappy, LZMA, BZ2, LZ4, LZ4F, LZ4HC, LZW, LZF, PGLZ (PostgreSQL LZ), RCOMP (Rice), ZFP, AEC, LERC, NPY, PNG, APNG, GIF, TIFF, WebP, QOI, JPEG 8-bit, JPEG 12-bit, Lossless JPEG (LJPEG, SOF3), JPEG 2000 (JP2, J2K), JPEG LS, JPEG XR (WDP, HD Photo), JPEG XL, MOZJPEG, AVIF, HEIF, RGBE (HDR), Jetraw, PackBits, Packed Integers, Delta, XOR Delta, Floating Point Predictor, Bitorder reversal, Byteshuffle, Bitshuffle, CMS (color space transformations), and Float24 (24-bit floating point).

... (truncated)

Changelog

Sourced from imagecodecs's changelog.

2023.9.18

  • Pass 7110 tests.
  • Rebuild with updated dependencies fixes CVE-2023-4863.

2023.9.4

  • Map avif_encode level parameter to quality (breaking).
  • Support monochrome images in avif_encode.
  • Add numthreads parameter to avif_decode (fix imread of AVIF).
  • Add experimental quantize filter (BitGroom, BitRound, GBR) via nc4var.c.
  • Add LZ4H5 codec.
  • Support more BCn compressed DDS fourcc types.
  • Require libavif 1.0.

2023.8.12

  • Add EER (Electron Event Representation) decoder.
  • Add option to pass initial value to crc32 and adler32 checksum functions.
  • Add fletcher32 and lookup3 checksum functions via HDF5's h5checksum.c.
  • Add Checksum codec for numcodecs.

2023.7.10

  • Rebuild with optimized compile flags.

2023.7.4

  • Add BCn and DDS decoder via bcdec library.
  • Add functions to transcode JPEG XL to/from JPEG (#78).
  • Add option to decode select frames from animated WebP.
  • Use legacy JPEG8 codec when building without libjpeg-turbo 3 (#65).
  • Change blosc2_encode defaults to match blosc2-python (breaking).
  • Fix segfault writing JPEG2K with more than 4 samples.
  • Fix some codecs returning bytearray by default.
  • Fully vendor cfitsio's ricecomp.c.
  • Drop support for Python 3.8 and numpy < 1.21 (NEP29).

2023.3.16

  • Require libjpeg-turbo 2.1.91 (3.0 beta) and c-blosc2 2.7.1.
  • Add experimental type hints.
  • Add SZIP codec via libaec library.
  • Use Zstd streaming API to decode blocks with unknown decompressed size.
  • Remove unused level, index, and numthreads parameters (breaking).
  • Make AEC and BLOSC constants enums (breaking).
  • Capitalize numcodecs class names (breaking).
  • Remove JPEG12 codec (breaking; use JPEG8 instead).
  • Encode and decode lossless and 12-bit JPEG with JPEG8 codec by default.
  • Remove JPEGSOF3 fallback in JPEG codec.

... (truncated)

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