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| Name: python310-tifffile | Distribution: openSUSE Tumbleweed |
| Version: 2024.9.20 | Vendor: openSUSE |
| Release: 1.2 | Build date: Sat Nov 9 16:50:42 2024 |
| Group: Unspecified | Build host: reproducible |
| Size: 2286397 | Source RPM: python-tifffile-2024.9.20-1.2.src.rpm |
| Packager: https://bugs.opensuse.org | |
| Url: https://github.com/cgohlke/tifffile/ | |
| Summary: Read and write TIFF files | |
Read and write TIFF files. Read image and metadata from many bio-scientific formats such as plain TIFF, BigTIFF, OME-TIFF, STK, LSM, SGI, NIH, ImageJ, MicroManager, MD GEL, and FluoView files. Write numpy arrays to TIFF, BigTIFF, and ImageJ hyperstack compatible files.
BSD-2-Clause
* Sat Nov 09 2024 Dirk Müller <dmueller@suse.com>
- update to 2024.9.20:
* Pass 5107 tests.
* Fix writing colormap to ImageJ files (breaking).
* Improve typing.
* Remove support for Python 3.9.
* Support writing OME Dataset and some StructuredAnnotations
elements.
* Fix LSM scan types and dimension orders (#269, breaking).
* Use IO[bytes] instead of BinaryIO for typing (#268).
* 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.
* Relax bitspersample check for JPEG, JPEG2K, and JPEGXL
compression (#265).
* Fix reading contiguous multi-page series via Zarr store
(#67).
* Fix integer overflow in product function caused by numpy
types.
* Allow tag reader functions to fail.
* Enable memmap to create empty files with non-native byte
order.
* Deprecate Python 3.9, support Python 3.13.
* Wed Jul 17 2024 Ben Greiner <code@bnavigator.de>
- Revert. Numpy 2 is supported since 2024.2.12
* Wed Jul 17 2024 Steve Kowalik <steven.kowalik@suse.com>
- Restrict numpy to < 2.
* Sat Jun 29 2024 Dirk Müller <dmueller@suse.com>
- update to 2024.6.18:
* Ensure TiffPage.nodata is castable to dtype (breaking, #260).
* Derive TiffPages, TiffPageSeries, FileSequence, StoredShape
from Sequence.
* Truncate circular IFD chain, do not raise TiffFileError
(breaking).
* Deprecate access to TiffPages.pages and FileSequence.files.
* Enable DeprecationWarning for enums in TIFF namespace.
* Remove some deprecated code (breaking).
* Add iccprofile property to TiffPage and parameter to
TiffWriter.write.
* Do not detect VSI as SIS format.
* Limit length of logged exception messages.
* Fix docstring examples not correctly rendered on GitHub
(#254, #255).
* Support reading JPEGXL compression in DNG 1.7.
* Read invalid TIFF created by IDEAS software.
* Fix reading incompletely written LSM.
* Fix reading Philips DP with extra rows of tiles (#253,
breaking).
* Fix compatibility issue with numpy 2 (#252).
* Fix write_fsspec when last row of tiles is missing in Philips
slide (#249).
* Add option not to quote file names in write_fsspec.
* Allow compress bilevel images with deflate, LZMA, and Zstd.
* Sun Mar 03 2024 Ben Greiner <code@bnavigator.de>
- Update to 2024.2.12
* Deprecate dtype, add chunkdtype parameter in
FileSequence.asarray.
* Add imreadargs parameters passed to FileSequence.imread.
- Release 2024.1.30
* Fix compatibility issue with numpy 2 (#238).
* Enable DeprecationWarning for tuple compression argument.
* Parse sequence of numbers in xml2dict.
- Don't test xarray on python39: no longer available
* Wed Dec 27 2023 Dirk Müller <dmueller@suse.com>
- update to 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.
* 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).
* 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.
* Tue Sep 12 2023 Markéta Machová <mmachova@suse.com>
- Update to 2023.8.30
* 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.
* Verify shaped metadata is compatible with page shape.
* Support out parameter when returning selection from imread (#222).
* Support exclusive file creation mode (#221, #223).
* Thu Aug 03 2023 Markéta Machová <mmachova@suse.com>
- Update to 2023.7.18
* Add option to return selection from imread
* Fix reading OME series with missing trailing frames
* Drop support for Python 3.8 and numpy < 1.21 (NEP29).
* Increase default strip size to 256 KB when writing with compression.
* Fix ZarrTiffStore with non-default chunkmode.
* Pass 4993 tests.
* Limit threading via TIFFFILE_NUM_THREADS environment variable
* Remove maxworkers parameter from tiff2fsspec (breaking).
* Wed May 31 2023 Dirk Müller <dmueller@suse.com>
- update to 2023.4.12:
* Pass 4988 tests.
* Do not write duplicate ImageDescription tags from extratags
(breaking).
* Support multifocal SVS files (#193).
* Log warning when filtering out extratags.
* Fix writing OME-TIFF with image description in extratags.
* Ignore invalid predictor tag value if prediction is not used.
* Raise KeyError if ZarrStore is missing requested chunk.
* 2023.3.21
* Fix reading MMstack with missing data (#187).
* Wed May 24 2023 Jan Engelhardt <jengelh@inai.de>
- Drop TM/R marks according to packaging guidelines.
* Sat Apr 01 2023 Ben Greiner <code@bnavigator.de>
- Update to 2023.3.15
* Pass 4980 tests.
* Fix corruption using tile generators with
prediction/compression (#185).
* Add parser for Micro-Manager MMStack series (breaking).
* Return micromanager_metadata IndexMap as numpy array
(breaking).
* Revert optimizations for Micro-Manager OME series.
* Do not use numcodecs zstd in write_fsspec (kerchunk issue 317).
* More type annotations.
- Release 2023.2.28
* Fix reading some Micro-Manager metadata from corrupted files.
* Speed up reading Micro-Manager indexmap for creation of OME
series.
- Release 2023.2.27
* Use Micro-Manager indexmap offsets to create virtual
TiffFrames.
* Fixes for future imagecodecs.
- Release 2023.2.3
* Fix overflow in calculation of databytecounts for large NDPI
files.
- Release 2023.2.2
* Fix regression reading layered NDPI files.
* Add option to specify offset in FileHandle.read_array.
- Release 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.
- Do not test xarry on python38: not supported anymore
* Tue Feb 21 2023 Steve Kowalik <steven.kowalik@suse.com>
- Inject multibuild to fix a bootstrapping issue.
* Sat Jan 21 2023 Ben Greiner <code@bnavigator.de>
- Update to 2022.10.10.
* Pass 4925 tests.
* 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.
- Release 2022.8.12
* Fix writing ImageJ format with hyperstack argument.
* Fix writing description with metadata disabled.
* Add option to disable writing shaped metadata in TiffWriter.
- Release 2022.8.8
* Fix regression using imread out argument (#147).
* Fix imshow show argument.
* Support fsspec OpenFile.
- Release 2022.8.3
* Fix regression writing default resolutionunit (#145).
* Add strptime function parsing common datetime formats.
- Release 2022.7.31
* Fix reading corrupted WebP compressed segments missing alpha
channel (#122).
* Fix regression reading compressed ImageJ files.
- Release 2022.7.28
* 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.
- Release 2022.5.4
* Allow to write NewSubfileType=0 (#132).
* Support writing iterators of strip or tile bytes.
* Convert iterables (not iterators) to NumPy arrays when writing.
* Explicitly specify optional keyword parameters for imread and
imwrite.
* Return number of written bytes from FileHandle write functions.
- Release 2022.4.28
* Add option to specify fsspec version 1 URL template name
(#131).
* Ignore invalid dates in UIC tags (#129).
* Fix zlib_encode and lzma_encode to work with non-contiguous
arrays (#128).
* Fix delta_encode to preserve byteorder of ndarrays.
* Move Imagecodecs fallback functions to private module and add
tests.
- Release 2022.4.26
* Fix AttributeError in TiffFile.shaped_metadata (#127).
* Fix TiffTag.overwrite with pre-packed binary value.
* Write sparse TIFF if tile iterator contains None.
* Raise ValueError when writing photometric mode with too few
samples.
* Improve test coverage.
- Release 2022.4.22
* Add type hints for Python 3.10 (WIP).
* Fix Mypy errors (breaking).
* Mark many parameters positional-only or keyword-only
(breaking).
* Remove deprecated pages parameter from imread (breaking).
* Remove deprecated compress and ijmetadata write parameters
(breaking).
* Remove deprecated fastij and movie parameters from TiffFile
(breaking).
* Remove deprecated multifile parameters from TiffFile
(breaking).
* Remove deprecated tif parameter from TiffTag.overwrite
(breaking).
* Remove deprecated file parameter from FileSequence.asarray
(breaking).
* Remove option to pass imread class to FileSequence (breaking).
* Remove optional parameters from __str__ functions (breaking).
* Rename TiffPageSeries.offset to dataoffset (breaking)
* Change TiffPage.pages to None if no SubIFDs are present
(breaking).
* Change TiffPage.index to int (breaking).
* Change TiffPage.is_contiguous, is_imagej, and is_shaped to bool
(breaking).
* Add TiffPage imagej_description and shaped_description
properties.
* Add TiffFormat abstract base class.
* Deprecate lazyattr and use functools.cached_property instead
(breaking).
* Julian_datetime raises ValueError for dates before year 1
(breaking).
* Regressed import time due to typing.
- Release 2022.4.8
* Add _ARRAY_DIMENSIONS attributes to ZarrTiffStore.
* Allow C instead of S axis when writing OME-TIFF.
* Fix writing OME-TIFF with separate samples.
* Fix reading unsqueezed pyramidal OME-TIFF series.
- Release 2022.3.25
* Fix another ValueError using ZarrStore with zarr >= 2.11.0
(tiffslide #25).
* Add parser for Hamamatsu streak metadata.
* Improve hexdump.
- Release 2022.3.16
* Use multi-threading to compress strips and tiles.
* Raise TiffFileError when reading corrupted strips and tiles
(#122).
* Fix ScanImage single channel count (#121).
* Add parser for AstroTIFF FITS metadata.
- Release 2022.2.9
* Fix ValueError using multiscale ZarrStore with zarr >= 2.11.0.
* Raise KeyError if ZarrStore does not contain key.
* Limit number of warnings for missing files in multifile series.
* Allow to save colormap to 32-bit ImageJ files (#115).
- Release 2022.2.2
* Fix TypeError when second ImageDescription tag contains
non-ASCII (#112).
* Fix parsing IJMetadata with many IJMetadataByteCounts (#111).
* Detect MicroManager NDTiffv2 header (not tested).
* Remove cache from ZarrFileSequenceStore (use
zarr.LRUStoreCache).
* Raise limit on maximum number of pages.
* Use J2K format when encoding JPEG2000 segments.
* Formally deprecate imsave and TiffWriter.save.
* Drop support for Python 3.7 and NumPy < 1.19 (NEP29).
- Release 2021.11.2
* Lazy-load non-essential tag values (breaking).
* Warn when reading from closed file.
* Support ImageJ prop metadata type (#103).
* Support writing indexed ImageJ format.
* Fix multi-threaded access of multi-page Zarr stores with
chunkmode 2.
* Raise error if truncate is used with compression, packints, or
tile.
* Read STK metadata without UIC2tag.
* Improve log and warning messages (WIP).
* Improve string representation of large tag values.
- Release 2021.10.12
* Revert renaming of file parameter in FileSequence.asarray
(breaking).
* Deprecate file parameter in FileSequence.asarray.
- Release 2021.10.10
* Disallow letters as indices in FileSequence; use categories
(breaking).
* Do not warn of missing files in FileSequence; use files_missing
property.
* Support predictors in ZarrTiffStore.write_fsspec.
* Add option to specify Zarr group name in write_fsspec.
* Add option to specify categories for FileSequence patterns
(#76).
* Add option to specify chunk shape and dtype for
ZarrFileSequenceStore.
* Add option to tile ZarrFileSequenceStore and
FileSequence.asarray.
* Add option to pass additional zattrs to Zarr stores.
* Detect Roche BIF files.
- Release 2021.8.30
* Fix horizontal differencing with non-native byte order.
* Fix multi-threaded access of memory-mappable, multi-page Zarr
stores (#67).
- Release 2021.8.8
* Fix tag offset and valueoffset for NDPI > 4 GB (#96).
- Release 2021.7.30
* Deprecate first parameter to TiffTag.overwrite (no longer
required).
* TiffTag init API change (breaking).
* Detect Ventana BIF series and warn that tiles are not stitched.
* Enable reading PreviewImage from RAW formats (#93, #94).
* Work around numpy.ndarray.tofile is very slow for
non-contiguous arrays.
* Fix issues with PackBits compression (requires imagecodecs
2021.7.30).
- Release 2021.7.2
* Decode complex integer images found in SAR GeoTIFF.
* Support reading NDPI with JPEG-XR compression.
* Deprecate TiffWriter RGB auto-detection, except for RGB24/48
and RGBA32/64.
- Release 2021.6.14
* Set stacklevel for deprecation warnings (#89).
* Fix svs_description_metadata for SVS with double header (#88,
breaking).
* Fix reading JPEG compressed CMYK images.
* Support ALT_JPEG and JPEG_2000_LOSSY compression found in
Bio-Formats.
* Log warning if TiffWriter auto-detects RGB mode (specify
photometric).
- Release 2021.6.6
* Fix TIFF.COMPESSOR typo (#85).
* Round resolution numbers that do not fit in 64-bit rationals
(#81).
* Add support for JPEG XL compression.
* Add Numcodecs compatible TIFF codec.
* Rename ZarrFileStore to ZarrFileSequenceStore (breaking).
* Add method to export fsspec ReferenceFileSystem from
ZarrFileStore.
* Fix fsspec ReferenceFileSystem v1 for multifile series.
* Fix creating OME-TIFF with micron character in OME-XML.
- Release 2021.4.8
* Fix reading OJPEG with wrong photometric or samplesperpixel
tags (#75).
* Fix fsspec ReferenceFileSystem v1 and JPEG compression.
* Use TiffTagRegistry for NDPI_TAGS, EXIF_TAGS, GPS_TAGS,
IOP_TAGS constants.
* Make TIFF.GEO_KEYS an Enum (breaking).
- Release 2021.3.31
* Use JPEG restart markers as tile offsets in NDPI.
* Support version 1 and more codecs in fsspec ReferenceFileSystem
(untested).
- Release 2021.3.17
* Fix regression reading multi-file OME-TIFF with missing files
(#72).
* Fix fsspec ReferenceFileSystem with non-native byte order
(#56).
- Release 2021.3.16
* TIFF is no longer a defended trademark.
* Add method to export fsspec ReferenceFileSystem from
ZarrTiffStore (#56).
- Release 2021.3.5
* Preliminary support for EER format (#68).
* Do not warn about unknown compression (#68).
- Release 2021.3.4
* Fix reading multi-file, multi-series OME-TIFF (#67).
* Detect ScanImage 2021 files (#46).
* Shape new version ScanImage series according to metadata
(breaking).
* Remove Description key from TiffFile.scanimage_metadata dict
(breaking).
* Also return ScanImage version from read_scanimage_metadata
(breaking).
* Fix docstrings.
- Release 2021.2.26
* Squeeze axes of LSM series by default (breaking).
* Add option to preserve single dimensions when reading from
series (WIP).
* Do not allow appending to OME-TIFF files.
* Fix reading STK files without name attribute in metadata.
* Make TIFF constants multi-thread safe and pickleable (#64).
* Add detection of NDTiffStorage MajorVersion to
read_micromanager_metadata.
* Support ScanImage v4 files in read_scanimage_metadata.
- Release 2021.2.1
* Fix multi-threaded access of ZarrTiffStores using same TiffFile
instance.
* Use fallback zlib and lzma codecs with imagecodecs lite builds.
* Open Olympus and Panasonic RAW files for parsing, albeit not
supported.
* Support X2 and X4 differencing found in DNG.
* Support reading JPEG_LOSSY compression found in DNG.
* Mon Feb 08 2021 Markéta Machová <mmachova@suse.com>
- Skip python36 because of imagecodecs
* Sun Jan 31 2021 andy great <andythe_great@pm.me>
- Add missing python_alternative.
* Mon Jan 25 2021 andy great <andythe_great@pm.me>
- Update to version 2021.1.14.
* Try ImageJ series if OME series fails
* Add option to use pages as chunks in ZarrFileStore (experimental).
* Fix reading from file objects with no readinto function.
- Updates for version 2021.1.11
* Fix test errors on PyPy.
* Fix decoding bitorder with imagecodecs >= 2021.1.11.
- Updates for version 2021.1.8
* Decode float24 using imagecodecs >= 2021.1.8.
* Consolidate reading of segments if possible.
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