--- - branch: MAIN date: Mon Apr 24 07:03:08 UTC 2023 files: - new: '1.13' old: '1.12' path: pkgsrc/graphics/py-tifffile/Makefile pathrev: pkgsrc/graphics/py-tifffile/Makefile@1.13 type: modified - new: '1.4' old: '1.3' path: pkgsrc/graphics/py-tifffile/PLIST pathrev: pkgsrc/graphics/py-tifffile/PLIST@1.4 type: modified - new: '1.11' old: '1.10' path: pkgsrc/graphics/py-tifffile/distinfo pathrev: pkgsrc/graphics/py-tifffile/distinfo@1.11 type: modified id: 20230424T070308Z.638e66f00c52be8b9034d55476815302971a8d9e log: | py-tifffile: updated to 2023.4.12 2023.4.12 - Pass 4988 tests. - Do not write duplicate ImageDescription tags from extratags (breaking). - Support multifocal SVS files - 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 2023.3.15 - Fix corruption using tile generators with prediction/compression - 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. 2023.2.28 - Fix reading some Micro-Manager metadata from corrupted files. - Speed up reading Micro-Manager indexmap for creation of OME series. 2023.2.27 - 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 - 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 - Relax detection of OME-XML - 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 - 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. 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. 2022.8.8 - Fix regression using imread out argument - Fix imshow show argument. - Support fsspec OpenFile. 2022.8.3 - Fix regression writing default resolutionunit - Add strptime function parsing common datetime formats. 2022.7.31 - Fix reading corrupted WebP compressed segments missing alpha channel - Fix regression reading compressed ImageJ files. 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 - 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 - 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 - Parse metaseries time values as datetime objects - 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. 2022.5.4 - Allow to write NewSubfileType=0 - 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. 2022.4.28 - Add option to specify fsspec version 1 URL template name - Ignore invalid dates in UIC tags - Fix zlib_encode and lzma_encode to work with non-contiguous arrays - Fix delta_encode to preserve byteorder of ndarrays. - Move Imagecodecs fallback functions to private module and add tests. 2022.4.26 - Fix AttributeError in TiffFile.shaped_metadata - 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. 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. 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. 2022.3.25 - Fix another ValueError using ZarrStore with zarr >= 2.11.0 - Add parser for Hamamatsu streak metadata. - Improve hexdump. 2022.3.16 - Use multi-threading to compress strips and tiles. - Raise TiffFileError when reading corrupted strips and tiles - Fix ScanImage single channel count - Add parser for AstroTIFF FITS metadata. 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 2022.2.2 - Fix TypeError when second ImageDescription tag contains non-ASCII - Fix parsing IJMetadata with many IJMetadataByteCounts - 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). module: pkgsrc subject: 'CVS commit: pkgsrc/graphics/py-tifffile' unixtime: '1682319788' user: adam