Revisions of python-tifffile
buildservice-autocommit
accepted
request 1155044
from
Markéta Machová (mcalabkova)
(revision 39)
baserev update by copy to link target
Markéta Machová (mcalabkova)
accepted
request 1154413
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Benjamin Greiner (bnavigator)
(revision 38)
- 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
buildservice-autocommit
accepted
request 1135343
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Dirk Mueller (dirkmueller)
(revision 37)
baserev update by copy to link target
Dirk Mueller (dirkmueller)
committed
(revision 36)
- 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. - Inject multibuild to fix a bootstrapping issue. - Add _constraints file to avoid OOM - Ignore test_write_ome, test_class_omexml_attributes, test_class_omexml_multiimage, and test_class_omexml because it - Fix ERROR: download_files is configured to fail when the upstream file is different than the committed file. - Fix spec file build condition. * Re-add pure Python PackBits decoder.
buildservice-autocommit
accepted
request 1111068
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Dirk Mueller (dirkmueller)
(revision 35)
baserev update by copy to link target
Dirk Mueller (dirkmueller)
accepted
request 1111047
from
Markéta Machová (mcalabkova)
(revision 34)
- 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).
buildservice-autocommit
accepted
request 1103855
from
Markéta Machová (mcalabkova)
(revision 33)
baserev update by copy to link target
Matej Cepl (mcepl)
accepted
request 1102181
from
Markéta Machová (mcalabkova)
(revision 32)
- 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).
buildservice-autocommit
accepted
request 1090095
from
Dirk Mueller (dirkmueller)
(revision 31)
baserev update by copy to link target
Dirk Mueller (dirkmueller)
committed
(revision 30)
Dirk Mueller (dirkmueller)
committed
(revision 29)
- 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).
buildservice-autocommit
accepted
request 1088888
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Matej Cepl (mcepl)
(revision 28)
baserev update by copy to link target
Matej Cepl (mcepl)
accepted
request 1088816
from
Jan Engelhardt (jengelh)
(revision 27)
- Drop TM/R marks according to packaging guidelines.
buildservice-autocommit
accepted
request 1076744
from
andy great (andythe_great)
(revision 26)
baserev update by copy to link target
andy great (andythe_great)
accepted
request 1076618
from
Benjamin Greiner (bnavigator)
(revision 25)
- 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
buildservice-autocommit
accepted
request 1066888
from
Steve Kowalik (StevenK)
(revision 24)
baserev update by copy to link target
Steve Kowalik (StevenK)
committed
(revision 23)
- Inject multibuild to fix a bootstrapping issue.
buildservice-autocommit
accepted
request 1060309
from
andy great (andythe_great)
(revision 22)
baserev update by copy to link target
andy great (andythe_great)
accepted
request 1060172
from
Benjamin Greiner (bnavigator)
(revision 21)
- 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.
buildservice-autocommit
accepted
request 870287
from
Markéta Machová (mcalabkova)
(revision 20)
baserev update by copy to link target
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