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2024.5.22

  • Pass 5084 tests.
  • 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.
  • Work around GitHub not rendering docstring examples (#254, #255).

2024.5.10

  • Support reading JPEGXL compression in DNG 1.7.
  • Read invalid TIFF created by IDEAS software.

2024.5.3

  • Fix reading incompletely written LSM.
  • Fix reading Philips DP with extra rows of tiles (#253, breaking).

2024.4.24

  • Fix compatibility issue with numpy 2 (#252).

2024.4.18

  • 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.

2024.2.12

  • Deprecate dtype, add chunkdtype parameter in FileSequence.asarray.
  • Add imreadargs parameters passed to FileSequence.imread.

2024.1.30

  • Fix compatibility issue with numpy 2 (#238).
  • Enable DeprecationWarning for tuple compression argument.
  • Parse sequence of numbers in xml2dict.

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.

2023.9.26

  • 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).

2023.9.18

  • 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.

2023.8.30

  • Support exclusive file creation mode (#221, #223).

2023.8.25

  • Verify shaped metadata is compatible with page shape.
  • Support out parameter when returning selection from imread (#222).

2023.8.12

  • 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.

2023.7.18

  • Limit threading via TIFFFILE_NUM_THREADS environment variable (#215).
  • Remove maxworkers parameter from tiff2fsspec (breaking).

2023.7.10

  • Increase default strip size to 256 KB when writing with compression.
  • Fix ZarrTiffStore with non-default chunkmode.

2023.7.4

  • Add option to return selection from imread (#200).
  • Fix reading OME series with missing trailing frames (#199).
  • Fix fsspec reference for WebP compressed segments missing alpha channel.
  • Fix linting issues.
  • Detect files written by Agilent Technologies.
  • Drop support for Python 3.8 and numpy < 1.21 (NEP29).

2023.4.12

  • 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).

2023.3.15

  • 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.

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 (#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.

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 (#147).
  • Fix imshow show argument.
  • Support fsspec OpenFile.

2022.8.3

  • Fix regression writing default resolutionunit (#145).
  • Add strptime function parsing common datetime formats.

2022.7.31

  • Fix reading corrupted WebP compressed segments missing alpha channel (#122).
  • 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 (#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.

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 (breaking).
  • 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 (#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.

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.

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 (tiffslide #25).
  • 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 (#122).
  • Fix ScanImage single channel count (#121).
  • 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 (#115).

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).

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.

2021.10.12

  • Revert renaming of file parameter in FileSequence.asarray (breaking).
  • Deprecate file parameter in FileSequence.asarray.

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.

2021.8.30

  • Fix horizontal differencing with non-native byte order.
  • Fix multi-threaded access of memory-mappable, multi-page Zarr stores (#67).

2021.8.8

  • Fix tag offset and valueoffset for NDPI > 4 GB (#96).

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).

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.

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).

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.

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).

2021.3.31

  • Use JPEG restart markers as tile offsets in NDPI.
  • Support version 1 and more codecs in fsspec ReferenceFileSystem (untested).

2021.3.17

  • Fix regression reading multi-file OME-TIFF with missing files (#72).
  • Fix fsspec ReferenceFileSystem with non-native byte order (#56).

2021.3.16

  • TIFF is no longer a defended trademark.
  • Add method to export fsspec ReferenceFileSystem from ZarrTiffStore (#56).

2021.3.5

  • Preliminary support for EER format (#68).
  • Do not warn about unknown compression (#68).

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.

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.

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.

2021.1.14

  • Try ImageJ series if OME series fails (#54)
  • Add option to use pages as chunks in ZarrFileStore (experimental).
  • Fix reading from file objects with no readinto function.

2021.1.11

  • Fix test errors on PyPy.
  • Fix decoding bitorder with imagecodecs >= 2021.1.11.

2021.1.8

  • Decode float24 using imagecodecs >= 2021.1.8.
  • Consolidate reading of segments if possible.

2020.12.8

  • Fix corrupted ImageDescription in multi shaped series if buffer too small.
  • Fix libtiff warning that ImageDescription contains null byte in value.
  • Fix reading invalid files using JPEG compression with palette colorspace.

2020.12.4

  • Fix reading some JPEG compressed CFA images.
  • Make index of SubIFDs a tuple.
  • Pass through FileSequence.imread arguments in imread.
  • Do not apply regex flags to FileSequence axes patterns (breaking).

2020.11.26

  • Add option to pass axes metadata to ImageJ writer.
  • Pad incomplete tiles passed to TiffWriter.write (#38).
  • Split TiffTag constructor (breaking).
  • Change TiffTag.dtype to TIFF.DATATYPES (breaking).
  • Add TiffTag.overwrite method.
  • Add script to change ImageDescription in files.
  • Add TiffWriter.overwrite_description method (WIP).

2020.11.18

  • Support writing SEPARATED color space (#37).
  • Use imagecodecs.deflate codec if available.
  • Fix SCN and NDPI series with Z dimensions.
  • Add TiffReader alias for TiffFile.
  • TiffPage.is_volumetric returns True if ImageDepth > 1.
  • Zarr store getitem returns NumPy arrays instead of bytes.

2020.10.1

  • Formally deprecate unused TiffFile parameters (scikit-image #4996).

2020.9.30

  • Allow to pass additional arguments to compression codecs.
  • Deprecate TiffWriter.save method (use TiffWriter.write).
  • Deprecate TiffWriter.save compress parameter (use compression).
  • Remove multifile parameter from TiffFile (breaking).
  • Pass all is_flag arguments from imread to TiffFile.
  • Do not byte-swap JPEG2000, WEBP, PNG, JPEGXR segments in TiffPage.decode.

2020.9.29

  • Fix reading files produced by ScanImage > 2015 (#29).

2020.9.28

  • Derive ZarrStore from MutableMapping.
  • Support zero shape ZarrTiffStore.
  • Fix ZarrFileStore with non-TIFF files.
  • Fix ZarrFileStore with missing files.
  • Cache one chunk in ZarrFileStore.
  • Keep track of already opened files in FileCache.
  • Change parse_filenames function to return zero-based indices.
  • Remove reopen parameter from asarray (breaking).
  • Rename FileSequence.fromfile to imread (breaking).

2020.9.22

  • Add experimental Zarr storage interface (WIP).
  • Remove unused first dimension from TiffPage.shaped (breaking).
  • Move reading of STK planes to series interface (breaking).
  • Always use virtual frames for ScanImage files.
  • Use DimensionOrder to determine axes order in OmeXml.
  • Enable writing striped volumetric images.
  • Keep complete dataoffsets and databytecounts for TiffFrames.
  • Return full size tiles from Tiffpage.segments.
  • Rename TiffPage.is_sgi property to is_volumetric (breaking).
  • Rename TiffPageSeries.is_pyramid to is_pyramidal (breaking).
  • Fix TypeError when passing jpegtables to non-JPEG decode method (#25).

2020.9.3

  • Do not write contiguous series by default (breaking).
  • Allow to write to SubIFDs (WIP).
  • Fix writing F-contiguous NumPy arrays (#24).

2020.8.25

  • Do not convert EPICS timeStamp to datetime object.
  • Read incompletely written Micro-Manager image file stack header (#23).
  • Remove tag 51123 values from TiffFile.micromanager_metadata (breaking).

2020.8.13

  • Use tifffile metadata over OME and ImageJ for TiffFile.series (breaking).
  • Fix writing iterable of pages with compression (#20).
  • Expand error checking of TiffWriter data, dtype, shape, and tile arguments.

2020.7.24

  • Parse nested OmeXml metadata argument (WIP).
  • Do not lazy load TiffFrame JPEGTables.
  • Fix conditionally skipping some tests.

2020.7.22

  • Do not auto-enable OME-TIFF if description is passed to TiffWriter.save.
  • Raise error writing empty bilevel or tiled images.
  • Allow to write tiled bilevel images.
  • Allow to write multi-page TIFF from iterable of single page images (WIP).
  • Add function to validate OME-XML.
  • Correct Philips slide width and length.

2020.7.17

  • Initial support for writing OME-TIFF (WIP).
  • Return samples as separate dimension in OME series (breaking).
  • Fix modulo dimensions for multiple OME series.
  • Fix some test errors on big endian systems (#18).
  • Fix BytesWarning.
  • Allow to pass TIFF.PREDICTOR values to TiffWriter.save.

2020.7.4

  • Deprecate support for Python 3.6 (NEP 29).
  • Move pyramidal subresolution series to TiffPageSeries.levels (breaking).
  • Add parser for SVS, SCN, NDPI, and QPI pyramidal series.
  • Read single-file OME-TIFF pyramids.
  • Read NDPI files > 4 GB (#15).
  • Include SubIFDs in generic series.
  • Preliminary support for writing packed integer arrays (#11, WIP).
  • Read more LSM info subrecords.
  • Fix missing ReferenceBlackWhite tag for YCbCr photometrics.
  • Fix reading lossless JPEG compressed DNG files.

2020.6.3

  • Support os.PathLike file names (#9).

2020.5.30

  • Re-add pure Python PackBits decoder.

2020.5.25

  • Make imagecodecs an optional dependency again.
  • Disable multi-threaded decoding of small LZW compressed segments.
  • Fix caching of TiffPage.decode method.
  • Fix xml.etree.cElementTree ImportError on Python 3.9.
  • Fix tostring DeprecationWarning.

2020.5.11

  • Fix reading ImageJ grayscale mode RGB images (#6).
  • Remove napari reader plugin.

2020.5.7

  • Add napari reader plugin (tentative).
  • Fix writing single tiles larger than image data (#3).
  • Always store ExtraSamples values in tuple (breaking).

2020.5.5

  • Allow to write tiled TIFF from iterable of tiles (WIP).
  • Add method to iterate over decoded segments of TiffPage (WIP).
  • Pass chunks of segments to ThreadPoolExecutor.map to reduce memory usage.
  • Fix reading invalid files with too many strips.
  • Fix writing over-aligned image data.
  • Detect OME-XML without declaration (#2).
  • Support LERC compression (WIP).
  • Delay load imagecodecs functions.
  • Remove maxsize parameter from asarray (breaking).
  • Deprecate ijmetadata parameter from TiffWriter.save (use metadata).

2020.2.16

  • Add method to decode individual strips or tiles.
  • Read strips and tiles in order of their offsets.
  • Enable multi-threading when decompressing multiple strips.
  • Replace TiffPage.tags dictionary with TiffTags (breaking).
  • Replace TIFF.TAGS dictionary with TiffTagRegistry.
  • Remove TIFF.TAG_NAMES (breaking).
  • Improve handling of TiffSequence parameters in imread.
  • Match last uncommon parts of file paths to FileSequence pattern (breaking).
  • Allow letters in FileSequence pattern for indexing well plate rows.
  • Allow to reorder axes in FileSequence.
  • Allow to write > 4 GB arrays to plain TIFF when using compression.
  • Allow to write zero size NumPy arrays to nonconformant TIFF (tentative).
  • Fix xml2dict.
  • Require imagecodecs >= 2020.1.31.
  • Remove support for imagecodecs-lite (breaking).
  • Remove verify parameter to asarray method (breaking).
  • Remove deprecated lzw_decode functions (breaking).
  • Remove support for Python 2.7 and 3.5 (breaking).

2019.7.26

  • Fix infinite loop reading more than two tags of same code in IFD.
  • Delay import of logging module.

2019.7.20

  • Fix OME-XML detection for files created by Imaris.
  • Remove or replace assert statements.

2019.7.2

  • Do not write SampleFormat tag for unsigned data types.
  • Write ByteCount tag values as SHORT or LONG if possible.
  • Allow to specify axes in FileSequence pattern via group names.
  • Add option to concurrently read FileSequence using threads.
  • Derive TiffSequence from FileSequence.
  • Use str(datetime.timedelta) to format Timer duration.
  • Use perf_counter for Timer if possible.

2019.6.18

  • Fix reading planar RGB ImageJ files created by Bio-Formats.
  • Fix reading single-file, multi-image OME-TIFF without UUID.
  • Presume LSM stores uncompressed images contiguously per page.
  • Reformat some complex expressions.

2019.5.30

  • Ignore invalid frames in OME-TIFF.
  • Set default subsampling to (2, 2) for RGB JPEG compression.
  • Fix reading and writing planar RGB JPEG compression.
  • Replace buffered_read with FileHandle.read_segments.
  • Include page or frame numbers in exceptions and warnings.
  • Add Timer class.

2019.5.22

  • Add optional chroma subsampling for JPEG compression.
  • Enable writing PNG, JPEG, JPEGXR, and JPEG2K compression (WIP).
  • Fix writing tiled images with WebP compression.
  • Improve handling GeoTIFF sparse files.

2019.3.18

  • Fix regression decoding JPEG with RGB photometrics.
  • Fix reading OME-TIFF files with corrupted but unused pages.
  • Allow to load TiffFrame without specifying keyframe.
  • Calculate virtual TiffFrames for non-BigTIFF ScanImage files > 2GB.
  • Rename property is_chroma_subsampled to is_subsampled (breaking).
  • Make more attributes and methods private (WIP).

2019.3.8

  • Fix MemoryError when RowsPerStrip > ImageLength.
  • Fix SyntaxWarning on Python 3.8.
  • Fail to decode JPEG to planar RGB (tentative).
  • Separate public from private test files (WIP).
  • Allow testing without data files or imagecodecs.

2019.2.22

  • Use imagecodecs-lite as fallback for imagecodecs.
  • Simplify reading NumPy arrays from file.
  • Use TiffFrames when reading arrays from page sequences.
  • Support slices and iterators in TiffPageSeries sequence interface.
  • Auto-detect uniform series.
  • Use page hash to determine generic series.
  • Turn off TiffPages cache (tentative).
  • Pass through more parameters in imread.
  • Discontinue movie parameter in imread and TiffFile (breaking).
  • Discontinue bigsize parameter in imwrite (breaking).
  • Raise TiffFileError in case of issues with TIFF structure.
  • Return TiffFile.ome_metadata as XML (breaking).
  • Ignore OME series when last dimensions are not stored in TIFF pages.

2019.2.10

  • Assemble IFDs in memory to speed-up writing on some slow media.
  • Handle discontinued arguments fastij, multifile_close, and pages.

2019.1.30

  • Use black background in imshow.
  • Do not write datetime tag by default (breaking).
  • Fix OME-TIFF with SamplesPerPixel > 1.
  • Allow 64-bit IFD offsets for NDPI (files > 4GB still not supported).

2019.1.4

  • Fix decoding deflate without imagecodecs.

2019.1.1

  • Update copyright year.
  • Require imagecodecs >= 2018.12.16.
  • Do not use JPEG tables from keyframe.
  • Enable decoding large JPEG in NDPI.
  • Decode some old-style JPEG.
  • Reorder OME channel axis to match PlanarConfiguration storage.
  • Return tiled images as contiguous arrays.
  • Add decode_lzw proxy function for compatibility with old czifile module.
  • Use dedicated logger.

2018.11.28

  • Make SubIFDs accessible as TiffPage.pages.
  • Make parsing of TiffSequence axes pattern optional (breaking).
  • Limit parsing of TiffSequence axes pattern to file names, not path names.
  • Do not interpolate in imshow if image dimensions <= 512, else use bilinear.
  • Use logging.warning instead of warnings.warn in many cases.
  • Fix NumPy FutureWarning for out == 'memmap'.
  • Adjust ZSTD and WebP compression to libtiff-4.0.10 (WIP).
  • Decode old-style LZW with imagecodecs >= 2018.11.8.
  • Remove TiffFile.qptiff_metadata (QPI metadata are per page).
  • Do not use keyword arguments before variable positional arguments.
  • Make either all or none return statements in function return expression.
  • Use pytest parametrize to generate tests.
  • Replace test classes with functions.

2018.11.6

  • Rename imsave function to imwrite.
  • Re-add Python implementations of packints, delta, and bitorder codecs.
  • Fix TiffFrame.compression AttributeError.

2018.10.18

  • Rename tiffile package to tifffile.

2018.10.10

  • Read ZIF, the Zoomable Image Format (WIP).
  • Decode YCbCr JPEG as RGB (tentative).
  • Improve restoration of incomplete tiles.
  • Allow to write grayscale with extrasamples without specifying planarconfig.
  • Enable decoding of PNG and JXR via imagecodecs.
  • Deprecate 32-bit platforms (too many memory errors during tests).

2018.9.27

  • Read Olympus SIS (WIP).
  • Allow to write non-BigTIFF files up to ~4 GB (fix).
  • Fix parsing date and time fields in SEM metadata.
  • Detect some circular IFD references.
  • Enable WebP codecs via imagecodecs.
  • Add option to read TiffSequence from ZIP containers.
  • Remove TiffFile.isnative.
  • Move TIFF struct format constants out of TiffFile namespace.

2018.8.31

  • Fix wrong TiffTag.valueoffset.
  • Towards reading Hamamatsu NDPI (WIP).
  • Enable PackBits compression of byte and bool arrays.
  • Fix parsing NULL terminated CZ_SEM strings.

2018.8.24

  • Move tifffile.py and related modules into tiffile package.
  • Move usage examples to module docstring.
  • Enable multi-threading for compressed tiles and pages by default.
  • Add option to concurrently decode image tiles using threads.
  • Do not skip empty tiles (fix).
  • Read JPEG and J2K compressed strips and tiles.
  • Allow floating-point predictor on write.
  • Add option to specify subfiletype on write.
  • Depend on imagecodecs package instead of _tifffile, lzma, etc modules.
  • Remove reverse_bitorder, unpack_ints, and decode functions.
  • Use pytest instead of unittest.

2018.6.20

  • Save RGBA with unassociated extrasample by default (breaking).
  • Add option to specify ExtraSamples values.

2018.6.17 (included with 0.15.1)

  • Towards reading JPEG and other compressions via imagecodecs package (WIP).
  • Read SampleFormat VOID as UINT.
  • Add function to validate TIFF using jhove -m TIFF-hul.
  • Save bool arrays as bilevel TIFF.
  • Accept pathlib.Path as filenames.
  • Move software argument from TiffWriter __init__ to save.
  • Raise DOS limit to 16 TB.
  • Lazy load LZMA and ZSTD compressors and decompressors.
  • Add option to save IJMetadata tags.
  • Return correct number of pages for truncated series (fix).
  • Move EXIF tags to TIFF.TAG as per TIFF/EP standard.

2018.2.18

  • Always save RowsPerStrip and Resolution tags as required by TIFF standard.
  • Do not use badly typed ImageDescription.
  • Coerce bad ASCII string tags to bytes.
  • Tuning of __str__ functions.
  • Fix reading undefined tag values.
  • Read and write ZSTD compressed data.
  • Use hexdump to print bytes.
  • Determine TIFF byte order from data dtype in imsave.
  • Add option to specify RowsPerStrip for compressed strips.
  • Allow memory-map of arrays with non-native byte order.
  • Attempt to handle ScanImage <= 5.1 files.
  • Restore TiffPageSeries.pages sequence interface.
  • Use numpy.frombuffer instead of fromstring to read from binary data.
  • Parse GeoTIFF metadata.
  • Add option to apply horizontal differencing before compression.
  • Towards reading PerkinElmer QPI (QPTIFF, no test files).
  • Do not index out of bounds data in tifffile.c unpackbits and decodelzw.

2017.9.29

  • Many backward incompatible changes improving speed and resource usage:
  • Add detail argument to __str__ function. Remove info functions.
  • Fix potential issue correcting offsets of large LSM files with positions.
  • Remove TiffFile sequence interface; use TiffFile.pages instead.
  • Do not make tag values available as TiffPage attributes.
  • Use str (not bytes) type for tag and metadata strings (WIP).
  • Use documented standard tag and value names (WIP).
  • Use enums for some documented TIFF tag values.
  • Remove memmap and tmpfile options; use out='memmap' instead.
  • Add option to specify output in asarray functions.
  • Add option to concurrently decode pages using threads.
  • Add TiffPage.asrgb function (WIP).
  • Do not apply colormap in asarray.
  • Remove colormapped, rgbonly, and scale_mdgel options from asarray.
  • Consolidate metadata in TiffFile _metadata functions.
  • Remove non-tag metadata properties from TiffPage.
  • Add function to convert LSM to tiled BIN files.
  • Align image data in file.
  • Make TiffPage.dtype a numpy.dtype.
  • Add ndim and size properties to TiffPage and TiffPageSeries.
  • Allow imsave to write non-BigTIFF files up to ~4 GB.
  • Only read one page for shaped series if possible.
  • Add memmap function to create memory-mapped array stored in TIFF file.
  • Add option to save empty arrays to TIFF files.
  • Add option to save truncated TIFF files.
  • Allow single tile images to be saved contiguously.
  • Add optional movie mode for files with uniform pages.
  • Lazy load pages.
  • Use lightweight TiffFrame for IFDs sharing properties with key TiffPage.
  • Move module constants to TIFF namespace (speed up module import).
  • Remove fastij option from TiffFile.
  • Remove pages parameter from TiffFile.
  • Remove TIFFfile alias.
  • Deprecate Python 2.
  • Require enum34 and futures packages on Python 2.7.
  • Remove Record class and return all metadata as dict instead.
  • Add functions to parse STK, MetaSeries, ScanImage, SVS, Pilatus metadata.
  • Read tags from EXIF and GPS IFDs.
  • Use pformat for tag and metadata values.
  • Fix reading some UIC tags.
  • Do not modify input array in imshow (fix).
  • Fix Python implementation of unpack_ints.

2017.5.23

  • Write correct number of SampleFormat values (fix).
  • Use Adobe deflate code to write ZIP compressed files.
  • Add option to pass tag values as packed binary data for writing.
  • Defer tag validation to attribute access.
  • Use property instead of lazyattr decorator for simple expressions.

2017.3.17

  • Write IFDs and tag values on word boundaries.
  • Read ScanImage metadata.
  • Remove is_rgb and is_indexed attributes from TiffFile.
  • Create files used by doctests.

2017.1.12 (included with scikit-image 0.14.x)

  • Read Zeiss SEM metadata.
  • Read OME-TIFF with invalid references to external files.
  • Rewrite C LZW decoder (5x faster).
  • Read corrupted LSM files missing EOI code in LZW stream.

2017.1.1

  • Add option to append images to existing TIFF files.
  • Read files without pages.
  • Read S-FEG and Helios NanoLab tags created by FEI software.
  • Allow saving Color Filter Array (CFA) images.
  • Add info functions returning more information about TiffFile and TiffPage.
  • Add option to read specific pages only.
  • Remove maxpages argument (breaking).
  • Remove test_tifffile function.

2016.10.28

  • Improve detection of ImageJ hyperstacks.
  • Read TVIPS metadata created by EM-MENU (by Marco Oster).
  • Add option to disable using OME-XML metadata.
  • Allow non-integer range attributes in modulo tags (by Stuart Berg).

2016.6.21

  • Do not always memmap contiguous data in page series.

2016.5.13

  • Add option to specify resolution unit.
  • Write grayscale images with extra samples when planarconfig is specified.
  • Do not write RGB color images with 2 samples.
  • Reorder TiffWriter.save keyword arguments (breaking).

2016.4.18

  • TiffWriter, imread, and imsave accept open binary file streams.

2016.04.13

  • Fix reversed fill order in 2 and 4 bps images.
  • Implement reverse_bitorder in C.

2016.03.18

  • Fix saving additional ImageJ metadata.

2016.2.22

  • Write 8 bytes double tag values using offset if necessary (bug fix).
  • Add option to disable writing second image description tag.
  • Detect tags with incorrect counts.
  • Disable color mapping for LSM.

2015.11.13

  • Read LSM 6 mosaics.
  • Add option to specify directory of memory-mapped files.
  • Add command line options to specify vmin and vmax values for colormapping.

2015.10.06

  • New helper function to apply colormaps.
  • Renamed is_palette attributes to is_indexed (breaking).
  • Color-mapped samples are now contiguous (breaking).
  • Do not color-map ImageJ hyperstacks (breaking).
  • Towards reading Leica SCN.

2015.9.25

  • Read images with reversed bit order (FillOrder is LSB2MSB).

2015.9.21

  • Read RGB OME-TIFF.
  • Warn about malformed OME-XML.

2015.9.16

  • Detect some corrupted ImageJ metadata.
  • Better axes labels for shaped files.
  • Do not create TiffTag for default values.
  • Chroma subsampling is not supported.
  • Memory-map data in TiffPageSeries if possible (optional).

2015.8.17

  • Write ImageJ hyperstacks (optional).
  • Read and write LZMA compressed data.
  • Specify datetime when saving (optional).
  • Save tiled and color-mapped images (optional).
  • Ignore void bytecounts and offsets if possible.
  • Ignore bogus image_depth tag created by ISS Vista software.
  • Decode floating-point horizontal differencing (not tiled).
  • Save image data contiguously if possible.
  • Only read first IFD from ImageJ files if possible.
  • Read ImageJ raw format (files larger than 4 GB).
  • TiffPageSeries class for pages with compatible shape and data type.
  • Try to read incomplete tiles.
  • Open file dialog if no filename is passed on command line.
  • Ignore errors when decoding OME-XML.
  • Rename decoder functions (breaking).

2014.8.24

  • TiffWriter class for incremental writing images.
  • Simplify examples.

2014.8.19

  • Add memmap function to FileHandle.
  • Add function to determine if image data in TiffPage is memory-mappable.
  • Do not close files if multifile_close parameter is False.

2014.8.10

  • Return all extrasamples by default (breaking).
  • Read data from series of pages into memory-mapped array (optional).
  • Squeeze OME dimensions (breaking).
  • Workaround missing EOI code in strips.
  • Support image and tile depth tags (SGI extension).
  • Better handling of STK/UIC tags (breaking).
  • Disable color mapping for STK.
  • Julian to datetime converter.
  • TIFF ASCII type may be NULL separated.
  • Unwrap strip offsets for LSM files greater than 4 GB.
  • Correct strip byte counts in compressed LSM files.
  • Skip missing files in OME series.
  • Read embedded TIFF files.

2014.2.05

  • Save rational numbers as type 5 (bug fix).

2013.12.20

  • Keep other files in OME multi-file series closed.
  • FileHandle class to abstract binary file handle.
  • Disable color mapping for bad OME-TIFF produced by bio-formats.
  • Read bad OME-XML produced by ImageJ when cropping.

2013.11.3

  • Allow zlib compress data in imsave function (optional).
  • Memory-map contiguous image data (optional).

2013.10.28

  • Read MicroManager metadata and little-endian ImageJ tag.
  • Save extra tags in imsave function.
  • Save tags in ascending order by code (bug fix).

2012.10.18

  • Accept file like objects (read from OIB files).

2012.8.21

  • Rename TIFFfile to TiffFile and TIFFpage to TiffPage.
  • TiffSequence class for reading sequence of TIFF files.
  • Read UltraQuant tags.
  • Allow float numbers as resolution in imsave function.

2012.8.3

  • Read MD GEL tags and NIH Image header.

2012.7.25

  • Read ImageJ tags.
  • …