- Update documentation.
- Bump dependencies.
- Improved validation of TIFF write arguments.
- Add ability to speciy store when writing Zarr e.g. zarr.SQliteStore.
- Update CLI:
- New
-s
argment forconvert
to specify store for zarr.
- New
- Bug fixes:
- Fix MPP writing for .dcm files.
- Fix parsing of NGFF metadata (zattrs JSON), including getting MPP.
- Bug fixes:
- Fix issue where
DICOMWSIReader
required user input at init. - Fix level offset when printing the level number during
TIFFWriter
pyramid building. - Refactor slow
DICOMWSIReader
init warning and only warn from the main process.
- Fix issue where
- Add DICOM writer.
- Avoid decoding entire TIFF before conversion starts.
- TIFFReader can now expose a dask array view (using tiffile Zarr view underneath).
- Add overwrite option to transcode CLI mode.
- Refactor to use persistent worker subprocesses. This avoids recreating the reader object for each region read. For some reader such as DICOMWSIReader this significantly improves performance.
- General refactoring and code cleanup.
- Bug fixes:
- Fix writing MPP for SVSWriter.
- Remove OpenSlide thumbnail generation method. This would cause the process to run out of memory for some files and the base implementation works just as well without this memory issue.
- Normalise TIFF array axes (to YXC order) when reading using tiffile.
- Bug fixes:
- Fix reading/writing JP2 resoluion metadata (vres/hres are in m not cm).
- Join child processes when finishing writing / exiting.
- Copy the reader tile size for transcode mode.
- Return None for MPP when JP2 has no resolution box.
- Set resolution units to cm when writing TIFFs.
- Use the MPP from the reader when writing JP2.
- Add a zarr intermediate for JP2 writing (allows different read and write tile sizes).
- Select Writer class based on file extension from CLI.
- Bug fixes:
- Fix writing MPP to NGFF v0.4.
- Change coordinate transformation ordering.
- Fix reading TIFF resolution tag. Previously only the numerator of the resolution fraction was being read.
- Other minor bug fixes.
- Add ability to write resolution metadata to JP2. Thanks to @quintusdias for helping get this implemented in glymur.
- Remove QOI codec code as this is not included in imagecodes. Thanks to Christoph Gohlke for adding this.
- Add a "How do I?" documentation page.
- Bug fixes:
- Fix parsing of OpenSlide MPP to float.
- Add ability to transcode/repackage to a TIFF file (from DICOM or SVS).
- Refactor
ZarrReaderWriter
to seperateZarrWriter
andZarrReader
. - Bug fixes:
- Fix thumbnaiul generation for zarr.
- Fix NGFF metadata
CoordinateTransformation
field default factor.
- Add ability to write JPEG compressed SVS files.
- Add support for thumbnail generation and a CLI command.
- Swap from strings to enums for codecs and color spaces.
- Remove unused CLI debug option.
- Add generation of OME-NGFF metadata (JSON .zattrs file).
- Add timeout when copying tiles to prevent indefinite hanging.
- Improve joining/termination of child processes at shutdown.
- Use the TIFF resolution tag if present.
- Add
get_tile
method to allReader
classes. - Update supported Python versions to 3.8, 3.9, 3.10.
- Bug fixes:
- Fix and issue with concatenation of pyramid downsamples.
- Add a custom Queue class for multiprocessing on macOS.
- Fix handling of
pyramid_downsamples
argument whenNone
.
- Add Support To Read DICOM WSI and transform to zarr.
- First release on PyPI.