--- a +++ b/HISTORY.md @@ -0,0 +1,110 @@ +# History + +## 0.9.0 (2023-05-25) + +- 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 for `convert` to specify store for zarr. +- Bug fixes: + - Fix MPP writing for .dcm files. + - Fix parsing of NGFF metadata (zattrs JSON), including getting MPP. + +## 0.8.2 (2023-04-02) + +- 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. + +## 0.8.0 (2023-04-01) + +- 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. + +## 0.7.0 (2022-12-15) + +- 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). + +## 0.6.1 (2022-10-21) + +- 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. + +## 0.6.0 (2022-10-03) + +- 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. + +## 0.5.1 (2022-06-27) + +- Bug fixes: + - Fix parsing of OpenSlide MPP to float. + +## 0.5.0 (2022-06-25) + +- Add ability to transcode/repackage to a TIFF file (from DICOM or SVS). +- Refactor `ZarrReaderWriter` to seperate `ZarrWriter` and `ZarrReader`. +- Bug fixes: + - Fix thumbnaiul generation for zarr. + - Fix NGFF metadata `CoordinateTransformation` field default factor. + +## 0.4.0 (2022-06-20) + +- 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. + +## 0.3.0 (2022-05-13) + +- 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 all `Reader` 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 when `None`. + +## 0.2.0 (2022-03-22) + +- Add Support To Read DICOM WSI and transform to zarr. + +## 0.1.0 (2022-02-22) + +- First release on PyPI.