# 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.