Webknossos

webknossos

Breaking Changes
- Consistently rename `organization_name` parameters to `organization_id` (except in deprecated `webknossos.client.download_dataset`). [639](https://github.com/scalableminds/webknossos-libs/pull/639)

Changed
- `MagView.compress` now skips in-place compression of already compressed mags. [667](https://github.com/scalableminds/webknossos-libs/pull/667)

Fixed
- Fixed compression of downsampled mags for layers with arbitrary and potentially mag-unaligned bounding boxes. [667](https://github.com/scalableminds/webknossos-libs/pull/667)


wkcuber

Fixed
- Fixed that wkcuber.downsampling didn't support anisotropic downsampling for some downsampling modes like `nearest`. [643](https://github.com/scalableminds/webknossos-libs/pull/643)

webknossos

Breaking Changes
- The annotation class now exposes `BoundingBox` objects instead of tuples. [646](https://github.com/scalableminds/webknossos-libs/pull/646)

Added
- Added `groups` and `graphs` property to skeleton.Group to access immediate child groups/graphs. [645](https://github.com/scalableminds/webknossos-libs/pull/645)
- The `BoundingBox` class now supports the following additional properties: `id`, `name`, `is_visible` and `color`. [646](https://github.com/scalableminds/webknossos-libs/pull/646)
- Added support for [Zarr](https://zarr.dev/) arrays in the `Dataset` classes. Users can set the `data_format` of layers to `zarr` to use Zarr for storing data. [#627](https://github.com/scalableminds/webknossos-libs/pull/627)
The current implementation has some limitations, e.g.:
* Only one type of compression (Blosc+Zstd) is implemented.
* Sharding is not available in Zarr, yet. Please use `chunks_per_shard = (1, 1, 1)`.
* Only local filesystem-based arrays are supported.
There are changes to the `datasource-properties.json` for Zarr layers compared to WKW layers:
* `dataFormat` needs to be changed to `zarr`.
* The list of mags is called `mags`, instead of `wkwResolutions`.
* Each mag is represented by an object with a single attribute `mag`, e.g. `{ "mag": [1, 1, 1] }`.

Changed
- Dataset: `block_len` and `file_len` attributes are now deprecated, but still available for backwards compatibility. Use `chunk_size` and `chunks_per_shard` instead. These new attributes are `Vec3Int`, so they can be set non-uniformly. However, WKW-backed layers still require uniform `chunk_size` and `chunks_per_shard`. [627](https://github.com/scalableminds/webknossos-libs/pull/627)

Fixed
- Fixed crash during downsampling and compression of segmentation layers. [657](https://github.com/scalableminds/webknossos-libs/pull/657)


wkcuber

Added
- Added logging to file in `./logs` directory. [641](https://github.com/scalableminds/webknossos-libs/pull/641)

webknossos

Changed
- Annotation: `Annotation.temporary_volume_layer_copy` now uses the NML-provided `scale`. [644](https://github.com/scalableminds/webknossos-libs/pull/644)
- Dataset: Moved the deprecation warning from `get_color_layers()` to the actually deprecated method `get_color_layer()`.
[635](https://github.com/scalableminds/webknossos-libs/pull/635)
- Inconsistent writes to datasets properties (e.g., caused due to multiprocessing) are detected automatically. The warning can be escalated to an exception with `warnings.filterwarnings("error", module="webknossos", message=r"\[WARNING\]")`. [633](https://github.com/scalableminds/webknossos-libs/pull/633)

Fixed
- Tests: The `./test.sh` script works on macOS again and doesn't throw Network Errors anymore. However the introduced fix could lead to slightly different behaviour on macOS tests vs CI tests, when UNIX socket communication is involved. [618](https://github.com/scalableminds/webknossos-libs/pull/618)


wkcuber

Fixed
- Fixed that wkcuber.downsampling didn't support an anisotropic mag for `--from`. [638](https://github.com/scalableminds/webknossos-libs/pull/638)

webknossos

Breaking Changes
- Changed the interface and behavior of `Annotation`s and `Skeleton`s, as well as nml-parsing related code.
[602](https://github.com/scalableminds/webknossos-libs/pull/602)
* `webknossos.skeleton.nml` is not exposed anymore. The previous functionality may be found in
`webknossos._nml` and `webknossos/annotation/_nml_conversion.py ` if needed, but please not that
this is not part of the public API and may change at any time. Please use the respective logic on the
`Annotation` class instead.
* The `name` attribute on the `Skeleton` class changed to `dataset_name`.
* The deprecated `Skeleton.offset` attribute is removed.
* The following attributes are removed from the `Skeleton` class, instead they are part of the
`Annotation` class now: `time`, `edit_position`, `edit_rotation`, `zoom_level`, `task_bounding_box`,
`user_bounding_boxes`.
* The following `Annotation` methods were renamed and their arguments changed slightly:
- `save_volume_annotation` ➜ `export_volume_layer_to_dataset`
- `temporary_volume_annotation_layer_copy` ➜ `temporary_volume_layer_copy`

Added
- Added new features to the `Annotation` and `Skeleton` classes. [602](https://github.com/scalableminds/webknossos-libs/pull/602)
* The `Skeleton` class has new attributes `description` and `organization_id`.
* The `Annotation` class has new attributes `username` and `annotation_id`, as well as the following
attributes that are proxies for the skeleton attributes: `dataset_name`, `scale`, `organization_id`, `description`
* `Annotation`s can now be initialized from their attributes and an optional skeleton.
* New methods on `Annotation`: `upload`, `add_volume_layer`, `delete_volume_layer`
* `Annotation.load()` and `annoation.save()` also works with `.nml` files.
- Added `MagView.get_views_on_disk()` as a shortcut to turning `get_bounding_boxes_on_disk` into views.
[621](https://github.com/scalableminds/webknossos-libs/pull/621)

Fixed
- Fixed the download of skeleton-only annotations. [602](https://github.com/scalableminds/webknossos-libs/pull/602)

webknossos

Added
- Added `allow_overwrite` parameter to `Layer.downsample()`. [614](https://github.com/scalableminds/webknossos-libs/pull/614)