v0.9.21

Release for v0.9.21

v0.9.20

webknossos

Fixed

• Fixed a bug where the server’s error message during dataset upload was not displayed to the user. #702

wkcuber

Breaking Changes

• Deprecated --wkw_file_len flags in favor of --chunks_per_shard. #679
• Deprecated wkcuber.api in favor of the high-level webknososs.Dataset API. #679
• Deprecated external use of wkcuber.utils. #679
• Remove the deprecated modules wkcuber.downsampling_utils and wkcuber.upsampling_utils. Use the high-level Layer.downsample and Layer.upsample methods in the webknossos package instead. #679

Added

• Added Zarr support for wkcuber, wkcuber.cubing, wkcuber.converter, wkcuber.convert_knossos, wkcuber.convert_image_stack_to_wkw, wkcuber.convert_nifti, wkcuber.convert_raw, wkcuber.convert_zarr, and wkcuber.recubing. These commands now take a --data_format flag that can either be wkw or zarr. Additionally, --chunk_size and --chunks_per_shard flag are available and take either a single number or a 3-tuple (e.g. 32,32,32). #689

v0.9.19

wkcuber

Added

• Added support for converting .bmp image files. #689

cluster_tools

Fixed

• Fixed that the ProcessPoolExecutor by the cluster tools would also create a checkpoint if the job failed. This was a regression introduced by #686. #692

v0.9.18

cluster_tools

Breaking Changes

• The cluster-tools serialize the output of a job in the format (wasSuccessful, result_value) to a pickle file if output_pickle_path is provided and multiprocessing is used. This is consistent with how it is already done when using a cluster executor (e.g., slurm). #686

v0.9.17

Release for v0.9.17

v0.9.16

Release for v0.9.16

v0.9.14

webknossos

Breaking Changes

• Dataset.download: The argument dataset_name was renamed to dataset_name_or_url. #660

Added

• Dataset.download now also accepts a URL, as well as a sharing_token, which can also be part of the URL. #660

v0.9.13

webknossos

Breaking Changes

• Consistently rename organization_name parameters to organization_id (except in deprecated webknossos.client.download_dataset). #639

Changed

• MagView.compress now skips in-place compression of already compressed mags. #667

Fixed

• Fixed compression of downsampled mags for layers with arbitrary and potentially mag-unaligned bounding boxes. #667

wkcuber

Fixed

• Fixed that wkcuber.downsampling didn't support anisotropic downsampling for some downsampling modes like nearest. #643

v0.9.12

webknossos

Breaking Changes

• The annotation class now exposes BoundingBox objects instead of tuples. #646

Added

• Added groups and graphs property to skeleton.Group to access immediate child groups/graphs. #645
• The BoundingBox class now supports the following additional properties: id, name, is_visible and color. #646
• Added support for Zarr arrays in the Dataset classes. Users can set the data_format of layers to zarr to use Zarr for storing data. #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

Fixed

• Fixed crash during downsampling and compression of segmentation layers. #657

wkcuber

Added

• Added logging to file in ./logs directory. #641

v0.9.11

Release for v0.9.11