v0.10.1

Release for v0.10.1

v0.10.0

webknossos

Breaking Changes

• Dataset.upload() now returns a RemoteDataset instead instead of the URL string. You can get the URL via remote_ds.url. #723
• User.teams now is a tuple instead of a list. #723
• The deprecated download_dataset function now requires the organization_id argument. #723

Added

• Added Dataset.open_remote(), which returns an object of the new RemoteDataset. #723
  This can
  • give the webknossos URL for the dataset as remote_ds.url,
  • read image data via the webknossos zarr interface, using the inherited Dataset methods, and
  • read and change the following dataset metadata as properties: display_name, description, tags, is_public, sharing_token, allowed_teams.
• Team instances also contain the organization_id. #723

v0.9.24

webknossos

Fixed

• Fixed upsampling with constant z in certain anisotropic cases. #720

v0.9.23

Release for v0.9.23

v0.9.22

webknossos

Breaking Changes

• Renamed some entities to comply with the webKnossos terminology. #704:
  • The Graph class changed to Tree, also related methods and attributes are renamed now, e.g. add_graph is now add_tree.
    All previous entities are still available, but deprecated.
  • scale has changed to voxel_size for datasets, skeletons and annotations.
    Changes in Dataset are backwards-compatible, but scale is deprecated.
    For Annotation and Skeletons the initializer only supports voxel_size, the scale attribute is deprecated
  • get_best_mag is deprecated, please use get_finest_mag instead
  • In layer.upscale, min_mag is deprecated in favor of finest_mag

Fixed

• Correctly maintain default_view_configuration property when downloading a dataset. #677

wkcuber

Breaking Changes

• Deprecated --scale in favor of --voxel_size. #704

Fixed

• Fixed a bug where upper-case file extensions would lead to errors during channel count detection. #709

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