v0.13.2

webknossos

Changed

• The convert command of the cli now has a --category flag, to select the LayerCategoryType.

cluster_tools

Added

• From now on the cluster tools will detect if slurm jobs were killed, because they exceeded the configured time limit, and throw a RemoteTimeLimitException indicating the issue instead of a generic RemoteException. If it is unclear whether a job was killed because of the time or memory limit, a RemoteResourceLimitException is thrown. #929

v0.13.1

webknossos

Changed

• The conversion folder structures to layer names does not allow slashes in the layer name anymore. #918

Fixed

• Fixed a bug where compression in add_layer_from_images uses too much memory #900

v0.13.0

webknossos

Added

• Added duration_in_seconds and modified to AnnotationInfo. #914
• Added zarrita storage backend for arrays. zarrita supports Zarr v2 and v3 including sharding. To activate zarrita, the environment variable WK_USE_ZARRITA must be set. #912
• Added a Zarr3 data format which supports sharding. #912

Changed

• Integrated the wkcuber CLI tool into webknossos package. #903
  • To get an overview of all webknossos subcommands type webknossos --help. If the usage of a single subcommand is of interest type webknossos <subcommand> --help
  • These commands were changed:
    • python -m wkcuber, python -m wkcuber.convert_image_stack_to_wkw -> webknossos convert
    • python -m wkcuber.export_wkw_as_tiff -> webknossos export-wkw-as-tiff
    • python -m wkcuber.convert_knossos -> webknossos convert-knossos
    • python -m wkcuber.convert_nifti -> webknossos convert-nifti
    • python -m wkcuber.convert_raw -> webknossos convert-raw
    • python -m wkcuber.downsampling -> webknossos downsample
    • python -m wkcuber.compress -> webknossos compress
    • python -m wkcuber.check_equality -> webknossos check-equality
  • There is one new command:
    • webknossos upload to upload a dataset to a WEBKNOSSOS server
  • These commands have been removed:
    • python -m wkcuber.cubing
    • python -m wkcuber.tile_cubing
    • python -m wkcuber.metadata
    • python -m wkcuber.recubing

Fixed

• Fixed a bug where upsampling of a layer would fail, if the layer had a bounding box that doesn't align with the from_mag mag. #915

wkcuber

The wkcuber package is now deprecated because the CLI was integrated into the webknossos package. Please use the CLI in the webknossos package instead.

v0.12.6

webknossos

Changed

• Upgrades wkw. #911

v0.12.5

webknossos

Added

• Added support for Python 3.11. #843

v0.12.4

webknossos

Added

• Group.add_tree now also accepts a tree object as a first parameter (instead of only a string). #891
• Group.remove_tree_by_id was added. #891

Changed

• Upgrades black, mypy, pylint, pytest. #873

Fixed

• Fixed poetry build backend for new versions of Poetry. #899
• Added axis_order fields for Zarr data format. #902

wkcuber

Changed

• Upgrades black, mypy, pylint, pytest. #873

cluster_tools

Changed

• Upgrades black, mypy, pylint, pytest. #873

v0.12.3

webknossos

Added

• Added support to import ImageJ Hyperstack tiff files via Dataset.from_images and dataset.add_layer_from_images. #877

Changed

• Dataset.from_images and dataset.add_layer_from_images now automatically convert big endian dtypes to their little endian counterparts by default. #877

Fixed

• Fixed reading czi files with non-zero axis offsets. #876

v0.12.2

webknossos

Commits

Added

• Added RemoteFolder for assigning remote datasets to a WEBKNOSSOS folder. #868

wkcuber

Fixed

• Fixed Docker container startup, by adding version information during build time. #872

v0.12.1

webknossos

Added

• Added read_only parameter for annotation.temporary_volume_layer_copy. #866

Changed

• in Dataset.layer_from_images, layer names generated from multiple input image channels no longer contain equal signs, yielding better url safety. #867

Fixed

• Fixed a bug where some czi, dm3, dm4 images could not be converted to wkw due to a too-strict check. #865
• Enforce read_only property of datasets also for down- and upsampling. #866

v0.12.0

webknossos

Breaking Changes

• Dropped support for Python 3.7. #833

Added

• Added support for Python 3.10. #833

wkcuber

Breaking Changes

• Dropped support for Python 3.7. #833

Added

• Added support for Python 3.10. #833