v0.14.1

webknossos

Commits

Added

• Adds support for Zarr3-based volume annotations as introduced in webknossos#7288. #952

Changed

• The WK_USE_ZARRITA env variable is no longer required. zarrita is always installed and now the default for Zarr and Zarr3 datasets. #950
• Updates various dependencies. #943

v0.14.0

webknossos

Breaking Changes

• wait_and_ensure_success from webknossos.utils now requires an executor argument. #943

Changed

• Updates various dependencies. #943

cluster_tools

Breaking Changes

• Dropped support for Python 3.7. #943
• Please use Executor.as_completed instead of concurrent.futures.as_completed because the latter will not work for DaskExecutor futures. #943

Added

• Added DaskScheduler (only Python >= 3.9). #943

Changed

• The exported Executor type is now implemented as a protocol. #943

v0.13.7

webknossos

Fixed

• Fixed a bug in writing compressed data. #942

v0.13.6

Release for v0.13.6

v0.13.5

webknossos

Added

• Added task_type property to Task class. #938

Fixed

• Fixed a bug where parallel access to the properties json leads to an JsonDecodeError in the webknossos CLI #919

v0.13.4

webknossos

Breaking Changes

• Task/Project management: open tasks have been renamed to pending. Use Task.status.pending_instance_count instead of Task.status.open_instance_count. #930

Fixed

• Fixed an infinite loop in the mag calculation during anisotropic downsampling in situations where the target mag cannot possibly be reached while adhering to the anisotropic downsampling scheme. #934

v0.13.3

webknossos

Added

• View has a map_chunk method now to run a function on each chunk and collect the results in a list.

Changed

• As WEBKNOSSOS does not require the largest segment id. It is also not mandatory in the WEBKNOSSOS libs anymore. #917 The method SegmentationLayer.refresh_largest_segment_id was added to lookup the highest value in segmentation data and set largest_segment_id accordingly.
• The convert command of the cli now has a --category flag, to select the LayerCategoryType.

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.