v0.9.10

webknossos

Changed

• Annotation: Annotation.temporary_volume_layer_copy now uses the NML-provided scale. #644
• Dataset: Moved the deprecation warning from get_color_layers() to the actually deprecated method get_color_layer().
  #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

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

wkcuber

Fixed

• Fixed that wkcuber.downsampling didn't support an anisotropic mag for --from. #638

v.0.9.9

webknossos

Breaking Changes

• Changed the interface and behavior of Annotations and Skeletons, as well as nml-parsing related code.
  #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
  • 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
  • Annotations 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

Fixed

• Fixed the download of skeleton-only annotations. #602

v0.9.8

webknossos

Added

• Added allow_overwrite parameter to Layer.downsample(). #614

v0.9.7

webknossos

Added

• Added only_setup_mag parameter to downsample-related methods in Layer. This parameter allows creating output magnifications before parallelizing downsampling invocations to avoid outdated writes to datasource-properties.json. #610
• Added Task.create() method to create tasks by prodiving a dataset name, location, and rotation. #605

cluster-tools

Added

• Added KubernetesExecutor for parallelizing Python scripts on a Kubernetes cluster. #600

v0.9.6

webknossos

Added

• Added apply_merger_mode.py example. #592
• Added support for reading from multiple volume layers in annotations. If an annotation contains multiple volume layers, the layer name has to be provided when reading from a volume layer in an annotation (in Annotation.save_volume_annotation() and Annotation.temporary_volume_annotation_layer_copy()). Also, added the method Annotation.get_volume_layer_names() to see available volume layers. #588

Changed

• Dataset writes in higher mags do not increase the bounding box if the written data fits in the rounded up box. #595

Fixed

• Dataset down- & upload: #595
  • Fixed download of higher mags.
  • Bounding box after download is set correctly (was inflated before when downloading higher mags).
  • The returned URL for uploads is corrected, this did not respect new_dataset_name before.

cluster-tools

Added

• Automatically detect when a multiprocessing context is set up without using an if __name__ == "__main__" guard in the main module. #598

v0.9.5

webknossos

Fixed

• Skeleton: Fixed a bug when comparing Graph instances, this fixes failing loads which had the error message Can only compare wk.Graph to another wk.Graph. before. #593

v0.9.4

webknossos

Added

• Added AnnotationInfo, Project and Task classes for handling annotation information and annotation project administration. #574:

Changed

• Lifted the restriction that BoundingBox cannot have a negative topleft (introduced in v0.9.0). Also, negative size dimensions are flipped, so that the topleft <= bottomright,
  e.g. BoundingBox((10, 10, 10), (-5, 5, 5)) -> BoundingBox((5, 10, 10), (5, 5, 5)). #589

v0.9.3

webknossos

Fixed

• dataset.upload(layers_to_link=…): Fixed a bug where the upload did not complete if layers_to_link contained layers present in uploading dataset. #584

v0.9.2

webknossos

Added

• A custom network request timeout can be set using webknossos_context(…, timeout=300) or export WK_TIMEOUT="300". #577

Changed

• The default network request timeout changed from ½min to 30 min. #577

v0.9.1

webknossos

Changed

• The signatures of (Mag)View.for_each_chunk and (Mag)View.for_zipped_chunks changed:
  • The previous argument work_on_chunk is now called func_per_chunk.
  • The various chunk_size arguments now have to be given in Mag(1). They now have default values.
• Deprecations in (Mag)View.get_buffered_slice_reader/_writer #564:
  • (Mag)View.get_buffered_slice_reader: using the parameters offset and size is deprecated.
    Please use the parameter relative_bounding_box or absolute_bounding_box (both in Mag(1)) instead.
    The old offset behavior was absolute for MagViews and relative for Views.
  • (Mag)View.get_buffered_slice_writer: using the parameter offset is deprecated.
    Please use the parameter relative_offset or absolute_offset (both in Mag(1)) instead.
    The old offset behavior was absolute for MagViews and relative for Views.

wkcuber

Added

• Added wkcuber.convert_zarr tool to convert zarr files to wkw datasets. #549

Fixed

• Fixed automatic conversion of 3D tiff files which only have a single page. #575