v0.8.21

downgrade typing-extensions for better dependency compatibility #472

v0.8.20

Breaking Changes

• BoundingBox.chunk()'s 2nd parameter chunk_border_alignments now does not accept a list with a single int anymore. #437

Fixed

• Make Views picklable. We now ignore the file handle when we pickle Views. #469

v0.8.19

Added

• Added a new Annotation class which includes skeletons as well as volume-annotations. #437
• Added dataset down- and upload as well as annotation download, see the examples learned_segmenter.py and upload_image_data.py. #437

Changed

• Views now always open the wkw.Dataset lazily. All explicit calls to View.open() and View.close() must be removed. #448

Fixed

• Fixed two bugs in cubing (regarding start_z and pad). As a result, the ImageConverters do no longer cache metadata. #460

v0.8.18

What's Changed

• Add shallow_copy_dataset method by @valentin-pinkau in #437
• Allow full Vec3IntLike as input for get_buffered_slice_writer by @fm3 in #438
• [wkcuber] Make tiff and czi reading more robust by @youri-k in #335
• Allow float numpy array in BoundingBox.contains by @fm3 in #450
• Forbid implicit optional in typing by @fm3 in #449
• Use Dataset API inside cubing by @rschwanhold in #418

Full Changelog: v0.8.17...v0.8.18

v0.8.17

wkcuber and webknossos:

• Updated scikit-image dependency to 0.18.3. #435

v0.8.16

wkcuber:

• Add jp2 support. #428
• Fixed the string translation for signed int layer. #428

webknossos python lib:

• Refactored the BufferedSliceWriter and added a BufferedSliceReader. #425
• Breaking changes in BufferedSliceWriter:
  • The data no longer gets transposed: previously the format of the slices was [y,x]; now it is [x,y]
  • The interface of the constructor was changed:
    • A View (or MagView) is now required as datasource
    • The parameter dimension can be used to specify the axis along the data is sliced
    • The offset is expected to be in the magnification of the view
  • This class is now supposed to be used within a context manager and the slices are written by sending them to the generator (see documentation of the class).
• BufferedSliceReader
  • This class was added complementary to the BufferedSliceWriter
• Added methods to get a BufferedSliceReader/BufferedSliceWriter from a View directly

v0.8.15

Fixed an indexing bug in webknossos.geometry.BoundingBox.to_slices() introduced in v0.8.15.

v0.8.14

wkcuber:

• Adjust downsampling scheme to always try to minimize the scaled difference between the different dimensions of a mag and renamed the sampling mode auto to anisotropic. #391
• Make parameter executor optional for View.for_each_chunk and View.for_zipped_chunks. #404
• Add option to rename foreign layer with add_{symlink,copy}_layer. #419
• Reverted that dataset.add_symlink_layer and dataset.add_copy_layer resolved the layer path if it was a symlink. #408

webknossos python package:

• Breaking changes were introduced for geometry classes in #421:

  • BoundingBox

    • is now immutable, use convenience methods, e.g. bb.with_topleft((0,0,0))
    • properties topleft and size are now Vec3Int instead of np.array, they are each immutable as well
    • all to_-conversions return a copy, some were renamed:
    • to_array → to_list
    • as_np → to_np
    • as_wkw → to_wkw_dict
    • from_wkw → from_wkw_dict
    • as_config → to_config_dict
    • as_checkpoint_name → to_checkpoint_name
    • as_tuple6 → to_tuple6
    • as_csv → to_csv
    • as_named_tuple → to_named_tuple
    • as_slices → to_slices
    • copy → (gone, immutable)

  • Mag

    • is now immutable
    • mag.mag is now mag._mag (considered private, use to_list instead if you really need it as list)
    • all to_-conversions return a copy, some were renamed:
    • to_array → to_list
    • scale_by → (gone, immutable)
    • divide_by → (gone, immutable)
    • as_np → to_np

• An immutable Vec3Int class was introduced that holds three integers and provides a number of convenience methods and accessors. #421

• BoundingBox and Mag are now immutable attr classes containing Vec3Int values. See breaking changes above.

v0.8.13

• Replaced the old properties classes of the Dataset API with attr-classes.
  • The Layer.rename() function is now replaced with the setter of Layer.name.
  • The functions Layer.get_view_configuration and Layer.set_view_conficuration are replaced by the property Layer.default_view_configuration. (Same applies to Dataset.get_view_configuration and Dataset.set_view_configuration)
  • Moved LayerViewConfiguration and DatasetViewConfiguration into properties.py
  • Removed Layer.set_bounding_box_offset and Layer.set_bounding_box_size.
  • Renamed Layer.get_bounding_box() to the property Layer.bounding_box. The method Layer.set_bounding_box is replaced with the setter of the property Layer.bounding_box.
• Reverted that dataset.add_symlink_layer and dataset.add_copy_layer resolved the layer path if it was a symlink. #408

v0.8.12

• Rollback scikit-image version from 0.18.0 to 0.16.2 because the newer version caused problems in voxelytics. #390