v2.0.7

webknossos

Changed

• Pinned tensorstore to <=0.1.71. #1276

v2.0.6

webknossos

Fixed

• Fixed an issue with uploading datasets where the dataset name is already in use. #1275

v2.0.5

webknossos

Changed

• Changed the default dimension separator for Zarr 2 arrays from . to /. #1274

v2.0.4

webknossos

Changed

• For Zarr3 datasets, the OME-Zarr 0.5 metadata is now written. #1272

Fixed

• Fixed an issue where it was attempted to overwrite the OME-Zarr metadata for symlinked layers. #1272

v2.0.3

Release for v2.0.3

v2.0.2

webknossos

Added

• Added tests for NDBoundingBox and VecInt classes. #1268

Changed

• Removed PimsImagejTiffReader in favor of the unified PimsTiffReader. #1269

Fixed

• Fixed issues with tiff conversion for tiff files that don't use pages for z and other axes. #1269

v2.0.1

webknossos

Added

• Added get_remote_annotations() to AnnotationInfo class to get a list of all remote Annotations of the current user. #1262

Fixed

• Fixed an issue with RemoteDataset.explore_and_add_remote() where including a remote dataset failed. #1261
• Fixed an issue with the Zarr array's shape when using Dataset.from_images. #1267

v2.0.0

webknossos

Breaking Changes

• Changed writing behavior. There is a new argument allow_resize for MagView.write, which defaults to False. If set to True, the bounding box of the underlying Layer will be resized to fit the to-be-written data. That largely mirrors the previous behavior. However, it is not safe for concurrent operations, so it is disabled by default. It is recommended to set the Layer.bounding_box to the desired size before writing. Additionally, by default, writes need to be aligned with the underlying shard grid to guard against concurrency issues and avoid performance footguns. There is a new argument allow_unaligned, which defaults to False. If set to True, the check for shard alignment is skipped.
• Deprecated chunks_per_shard arguments in favor of shard_shape, which equals to shard_shape = chunk_shape * chunks_per_shard. The shard shape is more intuitive, because it directly defines the size of shards instead of being a factor of the chunk shape.
• Deprecated dtype_per_layer argument, because it promotes the use of uncommon dtypes and leads to confusion with the other dtype_per_channel argument. With this change only the use of dtype_per_channel is encouraged.
• Removed deprecated functions, properties and arguments:
  • Functions:
    • open_annotation, use Annotation.load() instead
    • Dataset.get_color_layer, use Dataset.get_color_layers() instead
    • Dataset.get_segmentation_layer, use Dataset.get_segmentation_layers() instead
    • Dataset.create, use Dataset.__init__ instead
    • Dataset.get_or_create, use Dataset.__init__ with exist_ok=True instead
    • Layer.get_best_mag, use Layer.get_finest_mag instead
    • View.read_bbox, use read with relative_bounding_box or absolute_bounding_box instead
    • View.__enter__ and View.__exit__, context managers are not needed anymore
    • open_nml, use Skeleton.load() instead
    • Group.add_graph, use Group.add_tree instead
    • Group.get_max_graph_id, use Group.get_max_tree_id instead
    • Group.flattened_graphs, use Group.flattened_trees instead
    • Group.get_graph_by_id, use Group.get_tree_by_id instead
    • Skeleton.from_path, use Skeleton.load() instead
    • Skeleton.write, use Skeleton.save() instead
  • Properties:
    • Annotation.username, use Annotation.owner_name instead
    • Annotation.scale, use Annotation.voxel_size instead
    • Annotation.user_id, use Annotation.owner_id instead
    • ArrayInfo.shard_size, use ArrayInfo.shard_shape instead
    • Dataset.scale, use Dataset.voxel_size instead
    • MagView.global_offset, always (0, 0, 0, ...)
    • MagView.size, use mag_view.bounding_box.in_mag(mag_view.mag).bottomright
    • MagViewProperties.resolution, use MagViewProperties.mag instead
    • LayerProperties.resolutions, use LayerProperties.mags instead
    • View.header, use View.info instead
    • View.global_offset, use view.bounding_box.in_mag(view.mag).topleft instead
    • View.size, use view.bounding_box.in_mag(view.mag).size instead
    • Group.graphs, use Group.trees
    • Skeleton.scale, use Skeleton.voxel_size instead
  • Arguments:
    • annotation_type in Annotation.download, not needed anymore
    • annotation_type in Annotation.open_as_remote_dataset, not needed anymore
    • size in BufferedSliceReader.__init__, use relative_bounding_box or absolute_bounding_box instead
    • offset in BufferedSliceReader.__init__, use relative_bounding_box or absolute_bounding_box instead
    • offset in BufferedSliceWriter.__init__, use relative_bounding_box or absolute_bounding_box instead
    • json_update_allowed in BufferedSliceWriter.__init__, not supported anymore
    • offset in BufferedSliceWriter.reset_offset, use relative_offset or absolute_offset instead
    • scale in Dataset.__init__, use voxel_size or voxel_size_with_unit instead
    • dtype in Dataset.add_layer, use dtype_per_channel instead
    • dtype in Dataset.get_or_add_layer, use dtype_per_channel instead
    • chunk_size in Dataset.add_layer_from_images, use chunk_shape instead
    • chunk_size in Dataset.copy_dataset, use chunk_shape instead
    • block_len in Dataset.copy_dataset, use chunk_shape instead
    • file_len in Dataset.copy_dataset, use chunks_per_shard instead
    • args in Dataset.copy_dataset, use executor instead
    • chunk_size in Layer.add_mag, use chunk_shape instead
    • block_len in Layer.add_mag, use chunk_shape instead
    • file_len in Layer.add_mag, use chunks_per_shard instead
    • chunk_size in Layer.get_or_add_mag, use chunk_shape instead
    • block_len in Layer.get_or_add_mag, use chunk_shape instead
    • file_len in Layer.get_or_add_mag, use chunks_per_shard instead
    • args in Layer.downsample, use executor instead
    • args in Layer.downsample_mag, use executor instead
    • args in Layer.redownsample, use executor instead
    • args in Layer.downsample_mag_list, use executor instead
    • args in Layer.downsample_mag_list, use executor instead
    • buffer_edge_len in Layer.upsample, use buffer_shape instead
    • args in Layer.upsample, use executor instead
    • min_mag in Layer.upsample, use finest_mag instead
    • offset in MagView.write, use relative_offset, absolute_offset, relative_bounding_box, or absolute_bounding_box instead
    • json_update_allowed in MagView.write, use allow_resize instead
    • args in MagView.compress, use executor instead
    • offset in View.write, use relative_offset, absolute_offset, relative_bounding_box, or absolute_bounding_box instead
    • json_update_allowed in View.write, not supported anymore
    • offset in View.read, use relative_offset, absolute_offset, relative_bounding_box, or absolute_bounding_box instead
    • offset in View.get_view, use relative_offset, absolute_offset, relative_bounding_box, or absolute_bounding_box instead
    • offset in View.get_buffered_slice_writer, use relative_offset, absolute_offset, relative_bounding_box, or absolute_bounding_box instead
    • offset in View.get_buffered_slice_reader, use relative_bounding_box, or absolute_bounding_box instead
    • size in View.get_buffered_slice_reader, use relative_bounding_box, or absolute_bounding_box instead
    • chunk_size in View.for_each_chunk, use chunk_shape instead
    • source_chunk_size in View.for_zipped_chunks, use source_chunk_shape instead
    • target_chunk_size in View.for_zipped_chunks, use target_chunk_shape instead
    • args in View.content_is_equal, use executor instead
  • Classes:
    • Graph, use Tree instead
• Changed defaults:
  • exist_ok in Dataset.__init__ is now False
  • compress in Dataset.from_images is now True
  • compress in Dataset.add_layer_from_images is now True
  • DEFAULT_DATA_FORMAT is now Zarr3
  • compress in Layer.add_mag is now True
  • compress in Layer.upsample is now True
  • buffer_size in View.get_buffered_slice_reader is now computed from the shard shape
  • buffer_size in View.get_buffered_slice_writer is now computed from the shard shape
• Moved from positional argument to keyword-only argument:
  • json_update_allowed in MagView.write
  • organization_id, sharing_token, webknossos_url, bbox, layers, mags, path, exist_ok in Dataset.download
  • layers_to_link, jobs in Dataset.upload
  • dtype_per_layer, dtype_per_channel, num_channels, data_format, bounding_box in Dataset.add_layer
  • dtype_per_layer, dtype_per_channel, num_channels, data_format in Dataset.get_or_add_layer
  • data_format, mag, chunk_shape, chunks_per_shard, shard_shape, compress in Dataset.add_layer_from_images
  • chunk_shape, shard_shape, chunks_per_shard, data_format, compress, executor in Dataset.add_copy_layer
  • organization_id, tags, name, folder_id in Dataset.get_remote_datasets
  • make_relative in Dataset.add_symlink_layer
  • name, make_relative, layers_to_ignore in Dataset.shallow_copy_dataset
  • executor in Dataset.compress
  • sampling_mode, coarsest_mag, executor in Dataset.downsample
  • voxel_size, chunk_shape, shard_shape, chunks_per_shard, data_format, compress, executor, voxel_size_with_unit in Dataset.copy_dataset
  • chunk_shape, shard_shape, chunks_per_shard, compress in Layer.add_mag
  • chunk_shape, shard_shape, chunks_per_shard, compress in Layer.get_or_add_mag
  • extend_layer_bounding_box, chunk_shape, shard_shape, chunks_per_shard, compress, executor in Layer.add_copy_mag
  • make_relative, extend_layer_bounding_box in Layer.add_symlink_mag
  • extend_layer_bounding_box in Layer.add_remote_mag
  • extend_layer_bounding_box in Layer.add_fs_copy_mag
  • move, extend_layer_bounding_box in Layer.add_mag_from_zarrarray
  • from_mag, coarsest_mag, interpolation_mode, compress, sampling_mode, align_with_other_layers, buffer_shape, force_sampling_scheme, allow_overwrite, only_setup_mags, executor in Layer.downsample
  • interpolation_mode, compress, buffer_shape, allow_overwrite, only_setup_mag, executor in Layer.downsample_mag
  • interpolation_mode, compress, buffer_shape, executor in Layer.redownsample
  • interpolation_mode, compress, buffer_shape, allow_overwrite, only_setup_mags, executor in Layer.downsample_mag_list
  • finest_mag, compress, sampling_mode, align_with_other_layers, buffer_shape, executor in Layer.upsample
  • chunk_shape, executor in `SegmentationLayer.refresh_la...

v0.16.10

Release for v0.16.10

v0.16.9

webknossos

Fixed

• Fixed opening a renamed dataset via an annotation link. #1256