webknossos.dataset ¶

RemoteSegmentationLayer ¶

RemoteSegmentationLayer(
    dataset: RemoteDataset,
    properties: SegmentationLayerProperties,
    read_only: bool,
)

Bases: AbstractSegmentationLayer[RemoteAttachments], RemoteLayer

attachments `property` ¶

attachments: AttachmentsTypeT

Access, add and remove the attachments of this layer.

Attachments are additional files that can be attached to a segmentation layer. They can be used to store additional information, such as meshes, agglomerations, segment indices, cumsums and connectomes.

Examples:

# Add a mesh attachment to the segmentation layer
layer.attachments.add_mesh(
    mesh_path,
    name="meshfile",
    data_format=AttachmentDataFormat.Zarr3,
)

# Access the mesh attachment path
layer.attachments.meshes[0].path

# Remove the mesh attachment
layer.attachments.delete_attachment(layer.attachments.meshes[0])

bounding_box `property` `writable` ¶

bounding_box: NDBoundingBox

Gets the bounding box encompassing this layer's data.

Returns:

NDBoundingBox ( NDBoundingBox ) –

Bounding box with layer dimensions

category `property` ¶

category: LayerCategoryType

data_format `property` ¶

data_format: DataFormat

Gets the data storage format used by this layer.

Returns:

DataFormat ( DataFormat ) –

Format used to store data

Raises:

AssertionError –

If data_format is not set in properties

dataset `property` ¶

dataset: RemoteDataset

default_view_configuration `property` `writable` ¶

default_view_configuration: LayerViewConfiguration | None

Gets the default view configuration for this layer.

Returns:

LayerViewConfiguration | None –

LayerViewConfiguration | None: View configuration if set, otherwise None

dtype_per_channel `property` ¶

dtype_per_channel: dtype

Gets the data type used per channel.

Returns:

dtype –

np.dtype: NumPy data type for individual channels

dtype_per_layer `property` ¶

dtype_per_layer: str

Deprecated, use dtype_per_channel instead. Gets the data type used for the entire layer.

Returns:

str ( str ) –

Data type string (e.g. "uint8")

largest_segment_id `property` `writable` ¶

largest_segment_id: int | None

Gets the largest segment ID present in the data.

The largest segment ID is the highest numerical identifier assigned to any segment in this layer. This is useful for: - Allocating new segment IDs - Validating segment ID ranges - Optimizing data structures

Returns:

int | None –

int | None: The highest segment ID present, or None if no segments exist

mags `property` ¶

mags: Mapping[Mag, MagView]

Getter for dictionary containing all mags.

name `property` `writable` ¶

name: str

Returns the name of the layer.

num_channels `property` ¶

num_channels: int

Gets the number of channels in this layer.

Returns:

int ( int ) –

Number of channels

Raises:

AssertionError –

If num_channels is not set in properties

read_only `property` ¶

read_only: bool

Whether this layer is read-only.

Returns:

bool ( bool ) –

True if layer is read-only, False if writable

add_mag_as_copy ¶

add_mag_as_copy(
    foreign_mag_view_or_path: (
        PathLike | UPath | str | MagView
    ),
    transfer_mode: TransferMode = COPY,
    common_storage_path_prefix: str | None = None,
    overwrite_pending: bool = True,
) -> MagView[RemoteLayer]

Copies the data at foreign_mag_view_or_path which can belong to another dataset to the current remote dataset. Additionally, the relevant information from the datasource-properties.json of the other dataset are copied, too.

as_segmentation_layer ¶

as_segmentation_layer() -> RemoteSegmentationLayer

Casts into SegmentationLayer.

delete_mag ¶

delete_mag(mag: MagLike) -> None

download_mesh ¶

download_mesh(
    segment_id: int,
    output_dir: PathLike | UPath | str,
    mesh_file_name: str | None = None,
    datastore_url: str | None = None,
    lod: int = 0,
    mapping_name: str | None = None,
    mapping_type: (
        Literal["agglomerate", "json"] | None
    ) = None,
    mag: MagLike | None = None,
    seed_position: Vec3Int | None = None,
    token: str | None = None,
    sharing_token: str | None = None,
) -> UPath

downsample ¶

downsample(
    *,
    from_mag: Mag | None = None,
    coarsest_mag: Mag | None = None,
    interpolation_mode: str = "default",
    compress: bool | Zarr3Config = True,
    sampling_mode: str | SamplingModes = ANISOTROPIC,
    align_with_other_layers: bool = True,
    buffer_shape: Vec3Int | None = None,
    force_sampling_scheme: bool = False,
    transfer_mode: TransferMode = COPY,
    common_storage_path_prefix: str | None = None,
    overwrite_pending: bool = True,
    executor: Executor | None = None
) -> None

Downsample data from a source magnification to coarser magnifications.

Downsamples the data starting from from_mag until a magnification is >= max(coarsest_mag). Different sampling modes control how dimensions are downsampled.

Note that the data is written temporarily on the local disk and uploaded afterwards so some local disk space is required.

Parameters:

from_mag (Mag | None, default: None ) –

Source magnification to downsample from. Defaults to highest existing mag.
coarsest_mag (Mag | None, default: None ) –

Target magnification to stop at. Defaults to calculated value.
interpolation_mode (str, default: 'default' ) –

Interpolation method to use. Defaults to "default". Supported modes: "median", "mode", "nearest", "bilinear", "bicubic"
compress (bool | Zarr3Config, default: True ) –

Whether to compress the generated magnifications. For Zarr3 datasets, codec configuration and chunk key encoding may also be supplied. Defaults to True.
sampling_mode (str | SamplingModes, default: ANISOTROPIC ) –

How dimensions should be downsampled. Defaults to ANISOTROPIC.
align_with_other_layers (bool, default: True ) –

Whether to align the mag selection with the dataset’s other layers. True by default.
buffer_shape (Vec3Int | None, default: None ) –

Shape of processing buffer. Defaults to None.
force_sampling_scheme (bool, default: False ) –

Force invalid sampling schemes. Defaults to False.
common_storage_path_prefix (str | None, default: None ) –

Optional path prefix used when transfer_mode is either COPY or MOVE_AND_SYMLINK to select one of the available WEBKNOSSOS storages.
executor (Executor | None, default: None ) –

Executor for parallel processing. None by default.

Raises:

AssertionError –

If from_mag does not exist
RuntimeError –

If sampling scheme produces invalid magnifications
AttributeError –

If sampling_mode is invalid

get_finest_mag ¶

get_finest_mag() -> MagView[RemoteLayer]

get_mag ¶

get_mag(mag: MagLike) -> MagView[RemoteLayer]

refresh_largest_segment_id ¶

refresh_largest_segment_id(
    *,
    chunk_shape: Vec3Int | None = None,
    executor: Executor | None = None
) -> None

Updates largest_segment_id based on actual data content.

Scans through the data to find the highest segment ID value. Sets to None if data is empty.

Parameters:

chunk_shape (Vec3Int | None, default: None ) –

Shape of chunks for processing
executor (Executor | None, default: None ) –

Executor for parallel processing

webknossos.dataset ¶

RemoteSegmentationLayer ¶

attachments property ¶

bounding_box property writable ¶

category property ¶

data_format property ¶

dataset property ¶

default_view_configuration property writable ¶

dtype_per_channel property ¶

dtype_per_layer property ¶

largest_segment_id property writable ¶

mags property ¶

name property writable ¶

num_channels property ¶

read_only property ¶

add_mag_as_copy ¶

as_segmentation_layer ¶

delete_mag ¶

download_mesh ¶

downsample ¶

get_finest_mag ¶

get_mag ¶

refresh_largest_segment_id ¶

attachments `property` ¶

bounding_box `property` `writable` ¶

category `property` ¶

data_format `property` ¶

dataset `property` ¶

default_view_configuration `property` `writable` ¶

dtype_per_channel `property` ¶

dtype_per_layer `property` ¶

largest_segment_id `property` `writable` ¶

mags `property` ¶

name `property` `writable` ¶

num_channels `property` ¶

read_only `property` ¶