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webknossos.dataset.abstract_dataset

AbstractDataset 

AbstractDataset(
    dataset_properties: DatasetProperties, read_only: bool
)

Bases: Generic[LayerType, SegmentationLayerType]

default_view_configuration property writable 

default_view_configuration: DatasetViewConfiguration | None

Default view configuration for this dataset in webknossos.

Controls how the dataset is displayed in webknossos when first opened by a user, including position, zoom level, rotation etc.

Returns:

Examples:

ds.default_view_configuration = DatasetViewConfiguration(
    zoom=1.5,
    position=(100, 100, 100)
)

layers property 

layers: Mapping[str, LayerType]

Dictionary containing all layers of this dataset.

Returns:

  • Mapping[str, LayerType] –

    dict[str, Layer]: Dictionary mapping layer names to Layer objects

Examples:

for layer_name, layer in ds.layers.items():
   print(layer_name)

name property writable 

name: str

Name of this dataset as specified in datasource-properties.json.

Can be modified to rename the dataset. Changes are persisted to the properties file.

Returns:

  • str ( str ) –

    Current dataset name

Examples:

ds.name = "my_renamed_dataset"  # Updates the name in properties file

read_only property 

read_only: bool

Whether this dataset is opened in read-only mode.

When True, operations that would modify the dataset (adding layers, changing properties, etc.) are not allowed and will raise RuntimeError.

Returns:

  • bool ( bool ) –

    True if dataset is read-only, False otherwise

voxel_size property 

voxel_size: tuple[float, float, float]

Size of each voxel in nanometers along each dimension (x, y, z).

Returns:

  • tuple[float, float, float] –

    tuple[float, float, float]: Size of each voxel in nanometers for x,y,z dimensions

Examples:

vx, vy, vz = ds.voxel_size
print(f"X resolution is {vx}nm")

voxel_size_with_unit property 

voxel_size_with_unit: VoxelSize

Size of voxels including unit information.

Size of each voxel along each dimension (x, y, z), including unit specification. The default unit is nanometers.

Returns:

  • VoxelSize ( VoxelSize ) –

    Object containing voxel sizes and their units

calculate_bounding_box 

calculate_bounding_box() -> NDBoundingBox

Calculate the enclosing bounding box of all layers.

Finds the smallest box that contains all data from all layers in the dataset.

Returns:

  • NDBoundingBox ( NDBoundingBox ) –

    Bounding box containing all layer data

Examples:

bbox = ds.calculate_bounding_box()
print(f"Dataset spans {bbox.size} voxels")
print(f"Dataset starts at {bbox.topleft}")

get_color_layers 

get_color_layers() -> list[LayerType]

Get all color layers in the dataset.

Provides access to all layers with category 'color'. Useful when a dataset contains multiple color layers.

Returns:

  • list[LayerType] –

    list[Layer]: List of all color layers in order

Examples:

Print all color layer names: 

for layer in ds.get_color_layers():
    print(layer.name)
Note

If you need only a single color layer, consider using get_layer() with the specific layer name instead.

get_layer 

get_layer(layer_name: str) -> LayerType

Get a specific layer from this dataset.

Parameters:

  • layer_name (str) –

    Name of the layer to retrieve

Returns:

  • Layer ( LayerType ) –

    The requested layer object

Raises:

  • IndexError –

    If no layer with the given name exists

Examples:

color_layer = ds.get_layer("color")
seg_layer = ds.get_layer("segmentation")
Note

Use layers property to access all layers at once.

get_segmentation_layer 

get_segmentation_layer(
    layer_name: str,
) -> SegmentationLayerType

Get a segmentation layer by name.

Parameters:

  • layer_name (str) –

    Name of the layer to get

Returns:

  • SegmentationLayer ( SegmentationLayerType ) –

    The segmentation layer

get_segmentation_layers 

get_segmentation_layers() -> list[SegmentationLayerType]

Get all segmentation layers in the dataset.

Provides access to all layers with category 'segmentation'. Useful when a dataset contains multiple segmentation layers.

Returns:

  • list[SegmentationLayerType] –

    list[SegmentationLayer]: List of all segmentation layers in order

Examples:

Print all segmentation layer names: 

for layer in ds.get_segmentation_layers():
    print(layer.name)
Note

If you need only a single segmentation layer, consider using get_layer() with the specific layer name instead.