webknossos.dataset.properties

AxisProperties

bounds instance-attribute

bounds: tuple[int, int]

index instance-attribute

index: int

name instance-attribute

name: str

DatasetProperties

data_layers instance-attribute

data_layers: list[SegmentationLayerProperties | LayerProperties]

default_view_configuration class-attribute instance-attribute

default_view_configuration: DatasetViewConfiguration | None = None

id instance-attribute

id: dict[str, str]

scale instance-attribute

scale: VoxelSize

version instance-attribute

version: Literal[1]

update_for_layer

update_for_layer(layer_name: str, layer_properties: LayerProperties) -> None

DatasetViewConfiguration

Stores information on how the dataset is shown in webknossos by default.

four_bit class-attribute instance-attribute

four_bit: bool | None = None

interpolation class-attribute instance-attribute

interpolation: bool | None = None

loading_strategy class-attribute instance-attribute

loading_strategy: str | None = None

position class-attribute instance-attribute

position: tuple[int, int, int] | None = None

render_missing_data_black class-attribute instance-attribute

render_missing_data_black: bool | None = None

rotation class-attribute instance-attribute

rotation: tuple[int, int, int] | None = None

segmentation_pattern_opacity class-attribute instance-attribute

segmentation_pattern_opacity: int | None = None

zoom class-attribute instance-attribute

zoom: float | None = None

LayerProperties

bounding_box instance-attribute

bounding_box: NDBoundingBox

category instance-attribute

category: LayerCategoryType

data_format instance-attribute

data_format: DataFormat

default_view_configuration class-attribute instance-attribute

default_view_configuration: LayerViewConfiguration | None = None

element_class instance-attribute

element_class: str

mags instance-attribute

mags: list[MagViewProperties]

name instance-attribute

name: str

num_channels class-attribute instance-attribute

num_channels: int | None = None

LayerViewConfiguration

Stores information on how the dataset is shown in webknossos by default.

alpha class-attribute instance-attribute

alpha: float | None = None

Alpha value from 0 to 100. The WEBKNOSSOS default is 100 except for segmentation layers where it is 20.

color class-attribute instance-attribute

color: tuple[int, int, int] | None = None

Color in RGB from 0 to 255. The WEBKNOSSOS default is [255, 255, 255].

intensity_range class-attribute instance-attribute

intensity_range: tuple[float, float] | None = None

Min and max data value range (dependent on the layer's data type). Can be used to threshold the value range. The WEBKNOSSOS default is the full value range.

is_disabled class-attribute instance-attribute

is_disabled: bool | None = None

Disable a layer. The WEBKNOSSOS default is False.

is_in_edit_mode class-attribute instance-attribute

is_in_edit_mode: bool | None = None

Enable the histogram edit mode. The WEBKNOSSOS default is False.

is_inverted class-attribute instance-attribute

is_inverted: bool | None = None

Invert a layer. The WEBKNOSSOS default is False.

mapping class-attribute instance-attribute

mapping: dict[str, str] | None = None

Enables ID mapping for a segmentation layer and applies the selected mapping by default. The default WK behavior is to disable ID mapping. Expected values is a Dict with {"name": my_mapping_name, "type": "HDF5"}.

max class-attribute instance-attribute

max: float | None = None

Maximum data value that might be encountered. This will restrict the histogram in WEBKNOSSOS and possibly overwrite the max value of the intensityRange (if that is higher).

min class-attribute instance-attribute

min: float | None = None

Minimum data value that might be encountered. This will restrict the histogram in WEBKNOSSOS and possibly overwrite the min value of the intensityRange (if that is lower).

MagViewProperties

axis_order class-attribute instance-attribute

axis_order: dict[str, int] | None = None

cube_length class-attribute instance-attribute

cube_length: int | None = None

mag instance-attribute

mag: Mag

path class-attribute instance-attribute

path: str | None = None

SegmentationLayerProperties

Bases: LayerProperties

bounding_box instance-attribute

bounding_box: NDBoundingBox

category instance-attribute

category: LayerCategoryType

data_format instance-attribute

data_format: DataFormat

default_view_configuration class-attribute instance-attribute

default_view_configuration: LayerViewConfiguration | None = None

element_class instance-attribute

element_class: str

largest_segment_id class-attribute instance-attribute

largest_segment_id: int | None = None

mags instance-attribute

mags: list[MagViewProperties]

mappings class-attribute instance-attribute

mappings: list[str] = []

name instance-attribute

name: str

num_channels class-attribute instance-attribute

num_channels: int | None = None

VoxelSize

factor class-attribute instance-attribute

factor: tuple[float, float, float] = field(converter=float_tpl)

unit class-attribute instance-attribute

unit: LengthUnit = DEFAULT_LENGTH_UNIT

to_nanometer

to_nanometer() -> tuple[float, float, float]

SegmentationLayerProperties

Bases: LayerProperties

bounding_box instance-attribute

bounding_box: NDBoundingBox

category instance-attribute

category: LayerCategoryType

data_format instance-attribute

data_format: DataFormat

default_view_configuration class-attribute instance-attribute

default_view_configuration: LayerViewConfiguration | None = None

element_class instance-attribute

element_class: str

largest_segment_id class-attribute instance-attribute

largest_segment_id: int | None = None

mags instance-attribute

mags: list[MagViewProperties]

mappings class-attribute instance-attribute

mappings: list[str] = []

name instance-attribute

name: str

num_channels class-attribute instance-attribute

num_channels: int | None = None

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