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webknossos.dataset_properties.dataset_properties

AttachmentProperties

data_format instance-attribute 

data_format: AttachmentDataFormat

name instance-attribute 

name: str

path instance-attribute 

path: str

AttachmentsProperties

agglomerates class-attribute instance-attribute 

agglomerates: list[AttachmentProperties] | None = None

connectomes class-attribute instance-attribute 

connectomes: list[AttachmentProperties] | None = None

cumsum class-attribute instance-attribute 

cumsum: AttachmentProperties | None = None

meshes class-attribute instance-attribute 

meshes: list[AttachmentProperties] | None = None

segment_index class-attribute instance-attribute 

segment_index: AttachmentProperties | None = None

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]

id is a legacy field that is not used anymore. Its keys are name (dataset directory name) and team (organization id) However, webknossos will take both from the dataset path and not from what is here in the datasource-properties.json.

scale instance-attribute 

scale: VoxelSize

version instance-attribute 

version: int

A default version is set during structuring

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

Could be None for older datasource-proterties.json files.

SegmentationLayerProperties

Bases: LayerProperties

attachments class-attribute instance-attribute 

attachments: AttachmentsProperties = field(
    factory=AttachmentsProperties
)

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]