layers

ngtools.layers

A neuroglancer scene with a programmatic interface.

LayerFactory

Bases: type

Metaclass for layers.

call

__call__(arg=None, *args, **kwargs)

Parameters:

Name	Type	Description	Default
`arg`	`ng.Layer or [list of] (str \| dict \| None)`		`None`

Layer

Layer(*args, **kwargs)

Bases: Wraps(Layer)

Base class for all layers.

See ImageLayer, SegmentationLayer, MeshLayer for keyword-parameters specific to these layers types.

Parameters:

Name	Type	Description	Default
`json_data`	`dict \| Layer \| LayerDataSource \| str`	Either a Layer (or its JSON representation), or a data source (or its JSON representation).	required

Other Parameters:

Name	Type	Description
`type`	`(image, segmentation, mesh, annotation, pointAnnotation)`	Layer type -- guessed from source by default.
`source`	`[list of] LayerDataSource \| str`	Data source. Except if layer is a `PointAnnotationLayer`.
`layer_dimensions`	`CoordinateSpace`	Local dimensions specific to the layer.
`layer_position`	`CoordinateSpace`	Position within the local dimensions.
`local_velocity`	`DimensionPlaybackVelocity`	Speed for playback along local dimensions.
`tab`	`str`
`panels`	`list[LayerSidePanelState]`
`pick`	`bool`
`tool_bindings`	`dict[str, Tool \| str]`	Key binding to tools, specific to this layer.
`tool`	`Tool \| str`	Active tool (or tool name).

apply_transform

apply_transform(*args)

Apply an additional transform in model space.

ImageLayer

ImageLayer(*args, **kwargs)

Bases: _SourceMixin, Wraps(ImageLayer), Layer

Image layer.

See Layer for keyword parameters common to all layers.

Other Parameters:

Name	Type	Description
`source`	`[list of] LayerDataSource \| str`
`shader`	`str`	Default shader: `#uicontrol invlerp normalized void main() { emitGrayscale(normalized()); }`
`shader_controls`	`dict[str, float \| dict \| InvlerpParameters \| TransferFunctionParameters]`	InvlerpParameters: range: tuple[float, float] window: tuple[float, float] channel: list[int] TransferFunctionParameters: window: tuple[float, float] channel: list[int] controlPoints : list[list[float]] defaultColor : str
`opacity`	`float`
`blend`	`(default, additive)`
`volume_rendering_mode`	`bool \| {off, on, max, min}`
`volume_rendering_gain`	`float`
`volume_rendering_depth_samples`	`float`
`cross_section_render_scale`	`float`

apply_transform

apply_transform(*args)

Apply an additional transform in model space.

SegmentationLayer

SegmentationLayer(*args, **kwargs)

Bases: _SourceMixin, Wraps(SegmentationLayer), Layer

Segmentation layer.

See Layer for keyword parameters common to all layers.

Other Parameters:

Name	Type	Description
`source`	`[list of] LayerDataSource \| str`
`starred_segments`	`StarredSegments \| dict[int, bool]`
`equivalences`	`EquivalenceMap \| list[list[int]]`
`hide_segment_zero`	`bool`
`hover_highlight`	`bool`
`base_segment_coloring`	`bool`
`selected_alpha`	`float`
`not_selected_alpha`	`float`
`object_alpha`	`float`
`saturation`	`float`
`ignore_null_visible_set`	`bool`
`skeleton_rendering`	`SkeletonRenderingOptions \| dict`	shader : str, optional shader_controls : dict[str, float \| dict \| ng.InvlerpParameters \| ng.TransferFunctionParameters] - InvlerpParameters: range: tuple[float, float] window: tuple[float, float] channel: list[int] - TransferFunctionParameters: window: tuple[float, float] channel: list[int] controlPoints : list[list[float]] defaultColor : str mode2d : {"lines", "lines_and_points"}, optional line_width2d : float, default=2 mode3d: {"lines", "lines_and_points"}, optional line_width3d : float, default=3
`color_seed`	`int`
`cross_section_render_scale`	`float`
`mesh_render_scale`	`float`
`mesh_silhouette_rendering`	`float`
`segment_query`	`str`
`segment_colors`	`dict[uint64, str]`
`segment_default_color`	`str`
`linked_segmentation_group`	`str`
`linked_segmentation_color_group`	`str \| False`

apply_transform

apply_transform(*args)

Apply an additional transform in model space.

SkeletonLayerFactory

Bases: LayerFactory

Factory for skeletons.

SkeletonLayer

SkeletonLayer(*args, **kwargs)

Bases: SegmentationLayer

Skeleton layer.

apply_transform

apply_transform(*args)

Apply an additional transform in model space.

TractLayer

TractLayer(arg=None, *args, **kwargs)

Bases: SkeletonLayer

Tract layer.

apply_transform

apply_transform(*args)

Apply an additional transform in model space.

MeshLayer

MeshLayer(*args, **kwargs)

Bases: Layer

Common ancestors to all mesh layers.

See also: SingleMeshLayer, MultiscaleMeshLayer

apply_transform

apply_transform(*args)

Apply an additional transform in model space.

SingleMeshLayer

SingleMeshLayer(*args, **kwargs)

Bases: _SourceMixin, Wraps(SingleMeshLayer), MeshLayer

Single mesh layer.

See Layer for keyword parameters common to all layers.

See also: MeshLayer, MultiscaleMeshLayer.

Other Parameters:

Name	Type	Description
`source`	`[list of] LayerDataSource \| str`
`vertex_attribute_sources`	`list[str]`
`shader`	`str`	Default shader: `void main() { emitGray(); }`
`vertex_attribute_names`	`list[str]`

apply_transform

apply_transform(*args)

Apply an additional transform in model space.

MultiscaleMeshLayer

MultiscaleMeshLayer(*args, **kwargs)

Bases: SegmentationLayer

Multiscale mesh layer.

See also: MeshLayer, SingleMeshLayer.

Other Parameters:

Name	Type	Description
`render_scale`	`float`
`silhouette_rendering`	`float`

apply_transform

apply_transform(*args)

Apply an additional transform in model space.

AnnotationLayer

AnnotationLayer(*args, **kwargs)

Bases: _SourceMixin, Wraps(AnnotationLayer), Layer

Annotation layer.

See Layer for keyword parameters common to all layers.

Other Parameters:

Name	Type	Description
`source`	`[list of] LayerDataSource \| str`
`annotations`	`list[AnnotationBase \| dict]`	Valid annotations: `{ "point": PointAnnotation, "line": LineAnnotation, "axis_aligned_bounding_box": AxisAlignedBoundingBoxAnnotation, "ellipsoid": EllipsoidAnnotation, }`
`annotation_properties`	`list[AnnotationPropertySpec \| dict]`	id : str type : str description : str default : float \| str enum_values : list[int \| str] enum_labels : list[str]
`annotation_relationships`	`list[str]`
`linked_segmentation_layer`	`dict[str, str]`
`filter_by_segmentation`	`list[str]`
`ignore_null_segment_filter`	`bool`
`shader`	`str`	Default shader: `void main() { setColor(defaultColor()); }`
`shader_controls`	`dict[str, float \| dict \| InvlerpParameters \| TransferFunctionParameters]`	InvlerpParameters: range: tuple[float, float] window: tuple[float, float] channel: list[int] TransferFunctionParameters: window: tuple[float, float] channel: list[int] controlPoints : list[list[float]] defaultColor : str

apply_transform

apply_transform(*args)

Apply an additional transform in model space.

TractAnnotationLayer

TractAnnotationLayer(*args, **kwargs)

Bases: AnnotationLayer

Tract annotation layer.

apply_transform

apply_transform(*args)

Apply an additional transform in model space.

LocalAnnotationLayer

LocalAnnotationLayer(*args, **kwargs)

Bases: Wraps(LocalAnnotationLayer), AnnotationLayer

TODO.

apply_transform

apply_transform(*args)

Apply an additional transform in model space.

PointAnnotationLayer

PointAnnotationLayer(*args, **kwargs)

Bases: Wraps(PointAnnotationLayer), Layer

Point annotation layer.

Parameters:

Name	Type	Description	Default
`points`	`list[tuple[float, float, float]]`		required

apply_transform

apply_transform(*args)

Apply an additional transform in model space.

ManagedLayer

ManagedLayer(*args, **kwargs)

Bases: Wraps(ManagedLayer), _SourceMixin

Named layer.

Layers

Bases: Wraps(Layers)

List of named layers.