napari.layers.Labels#

class napari.layers.Labels(data, *, affine=None, axis_labels=None, blending='translucent', cache=True, colormap=None, depiction='volume', experimental_clipping_planes=None, features=None, iso_gradient_mode='fast', metadata=None, multiscale=None, name=None, opacity=0.7, plane=None, projection_mode='none', properties=None, rendering='iso_categorical', rotate=None, scale=None, shear=None, translate=None, units=None, visible=True)[source]#

Bases: ScalarFieldBase

Labels (or segmentation) layer.

An image-like layer where every pixel contains an integer ID corresponding to the region it belongs to.

Parameters:

data (array or list of array) – Labels data as an array or multiscale. Must be integer type or bools. Please note multiscale rendering is only supported in 2D. In 3D, only the lowest resolution scale is displayed.
affine (n-D array or napari.utils.transforms.Affine) – (N+1, N+1) affine transformation matrix in homogeneous coordinates. The first (N, N) entries correspond to a linear transform and the final column is a length N translation vector and a 1 or a napari Affine transform object. Applied as an extra transform on top of the provided scale, rotate, and shear values.
axis_labels (tuple of str, optional) – Dimension names of the layer data. If not provided, axis_labels will be set to (…, ‘axis -2’, ‘axis -1’).
blending (str) – One of a list of preset blending modes that determines how RGB and alpha values of the layer visual get mixed. Allowed values are {‘opaque’, ‘translucent’, and ‘additive’}.
cache (bool) – Whether slices of out-of-core datasets should be cached upon retrieval. Currently, this only applies to dask arrays.
colormap (CyclicLabelColormap or DirectLabelColormap or None) – Colormap to use for the labels. If None, a random colormap will be used.
depiction (str) – 3D Depiction mode. Must be one of {‘volume’, ‘plane’}. The default value is ‘volume’.
experimental_clipping_planes (list of dicts, list of ClippingPlane, or ClippingPlaneList) – Each dict defines a clipping plane in 3D in data coordinates. Valid dictionary keys are {‘position’, ‘normal’, and ‘enabled’}. Values on the negative side of the normal are discarded if the plane is enabled.
features (dict[str, array-like] or DataFrame) – Features table where each row corresponds to a label and each column is a feature. The first row corresponds to the background label.
iso_gradient_mode (str) – Method for calulating the gradient (used to get the surface normal) in the ‘iso_categorical’ rendering mode. Must be one of {‘fast’, ‘smooth’}. ‘fast’ uses a simple finite difference gradient in x, y, and z. ‘smooth’ uses an isotropic Sobel gradient, which is smoother but more computationally expensive. The default value is ‘fast’.
metadata (dict) – Layer metadata.
multiscale (bool) – Whether the data is a multiscale image or not. Multiscale data is represented by a list of array like image data. If not specified by the user and if the data is a list of arrays that decrease in shape then it will be taken to be multiscale. The first image in the list should be the largest. Please note multiscale rendering is only supported in 2D. In 3D, only the lowest resolution scale is displayed.
name (str) – Name of the layer.
opacity (float) – Opacity of the layer visual, between 0.0 and 1.0.
plane (dict or SlicingPlane) – Properties defining plane rendering in 3D. Properties are defined in data coordinates. Valid dictionary keys are {‘position’, ‘normal’, ‘thickness’, and ‘enabled’}.
projection_mode (str) – How data outside the viewed dimensions but inside the thick Dims slice will be projected onto the viewed dimensions
properties (dict {str: array (N,)} or DataFrame) – Properties for each label. Each property should be an array of length N, where N is the number of labels, and the first property corresponds to background.
rendering (str) – 3D Rendering mode used by vispy. Must be one {‘translucent’, ‘iso_categorical’}. ‘translucent’ renders without lighting. ‘iso_categorical’ uses isosurface rendering to calculate lighting effects on labeled surfaces. The default value is ‘iso_categorical’.
rotate (float, 3-tuple of float, or n-D array.) – If a float convert into a 2D rotation matrix using that value as an angle. If 3-tuple convert into a 3D rotation matrix, using a yaw, pitch, roll convention. Otherwise assume an nD rotation. Angles are assumed to be in degrees. They can be converted from radians with np.degrees if needed.
scale (tuple of float) – Scale factors for the layer.
shear (1-D array or n-D array) – Either a vector of upper triangular values, or an nD shear matrix with ones along the main diagonal.
translate (tuple of float) – Translation values for the layer.
units (tuple of str or pint.Unit, optional) – Units of the layer data in world coordinates. If not provided, the default units are assumed to be pixels.
visible (bool) – Whether the layer visual is currently being displayed.

data#

Integer label data as an array or multiscale. Can be N dimensional. Every pixel contains an integer ID corresponding to the region it belongs to. The label 0 is rendered as transparent. Please note multiscale rendering is only supported in 2D. In 3D, only the lowest resolution scale is displayed.

Type:: array or list of array

axis_labels#

Dimension names of the layer data.

Type:: tuple of str

multiscale#

Whether the data is a multiscale image or not. Multiscale data is represented by a list of array like image data. The first image in the list should be the largest. Please note multiscale rendering is only supported in 2D. In 3D, only the lowest resolution scale is displayed.

Type:: bool

metadata#

Labels metadata.

Type:: dict

num_colors#

Number of unique colors to use in colormap. DEPRECATED: set colormap directly, using napari.utils.colormaps.label_colormap.

Type:: int

features#

Features table where each row corresponds to a label and each column is a feature. The first row corresponds to the background label.

Type:: Dataframe-like

properties#

Properties for each label. Each property should be an array of length N, where N is the number of labels, and the first property corresponds to background.

Type:: dict {str: array (N,)}, DataFrame

color#

Custom label to color mapping. Values must be valid color names or RGBA arrays. While there is no limit to the number of custom labels, the the layer will render incorrectly if they map to more than 1024 distinct colors. DEPRECATED: set colormap directly, using napari.utils.colormaps.DirectLabelColormap.

Type:: dict of int to str or array

seed#

Seed for colormap random generator. DEPRECATED: set colormap directly, using napari.utils.colormaps.label_colormap.

Type:: float

opacity#

Opacity of the labels, must be between 0 and 1.

Type:: float

contiguous#

If True, the fill bucket changes only connected pixels of same label.

Type:: bool

n_edit_dimensions#

The number of dimensions across which labels will be edited.

Type:: int

contour#

If greater than 0, displays contours of labels instead of shaded regions with a thickness equal to its value. Must be >= 0.

Type:: int

brush_size#

Size of the paint brush in data coordinates.

Type:: float

selected_label#

Index of selected label. Can be greater than the current maximum label.

Type:: int

mode#

Interactive mode. The normal, default mode is PAN_ZOOM, which allows for normal interactivity with the canvas.

In PICK mode the cursor functions like a color picker, setting the clicked on label to be the current label. If the background is picked it will select the background label 0.

In PAINT mode the cursor functions like a paint brush changing any pixels it brushes over to the current label. If the background label 0 is selected than any pixels will be changed to background and this tool functions like an eraser. The size and shape of the cursor can be adjusted in the properties widget.

In FILL mode the cursor functions like a fill bucket replacing pixels of the label clicked on with the current label. It can either replace all pixels of that label or just those that are contiguous with the clicked on pixel. If the background label 0 is selected than any pixels will be changed to background and this tool functions like an eraser.

In ERASE mode the cursor functions similarly to PAINT mode, but to paint with background label, which effectively removes the label.

Type:: str

plane#

Properties defining plane rendering in 3D.

Type:: SlicingPlane

experimental_clipping_planes#

Clipping planes defined in data coordinates, used to clip the volume.

Type:: ClippingPlaneList

units#

Units of the layer data in world coordinates.

Type:: tuple of pint.Unit

Notes

_selected_color4-tuple or None: RGBA tuple of the color of the selected label, or None if the background label 0 is selected.

Methods

`as_layer_data_tuple`()
`bind_key`(key_bind[, func, overwrite])	Bind a key combination to a keymap.
`block_history`()	Context manager to group history-editing operations together.
`block_update_properties`()
`click_plane_from_click_data`(click_position, ...)	Calculate a (point, normal) plane parallel to the canvas in data coordinates, centered on the centre of rotation of the camera.
`create`(data[, meta, layer_type])	Create layer from data of type layer_type.
`data_setitem`(indices, value[, refresh])	Set indices in data to value, while writing to edit history.
`data_to_world`(position)	Convert from data coordinates to world coordinates.
`fill`(coord, new_label[, refresh])	Replace an existing label with a new label, either just at the connected component if the contiguous flag is True or everywhere if it is False, working in the number of dimensions specified by the n_edit_dimensions flag.
`get_color`(label)	Return the color corresponding to a specific label.
`get_ray_intersections`(position, ...[, world])	Get the start and end point for the ray extending from a point through the data bounding box.
`get_source_str`()
`get_status`([position, view_direction, ...])	Status message information of the data at a coordinate position.
`get_value`(position, *[, view_direction, ...])	Value of the data at a position.
`new_colormap`([seed])
`paint`(coord, new_label[, refresh])	Paint over existing labels with a new label, using the selected brush shape and size, either only on the visible slice or in all n dimensions.
`paint_polygon`(points, new_label)	Paint a polygon over existing labels with a new label.
`projected_distance_from_mouse_drag`(...)	Calculate the length of the projection of a line between two mouse clicks onto a vector (or array of vectors) in data coordinates.
`redo`()
`refresh`([event, thumbnail, data_displayed, ...])	Refresh all layer data based on current view slice.
`save`(path[, plugin])	Save this layer to `path` with default (or specified) plugin.
`set_view_slice`()
`swap_selected_and_background_labels`()	Swap between the selected label and the background label.
`undo`()
`update_transform_box_visibility`(visible)
`world_to_data`(position)	Convert from world coordinates to data coordinates.

Attributes

`ModeCallable`	alias of `Callable`[[`Layer`, `Event`], `None` \| `Generator`[`None`, `None`, `None`]]
`affine`	Extra affine transform to go from physical to world coordinates.
`axis_labels`	tuple of axis labels for the layer.
`blending`	Determines how RGB and alpha values get mixed.
`bounding_box`
`brush_size`	Size of the paint in world coordinates.
`brush_size_on_mouse_move`
`class_keymap`
`colormap`
`contiguous`	fill bucket changes only connected pixels of same label.
`contour`	displays contours of labels instead of shaded regions.
`cursor`	String identifying cursor displayed over canvas.
`cursor_size`	Size of cursor if custom.
`custom_interpolation_kernel_2d`
`data`	Image data.
`data_level`	Current level of multiscale, or 0 if image.
`data_raw`	Data, exactly as provided by the user.
`depiction`	The current 3D depiction mode.
`downsample_factors`	Downsample factors for each level of the multiscale.
`dtype`
`editable`	Whether the current layer data is editable from the viewer.
`experimental_clipping_planes`
`extent`	Extent of layer in data and world coordinates.
`features`	Dataframe-like features table.
`help`	displayed in status bar bottom right.
`interactive`
`iso_gradient_mode`	Return current gradient mode for isosurface rendering.
`keymap`
`level_shapes`	Shapes of each level of the multiscale or just of image.
`loaded`	True if this layer is fully loaded in memory, False otherwise.
`metadata`	Key/value map for user-stored data.
`mode`	Interactive mode.
`mouse_pan`	Determine if canvas interactive panning is enabled with the mouse.
`mouse_zoom`	Determine if canvas interactive zooming is enabled with the mouse.
`n_edit_dimensions`
`name`	Unique name of the layer.
`ndim`	Number of dimensions in the data.
`opacity`	Opacity value between 0.0 and 1.0.
`plane`
`preserve_labels`	Defines if painting should preserve existing labels.
`projection_mode`	Mode of projection of the thick slice onto the viewed dimensions.
`properties`	Properties for each label.
`rendering`	Return current rendering mode.
`rotate`	Rotation matrix in world coordinates.
`scale`	Anisotropy factors to scale data into world coordinates.
`selected_label`	Index of selected label.
`shear`	Shear matrix in world coordinates.
`show_selected_label`	Whether to filter displayed labels to only the selected label or not
`source`
`thumbnail`	Integer array of thumbnail for the layer
`translate`	Factors to shift the layer by in units of world coordinates.
`unique_id`	Unique ID of the layer.
`units`	List of units for the layer.
`visible`	Whether the visual is currently being displayed.

Details

property affine: Affine#

Extra affine transform to go from physical to world coordinates.

Type:: napari.utils.transforms.Affine

property axis_labels: tuple[str, ...]#: tuple of axis labels for the layer.

bind_key(key_bind: ~app_model.types._keys._keybindings.KeyBinding | str | int | ellipsis, func=<object object>, *, overwrite=False)#

Bind a key combination to a keymap.

Parameters:

keymap (dict of str: callable) – Keymap to modify.
key_bind (keybinding-like or ...) – Key combination. ... acts as a wildcard if no key combinations can be matched in the keymap (this will overwrite all key combinations further down the lookup chain).
func (callable, None, or ...) – Callable to bind to the key combination. If None is passed, unbind instead. ... acts as a blocker, effectively unbinding the key combination for all keymaps further down the lookup chain.
overwrite (bool, keyword-only, optional) – Whether to overwrite the key combination if it already exists.

Returns:

unbound – Callable unbound by this operation, if any.

Return type:

callable or None

Notes

Key combinations are represented in the form [modifier-]key, e.g. a, Control-c, or Control-Alt-Delete. Valid modifiers are Control, Alt, Shift, and Meta.

Letters will always be read as upper-case. Due to the native implementation of the key system, Shift pressed in certain key combinations may yield inconsistent or unexpected results. Therefore, it is not recommended to use Shift with non-letter keys. On OSX, Control is swapped with Meta such that pressing Command reads as Control.

Special keys include Shift, Control, Alt, Meta, Up, Down, Left, Right, PageUp, PageDown, Insert, Delete, Home, End, Escape, Backspace, F1, F2, F3, F4, F5, F6, F7, F8, F9, F10, F11, F12, Space, Enter, and Tab

Functions take in only one argument: the parent that the function was bound to.

By default, all functions are assumed to work on key presses only, but can be denoted to work on release too by separating the function into two statements with the yield keyword:

@viewer.bind_key('h')
def hello_world(viewer):
    # on key press
    viewer.status = 'hello world!'

    yield

    # on key release
    viewer.status = 'goodbye world :('

To create a keymap that will block others, bind_key(..., ...)`.

property blending: str#

Determines how RGB and alpha values get mixed.

Blending.OPAQUE: Allows for only the top layer to be visible and corresponds to depth_test=True, cull_face=False, blend=False.
Blending.TRANSLUCENT: Allows for multiple layers to be blended with different opacity and corresponds to depth_test=True, cull_face=False, blend=True, blend_func=(‘src_alpha’, ‘one_minus_src_alpha’), and blend_equation=(‘func_add’).
Blending.TRANSLUCENT_NO_DEPTH: Allows for multiple layers to be blended with different opacity, but no depth testing is performed. Corresponds to depth_test=False, cull_face=False, blend=True, blend_func=(‘src_alpha’, ‘one_minus_src_alpha’), and blend_equation=(‘func_add’).
Blending.ADDITIVE: Allows for multiple layers to be blended together with different colors and opacity. Useful for creating overlays. It corresponds to depth_test=False, cull_face=False, blend=True, blend_func=(‘src_alpha’, ‘one’), and blend_equation=(‘func_add’).
Blending.MINIMUM: Allows for multiple layers to be blended together such that the minimum of each RGB component and alpha are selected. Useful for creating overlays with inverted colormaps. It corresponds to depth_test=False, cull_face=False, blend=True, blend_equation=(‘min’).

Type:: Blending mode

block_history()[source]#

Context manager to group history-editing operations together.

While in the context, history atoms are grouped together into a “staged” history. When exiting the context, that staged history is committed to the undo history queue, and an event is emitted containing the change.

property brush_size#

Size of the paint in world coordinates.

Type:: float

click_plane_from_click_data(click_position: npt.ArrayLike, view_direction: npt.ArrayLike, dims_displayed: list[int]) → tuple[np.ndarray, np.ndarray]#

Calculate a (point, normal) plane parallel to the canvas in data coordinates, centered on the centre of rotation of the camera.

Parameters:

click_position (np.ndarray) – click position in world coordinates from mouse event.
view_direction (np.ndarray) – view direction in world coordinates from mouse event.
dims_displayed (List[int]) – dimensions of the data array currently in view.

Returns:

click_plane – tuple of (plane_position, plane_normal) in data coordinates.

Return type:

Tuple[np.ndarray, np.ndarray]

property contiguous#

fill bucket changes only connected pixels of same label.

Type:: bool

property contour: int#

displays contours of labels instead of shaded regions.

Type:: int

classmethod create(data: Any, meta: dict | None = None, layer_type: str | None = None) → Layer#

Create layer from data of type layer_type.

Primarily intended for usage by reader plugin hooks and creating a layer from an unwrapped layer data tuple.

Parameters:

data (Any) – Data in a format that is valid for the corresponding layer_type.
meta (dict, optional) – Dict of keyword arguments that will be passed to the corresponding layer constructor. If any keys in meta are not valid for the corresponding layer type, an exception will be raised.
layer_type (str) – Type of layer to add. Must be the (case insensitive) name of a Layer subclass. If not provided, the layer is assumed to be “image”, unless data.dtype is one of (np.int32, np.uint32, np.int64, np.uint64), in which case it is assumed to be “labels”.

Raises:

ValueError – If layer_type is not one of the recognized layer types.
TypeError – If any keyword arguments in meta are unexpected for the corresponding add_* method for this layer_type.

Examples

A typical use case might be to upack a tuple of layer data with a specified layer_type.

>>> data = (
...     np.random.random((10, 2)) * 20,
...     {'face_color': 'blue'},
...     'points',
... )
>>> Layer.create(*data)

property cursor: str#

String identifying cursor displayed over canvas.

Type:: str

property cursor_size: int#

Size of cursor if custom. None yields default size.

Type:: int

property data: LayerDataProtocol | MultiScaleData#

Image data.

Type:: array

property data_level: int#

Current level of multiscale, or 0 if image.

Type:: int

property data_raw: LayerDataProtocol | Sequence[LayerDataProtocol]#: Data, exactly as provided by the user.

data_setitem(indices, value, refresh=True)[source]#

Set indices in data to value, while writing to edit history.

Parameters:

indices (tuple of arrays of int) – Indices in data to overwrite. Must be a tuple of arrays of length equal to the number of data dimensions. (Fancy indexing in [2]).
value (int or array of int) – New label value(s). If more than one value, must match or broadcast with the given indices.
refresh (bool, default True) – whether to refresh the view, by default True

References

data_to_world(position)#

Convert from data coordinates to world coordinates.

Parameters:: position (tuple, list, 1D array) – Position in data coordinates. If longer then the number of dimensions of the layer, the later dimensions will be used.
Returns:: Position in world coordinates.
Return type:: tuple

property depiction#

The current 3D depiction mode.

Selects a preset depiction mode in vispy

volume: images are rendered as 3D volumes.
plane: images are rendered as 2D planes embedded in 3D.
plane position, normal, and thickness are attributes of layer.plane which can be modified directly.

property downsample_factors: ndarray#

Downsample factors for each level of the multiscale.

Type:: list

property editable: bool#

Whether the current layer data is editable from the viewer.

Type:: bool

property extent: Extent#

Extent of layer in data and world coordinates.

For image-like layers, these coordinates are the locations of the pixels in Layer.data which are treated like sample points that are centered in the rendered version of those pixels. For other layers, these coordinates are the points or vertices stored in Layer.data. Lower and upper bounds are inclusive.

property features#

Dataframe-like features table.

It is an implementation detail that this is a pandas.DataFrame. In the future, we will target the currently-in-development Data API dataframe protocol [1]. This will enable us to use alternate libraries such as xarray or cuDF for additional features without breaking existing usage of this.

If you need to specifically rely on the pandas API, please coerce this to a pandas.DataFrame using features_to_pandas_dataframe.

References

fill(coord, new_label, refresh=True)[source]#

Replace an existing label with a new label, either just at the connected component if the contiguous flag is True or everywhere if it is False, working in the number of dimensions specified by the n_edit_dimensions flag.

Parameters:

coord (sequence of float) – Position of mouse cursor in image coordinates.
new_label (int) – Value of the new label to be filled in.
refresh (bool) – Whether to refresh view slice or not. Set to False to batch paint calls.

get_color(label)[source]#: Return the color corresponding to a specific label.

get_ray_intersections(position: npt.ArrayLike, view_direction: npt.ArrayLike, dims_displayed: list[int], world: bool = True) → tuple[np.ndarray | None, np.ndarray | None]#

Get the start and end point for the ray extending from a point through the data bounding box.

Parameters:

position – the position of the point in nD coordinates. World vs. data is set by the world keyword argument.
view_direction (np.ndarray) – a unit vector giving the direction of the ray in nD coordinates. World vs. data is set by the world keyword argument.
dims_displayed (List[int]) – a list of the dimensions currently being displayed in the viewer.
world (bool) – True if the provided coordinates are in world coordinates. Default value is True.

Returns:

start_point (np.ndarray) – The point on the axis-aligned data bounding box that the cursor click intersects with. This is the point closest to the camera. The point is the full nD coordinates of the layer data. If the click does not intersect the axis-aligned data bounding box, None is returned.
end_point (np.ndarray) – The point on the axis-aligned data bounding box that the cursor click intersects with. This is the point farthest from the camera. The point is the full nD coordinates of the layer data. If the click does not intersect the axis-aligned data bounding box, None is returned.

Status message information of the data at a coordinate position.

Parameters:

position (tuple) – Position in either data or world coordinates.
view_direction (Optional[np.ndarray]) – A unit vector giving the direction of the ray in nD world coordinates. The default value is None.
dims_displayed (Optional[List[int]]) – A list of the dimensions currently being displayed in the viewer. The default value is None.
world (bool) – If True the position is taken to be in world coordinates and converted into data coordinates. False by default.

Returns:

source_info – Dict containing a information that can be used in a status update.

Return type:

dict

get_value(position: npt.ArrayLike, *, view_direction: npt.ArrayLike | None = None, dims_displayed: list[int] | None = None, world: bool = False) → tuple | None#

Value of the data at a position.

If the layer is not visible, return None.

Parameters:

position (tuple of float) – Position in either data or world coordinates.
view_direction (Optional[np.ndarray]) – A unit vector giving the direction of the ray in nD world coordinates. The default value is None.
dims_displayed (Optional[List[int]]) – A list of the dimensions currently being displayed in the viewer. The default value is None.
world (bool) – If True the position is taken to be in world coordinates and converted into data coordinates. False by default.

Returns:

value – Value of the data. If the layer is not visible return None.

Return type:

tuple, None

property help: str#

displayed in status bar bottom right.

Type:: str

property iso_gradient_mode#

Return current gradient mode for isosurface rendering.

Selects the finite-difference gradient method for the isosurface shader. Options include:

fast: use a simple finite difference gradient along each axis
smooth: use an isotropic Sobel gradient, smoother but more computationally expensive

Returns:: The current gradient mode
Return type:: str

property level_shapes: ndarray#

Shapes of each level of the multiscale or just of image.

Type:: array

property loaded: bool#

True if this layer is fully loaded in memory, False otherwise.

Layers that only support sync slicing are always fully loaded. Layers that support async slicing can be temporarily not loaded while slicing is occurring.

property metadata: dict#: Key/value map for user-stored data.

property mode#

Interactive mode. The normal, default mode is PAN_ZOOM, which allows for normal interactivity with the canvas.

In PICK mode the cursor functions like a color picker, setting the clicked on label to be the current label. If the background is picked it will select the background label 0.

In PAINT mode the cursor functions like a paint brush changing any pixels it brushes over to the current label. If the background label 0 is selected than any pixels will be changed to background and this tool functions like an eraser. The size and shape of the cursor can be adjusted in the properties widget.

In FILL mode the cursor functions like a fill bucket replacing pixels of the label clicked on with the current label. It can either replace all pixels of that label or just those that are contiguous with the clicked on pixel. If the background label 0 is selected than any pixels will be changed to background and this tool functions like an eraser.

In ERASE mode the cursor functions similarly to PAINT mode, but to paint with background label, which effectively removes the label.

Type:: MODE

property mouse_pan: bool#

Determine if canvas interactive panning is enabled with the mouse.

Type:: bool

property mouse_zoom: bool#

Determine if canvas interactive zooming is enabled with the mouse.

Type:: bool

property name: str#

Unique name of the layer.

Type:: str

property ndim: int#

Number of dimensions in the data.

Type:: int

property opacity: float#

Opacity value between 0.0 and 1.0.

Type:: float

paint(coord, new_label, refresh=True)[source]#

Paint over existing labels with a new label, using the selected brush shape and size, either only on the visible slice or in all n dimensions.

Parameters:

coord (sequence of int) – Position of mouse cursor in image coordinates.
new_label (int) – Value of the new label to be filled in.
refresh (bool) – Whether to refresh view slice or not. Set to False to batch paint calls.

paint_polygon(points, new_label)[source]#

Paint a polygon over existing labels with a new label.

Parameters:

points (list of coordinates) – List of coordinates of the vertices of a polygon.
new_label (int) – Value of the new label to be filled in.

property preserve_labels#

Defines if painting should preserve existing labels.

Default to false to allow paint on existing labels. When set to true, existing labels will be preserved during painting.

projected_distance_from_mouse_drag(start_position: npt.ArrayLike, end_position: npt.ArrayLike, view_direction: npt.ArrayLike, vector: np.ndarray, dims_displayed: list[int]) → npt.NDArray#

Calculate the length of the projection of a line between two mouse clicks onto a vector (or array of vectors) in data coordinates.

Parameters:

start_position (np.ndarray) – Starting point of the drag vector in data coordinates
end_position (np.ndarray) – End point of the drag vector in data coordinates
view_direction (np.ndarray) – Vector defining the plane normal of the plane onto which the drag vector is projected.
vector (np.ndarray) – (3,) unit vector or (n, 3) array thereof on which to project the drag vector from start_event to end_event. This argument is defined in data coordinates.
dims_displayed (List[int]) – (3,) list of currently displayed dimensions

Returns:

projected_distance

Return type:

(1, ) or (n, ) np.ndarray of float

property projection_mode#

Mode of projection of the thick slice onto the viewed dimensions.

The sliced data is described by an n-dimensional bounding box (“thick slice”), which needs to be projected onto the visible dimensions to be visible. The projection mode controls the projection logic.

property properties: dict[str, ndarray]#

Properties for each label.

Type:: dict {str
Type:: array (N,)}, DataFrame

refresh(event: Event | None = None, *, thumbnail: bool = True, data_displayed: bool = True, highlight: bool = True, extent: bool = True, force: bool = False) → None#: Refresh all layer data based on current view slice.

property rendering#

Return current rendering mode.

Selects a preset rendering mode in vispy that determines how lablels are displayed. Options include:

translucent: voxel colors are blended along the view ray until the result is opaque.
iso_categorical: isosurface for categorical data. Cast a ray until a non-background value is encountered. At that location, lighning calculations are performed to give the visual appearance of a surface.

Returns:: The current rendering mode
Return type:: str

property rotate: npt.NDArray#

Rotation matrix in world coordinates.

Type:: array

save(path: str, plugin: str | None = None) → list[str]#

Save this layer to path with default (or specified) plugin.

Parameters:

path (str) – A filepath, directory, or URL to open. Extensions may be used to specify output format (provided a plugin is available for the requested format).
plugin (str, optional) – Name of the plugin to use for saving. If None then all plugins corresponding to appropriate hook specification will be looped through to find the first one that can save the data.

Returns:

File paths of any files that were written.

Return type:

list of str

property scale: npt.NDArray#

Anisotropy factors to scale data into world coordinates.

Type:: array

property selected_label#

Index of selected label.

Type:: int

property shear: npt.NDArray#

Shear matrix in world coordinates.

Type:: array

property show_selected_label#: Whether to filter displayed labels to only the selected label or not

swap_selected_and_background_labels()[source]#: Swap between the selected label and the background label.

property thumbnail: npt.NDArray[np.uint8]#

Integer array of thumbnail for the layer

Type:: array

property translate: npt.NDArray#

Factors to shift the layer by in units of world coordinates.

Type:: array

property unique_id: Hashable#

Unique ID of the layer.

This is guaranteed to be unique to this specific layer instance over the lifetime of the program.

property units: tuple[Unit, ...]#: List of units for the layer.

property visible: bool#

Whether the visual is currently being displayed.

Type:: bool

world_to_data(position: npt.ArrayLike) → npt.NDArray#

Convert from world coordinates to data coordinates.

Parameters:: position (tuple, list, 1D array) – Position in world coordinates. If longer then the number of dimensions of the layer, the later dimensions will be used.
Returns:: Position in data coordinates.
Return type:: tuple