class napari.layers.Shapes(data=None, *, ndim=None, properties=None, property_choices=None, text=None, shape_type='rectangle', edge_width=1, edge_color='#777777', edge_color_cycle=None, edge_colormap='viridis', edge_contrast_limits=None, face_color='white', face_color_cycle=None, face_colormap='viridis', face_contrast_limits=None, z_index=0, name=None, metadata=None, scale=None, translate=None, rotate=None, shear=None, affine=None, opacity=0.7, blending='translucent', visible=True, experimental_clipping_planes=None)[source]

Bases: napari.layers.base.base.Layer

Shapes layer.

Parameters
  • data (list or array) – List of shape data, where each element is an (N, D) array of the N vertices of a shape in D dimensions. Can be an 3-dimensional array if each shape has the same number of vertices.

  • ndim (int) – Number of dimensions for shapes. When data is not None, ndim must be D. An empty shapes layer can be instantiated with arbitrary ndim.

  • properties (dict {str: array (N,)}, DataFrame) – Properties for each shape. Each property should be an array of length N, where N is the number of shapes.

  • property_choices (dict {str: array (N,)}) – possible values for each property.

  • text (str, dict) – Text to be displayed with the shapes. If text is set to a key in properties, the value of that property will be displayed. Multiple properties can be composed using f-string-like syntax (e.g., ‘{property_1}, {float_property:.2f}). A dictionary can be provided with keyword arguments to set the text values and display properties. See TextManager.__init__() for the valid keyword arguments. For example usage, see /napari/examples/add_shapes_with_text.py.

  • shape_type (string or list) – String of shape shape_type, must be one of “{‘line’, ‘rectangle’, ‘ellipse’, ‘path’, ‘polygon’}”. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • edge_width (float or list) – Thickness of lines and edges. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • edge_color (str, array-like) – If string can be any color name recognized by vispy or hex value if starting with #. If array-like must be 1-dimensional array with 3 or 4 elements. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • edge_color_cycle (np.ndarray, list) – Cycle of colors (provided as string name, RGB, or RGBA) to map to edge_color if a categorical attribute is used color the vectors.

  • edge_colormap (str, napari.utils.Colormap) – Colormap to set edge_color if a continuous attribute is used to set face_color.

  • edge_contrast_limits (None, (float, float)) – clims for mapping the property to a color map. These are the min and max value of the specified property that are mapped to 0 and 1, respectively. The default value is None. If set the none, the clims will be set to (property.min(), property.max())

  • face_color (str, array-like) – If string can be any color name recognized by vispy or hex value if starting with #. If array-like must be 1-dimensional array with 3 or 4 elements. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • face_color_cycle (np.ndarray, list) – Cycle of colors (provided as string name, RGB, or RGBA) to map to face_color if a categorical attribute is used color the vectors.

  • face_colormap (str, napari.utils.Colormap) – Colormap to set face_color if a continuous attribute is used to set face_color.

  • face_contrast_limits (None, (float, float)) – clims for mapping the property to a color map. These are the min and max value of the specified property that are mapped to 0 and 1, respectively. The default value is None. If set the none, the clims will be set to (property.min(), property.max())

  • z_index (int or list) – Specifier of z order priority. Shapes with higher z order are displayed ontop of others. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • name (str) – Name of the layer.

  • metadata (dict) – Layer metadata.

  • scale (tuple of float) – Scale factors for the layer.

  • translate (tuple of float) – Translation values for the layer.

  • 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.

  • 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.

  • 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.

  • opacity (float) – Opacity of the layer visual, between 0.0 and 1.0.

  • 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’}.

  • visible (bool) – Whether the layer visual is currently being displayed.

data

List of shape data, where each element is an (N, D) array of the N vertices of a shape in D dimensions.

Type

(N, ) list of array

properties

Properties for each shape. Each property should be an array of length N, where N is the number of shapes.

Type

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

text

Text to be displayed with the shapes. If text is set to a key in properties, the value of that property will be displayed. Multiple properties can be composed using f-string-like syntax (e.g., ‘{property_1}, {float_property:.2f}). For example usage, see /napari/examples/add_shapes_with_text.py.

Type

str, dict

shape_type

Name of shape type for each shape.

Type

(N, ) list of str

edge_color

Color of the shape border. Numeric color values should be RGB(A).

Type

str, array-like

face_color

Color of the shape face. Numeric color values should be RGB(A).

Type

str, array-like

edge_width

Edge width for each shape.

Type

(N, ) list of float

z_index

z-index for each shape.

Type

(N, ) list of int

current_edge_width

Thickness of lines and edges of the next shape to be added or the currently selected shape.

Type

float

current_edge_color

Color of the edge of the next shape to be added or the currently selected shape.

Type

str

current_face_color

Color of the face of the next shape to be added or the currently selected shape.

Type

str

selected_data

List of currently selected shapes.

Type

set

nshapes

Total number of shapes.

Type

int

mode

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

The SELECT mode allows for entire shapes to be selected, moved and resized.

The DIRECT mode allows for shapes to be selected and their individual vertices to be moved.

The VERTEX_INSERT and VERTEX_REMOVE modes allow for individual vertices either to be added to or removed from shapes that are already selected. Note that shapes cannot be selected in this mode.

The ADD_RECTANGLE, ADD_ELLIPSE, ADD_LINE, ADD_PATH, and ADD_POLYGON modes all allow for their corresponding shape type to be added.

Type

Mode

Notes

_data_dictDict of ShapeList

Dictionary containing all the shape data indexed by slice tuple

_data_viewShapeList

Object containing the currently viewed shape data.

_selected_data_historyset

Set of currently selected captured on press of <space>.

_selected_data_storedset

Set of selected previously displayed. Used to prevent rerendering the same highlighted shapes when no data has changed.

_selected_boxNone | np.ndarray

None if no shapes are selected, otherwise a 10x2 array of vertices of the interaction box. The first 8 points are the corners and midpoints of the box. The 9th point is the center of the box, and the last point is the location of the rotation handle that can be used to rotate the box.

_drag_startNone | np.ndarray

If a drag has been started and is in progress then a length 2 array of the initial coordinates of the drag. None otherwise.

_drag_boxNone | np.ndarray

If a drag box is being created to select shapes then this is a 2x2 array of the two extreme corners of the drag. None otherwise.

_drag_box_storedNone | np.ndarray

If a drag box is being created to select shapes then this is a 2x2 array of the two extreme corners of the drag that have previously been rendered. None otherwise. Used to prevent rerendering the same drag box when no data has changed.

_is_movingbool

Bool indicating if any shapes are currently being moved.

_is_selectingbool

Bool indicating if a drag box is currently being created in order to select shapes.

_is_creatingbool

Bool indicating if any shapes are currently being created.

_fixed_aspectbool

Bool indicating if aspect ratio of shapes should be preserved on resizing.

_aspect_ratiofloat

Value of aspect ratio to be preserved if _fixed_aspect is True.

_fixed_vertexNone | np.ndarray

If a scaling or rotation is in progress then a length 2 array of the coordinates that are remaining fixed during the move. None otherwise.

_fixed_indexint

If a scaling or rotation is in progress then the index of the vertex of the bounding box that is remaining fixed during the move. None otherwise.

_update_propertiesbool

Bool indicating if properties are to allowed to update the selected shapes when they are changed. Blocking this prevents circular loops when shapes are selected and the properties are changed based on that selection

_allow_thumbnail_updatebool

Flag set to true to allow the thumbnail to be updated. Blocking the thumbnail can be advantageous where responsiveness is critical.

_clipboarddict

Dict of shape objects that are to be used during a copy and paste.

_colorslist

List of supported vispy color names.

_vertex_sizefloat

Size of the vertices of the shapes and bounding box in Canvas coordinates.

_rotation_handle_lengthfloat

Length of the rotation handle of the bounding box in Canvas coordinates.

_input_ndimint

Dimensions of shape data.

_thumbnail_update_threshint

If there are more than this number of shapes, the thumbnail won’t update during interactive events

_property_choicesdict {str: array (N,)}

Possible values for the properties in Shapes.properties.

Methods

Attributes

add(data, *, shape_type='rectangle', edge_width=None, edge_color=None, face_color=None, z_index=None)[source]

Add shapes to the current layer.

Parameters
  • data (Array | Tuple(Array,str) | List[Array | Tuple(Array, str)] | Tuple(List[Array], str)) – List of shape data, where each element is either an (N, D) array of the N vertices of a shape in D dimensions or a tuple containing an array of the N vertices and the shape_type string. When a shape_type is present, it overrides keyword arg shape_type. Can be an 3-dimensional array if each shape has the same number of vertices.

  • shape_type (string | list) – String of shape shape_type, must be one of “{‘line’, ‘rectangle’, ‘ellipse’, ‘path’, ‘polygon’}”. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes. Overridden by data shape_type, if present.

  • edge_width (float | list) – thickness of lines and edges. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • edge_color (str | tuple | list) – If string can be any color name recognized by vispy or hex value if starting with #. If array-like must be 1-dimensional array with 3 or 4 elements. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • face_color (str | tuple | list) – If string can be any color name recognized by vispy or hex value if starting with #. If array-like must be 1-dimensional array with 3 or 4 elements. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • z_index (int | list) – Specifier of z order priority. Shapes with higher z order are displayed ontop of others. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

add_ellipses(data, *, edge_width=None, edge_color=None, face_color=None, z_index=None)[source]

Add ellipses to the current layer.

Parameters
  • data (Array | List[Array]) – List of ellipse data where each element is a (4, D) array of 4 vertices in D dimensions representing a bounding box, or a (2, D) array of center position and radii magnitudes in D dimensions. Can be a 3-dimensional array for multiple shapes, or list of 2 or 4 vertices for a single shape.

  • edge_width (float | list) – thickness of lines and edges. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • edge_color (str | tuple | list) – If string can be any color name recognized by vispy or hex value if starting with #. If array-like must be 1-dimensional array with 3 or 4 elements. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • face_color (str | tuple | list) – If string can be any color name recognized by vispy or hex value if starting with #. If array-like must be 1-dimensional array with 3 or 4 elements. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • z_index (int | list) – Specifier of z order priority. Shapes with higher z order are displayed ontop of others. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

add_lines(data, *, edge_width=None, edge_color=None, face_color=None, z_index=None)[source]

Add lines to the current layer.

Parameters
  • data (Array | List[Array]) – List of line data where each element is a (2, D) array of 2 vertices in D dimensions representing a line. Can be a 3-dimensional array for multiple shapes, or list of 2 vertices for a single shape.

  • edge_width (float | list) – thickness of lines and edges. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • edge_color (str | tuple | list) – If string can be any color name recognized by vispy or hex value if starting with #. If array-like must be 1-dimensional array with 3 or 4 elements. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • face_color (str | tuple | list) – If string can be any color name recognized by vispy or hex value if starting with #. If array-like must be 1-dimensional array with 3 or 4 elements. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • z_index (int | list) – Specifier of z order priority. Shapes with higher z order are displayed ontop of others. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

add_paths(data, *, edge_width=None, edge_color=None, face_color=None, z_index=None)[source]

Add paths to the current layer.

Parameters
  • data (Array | List[Array]) – List of path data where each element is a (V, D) array of V vertices in D dimensions representing a path. Can be a 3-dimensional array if all paths have same number of vertices, or a list of V vertices for a single path.

  • edge_width (float | list) – thickness of lines and edges. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • edge_color (str | tuple | list) – If string can be any color name recognized by vispy or hex value if starting with #. If array-like must be 1-dimensional array with 3 or 4 elements. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • face_color (str | tuple | list) – If string can be any color name recognized by vispy or hex value if starting with #. If array-like must be 1-dimensional array with 3 or 4 elements. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • z_index (int | list) – Specifier of z order priority. Shapes with higher z order are displayed ontop of others. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

add_polygons(data, *, edge_width=None, edge_color=None, face_color=None, z_index=None)[source]

Add polygons to the current layer.

Parameters
  • data (Array | List[Array]) – List of polygon data where each element is a (V, D) array of V vertices in D dimensions representing a polygon. Can be a 3-dimensional array if polygons have same number of vertices, or a list of V vertices for a single polygon.

  • edge_width (float | list) – thickness of lines and edges. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • edge_color (str | tuple | list) – If string can be any color name recognized by vispy or hex value if starting with #. If array-like must be 1-dimensional array with 3 or 4 elements. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • face_color (str | tuple | list) – If string can be any color name recognized by vispy or hex value if starting with #. If array-like must be 1-dimensional array with 3 or 4 elements. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • z_index (int | list) – Specifier of z order priority. Shapes with higher z order are displayed ontop of others. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

add_rectangles(data, *, edge_width=None, edge_color=None, face_color=None, z_index=None)[source]

Add rectangles to the current layer.

Parameters
  • data (Array | List[Array]) – List of rectangle data where each element is a (4, D) array of 4 vertices in D dimensions, or a (2, D) array of 2 vertices in D dimensions, where the vertices are top-left and bottom-right corners. Can be a 3-dimensional array for multiple shapes, or list of 2 or 4 vertices for a single shape.

  • edge_width (float | list) – thickness of lines and edges. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • edge_color (str | tuple | list) – If string can be any color name recognized by vispy or hex value if starting with #. If array-like must be 1-dimensional array with 3 or 4 elements. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • face_color (str | tuple | list) – If string can be any color name recognized by vispy or hex value if starting with #. If array-like must be 1-dimensional array with 3 or 4 elements. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

  • z_index (int | list) – Specifier of z order priority. Shapes with higher z order are displayed ontop of others. If a list is supplied it must be the same length as the length of data and each element will be applied to each shape otherwise the same value will be used for all shapes.

property affine

Extra affine transform to go from physical to world coordinates.

Type

napari.utils.transforms.Affine

bind_key(key, func=<object object>, *, overwrite=False)

Bind a key combination to a keymap.

Parameters
  • keymap (dict of str: callable) – Keymap to modify.

  • key (str 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

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’).

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’).

Type

Blending mode

block_thumbnail_update()[source]

Use this context manager to block thumbnail updates

property coordinates

Cursor position in data coordinates.

classmethod create(data, meta=None, layer_type=None)

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)
Return type

Layer

property current_edge_color

color of shape edges including lines and paths.

Type

str

property current_edge_width

Width of shape edges including lines and paths.

Type

float

property current_face_color

color of shape faces.

Type

str

property current_properties

properties for the next added shape.

Type

dict{str

Type

np.ndarray(1,)}

Return type

Dict[str, ndarray]

property cursor

String identifying cursor displayed over canvas.

Type

str

property cursor_size

Size of cursor if custom. None yields default size.

Type

int | None

property data

Each element is an (N, D) array of the vertices of a shape.

Type

list

property displayed_coordinates

List of currently displayed coordinates.

displayed_coordinates is deprecated and will be removed in version 0.4.9. It should no longer be used as layers should will soon not know which dimensions are displayed. Instead you should use `[layer.coordinates[d] for d in viewer.dims.displayed]

Type

list

property edge_color

Array of RGBA face colors for each shape

Type

(N x 4) np.ndarray

property edge_color_cycle

Color cycle for edge_color.

Can be a list of colors defined by name, RGB or RGBA

Type

Union[list, np.ndarray]

Return type

ndarray

property edge_color_mode

Edge color setting mode

DIRECT (default mode) allows each shape color to be set arbitrarily

CYCLE allows the color to be set via a color cycle over an attribute

COLORMAP allows color to be set via a color map over an attribute

Type

str

Return type

str

property edge_colormap

Return the colormap to be applied to a property to get the edge color.

Returns

colormap – The Colormap object.

Return type

napari.utils.Colormap

property edge_contrast_limits

contrast limits for mapping the edge_color colormap property to 0 and 1

Type

None, (float, float)

Return type

Tuple[float, float]

property edge_width

edge width for each shape.

Type

list of float

property editable

Whether the current layer data is editable from the viewer.

Type

bool

expand_shape(data)[source]

Expand shape from 2D to the full data dims.

expand_shape is deprecated and will be removed in version 0.4.9. It should no longer be used as layers should will soon not know which dimensions are displayed. Instead you should work with full nD shape data as much as possible.

Parameters

data (array) – 2D data array of shape to be expanded.

Returns

data_full – Full D dimensional data array of the shape.

Return type

array

property extent

Extent of layer in data and world coordinates.

Return type

Extent

property face_color

Array of RGBA face colors for each shape

Type

(N x 4) np.ndarray

property face_color_cycle

Color cycle for face_color Can be a list of colors defined by name, RGB or RGBA

Type

Union[np.ndarray, cycle]

Return type

ndarray

property face_color_mode

Face color setting mode

DIRECT (default mode) allows each shape color to be set arbitrarily

CYCLE allows the color to be set via a color cycle over an attribute

COLORMAP allows color to be set via a color map over an attribute

Type

str

Return type

str

property face_colormap

Return the colormap to be applied to a property to get the face color.

Returns

colormap – The Colormap object.

Return type

napari.utils.Colormap

property face_contrast_limits

clims for mapping the face_color colormap property to 0 and 1

Type

None, (float, float)

Return type

Optional[Tuple[float, float]]

get_index_and_intersection(position, view_direction, dims_displayed)[source]

Get the shape index and intersection point of the first shape (i.e., closest to start_point) “under” a mouse click.

See examples/add_points_on_nD_shapes.py for example usage.

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.

Return type

Tuple[Union[float, int], None]

Returns

  • value – The data value along the supplied ray.

  • intersection_point (np.ndarray) – (n,) array containing the point where the ray intersects the first shape (i.e., the shape most in the foreground). The coordinate is in layer coordinates.

get_ray_intersections(position, view_direction, dims_displayed, world=True)

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

Parameters
  • position (List[float]) – 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.

Return type

Union[Tuple[ndarray, ndarray], Tuple[None, None]]

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.

get_status(position, *, view_direction=None, dims_displayed=None, world=False)

Status message 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

msg – String containing a message that can be used as a status update.

Return type

string

get_value(position, *, view_direction=None, dims_displayed=None, world=False)

Value of the data at a position.

If the layer is not visible, return None.

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

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

Return type

tuple, None

property help

displayed in status bar bottom right.

Type

str

interaction_box(index)[source]

Create the interaction box around a shape or list of shapes. If a single index is passed then the boudning box will be inherited from that shapes interaction box. If list of indices is passed it will be computed directly.

Parameters

index (int | list) – Index of a single shape, or a list of shapes around which to construct the interaction box

Returns

box – 10x2 array of vertices of the interaction box. The first 8 points are the corners and midpoints of the box in clockwise order starting in the upper-left corner. The 9th point is the center of the box, and the last point is the location of the rotation handle that can be used to rotate the box

Return type

np.ndarray

property interactive

Determine if canvas pan/zoom interactivity is enabled.

Type

bool

property loaded

Return True if this layer is fully loaded in memory.

This base class says that layers are permanently in the loaded state. Derived classes that do asynchronous loading can override this.

Return type

bool

property metadata

Key/value map for user-stored data.

Return type

dict

property mode

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

The SELECT mode allows for entire shapes to be selected, moved and resized.

The DIRECT mode allows for shapes to be selected and their individual vertices to be moved.

The VERTEX_INSERT and VERTEX_REMOVE modes allow for individual vertices either to be added to or removed from shapes that are already selected. Note that shapes cannot be selected in this mode.

The ADD_RECTANGLE, ADD_ELLIPSE, ADD_LINE, ADD_PATH, and ADD_POLYGON modes all allow for their corresponding shape type to be added.

Type

MODE

move_to_back()[source]

Moves selected objects to be displayed behind all others.

move_to_front()[source]

Moves selected objects to be displayed in front of all others.

property name

Unique name of the layer.

Type

str

property ndim

Number of dimensions in the data.

Type

int

property nshapes

Total number of shapes.

Type

int

property opacity

Opacity value between 0.0 and 1.0.

Type

float

property position

Cursor position in world slice coordinates.

Type

tuple

property properties

Annotations for each shape

Type

dict {str

Type

np.ndarray (N,)}, DataFrame

Return type

Dict[str, ndarray]

refresh(event=None)

Refresh all layer data based on current view slice.

refresh_colors(update_color_mapping=False)[source]

Calculate and update face and edge colors if using a cycle or color map

Parameters

update_color_mapping (bool) – If set to True, the function will recalculate the color cycle map or colormap (whichever is being used). If set to False, the function will use the current color cycle map or color map. For example, if you are adding/modifying shapes and want them to be colored with the same mapping as the other shapes (i.e., the new shapes shouldn’t affect the color cycle map or colormap), set update_color_mapping=False. Default value is False.

refresh_text()[source]

Refresh the text values.

This is generally used if the properties were updated without changing the data

remove_selected()[source]

Remove any selected shapes.

property rotate

Rotation matrix in world coordinates.

Type

array

save(path, plugin=None)

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

Anisotropy factors to scale data into world coordinates.

Type

list

property selected

Whether this layer is selected or not.

Type

bool

property selected_data

set of currently selected shapes.

Type

set

property shape_type

name of shape type for each shape.

Type

list of str

property shear

Shear matrix in world coordinates.

Type

array

property text

The TextManager object containing the text properties

Type

TextManager

Return type

TextManager

property thumbnail

Integer array of thumbnail for the layer

Type

array

to_labels(labels_shape=None)[source]

Return an integer labels image.

Parameters

labels_shape (np.ndarray | tuple | None) – Tuple defining shape of labels image to be generated. If non specified, takes the max of all the vertiecs

Returns

labels – Integer array where each value is either 0 for background or an integer up to N for points inside the shape at the index value - 1. For overlapping shapes z-ordering will be respected.

Return type

np.ndarray

to_masks(mask_shape=None)[source]

Return an array of binary masks, one for each shape.

Parameters

mask_shape (np.ndarray | tuple | None) – tuple defining shape of mask to be generated. If non specified, takes the max of all the vertices

Returns

masks – Array where there is one binary mask for each shape

Return type

np.ndarray

property translate

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

Type

list

property translate_grid

Factors to shift the layer by.

Type

list

property visible

Whether the visual is currently being displayed.

Type

bool

world_to_data(position)

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

property z_index

z_index for each shape.

Type

list of int