napari.layers.Shapes

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 3dimensional 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 fstringlike 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, arraylike) – If string can be any color name recognized by vispy or hex value if starting with #. If arraylike must be 1dimensional 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, arraylike) – If string can be any color name recognized by vispy or hex value if starting with #. If arraylike must be 1dimensional 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, 3tuple of float, or nD array.) – If a float convert into a 2D rotation matrix using that value as an angle. If 3tuple 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 (1D array or nD array) – Either a vector of upper triangular values, or an nD shear matrix with ones along the main diagonal.
affine (nD 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 fstringlike syntax (e.g., ‘{property_1}, {float_property:.2f}). For example usage, see /napari/examples/add_shapes_with_text.py.

shape_type
¶ Name of shape type for each shape.
 Type
(N, ) list of str

edge_width
¶ Edge width for each shape.
 Type
(N, ) list of float

z_index
¶ zindex 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

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

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

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 3dimensional 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 arraylike must be 1dimensional 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 arraylike must be 1dimensional 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 3dimensional 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 arraylike must be 1dimensional 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 arraylike must be 1dimensional 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 3dimensional 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 arraylike must be 1dimensional 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 arraylike must be 1dimensional 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 3dimensional 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 arraylike must be 1dimensional 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 arraylike must be 1dimensional 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 3dimensional 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 arraylike must be 1dimensional 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 arraylike must be 1dimensional 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 topleft and bottomright corners. Can be a 3dimensional 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 arraylike must be 1dimensional 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 arraylike must be 1dimensional 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, keywordonly, 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
,Controlc
, orControlAltDelete
. Valid modifiers are Control, Alt, Shift, and Meta.Letters will always be read as uppercase. 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 nonletter 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

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_properties
¶ properties for the next added shape.

property
cursor_size
¶ Size of cursor if custom. None yields default size.
 Type
int  None

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

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

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

property
edge_colormap
¶ Return the colormap to be applied to a property to get the edge color.
 Returns
colormap – The Colormap object.
 Return type

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

property
edge_width
¶ edge width for each shape.
 Type
list of float

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

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

property
face_colormap
¶ Return the colormap to be applied to a property to get the face color.
 Returns
colormap – The Colormap object.
 Return type

property
face_contrast_limits
¶ clims for mapping the face_color colormap property to 0 and 1

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
 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
 Returns
start_point (np.ndarray) – The point on the axisaligned 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 axisaligned data bounding box, None is returned.
end_point (np.ndarray) – The point on the axisaligned 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 axisaligned 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

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 upperleft 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
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

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

property
properties
¶ Annotations for each shape

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

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
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 zordering 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

world_to_data
(position)¶ Convert from world coordinates to data coordinates.

property
z_index
¶ z_index for each shape.
 Type
list of int